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Tommasi S, Maurmo L, Rizzo A, Carella C, Ranieri G, De Summa S, Mannavola F, Chiurì VE, Guida M, Nisi C, Montrone M, Giotta F, Patruno M, Lacalamita R, Pilato B, Zito FA, Fucci L, Coppola CA, Ditonno P, Nardulli P, Quaresmini D, Strippoli S. The molecular tumor board as a step in cancer patient management: a southern Italian experience. Front Med (Lausanne) 2024; 11:1432628. [PMID: 39323465 PMCID: PMC11422073 DOI: 10.3389/fmed.2024.1432628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 08/21/2024] [Indexed: 09/27/2024] Open
Abstract
Introduction The management of cancer patients follows a Diagnostic Therapeutic and Care Pathway (PDTA) approach, aimed at achieving the optimal balance between care and quality of life. To support this process, precision medicine and innovative technologies [e.g., next-generation sequencing (NGS)] allow rapid identification of genetic-molecular alterations useful for the design of PDTA-approved therapies. If the standard approach proves inadequate, the Molecular Tumor Board (MTB), a group comprising specialists from diverse disciplines, can step in to evaluate a broader molecular profile, proposing potential therapies beyond evidence levels I-II or considering enrolment in clinical trials. Our aim is to analyze the role of the MTB in the entire management of patients in our institute and its impact on the strategy of personalized medicine, particularly when all approved treatments have failed. Materials and methods In alignment with European and national guidelines, a panel of clinicians and preclinical specialists from our institution was defined as the MTB core team. We designed and approved a procedure for the operation of this multidisciplinary group, which is the only one operating in the Puglia region. Results and discussion In 29 months (2021-2023), we discussed and analyzed 93 patients. A total of 44% presented pathogenic alterations, of which 40.4% were potentially actionable. Only 11 patients were proposed for enrollment in clinical trials, treatment with off-label drugs, or AIFA (the Italian pharmaceutical agency for drugs)-5% funding. Our process indicators, time to analysis, and number of patient cases discussed are in line with the median data of other European institutions. Such findings underscore both the importance and usefulness of the integration of an MTB process into the care of oncology patients.
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Affiliation(s)
- Stefania Tommasi
- Unità di Diagnostica Molecolare e Farmacogenetica, IRCCS Istituto Tumori Giovanni Paolo II Bari, Bari, Italy
| | - Leonarda Maurmo
- Unità di Diagnostica Molecolare e Farmacogenetica, IRCCS Istituto Tumori Giovanni Paolo II Bari, Bari, Italy
| | - Alessandro Rizzo
- Unità Operativa di Oncologia Medica, IRCCS Istituto Tumori Giovanni Paolo II Bari, Bari, Italy
| | - Claudia Carella
- Unità Operativa di Oncologia Medica, IRCCS Istituto Tumori Giovanni Paolo II Bari, Bari, Italy
| | - Girolamo Ranieri
- Unità di Oncologia Interventistica, IRCCS Istituto Tumori Giovanni Paolo II Bari, Bari, Italy
| | - Simona De Summa
- Unità di Diagnostica Molecolare e Farmacogenetica, IRCCS Istituto Tumori Giovanni Paolo II Bari, Bari, Italy
| | - Francesco Mannavola
- Unità di Oncologia Medica, Azienda Ospedaliera Policlinico Consorziale di Bari, Bari, Italy
| | | | - Michele Guida
- Unità Operativa di Oncologia Medica, IRCCS Istituto Tumori Giovanni Paolo II Bari, Bari, Italy
| | - Claudia Nisi
- Reparto di Oncologia, Ospedale San Giuseppe Moscati Taranto, Taranto, Italy
| | - Michele Montrone
- Unità Operativa di Oncologia Medica, IRCCS Istituto Tumori Giovanni Paolo II Bari, Bari, Italy
| | - Francesco Giotta
- Unità Operativa di Oncologia Medica, IRCCS Istituto Tumori Giovanni Paolo II Bari, Bari, Italy
| | - Margherita Patruno
- Centro Studi Tumori eredo-familiari, IRCCS Istituto Tumori Giovanni Paolo II Bari, Bari, Italy
| | - Rosanna Lacalamita
- Unità di Diagnostica Molecolare e Farmacogenetica, IRCCS Istituto Tumori Giovanni Paolo II Bari, Bari, Italy
| | - Brunella Pilato
- Unità di Diagnostica Molecolare e Farmacogenetica, IRCCS Istituto Tumori Giovanni Paolo II Bari, Bari, Italy
| | - Francesco Alfredo Zito
- Unità Operativa di Anatomia Patologica, IRCCS Istituto Tumori Giovanni Paolo II Bari, Bari, Italy
| | - Livia Fucci
- Unità Operativa di Anatomia Patologica, IRCCS Istituto Tumori Giovanni Paolo II Bari, Bari, Italy
| | - Claudio Antonio Coppola
- Unità di Diagnostica Molecolare e Farmacogenetica, IRCCS Istituto Tumori Giovanni Paolo II Bari, Bari, Italy
| | - Paolo Ditonno
- Unità Operativa di Ematologia, IRCCS Istituto Tumori Giovanni Paolo II Bari, Bari, Italy
| | - Patrizia Nardulli
- Unità Operativa Farmacia e U.M.A.C.A., IRCCS Istituto Tumori Giovanni Paolo II Bari, Bari, Italy
| | - Davide Quaresmini
- Unità Operativa di Oncologia Medica, IRCCS Istituto Tumori Giovanni Paolo II Bari, Bari, Italy
| | - Sabino Strippoli
- Unità Operativa di Oncologia Medica, IRCCS Istituto Tumori Giovanni Paolo II Bari, Bari, Italy
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Tsoulos N, Agiannitopoulos K, Potska K, Katseli A, Ntogka C, Pepe G, Bouzarelou D, Papathanasiou A, Grigoriadis D, Tsaousis GN, Gogas H, Troupis T, Papazisis K, Natsiopoulos I, Venizelos V, Amarantidis K, Giassas S, Papadimitriou C, Fountzilas E, Stathoulopoulou M, Koumarianou A, Xepapadakis G, Blidaru A, Zob D, Voinea O, Özdoğan M, Ergören MÇ, Hegmane A, Papadopoulou E, Nasioulas G, Markopoulos C. The Clinical and Genetic Landscape of Hereditary Cancer: Experience from a Single Clinical Diagnostic Laboratory. Cancer Genomics Proteomics 2024; 21:448-463. [PMID: 39191493 PMCID: PMC11363926 DOI: 10.21873/cgp.20463] [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: 06/26/2024] [Revised: 07/12/2024] [Accepted: 07/15/2024] [Indexed: 08/29/2024] Open
Abstract
BACKGROUND/AIM The application of next-generation sequencing (NGS) technology in the genetic investigation of hereditary cancer is important for clinical surveillance, therapeutic approach, and reducing the risk of developing new malignancies. The aim of the study was to explore genetic predisposition in individuals referred for hereditary cancer. MATERIALS AND METHODS A total of 8,261 individuals were referred for multigene genetic testing, during the period 2020-2023, in the laboratory, and underwent multigene genetic testing using NGS. Among the examined individuals, 56.17% were diagnosed with breast cancer, 6.77% with ovarian cancer, 2.88% with colorectal cancer, 1.91% with prostate cancer, 6.43% were healthy with a significant family history of cancer, while 3.06% had a different type of cancer and 0.21% had not provided any information. Additionally, in 85 women with breast cancer we performed whole exome sequencing analysis. RESULTS 20% of the examined individuals carried a pathogenic variant. Specifically, 54.8% of the patients had a pathogenic variant in a clinically significant gene (BRCA1, BRCA2, PALB2, RAD51C, PMS2, CDKN2A, MLH1, MSH2, TP53, MSH6, APC, RAD51D, PTEN, RET, CDH1, MEN1, and VHL). Among the different types of pathogenic variants detected, a significant percentage (6.52%) represented copy number variation (CNV). With WES analysis, the following findings were detected: CTC1: c.880C>T, p.(Gln294*); MLH3: c.405del, p.(Asp136Metfs*2), PPM1D: c.1426_1430del, p.(Glu476Leufs*3), and SDHB: c.395A>G, p.(His132Arg). CONCLUSION Comprehensive multigene genetic testing is necessary for appropriate clinical management of pathogenic variants' carriers. Additionally, the information obtained is important for determining the risk of malignancy development in family members of the examined individuals.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Helen Gogas
- First Department of Medicine, National and Kapodistrian University of Athens - School of Medicine, Athens, Greece
| | - Theodore Troupis
- School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | | | | | | | - Kyriakos Amarantidis
- Department of Medical Oncology, Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | | | - Christos Papadimitriou
- Oncology Unit, Aretaieion University Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Elena Fountzilas
- Department of Medical Oncology, St. Lukes's Clinic, Thessaloniki, Greece
| | | | - Anna Koumarianou
- Section of Medical Oncology, Attikon University Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | | | | | - Daniela Zob
- Oncology Department, "Prof. Dr. Al. Trestioreanu" Bucharest Oncology Institute, Bucharest, Romania
| | - Oana Voinea
- Department of Pathology, "Carol Davila" University of Medicine and Pharmacy, Bucharest, Romania
| | - Mustafa Özdoğan
- Division of Medical Oncology, Memorial Antalya Hospital, Antalya, Turkey
| | - Mahmut Çerkez Ergören
- Department of Medical Genetics, Faculty of Medicine, Near East University, Nicosia, Cyprus
| | - Alinta Hegmane
- Riga East University Hospital, Oncology Center of Latvia, Riga, Latvia
| | | | | | - Christos Markopoulos
- School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
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Nicholas C, Beharry A, Bendzsak AM, Bisson KR, Dadson K, Dudani S, Iafolla M, Irshad K, Perdrizet K, Raskin W, Singh R, Tsui DCC, Wang X, Yeung C, Cheema PK, Sheffield BS. Point of Care Liquid Biopsy for Cancer Treatment-Early Experience from a Community Center. Cancers (Basel) 2024; 16:2505. [PMID: 39061145 PMCID: PMC11274424 DOI: 10.3390/cancers16142505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 07/04/2024] [Accepted: 07/08/2024] [Indexed: 07/28/2024] Open
Abstract
Liquid biopsy is rapidly becoming an indispensable tool in the oncologist's arsenal; however, this technique remains elusive in a publicly funded healthcare system, and real-world evidence is needed to demonstrate utility and feasibility. Here, we describe the first experience of an in-house point of care liquid biopsy program at a Canadian community hospital. A retrospective review of consecutive cases that underwent plasma-based next-generation sequencing (NGS) was conducted. Liquid biopsy was initiated at the discretion of clinicians. Sequencing followed a point of care workflow using the Genexus™ integrated sequencer and the Oncomine precision assay, performed by histotechnologists. Results were reported by the attending pathologist. Eligible charts were reviewed for outcomes of interest, including the intent of the liquid biopsy, results of the liquid biopsy, and turnaround time from blood draw to results available. A total of 124 cases, with confirmed or suspected cancer, underwent liquid biopsy between January 2021 and November 2023. The median turnaround time for liquid biopsy results was 3 business days (range 1-12 days). The sensitivity of liquid biopsies was 71%, compared to tissue testing in cases with matched tissue results available for comparison. Common mutations included EGFR (29%), in 86 lung cancer patients, and PIK3CA (22%), identified in 13 breast cancer patients. Healthcare providers ordered liquid biopsies to inform diagnostic investigations and treatment decisions, and to determine progression or resistance mechanisms, as these reasons often overlapped. This study demonstrates that rapid in-house liquid biopsy using point of care methodology is feasible. The technique facilitates precision treatment and offers many additional advantages for cancer care.
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Affiliation(s)
- Champica Nicholas
- Osler Research Institute for Health Innovation, William Osler Health System, Brampton, ON L6R 3J7, Canada (P.K.C.)
- Division of Advanced Diagnostics, William Osler Health System, Brampton, ON L6R 3J7, Canada
| | - Andrea Beharry
- Osler Research Institute for Health Innovation, William Osler Health System, Brampton, ON L6R 3J7, Canada (P.K.C.)
- Division of Advanced Diagnostics, William Osler Health System, Brampton, ON L6R 3J7, Canada
| | - Anna M. Bendzsak
- Osler Research Institute for Health Innovation, William Osler Health System, Brampton, ON L6R 3J7, Canada (P.K.C.)
- Division of Thoracic Surgery, William Osler Health System, Brampton, ON L6R 3J7, Canada
| | - Kassandra R. Bisson
- Osler Research Institute for Health Innovation, William Osler Health System, Brampton, ON L6R 3J7, Canada (P.K.C.)
- Division of Advanced Diagnostics, William Osler Health System, Brampton, ON L6R 3J7, Canada
| | - Keith Dadson
- Thermo Fisher Scientific, Burlington, ON L7L 5Z1, Canada
| | - Shaan Dudani
- Osler Research Institute for Health Innovation, William Osler Health System, Brampton, ON L6R 3J7, Canada (P.K.C.)
- Division of Medical Oncology, William Osler Health System, Brampton, ON L6R 3J7, Canada
| | - Marco Iafolla
- Osler Research Institute for Health Innovation, William Osler Health System, Brampton, ON L6R 3J7, Canada (P.K.C.)
- Division of Medical Oncology, William Osler Health System, Brampton, ON L6R 3J7, Canada
- Department of Medicine, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Kashif Irshad
- Osler Research Institute for Health Innovation, William Osler Health System, Brampton, ON L6R 3J7, Canada (P.K.C.)
- Division of Thoracic Surgery, William Osler Health System, Brampton, ON L6R 3J7, Canada
| | - Kirstin Perdrizet
- Osler Research Institute for Health Innovation, William Osler Health System, Brampton, ON L6R 3J7, Canada (P.K.C.)
- Division of Medical Oncology, William Osler Health System, Brampton, ON L6R 3J7, Canada
- Department of Medicine, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - William Raskin
- Osler Research Institute for Health Innovation, William Osler Health System, Brampton, ON L6R 3J7, Canada (P.K.C.)
- Division of Medical Oncology, William Osler Health System, Brampton, ON L6R 3J7, Canada
| | - Raviya Singh
- Division of Medical Oncology, Scarborough Health Network, Scarborough, ON M1P 2V5, Canada
| | - David Chun Cheong Tsui
- Osler Research Institute for Health Innovation, William Osler Health System, Brampton, ON L6R 3J7, Canada (P.K.C.)
- Division of Medical Oncology, William Osler Health System, Brampton, ON L6R 3J7, Canada
| | - Xin Wang
- Division of Medical Oncology, UHN Princess Margaret Cancer Centre, Toronto, ON M5S 1A1, Canada
| | - Ching Yeung
- Osler Research Institute for Health Innovation, William Osler Health System, Brampton, ON L6R 3J7, Canada (P.K.C.)
- Division of Thoracic Surgery, William Osler Health System, Brampton, ON L6R 3J7, Canada
| | - Parneet K. Cheema
- Osler Research Institute for Health Innovation, William Osler Health System, Brampton, ON L6R 3J7, Canada (P.K.C.)
- Division of Medical Oncology, William Osler Health System, Brampton, ON L6R 3J7, Canada
- Department of Medicine, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Brandon S. Sheffield
- Osler Research Institute for Health Innovation, William Osler Health System, Brampton, ON L6R 3J7, Canada (P.K.C.)
- Division of Advanced Diagnostics, William Osler Health System, Brampton, ON L6R 3J7, Canada
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Singh H, Choudhary HB, Mandlik DS, Magre MS, Mohanto S, Ahmed MG, Singh BK, Mishra AK, Kumar A, Mishra A, Venkatachalam T, Chopra H. Molecular pathways and therapeutic strategies in dermatofibrosarcoma protuberans (DFSP): unravelling the tumor's genetic landscape. EXCLI JOURNAL 2024; 23:727-762. [PMID: 38983783 PMCID: PMC11231459 DOI: 10.17179/excli2024-7164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 04/26/2024] [Indexed: 07/11/2024]
Abstract
Dermatofibrosarcoma Protuberans (DFSP) is a rare soft tissue sarcoma distinguished by its infiltrative growth pattern and recurrence potential. Understanding the molecular characteristics of DFSP is essential for enhancing its diagnosis, prognosis, and treatment strategies. The paper provides an overview of DFSP, highlighting the significance of its molecular understanding. The gene expression profiling has uncovered unique molecular signatures in DFSP, highlighting its heterogeneity and potential therapeutic targets. The Platelet-Derived Growth Factor Receptors (PDGFRs) and Fibroblast Growth Factor Receptors (FGFRs) signaling pathways play essential roles in the progression and development of DFSP. The abnormal activation of these pathways presents opportunities for therapeutic interventions. Several emerging therapies, i.e., immunotherapies, immunomodulatory strategies, and immune checkpoint inhibitors, offer promising alternatives to surgical resection. In DFSP management, combination strategies, including rational combination therapies, aim to exploit the synergistic effects and overcome resistance. The article consisting future perspectives and challenges includes the discovery of prognostic and predictive biomarkers to improve risk stratification and treatment selection. Preclinical models, such as Patient-derived xenografts (PDX) and genetically engineered mouse models, help study the biology of DFSP and evaluate therapeutic interventions. The manuscript also covers small-molecule inhibitors, clinical trials, immune checkpoint inhibitors for DFSP treatment, combination therapies, rational therapies, and resistance mechanisms, which are unique and not broadly covered in recent pieces of literature. See also the graphical abstract(Fig. 1).
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Affiliation(s)
- Harpreet Singh
- School of Pharmaceutical Sciences, IFTM University, Moradabad, Uttar Pradesh, 244102, India
| | | | - Deepa Satish Mandlik
- Department of Pharmacology, BVDU, Poona College of Pharmacy, Pune, 411038, Maharashtra, India
| | - Manoj Subhash Magre
- Department of Pharmacology, BVDU, Poona College of Pharmacy, Pune, 411038, Maharashtra, India
| | - Sourav Mohanto
- Department of Pharmaceutics, Yenepoya Pharmacy College & Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, 575018, India
| | - Mohammed Gulzar Ahmed
- Department of Pharmaceutics, Yenepoya Pharmacy College & Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka, 575018, India
| | - Bhuvnesh Kumar Singh
- Faculty of Pharmacy, Moradabad Educational Trust, Moradabad, Uttar Pradesh, 244001, India
| | - Arun Kumar Mishra
- SOS School of Pharmacy, IFTM University, Moradabad, Uttar Pradesh, 244102, India
| | - Arvind Kumar
- School of Pharmaceutical Sciences, IFTM University, Moradabad, Uttar Pradesh, 244102, India
| | - Amrita Mishra
- School of Pharmaceutical Sciences, Delhi Pharmaceutical Sciences and Research University, New Delhi, 110017, India
| | - T. Venkatachalam
- Department of Pharmaceutical Chemistry, JKKMMRFs-Annai JKK Sampoorani Ammal College of Pharmacy, Komarapalayam, The Tamil Nadu Dr. MGR Medical University, Chennai, Tamil Nadu, 638183, India
| | - Hitesh Chopra
- Department of Biosciences, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai - 602105, Tamil Nadu, India
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Saeinasab M, Atlasi Y, M Matin M. Functional role of lncRNAs in gastrointestinal malignancies: the peculiar case of small nucleolar RNA host gene family. FEBS J 2024; 291:1353-1385. [PMID: 36282516 DOI: 10.1111/febs.16668] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/18/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022]
Abstract
Long noncoding RNAs (lncRNAs) play crucial roles in normal physiology and are often de-regulated in disease states such as cancer. Recently, a class of lncRNAs referred to as the small nucleolar RNA host gene (SNHG) family have emerged as important players in tumourigenesis. Here, we discuss new findings describing the role of SNHGs in gastrointestinal tumours and summarize the three main functions by which these lncRNAs promote carcinogenesis, namely: competing with endogenous RNAs, modulating protein function, and regulating epigenetic marking. Furthermore, we discuss how SNHGs participate in different hallmarks of cancer, and how this class of lncRNAs may serve as potential biomarkers in cancer diagnosis and therapy.
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Affiliation(s)
- Morvarid Saeinasab
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Iran
| | - Yaser Atlasi
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, UK
| | - Maryam M Matin
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Iran
- Novel Diagnostics and Therapeutics Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Iran
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Ferreira-Gonzalez A, Hocum B, Ko G, Shuvo S, Appukkuttan S, Babajanyan S. Next-Generation Sequencing Trends among Adult Patients with Select Advanced Tumor Types: A Real-World Evidence Evaluation. J Mol Diagn 2024; 26:292-303. [PMID: 38296192 DOI: 10.1016/j.jmoldx.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 10/10/2023] [Accepted: 01/02/2024] [Indexed: 02/06/2024] Open
Abstract
There are limited data on the prevalence of next-generation sequencing (NGS) in the United States, especially in light of the increasing importance of identifying actionable oncogenic variants due to molecular biomarker-based therapy approvals. This retrospective study of adult patients with select metastatic solid tumors and central nervous system tumors from the Optum Clinformatics Data Mart US health care claims database (January 1, 2014, to June 30, 2021; N = 63,209) examined NGS use trends over time. A modest increase in NGS was observed across tumor types from 2015 (0.0% to 1.5%) to 2021 (2.1% to 17.4%). A similar increase in NGS rates was also observed across key periods; however, rates in the final key period remained <10% for patients with breast, colorectal, head and neck, soft tissue sarcoma, and thyroid cancers, as well as central nervous system tumors. The median time to NGS from diagnosis was shortest among patients with non-small-cell lung cancer and longest for patients with breast cancer. Predictors of NGS varied by tumor type; test rates for minorities in select tumor types appeared comparable to the White population. Despite improving payer policies to expand coverage of NGS and molecular biomarker-based therapy approvals, NGS rates remained low across tumor types. Given the potential for improved patient outcomes with molecular biomarker-based therapy, further efforts to improve NGS rates are warranted.
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Affiliation(s)
| | - Brian Hocum
- Bayer HealthCare Pharmaceuticals, Inc., Whippany, New Jersey
| | - Gilbert Ko
- Bayer HealthCare Pharmaceuticals, Inc., Whippany, New Jersey.
| | - Sohul Shuvo
- Bayer HealthCare Pharmaceuticals, Inc., Whippany, New Jersey
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7
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Jalali P, Samii A, Rezaee M, Shahmoradi A, Pashizeh F, Salehi Z. UBE2C: A pan-cancer diagnostic and prognostic biomarker revealed through bioinformatics analysis. Cancer Rep (Hoboken) 2024; 7:e2032. [PMID: 38577722 PMCID: PMC10995712 DOI: 10.1002/cnr2.2032] [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: 11/07/2023] [Revised: 02/03/2024] [Accepted: 02/22/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND The diverse and complex attributes of cancer have made it a daunting challenge to overcome globally and remains to endanger human life. Detection of critical cancer-related gene alterations in solid tumor samples better defines patient diagnosis and prognosis, and indicates what targeted therapies must be administered to improve cancer patients' outcome. MATERIALS AND METHODS To identify genes that have aberrant expression across different cancer types, differential expressed genes were detected within the TCGA datasets. Subsequently, the DEGs common to all pan cancers were determined. Furthermore, various methods were employed to gain genetic alterations, co-expression genes network and protein-protein interaction (PPI) network, pathway enrichment analysis of common genes. Finally, the gene regulatory network was constructed. RESULTS Intersectional analysis identified UBE2C as a common DEG between all 28 types of studied cancers. Upregulated UBE2C expression was significantly correlated with OS and DFS of 10 and 9 types of cancer patients. Also, UBE2C can be a diagnostic factor in CESC, CHOL, GBM, and UCS with AUC = 100% and diagnose 19 cancer types with AUC ≥90%. A ceRNA network constructed including UBE2C, 41 TFs, 10 shared miRNAs, and 21 circRNAs and 128 lncRNAs. CONCLUSION In summary, UBE2C can be a theranostic gene, which may serve as a reliable biomarker in diagnosing cancers, improving treatment responses and increasing the overall survival of cancer patients and can be a promising gene to be target by cancer drugs in the future.
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Affiliation(s)
- Pooya Jalali
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Centre, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical SciencesTehranIran
| | - Amir Samii
- Department of Hematology and Blood TransfusionSchool of Allied Medical Sciences, Iran University of Medical SciencesTehranIran
| | - Malihe Rezaee
- Department of PharmacologySchool of Medicine, Shahid Beheshti University of Medical SciencesTehranIran
| | - Arvin Shahmoradi
- Department of Laboratory MedicineFaculty of Paramedical, Kurdistan University of Medical SciencesSanandajIran
| | - Fatemeh Pashizeh
- Department of Clinical ImmunologyShahid Sadoughi University of Medical SciencesYazdIran
| | - Zahra Salehi
- Hematology, Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical SciencesTehranIran
- Research Institute for Oncology, Hematology and Cell Therapy, Tehran University of Medical SciencesTehranIran
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8
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Rahman MM, Wang L, Rahman MM, Chen Y, Zhang W, Wang J, Lee LP, Wan Y. Rapid in situ mutation detection in extracellular vesicle-DNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.26.582068. [PMID: 38464277 PMCID: PMC10925088 DOI: 10.1101/2024.02.26.582068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
A PCR- and sequencing-free mutation detection assay facilitates cancer diagnosis and reduces over-reliance on specialized equipment. This benefit was highlighted during the pandemic when high demand for viral nucleic acid testing often sidelined mutation analysis. This shift led to substantial challenges for patients on targeted therapy in tracking mutations. Here, we report a 30-minute DNA mutation detection technique using Cas12a-loaded liposomes in a microplate reader, a fundamental laboratory tool. CRISPR-Cas12a complex and fluorescence-quenching (FQ) probes are introduced into tumor-derived extracellular vesicles (EV) through membrane fusion. When CRISPR-RNA hybridizes with the DNA target, activated Cas12a can trans-cleave FQ probes, resulting in fluorescence signals for the quantification of DNA mutation. Future advancements in multiplex and high-throughput mutation detection using this assay will streamline self-diagnosis and treatment monitoring at home.
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Affiliation(s)
- Md Mofizur Rahman
- The Pq Laboratory of BiomeDx/Rx, Department of Biomedical Engineering, Binghamton University, Binghamton, NY, USA
- Department of Pharmacy, Daffodil International University, Dhaka, Bangladesh
| | - Lixue Wang
- The Pq Laboratory of BiomeDx/Rx, Department of Biomedical Engineering, Binghamton University, Binghamton, NY, USA
- Department of Radiotherapy, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Md Motiar Rahman
- Department of Chemistry, Binghamton University, Binghamton, NY, USA
| | - Yundi Chen
- The Pq Laboratory of BiomeDx/Rx, Department of Biomedical Engineering, Binghamton University, Binghamton, NY, USA
| | - Wenlong Zhang
- Twist Bioscience Corporation, San Francisco, CA, USA
| | - Jing Wang
- Department of Hematology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
- Department of Oncology and Hematology, Yizheng Hospital of Nanjing Drum Tower Hospital Group, Yizheng, Jiangsu, China
| | - Luke P Lee
- Harvard Medical School, Harvard University; Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Bioengineering, Department of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, CA, USA
- Department of Biophysics, Institute of Quantum Biophysics, Sungkyunkwan University, Suwon, Korea
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, Korea
| | - Yuan Wan
- The Pq Laboratory of BiomeDx/Rx, Department of Biomedical Engineering, Binghamton University, Binghamton, NY, USA
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9
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Black JO, Al-Ibraheemi A, Arnold MA, Coffin CM, Davis JL, Parham DM, Rudzinski ER, Shenoy A, Surrey LF, Tan SY, Spunt SL. The Pathologic Diagnosis of Pediatric Soft Tissue Tumors in the Era of Molecular Medicine: The Sarcoma Pediatric Pathology Research Interest Group Perspective. Arch Pathol Lab Med 2024; 148:107-116. [PMID: 37196343 DOI: 10.5858/arpa.2022-0364-ra] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2023] [Indexed: 05/19/2023]
Abstract
CONTEXT.— Pediatric soft tissue tumors are one of the areas of pediatric pathology that frequently generate consult requests. Evolving classification systems, ancillary testing methods, new treatment options, research enrollment opportunities, and tissue archival processes create additional complexity in handling these unique specimens. Pathologists are at the heart of this critical decision-making, balancing responsibilities to consider expediency, accessibility, and cost-effectiveness of ancillary testing during pathologic examination and reporting. OBJECTIVE.— To provide a practical approach to handling pediatric soft tissue tumor specimens, including volume considerations, immunohistochemical staining panel recommendations, genetic and molecular testing approaches, and other processes that impact the quality and efficiency of tumor tissue triage. DATA SOURCES.— The World Health Organization Classification of Soft Tissue and Bone Tumors, 5th edition, other recent literature investigating tissue handling, and the collective clinical experience of the group are used in this manuscript. CONCLUSIONS.— Pediatric soft tissue tumors can be difficult to diagnose, and evaluation can be improved by adopting a thoughtful, algorithmic approach to maximize available tissue and minimize time to diagnosis.
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Affiliation(s)
- Jennifer O Black
- From the Department of Pathology and Laboratory Medicine, Children's Hospital of Colorado, Aurora (Black, Arnold)
| | - Alyaa Al-Ibraheemi
- the Department of Pathology, Children's Hospital Boston, Boston, Massachusetts (Al-Ibraheemi)
| | - Michael A Arnold
- From the Department of Pathology and Laboratory Medicine, Children's Hospital of Colorado, Aurora (Black, Arnold)
| | - Cheryl M Coffin
- the Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee (Coffin)
| | - Jessica L Davis
- From the Department of Pathology and Laboratory Medicine, Children's Hospital of Colorado, Aurora (Black, Arnold)
- the Department of Pathology and Laboratory Medicine, Oregon Health and Sciences University, Portland (Davis)
| | - David M Parham
- Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles (Parham)
| | - Erin R Rudzinski
- the Department of Laboratory Medicine and Pathology, Seattle Children's Hospital, Seattle, Washington (Rudzinski)
| | - Archana Shenoy
- the Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio (Shenoy)
| | - Lea F Surrey
- the Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania (Surrey)
| | - Serena Y Tan
- the Departments of Pathology (Tan) and Pediatrics (Spunt), Lucille Packard Children's Hospital, Stanford University School of Medicine, Stanford, California
| | - Sheri L Spunt
- the Departments of Pathology (Tan) and Pediatrics (Spunt), Lucille Packard Children's Hospital, Stanford University School of Medicine, Stanford, California
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10
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Blay E, Hardyman E, Morovic W. PCR-based analytics of gene therapies using adeno-associated virus vectors: Considerations for cGMP method development. Mol Ther Methods Clin Dev 2023; 31:101132. [PMID: 37964893 PMCID: PMC10641278 DOI: 10.1016/j.omtm.2023.101132] [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] [Indexed: 11/16/2023]
Abstract
The field of gene therapy has evolved and improved so that today the treatment of thousands of genetic diseases is now possible. An integral aspect of the drug development process is generating analytical methods to be used throughout clinical and commercial manufacturing. Enumeration and identification assays using genetic testing are critical to ensure the safety, efficacy, and stability of many active pharmaceutical ingredients. While nucleic acid-based methods are already reliable and rapid, there are unique biological, technological, and regulatory aspects in gene therapies that must be considered. This review surveys aspects of method development and validation using nucleic acid-based testing of gene therapies by focusing on adeno-associated virus (AAV) vectors and their co-transfection factors. Key differences between quantitative PCR and droplet digital technologies are discussed to show how improvements can be made while still adhering to regulatory guidance. Example validation parameters for AAV genome titers are described to demonstrate the scope of analytical development. Finally, several areas for improving analytical testing are presented to inspire future innovation, including next-generation sequencing and artificial intelligence. Reviewing the broad characteristics of gene therapy assessment serves as an introduction for new researchers, while clarifying processes for professionals already involved in pharmaceutical manufacturing.
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Affiliation(s)
- Emmanuel Blay
- Gene & Cell Therapy, PPD GMP Laboratories, Part of ThermoFisher Scientific, Middleton, WI, USA
| | - Elaine Hardyman
- Gene & Cell Therapy, PPD GMP Laboratories, Part of ThermoFisher Scientific, Middleton, WI, USA
| | - Wesley Morovic
- Gene & Cell Therapy, PPD GMP Laboratories, Part of ThermoFisher Scientific, Middleton, WI, USA
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11
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Zhang Z, Song W, Yan R. Gbp3 is associated with the progression of lupus nephritis by regulating cell proliferation, inflammation and pyroptosis. Autoimmunity 2023; 56:2250095. [PMID: 37621179 DOI: 10.1080/08916934.2023.2250095] [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: 03/09/2023] [Revised: 05/18/2023] [Accepted: 08/15/2023] [Indexed: 08/26/2023]
Abstract
Lupus nephritis (LN) is a major cause death in patients with systemic lupus erythematosus. We aimed to find the differentially expressed genes (DEGs) in LN and confirm the regulatory mechanism on LN. The mouse model of LN was constructed by subcutaneous injection of pristane. RNA-seq screened 392 up-regulated and 447 down-regulated DEGs in LN mouse model, and KEGG analysis found that the top 20 DEGs were enriched in arachidonic acid metabolism, tryptophan metabolism, etc. The hub genes, Kynu, Spidr, Gbp3, Cbr1, Cyp4b1, and Cndp2 were identified, in which Gbp3 was selected for following study. Afterwards, the function of Gbp3 on the proliferation, inflammation, and pyroptosis of LN was verified by CCK-8, ELISA, and WB in vitro. The results demonstrated that si-Gbp3 promoted cell proliferation and inhibited the levels of inflammatory factors (IL-1β, TNF-α and IL-8) and pyroptosis-related proteins (GSDMD, Caspase-1 and NLRP3) in a cell model of LN. In constrast, Gbp3 overexpression played an opposite role. In summary, Gbp3 promoted the progression of LN via inhibiting cell proliferation and facilitating inflammation and pyroptosis.
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Affiliation(s)
- Zhongfeng Zhang
- Department of Pathology, The Affiliated Hospital of Guizhou Medical University, Guiyang City, Guizhou Province, P.R. China
| | - Wenyu Song
- Department of Nephrology, The Affiliated Hospital of Guizhou Medical University, Guiyang City, Guizhou Province, P.R. China
| | - Run Yan
- Department of Nephrology, The Affiliated Hospital of Guizhou Medical University, Guiyang City, Guizhou Province, P.R. China
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12
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Golan T, Casolino R, Biankin AV, Hammel P, Whitaker KD, Hall MJ, Riegert-Johnson DL. Germline BRCA testing in pancreatic cancer: improving awareness, timing, turnaround, and uptake. Ther Adv Med Oncol 2023; 15:17588359231189127. [PMID: 37720496 PMCID: PMC10504836 DOI: 10.1177/17588359231189127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 07/04/2023] [Indexed: 09/19/2023] Open
Abstract
Prognosis is generally poor for patients with pancreatic ductal adenocarcinoma. However, patients with germline BRCA1 or BRCA2 mutations (gBRCAm) may benefit from first-line platinum-based chemotherapy and maintenance therapy with the poly(adenosine diphosphate-ribose) polymerase inhibitor olaparib following at least 16 weeks of first-line platinum-based chemotherapy without disease progression. Germline breast cancer gene (BRCA) testing is therefore important to ensure that patients receive the most effective treatment. In addition, testing for other DNA damage response gene mutations beyond gBRCAm may also guide treatment decisions. However, clinical pathways for genetic testing are often suboptimal, leading to delays in treatment initiation or missed opportunities for personalized therapy. Barriers to testing include low rates of referral and uptake, delays to referral and slow result turnaround times, cost, and biopsy and assay limitations if somatic testing is performed, leading to the requirement for subsequent dedicated germline testing. Low rates of referral may result from lack of awareness among physicians of the clinical value of testing, coupled with low confidence in interpreting test results and poor availability of genetic counseling services. Among patients, barriers to uptake may include similar lack of awareness of the clinical value of testing, anxiety regarding the implications of test results, lack of insurance coverage, fear of negative insurance implications, and socioeconomic factors. Potential solutions include innovative approaches to testing pathways, including 'mainstreaming' of testing in which BRCA tests are routinely arranged by the treating oncologist, with the involvement of genetic counselors if a patient is found to have a gBRCAm. More recently, the utility of multigene panel analyses has also been explored. Access to genetic counseling may also be improved through initiatives such as having a genetic counseling appointment for all new patient visits and telemedicine approaches, including the use of telephone consultations or DVD-assisted counseling. Educational programs will also be beneficial, and cost effectiveness is likely to improve as the number of targeted treatments increases and when the earlier detection of tumors in family members following cascade testing is considered.
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Affiliation(s)
- Talia Golan
- Institute of Oncology, Sheba Medical Center, Tel Hashomer 52621, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Raffaella Casolino
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
- Department of Medicine, University and Hospital Trust of Verona, Verona, Italy
| | - Andrew V. Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, UK
- South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales, Liverpool, Australia
| | - Pascal Hammel
- Department of Digestive and Medical Oncology, University Paris-Saclay, Paul Brousse Hospital (AP-HP), Villejuif, France
| | - Kristen D. Whitaker
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Michael J. Hall
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, USA
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13
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Asl ER, Sarabandi S, Shademan B, Dalvandi K, sheikhansari G, Nourazarian A. MicroRNA targeting: A novel therapeutic intervention for ovarian cancer. Biochem Biophys Rep 2023; 35:101519. [PMID: 37521375 PMCID: PMC10382632 DOI: 10.1016/j.bbrep.2023.101519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 08/01/2023] Open
Abstract
Ovarian cancer, a perilous form of cancer affecting the female reproductive system, exhibits intricate communication networks that contribute to its progression. This study aims to identify crucial molecular abnormalities linked to the disease to enhance diagnostic and therapeutic strategies. In particular, we investigate the role of microRNAs (miRNAs) as diagnostic biomarkers and explore their potential in treating ovarian cancer. By targeting miRNAs, which can influence multiple pathways and genes, substantial therapeutic benefits can be attained. In this review we want to shed light on the promising application of miRNA-based interventions and provide insights into the specific miRNAs implicated in ovarian cancer pathogenesis.
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Affiliation(s)
- Elmira Roshani Asl
- Social Determinants of Health Research Center, Saveh University of Medical Sciences, Saveh, Iran
| | - Sajed Sarabandi
- Department of Veterinary, Faculty of Medicine Sciences, Islamic Azad University of Karaj, Karaj, Iran
| | - Behrouz Shademan
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Kourosh Dalvandi
- Ministry of Health and Medical Education, Health Department, Tehran, Iran
| | | | - Alireza Nourazarian
- Department of Basic Medical Sciences, Khoy University of Medical Sciences, Khoy, Iran
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14
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Ciurea AM, Schenker M, Ciofiac CM, Streba L, Schenker R, Streba CT. Genomic Profiling - A Need for Clinical Decision? -Case Reports. CURRENT HEALTH SCIENCES JOURNAL 2023; 49:467-473. [PMID: 38314216 PMCID: PMC10832885 DOI: 10.12865/chsj.49.03.22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 06/21/2023] [Indexed: 02/06/2024]
Abstract
Cancer is still an important health issue worldwide due to increased incidence and mortality. Personalized medicine is the future of cancer treatment. Development in technology improved technical skills in DNA/RNA sequencing. NGS technology in solid-tumor samples can describe DNA or RNA analysis by including the entire genome to detect clinical relevant mutations. Genetic results may be considered having a dynamic impact because of heterogenous molecular alterations depending of time and treatment influence. We conducted a retrospective study of all NGS tests made in the last five years for the patients from 'Sf. Nectarie' Oncology Center, Craiova, Romania. We selected three relevant clinical cases where NGS analysis was performed and the results changed the perspective of the clinical decision. Our aim is to evaluate the importance of NGS results in clinical approach. Although medicine known an important development during the last decades, only a few patients can benefit of advanced personalized treatments. It is still hard to identify the alterations or gene mutations because of genetic tests are not easily available and only a small proportion of patients carries genetic alterations.
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Affiliation(s)
- Ana-Maria Ciurea
- Department of Oncology, University of Medicine and Pharmacy of Craiova, Romania
| | - Michael Schenker
- Department of Oncology, University of Medicine and Pharmacy of Craiova, Romania
| | - Cristina Mihaela Ciofiac
- Doctoral School, Department of Radiology and Medical Imaging, University of Medicine and Pharmacy of Craiova
| | - Liliana Streba
- Department of Oncology, University of Medicine and Pharmacy of Craiova, Romania
| | - Ramona Schenker
- Psychology Department, Sf Nectarie Oncology Center, Craiova, Romania
| | - Costin Teodor Streba
- Department of Pulmonology, University of Medicine and Pharmacy of Craiova, Romania
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15
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Paganin M, Tebaldi T, Lauria F, Viero G. Visualizing gene expression changes in time, space, and single cells with expressyouRcell. iScience 2023; 26:106853. [PMID: 37250782 PMCID: PMC10220493 DOI: 10.1016/j.isci.2023.106853] [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: 02/14/2023] [Revised: 05/05/2023] [Accepted: 05/05/2023] [Indexed: 05/31/2023] Open
Abstract
The last decade has witnessed massive advancements in high-throughput techniques capable of producing increasingly complex gene expression datasets across time and space and at the resolution of single cells. Yet, the large volume of big data available and the complexity of experimental designs hamper an easy understanding and effective communication of the results. We present expressyouRcell, an easy-to-use R package to map the multi-dimensional variations of transcript and protein levels in dynamic cell pictographs. expressyouRcell visualizes gene expression variations as pictographic representations of cell-type thematic maps. expressyouRcell visually reduces the complexity of displaying gene expression and protein level changes across multiple measurements (time points or single-cell trajectories) by generating dynamic representations of cellular pictographs. We applied expressyouRcell to single cell, bulk RNA sequencing (RNA-seq), and proteomics datasets, demonstrating its flexibility and usability in the visualization of complex variations in gene expression. Our approach improves the standard quantitative interpretation and communication of relevant results.
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Affiliation(s)
| | - Toma Tebaldi
- Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
- Department CIBIO, University of Trento, Trento, Italy
| | - Fabio Lauria
- Institute of Biophysics, CNR Unit Trento, Trento, Italy
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16
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Pennisi MS, Di Gregorio S, Tirrò E, Romano C, Duminuco A, Garibaldi B, Giuffrida G, Manzella L, Vigneri P, Palumbo GA. Additional Genetic Alterations and Clonal Evolution of MPNs with Double Mutations on the MPL Gene: Two Case Reports. Hematol Rep 2023; 15:317-324. [PMID: 37367082 DOI: 10.3390/hematolrep15020033] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/17/2023] [Accepted: 05/19/2023] [Indexed: 06/28/2023] Open
Abstract
Essential thrombocythemia (ET) and primary myelofibrosis (PMF) are two of the main BCR-ABL1-negative chronic myeloproliferative neoplasms (MPNs) characterized by abnormal megakaryocytic proliferation. Janus kinase 2 (JAK2) mutations are detected in 50-60% of ET and PMF, while myeloproliferative leukemia (MPL) virus oncogene mutations are present in 3-5% of cases. While Sanger sequencing is a valuable diagnostic tool to discriminate the most common MPN mutations, next-generation sequencing (NGS) is a more sensitive technology that also identifies concurrent genetic alterations. In this report, we describe two MPN patients with simultaneous double MPL mutations: a woman with ET presenting both MPLV501A-W515R and JAK2V617F mutations and a man with PMF displaying an uncommon double MPLV501A-W515L. Using colony-forming assays and NGS analyses, we define the origin and mutational landscape of these two unusual malignancies and uncover further gene alterations that may contribute to the pathogenesis of ET and PMF.
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Affiliation(s)
- Maria Stella Pennisi
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico "G. Rodolico-San Marco", 95123 Catania, Italy
| | - Sandra Di Gregorio
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico "G. Rodolico-San Marco", 95123 Catania, Italy
| | - Elena Tirrò
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico "G. Rodolico-San Marco", 95123 Catania, Italy
| | - Chiara Romano
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico "G. Rodolico-San Marco", 95123 Catania, Italy
| | - Andrea Duminuco
- Postgraduate School of Hematology, University of Catania, 95123 Catania, Italy
| | - Bruno Garibaldi
- Postgraduate School of Hematology, University of Catania, 95123 Catania, Italy
| | - Gaetano Giuffrida
- Hematology Unit and Bone Marrow Transplant, A.O.U. Policlinico "G. Rodolico-San Marco", 95123 Catania, Italy
| | - Livia Manzella
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico "G. Rodolico-San Marco", 95123 Catania, Italy
| | - Paolo Vigneri
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico "G. Rodolico-San Marco", 95123 Catania, Italy
| | - Giuseppe A Palumbo
- Department of Medical, Surgical Sciences and Advanced Technologies, "G.F. Ingrassia", University of Catania, 95123 Catania, Italy
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17
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Gajda-Walczak A, Potęga A, Kowalczyk A, Sek S, Zięba S, Kowalik A, Kudelski A, Nowicka AM. New, fast and cheap prediction tests for BRCA1 gene mutations identification in clinical samples. Sci Rep 2023; 13:7316. [PMID: 37147448 PMCID: PMC10163215 DOI: 10.1038/s41598-023-34588-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/03/2023] [Indexed: 05/07/2023] Open
Abstract
Despite significant progress in cancer therapy, cancer is still the second cause of mortality in the world. The necessity to make quick therapeutic decisions forces the development of procedures allowing to obtain a reliable result in a quick and unambiguous manner. Currently, detecting predictive mutations, including BRCA1, is the basis for effectively treating advanced breast cancer. Here, we present new insight on gene mutation detection. We propose a cheap BRCA1 mutation detection tests based on the surface plasmon resonance (SPR) or quartz crystal microbalance with energy dissipation (QCM-D) response changes recorded during a hybridization process of an oligonucleotide molecular probe with DNA fragments, with and without the BRCA1 mutation. The changes in the morphology of the formed DNA layer caused by the presence of the mutation were confirmed by atomic force microscopy. The unique property of the developed SPR and QCM tests is really short time of analysis: ca. 6 min for SPR and ca. 25 min for QCM. The proposed tests have been verified on 22 different DNA extracted from blood leukocytes collected from cancer patients: 17 samples from patients with various BRCA1 gene mutation variants including deletion, insertion and missense single-nucleotide and 5 samples from patients without any BRCA1 mutation. Our test is a response to the need of medical diagnostics for a quick, unambiguous test to identify mutations of the BRCA1 gene, including missense single-nucleotide (SNPs).
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Affiliation(s)
| | - Agnieszka Potęga
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdańsk University of Technology, Narutowicza 11/12 Str., 80-233, Gdańsk, Poland
| | - Agata Kowalczyk
- Faculty of Chemistry, University of Warsaw, Pasteura 1 Str., 02-093, Warsaw, Poland
| | - Slawomir Sek
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101 Str., 02-089, Warsaw, Poland
| | - Sebastian Zięba
- Molecular Diagnostics, Holy Cross Cancer Center, Stefana Artwińskiego 3 Str., 25-734, Kielce, Poland
| | - Artur Kowalik
- Molecular Diagnostics, Holy Cross Cancer Center, Stefana Artwińskiego 3 Str., 25-734, Kielce, Poland
- Division of Medical Biology, Institute of Biology, Jan Kochanowski University, Uniwersytecka 7 Str., 25-406, Kielce, Poland
| | - Andrzej Kudelski
- Faculty of Chemistry, University of Warsaw, Pasteura 1 Str., 02-093, Warsaw, Poland
| | - Anna M Nowicka
- Faculty of Chemistry, University of Warsaw, Pasteura 1 Str., 02-093, Warsaw, Poland.
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18
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Andalib KMS, Rahman MH, Habib A. Bioinformatics and cheminformatics approaches to identify pathways, molecular mechanisms and drug substances related to genetic basis of cervical cancer. J Biomol Struct Dyn 2023; 41:14232-14247. [PMID: 36852684 DOI: 10.1080/07391102.2023.2179542] [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: 10/17/2022] [Accepted: 02/07/2023] [Indexed: 03/01/2023]
Abstract
Cervical cancer (CC) is a global threat to women and our knowledge is frighteningly little about its underlying genomic contributors. Our research aimed to understand the underlying molecular and genetic mechanisms of CC by integrating bioinformatics and network-based study. Transcriptomic analyses of three microarray datasets identified 218 common differentially expressed genes (DEGs) within control samples and CC specimens. KEGG pathway analysis revealed pathways in cell cycle, drug metabolism, DNA replication and the significant GO terms were cornification, proteolysis, cell division and DNA replication. Protein-protein interaction (PPI) network analysis identified 20 hub genes and survival analyses validated CDC45, MCM2, PCNA and TOP2A as CC biomarkers. Subsequently, 10 transcriptional factors (TFs) and 10 post-transcriptional regulators were detected through TFs-DEGs and miRNAs-DEGs regulatory network assessment. Finally, the CC biomarkers were subjected to a drug-gene relationship analysis to find the best target inhibitors. Standard cheminformatics method including in silico ADMET and molecular docking study substantiated PD0325901 and Selumetinib as the most potent candidate-drug for CC treatment. Overall, this meticulous study holds promises for further in vitro and in vivo research on CC diagnosis, prognosis and therapies. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- K M Salim Andalib
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh
| | - Md Habibur Rahman
- Department of Computer Science and Engineering, Islamic University, Kushtia, Bangladesh
- Center for Advanced Bioinformatics and Artificial Intelligent Research, Islamic University, Kushtia, Bangladesh
| | - Ahsan Habib
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh
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19
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Pulumati A, Pulumati A, Dwarakanath BS, Verma A, Papineni RVL. Technological advancements in cancer diagnostics: Improvements and limitations. Cancer Rep (Hoboken) 2023; 6:e1764. [PMID: 36607830 PMCID: PMC9940009 DOI: 10.1002/cnr2.1764] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 10/20/2022] [Accepted: 11/27/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Cancer is characterized by the rampant proliferation, growth, and infiltration of malignantly transformed cancer cells past their normal boundaries into adjacent tissues. It is the leading cause of death worldwide, responsible for approximately 19.3 million new diagnoses and 10 million deaths globally in 2020. In the United States alone, the estimated number of new diagnoses and deaths is 1.9 million and 609 360, respectively. Implementation of currently existing cancer diagnostic techniques such as positron emission tomography (PET), X-ray computed tomography (CT), and magnetic resonance spectroscopy (MRS), and molecular diagnostic techniques, have enabled early detection rates and are instrumental not only for the therapeutic management of cancer patients, but also for early detection of the cancer itself. The effectiveness of these cancer screening programs are heavily dependent on the rate of accurate precursor lesion identification; an increased rate of identification allows for earlier onset treatment, thus decreasing the incidence of invasive cancer in the long-term, and improving the overall prognosis. Although these diagnostic techniques are advantageous due to lack of invasiveness and easier accessibility within the clinical setting, several limitations such as optimal target definition, high signal to background ratio and associated artifacts hinder the accurate diagnosis of specific types of deep-seated tumors, besides associated high cost. In this review we discuss various imaging, molecular, and low-cost diagnostic tools and related technological advancements, to provide a better understanding of cancer diagnostics, unraveling new opportunities for effective management of cancer, particularly in low- and middle-income countries (LMICs). RECENT FINDINGS Herein we discuss various technological advancements that are being utilized to construct an assortment of new diagnostic techniques that incorporate hardware, image reconstruction software, imaging devices, biomarkers, and even artificial intelligence algorithms, thereby providing a reliable diagnosis and analysis of the tumor. Also, we provide a brief account of alternative low cost-effective cancer therapy devices (CryoPop®, LumaGEM®, MarginProbe®) and picture archiving and communication systems (PACS), emphasizing the need for multi-disciplinary collaboration among radiologists, pathologists, and other involved specialties for improving cancer diagnostics. CONCLUSION Revolutionary technological advancements in cancer imaging and molecular biology techniques are indispensable for the accurate diagnosis and prognosis of cancer.
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Affiliation(s)
- Akhil Pulumati
- University of Missouri‐Kansas CityKansas CityMissouriUSA
| | - Anika Pulumati
- University of Missouri‐Kansas CityKansas CityMissouriUSA
| | - Bilikere S. Dwarakanath
- Central Research FacilitySri Ramachandra Institute of Higher Education and Research PorurChennaiIndia
- Department of BiotechnologyIndian Academy Degree CollegeBangaloreIndia
| | | | - Rao V. L. Papineni
- PACT & Health LLCBranfordConnecticutUSA
- Department of SurgeryUniversity of Kansas Medical CenterKansas CityKansasUSA
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20
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Cetintas VB, Duzgun Z, Akalin T, Ozgiray E, Dogan E, Yildirim Z, Akinturk N, Biceroglu H, Ertan Y, Kosova B. Molecular dynamic simulation and functional analysis of pathogenic PTEN mutations in glioblastoma. J Biomol Struct Dyn 2023; 41:11471-11483. [PMID: 36591942 DOI: 10.1080/07391102.2022.2162582] [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: 08/17/2022] [Accepted: 12/20/2022] [Indexed: 01/03/2023]
Abstract
PTEN, a dual-phosphatase and scaffold protein, is one of the most commonly mutated tumour suppressor gene across various cancer types in human. The aim of this study therefore was to investigate the stability, structural and functional effects, and pathogenicity of 12 missense PTEN mutations (R15S, E18G, G36R, N49I, Y68H, I101T, C105F, D109N, V133I, C136Y, R173C and N276S) found by next generation sequencing of the PTEN gene in tissue samples obtained from glioblastoma patients. Computational tools and molecular dynamic simulation programs were used to identify the deleterious effects of these mutations. Furthermore, PTEN mRNA and protein expression levels were evaluated by qRT-PCR, Western Blot, and immunohistochemistry staining methods. Various computational tools predicted strong deleterious effects for the G36R, C105F, C136Y and N276S mutations. Molecular dynamic simulation revealed a significant decrease in protein stability for the Y68H and N276S mutations when compared with the wild type protein; whereas, C105F, D109N, V133I and R173C showed partial stability reduction. Significant residual fluctuations were observed in the R15S, N49I and C136Y mutations and radius of gyration graphs revealed the most compact structure for D109N and least for C136Y. In summary, our study is the first one to show the presence of PTEN E18G, N49I, D109N and N276S mutations in glioblastoma patients; where, D109N is neutral and N276S is a damaging and disease-associated mutation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Zekeriya Duzgun
- Department of Medical Biology, Giresun University Faculty of Medicine, Giresun, Turkey
| | - Taner Akalin
- Department of Pathology, Ege University Faculty of Medicine, Izmir, Turkey
| | - Erkin Ozgiray
- Department of Neurosurgery, Ege University Faculty of Medicine, Izmir, Turkey
| | - Eda Dogan
- Department of Medical Biology, Ege University Faculty of Medicine, Izmir, Turkey
| | - Zafer Yildirim
- Department of Medical Biology, Ege University Faculty of Medicine, Izmir, Turkey
| | - Nevhis Akinturk
- Department of Neurosurgery, Ege University Faculty of Medicine, Izmir, Turkey
| | - Huseyin Biceroglu
- Department of Neurosurgery, Ege University Faculty of Medicine, Izmir, Turkey
| | - Yesim Ertan
- Department of Pathology, Ege University Faculty of Medicine, Izmir, Turkey
| | - Buket Kosova
- Department of Medical Biology, Ege University Faculty of Medicine, Izmir, Turkey
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21
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Arai H, Minami Y, Chi S, Utsu Y, Masuda S, Aotsuka N. Molecular-Targeted Therapy for Tumor-Agnostic Mutations in Acute Myeloid Leukemia. Biomedicines 2022; 10:3008. [PMID: 36551764 PMCID: PMC9775249 DOI: 10.3390/biomedicines10123008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/09/2022] [Accepted: 11/14/2022] [Indexed: 11/24/2022] Open
Abstract
Comprehensive genomic profiling examinations (CGPs) have recently been developed, and a variety of tumor-agnostic mutations have been detected, leading to the development of new molecular-targetable therapies across solid tumors. In addition, the elucidation of hereditary tumors, such as breast and ovarian cancer, has pioneered a new age marked by the development of new treatments and lifetime management strategies required for patients with potential or presented hereditary cancers. In acute myeloid leukemia (AML), however, few tumor-agnostic or hereditary mutations have been the focus of investigation, with associated molecular-targeted therapies remaining poorly developed. We focused on representative tumor-agnostic mutations such as the TP53, KIT, KRAS, BRCA1, ATM, JAK2, NTRK3, FGFR3 and EGFR genes, referring to a CGP study conducted in Japan, and we considered the possibility of developing molecular-targeted therapies for AML with tumor-agnostic mutations. We summarized the frequency, the prognosis, the structure and the function of these mutations as well as the current treatment strategies in solid tumors, revealed the genetical relationships between solid tumors and AML and developed tumor-agnostic molecular-targeted therapies and lifetime management strategies in AML.
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Affiliation(s)
- Hironori Arai
- Department of Hematology and Oncology, Japanese Red Cross Narita Hospital, Iidacho 286-0041, Japan
- Department of Hematology, National Cancer Center Hospital East, Kashiwa 277-8577, Japan
| | - Yosuke Minami
- Department of Hematology, National Cancer Center Hospital East, Kashiwa 277-8577, Japan
| | - SungGi Chi
- Department of Hematology, National Cancer Center Hospital East, Kashiwa 277-8577, Japan
| | - Yoshikazu Utsu
- Department of Hematology and Oncology, Japanese Red Cross Narita Hospital, Iidacho 286-0041, Japan
| | - Shinichi Masuda
- Department of Hematology and Oncology, Japanese Red Cross Narita Hospital, Iidacho 286-0041, Japan
| | - Nobuyuki Aotsuka
- Department of Hematology and Oncology, Japanese Red Cross Narita Hospital, Iidacho 286-0041, Japan
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22
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Tanvir I, Hassan A, Albeladi F. DNA Methylation and Epigenetic Events Underlying Renal Cell Carcinomas. Cureus 2022; 14:e30743. [DOI: 10.7759/cureus.30743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2022] [Indexed: 11/05/2022] Open
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23
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Ansari S, Yamaoka Y. Helicobacter pylori Infection, Its Laboratory Diagnosis, and Antimicrobial Resistance: a Perspective of Clinical Relevance. Clin Microbiol Rev 2022; 35:e0025821. [PMID: 35404105 PMCID: PMC9491184 DOI: 10.1128/cmr.00258-21] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Despite the recent decrease in overall prevalence of Helicobacter pylori infection, morbidity and mortality rates associated with gastric cancer remain high. The antimicrobial resistance developments and treatment failure are fueling the global burden of H. pylori-associated gastric complications. Accurate diagnosis remains the opening move for treatment and eradication of infections caused by microorganisms. Although several reports have been published on diagnostic approaches for H. pylori infection, most lack the data regarding diagnosis from a clinical perspective. Therefore, we provide an intensive, comprehensive, and updated description of the currently available diagnostic methods that can help clinicians, infection diagnosis professionals, and H. pylori researchers working on infection epidemiology to broaden their understanding and to select appropriate diagnostic methods. We also emphasize appropriate diagnostic approaches based on clinical settings (either clinical diagnosis or mass screening), patient factors (either age or other predisposing factors), and clinical factors (either upper gastrointestinal bleeding or partial gastrectomy) and appropriate methods to be considered for evaluating eradication efficacy. Furthermore, to cope with the increasing trend of antimicrobial resistance, a better understanding of its emergence and current diagnostic approaches for resistance detection remain inevitable.
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Affiliation(s)
- Shamshul Ansari
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu City, Oita, Japan
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu City, Oita, Japan
- Department of Medicine, Gastroenterology and Hepatology Section, Baylor College of Medicine, Houston, Texas, USA
- Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
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24
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Pavone G, Romano C, Martorana F, Motta L, Salvatorelli L, Zanghì AM, Magro G, Vigneri P. Giant Paratesticular Liposarcoma: Molecular Characterization and Management Principles with a Review of the Literature. Diagnostics (Basel) 2022; 12:diagnostics12092160. [PMID: 36140560 PMCID: PMC9498211 DOI: 10.3390/diagnostics12092160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/01/2022] [Accepted: 09/04/2022] [Indexed: 11/29/2022] Open
Abstract
Paratesticular liposarcomas are extremely rare malignant tumors originating from fat tissues, with an often-challenging diagnosis. We present here the case of a 76-year-old man with a giant paratesticular liposarcoma, initially misdiagnosed as a scrotal hernia. After two years, the progressively enlarging mass underwent surgical resection, and a diagnosis of well-differentiated liposarcoma (lipoma-like subtype) was made. Post-operative treatments were not indicated, and the patient remains relapse free. Next generation sequencing performed on the neoplastic tissue showed co-amplification of MDM2 and CDK4. These alterations are molecular hallmarks of well-differentiated liposarcomas and corroborate the histological diagnosis. Clinical and molecular features of the presented case are in line with the majority of previously published experiences. In conclusion, the presence of a liposarcoma should be taken into account during the diagnostic workup of scrotal masses, in order to minimize the rate of misdiagnosis and improper management. Molecular analysis may support histological characterization of these rare entities and potentially disclose novel therapeutic targets.
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Affiliation(s)
- Giuliana Pavone
- Division of Medical Oncology, A.O.U. Policlinico “G. Rodolico–San Marco”—Catania, Via Santa Sofia, 78, 95123 Catania, Italy
- Correspondence:
| | - Chiara Romano
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico “G. Rodolico–San Marco”—Catania, Via Santa Sofia, 78, 95123 Catania, Italy
- Department of Medical and Surgical Sciences and Advanced Technology G. F. Ingrassia, A.O.U. Policlinico “G. Rodolico–San Marco”—Catania, Via Santa Sofia, 87, 95123 Catania, Italy
| | - Federica Martorana
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy
| | - Lucia Motta
- Division of Medical Oncology, A.O.U. Policlinico “G. Rodolico–San Marco”—Catania, Via Santa Sofia, 78, 95123 Catania, Italy
| | - Lucia Salvatorelli
- Department of Medical and Surgical Sciences and Advanced Technology G. F. Ingrassia, A.O.U. Policlinico “G. Rodolico–San Marco”—Catania, Via Santa Sofia, 87, 95123 Catania, Italy
| | - Antonio Maria Zanghì
- Department of Medical and Surgical Sciences and Advanced Technology G. F. Ingrassia, A.O.U. Policlinico “G. Rodolico–San Marco”—Catania, Via Santa Sofia, 87, 95123 Catania, Italy
| | - Gaetano Magro
- Department of Medical and Surgical Sciences and Advanced Technology G. F. Ingrassia, A.O.U. Policlinico “G. Rodolico–San Marco”—Catania, Via Santa Sofia, 87, 95123 Catania, Italy
| | - Paolo Vigneri
- Division of Medical Oncology, A.O.U. Policlinico “G. Rodolico–San Marco”—Catania, Via Santa Sofia, 78, 95123 Catania, Italy
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico “G. Rodolico–San Marco”—Catania, Via Santa Sofia, 78, 95123 Catania, Italy
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy
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25
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Ding N, Luo H, Peng T, Zhang T, Li M, Deng Y, He Y. Bioinformatics analysis on differentially expressed genes between colorectal adenoma and colorectal adenocarcinoma. Scott Med J 2022; 67:178-188. [PMID: 36031809 DOI: 10.1177/00369330221122306] [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: 01/19/2023]
Abstract
BACKGROUND Colorectal adenoma (CRA) is the main cause of the progression of Colorectal adenocarcinoma (COAD). Therefore, it is very important to accurately reveal its developmental mechanism. METHODS Differential expression genes (DEGs) in three microarray datasets were screened using GEO and GEO2R. R packages were used for gene ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) path enrichment analysis. Hub genes screened by STRING, Cytoscape and CytoHubba were used. R was used for DEGs of hub genes, and Gene Expression Profiling Interactive Analysis (GEPIA2) database was used for prognostic Analysis. R-packet were used to analyze tumor pathology, tumour, lymph-nodes, and metastases (TNM) staging, enrichment, immune invasion and prognosis. RESULTS Among the 66 genes, including 36 up-regulated and 30 down-regulated genes. Survival analysis showed that COL1A1, COL5A2, COL5A1 and secreted protein acidic and rich in cysteine (SPARC) were associated with disease-free survival in patients. The four genes were related to tumor pathological stage, TNM stage and immune invasion. COL1A1 and COL5A2 were highly expressed in chromatin modification and cellular senescence. Low expression of COL5A1 and SPARC was significantly enriched in neutrophil degranulation and Wp VegfavegFR2 signaling pathways. CONCLUSIONS Obviously, these four key genes can serve as important targets for early diagnosis, treatment, immunity and prognosis of CRA to COAD.
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Affiliation(s)
- Ning Ding
- 118393Graduate School, Hunan University of Chinese Medicine, Changsha, P.R. China
| | - Hongbiao Luo
- Department of Anorectal Surgery, The Affiliated Hospital of Hunan Academy of Traditional Chinese Medicine, Changsha, P.R. China.,Department of Anorectal Surgery, 56696Chenzhou NO. 1 People's Hospital, Chenzhou, PR China
| | - Tianshu Peng
- Department of Anorectal Surgery, The Second Affiliated Hospital of Hunan University of Chinese Medicine, Changsha, P.R. China
| | - Tao Zhang
- 118393Graduate School, Hunan University of Chinese Medicine, Changsha, P.R. China
| | - Menglei Li
- 118393Graduate School, Hunan University of Chinese Medicine, Changsha, P.R. China
| | - Yu Deng
- 118393Graduate School, Hunan University of Chinese Medicine, Changsha, P.R. China
| | - Yongheng He
- Department of Anorectal Surgery, The Affiliated Hospital of Hunan Academy of Traditional Chinese Medicine, Changsha, P.R. China
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26
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Liquid Biopsy and Circulating Biomarkers for the Diagnosis of Precancerous and Cancerous Oral Lesions. Noncoding RNA 2022; 8:ncrna8040060. [PMID: 36005828 PMCID: PMC9414906 DOI: 10.3390/ncrna8040060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/21/2022] [Accepted: 08/08/2022] [Indexed: 12/19/2022] Open
Abstract
Oral cancer is one of the most common malignancies worldwide, accounting for 2% of all cases annually and 1.8% of all cancer deaths. To date, tissue biopsy and histopathological analyses are the gold standard methods for the diagnosis of oral cancers. However, oral cancer is generally diagnosed at advanced stages with a consequent poor 5-year survival (~50%) due to limited screening programs and inefficient physical examination strategies. To address these limitations, liquid biopsy is recently emerging as a novel minimally invasive tool for the early identification of tumors as well as for the evaluation of tumor heterogeneity and prognosis of patients. Several studies have demonstrated that liquid biopsy in oral cancer could be useful for the detection of circulating biomarkers including circulating tumor DNA (ctDNA), microRNAs (miRNAs), proteins, and exosomes, thus improving diagnostic strategies and paving the way to personalized medicine. However, the application of liquid biopsy in oral cancer is still limited and further studies are needed to better clarify its clinical impact. The present manuscript aims to provide an updated overview of the potential use of liquid biopsy as an additional tool for the management of oral lesions by describing the available methodologies and the most promising biomarkers.
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27
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Bozsodi A, Scholtz B, Papp G, Sapi Z, Biczo A, Varga PP, Lazary A. Potential molecular mechanism in self-renewal is associated with miRNA dysregulation in sacral chordoma - A next-generation RNA sequencing study. Heliyon 2022; 8:e10227. [PMID: 36033338 PMCID: PMC9404356 DOI: 10.1016/j.heliyon.2022.e10227] [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: 12/10/2021] [Revised: 05/24/2022] [Accepted: 08/04/2022] [Indexed: 12/04/2022] Open
Abstract
Background Chordoma, the most frequent malignant primary spinal neoplasm, characterized by a high rate of recurrence, is an orphan disease where the clarification of the molecular oncogenesis would be crucial to developing new, effective therapies. Dysregulated expression of non-coding RNAs, especially microRNAs (miRNA) has a significant role in cancer development. Methods Next-generation RNA sequencing (NGS) was used for the combinatorial analysis of mRNA-miRNA gene expression profiles in sacral chordoma and nucleus pulposus samples. Advanced bioinformatics workflow was applied to the data to predict miRNA-mRNA regulatory networks with altered activity in chordoma. Results A large set of significantly dysregulated miRNAs in chordoma and their differentially expressed target genes have been identified. Several molecular pathways related to tumorigenesis and the modulation of the immune system are predicted to be dysregulated due to aberrant miRNA expression in chordoma. We identified a gene set including key regulators of the Hippo pathway, which is targeted by differently expressed miRNAs, and validated their altered expression by RT-qPCR. These newly identified miRNA/RNA interactions are predicted to have a role in the self-renewal process of chordoma stem cells, which might sustain the high rate of recurrence for this tumor. Conclusions Our results can significantly contribute to the designation of possible targets for the development of anti-chordoma therapies.
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Affiliation(s)
- Arpad Bozsodi
- National Center for Spinal Disorders, Buda Health Center, Királyhágó u. 1-3, Budapest, H-1126, Hungary
- School of PhD Studies, Semmelweis University, Üllői út 26, Budapest, H-1085, Hungary
| | - Beata Scholtz
- Genomic Medicine and Bioinformatic Core Facility, Dept. of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Nagyerdei krt. 98, Debrecen, H-4032, Hungary
| | - Gergo Papp
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, Budapest, H-1085, Hungary
| | - Zoltan Sapi
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, Budapest, H-1085, Hungary
| | - Adam Biczo
- National Center for Spinal Disorders, Buda Health Center, Királyhágó u. 1-3, Budapest, H-1126, Hungary
| | - Peter Pal Varga
- National Center for Spinal Disorders, Buda Health Center, Királyhágó u. 1-3, Budapest, H-1126, Hungary
| | - Aron Lazary
- National Center for Spinal Disorders, Buda Health Center, Királyhágó u. 1-3, Budapest, H-1126, Hungary
- Department of Spine Surgery, Department of Orthopaedics, Semmelweis University, Királyhágó u. 1-3, Budapest, H-1126, Hungary
- Corresponding author.
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28
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Mass Spectrometry Imaging Spatial Tissue Analysis toward Personalized Medicine. LIFE (BASEL, SWITZERLAND) 2022; 12:life12071037. [PMID: 35888125 PMCID: PMC9318569 DOI: 10.3390/life12071037] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/04/2022] [Accepted: 07/10/2022] [Indexed: 12/19/2022]
Abstract
Novel profiling methodologies are redefining the diagnostic capabilities and therapeutic approaches towards more precise and personalized healthcare. Complementary information can be obtained from different omic approaches in combination with the traditional macro- and microscopic analysis of the tissue, providing a more complete assessment of the disease. Mass spectrometry imaging, as a tissue typing approach, provides information on the molecular level directly measured from the tissue. Lipids, metabolites, glycans, and proteins can be used for better understanding imbalances in the DNA to RNA to protein translation, which leads to aberrant cellular behavior. Several studies have explored the capabilities of this technology to be applied to tumor subtyping, patient prognosis, and tissue profiling for intraoperative tissue evaluation. In the future, intercenter studies may provide the needed confirmation on the reproducibility, robustness, and applicability of the developed classification models for tissue characterization to assist in disease management.
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29
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Li C, Hua K. Dissecting the Single-Cell Transcriptome Network of Immune Environment Underlying Cervical Premalignant Lesion, Cervical Cancer and Metastatic Lymph Nodes. Front Immunol 2022; 13:897366. [PMID: 35812401 PMCID: PMC9263187 DOI: 10.3389/fimmu.2022.897366] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/20/2022] [Indexed: 01/09/2023] Open
Abstract
Cervical cancer (CC) is one of the most common malignancy in women worldwide. It is characterized by a natural continuous phenomenon, that is, it is in the initial stage of HPV infection, progresses to intraepithelial neoplasia, and then develops into invasion and metastasis. Determining the complexity of tumor microenvironment (TME) can deepen our understanding of lesion progression and provide novel therapeutic strategies for CC. We performed the single-cell RNA sequencing on the normal cervix, intraepithelial neoplasia, primary tumor and metastatic lymph node tissues to describe the composition, lineage, and functional status of immune cells and mesenchymal cells at different stages of CC progression. A total of 59913 single cells were obtained and divided into 9 cellular clusters, including immune cells (T/NK cells, macrophages, B cells, plasma cells, mast cells and neutrophils) and mesenchymal cells (endothelial cells, smooth muscle cells and fibroblasts). Our results showed that there were distinct cell subpopulations in different stages of CC. High-stage intraepithelial neoplasia (HSIL) tissue exhibited a low, recently activated TME, and it was characterized by high infiltration of tissue-resident CD8 T cell, effector NK cells, Treg, DC1, pDC, and M1-like macrophages. Tumor tissue displayed high enrichment of exhausted CD8 T cells, resident NK cells and M2-like macrophages, suggesting immunosuppressive TME. Metastatic lymph node consisted of naive T cell, central memory T cell, circling NK cells, cytotoxic CD8+ T cells and effector memory CD8 T cells, suggesting an early activated phase of immune response. This study is the first to delineate the transcriptome profile of immune cells during CC progression using single-cell RNA sequencing. Our results indicated that HSIL exhibited a low, recently activated TME, tumor displayed immunosuppressive statue, and metastatic lymph node showed early activated phase of immune response. Our study enhanced the understanding of dynamic change of TME during CC progression and has implications for the development of novel treatments to inhibit the initiation and progression of CC.
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Affiliation(s)
- Chunbo Li
- Department of Obstetrics and Gynecology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Keqin Hua
- Department of Obstetrics and Gynecology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
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30
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Romano C, Di Gregorio S, Pennisi MS, Tirrò E, Broggi G, Caltabiano R, Manzella L, Ruggieri M, Vigneri P, Di Cataldo A. Multiple primary malignances managed with surgical excision: a case report with next generation sequencing analysis. Mol Biol Rep 2022; 49:9059-9064. [PMID: 35715605 DOI: 10.1007/s11033-022-07630-8] [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: 03/04/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Multiple primary malignancies (MPM) are defined as tumors originating in the same individual without any correlation between them. In addition to morphological and immunohistochemical analyses, sensitive DNA sequencing methods such as next generation sequencing (NGS) may help to discriminate the common or different genetic alterations driving each malignancy, to better diagnose these uncommon cases. METHODS AND RESULTS Here we report the case of a man who developed a poorly differentiated gastric adenocarcinoma invading the pancreas followed, two years later, by a colorectal cancer involving also the kidney and the diaphragm. Despite the advanced stage of both diseases, adjuvant chemotherapy was successful. While the second tumor was initially interpreted as a relapse of his stomach cancer, NGS-based mutation profiling of the two carcinomas revealed two distinct malignances, independently developing in different times and indicative of metachronous MPM. Indeed, sequencing of cancer-associated genes identified somatic mutations only in the first gastric cancer, besides germline variants on three different genes (PDGFRA, APC and TP53). However, analysis of both somatic and germline mutations with bio-informatics prediction tools failed to find a correlation between these variants and the unexpectedly good prognosis of both cancers. CONCLUSIONS In summary, NGS analysis contributed to defined different molecular profiles for two tumors developed in the span of two years, thus allowing diagnosing the case as MPN. However, NGS was unable to establish a direct correlation between the identified alterations and cancer development.
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Affiliation(s)
- Chiara Romano
- Department of Clinical and Experimental Medicine, University of Catania, 95123, Catania, Italy. .,Center of Experimental Oncology and Hematology, A.O.U. Policlinico "G. Rodolico - San Marco", 95123, Catania, Italy.
| | - Sandra Di Gregorio
- Department of Clinical and Experimental Medicine, University of Catania, 95123, Catania, Italy.,Center of Experimental Oncology and Hematology, A.O.U. Policlinico "G. Rodolico - San Marco", 95123, Catania, Italy
| | - Maria Stella Pennisi
- Department of Clinical and Experimental Medicine, University of Catania, 95123, Catania, Italy.,Center of Experimental Oncology and Hematology, A.O.U. Policlinico "G. Rodolico - San Marco", 95123, Catania, Italy
| | - Elena Tirrò
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico "G. Rodolico - San Marco", 95123, Catania, Italy.,Department of Surgical, Oncological and Stomatological Sciences, University of Palermo, 90127, Palermo, Italy
| | - Giuseppe Broggi
- Department of Medical, Surgical Sciences and Advanced Technologies "G.F. Ingrassia", Section of Anatomic Pathology, University of Catania, 95123, Catania, Italy
| | - Rosario Caltabiano
- Department of Medical, Surgical Sciences and Advanced Technologies "G.F. Ingrassia", Section of Anatomic Pathology, University of Catania, 95123, Catania, Italy
| | - Livia Manzella
- Department of Clinical and Experimental Medicine, University of Catania, 95123, Catania, Italy.,Center of Experimental Oncology and Hematology, A.O.U. Policlinico "G. Rodolico - San Marco", 95123, Catania, Italy
| | - Martino Ruggieri
- Unit of Rare Diseases of the Nervous System in Childhood, Department of Clinical and Experimental Medicine, Section of Pediatrics and Child Neuropsychiatry, University of Catania, 95123, Catania, Italy
| | - Paolo Vigneri
- Department of Clinical and Experimental Medicine, University of Catania, 95123, Catania, Italy.,Center of Experimental Oncology and Hematology, A.O.U. Policlinico "G. Rodolico - San Marco", 95123, Catania, Italy
| | - Antonio Di Cataldo
- Department of General Surgery and Medical-Surgical Specialties, University of Catania, 95123, Catania, Italy
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31
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Jerves T, Blau N, Ferreira CR. Clinical and biochemical footprints of inherited metabolic diseases. VIII. Neoplasias. Mol Genet Metab 2022; 136:118-124. [PMID: 35422340 PMCID: PMC9189061 DOI: 10.1016/j.ymgme.2022.03.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 12/21/2022]
Abstract
Cancer, caused by multiple cumulative pathogenic variants in tumor suppressor genes and proto-oncogenes, is a leading cause of mortality worldwide. The uncontrolled and rapid cell growth of the tumors requires a reprogramming of the complex cellular metabolic network to favor anabolism. Adequate management and treatment of certain inherited metabolic diseases might prevent the development of certain neoplasias, such as hepatocellular carcinoma in tyrosinemia type 1 or hepatocellular adenomas in glycogen storage disorder type 1a. We reviewed and updated the list of known metabolic etiologies associated with various types of benign and malignant neoplasias, finding 64 relevant inborn errors of metabolism. This is the eighth article of the series attempting to create a comprehensive list of clinical and metabolic differential diagnosis by system involvement.
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Affiliation(s)
- Teodoro Jerves
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nenad Blau
- Division of Metabolism, University Children's Hospital, Zürich, Switzerland.
| | - Carlos R Ferreira
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
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Actionable Mutation Profile of Sun-Protected Melanomas in South America. Am J Dermatopathol 2022; 44:741-747. [PMID: 35503891 DOI: 10.1097/dad.0000000000002213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
ABSTRACT Melanomas that arise in sun-protected sites, including acral and oral mucosal melanomas, are likely under the control of unique, specific mechanisms that lead to mutagenesis through various pathways. In this study, we examined somatic mutations in tumors by targeted sequencing using a custom Ion Ampliseq Panel, comprising hotspots of 14 genes that are frequently mutated in solid tumors. Tumor DNA was extracted from 9 formalin fixation, paraffin-embedded sun-protected melanomas (4 primary oral mucosal melanomas and 5 acral lentiginous melanomas), and we identified mutations in the NRAS, PIK3CA, EGFR, HRAS, ERBB2, and ROS1 genes. This study reveals new actionable mutations that are potential targets in the treatment of photo-protected melanomas. Additional studies on more of these melanoma subtypes could confirm our findings and identify new mutations.
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Lavoro A, Scalisi A, Candido S, Zanghì GN, Rizzo R, Gattuso G, Caruso G, Libra M, Falzone L. Identification of the most common BRCA alterations through analysis of germline mutation databases: Is droplet digital PCR an additional strategy for the assessment of such alterations in breast and ovarian cancer families? Int J Oncol 2022; 60:58. [PMID: 35383859 PMCID: PMC8997337 DOI: 10.3892/ijo.2022.5349] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/24/2022] [Indexed: 11/06/2022] Open
Abstract
Breast and ovarian cancer represent two of the most common tumor types in females worldwide. Over the years, several non‑modifiable and modifiable risk factors have been associated with the onset and progression of these tumors, including age, reproductive factors, ethnicity, socioeconomic status and lifestyle factors, as well as family history and genetic factors. Of note, BRCA1 and BRCA2 are two tumor suppressor genes with a key role in DNA repair processes, whose mutations may induce genomic instability and increase the risk of cancer development. Specifically, females with a family history of breast or ovarian cancer harboring BRCA1/2 germline mutations have a 60‑70% increased risk of developing breast cancer and a 15‑40% increased risk for ovarian cancer. Different databases have collected the most frequent germline mutations affecting BRCA1/2. Through the analysis of such databases, it is possible to identify frequent hotspot mutations that may be analyzed with next‑generation sequencing (NGS) and novel innovative strategies. In this context, NGS remains the gold standard method for the assessment of BRCA1/2 mutations, while novel techniques, including droplet digital PCR (ddPCR), may improve the sensitivity to identify such mutations in the hereditary forms of breast and ovarian cancer. On these bases, the present study aimed to provide an update of the current knowledge on the frequency of BRCA1/2 mutations and cancer susceptibility, focusing on the diagnostic potential of the most recent methods, such as ddPCR.
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Affiliation(s)
- Alessandro Lavoro
- Department of Biomedical and Biotechnological Sciences, University of Catania, I‑95123 Catania, Italy
| | - Aurora Scalisi
- Italian League Against Cancer, Section of Catania, I‑95122 Catania, Italy
| | - Saverio Candido
- Department of Biomedical and Biotechnological Sciences, University of Catania, I‑95123 Catania, Italy
| | - Guido Nicola Zanghì
- Department of General Surgery and Medical‑Surgical Specialties, Policlinico‑Vittorio Emanuele Hospital, University of Catania, I‑95123 Catania, Italy
| | - Roberta Rizzo
- Department of Biomedical and Biotechnological Sciences, University of Catania, I‑95123 Catania, Italy
| | - Giuseppe Gattuso
- Department of Biomedical and Biotechnological Sciences, University of Catania, I‑95123 Catania, Italy
| | - Giuseppe Caruso
- Department of Biomedical and Biotechnological Sciences, University of Catania, I‑95123 Catania, Italy
| | - Massimo Libra
- Department of Biomedical and Biotechnological Sciences, University of Catania, I‑95123 Catania, Italy
| | - Luca Falzone
- Epidemiology and Biostatistics Unit, National Cancer Institute IRCCS Fondazione 'G. Pascale', I‑80131 Naples, Italy
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Lechpammer M, Rao R, Shah S, Mirheydari M, Bhattacharya D, Koehler A, Toukam DK, Haworth KJ, Pomeranz Krummel D, Sengupta S. Advances in Immunotherapy for the Treatment of Adult Glioblastoma: Overcoming Chemical and Physical Barriers. Cancers (Basel) 2022; 14:1627. [PMID: 35406398 PMCID: PMC8997081 DOI: 10.3390/cancers14071627] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/18/2022] [Accepted: 03/22/2022] [Indexed: 02/07/2023] Open
Abstract
Glioblastoma, or glioblastoma multiforme (GBM, WHO Grade IV), is a highly aggressive adult glioma. Despite extensive efforts to improve treatment, the current standard-of-care (SOC) regimen, which consists of maximal resection, radiotherapy, and temozolomide (TMZ), achieves only a 12-15 month survival. The clinical improvements achieved through immunotherapy in several extracranial solid tumors, including non-small-cell lung cancer, melanoma, and non-Hodgkin lymphoma, inspired investigations to pursue various immunotherapeutic interventions in adult glioblastoma patients. Despite some encouraging reports from preclinical and early-stage clinical trials, none of the tested agents have been convincing in Phase III clinical trials. One, but not the only, factor that is accountable for the slow progress is the blood-brain barrier, which prevents most antitumor drugs from reaching the target in appreciable amounts. Herein, we review the current state of immunotherapy in glioblastoma and discuss the significant challenges that prevent advancement. We also provide thoughts on steps that may be taken to remediate these challenges, including the application of ultrasound technologies.
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Affiliation(s)
- Mirna Lechpammer
- Foundation Medicine, Inc., Cambridge, MA 02141, USA;
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Rohan Rao
- Department of Neurology and Rehabilitation Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; (R.R.); (D.B.); (A.K.); (D.K.T.)
| | - Sanjit Shah
- Department of Neurosurgery, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA;
| | - Mona Mirheydari
- Department of Internal Medicine, Division of Cardiovascular Health and Disease, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; (M.M.); (K.J.H.)
| | - Debanjan Bhattacharya
- Department of Neurology and Rehabilitation Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; (R.R.); (D.B.); (A.K.); (D.K.T.)
| | - Abigail Koehler
- Department of Neurology and Rehabilitation Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; (R.R.); (D.B.); (A.K.); (D.K.T.)
| | - Donatien Kamdem Toukam
- Department of Neurology and Rehabilitation Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; (R.R.); (D.B.); (A.K.); (D.K.T.)
| | - Kevin J. Haworth
- Department of Internal Medicine, Division of Cardiovascular Health and Disease, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; (M.M.); (K.J.H.)
| | - Daniel Pomeranz Krummel
- Department of Neurology and Rehabilitation Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; (R.R.); (D.B.); (A.K.); (D.K.T.)
| | - Soma Sengupta
- Department of Neurology and Rehabilitation Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; (R.R.); (D.B.); (A.K.); (D.K.T.)
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Cheng YH, Wang CH, Hsu KF, Lee GB. Integrated Microfluidic System for Cell-Free DNA Extraction from Plasma for Mutant Gene Detection and Quantification. Anal Chem 2022; 94:4311-4318. [PMID: 35235296 DOI: 10.1021/acs.analchem.1c04988] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ovarian cancer (OvCa) is among the most severe gynecologic cancers, yet individuals may be asymptomatic during its early stages. Routine, early screening for genetic abnormalities associated with OvCa could improve prognoses, and this can be achieved by detecting mutant genes in cell-free DNA (cfDNA). Herein, we developed an integrated microfluidic chip (IMC) that could extract cfDNA from plasma and automatically detect and quantify mutations in the OvCa biomarker BRCA1. The cfDNA extraction module relied on a vortex-type micromixer to mix cfDNA with magnetic beads surface-coated with cfDNA probes and could isolate 76% of molecules from a 200 μL plasma sample in 45 min. The cfDNA quantification module, which comprised a micropump that evenly distributed 4.5 μL of purified cfDNA into the on-chip, allele-specific quantitative polymerase chain reaction (qPCR) zones, was capable of quantifying mutant genes within 90 min. By automating the cfDNA extraction and qPCR processes, this IMC could be used for clinical screening for OvCa-associated mutations.
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Affiliation(s)
- Yu-Hung Cheng
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chih-Hung Wang
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Keng-Fu Hsu
- Department of Obstetrics and Gynecology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70403, Taiwan
| | - Gwo-Bin Lee
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan.,Institute of NanoEngineering and MicroSystems, National Tsing Hua University, Hsinchu 30013, Taiwan
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36
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Hechtman JF. NTRK insights: best practices for pathologists. Mod Pathol 2022; 35:298-305. [PMID: 34531526 PMCID: PMC8860742 DOI: 10.1038/s41379-021-00913-8] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/24/2021] [Accepted: 08/24/2021] [Indexed: 11/21/2022]
Abstract
Since the discovery of an oncogenic tropomyosin-receptor kinase (TRK) fusion protein in the early 1980s, our understanding of neurotrophic tropomyosin-receptor kinase (NTRK) fusions, their unique patterns of frequency in different tumor types, and methods to detect them have grown in scope and depth. Identification of these molecular alterations in the management of patients with cancer has become increasingly important with the emergence of histology-agnostic, US Food and Drug Administration-approved, effective TRK protein inhibitors. Herein, we review the biology of TRK in normal and malignant tissues, as well as the prevalence and enrichment patterns of these fusions across tumor types. Testing methods currently used to identify NTRK1-3 fusions will be reviewed in detail, with attention to newer assays including RNA-based next-generation sequencing. Recently proposed algorithms for NTRK fusion testing will be compared, and practical insights provided on how testing can best be implemented and communicated within the multidisciplinary healthcare team.
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Affiliation(s)
- Jaclyn F Hechtman
- Molecular Pathologist, Neogenomics 9490 NeoGenomics Way, Fort Myers, FL, 33912, USA.
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37
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Miao Y, Yang T, Yang S, Yang M, Mao C. Protein nanoparticles directed cancer imaging and therapy. NANO CONVERGENCE 2022; 9:2. [PMID: 34997888 PMCID: PMC8742799 DOI: 10.1186/s40580-021-00293-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/29/2021] [Indexed: 05/10/2023]
Abstract
Cancer has been a serious threat to human health. Among drug delivery carriers, protein nanoparticles are unique because of their mild and environmentally friendly preparation methods. They also inherit desired characteristics from natural proteins, such as biocompatibility and biodegradability. Therefore, they have solved some problems inherent to inorganic nanocarriers such as poor biocompatibility. Also, the surface groups and cavity of protein nanoparticles allow for easy surface modification and drug loading. Besides, protein nanoparticles can be combined with inorganic nanoparticles or contrast agents to form multifunctional theranostic platforms. This review introduces representative protein nanoparticles applicable in cancer theranostics, including virus-like particles, albumin nanoparticles, silk protein nanoparticles, and ferritin nanoparticles. It also describes the common methods for preparing them. It then critically analyzes the use of a variety of protein nanoparticles in improved cancer imaging and therapy.
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Affiliation(s)
- Yao Miao
- School of Materials Science and Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
| | - Tao Yang
- School of Materials Science and Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
| | - Shuxu Yang
- Department of Neurosurgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, 3 East Qingchun Road, Hangzhou, 310016, Zhejiang, China.
| | - Mingying Yang
- Institute of Applied Bioresource Research, College of Animal Science, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058, Zhejiang, China.
| | - Chuanbin Mao
- Department of Chemistry & Biochemistry, Stephenson Life Science Research Center, Institute for Biomedical Engineering, Science and Technology, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019-5251, USA.
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38
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Correa R, Alonso-Pupo N, Hernández Rodríguez EW. Multi-omics data integration approaches for precision oncology. Mol Omics 2022; 18:469-479. [DOI: 10.1039/d1mo00411e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Next-generation sequencing (NGS) has been pivotal to enhance the molecular characterization of human malignancies, allowing multiple omics data types to be available for cancer researchers and practitioners. In this context,...
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39
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Aleotti V, Catoni C, Poggiana C, Rosato A, Facchinetti A, Scaini MC. Methylation Markers in Cutaneous Melanoma: Unravelling the Potential Utility of Their Tracking by Liquid Biopsy. Cancers (Basel) 2021; 13:6217. [PMID: 34944843 PMCID: PMC8699653 DOI: 10.3390/cancers13246217] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/02/2021] [Accepted: 12/08/2021] [Indexed: 01/19/2023] Open
Abstract
Malignant melanoma is the most serious, life-threatening form of all dermatologic diseases, with a poor prognosis in the presence of metastases and advanced disease. Despite recent advances in targeted therapy and immunotherapy, there is still a critical need for a better understanding of the fundamental mechanisms behind melanoma progression and resistance onset. Recent advances in genome-wide methylation methods have revealed that aberrant changes in the pattern of DNA methylation play an important role in many aspects of cancer progression, including cell proliferation and migration, evasion of cell death, invasion, and metastasization. The purpose of the current review was to gather evidence regarding the usefulness of DNA methylation tracking in liquid biopsy as a potential biomarker in melanoma. We investigated the key genes and signal transduction pathways that have been found to be altered epigenetically in melanoma. We then highlighted the circulating tumor components present in blood, including circulating melanoma cells (CMC), circulating tumor DNA (ctDNA), and tumor-derived extracellular vesicles (EVs), as a valuable source for identifying relevant aberrations in DNA methylation. Finally, we focused on DNA methylation signatures as a marker for tracking response to therapy and resistance, thus facilitating personalized medicine and decision-making in the treatment of melanoma patients.
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Affiliation(s)
- Valentina Aleotti
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, 35128 Padua, Italy; (V.A.); (C.C.); (A.F.); (M.C.S.)
| | - Cristina Catoni
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, 35128 Padua, Italy; (V.A.); (C.C.); (A.F.); (M.C.S.)
| | - Cristina Poggiana
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, 35128 Padua, Italy; (V.A.); (C.C.); (A.F.); (M.C.S.)
| | - Antonio Rosato
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, 35128 Padua, Italy; (V.A.); (C.C.); (A.F.); (M.C.S.)
- Department of Surgery, Oncology and Gastroenterology, Oncology and Immunology Section, University of Padua, 35128 Padua, Italy
| | - Antonella Facchinetti
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, 35128 Padua, Italy; (V.A.); (C.C.); (A.F.); (M.C.S.)
- Department of Surgery, Oncology and Gastroenterology, Oncology and Immunology Section, University of Padua, 35128 Padua, Italy
| | - Maria Chiara Scaini
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, 35128 Padua, Italy; (V.A.); (C.C.); (A.F.); (M.C.S.)
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Current advances in prognostic and diagnostic biomarkers for solid cancers: Detection techniques and future challenges. Biomed Pharmacother 2021; 146:112488. [PMID: 34894516 DOI: 10.1016/j.biopha.2021.112488] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 11/19/2021] [Accepted: 11/30/2021] [Indexed: 12/20/2022] Open
Abstract
Solid cancers are one of the leading causes of cancer related deaths, characterized by rapid growth of tumour, and local and distant metastases. Current advances on multimodality care have substantially improved local control and metastasis-free survival of patients by resection of primary tumour. The major concern in disease prognosis is the timely detection of resectable or metastatic tumour, thus reinforcing the need for identification of biomarkers for premalignant lesions of solid cancer. This ultimately improves the outcome for the patients. Therefore, the purpose of this review is to update the recent advancements on prognostic and diagnostic biomarkers to enhance early detection of common solid cancers including, breast, lung, colorectal, prostate and stomach cancer. We also provide an insight into Food and Drug Administration (FDA)-approved solid cancers biomarkers; various conventional techniques used for detection of prognostic and diagnostic biomarkers and discuss approaches to turn challenges in this field into opportunities.
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Easwar A, Siddon AJ. Genetic Landscape of Myeloproliferative Neoplasms with an Emphasis on Molecular Diagnostic Laboratory Testing. Life (Basel) 2021; 11:1158. [PMID: 34833034 PMCID: PMC8625510 DOI: 10.3390/life11111158] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/18/2021] [Accepted: 10/27/2021] [Indexed: 12/27/2022] Open
Abstract
Chronic myeloproliferative neoplasms (MPNs) are hematopoietic stem cell neoplasms with driver events including the BCR-ABL1 translocation leading to a diagnosis of chronic myeloid leukemia (CML), or somatic mutations in JAK2, CALR, or MPL resulting in Philadelphia-chromosome-negative MPNs with constitutive activation of the JAK-STAT signaling pathway. In the Philadelphia-chromosome-negative MPNs, modern sequencing panels have identified a vast molecular landscape including additional mutations in genes involved in splicing, signal transduction, DNA methylation, and chromatin modification such as ASXL1, SF3B1, SRSF2, and U2AF1. These additional mutations often influence prognosis in MPNs and therefore are increasingly important for risk stratification. This review focuses on the molecular alterations within the WHO classification of MPNs and laboratory testing used for diagnosis.
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Affiliation(s)
- Arti Easwar
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06510, USA;
| | - Alexa J. Siddon
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06510, USA;
- Department of Pathology, Yale School of Medicine, New Haven, CT 06510, USA
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Bu Y, Chan YK, Wong HL, Poon SHL, Lo ACY, Shih KC, Tong L. A Review of the Impact of Alterations in Gut Microbiome on the Immunopathogenesis of Ocular Diseases. J Clin Med 2021; 10:jcm10204694. [PMID: 34682816 PMCID: PMC8541376 DOI: 10.3390/jcm10204694] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/01/2021] [Accepted: 10/09/2021] [Indexed: 12/11/2022] Open
Abstract
Recent studies have highlighted the association between ocular diseases and microbiota profiles of the host intestinal tract and oral cavity. There is mounting evidence supporting the existence of a 'gut-eye axis', whereby changes in gut microbiome alter host immunity, with consequential implications for ocular health and disease. In this review, we examined recent published findings on the association between gut microbiome and ocular morbidity, based on 25 original articles published between 2011 to 2020. The review included both clinical and in vivo animal studies, with particular focus on the influence of the microbiome on host immunity and metabolism. Significant associations between altered intestinal microbiome and specific ocular diseases and pathological processes, including Behçet's syndrome, autoimmune uveitis, age-related macular degeneration, choroidal neovascularization, bacterial keratitis, and Sjögren-like lacrimal keratoconjunctivitis have been demonstrated. Furthermore, alterations in the gut microbiome resulted in quantifiable changes in the host immune response, suggesting immunopathogenesis as the basis for the link between intestinal dysbiosis and ocular disease. We also examined and compared different techniques used in the identification and quantification of gut microorganisms. With our enhanced understanding of the potential role of gut commensals in ophthalmic disease, the stage is set for further studies on the underlying mechanisms linking the gut microbiome, the host immune response, and the pathogenesis of ophthalmic disease.
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Affiliation(s)
- Yashan Bu
- Department of Ophthalmology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (Y.B.); (Y.-K.C.); (H.-L.W.); (S.H.-L.P.); (A.C.-Y.L.)
| | - Yau-Kei Chan
- Department of Ophthalmology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (Y.B.); (Y.-K.C.); (H.-L.W.); (S.H.-L.P.); (A.C.-Y.L.)
| | - Ho-Lam Wong
- Department of Ophthalmology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (Y.B.); (Y.-K.C.); (H.-L.W.); (S.H.-L.P.); (A.C.-Y.L.)
| | - Stephanie Hiu-Ling Poon
- Department of Ophthalmology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (Y.B.); (Y.-K.C.); (H.-L.W.); (S.H.-L.P.); (A.C.-Y.L.)
| | - Amy Cheuk-Yin Lo
- Department of Ophthalmology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (Y.B.); (Y.-K.C.); (H.-L.W.); (S.H.-L.P.); (A.C.-Y.L.)
| | - Kendrick Co Shih
- Department of Ophthalmology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (Y.B.); (Y.-K.C.); (H.-L.W.); (S.H.-L.P.); (A.C.-Y.L.)
- Correspondence:
| | - Louis Tong
- Cornea and External Eye Disease Service, Singapore National Eye Centre, Singapore 168751, Singapore;
- Ocular Surface Research Group, Singapore Eye Research Institute, Singapore 169856, Singapore
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Soria X, Vilardell F, Maiques Ó, Barceló C, Sisó P, de la Rosa I, Velasco A, Cuevas D, Santacana M, Gatius S, Matías-Guiu X, Rodrigo A, Macià A, Martí RM. BRAFV600E Mutant Allele Frequency (MAF) Influences Melanoma Clinicopathologic Characteristics. Cancers (Basel) 2021; 13:5073. [PMID: 34680222 PMCID: PMC8533792 DOI: 10.3390/cancers13205073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/02/2021] [Accepted: 10/08/2021] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Cutaneous melanoma shows high variability regarding clinicopathological presentation, evolution and prognosis. METHODS Next generation sequencing was performed to analyze hotspot mutations in different areas of primary melanomas (MMp) and their paired metastases. Clinicopathological features were evaluated depending on the degree of variation of the BRAFV600E mutant allele frequency (MAF) in MMp. RESULTS In our cohort of 14 superficial spreading, 10 nodular melanomas and 52 metastases, 17/24 (71%) melanomas had a BRAFV600E mutation and 5/24 (21%) had a NRASQ61 mutation. We observed a high variation of BRAFV600E MAF (H-BRAFV600E) in 7/17 (41%) MMp. The H-BRAFV600E MMp were all located on the trunk, had lower Breslow and mitotic indexes and predominantly, a first nodal metastasis. Regions with spindled tumor cells (Spin) and high lymphocytic infiltrate (HInf) were more frequent in the H-BRAFV600E patients (4/7; 57%), whereas regions with epithelial tumor cells (Epit) and low lymphocytic infiltrate (LInf) were predominant (6/10; 60%) and exclusive in the low BRAFV600E MAF variation tumors (L-BRAFV600E). The H-BRAFV600E/Spin/HInf MMp patients had better prognostic features and nodal first metastasis. CONCLUSIONS The H-BRAFV600E MMp were located on the trunk, had better prognostic characteristics, such as lower Breslow and mitotic indexes as well as high lymphocytic infiltrate.
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Affiliation(s)
- Xavier Soria
- Department of Dermatology, Hospital Universitari Arnau de Vilanova de Lleida, Institut de Recerca Biomèdica de Lleida (IRBLleida), Universitat de Lleida, 25198 Lleida, Spain;
| | - Felip Vilardell
- Department of Pathology and Molecular Genetics, Hospital Universitari Arnau de Vilanova de Lleida, Institut de Recerca Biomèdica de Lleida (IRBLleida), Universitat de Lleida, 25198 Lleida, Spain; (F.V.); (A.V.); (D.C.); (M.S.); (S.G.); (X.M.-G.)
| | - Óscar Maiques
- Tumour Microenvironment, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK;
| | - Carla Barceló
- Oncological Pathology Group, Institut de Recerca Biomèdica de Lleida (IRBLleida), 25198 Lleida, Spain; (C.B.); (P.S.); (I.d.l.R.)
| | - Pol Sisó
- Oncological Pathology Group, Institut de Recerca Biomèdica de Lleida (IRBLleida), 25198 Lleida, Spain; (C.B.); (P.S.); (I.d.l.R.)
| | - Inés de la Rosa
- Oncological Pathology Group, Institut de Recerca Biomèdica de Lleida (IRBLleida), 25198 Lleida, Spain; (C.B.); (P.S.); (I.d.l.R.)
| | - Ana Velasco
- Department of Pathology and Molecular Genetics, Hospital Universitari Arnau de Vilanova de Lleida, Institut de Recerca Biomèdica de Lleida (IRBLleida), Universitat de Lleida, 25198 Lleida, Spain; (F.V.); (A.V.); (D.C.); (M.S.); (S.G.); (X.M.-G.)
- Centre of Biomedical Research on Cancer (CIBERONC), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Dolors Cuevas
- Department of Pathology and Molecular Genetics, Hospital Universitari Arnau de Vilanova de Lleida, Institut de Recerca Biomèdica de Lleida (IRBLleida), Universitat de Lleida, 25198 Lleida, Spain; (F.V.); (A.V.); (D.C.); (M.S.); (S.G.); (X.M.-G.)
- Centre of Biomedical Research on Cancer (CIBERONC), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Maria Santacana
- Department of Pathology and Molecular Genetics, Hospital Universitari Arnau de Vilanova de Lleida, Institut de Recerca Biomèdica de Lleida (IRBLleida), Universitat de Lleida, 25198 Lleida, Spain; (F.V.); (A.V.); (D.C.); (M.S.); (S.G.); (X.M.-G.)
- Centre of Biomedical Research on Cancer (CIBERONC), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Sònia Gatius
- Department of Pathology and Molecular Genetics, Hospital Universitari Arnau de Vilanova de Lleida, Institut de Recerca Biomèdica de Lleida (IRBLleida), Universitat de Lleida, 25198 Lleida, Spain; (F.V.); (A.V.); (D.C.); (M.S.); (S.G.); (X.M.-G.)
- Centre of Biomedical Research on Cancer (CIBERONC), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Xavier Matías-Guiu
- Department of Pathology and Molecular Genetics, Hospital Universitari Arnau de Vilanova de Lleida, Institut de Recerca Biomèdica de Lleida (IRBLleida), Universitat de Lleida, 25198 Lleida, Spain; (F.V.); (A.V.); (D.C.); (M.S.); (S.G.); (X.M.-G.)
- Centre of Biomedical Research on Cancer (CIBERONC), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
| | - Alberto Rodrigo
- Department of Medical Oncology, Hospital Universitari Arnau de Vilanova de Lleida, Institut de Recerca Biomèdica de Lleida (IRBLleida), Universitat de Lleida, 25198 Lleida, Spain;
| | - Anna Macià
- Unitat de Farmacologia- Department of Experimental Medicine, Universitat de Lleida, 25198 Lleida, Spain;
| | - Rosa M. Martí
- Department of Dermatology, Hospital Universitari Arnau de Vilanova de Lleida, Institut de Recerca Biomèdica de Lleida (IRBLleida), Universitat de Lleida, 25198 Lleida, Spain;
- Centre of Biomedical Research on Cancer (CIBERONC), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain
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44
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Nair SV, Madhulaxmi, Thomas G, Ankathil R. Next-Generation Sequencing in Cancer. J Maxillofac Oral Surg 2021; 20:340-344. [PMID: 34408360 DOI: 10.1007/s12663-020-01462-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 09/28/2020] [Indexed: 11/28/2022] Open
Abstract
Objective In this article, we provide a gestalt idea about NGS technologies and their applications in cancer research and molecular diagnosis. Background Next-generation sequencing (NGS) advancements like DNA sequencing and RNA sequencing allow uncovering of genomic, transcriptomic, and epigenomic scenes of individual malignant growths. An assortment of genomic abnormalities can be screened at the same time, for example common and uncommon variations, auxiliary variations like insertions and deletions, copy-number variation, and fusion transcripts. Conclusion NGS innovations together with bioinformatics investigation, which extend our insight, are progressively used to analyze multiple genes in a cost-effective way and have been applied in examining clinical cancer samples and offering NGS-based molecular diagnosis. Application NGS is progressively significant as a device for the diagnosis of cancers.
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Affiliation(s)
- S Vinod Nair
- Department of Oral and Maxillofacial Surgery, P.M.S Dental College, Vattapara, Trivandrum, India
| | - Madhulaxmi
- Department of Oral and Maxillofacial Surgery, Saveetha Dental College, Chennai, India
| | - Gigi Thomas
- Community Medicine, Regional Cancer Centre, Trivandrum, India
| | - Ravindran Ankathil
- Human Genome Centre, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, George Town, Malaysia
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Ficarazzi F, Vecchi M, Ferrari M, Pierotti MA. Towards population-based genetic screenings for breast and ovarian cancer: A comprehensive review from economic evaluations to patient perspectives. Breast 2021; 58:121-129. [PMID: 34022715 PMCID: PMC8164087 DOI: 10.1016/j.breast.2021.04.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 04/28/2021] [Accepted: 04/30/2021] [Indexed: 12/16/2022] Open
Abstract
Genetic testing for hereditary breast and ovarian cancer following genetic counseling is based on guidelines that take into account particular features of the personal and family history, and clinical criteria conferring a probability of having a BRCA mutation greater than 10% as a threshold for accessing the test. However, besides reducing mortality and social impact, the extension of screening programs also for healthy family members would allow a huge saving of the rising costs associated with these pathologies, supporting the choice of the "Test" strategy versus a "No Test" one. Analyses of different health care systems show that by applying the "Test" strategy on patients and their families, a decrease in breast and ovarian cancer cases is achieved, as well as a substantial decrease in costs of economic resources, including the costs of the clinical management of early detected tumors. In this review, we analyzed the most recent papers published on this topic and we summarized the findings on the economic evaluations related to breast and ovarian cancer population screenings. These results proved and validated that the population-wide testing approach is a more accurate screening and preventive intervention than traditional guidelines based on personal/family history and clinical criteria to reduce breast and ovarian cancer risk.
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Affiliation(s)
| | - Manuela Vecchi
- Cogentech Ltd Benefit Corp, Via Adamello 16, 20139, Milan, Italy
| | - Maurizio Ferrari
- Cogentech Ltd Benefit Corp, Via Adamello 16, 20139, Milan, Italy; Vita-Salute San Raffaele University, Via Olgettina 58, 20132, Milan, Italy
| | - Marco A Pierotti
- Cogentech Ltd Benefit Corp, Via Adamello 16, 20139, Milan, Italy; IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139, Milan, Italy.
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46
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García-Foncillas J, Argente J, Bujanda L, Cardona V, Casanova B, Fernández-Montes A, Horcajadas JA, Iñiguez A, Ortiz A, Pablos JL, Pérez Gómez MV. Milestones of Precision Medicine: An Innovative, Multidisciplinary Overview. Mol Diagn Ther 2021; 25:563-576. [PMID: 34331269 DOI: 10.1007/s40291-021-00544-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2021] [Indexed: 12/11/2022]
Abstract
Although the concept of precision medicine, in which healthcare is tailored to the molecular and clinical characteristics of each individual, is not new, its implementation in clinical practice has been heterogenous. In some medical specialties, precision medicine has gone from being just a promise to a reality that achieves better patient outcomes. This is a fact if we consider, for example, the great advances made in the genetic diagnosis and subsequent treatment of countless hereditary diseases, such as cystic fibrosis, which have improved the life expectancy of many of the affected children. In the field of oncology, the development of targeted therapies has prolonged the survival of patients with breast, lung, colorectal, melanoma, and hematological malignancies. In other disciplines, clinical milestones are perhaps less well known, but no less important. The current challenge is to expand and generalize the use of technologies that are central to precision medicine, such as massively parallel sequencing, to improve the management (prevention and treatment) of complex conditions such as cardiovascular, kidney, or autoimmune diseases. This process requires investment in specialized expertise, multidisciplinary collaboration, and the nationwide organization of genetic laboratories for diagnosis of specific diseases.
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Affiliation(s)
- Jesús García-Foncillas
- Department of Oncology, Oncohealth Institute, Fundacion Jimenez Diaz University Hospital, Autonomous University, Madrid, Spain. .,Medical Oncology Department, University Hospital Fundación Jiménez Díaz-Universidad Autonoma de Madrid, Madrid, Spain.
| | - Jesús Argente
- Department of Endocrinology, Instituto de Salud Carlos III, IMDEA Institute, Hospital Infantil Universitario Niño Jesús, Spanish PUBERE Registry, CIBER of Obesity and Nutrition (CIBEROBN), Universidad Autónoma de Madrid, Madrid, Spain.,Department of Pediatrics, Instituto de Salud Carlos III, IMDEA Institute, Hospital Infantil Universitario Niño Jesús, Spanish PUBERE Registry, CIBER of Obesity and Nutrition (CIBEROBN), Universidad Autónoma de Madrid, Madrid, Spain
| | - Luis Bujanda
- Department of Gastroenterology, Hospital Donostia/Instituto Biodonostia, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Universidad del País Vasco (UPV/EHU), San Sebastian, Spain
| | - Victoria Cardona
- Allergy Section, Department of Internal Medicine, Hospital Vall d'Hebron, Barcelona, Spain.,ARADyAL Research Network, Barcelona, Spain
| | - Bonaventura Casanova
- Neuroimmunology Unit, La Fe University and Polytechnic Hospital, Valencia, Spain.,Department of Medicine, Faculty of Medicine, University of Valencia, Valencia, Spain
| | - Ana Fernández-Montes
- Medical Oncology, Complejo Hospitalario Universitario de Ourense, Ourense, Spain
| | | | - Andrés Iñiguez
- Department of Cardiology, Hospital Álvaro Cunqueiro-Complejo Hospitalario Universitario, Vigo, Spain
| | - Alberto Ortiz
- Department of Nephrology and Hypertension, IIS-Fundación Jiménez Díaz-UAM, Madrid, Spain
| | - José L Pablos
- Grupo de Enfermedades Inflamatorias y Autoinmunes, Instituto de Investigación Hospital 12 de Octubre, Madrid, Spain.,Servicio de Reumatología, Hospital 12 de Octubre, Universidad Complutense de Madrid, Madrid, Spain
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47
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Hur JY, Lee KY. Characteristics and Clinical Application of Extracellular Vesicle-Derived DNA. Cancers (Basel) 2021; 13:3827. [PMID: 34359729 PMCID: PMC8345206 DOI: 10.3390/cancers13153827] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/25/2021] [Accepted: 07/27/2021] [Indexed: 02/06/2023] Open
Abstract
Extracellular vesicles (EVs) carry RNA, proteins, lipids, and diverse biomolecules for intercellular communication. Recent studies have reported that EVs contain double-stranded DNA (dsDNA) and oncogenic mutant DNA. The advantage of EV-derived DNA (EV DNA) over cell-free DNA (cfDNA) is the stability achieved through the encapsulation in the lipid bilayer of EVs, which protects EV DNA from degradation by external factors. The existence of DNA and its stability make EVs a useful source of biomarkers. However, fundamental research on EV DNA remains limited, and many aspects of EV DNA are poorly understood. This review examines the known characteristics of EV DNA, biogenesis of DNA-containing EVs, methylation, and next-generation sequencing (NGS) analysis using EV DNA for biomarker detection. On the basis of this knowledge, this review explores how EV DNA can be incorporated into diagnosis and prognosis in clinical settings, as well as gene transfer of EV DNA and its therapeutic potential.
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Affiliation(s)
- Jae Young Hur
- Precision Medicine Lung Cancer Center, Konkuk University Medical Center, Seoul 05030, Korea;
- Department of Pathology, Konkuk University Medical Center, Seoul 05030, Korea
| | - Kye Young Lee
- Precision Medicine Lung Cancer Center, Konkuk University Medical Center, Seoul 05030, Korea;
- Department of Pulmonary Medicine, Konkuk University School of Medicine, Seoul 05030, Korea
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48
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Al-Shamsi HO, Abu-Gheida I, Abdulsamad AS, AlAwadhi A, Alrawi S, Musallam KM, Arun B, Ibrahim NK. Molecular Spectra and Frequency Patterns of Somatic Mutations in Arab Women with Breast Cancer. Oncologist 2021; 26:e2086-e2089. [PMID: 34327780 DOI: 10.1002/onco.13916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 07/12/2021] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND The role of somatic mutations in breast cancer prognosis and management continues to be recognized. However, data on the molecular profiles of Arab women are limited. MATERIALS AND METHODS This was a cross-sectional study based on medical chart review of all Arab women diagnosed with breast cancer at a single institution between 2010 and 2018 who underwent next-generation sequencing with Ampliseq 46-Gene or 50-Gene. RESULTS A total of 78 Arab women were identified, with a median age at diagnosis of 52.3 years (range: 37-82 years; 38.5% ≤50 years). The majority of patients had stage III or IV disease (74.4%). Next-generation sequencing revealed the following somatic mutation rates: TP53, 23.1%; ATM, 2.6%; IDH1, 2.6%; IDH2, 3.8%; PTEN, 7.7%; PIK3CA, 15.4%; APC, 7.7%; NPM1, 2.5%; MPL, 1.3%; JAK2, 2.5%; KIT, 7.7%; KRAS, 3.8%; and NRAS, 3.8%. CONCLUSION Our study illustrates frequencies of somatic mutations in Arab women with breast cancer and suggests potential variations from estimates reported in the Western population. These data calls for larger epidemiologic studies considering the evolving role of such mutations in prognostication and personalized management.
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Affiliation(s)
- Humaid O Al-Shamsi
- Departments of Oncology, Burjeel Cancer Institute, Burjeel Medical City, Abu Dhabi, United Arab Emirates.,Departments of Radiation Oncology, Burjeel Cancer Institute, Burjeel Medical City, Abu Dhabi, United Arab Emirates.,Innovation and Research Center, Burjeel Cancer Institute, Burjeel Medical City, Abu Dhabi, United Arab Emirates.,College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Ibrahim Abu-Gheida
- Departments of Radiation Oncology, Burjeel Cancer Institute, Burjeel Medical City, Abu Dhabi, United Arab Emirates.,Innovation and Research Center, Burjeel Cancer Institute, Burjeel Medical City, Abu Dhabi, United Arab Emirates.,College of Medicine and Health Sciences, United Arab Emirates University, Abu Dhabi, United Arab Emirates
| | | | | | - Sadir Alrawi
- Departments of Oncology, Burjeel Cancer Institute, Burjeel Medical City, Abu Dhabi, United Arab Emirates
| | - Khaled M Musallam
- Innovation and Research Center, Burjeel Cancer Institute, Burjeel Medical City, Abu Dhabi, United Arab Emirates
| | - Banu Arun
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Nuhad K Ibrahim
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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49
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Huang Y, Zheng Y, Shao X, Shi L, Li G, Huang P. Long non-coding RNA TPT1-AS1 sensitizes breast cancer cell to paclitaxel and inhibits cell proliferation by miR-3156-5p/caspase 2 axis. Hum Cell 2021; 34:1244-1254. [PMID: 33999360 DOI: 10.1007/s13577-021-00541-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 04/26/2021] [Indexed: 12/24/2022]
Abstract
Long non-coding RNAs (lncRNAs) are key modulators during cancer progression. Application of using lncRNA expression to evaluate patient prognosis and sensitivity to treatment is highly anticipated, yet the expression and mechanism of many lncRNAs remain unknown. Herein, we projected for the investigation of TPT1-AS1 function in breast cancer. TPT1-AS1 was assessed by bioinformatic analysis of publicly available datasets and quantitative real-time PCR (qRT-PCR). Cell sensitivity to paclitaxel and cell proliferation was measured by flow cytometry and CCK-8. Interaction among TPT1-AS1, microRNA (miRNA, miR)-3156-5p and Caspase 2 (CASP2) was studied by bioinformatic analysis, qRT-PCR, western blot as well as dual luciferase reporter assay. Herein, TPT1-AS1 was significantly diminished in breast cancer from publicly available datasets and our collected samples. In breast cancer cells, TPT1-AS1 overexpression repressed cell proliferation and sensitized breast cancer cells to paclitaxel. RegRNA 2.0 predicted a potential interaction between TPT1-AS1 and miR-3156-5p which was confirmed by qRT-PCR as well as dual luciferase reporter assay. CASP2, a proapoptotic gene, was corroborated to be targeted by miR-3156-5p. Meanwhile, TPT1-AS1 upregulated CASP2 in breast cancer cells, and its biological function was reversed by CASP2 knockdown. Collectively, TPT1-AS1 diminished cell proliferation and sensitized cells to chemotherapy by sponging miR-3156-5p and upregulating CASP2, acting as a biomarker for patients with breast cancer.
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Affiliation(s)
- Yuan Huang
- Department of Breast Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), No 1, East Banshan Road, Gongshu District, Hangzhou, Zhejiang, 310022, People's Republic of China
- Department of Breast Medical Oncology, Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, People's Republic of China
| | - Yabing Zheng
- Department of Breast Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), No 1, East Banshan Road, Gongshu District, Hangzhou, Zhejiang, 310022, People's Republic of China.
- Department of Breast Medical Oncology, Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, People's Republic of China.
| | - Xiying Shao
- Department of Breast Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), No 1, East Banshan Road, Gongshu District, Hangzhou, Zhejiang, 310022, People's Republic of China
- Department of Breast Medical Oncology, Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, People's Republic of China
| | - Lei Shi
- Department of Breast Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), No 1, East Banshan Road, Gongshu District, Hangzhou, Zhejiang, 310022, People's Republic of China
- Department of Breast Medical Oncology, Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, People's Republic of China
| | - Guangliang Li
- Department of Breast Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), No 1, East Banshan Road, Gongshu District, Hangzhou, Zhejiang, 310022, People's Republic of China
- Department of Breast Medical Oncology, Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, People's Republic of China
| | - Ping Huang
- Department of Breast Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), No 1, East Banshan Road, Gongshu District, Hangzhou, Zhejiang, 310022, People's Republic of China
- Department of Breast Medical Oncology, Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, People's Republic of China
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50
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Clonal Hematopoiesis after Autologous Stem Cell Transplantation Does Not Confer Adverse Prognosis in Patients with AML. Cancers (Basel) 2021; 13:cancers13133190. [PMID: 34202404 PMCID: PMC8267699 DOI: 10.3390/cancers13133190] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 11/29/2022] Open
Abstract
Simple Summary Around 50% of patients with acute myeloid leukemia (AML) achieve a definite cure with intensive chemotherapy and consolidation, but relapse remains the main cause of death. Clonal hematopoiesis (CH) describes the presence of a clonal subset of myeloid precursors without known hematologic disease. We aimed to investigate whether the presence of CH-related mutations in the three most common genes (DNMT3A, TET2, and ASXL1, called DTA mutations) after autologous stem cell transplantation (ASCT) influence the outcome and retrospectively analyzed samples of 110 AML patients. We found no significant impact from the presence of DTA-CH on progression-free or overall survival. Thus, the persistence of DTA mutations after induction treatment should not prevent AML patients in first remission from ASCT consolidation. These results should undergo verification in independent cohorts. Abstract Introduction: Despite a 50% cure rate, relapse remains the main cause of death in patients with acute myeloid leukemia (AML) consolidated with autologous stem cell transplantation (ASCT) in first remission (CR1). Clonal hematopoiesis of indeterminate potential (CH) increases the risk for hematological and cardiovascular disorders and death. The impact of CH persisting after ASCT in AML patients is unclear. Materials and Methods: We retrospectively investigated the prognostic value of persisting DNMT3A, TET2, or ASXL1 (DTA) mutations after ASCT. Patients underwent stratification depending on the presence of DTA mutations. Results: We investigated 110 consecutive AML patients receiving ASCT in CR1 after two induction cycles at our center between 2007 and 2020. CH-related mutations were present in 31 patients (28.2%) after ASCT. The baseline characteristics were similar between patients with or without persisting DTA mutations after ASCT. The median progression free survival was 26.9 months in patients without DTA mutations and 16.7 months in patients with DTA mutations (HR 0.75 (0.42–1.33), p = 0.287), and the median overall survival was 80.9 and 54.4 months (HR 0.79 (0.41–1.51), p = 0.440), respectively. Conclusion: We suggest that DTA-CH after ASCT is not associated with an increased risk of relapse or death. The persistence of DTA mutations after induction should not prevent AML patients in CR1 from ASCT consolidation. Independent studies should confirm these data.
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