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Budhbaware T, Rathored J, Shende S. Molecular methods in cancer diagnostics: a short review. Ann Med 2024; 56:2353893. [PMID: 38753424 PMCID: PMC11100444 DOI: 10.1080/07853890.2024.2353893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND One of the ailments with the greatest fatality rates in the 21st century is cancer. Globally, molecular methods are widely employed to treat cancer-related disorders, and the body of research on this subject is growing yearly. A thorough and critical summary of the data supporting molecular methods for illnesses linked to cancer is required. OBJECTIVE In order to guide clinical practice and future research, it is important to examine and summarize the systematic reviews (SRs) that evaluate the efficacy and safety of molecular methods for disorders associated to cancer. METHODS We developed a comprehensive search strategy to find relevant articles from electronic databases like PubMed, Google Scholar, Web of Science (WoS), or Scopus. We looked through the literature and determined which diagnostic methods in cancer genetics were particularly reliable. We used phrases like 'cancer genetics', genetic susceptibility, Hereditary cancer, cancer risk assessment, 'cancer diagnostic tools', cancer screening', biomarkers, and molecular diagnostics, reviews and meta-analyses evaluating the efficacy and safety of molecular therapies for cancer-related disorders. Research that only consider treatment modalities that don't necessitate genetic or molecular diagnostics fall under the exclusion criteria. RESULTS The results of this comprehensive review clearly demonstrate the transformative impact of molecular methods in the realm of cancer genetics.This review underscores how these technologies have empowered researchers and clinicians to identify and understand key genetic alterations that drive malignancy, ranging from point mutations to structural variations. Such insights are instrumental in pinpointing critical oncogenic drivers and potential therapeutic targets, thus opening the door for methods in precision medicine that can significantly improve patient outcomes. LIMITATION The search does not specify a timeframe for publication inclusion, it may have missed recent advancements or changes in the field's landscape of molecular methods for cancer. As a result, it may not have included the most recent developments in the field. CONCLUSION After conducting an in-depth study on the molecular methods in cancer genetics, it is evident that these cutting-edge technologies have revolutionized the field of oncology, providing researchers and clinicians with powerful tools to unravel the complexities of cancer at the genetic level. The integration of molecular methods techniques has not only enhanced our understanding of cancer etiology, progression, and treatment response but has also opened new avenues for personalized medicine and targeted therapies, leading to improved patient outcomes.
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Affiliation(s)
- Tanushree Budhbaware
- Department of ‘School of Allied Health Sciences’, Central Research Laboratory (CRL) and Molecular Diagnostics, Datta Meghe Institute of Higher Education and Research, Sawangi (Meghe), Wardha, India
| | - Jaishriram Rathored
- Department of ‘School of Allied Health Sciences’, Central Research Laboratory (CRL) and Molecular Diagnostics, Datta Meghe Institute of Higher Education and Research, Sawangi (Meghe), Wardha, India
| | - Sandesh Shende
- Department of ‘School of Allied Health Sciences’, Central Research Laboratory (CRL) and Molecular Diagnostics, Datta Meghe Institute of Higher Education and Research, Sawangi (Meghe), Wardha, India
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2
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Golestan A, Tahmasebi A, Maghsoodi N, Faraji SN, Irajie C, Ramezani A. Unveiling promising breast cancer biomarkers: an integrative approach combining bioinformatics analysis and experimental verification. BMC Cancer 2024; 24:155. [PMID: 38291367 PMCID: PMC10829368 DOI: 10.1186/s12885-024-11913-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 01/23/2024] [Indexed: 02/01/2024] Open
Abstract
BACKGROUND Breast cancer remains a significant health challenge worldwide, necessitating the identification of reliable biomarkers for early detection, accurate prognosis, and targeted therapy. MATERIALS AND METHODS Breast cancer RNA expression data from the TCGA database were analyzed to identify differentially expressed genes (DEGs). The top 500 up-regulated DEGs were selected for further investigation using random forest analysis to identify important genes. These genes were evaluated based on their potential as diagnostic biomarkers, their overexpression in breast cancer tissues, and their low median expression in normal female tissues. Various validation methods, including online tools and quantitative Real-Time PCR (qRT-PCR), were used to confirm the potential of the identified genes as breast cancer biomarkers. RESULTS The study identified four overexpressed genes (CACNG4, PKMYT1, EPYC, and CHRNA6) among 100 genes with higher importance scores. qRT-PCR analysis confirmed the significant upregulation of these genes in breast cancer patients compared to normal samples. CONCLUSIONS These findings suggest that CACNG4, PKMYT1, EPYC, and CHRNA6 may serve as valuable biomarkers for breast cancer diagnosis, and PKMYT1 may also have prognostic significance. Furthermore, CACNG4, CHRNA6, and PKMYT1 show promise as potential therapeutic targets. These findings have the potential to advance diagnostic methods and therapeutic approaches for breast cancer.
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Affiliation(s)
- Ali Golestan
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Nafiseh Maghsoodi
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Nooreddin Faraji
- Department of Pathology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Cambyz Irajie
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amin Ramezani
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran.
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
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3
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Neagu AN, Whitham D, Bruno P, Morrissiey H, Darie CA, Darie CC. Omics-Based Investigations of Breast Cancer. Molecules 2023; 28:4768. [PMID: 37375323 DOI: 10.3390/molecules28124768] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/08/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Breast cancer (BC) is characterized by an extensive genotypic and phenotypic heterogeneity. In-depth investigations into the molecular bases of BC phenotypes, carcinogenesis, progression, and metastasis are necessary for accurate diagnoses, prognoses, and therapy assessments in predictive, precision, and personalized oncology. This review discusses both classic as well as several novel omics fields that are involved or should be used in modern BC investigations, which may be integrated as a holistic term, onco-breastomics. Rapid and recent advances in molecular profiling strategies and analytical techniques based on high-throughput sequencing and mass spectrometry (MS) development have generated large-scale multi-omics datasets, mainly emerging from the three "big omics", based on the central dogma of molecular biology: genomics, transcriptomics, and proteomics. Metabolomics-based approaches also reflect the dynamic response of BC cells to genetic modifications. Interactomics promotes a holistic view in BC research by constructing and characterizing protein-protein interaction (PPI) networks that provide a novel hypothesis for the pathophysiological processes involved in BC progression and subtyping. The emergence of new omics- and epiomics-based multidimensional approaches provide opportunities to gain insights into BC heterogeneity and its underlying mechanisms. The three main epiomics fields (epigenomics, epitranscriptomics, and epiproteomics) are focused on the epigenetic DNA changes, RNAs modifications, and posttranslational modifications (PTMs) affecting protein functions for an in-depth understanding of cancer cell proliferation, migration, and invasion. Novel omics fields, such as epichaperomics or epimetabolomics, could investigate the modifications in the interactome induced by stressors and provide PPI changes, as well as in metabolites, as drivers of BC-causing phenotypes. Over the last years, several proteomics-derived omics, such as matrisomics, exosomics, secretomics, kinomics, phosphoproteomics, or immunomics, provided valuable data for a deep understanding of dysregulated pathways in BC cells and their tumor microenvironment (TME) or tumor immune microenvironment (TIMW). Most of these omics datasets are still assessed individually using distinct approches and do not generate the desired and expected global-integrative knowledge with applications in clinical diagnostics. However, several hyphenated omics approaches, such as proteo-genomics, proteo-transcriptomics, and phosphoproteomics-exosomics are useful for the identification of putative BC biomarkers and therapeutic targets. To develop non-invasive diagnostic tests and to discover new biomarkers for BC, classic and novel omics-based strategies allow for significant advances in blood/plasma-based omics. Salivaomics, urinomics, and milkomics appear as integrative omics that may develop a high potential for early and non-invasive diagnoses in BC. Thus, the analysis of the tumor circulome is considered a novel frontier in liquid biopsy. Omics-based investigations have applications in BC modeling, as well as accurate BC classification and subtype characterization. The future in omics-based investigations of BC may be also focused on multi-omics single-cell analyses.
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Affiliation(s)
- Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, "Alexandru Ioan Cuza" University of Iasi, Carol I Bvd, No. 20A, 700505 Iasi, Romania
| | - Danielle Whitham
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Pathea Bruno
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Hailey Morrissiey
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Celeste A Darie
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Costel C Darie
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
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4
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Zheng H, Zhao H, Zhang W, Zhang Y, Zhang Y, Ye B, Guo Q. Epstein-Barr virus immediate-early protein Zta mediates the proliferation and migration of HER2-overexpressing cancer cells. Arch Virol 2023; 168:150. [PMID: 37133552 DOI: 10.1007/s00705-023-05774-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/27/2023] [Indexed: 05/04/2023]
Abstract
Epstein-Barr virus immediate-early protein Zta plays an active role in altering cellular gene expression, which may be fundamentally linked to the viral life cycle, cell cycle, cell growth, and differentiation. HER2 is associated with a wide variety of human cancers, and its knockdown significantly reverses the malignant features of HER2-positive cancers. The aim of this study was to investigate the potential role of Zta in regulating HER2 expression and phenotype changes of MDA-MB-453 cells. Our results indicate that ectopic expression of Zta resulted in downregulation of the HER2 protein in cancer cells (MDA-MB-453, SKBR-3, BT474, and SKOV-3). The Zta protein significantly decreased HER2 mRNA and protein expression in MDA-MB-453 cells in a dose-dependent manner. Mechanistically, Zta recognized and targeted the promoter of HER2 gene, reducing the transcriptional activity of the HER2 gene. Zta induced G0/G1 arrest of MDA-MB-453 cells, inhibiting their proliferation and migration activity. These data suggest that Zta may act as a transforming suppressor of the HER2 gene.
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Affiliation(s)
- Hongling Zheng
- Department of Emergency, Jinan Children's Hospital, Jinan, 250022, People's Republic of China
| | - Haitao Zhao
- Department of Hematology, Binzhou People's Hospital, Binzhou, 256600, People's Republic of China
| | - Wei Zhang
- Department of Emergency, Jinan Children's Hospital, Jinan, 250022, People's Republic of China
| | - Yan Zhang
- Department of Emergency, Jinan Children's Hospital, Jinan, 250022, People's Republic of China
| | - Yun Zhang
- Department of Respiratory, Jinan Children's Hospital, Jinan, 250022, People's Republic of China
| | - Bing Ye
- Department of Emergency, Jinan Children's Hospital, Jinan, 250022, People's Republic of China.
| | - Qingwei Guo
- Department of Hematology and Oncology, Jinan Children's Hospital, Jinan, 250022, People's Republic of China.
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5
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Kringelbach T, Højgaard M, Rohrberg K, Spanggaard I, Laursen BE, Ladekarl M, Haslund CA, Harsløf L, Belcaid L, Gehl J, Søndergaard L, Eefsen RL, Hansen KH, Kodahl AR, Jensen LH, Holt MI, Oellegaard TH, Yde CW, Ahlborn LB, Lassen U. ProTarget: a Danish Nationwide Clinical Trial on Targeted Cancer Treatment based on genomic profiling - a national, phase 2, prospective, multi-drug, non-randomized, open-label basket trial. BMC Cancer 2023; 23:182. [PMID: 36814246 PMCID: PMC9948467 DOI: 10.1186/s12885-023-10632-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 02/10/2023] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND An increasing number of trials indicate that treatment outcomes in cancer patients with metastatic disease are improved when targeted treatments are matched with druggable genomic alterations in individual patients (pts). An estimated 30-80% of advanced solid tumors harbor actionable genomic alterations. However, the efficacy of personalized cancer treatment is still scarcely investigated in larger, controlled trials due to the low frequency and heterogenous distribution of druggable alterations among different histologic tumor types. Therefore, the overall effect of targeted cancer treatment on clinical outcomes still needs investigation. STUDY DESIGN/METHODS ProTarget is a national, non-randomized, multi-drug, open-label, pan-cancer phase 2 trial aiming to investigate the anti-tumor activity and toxicity of currently 13 commercially available, EMA-approved targeted therapies outside the labeled indication for treatment of advanced malignant diseases, harboring specific actionable genomic alterations. The trial involves the Danish National Molecular Tumor Board for confirmation of drug-variant matches. Key inclusion criteria include a) measurable disease (RECIST v.1.1), b) ECOG performance status 0-2, and c) an actionable genomic alteration matching one of the study drugs. Key exclusion criteria include a) cancer type within the EMA-approved label of the selected drug, and b) genomic alterations known to confer drug resistance. Initial drug dose, schedule and dose modifications are according to the EMA-approved label. The primary endpoint is objective response or stable disease at 16 weeks. Pts are assigned to cohorts defined by the selected drug, genomic alteration, and tumor histology type. Cohorts are monitored according to a Simon's two-stage-based design. Response is assessed every 8 weeks for the first 24 weeks, then every 12 weeks. The trial is designed similar to the Dutch DRUP and the ASCO TAPUR trials and is a partner in the Nordic Precision Cancer Medicine Trial Network. In ProTarget, serial fresh tumor and liquid biopsies are mandatory and collected for extensive translational research including whole genome sequencing, array analysis, and RNA sequencing. DISCUSSION The ProTarget trial will identify new predictive biomarkers for targeted treatments and provide new data and essential insights in molecular pathways involved in e.g., resistance mechanisms and thereby potentially evolve and expand the personalized cancer treatment strategy. PROTOCOL VERSION 16, 09-MAY-2022. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT04341181. Secondary Identifying No: ML41742. EudraCT No: 2019-004771-40.
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Affiliation(s)
- Tina Kringelbach
- grid.475435.4Department of Oncology, Phase 1 Unit, Rigshospitalet, Blegdamsvej 9, Copenhagen, Denmark
| | - Martin Højgaard
- grid.475435.4Department of Oncology, Phase 1 Unit, Rigshospitalet, Blegdamsvej 9, Copenhagen, Denmark
| | - Kristoffer Rohrberg
- grid.475435.4Department of Oncology, Phase 1 Unit, Rigshospitalet, Blegdamsvej 9, Copenhagen, Denmark
| | - Iben Spanggaard
- grid.475435.4Department of Oncology, Phase 1 Unit, Rigshospitalet, Blegdamsvej 9, Copenhagen, Denmark
| | - Britt Elmedal Laursen
- grid.7048.b0000 0001 1956 2722Department of Molecular Medicine/Department of Oncology, Aarhus University Hospital, and Institute of Biomedicine, Pharmacology/Precision Medicine, Aarhus University, Aarhus, Denmark
| | - Morten Ladekarl
- grid.27530.330000 0004 0646 7349Department of Oncology, Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Charlotte Aaquist Haslund
- grid.27530.330000 0004 0646 7349Department of Oncology, Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Laurine Harsløf
- grid.475435.4Department of Oncology, Phase 1 Unit, Rigshospitalet, Blegdamsvej 9, Copenhagen, Denmark
| | - Laila Belcaid
- grid.475435.4Department of Oncology, Phase 1 Unit, Rigshospitalet, Blegdamsvej 9, Copenhagen, Denmark
| | - Julie Gehl
- grid.476266.7Department of Clinical Oncology and Palliative Care, Zealand University Hospital, Roskilde, Denmark ,grid.5254.60000 0001 0674 042XDepartment of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lise Søndergaard
- grid.476266.7Department of Clinical Oncology and Palliative Care, Zealand University Hospital, Roskilde, Denmark
| | | | - Karin Holmskov Hansen
- grid.7143.10000 0004 0512 5013Department of Oncology, Clinic of Precision Medicine, Odense University Hospital, Odense, Denmark
| | - Annette Raskov Kodahl
- grid.7143.10000 0004 0512 5013Department of Oncology, Clinic of Precision Medicine, Odense University Hospital, Odense, Denmark ,grid.10825.3e0000 0001 0728 0170Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Lars Henrik Jensen
- grid.417271.60000 0004 0512 5814Department of Oncology, Vejle Hospital and University Hospital of Southern Denmark, Vejle, Denmark
| | - Marianne Ingerslev Holt
- grid.417271.60000 0004 0512 5814Department of Clinical Genetics, Vejle Hospital and University Hospital of Southern Denmark, Vejle, Denmark
| | - Trine Heide Oellegaard
- grid.7048.b0000 0001 1956 2722Department of Oncology, Goedstrup Hospital, Goedstrup, and Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | | | | | - Ulrik Lassen
- Department of Oncology, Phase 1 Unit, Rigshospitalet, Blegdamsvej 9, Copenhagen, Denmark.
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Bai X, Tang J. TRIM proteins in breast cancer: Function and mechanism. Biochem Biophys Res Commun 2023; 640:26-31. [PMID: 36495607 DOI: 10.1016/j.bbrc.2022.11.103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022]
Abstract
Breast cancer is the most prevalent malignancy in the world, and despite tremendous progress in current treatment strategies, recurrence, metastasis and drug resistance of breast cancer remain the major causes of death in patients. Tripartite motif (TRIM) family proteins play a critical role in the tumor progression such as cell proliferation, migration, invasion, and metastasis. Accumulating evidence suggests that the TRIM protein family serve as cancer suppressor proteins or oncoproteins in breast cancer. This review focused on the roles and molecular mechanisms of TRIM protein in breast cancer. Importantly, it provides new insights that TRIM proteins may be ideal targets to treat breast cancer.
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Affiliation(s)
- Xin Bai
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, Gansu, 730000, PR China
| | - Jianming Tang
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, Gansu, 730000, PR China.
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7
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Kodariah R, Fadilah F, Paramita RI, Erlina L, Istiadi KA, Billianti YD, Saraswati M, Panigoro SS. Raw fastq data for hotspot regions of cancer-related 50 genes using fresh frozen breast carcinoma tissues obtained from IMERI-FMUI biobank collections. Front Genet 2022; 13:973453. [PMID: 36386824 PMCID: PMC9644235 DOI: 10.3389/fgene.2022.973453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 10/14/2022] [Indexed: 11/23/2022] Open
Affiliation(s)
- Ria Kodariah
- Master’s Programme in Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
- Department of Anatomical Pathology, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Fadilah Fadilah
- Master’s Programme in Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
- Department of Medical Chemistry, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
- Bioinformatics Core Facilities-IMERI, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
- *Correspondence: Fadilah Fadilah, ; Rafika Indah Paramita,
| | - Rafika Indah Paramita
- Master’s Programme in Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
- Department of Medical Chemistry, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
- Bioinformatics Core Facilities-IMERI, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
- *Correspondence: Fadilah Fadilah, ; Rafika Indah Paramita,
| | - Linda Erlina
- Master’s Programme in Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
- Department of Medical Chemistry, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
- Bioinformatics Core Facilities-IMERI, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Khaerunnisa Anbar Istiadi
- Bioinformatics Core Facilities-IMERI, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
- Department of Biology, Institut Teknologi Sumatera, Lampung, Indonesia
| | - Yayi Dwina Billianti
- Master’s Programme in Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
- Department of Anatomical Pathology, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Meilania Saraswati
- Master’s Programme in Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
- Department of Anatomical Pathology, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Sonar Soni Panigoro
- Master’s Programme in Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
- Surgical Oncology Division, Department of Surgery, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
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Rosenquist R, Cuppen E, Buettner R, Caldas C, Dreau H, Elemento O, Frederix G, Grimmond S, Haferlach T, Jobanputra V, Meggendorfer M, Mullighan CG, Wordsworth S, Schuh A. Clinical utility of whole-genome sequencing in precision oncology. Semin Cancer Biol 2022; 84:32-39. [PMID: 34175442 DOI: 10.1016/j.semcancer.2021.06.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 06/02/2021] [Accepted: 06/22/2021] [Indexed: 12/14/2022]
Abstract
Precision diagnostics is one of the two pillars of precision medicine. Sequencing efforts in the past decade have firmly established cancer as a primarily genetically driven disease. This concept is supported by therapeutic successes aimed at particular pathways that are perturbed by specific driver mutations in protein-coding domains and reflected in three recent FDA tissue agnostic cancer drug approvals. In addition, there is increasing evidence from studies that interrogate the entire genome by whole-genome sequencing that acquired global and complex genomic aberrations including those in non-coding regions of the genome might also reflect clinical outcome. After addressing technical, logistical, financial and ethical challenges, national initiatives now aim to introduce clinical whole-genome sequencing into real-world diagnostics as a rational and potentially cost-effective tool for response prediction in cancer and to identify patients who would benefit most from 'expensive' targeted therapies and recruitment into clinical trials. However, so far, this has not been accompanied by a systematic and prospective evaluation of the clinical utility of whole-genome sequencing within clinical trials of uniformly treated patients of defined clinical outcome. This approach would also greatly facilitate novel predictive biomarker discovery and validation, ultimately reducing size and duration of clinical trials and cost of drug development. This manuscript is the third in a series of three to review and critically appraise the potential and challenges of clinical whole-genome sequencing in solid tumors and hematological malignancies.
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Affiliation(s)
- Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Solna, Sweden
| | - Edwin Cuppen
- Hartwig Medical Foundation, Amsterdam, The Netherlands; Center for Molecular Medicine and Oncode Institute, University Medical Center, Utrecht, The Netherlands
| | | | - Carlos Caldas
- Cancer Research UK Cambridge Institute and Department of Oncology, University of Cambridge, United Kingdom
| | - Helene Dreau
- NIHR Oxford Biomedical Research Centre and Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Olivier Elemento
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, United States; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, United States
| | - Geert Frederix
- Julius Center for Health Sciences and Primary Care, University Medical Center, Utrecht, The Netherlands
| | - Sean Grimmond
- Centre for Cancer Research, University of Melbourne, Melbourne, Australia
| | | | - Vaidehi Jobanputra
- New York Genome Center, 101 Avenue of the Americas, New York, NY 100132, United States; Columbia University Medical Center, 650 W 168th St, New York, NY 10032, United States
| | | | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, United States
| | - Sarah Wordsworth
- Nuffield Department of Population Health and Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Anna Schuh
- NIHR Oxford Biomedical Research Centre and Department of Oncology, University of Oxford, Oxford, United Kingdom.
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9
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Dotolo S, Esposito Abate R, Roma C, Guido D, Preziosi A, Tropea B, Palluzzi F, Giacò L, Normanno N. Bioinformatics: From NGS Data to Biological Complexity in Variant Detection and Oncological Clinical Practice. Biomedicines 2022; 10:biomedicines10092074. [PMID: 36140175 PMCID: PMC9495893 DOI: 10.3390/biomedicines10092074] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/12/2022] [Accepted: 08/22/2022] [Indexed: 11/22/2022] Open
Abstract
The use of next-generation sequencing (NGS) techniques for variant detection has become increasingly important in clinical research and in clinical practice in oncology. Many cancer patients are currently being treated in clinical practice or in clinical trials with drugs directed against specific genomic alterations. In this scenario, the development of reliable and reproducible bioinformatics tools is essential to derive information on the molecular characteristics of each patient’s tumor from the NGS data. The development of bioinformatics pipelines based on the use of machine learning and statistical methods is even more relevant for the determination of complex biomarkers. In this review, we describe some important technologies, computational algorithms and models that can be applied to NGS data from Whole Genome to Targeted Sequencing, to address the problem of finding complex cancer-associated biomarkers. In addition, we explore the future perspectives and challenges faced by bioinformatics for precision medicine both at a molecular and clinical level, with a focus on an emerging complex biomarker such as homologous recombination deficiency (HRD).
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Affiliation(s)
- Serena Dotolo
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori—IRCCS—Fondazione G. Pascale, 80131 Naples, Italy
| | - Riziero Esposito Abate
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori—IRCCS—Fondazione G. Pascale, 80131 Naples, Italy
| | - Cristin Roma
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori—IRCCS—Fondazione G. Pascale, 80131 Naples, Italy
| | - Davide Guido
- Bioinformatics Research Core Facility, Gemelli Science and Technology Park (GSTeP), Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Largo A. Gemelli, 8, 00168 Rome, Italy
| | - Alessia Preziosi
- Bioinformatics Research Core Facility, Gemelli Science and Technology Park (GSTeP), Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Largo A. Gemelli, 8, 00168 Rome, Italy
| | - Beatrice Tropea
- Bioinformatics Research Core Facility, Gemelli Science and Technology Park (GSTeP), Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Largo A. Gemelli, 8, 00168 Rome, Italy
| | - Fernando Palluzzi
- Bioinformatics Research Core Facility, Gemelli Science and Technology Park (GSTeP), Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Largo A. Gemelli, 8, 00168 Rome, Italy
| | - Luciano Giacò
- Bioinformatics Research Core Facility, Gemelli Science and Technology Park (GSTeP), Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Largo A. Gemelli, 8, 00168 Rome, Italy
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori—IRCCS—Fondazione G. Pascale, 80131 Naples, Italy
- Correspondence:
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10
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Hussen BM, Abdullah ST, Salihi A, Sabir DK, Sidiq KR, Rasul MF, Hidayat HJ, Ghafouri-Fard S, Taheri M, Jamali E. The emerging roles of NGS in clinical oncology and personalized medicine. Pathol Res Pract 2022; 230:153760. [PMID: 35033746 DOI: 10.1016/j.prp.2022.153760] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/29/2021] [Accepted: 01/06/2022] [Indexed: 02/07/2023]
Abstract
Next-generation sequencing (NGS) has been increasingly popular in genomics studies over the last decade, as new sequencing technology has been created and improved. Recently, NGS started to be used in clinical oncology to improve cancer therapy through diverse modalities ranging from finding novel and rare cancer mutations, discovering cancer mutation carriers to reaching specific therapeutic approaches known as personalized medicine (PM). PM has the potential to minimize medical expenses by shifting the current traditional medical approach of treating cancer and other diseases to an individualized preventive and predictive approach. Currently, NGS can speed up in the early diagnosis of diseases and discover pharmacogenetic markers that help in personalizing therapies. Despite the tremendous growth in our understanding of genetics, NGS holds the added advantage of providing more comprehensive picture of cancer landscape and uncovering cancer development pathways. In this review, we provided a complete overview of potential NGS applications in scientific and clinical oncology, with a particular emphasis on pharmacogenomics in the direction of precision medicine treatment options.
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Affiliation(s)
- Bashdar Mahmud Hussen
- Department Pharmacognosy, College of Pharmacy, Hawler Medical University, Kurdistan Region, Erbil, Iraq; Center of Research and Strategic Studies, Lebanese French University, Kurdistan Region, Erbil, Iraq
| | - Sara Tharwat Abdullah
- Department of Pharmacology and Toxicology, College of Pharmacy, Hawler Medical University, Erbil, Iraq
| | - Abbas Salihi
- Center of Research and Strategic Studies, Lebanese French University, Kurdistan Region, Erbil, Iraq; Department of Biology, College of Science, Salahaddin University, Kurdistan Region, Erbil, Iraq
| | - Dana Khdr Sabir
- Department of Medical Laboratory Sciences, Charmo University, Kurdistan Region, Iraq
| | - Karzan R Sidiq
- Department of Biology, College of Education, University of Sulaimani, Sulaimani 334, Kurdistan, Iraq
| | - Mohammed Fatih Rasul
- Department of Medical Analysis, Faculty of Applied Science, Tishk International University, Kurdistan Region, Erbil, Iraq
| | - Hazha Jamal Hidayat
- Department of Biology, College of Education, Salahaddin University, Kurdistan Region, Erbil, Iraq
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany; Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Elena Jamali
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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11
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A catalog of curated breast cancer genes. Breast Cancer Res Treat 2021; 191:431-441. [PMID: 34755241 PMCID: PMC8763822 DOI: 10.1007/s10549-021-06441-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 10/21/2021] [Indexed: 12/01/2022]
Abstract
Purpose Decades of research have identified multiple genetic variants associated with breast cancer etiology. However, there is no database that archives breast cancer genes and variants responsible for predisposition. We set out to build a dynamic repository of curated breast cancer genes. Methods A comprehensive literature search was performed in PubMed and Google Scholar, followed by data extraction and harmonization for downstream analysis. Results Using a subset of 345 studies, we cataloged 652 breast cancer-associated loci across the genome. A majority of these were present in the non-coding region (i.e., intergenic (101) and intronic (345)), whereas only 158 were located within an exon. Using the odds ratio, we identified 429 loci to increase the disease risk and 198 to confer protection against breast cancer, whereas 25 were identified to both increase disease risk and confer protection against breast cancer. Chromosomal ideogram analysis indicated that chromosomes 17 and 19 have the highest density of breast cancer loci. We manually annotated and collated breast cancer genes in which a previous association between rare-monogenic variant and breast cancer has been documented. Finally, network and functional enrichment analysis revealed that steroid metabolism and DNA repair pathways were predominant among breast cancer genes and variants. Conclusions We have built an online interactive catalog of curated breast cancer genes (https://cbcg.dk). This will expedite clinical diagnostics and support the ongoing efforts in managing breast cancer etiology. Moreover, the database will serve as an essential repository when designing new breast cancer multigene panels. Supplementary Information The online version contains supplementary material available at 10.1007/s10549-021-06441-y.
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12
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Wen LJ, Wang YS, Tan PY. miR-515-5p inhibits the proliferation, migration and invasion of human breast cancer cells by targeting CBX4. Exp Ther Med 2021; 22:1328. [PMID: 34630682 PMCID: PMC8495589 DOI: 10.3892/etm.2021.10763] [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: 07/10/2020] [Accepted: 07/30/2021] [Indexed: 01/02/2023] Open
Abstract
microRNA (miR)-515-5p has been previously suggested to function as a tumor suppressor in various types of human cancer. Therefore, the role of miR-515-5p in breast cancer (BC) was explored in the present study. A series of assays were performed to study the function of miR-515-p in BC cells, including Cell Counting Kit-8, TUNEL, flow cytometric and colony formation to detect cell viability and apoptosis, wound healing and Transwell assays to measure cell motility. In addition, reverse transcription quantitative PCR and western blot analysis were used to assess miR-515-5p, CBX4, Cox-2, MMP2, MMP9, CDK2, p21 and Cyclin D1 respectively. Bioinformatics and dual-luciferase reporter assays were used to analyze the target genes of miR-515-5p, which confirmed the direct binding between miR-515-5p and polycomb chromobox 4 (CBX4). It was found that the expression of miR-515-5p is lower in BC cells compared with that in normal breast cells (MCF10A). Overexpression of miR-515-5p using the miR-515 mimic was found to reduce cell viability, facilitate cell apoptosis, inhibit cell proliferation and arrest cell cycle progressio at G1 phase. In addition, miR-515-5p overexpression could inhibit cell migration and invasion, whilst decreasing the expression levels of prostaglandin-endoperoxide synthase 2, MMP2 and MMP9 proteins. In addition, miR-515-5p overexpression could reduce the expression levels of CBX4 in MCF7 and ZR-75-30 cells. By contrast, overexpression of CBX4 reversed the effects of the miR-515-5p mimic transfection on cell proliferation, migration and invasion in MCF7 and ZR-75-30 cells. In combination, these results suggest that miR-515-5p inhibits BC cell proliferation, migration and invasion by directly targeting CBX4.
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Affiliation(s)
- Liu-Jing Wen
- Department of Pharmacy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, P.R. China
| | - Yue-Sheng Wang
- Department of Dentistry, Second Hospital Affiliated to Tianjin Medical University, Tianjin 300211, P.R. China
| | - Pei-Yi Tan
- Department of Pharmacy, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin 300193, P.R. China
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13
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Karimi MR, Karimi AH, Abolmaali S, Sadeghi M, Schmitz U. Prospects and challenges of cancer systems medicine: from genes to disease networks. Brief Bioinform 2021; 23:6361045. [PMID: 34471925 PMCID: PMC8769701 DOI: 10.1093/bib/bbab343] [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: 05/04/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 12/20/2022] Open
Abstract
It is becoming evident that holistic perspectives toward cancer are crucial in deciphering the overwhelming complexity of tumors. Single-layer analysis of genome-wide data has greatly contributed to our understanding of cellular systems and their perturbations. However, fundamental gaps in our knowledge persist and hamper the design of effective interventions. It is becoming more apparent than ever, that cancer should not only be viewed as a disease of the genome but as a disease of the cellular system. Integrative multilayer approaches are emerging as vigorous assets in our endeavors to achieve systemic views on cancer biology. Herein, we provide a comprehensive review of the approaches, methods and technologies that can serve to achieve systemic perspectives of cancer. We start with genome-wide single-layer approaches of omics analyses of cellular systems and move on to multilayer integrative approaches in which in-depth descriptions of proteogenomics and network-based data analysis are provided. Proteogenomics is a remarkable example of how the integration of multiple levels of information can reduce our blind spots and increase the accuracy and reliability of our interpretations and network-based data analysis is a major approach for data interpretation and a robust scaffold for data integration and modeling. Overall, this review aims to increase cross-field awareness of the approaches and challenges regarding the omics-based study of cancer and to facilitate the necessary shift toward holistic approaches.
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Affiliation(s)
| | | | | | - Mehdi Sadeghi
- Department of Cell & Molecular Biology, Semnan University, Semnan, Iran
| | - Ulf Schmitz
- Department of Molecular & Cell Biology, James Cook University, Townsville, QLD 4811, Australia
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14
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Barba D, León-Sosa A, Lugo P, Suquillo D, Torres F, Surre F, Trojman L, Caicedo A. Breast cancer, screening and diagnostic tools: All you need to know. Crit Rev Oncol Hematol 2020; 157:103174. [PMID: 33249359 DOI: 10.1016/j.critrevonc.2020.103174] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 09/18/2020] [Accepted: 11/05/2020] [Indexed: 02/06/2023] Open
Abstract
Breast cancer is one of the most frequent malignancies among women worldwide. Methods for screening and diagnosis allow health care professionals to provide personalized treatments that improve the outcome and survival. Scientists and physicians are working side-by-side to develop evidence-based guidelines and equipment to detect cancer earlier. However, the lack of comprehensive interdisciplinary information and understanding between biomedical, medical, and technology professionals makes innovation of new screening and diagnosis tools difficult. This critical review gathers, for the first time, information concerning normal breast and cancer biology, established and emerging methods for screening and diagnosis, staging and grading, molecular and genetic biomarkers. Our purpose is to address key interdisciplinary information about these methods for physicians and scientists. Only the multidisciplinary interaction and communication between scientists, health care professionals, technical experts and patients will lead to the development of better detection tools and methods for an improved screening and early diagnosis.
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Affiliation(s)
- Diego Barba
- Escuela de Medicina, Universidad San Francisco de Quito USFQ, Quito, Ecuador; Instituto de Investigaciones en Biomedicina, Universidad San Francisco de Quito USFQ, Quito, Ecuador; Mito-Act Research Consortium, Quito, Ecuador
| | - Ariana León-Sosa
- Escuela de Medicina, Universidad San Francisco de Quito USFQ, Quito, Ecuador; Instituto de Investigaciones en Biomedicina, Universidad San Francisco de Quito USFQ, Quito, Ecuador; Mito-Act Research Consortium, Quito, Ecuador
| | - Paulina Lugo
- Hospital de los Valles HDLV, Quito, Ecuador; Fundación Ayuda Familiar y Comunitaria AFAC, Quito, Ecuador
| | - Daniela Suquillo
- Instituto de Investigaciones en Biomedicina, Universidad San Francisco de Quito USFQ, Quito, Ecuador; Mito-Act Research Consortium, Quito, Ecuador; Ingeniería en Procesos Biotecnológicos, Colegio de Ciencias Biológicas y Ambientales COCIBA, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Fernando Torres
- Escuela de Medicina, Universidad San Francisco de Quito USFQ, Quito, Ecuador; Hospital de los Valles HDLV, Quito, Ecuador
| | - Frederic Surre
- University of Glasgow, James Watt School of Engineering, Glasgow, G12 8QQ, United Kingdom
| | - Lionel Trojman
- LISITE, Isep, 75006, Paris, France; Universidad San Francisco de Quito USFQ, Colegio de Ciencias e Ingenierías Politécnico - USFQ, Instituto de Micro y Nanoelectrónica, IMNE, USFQ, Quito, Ecuador
| | - Andrés Caicedo
- Escuela de Medicina, Universidad San Francisco de Quito USFQ, Quito, Ecuador; Instituto de Investigaciones en Biomedicina, Universidad San Francisco de Quito USFQ, Quito, Ecuador; Mito-Act Research Consortium, Quito, Ecuador; Sistemas Médicos SIME, Universidad San Francisco de Quito USFQ, Quito, Ecuador.
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15
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Panigoro SS, Siswiandari KM, Paramita RI, Fadilah F, Erlina L. Targeted genome sequencing data of young women breast cancer patients in Cipto Mangunkusumo national hospital, Jakarta. Data Brief 2020; 32:106138. [PMID: 32904294 PMCID: PMC7452687 DOI: 10.1016/j.dib.2020.106138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/30/2020] [Accepted: 07/31/2020] [Indexed: 11/30/2022] Open
Abstract
Breast cancer is the most common cancer in women, accounting for approximately 25% of all cancer cases worldwide. Some breast cancer patients are genetically predisposed to genes involved in genomic stability. We report the targeted genome sequencing data of 24 young women (aged below 45 years) breast cancer patients admitted to Cipto Mangunkusumo National Hospital, Jakarta, Indonesia. These data will be useful in detecting the genome markers of breast cancer and in deciding the diagnostics and therapies. DNA sequences were obtained using the Illumina NextSeq 500 platform. FASTQ raw files are available under BioProject accession number PRJNA606794 and Sequence Read Archive accession numbers SRR11774092–SRR11774115.
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Affiliation(s)
- Sonar Soni Panigoro
- Surgical Oncology Division, Department of Surgery, Faculty of Medicine, Universitas Indonesia, Jalan Salemba Raya number 6, Jakarta 10430, Indonesia
| | - Kristina Maria Siswiandari
- Surgical Oncology Division, Department of Surgery, Faculty of Medicine, Universitas Indonesia, Jalan Salemba Raya number 6, Jakarta 10430, Indonesia
| | - Rafika Indah Paramita
- Department of Medical Chemistry, Faculty of Medicine, Universitas Indonesia, Jalan Salemba Raya number 4, Jakarta 10430, Indonesia.,Bioinformatics Core Facilities-IMERI, Faculty of Medicine, Universitas Indonesia, Jalan Salemba Raya number 6, Jakarta 10430, Indonesia
| | - Fadilah Fadilah
- Department of Medical Chemistry, Faculty of Medicine, Universitas Indonesia, Jalan Salemba Raya number 4, Jakarta 10430, Indonesia.,Bioinformatics Core Facilities-IMERI, Faculty of Medicine, Universitas Indonesia, Jalan Salemba Raya number 6, Jakarta 10430, Indonesia
| | - Linda Erlina
- Department of Medical Chemistry, Faculty of Medicine, Universitas Indonesia, Jalan Salemba Raya number 4, Jakarta 10430, Indonesia.,Bioinformatics Core Facilities-IMERI, Faculty of Medicine, Universitas Indonesia, Jalan Salemba Raya number 6, Jakarta 10430, Indonesia
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16
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Feng Y, Guo C, Wang H, Zhao L, Wang W, Wang T, Feng Y, Yuan K, Huang G. Fibrinogen-Like Protein 2 (FGL2) is a Novel Biomarker for Clinical Prediction of Human Breast Cancer. Med Sci Monit 2020; 26:e923531. [PMID: 32716910 PMCID: PMC7409386 DOI: 10.12659/msm.923531] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 05/04/2020] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Fibrinogen-like protein 2 (FGL2) is a member of the fibrinogen-like protein family and possesses important regulatory functions in both innate and adaptive immune responses. FGL2 is overexpressed in glioma, and its expression level is negatively associated with the prognosis of glioma patients. However, the diagnostic value of FGL2 is unknown in breast carcinoma. MATERIAL AND METHODS We comprehensively analyzed the expression pattern of FGL2 in breast cancer. Several online databases - TCGA, Oncomine, GEPIA, Kaplan-Meier plotter, and PrognoScan - were used in this study. RESULTS Based on the TCGA dataset and Oncomine database, we found that the expression level of FGL2 was remarkably lower in breast cancer compared with adjacent normal tissues. Clinical data showed that the expression level of FGL2 was significantly associated with radiation therapy, PR status, and tumor stage. Bioinformatics analysis of the GEPIA, Kaplan-Meier plotter, and PrognoScan databases showed that lower FGL2 expression levels were associated with a worse prognosis in breast cancer patients. Furthermore, the expression level of FGL2 was positively correlated with the immune cell infiltrations in breast cancer, especially those cells with high antitumor activities. GO, KEGG, and GSEA analyses also validated that FGL2 was closely related to genes involved in the immune response, signal transduction, and T cell receptor signaling pathway in breast cancer. CONCLUSIONS The results demonstrated that high expression of FGL2 is a useful marker for breast cancer treatment and appears to be correlated with enhanced antitumor activities in breast cancer patients.
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Affiliation(s)
- Yanyan Feng
- Department of Immunology and Microbiology, School of Life Sciences, Beijing University of Chinese Medicine, Beijing, P.R. China
| | - Chunguang Guo
- Department of Abdominal Surgical Oncology, Cancer Institute (Hospital), Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P.R. China
| | - Hesong Wang
- Department of Immunology and Microbiology, School of Life Sciences, Beijing University of Chinese Medicine, Beijing, P.R. China
| | - Lu Zhao
- Department of Immunology and Microbiology, School of Life Sciences, Beijing University of Chinese Medicine, Beijing, P.R. China
| | - Wei Wang
- Department of Immunology and Microbiology, School of Life Sciences, Beijing University of Chinese Medicine, Beijing, P.R. China
| | - Ting Wang
- Department of Immunology and Microbiology, School of Life Sciences, Beijing University of Chinese Medicine, Beijing, P.R. China
| | - Yuyin Feng
- Department of Biochemistry, School of Life Sciences, Beijing University of Chinese Medicine, Beijing, P.R. China
| | - Kai Yuan
- Department of Immunology and Microbiology, School of Life Sciences, Beijing University of Chinese Medicine, Beijing, P.R. China
| | - Guangrui Huang
- Department of Biochemistry, School of Life Sciences, Beijing University of Chinese Medicine, Beijing, P.R. China
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17
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Adhikari A, Mandal P, Biswas S, Giri A, Gupta A, Bhattacharya A. Comparison of histopathological grading and staging of breast cancer with p53-positive and transforming growth factor-beta receptor 2-negative immunohistochemical marker expression cases. CANCER TRANSLATIONAL MEDICINE 2020. [DOI: 10.4103/ctm.ctm_4_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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18
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Abstract
Breast cancer is one of the most leading causes of death for women worldwide. According to statistics published by the International Agency for Research on Cancer (IARC), the incidence of breast cancer is on the rise year by year in most parts of the world. The existence of heterogeneity limits the early diagnosis and targeted therapy of breast cancer. Nowadays, precision medicine brings a new perspective to personalized diagnosis and targeted therapy, overcomes the heterogeneity of different patients, and provides an opportunity for screening of high-risk populations. As a clinician, we are committed to using genomic to provide a favorable perspective in the field of breast cancer. The current review describes the recent advances in the understanding of precision medicine for breast cancer in the aspect of the genomics which could be applied to improve our ability to diagnose and treat breast cancer individually and effectively.
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19
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Breast Cancer in Young Women: Status Quo and Advanced Disease Management by a Predictive, Preventive, and Personalized Approach. Cancers (Basel) 2019; 11:cancers11111791. [PMID: 31739537 PMCID: PMC6896106 DOI: 10.3390/cancers11111791] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/08/2019] [Accepted: 11/12/2019] [Indexed: 12/24/2022] Open
Abstract
Why does healthcare of breast cancer (BC) patients, especially in a young population, matter and why are innovative strategies by predictive, preventive, and personalized medicine (PPPM) strongly recommended to replace current reactive medical approach in BC management? Permanent increase in annual numbers of new BC cases with particularly quick growth of premenopausal BC patients, an absence of clearly described risk factors for those patients, as well as established screening tools and programs represent important reasons to focus on BC in young women. Moreover, "young" BC cases are frequently "asymptomatic", difficult to diagnose, and to treat effectively on time. The objective of this article is to update the knowledge on BC in young females, its unique molecular signature, newest concepts in diagnostics and therapy, and to highlight the concepts of predictive, preventive, and personalized medicine with a well-acknowledged potential to advance the overall disease management.
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20
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Marchini A, Daeffler L, Pozdeev VI, Angelova A, Rommelaere J. Immune Conversion of Tumor Microenvironment by Oncolytic Viruses: The Protoparvovirus H-1PV Case Study. Front Immunol 2019; 10:1848. [PMID: 31440242 PMCID: PMC6692828 DOI: 10.3389/fimmu.2019.01848] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 07/23/2019] [Indexed: 12/21/2022] Open
Abstract
Cancer cells utilize multiple mechanisms to evade and suppress anticancer immune responses creating a “cold” immunosuppressive tumor microenvironment. Oncolytic virotherapy is emerging as a promising approach to revert tumor immunosuppression and enhance the efficacy of other forms of immunotherapy. Growing evidence indicates that oncolytic viruses (OVs) act in a multimodal fashion, inducing immunogenic cell death and thereby eliciting robust anticancer immune responses. In this review, we summarize information about OV-mediated immune conversion of the tumor microenvironment. As a case study we focus on the rodent protoparvovirus H-1PV and its dual role as an oncolytic and immune modulatory agent. Potential strategies to improve H-1PV anticancer efficacy are also discussed.
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Affiliation(s)
- Antonio Marchini
- Laboratory of Oncolytic Virus Immuno-Therapeutics, Luxembourg Institute of Health, Luxembourg, Luxembourg.,Laboratory of Oncolytic Virus Immuno-Therapeutics, German Cancer Research Center, Heidelberg, Germany
| | - Laurent Daeffler
- Université de Strasbourg, IPHC, Strasbourg, France.,CNRS, UMR7178, Strasbourg, France
| | - Vitaly I Pozdeev
- Laboratory of Oncolytic Virus Immuno-Therapeutics, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Assia Angelova
- Infection, Inflammation and Cancer Program, German Cancer Research Center, Heidelberg, Germany
| | - Jean Rommelaere
- Infection, Inflammation and Cancer Program, German Cancer Research Center, Heidelberg, Germany
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21
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Rossing M, Sørensen CS, Ejlertsen B, Nielsen FC. Whole genome sequencing of breast cancer. APMIS 2019; 127:303-315. [PMID: 30689231 PMCID: PMC6850492 DOI: 10.1111/apm.12920] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 12/16/2018] [Indexed: 12/29/2022]
Abstract
Breast cancer was the first to take advantage of targeted therapy using endocrine therapy, and for up to 20% of all breast cancer patients a further significant improvement has been obtained by HER2‐targeted therapy. Greater insight in precision medicine is to some extent driven by technical and computational progress, with the first wave of a true technical advancement being the application of transcriptomic analysis. Molecular subtyping further improved our understanding of breast cancer biology and has through a new tumor classification enabled allocation of personalized treatment regimens. The next wave in technical progression must be next‐generation‐sequencing which is currently providing new and exciting results. Large‐scale sequencing data unravel novel somatic and potential targetable mutations as well as allowing the identification of new candidate genes predisposing for familial breast cancer. So far, around 15% of all breast cancer patients are genetically predisposed with most genes being factors in pathways implicated in genome maintenance. This review focuses on whole‐genome sequencing and the new possibilities that this technique, together with other high‐throughput analytic approaches, provides for a more individualized treatment course of breast cancer patients.
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Affiliation(s)
- Maria Rossing
- Centre for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Bent Ejlertsen
- Danish Breast Cancer Cooperative Group & Department of Clinical Oncology Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Finn Cilius Nielsen
- Centre for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
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