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Olmez OF, Bilici A, Er O, Bisgin A, Sevinc A, Akman T, Uslu R, Mandel NM, Yalcin S, Teomete M, Gorumlu G, Demir A, Namal E, Alici S, Selcukbiricik F, Bavbek S, Paksoy F, Basaran G, Ozer L, Sener N, Harputluoglu H. Beyond traditional therapies: clinical significance of complex molecular profiling in patients with advanced solid tumours-results from a Turkish multi-centre study. Jpn J Clin Oncol 2024; 54:562-568. [PMID: 38271177 DOI: 10.1093/jjco/hyae002] [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: 09/10/2023] [Accepted: 01/06/2024] [Indexed: 01/27/2024] Open
Abstract
OBJECTIVE The objective of this multi-centre, real-world study was to examine the potential influence of comprehensive molecular profiling on the development of treatment decisions or adjustments for patients with advanced solid malignancies. We then evaluated the impact of these informed choices on patient treatment outcomes. METHODS The study encompassed 234 adult patients (mean age: 52.7 ± 14.3 years, 54.7% women) who were diagnosed with solid tumours at 21 different medical centres in Turkey. Remarkably, 67.9% of the patients exhibited metastasis at the time of diagnosis. We utilized an OncoDNA (Gosselies, Belgium) platform (OncoDEEP) integrating next-generation sequencing with additional tests to harvest complex molecular profiling data. The results were analyzed in relation with two specific outcomes: (i) the impact on therapeutic decisions, including formulation or modifications, and (ii) associated treatment response. RESULTS Out of the 228 patients with final molecular profiling results, 118 (50.4%) had their treatment modified, whilst the remaining 110 (47.0%) did not. The response rates were comparable, with 3.9 versus 3.4% for complete response, 13.6 versus 29.3% for partial response, 66.9 versus 51.7% for progressive disease and 15.5 versus 15.5% for stable disease for treatments informed and not informed by complex molecular profiling, respectively (P = 0.16). CONCLUSION Our real-world findings highlight the significant impact of complex molecular profiling on the treatment decisions made by oncologists for a substantial portion of patients with advanced solid tumours. Regrettably, no significant advantage was detected in terms of treatment response or disease control rates.
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Affiliation(s)
- Omer Fatih Olmez
- Medical Oncology, Medipol University Faculty of Medicine Medipol Mega Hospital, Bagcilar, Istanbul
| | - Ahmet Bilici
- Medical Oncology, Medipol University Faculty of Medicine Medipol Mega Hospital, Bagcilar, Istanbul
| | - Ozlem Er
- Medical Oncology, Acibadem MAA University Acibadem Maslak Hospital, Istanbul
| | - Atil Bisgin
- Cukurova University AGENTEM (Adana Genetic Diseases Diagnosis and Treatment Center), Adana & Cukurova Technopolis InfoGenom, Adana
| | - Alper Sevinc
- Medical Oncology, Medical Park Gaziantep Hospital, Gaziantep
| | | | | | | | - Suayib Yalcin
- Department of Medical Oncology, Hacettepe University Faculty of Medicine, Ankara
| | - Mehmet Teomete
- Medical Oncology, Acibadem MAA University Acibadem Altunizade Hospital, Istanbul
| | | | - Atakan Demir
- Medical Oncology, Acibadem MAA University Acibadem Maslak Hospital, Istanbul
| | - Esat Namal
- Medical Oncology, Florence Nightingale Sisli Hospital, Istanbul
| | - Suleyman Alici
- Medical Oncology, Acibadem MAA University Acibadem Altunizade Hospital, Istanbul
| | | | | | - Fatma Paksoy
- Medical Oncology, Medical Park Goztepe Hospital, Istanbul
| | - Gul Basaran
- Medical Oncology, Acibadem MAA University Acibadem Altunizade Hospital, Istanbul
| | - Leyla Ozer
- Medical Oncology, Acıbadem MAA University Acibadem Atakent Hospital, Istanbul
| | - Nur Sener
- Medical Oncology, Florence Nightingale Atasehir Hospital, Istanbul
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Niu X, Zhao K, Zheng Y, Wang Y, Liu R, Zhang Y, Wang L, Wu Y, Bai X, Qiao B. ANXA13 promotes cell proliferation and invasion and attenuates apoptosis in renal cell carcinoma. Heliyon 2023; 9:e18009. [PMID: 37520951 PMCID: PMC10374933 DOI: 10.1016/j.heliyon.2023.e18009] [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: 09/15/2022] [Revised: 06/20/2023] [Accepted: 07/05/2023] [Indexed: 08/01/2023] Open
Abstract
Purpose Emerging evidences have demonstrated that annexin A13 (ANXA13) is closely related to the occurrence and development of malignant tumors. However, the functions and underlying molecular mechanisms of ANXA13 in Clear cell renal cell carcinoma (ccRCC) have not been defined. Therefore, this study aimed to clarify the potential role of ANXA13 in regulating the proliferation, migration, invasion, cell cycle, and apoptosis of ccRCC cells. Patients and methods The quantitative real-time PCR (qRT-PCR) and western blotting was performed for detecting the ANXA13 expression in ccRCC tissues at the mRNA and protein levels, respectively. The GEPIA2 databases were used to derive data for analyzing the ANXA13 expression in pan-cancer and ccRCC clinical features. Cell Counting and colony formation assays, as well as flow cytometry, were used to detect cell proliferation, apoptosis, or cell cycle. The wound healing assay was used to evaluate the migration ability of cells, and the Trans-well assay was conducted to determine the cell invasiveness. Results ANXA13 was upregulated in ccRCC cells and human ccRCC tissues. Furthermore, siANXA13 inhibited ccRCC cell proliferation, migration, invasion and induced cell apoptosis. Conclusion ANXA13 was upregulated in ccRCC. ANXA13 promotes tumorigenic traits of ccRCC cell lines in vitro. ANXA13 is a potential novel biomarker and a potential therapeutic target in ccRCC.
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Affiliation(s)
- Xiaoyu Niu
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Keyuan Zhao
- Department of Urology, Shaoxing People's Hospital, Shaoxing, Zhejiang, 312000, China
| | - Yuanyuan Zheng
- National Engineering Laboratory for Internet Medical Systems and Applications, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Yapeng Wang
- Department of Urology, Daping Hospital, Army Medical University, Chongqing, 404100, China
| | - Ruoyang Liu
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Yiming Zhang
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Lihui Wang
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Yongjun Wu
- College of Public Health, Zhengzhou University, Zhengzhou, Henan, 450001, China
- The Key Laboratory of Nanomedicine and Health Inspection of Zhengzhou, Zhengzhou, Henan, 450001, China
| | - Xuefeng Bai
- The Key Laboratory of Nanomedicine and Health Inspection of Zhengzhou, Zhengzhou, Henan, 450001, China
| | - Baoping Qiao
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
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Schettini F, De Bonis MV, Strina C, Milani M, Ziglioli N, Aguggini S, Ciliberto I, Azzini C, Barbieri G, Cervoni V, Cappelletti MR, Ferrero G, Ungari M, Locci M, Paris I, Scambia G, Ruocco G, Generali D. Computational reactive-diffusive modeling for stratification and prognosis determination of patients with breast cancer receiving Olaparib. Sci Rep 2023; 13:11951. [PMID: 37488154 PMCID: PMC10366144 DOI: 10.1038/s41598-023-38760-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 07/14/2023] [Indexed: 07/26/2023] Open
Abstract
Mathematical models based on partial differential equations (PDEs) can be exploited to handle clinical data with space/time dimensions, e.g. tumor growth challenged by neoadjuvant therapy. A model based on simplified assessment of tumor malignancy and pharmacodynamics efficiency was exercised to discover new metrics of patient prognosis in the OLTRE trial. We tested in a 17-patients cohort affected by early-stage triple negative breast cancer (TNBC) treated with 3 weeks of olaparib, the capability of a PDEs-based reactive-diffusive model of tumor growth to efficiently predict the response to olaparib in terms of SUVmax detected at 18FDG-PET/CT scan, by using specific terms to characterize tumor diffusion and proliferation. Computations were performed with COMSOL Multiphysics. Driving parameters governing the mathematical model were selected with Pearson's correlations. Discrepancies between actual and computed SUVmax values were assessed with Student's t test and Wilcoxon rank sum test. The correlation between post-olaparib true and computed SUVmax was assessed with Pearson's r and Spearman's rho. After defining the proper mathematical assumptions, the nominal drug efficiency (εPD) and tumor malignancy (rc) were computationally evaluated. The former parameter reflected the activity of olaparib on the tumor, while the latter represented the growth rate of metabolic activity as detected by SUVmax. εPD was found to be directly dependent on basal tumor-infiltrating lymphocytes (TILs) and Ki67% and was detectable through proper linear regression functions according to TILs values, while rc was represented by the baseline Ki67-to-TILs ratio. Predicted post-olaparib SUV*max did not significantly differ from original post-olaparib SUVmax in the overall, gBRCA-mutant and gBRCA-wild-type subpopulations (p > 0.05 in all cases), showing strong positive correlation (r = 0.9 and rho = 0.9, p < 0.0001 both). A model of simplified tumor dynamics was exercised to effectively produce an upfront prediction of efficacy of 3-week neoadjuvant olaparib in terms of SUVmax. Prospective evaluation in independent cohorts and correlation of these outcomes with more recognized efficacy endpoints is now warranted for model confirmation and tailoring of escalated/de-escalated therapeutic strategies for early-TNBC patients.
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Affiliation(s)
- Francesco Schettini
- Medical Oncology Department, Hospital Clinic of Barcelona, C. Villaroel 170, 08036, Barcelona, Spain.
- Translational Genomics and Targeted Therapies in Solid Tumors, August Pi I Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain.
- Faculty of Medicine, University of Barcelona, Barcelona, Spain.
| | - Maria Valeria De Bonis
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Carla Strina
- Department of Medicine, Surgery and Health Sciences, Cattinara Hospital, University of Trieste, Strada di Fiume 447, 34149, Trieste, Italy
| | - Manuela Milani
- Department of Medicine, Surgery and Health Sciences, Cattinara Hospital, University of Trieste, Strada di Fiume 447, 34149, Trieste, Italy
| | - Nicoletta Ziglioli
- Department of Medicine, Surgery and Health Sciences, Cattinara Hospital, University of Trieste, Strada di Fiume 447, 34149, Trieste, Italy
| | - Sergio Aguggini
- Department of Medicine, Surgery and Health Sciences, Cattinara Hospital, University of Trieste, Strada di Fiume 447, 34149, Trieste, Italy
| | - Ignazio Ciliberto
- Department of Medicine, Surgery and Health Sciences, Cattinara Hospital, University of Trieste, Strada di Fiume 447, 34149, Trieste, Italy
| | - Carlo Azzini
- Department of Medicine, Surgery and Health Sciences, Cattinara Hospital, University of Trieste, Strada di Fiume 447, 34149, Trieste, Italy
| | - Giuseppina Barbieri
- Department of Medicine, Surgery and Health Sciences, Cattinara Hospital, University of Trieste, Strada di Fiume 447, 34149, Trieste, Italy
| | - Valeria Cervoni
- Department of Medicine, Surgery and Health Sciences, Cattinara Hospital, University of Trieste, Strada di Fiume 447, 34149, Trieste, Italy
| | - Maria Rosa Cappelletti
- Department of Medicine, Surgery and Health Sciences, Cattinara Hospital, University of Trieste, Strada di Fiume 447, 34149, Trieste, Italy
| | | | - Marco Ungari
- UO Anatomia Patologica ASST di Cremona, Cremona, Italy
| | - Mariavittoria Locci
- Department of Neuroscience, Reproductive Sciences and Dentistry, University of Naples Federico II, Naples, Italy
| | - Ida Paris
- Department of Woman and Child Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Giovanni Scambia
- Department of Woman and Child Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Università Cattolica del Sacro Cuore, Rome, Italy
| | - Gianpaolo Ruocco
- Modeling and Prototyping Laboratory, College of Engineering, University of Basilicata, Potenza, Italy
| | - Daniele Generali
- Department of Medicine, Surgery and Health Sciences, Cattinara Hospital, University of Trieste, Strada di Fiume 447, 34149, Trieste, Italy.
- Multidisciplinary Unit of Breast Pathology and Translational Research, Cremona Hospital, Cremona, Italy.
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Wang X, Liu D, Luo J, Kong D, Zhang Y. Exploring the Role of Enhancer-Mediated Transcriptional Regulation in Precision Biology. Int J Mol Sci 2023; 24:10843. [PMID: 37446021 PMCID: PMC10342031 DOI: 10.3390/ijms241310843] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/18/2023] [Accepted: 06/25/2023] [Indexed: 07/15/2023] Open
Abstract
The emergence of precision biology has been driven by the development of advanced technologies and techniques in high-resolution biological research systems. Enhancer-mediated transcriptional regulation, a complex network of gene expression and regulation in eukaryotes, has attracted significant attention as a promising avenue for investigating the underlying mechanisms of biological processes and diseases. To address biological problems with precision, large amounts of data, functional information, and research on the mechanisms of action of biological molecules is required to address biological problems with precision. Enhancers, including typical enhancers and super enhancers, play a crucial role in gene expression and regulation within this network. The identification and targeting of disease-associated enhancers hold the potential to advance precision medicine. In this review, we present the concepts, progress, importance, and challenges in precision biology, transcription regulation, and enhancers. Furthermore, we propose a model of transcriptional regulation for multi-enhancers and provide examples of their mechanisms in mammalian cells, thereby enhancing our understanding of how enhancers achieve precise regulation of gene expression in life processes. Precision biology holds promise in providing new tools and platforms for discovering insights into gene expression and disease occurrence, ultimately benefiting individuals and society as a whole.
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Affiliation(s)
- Xueyan Wang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (D.L.); (J.L.); (D.K.)
| | - Danli Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (D.L.); (J.L.); (D.K.)
| | - Jing Luo
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (D.L.); (J.L.); (D.K.)
| | - Dashuai Kong
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (D.L.); (J.L.); (D.K.)
| | - Yubo Zhang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (D.L.); (J.L.); (D.K.)
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5
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Mohd Yunos RI, Ab Mutalib NS, Khoo JS, Saidin S, Ishak M, Syafruddin SE, Tieng FYF, Md Yusof NF, Abd Razak MR, Mahamad Nadzir N, Abu N, Rose IM, Sagap I, Mazlan L, Jamal R. Whole genome sequencing of Malaysian colorectal cancer patients reveals specific druggable somatic mutations. Front Mol Biosci 2023; 9:997747. [PMID: 36866106 PMCID: PMC9972984 DOI: 10.3389/fmolb.2022.997747] [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: 07/19/2022] [Accepted: 09/20/2022] [Indexed: 02/16/2023] Open
Abstract
The incidences of colorectal cancer (CRC) are continuously increasing in some areas of the world, including Malaysia. In this study, we aimed to characterize the landscape of somatic mutations using the whole-genome sequencing approach and identify druggable somatic mutations specific to Malaysian patients. Whole-genome sequencing was performed on the genomic DNA obtained from 50 Malaysian CRC patients' tissues. We discovered the top significantly mutated genes were APC, TP53, KRAS, TCF7L2 and ACVR2A. Four novel, non-synonymous variants were identified in three genes, which were KDM4E, MUC16 and POTED. At least one druggable somatic alteration was identified in 88% of our patients. Among them were two frameshift mutations in RNF43 (G156fs and P192fs) predicted to have responsive effects against the Wnt pathway inhibitor. We found that the exogenous expression of this RNF43 mutation in CRC cells resulted in increased cell proliferation and sensitivity against LGK974 drug treatment and G1 cell cycle arrest. In conclusion, this study uncovered our local CRC patients' genomic landscape and druggable alterations. It also highlighted the role of specific RNF43 frameshift mutations, which unveil the potential of an alternative treatment targeting the Wnt/β-Catenin signalling pathway and could be beneficial, especially to Malaysian CRC patients.
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Affiliation(s)
| | - Nurul-Syakima Ab Mutalib
- UKM Medical Molecular Biology Institute (UMBI), Kuala Lumpur, Malaysia,*Correspondence: Nurul-Syakima Ab Mutalib, ; Rahman Jamal,
| | | | - Sazuita Saidin
- UKM Medical Molecular Biology Institute (UMBI), Kuala Lumpur, Malaysia
| | - Muhiddin Ishak
- UKM Medical Molecular Biology Institute (UMBI), Kuala Lumpur, Malaysia
| | | | | | | | | | | | - Nadiah Abu
- UKM Medical Molecular Biology Institute (UMBI), Kuala Lumpur, Malaysia
| | - Isa Md Rose
- Department of Pathology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Ismail Sagap
- Department of Surgery, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Luqman Mazlan
- Department of Surgery, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Rahman Jamal
- UKM Medical Molecular Biology Institute (UMBI), Kuala Lumpur, Malaysia,*Correspondence: Nurul-Syakima Ab Mutalib, ; Rahman Jamal,
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6
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López-Guerrero JA, Mendiola M, Pérez-Fidalgo JA, Romero I, Torres A, Recalde D, Molina E, Gómez-Raposo C, Levin AM, Herrero A, Alarcón J, Esteban C, Marquina G, Rubio MJ, Guerra E, Sánchez-Lorenzo L, Gálvez-Montosa F, de Juan A, Churruca C, Gallego A, González-Martín A. Prospective Real-World Gynaecological Cancer Clinical Registry with Associated Biospecimens: A Collaborative Model to Promote Translational Research between GEICO and the Spanish Biobank Network. Cancers (Basel) 2022; 14:cancers14081965. [PMID: 35454870 PMCID: PMC9031046 DOI: 10.3390/cancers14081965] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/07/2022] [Accepted: 04/08/2022] [Indexed: 02/04/2023] Open
Abstract
Patient registries linked to biorepositories constitute a valuable asset for clinical and translational research in oncology. The Spanish Group of Ovarian Cancer Research (GEICO), in collaboration with the Spanish Biobank Network (RNBB), has developed a multicentre, multistakeholder, prospective virtual clinical registry (VCR) associated with biobanks for the collection of real-world data and biological samples of gynaecological cancer patients. This collaborative project aims to promote research by providing broad access to high-quality clinical data and biospecimens for future research according to the needs of investigators and to increase diagnostic and therapeutic opportunities for gynaecological cancer patients in Spain. The VCR will include the participation of more than 60 Spanish hospitals entering relevant clinical information in harmonised electronic case report forms (eCRFs) in four different cohorts: ovarian, endometrial, cervical, and rare gynaecological cancers (gestational trophoblastic disease). Initial data for the cases included till December 2021 are presented. The model described herein establishes a real-world win-win collaboration between multicentre structures, promoted and supported by GEICO, that will contribute to the success of translational research in gynaecological cancer.
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Affiliation(s)
- José Antonio López-Guerrero
- Laboratorio de Biología Molecular y Biobanco, Fundación Instituto Valenciano de Oncología, 46009 Valencia, Spain
- Unidad Mixta de Investigación en Cáncer IVO-CIPF, Centro de Investigación Príncipe Felipe (CIPF), 46012 Valencia, Spain
- Departamento de Patología, Facultad de Medicina, Universidad Católica de Valencia ‘San Vicente Martir’, 46001 Valencia, Spain
- Correspondence: ; Tel.: +34-961114337
| | - Marta Mendiola
- Laboratorio de Patología Molecular y Dianas Terapéuticas, Instituto de Investigación Hospital Universitario La Paz (IdiPAZ), 28029 Madrid, Spain;
- Centro de Investigación Biomédica en Red de Cáncer, CIBERONC, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - José Alejandro Pérez-Fidalgo
- Departamento de Oncología Médica, Hospital Clinico de Valencia, Instituto de Investigación Sanitaria INCLIVA, Universidad de Valencia, CIBERONC, 46010 Valencia, Spain;
| | - Ignacio Romero
- Department of Medical Oncology, Fundación Instituto Valenciano de Oncología, 46009 Valencia, Spain;
| | - Ana Torres
- Biobanco del Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain;
| | - Delia Recalde
- Biobanco del Sistema de Salud de Aragón, 50009 Zaragoza, Spain;
| | - Elena Molina
- Biobanco del Hospital Clínico San Carlos, 28040 Madrid, Spain;
| | - César Gómez-Raposo
- Department of Medical Oncology, Hospital Universitario Infanta Sofía, 28703 Madrid, Spain;
| | - Ana M. Levin
- Grupo Español de Investigación en Cáncer de Ovario, 28003 Madrid, Spain;
| | - Ana Herrero
- Department of Medical Oncology, Hospital Universitario Miguel Servet, 50009 Zaragoza, Spain;
| | - Jesús Alarcón
- Department of Medical Oncology, Hospital Universitario Son Espases, 07120 Palma, Spain;
| | - Carmen Esteban
- Department of Medical Oncology, Hospital Virgen de la Salud, 45004 Toledo, Spain;
| | - Gloria Marquina
- Department of Medical Oncology, Hospital Clínico San Carlos, 28040 Madrid, Spain;
| | - María Jesús Rubio
- Department of Medical Oncology, Hospital Universitario Reina Sofía, 14004 Córdoba, Spain;
| | - Eva Guerra
- Department of Medical Oncology, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain;
| | - Luisa Sánchez-Lorenzo
- Department of Medical Oncology, Clínica Universidad de Navarra, 28027 Madrid, Spain; (L.S.-L.); (A.G.-M.)
| | | | - Ana de Juan
- Department of Medical Oncology, Hospital Univeristario Marqués de Valdecilla, 39008 Santander, Spain;
| | - Cristina Churruca
- Department of Medical Oncology, Hospital Universitario Donostia, 20014 Donostia, Spain;
| | - Alejandro Gallego
- Department of Medical Oncology, Hospital Universitario La Paz, 28029 Madrid, Spain;
| | - Antonio González-Martín
- Department of Medical Oncology, Clínica Universidad de Navarra, 28027 Madrid, Spain; (L.S.-L.); (A.G.-M.)
- Programa de Tumores Sólidos, Centro de Investigación de Medicina Aplicada (CIMA), 31008 Pamplona, Spain
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7
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Wenmaekers S, Viergever BJ, Kumar G, Kranenburg O, Black PC, Daugaard M, Meijer RP. A Potential Role for HUWE1 in Modulating Cisplatin Sensitivity. Cells 2021; 10:cells10051262. [PMID: 34065298 PMCID: PMC8160634 DOI: 10.3390/cells10051262] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 12/25/2022] Open
Abstract
Cisplatin is a widely used antineoplastic agent, whose efficacy is limited by primary and acquired therapeutic resistance. Recently, a bladder cancer genome-wide CRISPR/Cas9 knock-out screen correlated cisplatin sensitivity to multiple genetic biomarkers. Among the screen’s top hits was the HECT domain-containing ubiquitin E3 ligase (HUWE1). In this review, HUWE1 is postulated as a therapeutic response modulator, affecting the collision between platinum-DNA adducts and the replication fork, the primary cytotoxic action of platins. HUWE1 can alter the cytotoxic response to platins by targeting essential components of the DNA damage response including BRCA1, p53, and Mcl-1. Deficiency of HUWE1 could lead to enhanced DNA damage repair and a dysfunctional apoptotic apparatus, thereby inducing resistance to platins. Future research on the relationship between HUWE1 and platins could generate new mechanistic insights into therapy resistance. Ultimately, HUWE1 might serve as a clinical biomarker to tailor cancer treatment strategies, thereby improving cancer care and patient outcomes.
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Affiliation(s)
- Stijn Wenmaekers
- Laboratory Translational Oncology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands; (S.W.); (B.J.V.); (O.K.)
- Department of Oncological Urology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands
| | - Bastiaan J. Viergever
- Laboratory Translational Oncology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands; (S.W.); (B.J.V.); (O.K.)
- Department of Oncological Urology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands
| | - Gunjan Kumar
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC V5Z 1M9, Canada; (G.K.); (P.C.B.)
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada
| | - Onno Kranenburg
- Laboratory Translational Oncology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands; (S.W.); (B.J.V.); (O.K.)
| | - Peter C. Black
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC V5Z 1M9, Canada; (G.K.); (P.C.B.)
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada
| | - Mads Daugaard
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC V5Z 1M9, Canada; (G.K.); (P.C.B.)
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada
- Correspondence: (M.D.); (R.P.M.)
| | - Richard P. Meijer
- Laboratory Translational Oncology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands; (S.W.); (B.J.V.); (O.K.)
- Department of Oncological Urology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands
- Correspondence: (M.D.); (R.P.M.)
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Ülgen E, Can Ö, Bilguvar K, Akyerli Boylu C, Kılıçturgay Yüksel Ş, Erşen Danyeli A, Sezerman OU, Yakıcıer MC, Pamir MN, Özduman K. Sequential filtering for clinically relevant variants as a method for clinical interpretation of whole exome sequencing findings in glioma. BMC Med Genomics 2021; 14:54. [PMID: 33622343 PMCID: PMC7903763 DOI: 10.1186/s12920-021-00904-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/02/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In the clinical setting, workflows for analyzing individual genomics data should be both comprehensive and convenient for clinical interpretation. In an effort for comprehensiveness and practicality, we attempted to create a clinical individual whole exome sequencing (WES) analysis workflow, allowing identification of genomic alterations and presentation of neurooncologically-relevant findings. METHODS The analysis workflow detects germline and somatic variants and presents: (1) germline variants, (2) somatic short variants, (3) tumor mutational burden (TMB), (4) microsatellite instability (MSI), (5) somatic copy number alterations (SCNA), (6) SCNA burden, (7) loss of heterozygosity, (8) genes with double-hit, (9) mutational signatures, and (10) pathway enrichment analyses. Using the workflow, 58 WES analyses from matched blood and tumor samples of 52 patients were analyzed: 47 primary and 11 recurrent diffuse gliomas. RESULTS The median mean read depths were 199.88 for tumor and 110.955 for normal samples. For germline variants, a median of 22 (14-33) variants per patient was reported. There was a median of 6 (0-590) reported somatic short variants per tumor. A median of 19 (0-94) broad SCNAs and a median of 6 (0-12) gene-level SCNAs were reported per tumor. The gene with the most frequent somatic short variants was TP53 (41.38%). The most frequent chromosome-/arm-level SCNA events were chr7 amplification, chr22q loss, and chr10 loss. TMB in primary gliomas were significantly lower than in recurrent tumors (p = 0.002). MSI incidence was low (6.9%). CONCLUSIONS We demonstrate that WES can be practically and efficiently utilized for clinical analysis of individual brain tumors. The results display that NOTATES produces clinically relevant results in a concise but exhaustive manner.
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Affiliation(s)
- Ege Ülgen
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Özge Can
- Department of Medical Engineering, Faculty of Engineering, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Kaya Bilguvar
- Department of Genetics, School of Medicine, Yale University, New Haven, CT, USA
- Yale Center for Genome Analysis, West Haven, CT, USA
| | - Cemaliye Akyerli Boylu
- Department of Medical Biology, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Şirin Kılıçturgay Yüksel
- Department of Medical Biology, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Ayça Erşen Danyeli
- Department of Pathology, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - O Uğur Sezerman
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - M Cengiz Yakıcıer
- Department of Molecular Biology, School of Arts and Sciences, Acibadem Mehmet Ali Aydinlar University Istanbul, Istanbul, Turkey
| | - M Necmettin Pamir
- Department of Neurosurgery, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Altunizade Mahallesi, Yurtcan Sok. No:1, Üsküdar, Istanbul, 34662, Turkey
| | - Koray Özduman
- Department of Neurosurgery, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Altunizade Mahallesi, Yurtcan Sok. No:1, Üsküdar, Istanbul, 34662, Turkey.
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Eslami-S Z, Cortés-Hernández LE, Alix-Panabières C. Epithelial Cell Adhesion Molecule: An Anchor to Isolate Clinically Relevant Circulating Tumor Cells. Cells 2020; 9:cells9081836. [PMID: 32764280 PMCID: PMC7464831 DOI: 10.3390/cells9081836] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/31/2020] [Accepted: 08/03/2020] [Indexed: 12/13/2022] Open
Abstract
In the last few decades, the epithelial cell adhesion molecule (EpCAM) has received increased attention as the main membrane marker used in many enrichment technologies to isolate circulating tumor cells (CTCs). Although there has been a great deal of progress in the implementation of EpCAM-based CTC detection technologies in medical settings, several issues continue to limit their clinical utility. The biology of EpCAM and its role are not completely understood but evidence suggests that the expression of this epithelial cell-surface protein is crucial for metastasis-competent CTCs and may not be lost completely during the epithelial-to-mesenchymal transition. In this review, we summarize the most significant advantages and disadvantages of using EpCAM as a marker for CTC enrichment and its potential biological role in the metastatic cascade.
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