1
|
Laus AC, Gomes INF, da Silva ALV, da Silva LS, Milan MB, AparecidaTeixeira S, Martin ACBM, do Nascimento Braga Pereira L, de Carvalho CEB, Crovador CS, de Paula FE, Nascimento FC, de Freitas HT, de Lima Vazquez V, Reis RM, da Silva-Oliveira RJ. Establishment and molecular characterization of HCB-541, a novel and aggressive human cutaneous squamous cell carcinoma cell line. Hum Cell 2024; 37:1170-1183. [PMID: 38565739 PMCID: PMC11194207 DOI: 10.1007/s13577-024-01054-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 03/04/2024] [Indexed: 04/04/2024]
Abstract
Cutaneous squamous cell carcinoma (cSCC) is a common type of skin cancer that can result in significant morbidity, although it is usually well-managed and rarely metastasizes. However, the lack of commercially available cSCC cell lines hinders our understanding of this disease. This study aims to establish and characterize a new metastatic cSCC cell line derived from a Brazilian patient. A tumor biopsy was taken from a metastatic cSCC patient, immortalized, and named HCB-541 after several passages. The cytokeratin expression profile, karyotypic alterations, mutational analysis, mRNA and protein differential expression, tumorigenic capacity in xenograft models, and drug sensitivity were analyzed. The HCB-541 cell line showed a doubling time between 20 and 30 h and high tumorigenic capacity in the xenograft mouse model. The HCB-541 cell line showed hypodiploid and hypotetraploidy populations. We found pathogenic mutations in TP53 p.(Arg248Leu), HRAS (Gln61His) and TERT promoter (C228T) and high-level microsatellite instability (MSI-H) in both tumor and cell line. We observed 37 cancer-related genes differentially expressed when compared with HACAT control cells. The HCB-541 cells exhibited high phosphorylated levels of EGFR, AXL, Tie, FGFR, and ROR2, and high sensitivity to cisplatin, carboplatin, and EGFR inhibitors. Our study successfully established HCB-541, a new cSCC cell line that could be useful as a valuable biological model for understanding the biology and therapy of metastatic skin cancer.
Collapse
Affiliation(s)
- Ana Carolina Laus
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela, 1331, Barretos, São Paulo, Zip Code: 14784 400, Brazil
| | - Izabela Natalia Faria Gomes
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela, 1331, Barretos, São Paulo, Zip Code: 14784 400, Brazil
| | - Aline Larissa Virginio da Silva
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela, 1331, Barretos, São Paulo, Zip Code: 14784 400, Brazil
| | - Luciane Sussuchi da Silva
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela, 1331, Barretos, São Paulo, Zip Code: 14784 400, Brazil
| | - Mirella Baroni Milan
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela, 1331, Barretos, São Paulo, Zip Code: 14784 400, Brazil
| | - Silvia AparecidaTeixeira
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela, 1331, Barretos, São Paulo, Zip Code: 14784 400, Brazil
| | - Ana Carolina Baptista Moreno Martin
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela, 1331, Barretos, São Paulo, Zip Code: 14784 400, Brazil
| | - Letícia do Nascimento Braga Pereira
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela, 1331, Barretos, São Paulo, Zip Code: 14784 400, Brazil
| | | | - Camila Souza Crovador
- Department of Surgery of Melanoma and Sarcoma, Barretos Cancer Hospital, São Paulo, Brazil
| | - Flávia Escremin de Paula
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela, 1331, Barretos, São Paulo, Zip Code: 14784 400, Brazil
| | - Flávia Caroline Nascimento
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela, 1331, Barretos, São Paulo, Zip Code: 14784 400, Brazil
| | - Helder Teixeira de Freitas
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela, 1331, Barretos, São Paulo, Zip Code: 14784 400, Brazil
| | - Vinicius de Lima Vazquez
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela, 1331, Barretos, São Paulo, Zip Code: 14784 400, Brazil
- Department of Surgery of Melanoma and Sarcoma, Barretos Cancer Hospital, São Paulo, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela, 1331, Barretos, São Paulo, Zip Code: 14784 400, Brazil
- Life and Health Sciences Research Institute (ICVS) Medical School, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
- Barretos School of Health Sciences, Dr. Paulo Prata-FACISB, Barretos, São Paulo, Brazil
| | - Renato José da Silva-Oliveira
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela, 1331, Barretos, São Paulo, Zip Code: 14784 400, Brazil.
- Barretos School of Health Sciences, Dr. Paulo Prata-FACISB, Barretos, São Paulo, Brazil.
| |
Collapse
|
2
|
Xu Y, Sun X, Tong Y. Interleukin-12 in multimodal tumor therapies for induction of anti-tumor immunity. Discov Oncol 2024; 15:170. [PMID: 38753073 PMCID: PMC11098992 DOI: 10.1007/s12672-024-01011-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 05/03/2024] [Indexed: 05/19/2024] Open
Abstract
Interleukin-12 (IL-12) can be used as an immunomodulator in cancer immunotherapy. And it has demonstrated enormous potential in inhibiting tumor growth and improving the tumor microenvironment (TME) by several preclinical models. However, some disappointing results have showed in the early clinical trials when IL-12 used as a single agent for systemic cancer therapy. Combination therapy is an effective way to significantly fulfill the great potential of IL-12 as an immunomodulator. Here, we discuss the effects of IL-12 combined with traditional methods (chemotherapy, radiotherapy and surgery), targeted therapy or immunotherapy in the preclinical and clinical studies. Moreover, we summarized the potential mechanism underlying the anti-tumor effect of IL-12 in the combination strategies. And we also discussed the delivery methods and tumor-targeted modification of IL-12 and outlines future prospects for IL-12 as an immunomodulator.
Collapse
Affiliation(s)
- Yulian Xu
- College of Life Sciences, China Jiliang University, 168 Xueyuan Street, Hangzhou, Zhejiang, China
| | - Xueli Sun
- College of Life Sciences, China Jiliang University, 168 Xueyuan Street, Hangzhou, Zhejiang, China
| | - Yunguang Tong
- College of Life Sciences, China Jiliang University, 168 Xueyuan Street, Hangzhou, Zhejiang, China.
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
- Omigen, Inc, Hangzhou, 310018, Zhejiang, China.
| |
Collapse
|
3
|
Ghosh S, Choudhury D, Ghosh D, Mondal M, Singha D, Malakar P. Characterization of polyploidy in cancer: Current status and future perspectives. Int J Biol Macromol 2024; 268:131706. [PMID: 38643921 DOI: 10.1016/j.ijbiomac.2024.131706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 04/23/2024]
Abstract
Various cancers frequently exhibit polyploidy, observed in a condition where a cell possesses more than two sets of chromosomes, which is considered a hallmark of the disease. The state of polyploidy often leads to aneuploidy, where cells possess an abnormal number or structure of chromosomes. Recent studies suggest that oncogenes contribute to aneuploidy. This finding significantly underscores its impact on cancer. Cancer cells exposed to certain chemotherapeutic drugs tend to exhibit an increased incidence of polyploidy. This occurrence is strongly associated with several challenges in cancer treatment, including metastasis, resistance to chemotherapy and the recurrence of malignant tumors. Indeed, it poses a significant hurdle to achieve complete tumor eradication and effective cancer therapy. Recently, there has been a growing interest in the field of polyploidy related to cancer for developing effective anti-cancer therapies. Polyploid cancer cells confer both advantages and disadvantages to tumor pathogenicity. This review delineates the diverse characteristics of polyploid cells, elucidates the pivotal role of polyploidy in cancer, and explores the advantages and disadvantages it imparts to cancer cells, along with the current approaches tried in lab settings to target polyploid cells. Additionally, it considers experimental strategies aimed at addressing the outstanding questions within the realm of polyploidy in relation to cancer.
Collapse
Affiliation(s)
- Srijonee Ghosh
- Department of Biomedical Science and Technology, School of Biological Sciences, Ramakrishna Mission Vivekananda Educational Research Institute (RKMVERI), Kolkata, India
| | - Debopriya Choudhury
- Department of Biomedical Science and Technology, School of Biological Sciences, Ramakrishna Mission Vivekananda Educational Research Institute (RKMVERI), Kolkata, India
| | - Dhruba Ghosh
- Department of Biomedical Science and Technology, School of Biological Sciences, Ramakrishna Mission Vivekananda Educational Research Institute (RKMVERI), Kolkata, India
| | - Meghna Mondal
- Department of Biomedical Science and Technology, School of Biological Sciences, Ramakrishna Mission Vivekananda Educational Research Institute (RKMVERI), Kolkata, India
| | - Didhiti Singha
- Department of Biomedical Science and Technology, School of Biological Sciences, Ramakrishna Mission Vivekananda Educational Research Institute (RKMVERI), Kolkata, India
| | - Pushkar Malakar
- Department of Biomedical Science and Technology, School of Biological Sciences, Ramakrishna Mission Vivekananda Educational Research Institute (RKMVERI), Kolkata, India.
| |
Collapse
|
4
|
Alabi OA, Okorie B, Simon-Oke IA, Atanda HC, Olumurewa JAV, Adebo TC. Cellular toxicity and DNA damage induced by Newbouldia laevis used for male infertility treatment in prokaryotic and eukaryotic models. PROTOPLASMA 2024; 261:53-64. [PMID: 37438649 DOI: 10.1007/s00709-023-01880-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 06/30/2023] [Indexed: 07/14/2023]
Abstract
Leaves of Newbouldia laevis have been extensively used in solving problems associated with infertility and childbirth in many African countries. Yet, information is very limited on the DNA damaging potential of this plant. This study evaluated the cytogenotoxic effect of the aqueous extract of N. laevis leaf using prokaryotic models (Ames Salmonella fluctuation test using TA100 and TA98 strains of Salmonella typhimurium and SOS Chromotest with Escherichia coli PQ37) and eukaryotic model (Allium cepa root cells). Identification of the volatile organic compounds (VOCs) and phytochemical screening of the plant extract were also performed. Onion bulbs were grown on each concentration (1 to 50%; v/v, extract/tap water) of the extract for chromosomal aberrations and root growth analyses. Results of the Ames test indicated that the extract is mutagenic while the SOS Chromotest results showed good complementation to the Ames test results, although the E. coli PQ37 system showed slightly higher sensitivity in the detection of mutagenicity and genotoxicity of the extract. The plant extract was cytotoxic when compared to the control, inducing a significant (p < 0.05) concentration-dependent inhibition of root growth from 5 to 50% concentrations. At 50% concentration, the extract completely inhibited cell division in the A. cepa. Also, chromosomal aberration increased significantly (p < 0.05) in exposed onions from 5 to 20% concentrations. The mutagenicity and cytogenotoxicity recorded in this report were believed to be caused by the presence of VOCs such as 1,2,3-benzene-triol, 1,2-benzenediol, and 5-hydroxymethylfurfural, and alkaloids in the extract an indication of the cytogenotoxicity of the aqueous extract of N. laevis leaf even at low concentration.
Collapse
Affiliation(s)
- Okunola Adenrele Alabi
- Department of Biology, Federal University of Technology, Akure, Ondo State, Nigeria.
- Department of Biotechnology, Federal University of Technology, Akure, Ondo State, Nigeria.
| | - Benson Okorie
- Department of Biotechnology, Federal University of Technology, Akure, Ondo State, Nigeria
| | - Iyabo A Simon-Oke
- Department of Biology, Federal University of Technology, Akure, Ondo State, Nigeria
| | - Halimat Chisom Atanda
- Department of Biotechnology, Federal University of Technology, Akure, Ondo State, Nigeria
| | - John A V Olumurewa
- Department of Biotechnology, Federal University of Technology, Akure, Ondo State, Nigeria
| | - Taiwo Cosmas Adebo
- Department of Biology, Federal University of Technology, Akure, Ondo State, Nigeria
| |
Collapse
|
5
|
Khan SM, Das T, Chakraborty S, Choudhury AMAR, Karim HF, Mostofa MA, Ahmed HU, Hossain MA, Le Calvez-Kelm F, Hosen MI, Shekhar HU. A transcriptome study of p53-pathway related prognostic gene signature set in bladder cancer. Heliyon 2023; 9:e21058. [PMID: 37876438 PMCID: PMC10590981 DOI: 10.1016/j.heliyon.2023.e21058] [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: 10/14/2022] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 10/26/2023] Open
Abstract
p53 pathway is important in tumorigenesis. However, no study has been performed to specifically investigate the role of p53 pathway genes in bladder cancer (BLCA). In this study, transcriptomics data of muscle invasive bladder cancer patients (n = 411) from The Cancer Genome Atlas (TCGA) were investigated. Using the hallmark p53 pathway gene set, the Non-Negative Matrix factorization (NMF) analysis identified two subtypes (C1 and C2). Clinical, survival, and immunological analysis were done to validate distinct characteristics of the subtypes. Pathway enrichment analysis showed the subtype C1 with poor prognosis having enrichment in genes of the immunity related pathways, where C2 subtype with better prognosis being enriched in genes of the steroid synthesis and drug metabolism pathways. A signature gene set consisting of MDGA2, GNLY, GGT2, UGT2B4, DLX1, and DSC1 was created followed by a risk model. Their expressions were analyzed in RNA extracted from the blood and matched tumor tissues of BLCA patients (n = 10). DSC1 had significant difference of expression (p = 0.005) between the blood and tumor tissues in our BLCA samples. Contrary to the usual normal bladder tissue to blood ratio, DLX1 expression was lower (p = 0.02734) in tumor tissues than in blood. Being the first research of p53 pathway related signature gene set in bladder cancer, this study potentially has a substantial impact on the development of biomarkers for BLCA.
Collapse
Affiliation(s)
- Safayat Mahmud Khan
- Clinical Biochemistry and Translational Medicine Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Tonmoy Das
- Systems Cell-Signalling Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Sajib Chakraborty
- Systems Cell-Signalling Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | | | - Howlader Fazlul Karim
- Department. Uro-Oncology, National Institute of Cancer Research Hospital, Bangladesh
| | - Munshi Akid Mostofa
- Department. Uro-Oncology, National Institute of Cancer Research Hospital, Bangladesh
| | - Hasib Uddin Ahmed
- Clinical Biochemistry and Translational Medicine Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Md Akmal Hossain
- Clinical Biochemistry and Translational Medicine Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Florence Le Calvez-Kelm
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC), 69372, Lyon, France
| | - Md Ismail Hosen
- Clinical Biochemistry and Translational Medicine Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Hossain Uddin Shekhar
- Clinical Biochemistry and Translational Medicine Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| |
Collapse
|
6
|
Fischer GM, Gliem TJ, Greipp PT, Rosenberg AE, Folpe AL, Hornick JL. Anaplastic Kaposi Sarcoma: A Clinicopathologic and Molecular Genetic Analysis. Mod Pathol 2023; 36:100191. [PMID: 37080393 DOI: 10.1016/j.modpat.2023.100191] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/31/2023] [Accepted: 04/10/2023] [Indexed: 04/22/2023]
Abstract
Kaposi sarcoma (KS) is a human herpesvirus 8 (HHV8)-associated vascular proliferation that most often involves the skin. Rarely, KS shows marked nuclear atypia or pleomorphism; such examples are known as "anaplastic" KS. This poorly characterized variant often pursues an aggressive course; little is known of its genetic landscape. This study evaluated the clinicopathologic and genomic features of anaplastic KS. We identified 9 anaplastic KS cases from 7 patients and 8 conventional KS cases, including a matched conventional KS and primary metastasis anaplastic KS pair from a single patient (anaplastic KS diagnosed 9 years after conventional KS). All patients with anaplastic KS were men, aged 51 to 82 years, who had locally aggressive tumors predominantly affecting the soft tissue and bone of the lower extremities (5/7 patients). Four patients were known to be HIV positive (all on antiretrovirals), 2 were HIV negative, and 1 was of unknown HIV status. The tumors showed angiosarcoma-like or pleomorphic spindle cell sarcoma morphology. Plasma cell-rich chronic inflammation and hemosiderin deposition were commonly present. Single-nucleotide polymorphism-based chromosomal microarray analysis showed the anaplastic KS cohort to demonstrate highly recurrent whole chromosome (chr) gains of chr 7, 11, 19, and 21, which primarily affected olfactory and G protein-coupled receptor signaling and losses of chr6_q and chrY. Compared with conventional KS, anaplastic KS cases showed significantly more total copy number alterations and more frequent gains of chr7 and chr11_q13.1 (MARK2, RELA, and ESRRA, including high copy number gain in 1 case). Pathway analysis demonstrated that these gains preferentially affected genes that facilitate cyclin-dependent cell signaling. Furthermore, anaplastic KS cases were phylogenetically distinct from conventional KS cases, including the patient-matched primary metastasis anaplastic KS pair and conventional KS. Our study is the first to demonstrate that a more complex genome and distinct copy number alterations distinguish anaplastic KS from conventional KS. Gains of chr7 and chr11_q13.1 appear central to biological transformation.
Collapse
Affiliation(s)
- Grant M Fischer
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Troy J Gliem
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Patricia T Greipp
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Andrew E Rosenberg
- Department of Pathology and Laboratory Medicine, University of Miami Miller School of Medicine, Miami, Florida
| | - Andrew L Folpe
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Jason L Hornick
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.
| |
Collapse
|
7
|
de Alencar MVOB, Islam MT, da Mata AMOF, Dos Reis AC, de Lima RMT, de Oliveira Ferreira JR, de Castro E Sousa JM, Ferreira PMP, de Carvalho Melo-Cavalcante AA, Rauf A, Hemeg HA, Alsharif KF, Khan H. Anticancer effects of phytol against Sarcoma (S-180) and Human Leukemic (HL-60) cancer cells. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:80996-81007. [PMID: 37308630 DOI: 10.1007/s11356-023-28036-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/29/2023] [Indexed: 06/14/2023]
Abstract
Phytol (Pyt), a diterpenoid, possesses many important bioactivities. This study evaluates the anticancer effects of Pyt on sarcoma 180 (S-180) and human leukemia (HL-60) cell lines. For this purpose, cells were treated with Pyt (4.72, 7.08, or 14.16 μM) and a cell viability assay was performed. Additionally, the alkaline comet assay and micronucleus test with cytokinesis were also performed using doxorubicin (6 μM) and hydrogen peroxide (10 mM) as positive controls and stressors, respectively. Results revealed that Pyt significantly reduced the viability and rate of division in S-180 and HL-60 cells with IC50 values of 18.98 ± 3.79 and 1.17 ± 0.34 μM, respectively. Pyt at 14.16 μM exerted aneugenic and/or clastogenic effects in S-180 and HL-60 cells, where the number of micronuclei and other nuclear abnormalities (e.g., nucleoplasmic bridges and nuclear buds) were frequently observed. Moreover, Pyt at all concentrations induced apoptosis and showed necrosis at 14.16 μM, suggesting its anticancer effects on the tested cancer cell lines. Taken together, Pyt showed promising anticancer effects, possibly through inducing apoptosis and necrosis mechanisms, and it exerted aneugenic and/or clastogenic effects on the S-180 and HL-60 cell lines.
Collapse
Affiliation(s)
- Marcus Vinícius Oliveira Barros de Alencar
- Postgraduate Program in Biotechnology (RENORBIO), Federal University of Piauí, Teresina, 64.049-550, Brazil
- Biomedical Sciences Research and Innovation Laboratory, Postgraduate Program in Biotechnology, INTA University Center, Sobral, 62.011-230, Brazil
- Laboratory of Toxicological Genetics, Department of Biochemistry and Pharmacology, Federal University of Piauí, Teresina, Piauí, 64.049-550, Brazil
| | - Muhammad Torequl Islam
- Postgraduate Program in Biotechnology (RENORBIO), Federal University of Piauí, Teresina, 64.049-550, Brazil
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
| | - Ana Maria Oliveira Ferreira da Mata
- Postgraduate Program in Biotechnology (RENORBIO), Federal University of Piauí, Teresina, 64.049-550, Brazil
- Laboratory of Toxicological Genetics, Department of Biochemistry and Pharmacology, Federal University of Piauí, Teresina, Piauí, 64.049-550, Brazil
| | - Antonielly Campinho Dos Reis
- Postgraduate Program in Biotechnology (RENORBIO), Federal University of Piauí, Teresina, 64.049-550, Brazil
- Laboratory of Toxicological Genetics, Department of Biochemistry and Pharmacology, Federal University of Piauí, Teresina, Piauí, 64.049-550, Brazil
| | - Rosália Maria Torres de Lima
- Postgraduate Program in Biotechnology (RENORBIO), Federal University of Piauí, Teresina, 64.049-550, Brazil
- Laboratory of Toxicological Genetics, Department of Biochemistry and Pharmacology, Federal University of Piauí, Teresina, Piauí, 64.049-550, Brazil
| | | | - João Marcelo de Castro E Sousa
- Postgraduate Program in Biotechnology (RENORBIO), Federal University of Piauí, Teresina, 64.049-550, Brazil
- Laboratory of Toxicological Genetics, Department of Biochemistry and Pharmacology, Federal University of Piauí, Teresina, Piauí, 64.049-550, Brazil
| | - Paulo Michel Pinheiro Ferreira
- Postgraduate Program in Biotechnology (RENORBIO), Federal University of Piauí, Teresina, 64.049-550, Brazil
- Laboratory of Experimental Cancerology, Department of Biophysics and Physiology, Federal University of Piauí, Teresina, 64.049-550, Brazil
| | - Ana Amélia de Carvalho Melo-Cavalcante
- Postgraduate Program in Biotechnology (RENORBIO), Federal University of Piauí, Teresina, 64.049-550, Brazil
- Laboratory of Toxicological Genetics, Department of Biochemistry and Pharmacology, Federal University of Piauí, Teresina, Piauí, 64.049-550, Brazil
| | - Abdur Rauf
- Department of Chemistry, University of Swabi, Anbar, Swabi, Khyber Pakhtunkhwa, 23430, Pakistan
| | - Hassan A Hemeg
- Department of Medical Laboratory Technology, College of Applied Medical Sciences, Taibah University, Al-Medinah Al-Monawara, 41411, Saudi Arabia
| | - Khalaf F Alsharif
- Department of Clinical Laboratory, College of Applied Medical Science, Taif University, Taif, 21944, Saudi Arabia
| | - Haroon Khan
- Department of Pharmacy, Abdul Wali Khan University Mardan, Mardan, 23200, Pakistan.
| |
Collapse
|
8
|
Fischer GM, Lindeman NI, Ligon AH, Russell-Goldman E. Proliferating Pilar Tumors Are Characterized by Recurrent 15q, 6q, and 6p22.2 Alterations. Am J Dermatopathol 2023; 45:217-226. [PMID: 36346171 DOI: 10.1097/dad.0000000000002308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
ABSTRACT Proliferating pilar tumors (PPTs) are rare neoplasms of external root sheath derivation, which most commonly occur on the scalp of elderly women. Although typically showing classic histologic features such as trichilemmal type keratinization, a lobular architecture and peripheral palisading, squamous cell carcinoma (SCC) remains a common diagnostic pitfall. Therefore, we sought to explore the molecular pathogenesis of PPTs and compare it with that of cutaneous squamous cell carcinoma (cSCC). Herein, we describe the use of a next-generation DNA sequencing platform to provide the most comprehensive molecular genetic analysis to date of a cohort of 5 PPTs and compare them to 5 head and neck cutaneous SCCs. Recurrent broad arm-level gains of 15q and concurrent single-copy losses of 6q and 6p22.2 were observed in 4 of 5 (80%) PPT cases. Other recurrent mutations or alterations of significance were not found in PPTs. Notably, these chromosomal changes were not identified in any of the 5 cutaneous SCCs, which instead showed recurrent alterations in the known SCC driver genes TP53 , CDKN2A , and NOTCH1 . Here, we show for the first time that PPTs are molecularly distinct from cutaneous SCC and provide evidence that recurrent alterations in chromosome 15 and chromosome 6 are central to the pathogenesis of PPTs.
Collapse
Affiliation(s)
- Grant M Fischer
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
| | | | | | | |
Collapse
|
9
|
METAXAS GEORGIOSI, TSIAMBAS EVANGELOS, MARINOPOULOS SPYRIDON, SPYROPOULOU DESPOINA, MANAIOS LOUKAS, ADAMOPOULOU MARIA, FALIDAS EVANGELOS, PESCHOS DIMITRIOS, KALKANI HELEN, DIMITRAKAKIS CONSTANTINE. Epigenetic Mechanisms in Breast Adenocarcinoma: Novel DNA Methylation Patterns. CANCER DIAGNOSIS & PROGNOSIS 2022; 2:603-608. [PMID: 36340455 PMCID: PMC9628153 DOI: 10.21873/cdp.10149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/08/2022] [Indexed: 11/11/2022]
Abstract
Breast adenocarcinoma is a leading cause of death in females worldwide. A broad spectrum of genetic and epigenetic alterations has been already identified and reported in millions of examined cancerous substrates, evidence of a high-level genomic heterogeneity that characterizes these malignancies. Concerning epigenetic changes and imbalances that critically affect progression and prognosis in the corresponding patients, DNA methylation, histone modifications (acetylation), micro-RNAs (miRs) alterations and chromatin re-organization represent the main mechanisms. Referring to DNA methylation, promoter hyper-hypo methylation in critical tumour suppressor and oncogenes is implicated in normal epithelia transformation to their neoplastic and finally malignant cyto-phenotypes. The current review is focused on the different methylation patterns and mechanisms detected in breast adenocarcinoma and their impact on the corresponding groups of patient response to specific chemotherapeutic regimens and life span prognosis.
Collapse
Affiliation(s)
- GEORGIOS I. METAXAS
- Breast Unit, 1st Department of Obstetrics and Gynecology, Alexandra Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | | | - SPYRIDON MARINOPOULOS
- Breast Unit, 1st Department of Obstetrics and Gynecology, Alexandra Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - DESPOINA SPYROPOULOU
- Department of Radiation Oncology, Medical School, University of Patras, Patras, Greece
| | - LOUKAS MANAIOS
- Department of Surgery, Bioclinic Medical Center, Athens, Greece
| | - MARIA ADAMOPOULOU
- Laboratory of Molecular Microbiology and Immunology, Department of Biomedical Sciences, School of Health and Care Sciences, University of West Attica, Athens, Greece
| | | | - DIMITRIOS PESCHOS
- Department of Physiology, School of Medicine, University of Ioannina, Ioannina, Greece
| | - HELEN KALKANI
- Leucippus Technology Park, NCSR Demokritos, Athens, Greece
| | - CONSTANTINE DIMITRAKAKIS
- Breast Unit, 1st Department of Obstetrics and Gynecology, Alexandra Hospital, National and Kapodistrian University of Athens, Athens, Greece
| |
Collapse
|
10
|
Souto EB, da Ana R, Vieira V, Fangueiro JF, Dias-Ferreira J, Cano A, Zielińska A, Silva AM, Staszewski R, Karczewski J. Non-melanoma skin cancers: physio-pathology and role of lipid delivery systems in new chemotherapeutic treatments. Neoplasia 2022; 30:100810. [PMID: 35649306 PMCID: PMC9160356 DOI: 10.1016/j.neo.2022.100810] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 05/16/2022] [Indexed: 12/19/2022]
Abstract
Non-melanoma carcinoma has high incidence rates and has two most common subtypes: basal cell carcinoma and squamous cell carcinoma. This type of carcinoma is usually not fatal; however, it can destroy sensory organs such as the nose, ears, and lips. The treatment of these injuries using non-invasive methods is thus strongly recommended. Some treatments for non-melanoma carcinoma are already well defined, such as surgery, cryosurgery, curettage and electrode section, and radiotherapy; however, these conventional treatments cause inflammation and scarring. In the non-surgical treatment of non-melanoma carcinoma, the topical administration of chemotherapeutic drugs contributes for an effective treatment with reduced side effects. However, the penetration of anticancer drugs in the deeper layers of the skin is required. Lipid delivery systems (liposomes, solid lipid nanoparticles, nanostructured lipid carriers) have been developed to overcome epidermal barrier of the skin and to allow the drugs to reach tumor cells. These lipid nanoparticles contribute to control the release profile of the loaded chemotherapeutic drugs, maintaining their stability and increasing death of tumor cells. In this review, the characteristics of non-melanoma carcinoma will be discussed, describing the main existing treatments, together with the contribution of lipid delivery systems as an innovative approach to increase the effectiveness of topical therapies for non-melanoma carcinomas.
Collapse
Affiliation(s)
- Eliana B Souto
- Department of Pharmaceutical Technology, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; REQUIMTE/UCIBIO, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal.
| | - Raquel da Ana
- Department of Pharmaceutical Technology, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Vânia Vieira
- Faculty of Health Sciences, University Fernando Pessoa, Rua Carlos da Maia, 296, 4200-150, Porto, Porto, Portugal
| | - Joana F Fangueiro
- Faculty of Health Sciences, University Fernando Pessoa, Rua Carlos da Maia, 296, 4200-150, Porto, Porto, Portugal
| | - João Dias-Ferreira
- Faculdade de Medicina, Universidade do Porto, Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal
| | - Amanda Cano
- Department of Pharmacy, Pharmaceutical Technology and Physical Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, 08007 Barcelona, Spain; Institute of Nanoscience and Nanotechnology (IN2UB), 08007 Barcelona, Spain
| | - Aleksandra Zielińska
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479 Poznań, Poland
| | - Amélia M Silva
- Department of Biology and Environment, University of Trás-os-Montes e Alto Douro, UTAD, Quinta de Prados, P-5001-801 Vila Real, Portugal; Centre for Research and Technology of Agro-Environmental and Biological Sciences, CITAB, UTAD, Quinta de Prados, P-5001-801 Vila Real, Portugal
| | - Rafał Staszewski
- Department of Hypertension Angiology and Internal Medicine, Poznan University of Medical Sciences, 61-701 Poznań, Poland
| | - Jacek Karczewski
- Department of Environmental Medicine, Poznan University of Medical Sciences, 61-701 Poznań, Poland; Department of Gastroenterology, Dietetics and Internal Diseases, H. Swiecicki University Hospital, Poznan University of Medical Sciences, 60-355 Poznan, Poland.
| |
Collapse
|
11
|
Tao R, Wang Y, Hu Y, Jiao Y, Zhou L, Jiang L, Li L, He X, Li M, Yu Y, Chen Q, Yao S. WT-PE: Prime editing with nuclease wild-type Cas9 enables versatile large-scale genome editing. Signal Transduct Target Ther 2022; 7:108. [PMID: 35440051 PMCID: PMC9018734 DOI: 10.1038/s41392-022-00936-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/16/2022] [Accepted: 02/21/2022] [Indexed: 02/08/2023] Open
Abstract
Large scale genomic aberrations including duplication, deletion, translocation, and other structural changes are the cause of a subtype of hereditary genetic disorders and contribute to onset or progress of cancer. The current prime editor, PE2, consisting of Cas9-nickase and reverse transcriptase enables efficient editing of genomic deletion and insertion, however, at small scale. Here, we designed a novel prime editor by fusing reverse transcriptase (RT) to nuclease wild-type Cas9 (WT-PE) to edit large genomic fragment. WT-PE system simultaneously introduced a double strand break (DSB) and a single 3' extended flap in the target site. Coupled with paired prime editing guide RNAs (pegRNAs) that have complementary sequences in their 3' terminus while target different genomic regions, WT-PE produced bi-directional prime editing, which enabled efficient and versatile large-scale genome editing, including large fragment deletion up to 16.8 megabase (Mb) pairs and chromosomal translocation. Therefore, our WT-PE system has great potential to model or treat diseases related to large-fragment aberrations.
Collapse
Affiliation(s)
- Rui Tao
- From laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China
| | - Yanhong Wang
- From laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China
| | - Yun Hu
- From laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China
| | - Yaoge Jiao
- From laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China
| | - Lifang Zhou
- From laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China
| | - Lurong Jiang
- From laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China
| | - Li Li
- From laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China
| | - Xingyu He
- From laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China
| | - Min Li
- From laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China
| | - Yamei Yu
- From laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China
| | - Qiang Chen
- From laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China
| | - Shaohua Yao
- From laboratory of Biotherapy, National Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan university, Renmin Nanlu 17, Chengdu, 610041, Sichuan, China.
| |
Collapse
|
12
|
Tang X, Chen F, Xie LC, Liu SX, Mai HR. Targeting metabolism: A potential strategy for hematological cancer therapy. World J Clin Cases 2022; 10:2990-3004. [PMID: 35647127 PMCID: PMC9082716 DOI: 10.12998/wjcc.v10.i10.2990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 11/01/2021] [Accepted: 02/27/2022] [Indexed: 02/06/2023] Open
Abstract
Most hematological cancer-related relapses and deaths are caused by metastasis; thus, the importance of this process as a target of therapy should be considered. Hematological cancer is a type of cancer in which metabolism plays an essential role in progression. Therefore, we are required to block fundamental metastatic processes and develop specific preclinical and clinical strategies against those biomarkers involved in the metabolic regulation of hematological cancer cells, which do not rely on primary tumor responses. To understand progress in this field, we provide a summary of recent developments in the understanding of metabolism in hematological cancer and a general understanding of biomarkers currently used and under investigation for clinical and preclinical applications involving drug development. The signaling pathways involved in cancer cell metabolism are highlighted and shed light on how we could identify novel biomarkers involved in cancer development and treatment. This review provides new insights into biomolecular carriers that could be targeted as anticancer biomarkers.
Collapse
Affiliation(s)
- Xue Tang
- Department of Hematology and Oncology, Shenzhen Children’s Hospital, Shenzhen 518038, Guangdong Province, China
| | - Fen Chen
- Department of Hematology and Oncology, Shenzhen Children’s Hospital, Shenzhen 518038, Guangdong Province, China
| | - Li-Chun Xie
- Department of Hematology and Oncology, Shenzhen Children’s Hospital, Shenzhen 518038, Guangdong Province, China
| | - Si-Xi Liu
- Department of Hematology and Oncology, Shenzhen Children’s Hospital, Shenzhen 518038, Guangdong Province, China
| | - Hui-Rong Mai
- Department of Hematology and Oncology, Shenzhen Children’s Hospital, Shenzhen 518038, Guangdong Province, China
| |
Collapse
|
13
|
Schaap-Johansen AL, Vujović M, Borch A, Hadrup SR, Marcatili P. T Cell Epitope Prediction and Its Application to Immunotherapy. Front Immunol 2021; 12:712488. [PMID: 34603286 PMCID: PMC8479193 DOI: 10.3389/fimmu.2021.712488] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 07/12/2021] [Indexed: 12/13/2022] Open
Abstract
T cells play a crucial role in controlling and driving the immune response with their ability to discriminate peptides derived from healthy as well as pathogenic proteins. In this review, we focus on the currently available computational tools for epitope prediction, with a particular focus on tools aimed at identifying neoepitopes, i.e. cancer-specific peptides and their potential for use in immunotherapy for cancer treatment. This review will cover how these tools work, what kind of data they use, as well as pros and cons in their respective applications.
Collapse
Affiliation(s)
| | - Milena Vujović
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Annie Borch
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Sine Reker Hadrup
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Paolo Marcatili
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| |
Collapse
|
14
|
Zhang W, Zhang YM, Gao Y, Zhang S, Chu W, Wei G, Li K, He X, Chen L, Guo L, Luan S, Zhang P. A novel decision tree model based on chromosome imbalances in cell-free DNA and CA-125 in the differential diagnosis of ovarian cancer. Int J Biol Markers 2021; 36:3-13. [PMID: 34053311 DOI: 10.1177/1724600821992356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OBJECTIVE CA-125 is widely used as biomarker of ovarian cancer. However, CA-125 suffers low accuracy. We developed a hybrid analytical model, the Ovarian Cancer Decision Tree (OCDT), employing a two-layer decision tree, which considers genetic alteration information from cell-free DNA along with CA-125 value to distinguish malignant tumors from benign tumors. METHODS We consider major copy number alterations at whole chromosome and chromosome-arm level as the main feature of our detection model. Fifty-eight patients diagnosed with malignant tumors, 66 with borderline tumors, and 10 with benign tumors were enrolled. RESULTS Genetic analysis revealed significant arm-level imbalances in most malignant tumors, especially in high-grade serous cancers in which 12 chromosome arms with significant aneuploidy (P<0.01) were identified, including 7 arms with significant gains and 5 with significant losses. The area under receiver operating characteristic curve (AUC) was 0.8985 for copy number variations analysis, compared to 0.8751 of CA125. The OCDT was generated with a cancerous score (CScore) threshold of 5.18 for the first level, and a CA-125 value of 103.1 for the second level. Our most optimized OCDT model achieved an AUC of 0.975. CONCLUSIONS The results suggested that genetic variations extracted from cfDNA can be combined with CA-125, and together improved the differential diagnosis of malignant from benign ovarian tumors. The model would aid in the pre-operative assessment of women with adnexal masses. Future clinical trials need to be conducted to further evaluate the value of CScore in clinical settings and search for the optimal threshold for malignancy detection.
Collapse
Affiliation(s)
- Weina Zhang
- Department of Gynecology, Qingdao Municipal Hospital, Qingdao, Shandong Province, China
| | - Yu-Min Zhang
- Biological Testing Department, Heze Food and Drug Testing Institute, Heze, Shandong Province, China
| | - Yuan Gao
- Department of Gynecology, Qingdao Municipal Hospital, Qingdao, Shandong Province, China
| | - Shengmiao Zhang
- Department of Gynecology, Qingdao Municipal Hospital, Qingdao, Shandong Province, China
| | - Weixin Chu
- Department of Gynecology, Qingdao Municipal Hospital, Qingdao, Shandong Province, China
| | - Guopeng Wei
- Research Lab, Gezhi Genomics, Nanjing, Jiangsu Province, China
| | - Ke Li
- Research Lab, Gezhi Genomics, Nanjing, Jiangsu Province, China
| | - Xuesong He
- Research Lab, Gezhi Genomics, Nanjing, Jiangsu Province, China
| | - Long Chen
- Department of Gynecology, Qingdao Municipal Hospital, Qingdao, Shandong Province, China
| | - Li Guo
- Department of Gynecology, Qingdao Municipal Hospital, Qingdao, Shandong Province, China
| | - Shufang Luan
- Department of Gynecology, Qingdao Municipal Hospital, Qingdao, Shandong Province, China
| | - Ping Zhang
- Department of Gynecology, Qingdao Municipal Hospital, Qingdao, Shandong Province, China
| |
Collapse
|
15
|
Miszczyk J, Przydacz M, Zembrzuski M, Chłosta PL. Investigation of Chromosome 1 Aberrations in the Lymphocytes of Prostate Cancer and Benign Prostatic Hyperplasia Patients by Fluorescence in situ Hybridization. Cancer Manag Res 2021; 13:4291-4298. [PMID: 34103984 PMCID: PMC8178583 DOI: 10.2147/cmar.s293249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 05/04/2021] [Indexed: 11/23/2022] Open
Abstract
Purpose Radiotherapy is one of the most common treatments for prostate cancer. Finding a useful predictor of the therapeutic outcome is crucial as it increases the efficacy of treatment planning. This study investigated the individual susceptibility to radiation based on chromosome 1 aberration frequency measured by the FISH (fluorescence in situ hybridization) method. Patients and Methods Whole blood samples were collected from 27 prostate cancer (PCa) patients and 32 subjects with benign prostatic hyperplasia (BPH), who were considered as a control group. Samples were irradiated with 2 Gy of x-rays, cultured, harvested, and used in the FISH procedure. Results After irradiation, significantly higher levels of all studied chromosome 1 aberrations (except for deletions) in the group of PCa patients were revealed. Furthermore, in the lymphocytes of cancer patients, nearly five-fold higher frequencies of acentric fragments were observed compared to the BPH group. The highest individual radiosensitivities for all estimated biomarkers were seen in PCa patient cells who reported cancer incidence in the immediate family (CIF+). Conclusion The differences in chromosome 1 aberrations between PCa and BPH demonstrate that lymphocytes taken from patients with prostate cancer have higher radiosensitivity which might be related to hereditary or familiar inclinations. Therefore, this technique may find future application in searching biomarkers of the cellular radiotherapy response in prostate cancer patients.
Collapse
Affiliation(s)
- Justyna Miszczyk
- Department of Experimental Physics of Complex Systems, The H. Niewodniczański Institute of Nuclear Physics PAN, Krakow, Poland
| | - Mikołaj Przydacz
- Department of Urology, Jagiellonian University Medical College, Krakow, Poland
| | - Michał Zembrzuski
- Department of Urology, Jagiellonian University Medical College, Krakow, Poland
| | - Piotr L Chłosta
- Department of Urology, Jagiellonian University Medical College, Krakow, Poland
| |
Collapse
|
16
|
Pires JG, da Silva GF, Weyssow T, Conforte AJ, Pagnoncelli D, da Silva FAB, Carels N. Galaxy and MEAN Stack to Create a User-Friendly Workflow for the Rational Optimization of Cancer Chemotherapy. Front Genet 2021; 12:624259. [PMID: 33679888 PMCID: PMC7935533 DOI: 10.3389/fgene.2021.624259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 01/22/2021] [Indexed: 12/24/2022] Open
Abstract
One aspect of personalized medicine is aiming at identifying specific targets for therapy considering the gene expression profile of each patient individually. The real-world implementation of this approach is better achieved by user-friendly bioinformatics systems for healthcare professionals. In this report, we present an online platform that endows users with an interface designed using MEAN stack supported by a Galaxy pipeline. This pipeline targets connection hubs in the subnetworks formed by the interactions between the proteins of genes that are up-regulated in tumors. This strategy has been proved to be suitable for the inhibition of tumor growth and metastasis in vitro. Therefore, Perl and Python scripts were enclosed in Galaxy for translating RNA-seq data into protein targets suitable for the chemotherapy of solid tumors. Consequently, we validated the process of target diagnosis by (i) reference to subnetwork entropy, (ii) the critical value of density probability of differential gene expression, and (iii) the inhibition of the most relevant targets according to TCGA and GDC data. Finally, the most relevant targets identified by the pipeline are stored in MongoDB and can be accessed through the aforementioned internet portal designed to be compatible with mobile or small devices through Angular libraries.
Collapse
Affiliation(s)
- Jorge Guerra Pires
- Plataforma de Modelagem de Sistemas Biológicos, Center for Technology Development in Health (CDTS), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Gilberto Ferreira da Silva
- Plataforma de Modelagem de Sistemas Biológicos, Center for Technology Development in Health (CDTS), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Thomas Weyssow
- Informatic Department, Free University of Brussels (ULB), Brussels, Belgium
| | - Alessandra Jordano Conforte
- Plataforma de Modelagem de Sistemas Biológicos, Center for Technology Development in Health (CDTS), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil.,Laboratório de Modelagem Computacional de Sistemas Biológicos, Scientific Computing Program, FIOCRUZ, Rio de Janeiro, Brazil
| | | | - Fabricio Alves Barbosa da Silva
- Laboratório de Modelagem Computacional de Sistemas Biológicos, Scientific Computing Program, FIOCRUZ, Rio de Janeiro, Brazil
| | - Nicolas Carels
- Plataforma de Modelagem de Sistemas Biológicos, Center for Technology Development in Health (CDTS), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| |
Collapse
|
17
|
Han T, Jing X, Bao J, Zhao L, Zhang A, Miao R, Guo H, Zhou B, Zhang S, Sun J, Shi J. H. pylori infection alters repair of DNA double-strand breaks via SNHG17. J Clin Invest 2021; 130:3901-3918. [PMID: 32538894 DOI: 10.1172/jci125581] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 04/14/2020] [Indexed: 12/15/2022] Open
Abstract
Chronic infections can lead to carcinogenesis through inflammation-related mechanisms. Chronic infection of the human gastric mucosa with Helicobacter pylori is a well-known risk factor for gastric cancer. However, the mechanisms underlying H. pylori-induced gastric carcinogenesis are incompletely defined. We aimed to screen and clarify the functions of long noncoding RNAs (lncRNAs) that are differentially expressed in H. pylori-related gastric cancer. We found that lncRNA SNHG17 was upregulated by H. pylori infection and markedly increased the levels of double-strand breaks (DSBs). SNHG17 overexpression correlated with poor overall survival in patients with gastric cancer. The recruitment of NONO by overabundant nuclear SNHG17, along with the role of cytoplasmic SNHG17 as a decoy for miR-3909, which regulates Rad51 expression, shifted the DSB repair balance from homologous recombination toward nonhomologous end joining. Notably, during chronic H. pylori infection, SNHG17 knockdown inhibited chromosomal aberrations. Our findings suggest that spatially independent deregulation of the SNHG17/NONO and SNHG17/miR-3909/RING1/Rad51 pathways upon H. pylori infection promotes tumorigenesis in gastric cancer by altering the DNA repair system, which is critical for the maintenance of genomic stability. Upregulation of SNHG17 by H. pylori infection might be an undefined link between cancer and inflammation.
Collapse
Affiliation(s)
- Taotao Han
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaohui Jing
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiayu Bao
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lianmei Zhao
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Research Center, Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, China
| | - Aidong Zhang
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Renling Miao
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hui Guo
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Baoguo Zhou
- Department of General Surgery, First Affiliated Hospital of Harbin Medical University, Heilongjiang, China
| | - Shang Zhang
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiazeng Sun
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Juan Shi
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| |
Collapse
|
18
|
LAMP3 (CD208) Expression in Squamous Cell Carcinoma and Epithelial Dysplasia of the Oral Cavity and Clinicopathological Characteristics of Unfavorable Prognosis. Rep Biochem Mol Biol 2021; 9:379-384. [PMID: 33969129 DOI: 10.52547/rbmb.9.4.373] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Background This study aimed to evaluate LAMP3 (CD208) gene expression in oral squamous cell carcinoma (OSCC) and dysplastic oral epithelium by quantitative real-time polymerase chain reaction (qPCR) and compare LAMP3 expression in different disease grades and stages. Methods In this study, 60 OSCC and dysplastic oral epithelium samples were obtained from the Mashhad University of Medical Sciences together with their demographic and clinicopathological documents. LAMP3 expression was measured by qPCR. Results LAMP3 expression was significantly greater in OSCC than in dysplasia samples (P=0.001), in grade III OSCC than in grades I and II, and also greater in advanced than in early OSCC disease stage (P=0.001). Conclusion The significantly greater LAMP3 expression in OSCC than in dysplastic epithelium indicates a role for LAMP3 in carcinogenesis in oral mucosa. Our results suggest LAMP3 may be useful as an anticancer target and/or to predict disease pathogenesis in OSCC patient's cells.
Collapse
|
19
|
Impact of infections, preneoplasia and cancer on micronucleus formation in urothelial and cervical cells: A systematic review. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2020; 787:108361. [PMID: 34083051 DOI: 10.1016/j.mrrev.2020.108361] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/03/2020] [Accepted: 12/05/2020] [Indexed: 11/24/2022]
Abstract
Approximately 165,000 and 311,000 individuals die annually from urothelial (UC) and cervical (CC) cancer. The therapeutic success of these cancers depends strongly on their early detection and could be improved by use of additional diagnostic tools. We evaluated the current knowledge of the use of micronucleus (MN) assays (which detect structural and numerical chromosomal aberrations) with urine- (UDC) and cervix-derived (CDC) cells for the identification of humans with increased risks and for the diagnosis of UC and CC. Several findings indicate that MN rates in UDC are higher in individuals with inflammation and schistosomiasis that are associated with increased prevalence of UC; furthermore, higher MN rates were also found in CDC in women with HPV, Candidiasis and Trichomonas infections which increase the risks for CC. Only few studies were published on MN rates in UDS in patients with UC, two concern the detection of recurrent bladder tumors. Strong correlations were found in individuals with abnormal CC cells that are scored in Pap tests and histopathological abnormalities. In total, 16 studies were published which concerned these topics. MN rates increased in the order: inflammation < ASC-US/ASC-H < LSIL < HSIL < CC. It is evident that MNi numbers increase with the risk to develop CC and with the degree of malignant transformation. Overall, the evaluation of the literature indicates that MNi are useful additional biomarkers for the prognosis and detection of CC and possibly also for UC. In regard to the diagnosis/surveillance of UC, further investigations are needed to draw firm conclusions, but the currently available data are promising. In general, further standardization of the assays is needed (i.e. definition of optimal cell numbers and of suitable stains as well as elucidation of the usefulness of parameters reflecting cytotoxicity and mitotic activity) before MN trials can be implemented in routine screening.
Collapse
|
20
|
Ibragimova MK, Tsyganov MM, Slonimskaya EM, Litviakov NV. Aberrations of the number of copies (CNA) in the genome of luminal B breast tumor. BULLETIN OF SIBERIAN MEDICINE 2020. [DOI: 10.20538/1682-0363-2020-3-22-28] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- M. K. Ibragimova
- Саnсеr Rеsеаrсh Institute, Tomsk National Research Medical Center of Russian Academy of Sciences
| | - M. M. Tsyganov
- Саnсеr Rеsеаrсh Institute, Tomsk National Research Medical Center of Russian Academy of Sciences
| | | | - N. V. Litviakov
- Саnсеr Rеsеаrсh Institute, Tomsk National Research Medical Center of Russian Academy of Sciences
| |
Collapse
|
21
|
SMURF2 prevents detrimental changes to chromatin, protecting human dermal fibroblasts from chromosomal instability and tumorigenesis. Oncogene 2020; 39:3396-3410. [PMID: 32103168 DOI: 10.1038/s41388-020-1226-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 02/13/2020] [Accepted: 02/17/2020] [Indexed: 01/17/2023]
Abstract
E3 ubiquitin ligases (E3s) play essential roles in the maintenance of tissue homeostasis under normal and stress conditions, as well as in disease states, particularly in cancer. However, the role of E3s in the initiation of human tumors is poorly understood. Previously, we reported that genetic ablation of the HECT-type E3 ubiquitin ligase Smurf2 induces carcinogenesis in mice; but whether and how these findings are pertinent to the inception of human cancer remain unknown. Here we show that SMURF2 is essential to protect human dermal fibroblasts (HDFs) from malignant transformation, and its depletion converts HDFs into tumorigenic entity. This phenomenon was associated with the radical changes in chromatin structural and epigenetic landscape, dysregulated gene expression and cell-cycle control, mesenchymal-to-epithelial transition and impaired DNA damage response. Furthermore, we show that SMURF2-mediated tumor suppression is interlinked with SMURF2's ability to regulate the expression of two central chromatin modifiers-an E3 ubiquitin ligase RNF20 and histone methyltransferase EZH2. Silencing these factors significantly reduced the growth and transformation capabilities of SMURF2-depleted cells. Finally, we demonstrate that SMURF2-compromised HDFs are highly tumorigenic in nude mice. These findings suggest the critical role that SMURF2 plays in preventing malignant alterations, chromosomal instability and cancer.
Collapse
|
22
|
Kyrodimos E, Papanikolaou V, Tsiambas E, Kikidis D, Peschos D, Ragos V, Mastronikolis N, Riziotis C, Chrysovergis A. Cyclin D1 Gene Numerical Imbalances in Laryngeal Squamous Cell Carcinoma: A Tissue Microarray Grid Based Analysis. Asian Pac J Cancer Prev 2020; 21:379-384. [PMID: 32102514 PMCID: PMC7332136 DOI: 10.31557/apjcp.2020.21.2.379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Deregulation of critical proteins involved in cell cycle stability, such as cyclins, is a frequent genetic event in the development and progression of solid malignancies. Concerning laryngeal squamous cell carcinoma (LSCC), cyclin D1 oncogenic transformation leads to an aberrant protein expression and seems to affect the biological behaviour of the neoplasm. The aim of this study was to determine the correlation of cyclin D1 numerical imbalances with the corresponding protein expression levels in LSCCs. MATERIAL AND METHOD Using tissue microarray (TMA) technology, fifty (n=50) histologically confirmed primary LSSCs were cored at a diameter of 1.5 mm. Immunohistochemistry (IHC) and chromogenic in situ hybridization (CISH) analyses were applied. Concerning the screening process in CISH slides, a novel real-time reference and calibration grid platform was implemented. RESULTS Protein overexpression was observed in 22/50 (44%) cases; whereas, gene amplification was seen in 13/50 (26%) cases (p=0.02). Combined protein/ gene deregulation was associated with the stage of malignancy (p= 0.0014, p=0.001), whereas overall protein expression was strongly correlated with the grade of tumour (p= 0.001). CONCLUSION Cyclin D1 gene amplification led to aberrant protein expression in LSCCs and it was also correlated with an aggressive biological behaviour. To best of our knowledge, this study was the first described grid based CISH analysis under conventional bright field microscopy for detecting gene numerical imbalances while providing a novel and accurate description for screening-mapping process in the entire slide area.<br />.
Collapse
Affiliation(s)
- Efthymios Kyrodimos
- 1st ENT Dept, Hippocration Hospital, Medical School, University of Athens, Athens, Greece
| | - Vasileios Papanikolaou
- 1st ENT Dept, Hippocration Hospital, Medical School, University of Athens, Athens, Greece
| | - Evangelos Tsiambas
- Department of Pathology-Cytology, 401 GAH, Athens, Greece.,Department of Pathology, 417 VA Hospital (NIMTS), Athens, Greece
| | - Dimitrios Kikidis
- 1st ENT Dept, Hippocration Hospital, Medical School, University of Athens, Athens, Greece
| | - Dimitrios Peschos
- Department of Physiology, Medical School, University of Ioannina, Greece
| | - Vasileios Ragos
- Department of Maxillofacial, Medical School, University of Ioannina, Greece
| | - Nicholas Mastronikolis
- Department of Otorhinolaryngology, Head and Neck Surgery, Medical School, University of Patras, Greece
| | - Christos Riziotis
- Theoretical and Physical Chemistry Institute, Photonics for Nanoapplications Laboratory, National Hellenic Research Foundation, Athens, Greece
| | | |
Collapse
|
23
|
Cytogenetics and Cytogenomics Evaluation in Cancer. Int J Mol Sci 2019; 20:ijms20194711. [PMID: 31547595 PMCID: PMC6801775 DOI: 10.3390/ijms20194711] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 09/06/2019] [Accepted: 09/09/2019] [Indexed: 02/07/2023] Open
Abstract
The availability of cytogenetics and cytogenomics technologies improved the detection and identification of tumor molecular signatures as well as the understanding of cancer initiation and progression. The use of large-scale and high-throughput cytogenomics technologies has led to a fast identification of several cancer candidate biomarkers associated with diagnosis, prognosis, and therapeutics. The advent of array comparative genomic hybridization and next-generation sequencing technologies has significantly improved the knowledge about cancer biology, underlining driver genes to guide targeted therapy development, drug-resistance prediction, and pharmacogenetics. However, few of these candidate biomarkers have made the transition to the clinic with a clear benefit for the patients. Technological progress helped to demonstrate that cellular heterogeneity plays a significant role in tumor progression and resistance/sensitivity to cancer therapies, representing the major challenge of precision cancer therapy. A paradigm shift has been introduced in cancer genomics with the recent advent of single-cell sequencing, since it presents a lot of applications with a clear benefit to oncological patients, namely, detection of intra-tumoral heterogeneity, mapping clonal evolution, monitoring the development of therapy resistance, and detection of rare tumor cell populations. It seems now evident that no single biomarker could provide the whole information necessary to early detect and predict the behavior and prognosis of tumors. The promise of precision medicine is based on the molecular profiling of tumors being vital the continuous progress of high-throughput technologies and the multidisciplinary efforts to catalogue chromosomal rearrangements and genomic alterations of human cancers and to do a good interpretation of the relation genotype-phenotype.
Collapse
|
24
|
Chromosomal Density of Cancer Up-Regulated Genes, Aberrant Enhancer Activity and Cancer Fitness Genes Are Associated with Transcriptional Cis-Effects of Broad Copy Number Gains in Colorectal Cancer. Int J Mol Sci 2019; 20:ijms20184652. [PMID: 31546890 PMCID: PMC6770609 DOI: 10.3390/ijms20184652] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/15/2019] [Accepted: 09/16/2019] [Indexed: 12/31/2022] Open
Abstract
Broad Copy Number Gains (BCNGs) are copy-number increases of chromosomes or large segments of chromosomal arms. Publicly-available single-nucleotide polymorphism (SNP) array and RNA-Seq data of colon adenocarcinoma (COAD) samples from The Cancer Genome Atlas (TCGA) consortium allowed us to design better control groups in order to identify changes in expression due to highly recurrent BCNGs (in chromosomes 20, 8, 7, 13). We identified: (1) Overexpressed Transcripts (OverT), transcripts whose expression increases in "COAD groups bearing a specific BCNG" in comparison to "control COAD groups" not bearing it, and (2) up-regulated/down-regulated transcripts, transcripts whose expression increases/decreases in COAD groups in comparison to normal colon tissue. An analysis of gene expression reveals a correlation between the density of up-regulated genes per selected chromosome and the recurrence rate of their BCNGs. We report an enrichment of gained enhancer activity and of cancer fitness genes among OverT genes. These results support the hypothesis that the chromosomal density of overexpressed cancer fitness genes might play a significant role in the selection of gained chromosomes during cancer evolution. Analysis of functional pathways associated with OverT suggest that some multi-subunit protein complexes (eIF2, eIF3, CSTF and CPSF) are candidate targets for silencing transcriptional therapy.
Collapse
|
25
|
Wilhelm T, Olziersky AM, Harry D, De Sousa F, Vassal H, Eskat A, Meraldi P. Mild replication stress causes chromosome mis-segregation via premature centriole disengagement. Nat Commun 2019; 10:3585. [PMID: 31395887 PMCID: PMC6687892 DOI: 10.1038/s41467-019-11584-0] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 07/23/2019] [Indexed: 01/19/2023] Open
Abstract
Replication stress, a hallmark of cancerous and pre-cancerous lesions, is linked to structural chromosomal aberrations. Recent studies demonstrated that it could also lead to numerical chromosomal instability (CIN). The mechanism, however, remains elusive. Here, we show that inducing replication stress in non-cancerous cells stabilizes spindle microtubules and favours premature centriole disengagement, causing transient multipolar spindles that lead to lagging chromosomes and micronuclei. Premature centriole disengagement depends on the G2 activity of the Cdk, Plk1 and ATR kinases, implying a DNA-damage induced deregulation of the centrosome cycle. Premature centriole disengagement also occurs spontaneously in some CIN+ cancer cell lines and can be suppressed by attenuating replication stress. Finally, we show that replication stress potentiates the effect of the chemotherapeutic agent taxol, by increasing the incidence of multipolar cell divisions. We postulate that replication stress in cancer cells induces numerical CIN via transient multipolar spindles caused by premature centriole disengagement. Chromosome instability can be caused by replication stress, although the mechanism is unclear. Here, the authors show that inducing mild replication stress in cancerous and non-cancerous cell lines leads to centriole disengagement and the subsequent formation of lagging chromosomes and micronuclei.
Collapse
Affiliation(s)
- Therese Wilhelm
- Department of Cell Physiology and Metabolism, University of Geneva, 1211, Geneva 4, Switzerland. .,Department of Genetic Stability and Oncogenesis, Institut Gustave Roussy, CNRS UMR8200, 94805, Villejuif, France.
| | - Anna-Maria Olziersky
- Department of Cell Physiology and Metabolism, University of Geneva, 1211, Geneva 4, Switzerland
| | - Daniela Harry
- Department of Cell Physiology and Metabolism, University of Geneva, 1211, Geneva 4, Switzerland
| | - Filipe De Sousa
- Department of Cell Physiology and Metabolism, University of Geneva, 1211, Geneva 4, Switzerland
| | - Helène Vassal
- Department of Cell Physiology and Metabolism, University of Geneva, 1211, Geneva 4, Switzerland.,National Institute of Applied Sciences, Villeurbanne, 69621, France
| | - Anja Eskat
- Department of Cell Physiology and Metabolism, University of Geneva, 1211, Geneva 4, Switzerland.,Clinical Trials Center, University Hospital Zurich, 8091, Zurich, Switzerland
| | - Patrick Meraldi
- Department of Cell Physiology and Metabolism, University of Geneva, 1211, Geneva 4, Switzerland. .,Translational Research Centre in Onco-hematology, University of Geneva, 1211, Geneva 4, Switzerland.
| |
Collapse
|
26
|
Hjaltelin JX, Izarzugaza JMG, Jensen LJ, Russo F, Westergaard D, Brunak S. Identification of hyper-rewired genomic stress non-oncogene addiction genes across 15 cancer types. NPJ Syst Biol Appl 2019; 5:27. [PMID: 31396397 PMCID: PMC6685999 DOI: 10.1038/s41540-019-0104-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 06/26/2019] [Indexed: 12/24/2022] Open
Abstract
Non-oncogene addiction (NOA) genes are essential for supporting the stress-burdened phenotype of tumours and thus vital for their survival. Although NOA genes are acknowledged to be potential drug targets, there has been no large-scale attempt to identify and characterise them as a group across cancer types. Here we provide the first method for the identification of conditional NOA genes and their rewired neighbours using a systems approach. Using copy number data and expression profiles from The Cancer Genome Atlas (TCGA) we performed comparative analyses between high and low genomic stress tumours for 15 cancer types. We identified 101 condition-specific differential coexpression modules, mapped to a high-confidence human interactome, comprising 133 candidate NOA rewiring hub genes. We observe that most modules lose coexpression in the high-stress state and that activated stress modules and hubs take part in homoeostasis maintenance processes such as chromosome segregation, oxireductase activity, mitotic checkpoint (PLK1 signalling), DNA replication initiation and synaptic signalling. We furthermore show that candidate NOA rewiring hubs are unique for each cancer type, but that their respective rewired neighbour genes largely are shared across cancer types.
Collapse
Affiliation(s)
- Jessica Xin Hjaltelin
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Jose M. G. Izarzugaza
- Department of Bio and Health Informatics, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Lars Juhl Jensen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Francesco Russo
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - David Westergaard
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark
- Copenhagen University Hospital, Rigshospitalet, Blegdamsvej 9, DK-2100 Copenhagen, Denmark
| |
Collapse
|
27
|
Personalized medicine: From diagnostic to adaptive. Biomed J 2019; 45:132-142. [PMID: 35590431 PMCID: PMC9133264 DOI: 10.1016/j.bj.2019.05.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 11/26/2018] [Accepted: 05/08/2019] [Indexed: 12/12/2022] Open
Abstract
Personalized therapy has made great strides but suffers from the lack of companion diagnostics. With the dawn of extracellular vesicle (EV) based liquid biopsies fast approaching, this article proposes a novel approach to cancer treatment – adaptive therapy. Already being implemented in the field of radiation oncology, adaptive radiation therapy utilizes cutting-edge imaging techniques as a viable means to monitor a patient's tumor throughout the entire treatment cycle by adapting the dosage and alignment to match the dynamic tumor. Through an EV liquid biopsy, medical oncologists will also soon have the means to continuously monitor a patient's tumor as it changes over time. With this information, physicians will be able to “adapt” pre-planned therapies concurrently with the fluctuating tumor environment, thus creating a more precise personalized medicine. In this article, a theory for adaptive medicine and the current state of the field with an outlook on future challenges are discussed.
Collapse
|
28
|
Circulating Cell-Free DNA-Diagnostic and Prognostic Applications in Personalized Cancer Therapy. Ther Drug Monit 2019; 41:115-120. [PMID: 30883505 DOI: 10.1097/ftd.0000000000000566] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Genomic analyses in oncologic care allow for the development of more precise clinical laboratory tests that will be critical for personalized pharmacotherapy. Traditional biopsy-based approaches are limited by the availability of sequential tissue specimens to detect resistance. Blood-based genomic profiling ("liquid biopsy") is useful for longitudinal monitoring of tumor genomes and can complement biopsies. Tumor-associated mutations can be identified in cell-free tumor DNA (ctDNA) from patient blood samples and used for monitoring disease activity. The US Food and Drug Administration approved a liquid biopsy test for EGFR-activating mutations in patients with non-small-cell lung cancer as a companion diagnostic for therapy selection. ctDNA also allows for the identification of mutations selected by treatment such as EGFR T790M in non-small-cell lung cancer. ctDNA can also detect mutations such as KRAS G12V in colorectal cancer and BRAF V600E/V600K in melanoma. Chromosomal aberration pattern analysis by low-coverage whole genome sequencing is a new, broader approach. Genomic imbalances detected in cell-free DNA (cfDNA) can be used to compute a copy number instability (CNI) score. In clinical studies, it was demonstrated that the change in CNI score can serve as an early predictor of therapeutic response to chemotherapy/immunotherapy of many cancer types. In multivariable models, it could be shown that the CNI score was superior to clinical parameters for prediction of overall survival in patients with head and neck cancer. There is emerging evidence for the clinical validity of ctDNA testing regarding identification of candidates for targeted therapies, prediction of therapeutic response, early detection of recurrence, resistance mutation detection, measuring genetic heterogeneity, tumor burden monitoring, and risk stratification. Improvement of sensitivity to detect tumors at very early stages is difficult due to insufficient mutant DNA fraction of ≤0.01%. Further developments will include validation in prospective multicenter interventional outcome studies and the development of digital platforms to integrate diagnostic data.
Collapse
|
29
|
Calling Variants in the Clinic: Informed Variant Calling Decisions Based on Biological, Clinical, and Laboratory Variables. Comput Struct Biotechnol J 2019; 17:561-569. [PMID: 31049166 PMCID: PMC6482431 DOI: 10.1016/j.csbj.2019.04.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 03/12/2019] [Accepted: 04/03/2019] [Indexed: 01/10/2023] Open
Abstract
Deep sequencing genomic analysis is becoming increasingly common in clinical research and practice, enabling accurate identification of diagnostic, prognostic, and predictive determinants. Variant calling, distinguishing between true mutations and experimental errors, is a central task of genomic analysis and often requires sophisticated statistical, computational, and/or heuristic techniques. Although variant callers seek to overcome noise inherent in biological experiments, variant calling can be significantly affected by outside factors including those used to prepare, store, and analyze samples. The goal of this review is to discuss known experimental features, such as sample preparation, library preparation, and sequencing, alongside diverse biological and clinical variables, and evaluate their effect on variant caller selection and optimization.
Collapse
|
30
|
Maccormick TM, Carvalho CES, Bravo Neto GP, Carvalho MDGDC. Comparative analysis of glutathione transferase genetic polymorphism, Helicobacter pylori and Epstein-Barr virus between the tumor area and the proximal and distal resection margins of gastric cancer. Rev Col Bras Cir 2019; 46:e2068. [PMID: 30726307 DOI: 10.1590/0100-6991e-20192068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 12/30/2018] [Indexed: 01/18/2023] Open
Abstract
OBJECTIVE to compare the polymorphism of the Glutathione S-transferase theta 1 (GSTT1) and Glutathione S-transferase mu 1 (GSTM1) genes from the tumor area with the proximal and distal margins of stomach specimens resected from patients with gastric cancer, and to investigate the presence of Epstein-Barr virus (EBV) DNA and Helicobacter pylori. METHODS we prospectively collected tissue specimens from the tumor area and from the proximal and distal resection margins of the stomachs of ten patients with gastric adenocarcinoma who underwent gastrectomy with D2 lymphadenectomy, and submitted these specimens to DNA extraction. We compared the tumor area with the proximal and distal margins of the resected stomachs for polymorphism of GSTT1 and GSTM1 genes and investigated the presence of EBV-DNA and H. pylori. We used the p53 exon 5 gene as an internal control of the multiplex PCR reaction. RESULTS in one patient, we detected null GSTT1 and GSTM1 genotypes in the tumor area, in contrast to the presence of both genes in the proximal and distal margins. We found EBV-DNA and H. pylori in the tumor area and also in the proximal and distal margins. In another patient, the proximal margin was negative for GSTT1, and EBV-DNA was negative in the distal margin. In three patients, EBV-DNA was negative only in the distal margin. CONCLUSION this is the first report where different genotypes, EBV-DNA and H. pylori infection were observed in the same patient, indicating a probable deletion of these genes in response to tumor progression and intratumoral heterogeneity.
Collapse
|
31
|
Abstract
Somatic structural variants undoubtedly play important roles in driving tumourigenesis. This is evident despite the substantial technical challenges that remain in accurately detecting structural variants and their breakpoints in tumours and in spite of our incomplete understanding of the impact of structural variants on cellular function. Developments in these areas of research contribute to the ongoing discovery of structural variation with a clear impact on the evolution of the tumour and on the clinical importance to the patient. Recent large whole genome sequencing studies have reinforced our impression of each tumour as a unique combination of mutations but paradoxically have also discovered similar genome-wide patterns of single-nucleotide and structural variation between tumours. Statistical methods have been developed to deconvolute mutation patterns, or signatures, that recur across samples, providing information about the mutagens and repair processes that may be active in a given tumour. These signatures can guide treatment by, for example, highlighting vulnerabilities in a particular tumour to a particular chemotherapy. Thus, although the complete reconstruction of the full evolutionary trajectory of a tumour genome remains currently out of reach, valuable data are already emerging to improve the treatment of cancer.
Collapse
Affiliation(s)
- Ailith Ewing
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH42XU, UK
| | - Colin Semple
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH42XU, UK
| |
Collapse
|
32
|
de Alencar MVOB, Islam MT, de Lima RMT, Paz MFCJ, dos Reis AC, da Mata AMOF, Filho JWGDO, Cerqueira GS, Ferreira PMP, e Sousa JMDC, Mubarak MS, Melo-Cavalcante AADC. Phytol as an anticarcinogenic and antitumoral agent: An in vivo study in swiss mice with DMBA-Induced breast cancer. IUBMB Life 2018; 71:200-212. [DOI: 10.1002/iub.1952] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 09/03/2018] [Accepted: 09/06/2018] [Indexed: 12/17/2022]
Affiliation(s)
| | - Muhammad Torequl Islam
- Department for Management of Science and Technology Development; Ton Duc Thang University; Ho Chi Minh City Vietnam
- Faculty of Pharmacy; Ton Duc Thang University; Ho Chi Minh City Vietnam
| | | | | | | | | | | | | | - Paulo Michel Pinheiro Ferreira
- Postgraduate Program in Biotechnology (RENORBIO); Federal University of Piauí; Teresina Piauí Brazil
- Postgraduate Program in Pharmaceutical Sciences; Federal University of Piauí; Teresina Piauí Brazil
- Department of Biophysics and Physiology; Laboratory of Experimental Cancerology, Federal University of Piauí; Teresina Piauí Brazil
| | - João Marcelo de Castro e Sousa
- Postgraduate Program in Pharmaceutical Sciences; Federal University of Piauí; Teresina Piauí Brazil
- Department of Biological Sciences; Federal University of Piauí; Picos Piauí Brazil
| | | | - Ana Amélia de Carvalho Melo-Cavalcante
- Postgraduate Program in Biotechnology (RENORBIO); Federal University of Piauí; Teresina Piauí Brazil
- Postgraduate Program in Pharmaceutical Sciences; Federal University of Piauí; Teresina Piauí Brazil
| |
Collapse
|
33
|
Pan Y, Tong JHM, Kang W, Lung RWM, Chak WP, Chung LY, Wu F, Li H, Yu J, Chan AWH, To KF. EXOSC4 functions as a potential oncogene in development and progression of colorectal cancer. Mol Carcinog 2018; 57:1780-1791. [DOI: 10.1002/mc.22896] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 08/13/2018] [Accepted: 08/26/2018] [Indexed: 12/21/2022]
Affiliation(s)
- Yi Pan
- Department of Anatomical and Cellular Pathology; State Key Laboratory in Oncology in South China; Prince of Wales Hospital; The Chinese University of Hong Kong; Hong Kong SAR China
- Li Ka Shing Institute of Health Science; The Chinese University of Hong Kong; Sir Y.K. Pao Cancer Center; Hong Kong SAR China
- Institute of Digestive Disease; Partner State Key Laboratory of Digestive Disease; The Chinese University of Hong Kong; Hong Kong SAR China
- Department of Pathology; Chinese Academy of Medical Sciences and Peking Union Medical College; National Cancer Center/Cancer Hospital; Beijing China
| | - Joanna H. M. Tong
- Department of Anatomical and Cellular Pathology; State Key Laboratory in Oncology in South China; Prince of Wales Hospital; The Chinese University of Hong Kong; Hong Kong SAR China
- Li Ka Shing Institute of Health Science; The Chinese University of Hong Kong; Sir Y.K. Pao Cancer Center; Hong Kong SAR China
- Institute of Digestive Disease; Partner State Key Laboratory of Digestive Disease; The Chinese University of Hong Kong; Hong Kong SAR China
| | - Wei Kang
- Department of Anatomical and Cellular Pathology; State Key Laboratory in Oncology in South China; Prince of Wales Hospital; The Chinese University of Hong Kong; Hong Kong SAR China
- Li Ka Shing Institute of Health Science; The Chinese University of Hong Kong; Sir Y.K. Pao Cancer Center; Hong Kong SAR China
- Institute of Digestive Disease; Partner State Key Laboratory of Digestive Disease; The Chinese University of Hong Kong; Hong Kong SAR China
| | - Raymond W. M. Lung
- Department of Anatomical and Cellular Pathology; State Key Laboratory in Oncology in South China; Prince of Wales Hospital; The Chinese University of Hong Kong; Hong Kong SAR China
- Li Ka Shing Institute of Health Science; The Chinese University of Hong Kong; Sir Y.K. Pao Cancer Center; Hong Kong SAR China
- Institute of Digestive Disease; Partner State Key Laboratory of Digestive Disease; The Chinese University of Hong Kong; Hong Kong SAR China
| | - Wing Po Chak
- Department of Anatomical and Cellular Pathology; State Key Laboratory in Oncology in South China; Prince of Wales Hospital; The Chinese University of Hong Kong; Hong Kong SAR China
- Li Ka Shing Institute of Health Science; The Chinese University of Hong Kong; Sir Y.K. Pao Cancer Center; Hong Kong SAR China
| | - Lau Ying Chung
- Department of Anatomical and Cellular Pathology; State Key Laboratory in Oncology in South China; Prince of Wales Hospital; The Chinese University of Hong Kong; Hong Kong SAR China
- Li Ka Shing Institute of Health Science; The Chinese University of Hong Kong; Sir Y.K. Pao Cancer Center; Hong Kong SAR China
| | - Feng Wu
- Department of Anatomical and Cellular Pathology; State Key Laboratory in Oncology in South China; Prince of Wales Hospital; The Chinese University of Hong Kong; Hong Kong SAR China
- Li Ka Shing Institute of Health Science; The Chinese University of Hong Kong; Sir Y.K. Pao Cancer Center; Hong Kong SAR China
- Institute of Digestive Disease; Partner State Key Laboratory of Digestive Disease; The Chinese University of Hong Kong; Hong Kong SAR China
| | - Hui Li
- Department of Anatomical and Cellular Pathology; State Key Laboratory in Oncology in South China; Prince of Wales Hospital; The Chinese University of Hong Kong; Hong Kong SAR China
- Li Ka Shing Institute of Health Science; The Chinese University of Hong Kong; Sir Y.K. Pao Cancer Center; Hong Kong SAR China
- Institute of Digestive Disease; Partner State Key Laboratory of Digestive Disease; The Chinese University of Hong Kong; Hong Kong SAR China
| | - Jun Yu
- Institute of Digestive Disease; Partner State Key Laboratory of Digestive Disease; The Chinese University of Hong Kong; Hong Kong SAR China
- Department of Medicine and Therapeutics; The Chinese University of Hong Kong; Hong Kong SAR China
| | - Anthony W. H. Chan
- Department of Anatomical and Cellular Pathology; State Key Laboratory in Oncology in South China; Prince of Wales Hospital; The Chinese University of Hong Kong; Hong Kong SAR China
- Li Ka Shing Institute of Health Science; The Chinese University of Hong Kong; Sir Y.K. Pao Cancer Center; Hong Kong SAR China
| | - Ka Fai To
- Department of Anatomical and Cellular Pathology; State Key Laboratory in Oncology in South China; Prince of Wales Hospital; The Chinese University of Hong Kong; Hong Kong SAR China
- Li Ka Shing Institute of Health Science; The Chinese University of Hong Kong; Sir Y.K. Pao Cancer Center; Hong Kong SAR China
- Institute of Digestive Disease; Partner State Key Laboratory of Digestive Disease; The Chinese University of Hong Kong; Hong Kong SAR China
| |
Collapse
|
34
|
Tyrrell HE, Kerr D. Prognostic markers for colorectal cancer. Oncotarget 2018; 9:33060-33061. [PMID: 30237850 PMCID: PMC6145697 DOI: 10.18632/oncotarget.26012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 08/15/2018] [Indexed: 11/25/2022] Open
|
35
|
Wise SS, Aboueissa AEM, Martino J, Wise JP. Hexavalent Chromium-Induced Chromosome Instability Drives Permanent and Heritable Numerical and Structural Changes and a DNA Repair-Deficient Phenotype. Cancer Res 2018; 78:4203-4214. [PMID: 29880483 PMCID: PMC6072558 DOI: 10.1158/0008-5472.can-18-0531] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 05/03/2018] [Accepted: 06/04/2018] [Indexed: 11/16/2022]
Abstract
A key hypothesis for how hexavalent chromium [Cr(VI)] causes cancer is that it drives chromosome instability (CIN), which leads to neoplastic transformation. Studies show chronic Cr(VI) can affect DNA repair and induce centrosome amplification, which can lead to structural and numerical CIN. However, no studies have considered whether these outcomes are transient or permanent. In this study, we exposed human lung cells to particulate Cr(VI) for three sequential 24-hour periods, each separated by about a month. After each treatment, cells were seeded at colony-forming density, cloned, expanded, and retreated, creating three generations of clonal cell lines. Each generation of clones was tested for chromium sensitivity, chromosome complement, DNA repair capacity, centrosome amplification, and the ability to grow in soft agar. After the first treatment, Cr(VI)-treated clones exhibited a normal chromosome complement, but some clones showed a repair-deficient phenotype and amplified centrosomes. After the second exposure, more than half of the treated clones acquired an abnormal karyotype including numerical and structural alterations, with many exhibiting deficient DNA double-strand break repair and amplified centrosomes. The third treatment produced new abnormal clones, with previously abnormal clones acquiring additional abnormalities and most clones exhibiting repair deficiency. CIN, repair deficiency, and amplified centrosomes were all permanent and heritable phenotypes of repeated Cr(VI) exposure. These outcomes support the hypothesis that CIN is a key mechanism of Cr(VI)-induced carcinogenesis.Significance: Chromium, a major public health concern and human lung carcinogen, causes fundamental changes in chromosomes and DNA repair in human lung cells. Cancer Res; 78(15); 4203-14. ©2018 AACR.
Collapse
Affiliation(s)
- Sandra S Wise
- Wise Laboratory of Environmental and Genetic Toxicology, Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, Kentucky
| | | | - Julieta Martino
- Wise Laboratory of Environmental and Genetic Toxicology, Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, Kentucky
| | - John Pierce Wise
- Wise Laboratory of Environmental and Genetic Toxicology, Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, Kentucky.
| |
Collapse
|
36
|
Toropov AA, Toropova AP, Raitano G, Benfenati E. CORAL: Building up QSAR models for the chromosome aberration test. Saudi J Biol Sci 2018; 26:1101-1106. [PMID: 31516335 PMCID: PMC6734133 DOI: 10.1016/j.sjbs.2018.05.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 04/23/2018] [Accepted: 05/06/2018] [Indexed: 12/13/2022] Open
Abstract
A high level of chromosomal aberrations in peripheral blood lymphocytes may be an early marker of cancer risk, but data on risk of specific cancers and types of chromosomal aberrations are limited. Consequently, the development of predictive models for chromosomal aberrations test is important task. Majority of models for chromosomal aberrations test are so-called knowledge-based rules system. The CORAL software (http://www.insilico.eu/coral, abbreviation of “CORrelation And Logic”) is an alternative for knowledge-based rules system. In contrast to knowledge-based rules system, the CORAL software gives possibility to estimate the influence upon the predictive potential of a model of different molecular alerts as well as different splits into the training set and validation set. This possibility is not available for the approaches based on the knowledge-based rules system. Quantitative Structure–Activity Relationships (QSAR) for chromosome aberration test are established for five random splits into the training, calibration, and validation sets. The QSAR approach is based on representation of the molecular structure by simplified molecular input-line entry system (SMILES) without data on physicochemical and/or biochemical parameters. In spite of this limitation, the statistical quality of these models is quite good.
Collapse
Affiliation(s)
| | - Alla P. Toropova
- Corresponding author at: Laboratory of Environmental Chemistry and Toxicology, IRCCS – Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa 19, 20156 Milano, Italy.
| | | | | |
Collapse
|
37
|
Wemmert S, Linxweiler M, Lerner C, Bochen F, Kulas P, Linxweiler J, Smola S, Urbschat S, Wagenpfeil S, Schick B. Combinational chromosomal aneuploidies and HPV status for prediction of head and neck squamous cell carcinoma prognosis in biopsies and cytological preparations. J Cancer Res Clin Oncol 2018; 144:1129-1141. [PMID: 29560516 DOI: 10.1007/s00432-018-2629-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 03/15/2018] [Indexed: 01/12/2023]
Abstract
PURPOSE Head and neck squamous cell carcinoma (HNSCC) is one of the most common human cancer types with a very poor prognosis despite improvements in therapeutic modalities. The major known risk factors are tobacco use and alcohol consumption or infection with high-risk human papilloma viruses (HPV), especially in oropharyngeal tumors. The current management based on the assessment of a variety of clinical and pathological parameters does not sufficiently predict outcome. METHODS Chromosomal alterations detected in HNSCCs were characterized by metaphase comparative genomic hybridization (CGH) and correlated with clinical parameters as well as survival time. Candidate regions were validated by quantitative polymerase chain reaction, fluorescence-in situ-hybridization (FISH) on dapped tumor tissue and liquid-based cytological smear preparations. In addition, HPV status was determined by polymerase chain reaction and simultaneous immunocytochemical p16INK4a-Ki67 staining. RESULTS The most frequent DNA copy number gains were observed on chromosome arms 3q, 8q, 5p, 7q, 12p, and 12q. DNA copy number decreases occurred most frequently at 3p, 17p, 4q, and 5q. FISH analysis verified in part the observed alterations by CGH on dapped tissues and was especially able to detect the most frequent DNA copy changes in cytological specimens. CONCLUSION The combination of HPV status and prognostic copy number alteration detected by FISH in biopsies or cytological specimens may be an applicable protocol for screening head and neck cancer patients prior to therapy.
Collapse
Affiliation(s)
- Silke Wemmert
- Department of Otorhinolaryngology, Saarland University Medical Center, Kirrberger Street 100, 66421, Homburg (Saar), Germany.
| | - Maximilian Linxweiler
- Department of Otorhinolaryngology, Saarland University Medical Center, Kirrberger Street 100, 66421, Homburg (Saar), Germany
| | - Cornelia Lerner
- Department of Otorhinolaryngology, Saarland University Medical Center, Kirrberger Street 100, 66421, Homburg (Saar), Germany
| | - Florian Bochen
- Department of Otorhinolaryngology, Saarland University Medical Center, Kirrberger Street 100, 66421, Homburg (Saar), Germany
| | - Philipp Kulas
- Department of Otorhinolaryngology, Saarland University Medical Center, Kirrberger Street 100, 66421, Homburg (Saar), Germany
| | | | - Sigrun Smola
- Institute of Virology, Saarland University Medical Center, Homburg (Saar), Germany
| | - Steffi Urbschat
- Department of Neurosurgery, Saarland University, Homburg (Saar), Germany
| | - Stefan Wagenpfeil
- Institute for Medical Biometry, Epidemiology and Medical Informatics, Saarland University, Homburg (Saar), Germany
| | - Bernhard Schick
- Department of Otorhinolaryngology, Saarland University Medical Center, Kirrberger Street 100, 66421, Homburg (Saar), Germany
| |
Collapse
|
38
|
Baird DM, Hendrickson EA. Telomeres and Chromosomal Translocations : There's a Ligase at the End of the Translocation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1044:89-112. [PMID: 29956293 DOI: 10.1007/978-981-13-0593-1_7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Chromosomal translocations are now well understood to not only constitute signature molecular markers for certain human cancers but often also to be causative in the genesis of that tumor. Despite the obvious importance of such events, the molecular mechanism of chromosomal translocations in human cells remains poorly understood. Part of the explanation for this dearth of knowledge is due to the complexity of the reaction and the need to archaeologically work backwards from the final product (a translocation) to the original unrearranged chromosomes to infer mechanism. Although not definitive, these studies have indicated that the aberrant usage of endogenous DNA repair pathways likely lies at the heart of the problem. An equally obfuscating aspect of this field, however, has also originated from the unfortunate species-specific differences that appear to exist in the relevant model systems that have been utilized to investigate this process. Specifically, yeast and murine systems (which are often used by basic science investigators) rely on different DNA repair pathways to promote chromosomal translocations than human somatic cells. In this chapter, we will review some of the basic concepts of chromosomal translocations and the DNA repair systems thought to be responsible for their genesis with an emphasis on underscoring the differences between other species and human cells. In addition, we will focus on a specific subset of translocations that involve the very end of a chromosome (a telomere). A better understanding of the relationship between DNA repair pathways and chromosomal translocations is guaranteed to lead to improved therapeutic treatments for cancer.
Collapse
Affiliation(s)
- Duncan M Baird
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Eric A Hendrickson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, MN, USA.
| |
Collapse
|
39
|
Oellerich M, Schütz E, Beck J, Kanzow P, Plowman PN, Weiss GJ, Walson PD. Using circulating cell-free DNA to monitor personalized cancer therapy. Crit Rev Clin Lab Sci 2017; 54:205-218. [PMID: 28393575 DOI: 10.1080/10408363.2017.1299683] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Michael Oellerich
- Department of Clinical Pharmacology, University Medical Center Göttingen, Göttingen, Germany
| | | | - Julia Beck
- Chronix Biomedical GmbH, Göttingen, Germany
| | - Philipp Kanzow
- Department of Clinical Pharmacology, University Medical Center Göttingen, Göttingen, Germany
| | - Piers N. Plowman
- Department of Clinical Oncology, St. Bartholomew’s Hospital, West Smithfield, London, UK
| | - Glen J. Weiss
- Cancer Treatment Centers of America, Goodyear, AZ, USA
| | - Philip D. Walson
- Department of Clinical Pharmacology, University Medical Center Göttingen, Göttingen, Germany
| |
Collapse
|
40
|
Hughesman CB, Lu XJD, Liu KYP, Zhu Y, Poh CF, Haynes C. A Robust Protocol for Using Multiplexed Droplet Digital PCR to Quantify Somatic Copy Number Alterations in Clinical Tissue Specimens. PLoS One 2016; 11:e0161274. [PMID: 27537682 PMCID: PMC4990255 DOI: 10.1371/journal.pone.0161274] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 06/25/2016] [Indexed: 12/24/2022] Open
Abstract
The ability of droplet digital PCR (ddPCR) to accurately determine the concentrations of amplifiable targets makes it a promising platform for measuring copy number alterations (CNAs) in genomic biomarkers. However, its application to clinical samples, particularly formalin-fixed paraffin-embedded specimens, will require strategies to reliably determine CNAs in DNA of limited quantity and quality. When applied to cancerous tissue, those methods must also account for global genetic instability and the associated probability that the abundance(s) of one or more chosen reference loci do not represent the average ploidy of cells comprising the specimen. Here we present an experimental design strategy and associated data analysis tool that enables accurate determination of CNAs in a panel of biomarkers using multiplexed ddPCR. The method includes strategies to optimize primer and probes design to cleanly segregate droplets in the data output from reaction wells amplifying multiple independent templates, and to correct for bias from artifacts such as DNA fragmentation. We demonstrate how a panel of reference loci can be used to determine a stable CNA-neutral benchmark. These innovations, when taken together, provide a comprehensive strategy that can be used to reliably detect biomarker CNAs in DNA extracted from either frozen or FFPE tissue biopsies.
Collapse
Affiliation(s)
- Curtis B. Hughesman
- Department of Oral Medical Biological Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - X. J. David Lu
- Department of Oral Medical Biological Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Kelly Y. P. Liu
- Department of Oral Medical Biological Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Yuqi Zhu
- Department of Oral Medical Biological Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Catherine F. Poh
- Department of Oral Medical Biological Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, V6T 2B5, Canada
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, V5Z 1L3, Canada
- * E-mail: (CH); (CP)
| | - Charles Haynes
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
- RES’EAU NSERC Research Network, Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
- * E-mail: (CH); (CP)
| |
Collapse
|