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Wang H, Gao Y, Bai J, Liu H, Li Y, Zhang J, Ma C, Zhao X, Zhang L, Wan K, Zhu D. CircLMBR1 inhibits phenotypic transformation of hypoxia-induced pulmonary artery smooth muscle via the splicing factor PUF60. Eur J Pharmacol 2024; 980:176855. [PMID: 39059570 DOI: 10.1016/j.ejphar.2024.176855] [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: 04/15/2024] [Revised: 07/04/2024] [Accepted: 07/24/2024] [Indexed: 07/28/2024]
Abstract
Phenotypic transformation of pulmonary artery smooth muscle cells (PASMCs) contributes to vascular remodeling in hypoxic pulmonary hypertension (PH). Recent studies have suggested that circular RNAs (circRNAs) may play important roles in the vascular remodeling of hypoxia-induced PH. However, whether circRNAs cause pulmonary vascular remodeling by regulating the phenotypic transformation in PH has not been investigated. Microarray and RT-qPCR analysis identified that circLMBR1, a novel circRNA, decreased in mouse lung tissues of the hypoxia-SU5416 PH model, as well as in human PASMCs and mouse PASMCs exposed to hypoxia. Overexpression of circLMBR1 in the Semaxinib (SU5416) mouse model ameliorated hypoxia-induced PH and vascular remodeling in the lungs. Notably, circLMBR1 was mainly distributed in the nucleus and bound to the splicing factor PUF60. CircLMBR1 suppressed the phenotypic transformation of human PASMCs and vascular remodeling by inhibiting PUF60 expression. Furthermore, we identified U2AF65 as the downstream regulatory factor of PUF60. U2AF65 directly interacted with the pre-mRNA of the contractile phenotype marker smooth muscle protein 22-α (SM22α) and inhibited its splicing. Meanwhile, hypoxia exposure increased the formation of the PUF60-U2AF65 complex, thereby inhibiting SM22α production and inducing the transition of human PASMCs from a contractile phenotype to a synthetic phenotype. Overall, our results verified the important role of circLMBR1 in the pathological process of PH. We also proposed a new circLMBR1/PUF60-U2AF65/pre-SM22α pathway that could regulate the phenotypic transformation and proliferation of human PASMCs. This study may provide new perspectives for the diagnosis and treatment of PH.
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MESH Headings
- Pulmonary Artery/metabolism
- Pulmonary Artery/pathology
- Pulmonary Artery/drug effects
- Animals
- Humans
- Mice
- Vascular Remodeling/drug effects
- Vascular Remodeling/genetics
- Myocytes, Smooth Muscle/metabolism
- Myocytes, Smooth Muscle/drug effects
- Myocytes, Smooth Muscle/pathology
- Phenotype
- RNA, Circular/genetics
- RNA, Circular/metabolism
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/pathology
- Muscle, Smooth, Vascular/drug effects
- Male
- Splicing Factor U2AF/genetics
- Splicing Factor U2AF/metabolism
- Hypertension, Pulmonary/metabolism
- Hypertension, Pulmonary/pathology
- Hypertension, Pulmonary/genetics
- Hypoxia/metabolism
- Hypoxia/genetics
- Mice, Inbred C57BL
- Cell Hypoxia
- Indoles/pharmacology
- Pyrroles
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Affiliation(s)
- Hongdan Wang
- Central Laboratory of Harbin Medical University (Daqing), Daqing, 163319, PR China; College of Pharmacy, Harbin Medical University, Harbin, 150081, PR China
| | - Yupei Gao
- Central Laboratory of Harbin Medical University (Daqing), Daqing, 163319, PR China; College of Pharmacy, Harbin Medical University, Harbin, 150081, PR China
| | - June Bai
- Central Laboratory of Harbin Medical University (Daqing), Daqing, 163319, PR China; College of Pharmacy, Harbin Medical University, Harbin, 150081, PR China
| | - Huiyu Liu
- Central Laboratory of Harbin Medical University (Daqing), Daqing, 163319, PR China; College of Pharmacy, Harbin Medical University, Harbin, 150081, PR China
| | - Yiying Li
- Central Laboratory of Harbin Medical University (Daqing), Daqing, 163319, PR China; College of Pharmacy, Harbin Medical University, Harbin, 150081, PR China
| | - Junting Zhang
- Central Laboratory of Harbin Medical University (Daqing), Daqing, 163319, PR China; College of Pharmacy, Harbin Medical University, Harbin, 150081, PR China
| | - Cui Ma
- Central Laboratory of Harbin Medical University (Daqing), Daqing, 163319, PR China; College of Medical Laboratory Science and Technology, Harbin Medical University (Daqing), Daqing, 163319, PR China
| | - Xijuan Zhao
- Central Laboratory of Harbin Medical University (Daqing), Daqing, 163319, PR China; College of Medical Laboratory Science and Technology, Harbin Medical University (Daqing), Daqing, 163319, PR China
| | - Lixin Zhang
- Central Laboratory of Harbin Medical University (Daqing), Daqing, 163319, PR China; College of Medical Laboratory Science and Technology, Harbin Medical University (Daqing), Daqing, 163319, PR China
| | - Kuiyu Wan
- Central Laboratory of Harbin Medical University (Daqing), Daqing, 163319, PR China
| | - Daling Zhu
- Central Laboratory of Harbin Medical University (Daqing), Daqing, 163319, PR China; College of Pharmacy, Harbin Medical University, Harbin, 150081, PR China; Key Laboratory of Cardiovascular Medicine Research, Ministry of Education, Harbin Medical University, Harbin, 150081, PR China.
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2
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Yan L, Fu K, Li L, Li Q, Zhou X. Potential of sonobiopsy as a novel diagnosis tool for brain cancer. MOLECULAR THERAPY. ONCOLOGY 2024; 32:200840. [PMID: 39077551 PMCID: PMC11284684 DOI: 10.1016/j.omton.2024.200840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
Brain tumors have a poor prognosis. Early, accurate diagnosis and treatment are crucial. Although brain surgical biopsy can provide an accurate diagnosis, it is highly invasive and risky and is not suitable for follow-up examination. Blood-based liquid biopsies have a low detection rate of tumor biomarkers and limited evaluation ability due to the existence of the blood-brain barrier (BBB). The BBB is composed of brain capillary endothelial cells through tight junctions, which prevents the release of brain tumor markers to the human peripheral circulation, making it more difficult to diagnose, predict prognosis, and evaluate therapeutic response through brain tumor markers than other tumors. Focused ultrasound (FUS)-enabled liquid biopsy (sonobiopsy) is an emerging technique using FUS to promote the release of tumor markers into the circulatory system and cerebrospinal fluid, thus facilitating tumor detection. The feasibility and safety data from both animal models and clinical trials support sonobiopsy as a great potential in the diagnosis of brain diseases.
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Affiliation(s)
- Li Yan
- Institute of Medical Research, Northwestern Polytechnical University, Xi’an, China
| | - Kang Fu
- Institute of Medical Research, Northwestern Polytechnical University, Xi’an, China
| | - Le Li
- Institute of Medical Research, Northwestern Polytechnical University, Xi’an, China
| | - Qing Li
- Ultrasound Diagnosis and Treatment Center, Xi’an International Medical Center Hospital, Xi’an, China
| | - Xiaodong Zhou
- Ultrasound Diagnosis and Treatment Center, Xi’an International Medical Center Hospital, Xi’an, China
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3
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Hu L, Ji YY, Zhu P, Lu RQ. Mutation-Selected Amplification droplet digital PCR: A new single nucleotide variant detection assay for TP53 R249S mutant in tumor and plasma samples. Anal Chim Acta 2024; 1318:342929. [PMID: 39067934 DOI: 10.1016/j.aca.2024.342929] [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: 03/01/2024] [Revised: 06/21/2024] [Accepted: 06/30/2024] [Indexed: 07/30/2024]
Abstract
The early detection of gene mutations in physiological and pathological processes is a powerful approach to guide decisions in precision medicine. However, detecting low-copy mutant DNA from clinical samples poses a challenge due to the enrichment of wild-type DNA backgrounds. In this study, we devised a novel strategy, named Mutation-Selected Amplification droplet digital PCR (MSA-ddPCR), to quantitatively analyze single nucleotide variants (SNVs) at low variant allele frequencies (VAFs). Using TP53R249S (a hotspot mutation associated with hepatocellular carcinoma) as a model, we optimized the concentration ratio of primers, the annealing temperature and nucleic acid amplification modifiers. Subsequently, we evaluated the linear range and precision of MSA-ddPCR by detecting TP53R249S and TP53wild-type (TP53WT) plasmid DNA, respectively. MSA-ddPCR demonstrated superior ability to discriminate between mutant DNA and wild-type DNA compared to traditional TaqMan-MGB PCR. We further applied MSA-ddPCR to analyze the TP53R249S mutation in 20 plasma samples and 15 formalin-fixed paraffin-embedded (FFPE) tissue samples, and assessed the agreement rates between MSA-ddPCR and amplicon high-throughput sequencing. The results showed that the limit of blanks of MSA-ddPCR are 0.449 copies μL-1 in the FAM channel and 0.452 copies μL-1 in the VIC channel. MSA-ddPCR could accurately quantify VAFs as low as 0.01 %, surpassing existing PCR and next-generation sequencing (NGS) methods. In the detection of clinical samples, a high correlation was found between MSA-ddPCR and amplicon high-throughput sequencing. Additionally, MSA-ddPCR outperformed sequencing methods in terms of detection time and simplicity of data analysis. MSA-ddPCR can be easily implemented into clinical practice and serve as a robust tool for detecting mutant genes due to its high sensitivity and accuracy.
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Affiliation(s)
- Ling Hu
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical School, Fudan University, Shanghai, 20032, China
| | - Yuan-Ye Ji
- Department of Medical Laboratory, Ningbo No.2 Hospital, Ningbo, 315010, China
| | - Peng Zhu
- Department of Medical Laboratory, Ningbo No.2 Hospital, Ningbo, 315010, China; Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315010, China.
| | - Ren-Quan Lu
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical School, Fudan University, Shanghai, 20032, China.
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4
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Batool SM, Escobedo AK, Hsia T, Ekanayake E, Khanna SK, Gamblin AS, Zheng H, Skog J, Miller JJ, Stemmer-Rachamimov AO, Cahill DP, Balaj L, Carter BS. Clinical utility of a blood based assay for the detection of IDH1.R132H-mutant gliomas. Nat Commun 2024; 15:7074. [PMID: 39152110 PMCID: PMC11329733 DOI: 10.1038/s41467-024-51332-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 08/05/2024] [Indexed: 08/19/2024] Open
Abstract
Glioma represents the most common central nervous system neoplasm in adults. Current classification scheme utilizes molecular alterations, particularly IDH1.R132H, to stratify lesions into distinct prognostic groups. Identification of the single nucleotide variant through traditional tissue biopsy assessment poses procedural risks and does not fully reflect the heterogeneous and evolving tumor landscape. Here, we introduce a liquid biopsy assay, mt-IDH1dx. The blood-based test allows minimally invasive detection of tumor-derived extracellular vesicle RNA using only 2 ml plasma volume. We perform rigorous, blinded validation testing across the study population (n = 133), comprising of IDH1.R132H patients (n = 80), IDH1 wild-type gliomas (n = 44), and age matched healthy controls (n = 9). Results from our plasma testing demonstrate an overall sensitivity of 75.0% (95% CI: 64.1%-84.0%), specificity 88.7% (95% CI: 77.0%-95.7%), positive predictive value 90.9%, and negative predictive value 70.1% compared to the tissue gold standard. In addition to fundamental diagnostic applications, the study also highlights the utility of mt-IDH1dx platform for blood-based monitoring and surveillance, offering valuable prognostic information. Finally, the optimized workflow enables rapid and efficient completion of both tumor tissue and plasma testing in under 4 hours from the time of sampling.
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Affiliation(s)
- Syeda Maheen Batool
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ana K Escobedo
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Tiffaney Hsia
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Emil Ekanayake
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Sirena K Khanna
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Austin S Gamblin
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Hui Zheng
- Center for Biostatistics, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Johan Skog
- Exosome Diagnostics, a Bio-Techne Brand, Waltham, MA, USA
| | - Julie J Miller
- Translational Neuro-Oncology Laboratory, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Center for Neuro-Oncology, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Daniel P Cahill
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Leonora Balaj
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Bob S Carter
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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5
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Li K, Zhu Q, Yang J, Zheng Y, Du S, Song M, Peng Q, Yang R, Liu Y, Qi L. Imaging and Liquid Biopsy for Distinguishing True Progression From Pseudoprogression in Gliomas, Current Advances and Challenges. Acad Radiol 2024; 31:3366-3383. [PMID: 38614827 DOI: 10.1016/j.acra.2024.03.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 01/14/2024] [Accepted: 03/18/2024] [Indexed: 04/15/2024]
Abstract
RATIONALE AND OBJECTIVES Gliomas are aggressive brain tumors with a poor prognosis. Assessing treatment response is challenging because magnetic resonance imaging (MRI) may not distinguish true progression (TP) from pseudoprogression (PsP). This review aims to discuss imaging techniques and liquid biopsies used to distinguish TP from PsP. MATERIALS AND METHODS This review synthesizes existing literature to examine advances in imaging techniques, such as magnetic resonance diffusion imaging (MRDI), perfusion-weighted imaging (PWI) MRI, and liquid biopsies, for identifying TP or PsP through tumor markers and tissue characteristics. RESULTS Advanced imaging techniques, including MRDI and PWI MRI, have proven effective in delineating tumor tissue properties, offering valuable insights into glioma behavior. Similarly, liquid biopsy has emerged as a potent tool for identifying tumor-derived markers in biofluids, offering a non-invasive glimpse into tumor evolution. Despite their promise, these methodologies grapple with significant challenges. Their sensitivity remains inconsistent, complicating the accurate differentiation between TP and PSP. Furthermore, the absence of standardized protocols across platforms impedes the reliability of comparisons, while inherent biological variability adds complexity to data interpretation. CONCLUSION Their potential applications have been highlighted, but gaps remain before routine clinical use. Further research is needed to develop and validate these promising methods for distinguishing TP from PsP in gliomas.
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Affiliation(s)
- Kaishu Li
- Department of Neurosurgery, Affiliated Qingyuan Hospital,Guangzhou Medical University,Qingyuan People's Hospital, Qingyuan 511518, China; Department of Neurosurgery & Medical Research Center, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), 1# Jiazi Road, Foshan, Guangdong 528300, China.; Department of Neurosurgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Qihui Zhu
- Department of Neurosurgery, Affiliated Qingyuan Hospital,Guangzhou Medical University,Qingyuan People's Hospital, Qingyuan 511518, China
| | - Junyi Yang
- Department of Neurosurgery, Affiliated Qingyuan Hospital,Guangzhou Medical University,Qingyuan People's Hospital, Qingyuan 511518, China
| | - Yin Zheng
- Department of Neurosurgery, Affiliated Qingyuan Hospital,Guangzhou Medical University,Qingyuan People's Hospital, Qingyuan 511518, China
| | - Siyuan Du
- Institute of Digestive Disease of Guangzhou Medical University, Affiliated Qingyuan Hospital,Guangzhou Medical University,Qingyuan People's Hospital, Qingyuan 511518, China
| | - Meihui Song
- Institute of Digestive Disease of Guangzhou Medical University, Affiliated Qingyuan Hospital,Guangzhou Medical University,Qingyuan People's Hospital, Qingyuan 511518, China
| | - Qian Peng
- Institute of Digestive Disease of Guangzhou Medical University, Affiliated Qingyuan Hospital,Guangzhou Medical University,Qingyuan People's Hospital, Qingyuan 511518, China
| | - Runwei Yang
- Department of Neurosurgery & Medical Research Center, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), 1# Jiazi Road, Foshan, Guangdong 528300, China
| | - Yawei Liu
- Department of Neurosurgery & Medical Research Center, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), 1# Jiazi Road, Foshan, Guangdong 528300, China
| | - Ling Qi
- Institute of Digestive Disease of Guangzhou Medical University, Affiliated Qingyuan Hospital,Guangzhou Medical University,Qingyuan People's Hospital, Qingyuan 511518, China.
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6
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Berzero G, Pieri V, Palazzo L, Finocchiaro G, Filippi M. Liquid biopsy in brain tumors: moving on, slowly. Curr Opin Oncol 2024:00001622-990000000-00195. [PMID: 39011725 DOI: 10.1097/cco.0000000000001079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
PURPOSE OF REVIEW Due to limited access to the tumor, there is an obvious clinical potential for liquid biopsy in patients with primary brain tumors. Here, we review current approaches, present limitations to be dealt with, and new promising data that may impact the field. RECENT FINDINGS The value of circulating tumor cell-free DNA (ctDNA) in the cerebrospinal fluid (CSF) for the noninvasive diagnosis of primary brain tumors has been confirmed in several reports. The detection of ctDNA in the peripheral blood is desirable for patient follow-up but requires ultrasensitive methods to identify low mutant allelic frequencies. Digital PCR approaches and targeted gene panels have been used to identify recurrent hotspot mutations and copy number variations (CNVs) from CSF or plasma. Tumor classification from circulating methylomes in plasma has been actively pursued, although the need of advanced bioinformatics currently hampers clinical application. The use of focused ultrasounds to open the blood-brain barrier may represent a way to enrich of ctDNA the peripheral blood and enhance plasma-based liquid biopsy. SUMMARY Monitoring CNVs and hotspot mutations by liquid biopsy is a promising tool to detect minimal residual disease and strengthen response assessment in patients with primary brain tumors. Novel methods to increase the relative and/or absolute amount of ctDNA can improve the clinical potential of plasma-based liquid biopsies.
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Affiliation(s)
- Giulia Berzero
- Neurology Unit, IRCCS Ospedale San Raffaele
- Vita-Salute San Raffaele University
| | - Valentina Pieri
- Neurology Unit, IRCCS Ospedale San Raffaele
- Vita-Salute San Raffaele University
| | - Leonardo Palazzo
- Neurology Unit, IRCCS Ospedale San Raffaele
- Vita-Salute San Raffaele University
| | | | - Massimo Filippi
- Neurology Unit, IRCCS Ospedale San Raffaele
- Vita-Salute San Raffaele University
- Neurorehabilitation Unit, Neurophysiology Unit, Neuroimaging Research Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS Ospedale San Raffaele, Milan, Italy
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7
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Rosas-Alonso R, Colmenarejo-Fernández J, Pernía O, Burdiel M, Rodríguez-Antolín C, Losantos-García I, Rubio T, Moreno-Velasco R, Esteban-Rodríguez I, Martínez-Marín V, Yubero P, Costa-Fraga N, Díaz-Lagares A, López-López R, Díaz-Martin E, García JF, Sánchez CV, Gandía-González ML, Moreno-Bueno G, de Castro J, de Cáceres II. Evaluation of the clinical use of MGMT methylation in extracellular vesicle-based liquid biopsy as a tool for glioblastoma patient management. Sci Rep 2024; 14:11398. [PMID: 38762534 PMCID: PMC11102540 DOI: 10.1038/s41598-024-62061-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 05/13/2024] [Indexed: 05/20/2024] Open
Abstract
Glioblastoma (GB) is a devastating tumor of the central nervous system characterized by a poor prognosis. One of the best-established predictive biomarker in IDH-wildtype GB is O6-methylguanine-DNA methyltransferase (MGMT) methylation (mMGMT), which is associated with improved treatment response and survival. However, current efforts to monitor GB patients through mMGMT detection have proven unsuccessful. Small extracellular vesicles (sEVs) hold potential as a key element that could revolutionize clinical practice by offering new possibilities for liquid biopsy. This study aimed to determine the utility of sEV-based liquid biopsy as a predictive biomarker and disease monitoring tool in patients with IDH-wildtype GB. Our findings show consistent results with tissue-based analysis, achieving a remarkable sensitivity of 85.7% for detecting mMGMT in liquid biopsy, the highest reported to date. Moreover, we suggested that liquid biopsy assessment of sEV-DNA could be a powerful tool for monitoring disease progression in IDH-wildtype GB patients. This study highlights the critical significance of overcoming molecular underdetection, which can lead to missed treatment opportunities and misdiagnoses, possibly resulting in ineffective therapies. The outcomes of our research significantly contribute to the field of sEV-DNA-based liquid biopsy, providing valuable insights into tumor tissue heterogeneity and establishing it as a promising tool for detecting GB biomarkers. These results have substantial implications for advancing predictive and therapeutic approaches in the context of GB and warrant further exploration and validation in clinical settings.
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Affiliation(s)
- Rocío Rosas-Alonso
- Cancer Epigenetics Laboratory, INGEMM, La Paz University Hospital, Paseo La Castellana 261, Edificio Bloque Quirúrgico Planta-2, 28046, Madrid, Spain.
- Biomarkers and Experimental Therapeutics in Cancer, IdiPAZ, Madrid, Spain.
| | - Julian Colmenarejo-Fernández
- Cancer Epigenetics Laboratory, INGEMM, La Paz University Hospital, Paseo La Castellana 261, Edificio Bloque Quirúrgico Planta-2, 28046, Madrid, Spain
- Biomarkers and Experimental Therapeutics in Cancer, IdiPAZ, Madrid, Spain
| | - Olga Pernía
- Cancer Epigenetics Laboratory, INGEMM, La Paz University Hospital, Paseo La Castellana 261, Edificio Bloque Quirúrgico Planta-2, 28046, Madrid, Spain
- Biomarkers and Experimental Therapeutics in Cancer, IdiPAZ, Madrid, Spain
| | - Miranda Burdiel
- Cancer Epigenetics Laboratory, INGEMM, La Paz University Hospital, Paseo La Castellana 261, Edificio Bloque Quirúrgico Planta-2, 28046, Madrid, Spain
- Biomarkers and Experimental Therapeutics in Cancer, IdiPAZ, Madrid, Spain
| | - Carlos Rodríguez-Antolín
- Cancer Epigenetics Laboratory, INGEMM, La Paz University Hospital, Paseo La Castellana 261, Edificio Bloque Quirúrgico Planta-2, 28046, Madrid, Spain
- Biomarkers and Experimental Therapeutics in Cancer, IdiPAZ, Madrid, Spain
| | | | - Tania Rubio
- Cancer Epigenetics Laboratory, INGEMM, La Paz University Hospital, Paseo La Castellana 261, Edificio Bloque Quirúrgico Planta-2, 28046, Madrid, Spain
- Biomarkers and Experimental Therapeutics in Cancer, IdiPAZ, Madrid, Spain
| | - Rocío Moreno-Velasco
- Cancer Epigenetics Laboratory, INGEMM, La Paz University Hospital, Paseo La Castellana 261, Edificio Bloque Quirúrgico Planta-2, 28046, Madrid, Spain
- Biomarkers and Experimental Therapeutics in Cancer, IdiPAZ, Madrid, Spain
| | - Isabel Esteban-Rodríguez
- Biomarkers and Experimental Therapeutics in Cancer, IdiPAZ, Madrid, Spain
- Department of Pathology, La Paz University Hospital, Madrid, Spain
| | | | - Paloma Yubero
- Department of Medical Oncology, La Paz University Hospital, Madrid, Spain
| | - Nicolas Costa-Fraga
- Cancer Epigenomics Laboratory, Epigenomics Unit, Translational Medical Oncology Group (ONCOMET), IDIS, University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
| | - Angel Díaz-Lagares
- Cancer Epigenomics Laboratory, Epigenomics Unit, Translational Medical Oncology Group (ONCOMET), IDIS, University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Rafael López-López
- Cancer Epigenomics Laboratory, Epigenomics Unit, Translational Medical Oncology Group (ONCOMET), IDIS, University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
- Department of Medical Oncology, University Hospital Complex of Santiago de Compostela, Santiago de Compostela, Spain
| | | | - Juan F García
- MD Anderson International Foundation, Madrid, Spain
- Department of Pathology, MD Anderson Cancer Center, Madrid, Spain
| | | | | | - Gema Moreno-Bueno
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
- MD Anderson International Foundation, Madrid, Spain
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM), Instituto de Investigaciones Biomédicas 'Alberto Sols' (CSIC-UAM), IdiPAZ, Madrid, Spain
| | - Javier de Castro
- Biomarkers and Experimental Therapeutics in Cancer, IdiPAZ, Madrid, Spain
- Department of Medical Oncology, La Paz University Hospital, Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Inmaculada Ibánez de Cáceres
- Cancer Epigenetics Laboratory, INGEMM, La Paz University Hospital, Paseo La Castellana 261, Edificio Bloque Quirúrgico Planta-2, 28046, Madrid, Spain.
- Biomarkers and Experimental Therapeutics in Cancer, IdiPAZ, Madrid, Spain.
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8
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Schreck KC, Strowd RE, Nabors LB, Ellingson BM, Chang M, Tan SK, Abdullaev Z, Turakulov R, Aldape K, Danda N, Desideri S, Fisher J, Iacoboni M, Surakus T, Rudek MA, Bettegowda C, Grossman SA, Ye X. Response Rate and Molecular Correlates to Encorafenib and Binimetinib in BRAF-V600E Mutant High-Grade Glioma. Clin Cancer Res 2024; 30:2048-2056. [PMID: 38446982 PMCID: PMC11096001 DOI: 10.1158/1078-0432.ccr-23-3241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/25/2024] [Accepted: 03/04/2024] [Indexed: 03/08/2024]
Abstract
PURPOSE Although fewer than 5% of high-grade gliomas (HGG) are BRAF-V600E mutated, these tumors are notable as BRAF-targeted therapy shows efficacy for some populations. The purpose of this study was to evaluate response to the combination of encorafenib with binimetinib in adults with recurrent BRAF-V600-mutated HGG. PATIENTS AND METHODS In this phase 2, open-label, Adult Brain Tumor Consortium (ABTC) trial (NCT03973918), encorafenib and binimetinib were administered at their FDA-approved doses continuously in 28-day cycles. Eligible patients were required to have HGG or glioblastoma with a BRAF-V600E alteration that was recurrent following at least one line of therapy, including radiotherapy. RESULTS Five patients enrolled between January 2020 and administrative termination in November 2021 (due to closure of the ABTC). Enrolled patients received treatment for 2 to 40 months; currently one patient remains on treatment. Centrally determined radiographic response rate was 60%, with one complete response and two partial responses. Methylation profiling revealed that all tumors cluster most closely with anaplastic pleomorphic xanthoastrocytoma (PXA). Transcriptional profile for MAPK-response signature was similar across all tumors at baseline and did not correlate with response in this small population. Circulating tumor DNA measured in plasma samples before treatment, during response, and upon progression showed feasibility of detection for the BRAF-V600E alteration. No new safety signal was detected. CONCLUSIONS Encorafenib and binimetinib exhibit positive tumor responses in patients with recurrent BRAF-V600E mutant HGG in this small series, warranting therapeutic consideration. Although toxicity remains a concern for BRAF-targeted therapies, no new safety signal was observed in these patients.
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Affiliation(s)
- Karisa C Schreck
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | - Roy E Strowd
- Department of Neurology, Wake Forest University School of Medicine, Winston Salem, North Carolina
| | - Louis B Nabors
- Department of Neurology, Heersink School of Medicine, University of Alabama at Birmingham, Alabama
| | - Benjamin M Ellingson
- Department of Radiological Sciences, UCLA Brain Tumor Imaging Laboratory, University of California Los Angeles, Los Angeles, California
| | - Michael Chang
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sze K Tan
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Zied Abdullaev
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Rust Turakulov
- Victorian Comprehensive Cancer Center, Melbourne, Victoria, Australia
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Neeraja Danda
- Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | - Serena Desideri
- Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | - Joy Fisher
- Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | | | - Trisha Surakus
- Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | | | - Chetan Bettegowda
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Xiaobu Ye
- Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
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9
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Roda D, Veiga P, Melo JB, Carreira IM, Ribeiro IP. Principles in the Management of Glioblastoma. Genes (Basel) 2024; 15:501. [PMID: 38674436 PMCID: PMC11050118 DOI: 10.3390/genes15040501] [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: 03/15/2024] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
Glioblastoma, the most aggressive and common malignant primary brain tumour, is characterized by infiltrative growth, abundant vascularization, and aggressive clinical evolution. Patients with glioblastoma often face poor prognoses, with a median survival of approximately 15 months. Technological progress and the subsequent improvement in understanding the pathophysiology of these tumours have not translated into significant achievements in therapies or survival outcomes for patients. Progress in molecular profiling has yielded new omics data for a more refined classification of glioblastoma. Several typical genetic and epigenetic alterations in glioblastoma include mutations in genes regulating receptor tyrosine kinase (RTK)/rat sarcoma (RAS)/phosphoinositide 3-kinase (PI3K), p53, and retinoblastoma protein (RB) signalling, as well as mutation of isocitrate dehydrogenase (IDH), methylation of O6-methylguanine-DNA methyltransferase (MGMT), amplification of epidermal growth factor receptor vIII, and codeletion of 1p/19q. Certain microRNAs, such as miR-10b and miR-21, have also been identified as prognostic biomarkers. Effective treatment options for glioblastoma are limited. Surgery, radiotherapy, and alkylating agent chemotherapy remain the primary pillars of treatment. Only promoter methylation of the gene MGMT predicts the benefit from alkylating chemotherapy with temozolomide and it guides the choice of first-line treatment in elderly patients. Several targeted strategies based on tumour-intrinsic dominant signalling pathways and antigenic tumour profiles are under investigation in clinical trials. This review explores the potential genetic and epigenetic biomarkers that could be deployed as analytical tools in the diagnosis and prognostication of glioblastoma. Recent clinical advancements in treating glioblastoma are also discussed, along with the potential of liquid biopsies to advance personalized medicine in the field of glioblastoma, highlighting the challenges and promises for the future.
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Affiliation(s)
- Domingos Roda
- Algarve Radiation Oncology Unit—Joaquim Chaves Saúde (JCS), 8000-316 Faro, Portugal;
| | - Pedro Veiga
- Institute of Cellular and Molecular Biology, Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal; (P.V.); (J.B.M.)
| | - Joana Barbosa Melo
- Institute of Cellular and Molecular Biology, Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal; (P.V.); (J.B.M.)
- Coimbra Institute for Clinical and Biomedical Research (iCBR) and Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB) and Clinical Academic Center of Coimbra (CACC), University of Coimbra, 3000-548 Coimbra, Portugal
| | - Isabel Marques Carreira
- Institute of Cellular and Molecular Biology, Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal; (P.V.); (J.B.M.)
- Coimbra Institute for Clinical and Biomedical Research (iCBR) and Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB) and Clinical Academic Center of Coimbra (CACC), University of Coimbra, 3000-548 Coimbra, Portugal
| | - Ilda Patrícia Ribeiro
- Institute of Cellular and Molecular Biology, Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal; (P.V.); (J.B.M.)
- Coimbra Institute for Clinical and Biomedical Research (iCBR) and Center of Investigation on Environment Genetics and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB) and Clinical Academic Center of Coimbra (CACC), University of Coimbra, 3000-548 Coimbra, Portugal
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10
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Otsuji R, Fujioka Y, Hata N, Kuga D, Hatae R, Sangatsuda Y, Nakamizo A, Mizoguchi M, Yoshimoto K. Liquid Biopsy for Glioma Using Cell-Free DNA in Cerebrospinal Fluid. Cancers (Basel) 2024; 16:1009. [PMID: 38473369 DOI: 10.3390/cancers16051009] [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: 12/25/2023] [Revised: 02/24/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Glioma is one of the most common primary central nervous system (CNS) tumors, and its molecular diagnosis is crucial. However, surgical resection or biopsy is risky when the tumor is located deep in the brain or brainstem. In such cases, a minimally invasive approach to liquid biopsy is beneficial. Cell-free DNA (cfDNA), which directly reflects tumor-specific genetic changes, has attracted attention as a target for liquid biopsy, and blood-based cfDNA monitoring has been demonstrated for other extra-cranial cancers. However, it is still challenging to fully detect CNS tumors derived from cfDNA in the blood, including gliomas, because of the unique structure of the blood-brain barrier. Alternatively, cerebrospinal fluid (CSF) is an ideal source of cfDNA and is expected to contribute significantly to the liquid biopsy of gliomas. Several successful studies have been conducted to detect tumor-specific genetic alterations in cfDNA from CSF using digital PCR and/or next-generation sequencing. This review summarizes the current status of CSF-based cfDNA-targeted liquid biopsy for gliomas. It highlights how the approaches differ from liquid biopsies of other extra-cranial cancers and discusses the current issues and prospects.
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Affiliation(s)
- Ryosuke Otsuji
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yutaka Fujioka
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Nobuhiro Hata
- Department of Neurosurgery, Oita University Faculty of Medicine, Yufu 879-5593, Japan
| | - Daisuke Kuga
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Ryusuke Hatae
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yuhei Sangatsuda
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Akira Nakamizo
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Masahiro Mizoguchi
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
- Department of Neurosurgery, National Hospital Organization Kyushu Medical Center, Clinical Research Institute, Fukuoka 810-8563, Japan
| | - Koji Yoshimoto
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
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11
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Iv M, Naya L, Sanan S, Van Buskirk SL, Nagpal S, Thomas RP, Recht LD, Patel CB. Tumor treating fields increases blood-brain barrier permeability and relative cerebral blood volume in patients with glioblastoma. Neuroradiol J 2024; 37:107-118. [PMID: 37931176 PMCID: PMC10863570 DOI: 10.1177/19714009231207083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND AND OBJECTIVE 200 kHz tumor treating fields (TTFields) is clinically approved for newly-diagnosed glioblastoma (nGBM). Because its effects on conventional surveillance MRI brain scans are equivocal, we investigated its effects on perfusion MRI (pMRI) brain scans. METHODS Each patient underwent institutional standard pMRI: dynamic contrast-enhanced (DCE) and dynamic susceptibility contrast (DSC) pMRI at three time points: baseline, 2-, and 6-months on-adjuvant therapy. At each timepoint, the difference between T1 pre- versus post-contrast tumor volume (ΔT1) and these pMRI metrics were evaluated: normalized and standardized relative cerebral blood volume (nRCBV, sRCBV); fractional plasma volume (Vp), volume of extravascular extracellular space (EES) per volume of tissue (Ve), blood-brain barrier (BBB) permeability (Ktrans), and time constant for gadolinium reflux from EES back into the vascular system (Kep). Between-group comparisons were performed using rank-sum analysis, and bootstrapping evaluated likely reproducibility of the results. RESULTS Among 13 pMRI datasets (11 nGBM, 2 recurrent GBM), therapies included temozolomide-only (n = 9) and temozolomide + TTFields (n = 4). No significant differences were found in patient or tumor characteristics. Compared to temozolomide-only, temozolomide + TTFields did not significantly affect the percent-change in pMRI metrics from baseline to 2 months. But during the 2- to 6-month period, temozolomide + TTFields significantly increased the percent-change in nRCBV (+26.9% [interquartile range 55.1%] vs -39.1% [37.0%], p = 0.049), sRCBV (+9.5% [39.7%] vs -30.5% [39.4%], p = 0.049), Ktrans (+54.6% [1768.4%] vs -26.9% [61.2%], p = 0.024), Ve (+111.0% [518.1%] vs -13.0% [22.5%], p = 0.048), and Vp (+98.8% [2172.4%] vs -24.6% [53.3%], p = 0.024) compared to temozolomide-only. CONCLUSION Using pMRI, we provide initial in-human validation of pre-clinical studies regarding the effects of TTFields on tumor blood volume and BBB permeability in GBM.
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Affiliation(s)
- Michael Iv
- Division of Neuroradiology, Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lewis Naya
- Stanford Cancer Institute, Stanford, CA, USA
| | - Sajal Sanan
- School of Medicine, University of Washington, Seattle, WA, USA
| | - Samuel L Van Buskirk
- Department of Psychology, University of Texas at San Antonio, San Antonio, TX, USA
| | - Seema Nagpal
- Division of Neuro-Oncology, Department of Neurology, Stanford University School of Medicine, Stanford, CA, USA
| | - Reena P Thomas
- Division of Neuro-Oncology, Department of Neurology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lawrence D Recht
- Division of Neuro-Oncology, Department of Neurology, Stanford University School of Medicine, Stanford, CA, USA
| | - Chirag B Patel
- Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Cancer Biology Program, The University of Texas MD Anderson Cancer Center, University of Texas at Houston Graduate School of Biomedical Sciences (GSBS), Houston, TX, USA
- Neuroscience Graduate Program, The University of Texas MD Anderson Cancer Center-University of Texas at Houston Graduate School of Biomedical Sciences (GSBS), USA
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12
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Brooks AM, Vornoli A, Kovi RC, Ton TVT, Xu M, Mashal A, Tibaldi E, Gnudi F, Li JL, Sills RC, Bucher JR, Mandrioli D, Belpoggi F, Pandiri AR. Genetic profiling of rat gliomas and cardiac schwannomas from life-time radiofrequency radiation exposure study using a targeted next-generation sequencing gene panel. PLoS One 2024; 19:e0296699. [PMID: 38232086 PMCID: PMC10793937 DOI: 10.1371/journal.pone.0296699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/17/2023] [Indexed: 01/19/2024] Open
Abstract
The cancer hazard associated with lifetime exposure to radiofrequency radiation (RFR) was examined in Sprague Dawley (SD) rats at the Ramazzini Institute (RI), Italy. There were increased incidences of gliomas and cardiac schwannomas. The translational relevance of these rare rat tumors for human disease is poorly understood. We examined the genetic alterations in RFR-derived rat tumors through molecular characterization of important cancer genes relevant for human gliomagenesis. A targeted next-generation sequencing (NGS) panel was designed for rats based on the top 23 orthologous human glioma-related genes. Single-nucleotide variants (SNVs) and small insertion and deletions (indels) were characterized in the rat gliomas and cardiac schwannomas. Translational relevance of these genetic alterations in rat tumors to human disease was determined through comparison with the Catalogue of Somatic Mutations in Cancer (COSMIC) database. These data suggest that rat gliomas resulting from life-time exposure to RFR histologically resemble low grade human gliomas but surprisingly no mutations were detected in rat gliomas that had homology to the human IDH1 p.R132 or IDH2 p.R172 suggesting that rat gliomas are primarily wild-type for IDH hotspot mutations implicated in human gliomas. The rat gliomas appear to share some genetic alterations with IDH1 wildtype human gliomas and rat cardiac schwannomas also harbor mutations in some of the queried cancer genes. These data demonstrate that targeted NGS panels based on tumor specific orthologous human cancer driver genes are an important tool to examine the translational relevance of rodent tumors resulting from chronic/life-time rodent bioassays.
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Affiliation(s)
- Ashley M. Brooks
- Integrative Bioinformatics Support Group, Division of Intramural Research, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | - Andrea Vornoli
- Comparative and Molecular Pathogenesis Branch, Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
- Cesare Maltoni Cancer Research Center, Ramazzini Institute, Bologna, Italy
| | - Ramesh C. Kovi
- Comparative and Molecular Pathogenesis Branch, Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
- Experimental Pathology Laboratories, Inc., Research Triangle Park, North Carolina, United States of America
| | - Thai Vu T. Ton
- Comparative and Molecular Pathogenesis Branch, Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | - Miaofei Xu
- Comparative and Molecular Pathogenesis Branch, Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | - Ahmed Mashal
- Comparative and Molecular Pathogenesis Branch, Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | - Eva Tibaldi
- Cesare Maltoni Cancer Research Center, Ramazzini Institute, Bologna, Italy
| | - Federica Gnudi
- Cesare Maltoni Cancer Research Center, Ramazzini Institute, Bologna, Italy
| | - Jian-Liang Li
- Integrative Bioinformatics Support Group, Division of Intramural Research, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | - Robert C. Sills
- Comparative and Molecular Pathogenesis Branch, Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | - John R. Bucher
- Comparative and Molecular Pathogenesis Branch, Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | - Daniele Mandrioli
- Cesare Maltoni Cancer Research Center, Ramazzini Institute, Bologna, Italy
| | - Fiorella Belpoggi
- Cesare Maltoni Cancer Research Center, Ramazzini Institute, Bologna, Italy
| | - Arun R. Pandiri
- Comparative and Molecular Pathogenesis Branch, Division of Translational Toxicology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
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13
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Crucitta S, Pasqualetti F, Gonnelli A, Ruglioni M, Luculli GI, Cantarella M, Ortenzi V, Scatena C, Paiar F, Naccarato AG, Danesi R, Del Re M. IDH1 mutation is detectable in plasma cell-free DNA and is associated with survival outcome in glioma patients. BMC Cancer 2024; 24:31. [PMID: 38172718 PMCID: PMC10763009 DOI: 10.1186/s12885-023-11726-0] [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: 11/02/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Circulating cell-free DNA (cfDNA, liquid biopsy) is a powerful tool to detect molecular alterations. However, depending on tumor characteristics, biology and anatomic localization, cfDNA detection and analysis may be challenging. Gliomas are enclosed into an anatomic sanctuary, which obstacles the release of cfDNA into the peripheral blood. Therefore, the advantages of using liquid biopsy for brain tumors is still to be confirmed. The present study evaluates the ability of liquid biopsy to detect IDH1 mutations and its correlation with survival and clinical characteristics of glioma patients. METHODS Blood samples obtained from glioma patients were collected after surgery prior to the adjuvant therapy. cfDNA was extracted from plasma and IDH1 p.R132H mutation analysis was performed on a digital droplet PCR. χ2-test and Cohen k were used to assess the correlation between plasma and tissue IDH1 status, while Kaplan Meier curve and Cox regression analysis were applied to survival analysis. Statistical calculations were performed by MedCalc and GraphPad Prism software. RESULTS A total of 67 samples were collected. A concordance between IDH1 status in tissue and in plasma was found (p = 0.0024), and the presence of the IDH1 mutation both in tissue (138.8 months vs 24.4, p < 0.0001) and cfDNA (116.3 months vs 35.8, p = 0.016) was associated with longer median OS. A significant association between IDH1 mutation both in tissue and cfDNA, age, tumor grade and OS was demonstrated by univariate Cox regression analysis. No statistically significant association between IDH1 mutation and tumor grade was found (p = 0.10). CONCLUSIONS The present study demonstrates that liquid biopsy may be used in brain tumors to detect IDH1 mutation which represents an important prognostic biomarker in patients with different types of gliomas, being associated to OS.
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Affiliation(s)
- Stefania Crucitta
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Francesco Pasqualetti
- Radiation Oncology, Department of Medicine and Oncology, University of Pisa, Pisa, Italy
- Department of Oncology, University of Oxford, Oxford, UK
| | - Alessandra Gonnelli
- Radiation Oncology, Department of Medicine and Oncology, University of Pisa, Pisa, Italy
| | - Martina Ruglioni
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Giovanna Irene Luculli
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Martina Cantarella
- Radiation Oncology, Department of Medicine and Oncology, University of Pisa, Pisa, Italy
| | - Valerio Ortenzi
- Division of Pathology, Department of Translational Research & New Technologies in Medicine & Surgery, University of Pisa, Pisa, Italy
| | - Cristian Scatena
- Division of Pathology, Department of Translational Research & New Technologies in Medicine & Surgery, University of Pisa, Pisa, Italy
| | - Fabiola Paiar
- Radiation Oncology, Department of Medicine and Oncology, University of Pisa, Pisa, Italy
| | - Antonio Giuseppe Naccarato
- Division of Pathology, Department of Translational Research & New Technologies in Medicine & Surgery, University of Pisa, Pisa, Italy
| | - Romano Danesi
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy.
- Department of Oncology and Hemato-Oncology, University of Milano, Via Festa del Perdono, 7, Milano, 20122, Italy.
| | - Marzia Del Re
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
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14
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Jones JJ, Nguyen H, Wong SQ, Whittle J, Iaria J, Stylli S, Towner J, Pieters T, Gaillard F, Kaye AH, Drummond KJ, Morokoff AP. Plasma ctDNA liquid biopsy of IDH1, TERTp, and EGFRvIII mutations in glioma. Neurooncol Adv 2024; 6:vdae027. [PMID: 38572065 PMCID: PMC10989869 DOI: 10.1093/noajnl/vdae027] [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] [Indexed: 04/05/2024] Open
Abstract
Background Circulating tumor DNA has emerging clinical applications in several cancers; however, previous studies have shown low sensitivity in glioma. We investigated if 3 key glioma gene mutations IDH1, TERTp, and EGFRvIII could be reliably detected in plasma by droplet digital polymerase chain reaction (ddPCR) thereby demonstrating the potential of this technique for glioma liquid biopsy. Methods We analyzed 110 glioma patients from our biobank with a total of 359 plasma samples (median 4 samples per patient). DNA was isolated from plasma and analyzed for IDH1, TERTp, and EGFRvIII mutations using ddPCR. Results Total cfDNA was significantly associated with tumor grade, tumor volume, and both overall and progression-free survival for all gliomas as well as the grade 4 glioblastoma subgroup, but was not reliably associated with changes in tumor volume/progression during the patients' postoperative time course. IDH1 mutation was detected with 84% overall sensitivity across all plasma samples and 77% in the preoperative samples alone; however, IDH1 mutation plasma levels were not associated with tumor progression or survival. IDH1m plasma levels were not associated with pre- or postsurgery progression or survival. The TERTp C228T mutation was detected in the plasma ctDNA in 88% but the C250T variant in only 49% of samples. The EGFRvIII mutation was detected in plasma in 5 out of 7 patients (71%) with tissue EGFRvIII mutations in tumor tissue. Conclusions Plasma ctDNA mutations detected with ddPCR provide excellent diagnostic sensitivity for IDH1, TERTp-C228T, and EGFRvIII mutations in glioma patients. Total cfDNA may also assist with prognostic information. Further studies are needed to validate these findings and the clinical role of ctDNA in glioma.
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Affiliation(s)
- Jordan J Jones
- Department of Surgery, University of Melbourne, Victoria, Australia
- Department of Neurosurgery, Royal Melbourne Hospital, Victoria, Australia
| | - Hong Nguyen
- Department of Surgery, University of Melbourne, Victoria, Australia
| | | | | | - Josie Iaria
- Department of Surgery, University of Melbourne, Victoria, Australia
| | - Stanley Stylli
- Department of Surgery, University of Melbourne, Victoria, Australia
| | - James Towner
- Department of Neurosurgery, Royal Melbourne Hospital, Victoria, Australia
| | - Thomas Pieters
- Department of Neurosurgery, Royal Melbourne Hospital, Victoria, Australia
| | - Frank Gaillard
- Department of Radiology, University of Melbourne, Victoria, Australia
| | - Andrew H Kaye
- Department of Surgery, University of Melbourne, Victoria, Australia
- Department of Neurosurgery, Royal Melbourne Hospital, Victoria, Australia
| | - Katharine J Drummond
- Department of Surgery, University of Melbourne, Victoria, Australia
- Department of Neurosurgery, Royal Melbourne Hospital, Victoria, Australia
| | - Andrew P Morokoff
- Department of Surgery, University of Melbourne, Victoria, Australia
- Department of Neurosurgery, Royal Melbourne Hospital, Victoria, Australia
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15
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Robinson SD, de Boisanger J, Pearl FMG, Critchley G, Rosenfelder N, Giamas G. A brain metastasis liquid biopsy: Where are we now? Neurooncol Adv 2024; 6:vdae066. [PMID: 38770219 PMCID: PMC11102938 DOI: 10.1093/noajnl/vdae066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024] Open
Abstract
Brain metastases remain a challenging and feared complication for patients with cancer and research in this area has lagged behind research into metastases to other organs. Due to their location and the risks associated with neurosurgical biopsies, the biology underpinning brain metastases response to treatment and evolution over time remains poorly understood. Liquid biopsies are proposed to overcome many of the limitations present with tissue biopsies, providing a better representation of tumor heterogeneity, facilitating repeated sampling, and providing a noninvasive assessment of tumor biology. Several different liquid biopsy approaches have been investigated including circulating tumor cells, circulating tumor DNA, extracellular vesicles, and tumor-educated platelets; however, these have generally been less effective in assessing brain metastases compared to metastases to other organs requiring improved techniques to investigate these approaches, studies combining different liquid biopsy approaches and/or novel liquid biopsy approaches. Through this review, we highlight the current state of the art and define key unanswered questions related to brain metastases liquid biopsies.
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Affiliation(s)
- Stephen David Robinson
- Sussex Cancer Centre, University Hospitals Sussex NHS Foundation Trust, Brighton, UK
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - James de Boisanger
- Neuro-Oncology Unit, The Royal Marsden Hospital NHS Foundation Trust, London, UK
| | - Frances M G Pearl
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Giles Critchley
- Department of Neurosurgery, University Hospitals Sussex NHS Foundation Trust, Brighton, UK
- Section of Neurosurgery, Department of Surgical Sciences, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Nicola Rosenfelder
- Neuro-Oncology Unit, The Royal Marsden Hospital NHS Foundation Trust, London, UK
| | - Georgios Giamas
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
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16
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Foster JB, Koptyra MP, Bagley SJ. Recent Developments in Blood Biomarkers in Neuro-oncology. Curr Neurol Neurosci Rep 2023; 23:857-867. [PMID: 37943477 DOI: 10.1007/s11910-023-01321-y] [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] [Accepted: 10/31/2023] [Indexed: 11/10/2023]
Abstract
PURPOSE OF REVIEW Given the invasive and high-risk nature of brain surgery, the need for non-invasive biomarkers obtained from the peripheral blood is greatest in tumors of the central nervous system (CNS). In this comprehensive review, we highlight recent advances in blood biomarker development for adult and pediatric brain tumors. RECENT FINDINGS We summarize recent blood biomarker development for CNS tumors across multiple key analytes, including peripheral blood mononuclear cells, cell-free DNA, cell-free RNA, proteomics, circulating tumor cells, and tumor-educated platelets. We also discuss methods for enhancing blood biomarker detection through transient opening of the blood-brain barrier. Although blood-based biomarkers are not yet used in routine neuro-oncology practice, this field is advancing rapidly and holds great promise for improved and non-invasive management of patients with brain tumors. Prospective and adequately powered studies are needed to confirm the clinical utility of any blood biomarker prior to widespread clinical implementation.
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Affiliation(s)
- Jessica B Foster
- Division of Oncology, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mateusz P Koptyra
- Center for Data-Driven Discovery in Biomedicine (D3b), Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Stephen J Bagley
- Division of Hematology/Oncology, Hospital of the University of Pennsylvania, Perelman School of Medicine, University of Pennsylvania, 10th Floor Perelman Center, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA.
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17
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Trivedi R, Bhat KP. Liquid biopsy: creating opportunities in brain space. Br J Cancer 2023; 129:1727-1746. [PMID: 37752289 PMCID: PMC10667495 DOI: 10.1038/s41416-023-02446-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 09/10/2023] [Accepted: 09/15/2023] [Indexed: 09/28/2023] Open
Abstract
In recent years, liquid biopsy has emerged as an alternative method to diagnose and monitor tumors. Compared to classical tissue biopsy procedures, liquid biopsy facilitates the repetitive collection of diverse cellular and acellular analytes from various biofluids in a non/minimally invasive manner. This strategy is of greater significance for high-grade brain malignancies such as glioblastoma as the quantity and accessibility of tumors are limited, and there are collateral risks of compromised life quality coupled with surgical interventions. Currently, blood and cerebrospinal fluid (CSF) are the most common biofluids used to collect circulating cells and biomolecules of tumor origin. These liquid biopsy analytes have created opportunities for real-time investigations of distinct genetic, epigenetic, transcriptomics, proteomics, and metabolomics alterations associated with brain tumors. This review describes different classes of liquid biopsy biomarkers present in the biofluids of brain tumor patients. Moreover, an overview of the liquid biopsy applications, challenges, recent technological advances, and clinical trials in the brain have also been provided.
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Affiliation(s)
- Rakesh Trivedi
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Krishna P Bhat
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
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18
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Grebstad Tune B, Sareen H, Powter B, Kahana-Edwin S, Cooper A, Koh ES, Lee CS, Po JW, McCowage G, Dexter M, Cain L, O'Neill G, Prior V, Karpelowsky J, Tsoli M, Baumbusch LO, Ziegler D, Roberts TL, DeSouza P, Becker TM, Ma Y. From Pediatric to Adult Brain Cancer: Exploring Histone H3 Mutations in Australian Brain Cancer Patients. Biomedicines 2023; 11:2907. [PMID: 38001908 PMCID: PMC10669073 DOI: 10.3390/biomedicines11112907] [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: 09/29/2023] [Revised: 10/14/2023] [Accepted: 10/19/2023] [Indexed: 11/26/2023] Open
Abstract
Genetic histone variants have been implicated in cancer development and progression. Mutations affecting the histone 3 (H3) family, H3.1 (encoded by HIST1H3B and HIST1H3C) and H3.3 (encoded by H3F3A), are mainly associated with pediatric brain cancers. While considered poor prognostic brain cancer biomarkers in children, more recent studies have reported H3 alterations in adult brain cancer as well. Here, we established reliable droplet digital PCR based assays to detect three histone mutations (H3.3-K27M, H3.3-G34R, and H3.1-K27M) primarily linked to childhood brain cancer. We demonstrate the utility of our assays for sensitively detecting these mutations in cell-free DNA released from cultured diffuse intrinsic pontine glioma (DIPG) cells and in the cerebral spinal fluid of a pediatric patient with DIPG. We further screened tumor tissue DNA from 89 adult patients with glioma and 1 with diffuse hemispheric glioma from Southwestern Sydney, Australia, an ethnically diverse region, for these three mutations. No histone mutations were detected in adult glioma tissue, while H3.3-G34R presence was confirmed in the diffuse hemispheric glioma patient.
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Affiliation(s)
- Benedicte Grebstad Tune
- Department of Pediatric Research, Division of Paediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, 0372 Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St, Liverpool, NSW 2170, Australia
| | - Heena Sareen
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St, Liverpool, NSW 2170, Australia
- South Western Sydney Clinical School, University of New South Wales, Goulburn St, Liverpool, NSW 2170, Australia
| | - Branka Powter
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St, Liverpool, NSW 2170, Australia
| | - Smadar Kahana-Edwin
- Children's Cancer Research Unit, Kids Research, The Children's Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Adam Cooper
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St, Liverpool, NSW 2170, Australia
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia
| | - Eng-Siew Koh
- South Western Sydney Clinical School, University of New South Wales, Goulburn St, Liverpool, NSW 2170, Australia
- Department of Radiation Oncology, Liverpool Hospital, Liverpool, NSW 2170, Australia
| | - Cheok S Lee
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia
- Department of Radiation Oncology, Liverpool Hospital, Liverpool, NSW 2170, Australia
| | - Joseph W Po
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St, Liverpool, NSW 2170, Australia
| | - Geoff McCowage
- Cancer Centre for Children, The Children Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Mark Dexter
- Neurosurgery, The Children Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Lucy Cain
- Cancer Centre for Children, The Children Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Geraldine O'Neill
- Children's Cancer Research Unit, Kids Research, The Children's Hospital at Westmead, Westmead, NSW 2145, Australia
- The University of Sydney Children's Hospital Westmead Clinical School, Faculty of Medicine & Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Victoria Prior
- Children's Cancer Research Unit, Kids Research, The Children's Hospital at Westmead, Westmead, NSW 2145, Australia
- The University of Sydney Children's Hospital Westmead Clinical School, Faculty of Medicine & Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Jonathan Karpelowsky
- Children's Cancer Research Unit, Kids Research, The Children's Hospital at Westmead, Westmead, NSW 2145, Australia
- Paediatric Oncology and Thoracic Surgery, The Children's Hospital at Westmead, Westmead, NSW 2145, Australia
- Division of Child and Adolescent Health, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Maria Tsoli
- Children's Cancer Institute, Randwick, NSW 2031, Australia
| | - Lars O Baumbusch
- Department of Pediatric Research, Division of Paediatric and Adolescent Medicine, Oslo University Hospital Rikshospitalet, 0372 Oslo, Norway
- Faculty of Health, Welfare and Organization, Østfold University College, 1757 Halden, Norway
| | - David Ziegler
- Children's Cancer Institute, Randwick, NSW 2031, Australia
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW 2052, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Kensington, NSW 2052, Australia
| | - Tara L Roberts
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St, Liverpool, NSW 2170, Australia
- South Western Sydney Clinical School, University of New South Wales, Goulburn St, Liverpool, NSW 2170, Australia
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia
| | - Paul DeSouza
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St, Liverpool, NSW 2170, Australia
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia
| | - Therese M Becker
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St, Liverpool, NSW 2170, Australia
- South Western Sydney Clinical School, University of New South Wales, Goulburn St, Liverpool, NSW 2170, Australia
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia
| | - Yafeng Ma
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St, Liverpool, NSW 2170, Australia
- South Western Sydney Clinical School, University of New South Wales, Goulburn St, Liverpool, NSW 2170, Australia
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia
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19
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Penkova A, Kuziakova O, Gulaia V, Tiasto V, Goncharov NV, Lanskikh D, Zhmenia V, Baklanov I, Farniev V, Kumeiko V. Comprehensive clinical assays for molecular diagnostics of gliomas: the current state and future prospects. Front Mol Biosci 2023; 10:1216102. [PMID: 37908227 PMCID: PMC10613994 DOI: 10.3389/fmolb.2023.1216102] [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: 06/08/2023] [Accepted: 09/04/2023] [Indexed: 11/02/2023] Open
Abstract
Glioma is one of the most intractable types of cancer, due to delayed diagnosis at advanced stages. The clinical symptoms of glioma are unclear and due to a variety of glioma subtypes, available low-invasive testing is not effective enough to be introduced into routine medical laboratory practice. Therefore, recent advances in the clinical diagnosis of glioma have focused on liquid biopsy approaches that utilize a wide range of techniques such as next-generation sequencing (NGS), droplet-digital polymerase chain reaction (ddPCR), and quantitative PCR (qPCR). Among all techniques, NGS is the most advantageous diagnostic method. Despite the rapid cheapening of NGS experiments, the cost of such diagnostics remains high. Moreover, high-throughput diagnostics are not appropriate for molecular profiling of gliomas since patients with gliomas exhibit only a few diagnostic markers. In this review, we highlighted all available assays for glioma diagnosing for main pathogenic glioma DNA sequence alterations. In the present study, we reviewed the possibility of integrating routine molecular methods into the diagnosis of gliomas. We state that the development of an affordable assay covering all glioma genetic aberrations could enable early detection and improve patient outcomes. Moreover, the development of such molecular diagnostic kits could potentially be a good alternative to expensive NGS-based approaches.
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Affiliation(s)
- Alina Penkova
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Olga Kuziakova
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Valeriia Gulaia
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Vladlena Tiasto
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Nikolay V. Goncharov
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
- A. V. Zhirmunsky National Scientific Center of Marine Biology, FEB RAS, Vladivostok, Russia
| | - Daria Lanskikh
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Valeriia Zhmenia
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Ivan Baklanov
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
- A. V. Zhirmunsky National Scientific Center of Marine Biology, FEB RAS, Vladivostok, Russia
| | - Vladislav Farniev
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Vadim Kumeiko
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
- A. V. Zhirmunsky National Scientific Center of Marine Biology, FEB RAS, Vladivostok, Russia
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20
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Berzero G, Pieri V, Mortini P, Filippi M, Finocchiaro G. The coming of age of liquid biopsy in neuro-oncology. Brain 2023; 146:4015-4024. [PMID: 37289981 PMCID: PMC10545511 DOI: 10.1093/brain/awad195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 04/05/2023] [Accepted: 05/16/2023] [Indexed: 06/10/2023] Open
Abstract
The clinical role of liquid biopsy in oncology is growing significantly. In gliomas and other brain tumours, targeted sequencing of cell-free DNA (cfDNA) from CSF may help differential diagnosis when surgery is not recommended and be more representative of tumour heterogeneity than surgical specimens, unveiling targetable genetic alterations. Given the invasive nature of lumbar puncture to obtain CSF, the quantitative analysis of cfDNA in plasma is a lively option for patient follow-up. Confounding factors may be represented by cfDNA variations due to concomitant pathologies (inflammatory diseases, seizures) or clonal haematopoiesis. Pilot studies suggest that methylome analysis of cfDNA from plasma and temporary opening of the blood-brain barrier by ultrasound have the potential to overcome some of these limitations. Together with this, an increased understanding of mechanisms modulating the shedding of cfDNA by the tumour may help to decrypt the meaning of cfDNA kinetics in blood or CSF.
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Affiliation(s)
- Giulia Berzero
- Neurology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Valentina Pieri
- Neurology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Pietro Mortini
- Vita-Salute San Raffaele University, 20132 Milan, Italy
- Department of Neurosurgery and Gamma Knife Radiosurgery, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Massimo Filippi
- Neurology Unit, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- Vita-Salute San Raffaele University, 20132 Milan, Italy
- Neurorehabilitation Unit; Neurophysiology Unit; Neuroimaging Research Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
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21
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Yuan J, Xu L, Chien CY, Yang Y, Yue Y, Fadera S, Stark AH, Schwetye KE, Nazeri A, Desai R, Athiraman U, Chaudhuri AA, Chen H, Leuthardt EC. First-in-human prospective trial of sonobiopsy in high-grade glioma patients using neuronavigation-guided focused ultrasound. NPJ Precis Oncol 2023; 7:92. [PMID: 37717084 PMCID: PMC10505140 DOI: 10.1038/s41698-023-00448-y] [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: 03/20/2023] [Accepted: 09/05/2023] [Indexed: 09/18/2023] Open
Abstract
Sonobiopsy is an emerging technology that combines focused ultrasound (FUS) with microbubbles to enrich circulating brain disease-specific biomarkers for noninvasive molecular diagnosis of brain diseases. Here, we report the first-in-human prospective trial of sonobiopsy in high-grade glioma patients to evaluate its feasibility and safety in enriching plasma circulating tumor biomarkers. A nimble FUS device integrated with a clinical neuronavigation system was used to perform sonobiopsy following an established clinical workflow for neuronavigation. Analysis of blood samples collected before and after FUS sonication showed that sonobiopsy enriched plasma circulating tumor DNA (ctDNA), including a maximum increase of 1.6-fold for the mononucleosome cell-free DNA (cfDNA) fragments (120-280 bp), 1.9-fold for the patient-specific tumor variant ctDNA level, and 5.6-fold for the TERT mutation ctDNA level. Histological analysis of surgically resected tumors confirmed the safety of the procedure. Transcriptome analysis of sonicated and nonsonicated tumor tissues found that FUS sonication modulated cell physical structure-related genes. Only 2 out of 17,982 total detected genes related to the immune pathways were upregulated. These feasibility and safety data support the continued investigation of sonobiopsy for noninvasive molecular diagnosis of brain diseases.
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Affiliation(s)
- Jinyun Yuan
- Department of Biomedical Engineering, Washington University in St. Louis, Saint Louis, MO, 63130, USA
| | - Lu Xu
- Department of Biomedical Engineering, Washington University in St. Louis, Saint Louis, MO, 63130, USA
| | - Chih-Yen Chien
- Department of Biomedical Engineering, Washington University in St. Louis, Saint Louis, MO, 63130, USA
| | - Yaoheng Yang
- Department of Biomedical Engineering, Washington University in St. Louis, Saint Louis, MO, 63130, USA
| | - Yimei Yue
- Department of Biomedical Engineering, Washington University in St. Louis, Saint Louis, MO, 63130, USA
| | - Siaka Fadera
- Department of Biomedical Engineering, Washington University in St. Louis, Saint Louis, MO, 63130, USA
| | - Andrew H Stark
- Department of Biomedical Engineering, Washington University in St. Louis, Saint Louis, MO, 63130, USA
| | - Katherine E Schwetye
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Arash Nazeri
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Rupen Desai
- Department of Neurosurgery, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Umeshkumar Athiraman
- Department of Anesthesia, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Aadel A Chaudhuri
- Department of Biomedical Engineering, Washington University in St. Louis, Saint Louis, MO, 63130, USA
- Department of Radiation Oncology, Washington University School of Medicine, Saint Louis, MO, 63108, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Computer Science and Engineering, Washington University in St. Louis, Saint Louis, MO, 63130, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Hong Chen
- Department of Biomedical Engineering, Washington University in St. Louis, Saint Louis, MO, 63130, USA.
- Department of Neurosurgery, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Division of Neurotechnology, Department of Neurosurgery, Washington University School of Medicine, Saint Louis, MO, 63110, USA.
| | - Eric C Leuthardt
- Department of Biomedical Engineering, Washington University in St. Louis, Saint Louis, MO, 63130, USA.
- Department of Neurosurgery, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Division of Neurotechnology, Department of Neurosurgery, Washington University School of Medicine, Saint Louis, MO, 63110, USA.
- Department of Neuroscience, Washington University School of Medicine, Saint Louis, MO, 63110, USA.
- Center for Innovation in Neuroscience and Technology, Washington University School of Medicine, Saint Louis, MO, 63110, USA.
- Department of Mechanical Engineering and Materials Science, Washington University in St. Louis, Saint Louis, MO, 63130, USA.
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22
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Skouras P, Markouli M, Kalamatianos T, Stranjalis G, Korkolopoulou P, Piperi C. Advances on Liquid Biopsy Analysis for Glioma Diagnosis. Biomedicines 2023; 11:2371. [PMID: 37760812 PMCID: PMC10525418 DOI: 10.3390/biomedicines11092371] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/16/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
Gliomas comprise the most frequent primary central nervous system (CNS) tumors, characterized by remarkable genetic and epigenetic heterogeneity, difficulty in monitoring, and increased relapse and mortality rates. Tissue biopsy is an established method of tumor cell collection and analysis that enables diagnosis, classification of different tumor types, and prediction of prognosis upon confirmation of tumor's location for surgical removal. However, it is an invasive and often challenging procedure that cannot be used for frequent patient screening, detection of mutations, disease monitoring, or resistance to therapy. To this end, the minimally invasive procedure of liquid biopsy has emerged, allowing effortless tumor sampling and enabling continuous monitoring. It is considered a novel preferable way to obtain faster data on potential tumor risk, personalized diagnosis, prognosis, and recurrence evaluation. The purpose of this review is to describe the advances on liquid biopsy for glioma diagnosis and management, indicating several biomarkers that can be utilized to analyze tumor characteristics, such as cell-free DNA (cfDNA), cell-free RNA (cfRNA), circulating proteins, circulating tumor cells (CTCs), and exosomes. It further addresses the benefit of combining liquid biopsy with radiogenomics to facilitate early and accurate diagnoses, enable precise prognostic assessments, and facilitate real-time disease monitoring, aiming towards more optimal treatment decisions.
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Affiliation(s)
- Panagiotis Skouras
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece;
- 1st Department of Neurosurgery, Evangelismos Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece; (T.K.); (G.S.)
| | - Mariam Markouli
- Department of Medicine, Boston Medical Center, Boston University School of Medicine, Boston, MA 02118, USA;
| | - Theodosis Kalamatianos
- 1st Department of Neurosurgery, Evangelismos Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece; (T.K.); (G.S.)
| | - George Stranjalis
- 1st Department of Neurosurgery, Evangelismos Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece; (T.K.); (G.S.)
| | - Penelope Korkolopoulou
- Department of Pathology, Medical School, National and Kapodistrian University of Athens, 75 M. Asias Street, 11527 Athens, Greece;
| | - Christina Piperi
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece;
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23
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Lin F, Huang J, Zhu W, Jiang T, Guo J, Xia W, Chen M, Guo L, Deng W, Lin H. Prognostic value and immune landscapes of TERT promoter methylation in triple negative breast cancer. Front Immunol 2023; 14:1218987. [PMID: 37575241 PMCID: PMC10416624 DOI: 10.3389/fimmu.2023.1218987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 07/14/2023] [Indexed: 08/15/2023] Open
Abstract
Background Treatment options for patients with triple-negative breast cancer (TNBC) remain limited to mainstay therapies owing to a lack of efficacious therapeutic targets. Accordingly, there is an urgent need to discover and identify novel molecular targets for the treatment and diagnosis of this disease. In this study, we analyzed the correlation of telomerase reverse transcriptase (TERT) methylation status with TERT expression, prognosis, and immune infiltration in TNBC and identified the role of TERT methylation in the regulation TNBC prognosis and immunotherapy. Methods Data relating to the transcriptome, clinicopathological characteristics and methylation of TNBC patients were obtained from The Cancer Genome Atlas (TCGA) database. TERT expression levels and differential methylation sites (DMSs) were detected. The correlations between TERT expression and DMSs were calculated. Kaplan-Meier curves was plotted to analyze the relationship between the survival of TNBC patients and the DMSs. The correlations of DMSs and TERT expression with several immunological characteristics of immune microenvironment (immune cell infiltration, immunomodulators, immune-related biological pathways, and immune checkpoints) were assessed. The results were validated using 40 TNBC patients from Sun Yat-sen University Cancer Center (SYSUCC). Results Six DMSs were identified. Among them, four sites (cg11625005, cg07380026, cg17166338, and cg26006951) were within the TERT promoter, in which two sites (cg07380026 and cg26006951) were significantly related to the prognosis of patients with TNBC. Further validation using 40 TNBC samples from SYSUCC showed that the high methylation of the cg26006951 CpG site was associated with poor survival prognosis (P=0.0022). TERT expression was significantly correlated with pathological N stage and clinical stage, and cg07380026 were significantly associated with pathological T and N stages in the TCGA cohort. Moreover, the methylation site cg26006951, cg07380026 and TERT expression were significantly correlated with immune cell infiltration, common immunomodulators, and the level of the immune checkpoint receptor lymphocyte activation gene 3 (LAG-3) in TNBC patients. Conclusion TERT promotertypermethylation plays an important role in TERT expression regulation and tumor microenvironment in TNBC. It is associated with overall survival and LAG-3 expression. TERT promoter hypermethylation may be a potential molecular biomarker for predicting response to the TERT inhibitors and immune checkpoint inhibitors in TNBC.
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Affiliation(s)
| | | | | | | | | | | | | | - Ling Guo
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wuguo Deng
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Huanxin Lin
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, China
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24
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Wu Y, Wang X, Zhang M, Wu D. Molecular Biomarkers and Recent Liquid Biopsy Testing Progress: A Review of the Application of Biosensors for the Diagnosis of Gliomas. Molecules 2023; 28:5660. [PMID: 37570630 PMCID: PMC10419986 DOI: 10.3390/molecules28155660] [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: 05/25/2023] [Revised: 07/19/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023] Open
Abstract
Gliomas are the most common primary central nervous system tumors, with a high mortality rate. Early and accurate diagnosis of gliomas is critical for successful treatment. Biosensors are significant in the detection of molecular biomarkers because they are simple to use, portable, and capable of real-time analysis. This review discusses several important molecular biomarkers as well as various biosensors designed for glioma diagnosis, such as electrochemical biosensors and optical biosensors. We present our perspectives on the existing challenges and hope that this review can promote the improvement of biosensors.
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Affiliation(s)
- Yuanbin Wu
- Department of Emergency Medicine, The Seventh Medical Center, Chinese PLA General Hospital, Beijing 100700, China;
| | - Xuning Wang
- Department of General Surgery, The Air Force Hospital of Northern Theater PLA, Shenyang 110042, China
| | - Meng Zhang
- Department of Neurosurgery, The Second Hospital of Southern Theater of Chinese Navy, Sanya 572000, China
| | - Dongdong Wu
- Department of Neurosurgery, The First Medical Centre, Chinese PLA General Hospital, Beijing 100853, China
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25
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Bhargav AG, Domino JS, Alvarado AM, Tuchek CA, Akhavan D, Camarata PJ. Advances in computational and translational approaches for malignant glioma. Front Physiol 2023; 14:1219291. [PMID: 37405133 PMCID: PMC10315500 DOI: 10.3389/fphys.2023.1219291] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 06/05/2023] [Indexed: 07/06/2023] Open
Abstract
Gliomas are the most common primary brain tumors in adults and carry a dismal prognosis for patients. Current standard-of-care for gliomas is comprised of maximal safe surgical resection following by a combination of chemotherapy and radiation therapy depending on the grade and type of tumor. Despite decades of research efforts directed towards identifying effective therapies, curative treatments have been largely elusive in the majority of cases. The development and refinement of novel methodologies over recent years that integrate computational techniques with translational paradigms have begun to shed light on features of glioma, previously difficult to study. These methodologies have enabled a number of point-of-care approaches that can provide real-time, patient-specific and tumor-specific diagnostics that may guide the selection and development of therapies including decision-making surrounding surgical resection. Novel methodologies have also demonstrated utility in characterizing glioma-brain network dynamics and in turn early investigations into glioma plasticity and influence on surgical planning at a systems level. Similarly, application of such techniques in the laboratory setting have enhanced the ability to accurately model glioma disease processes and interrogate mechanisms of resistance to therapy. In this review, we highlight representative trends in the integration of computational methodologies including artificial intelligence and modeling with translational approaches in the study and treatment of malignant gliomas both at the point-of-care and outside the operative theater in silico as well as in the laboratory setting.
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Affiliation(s)
- Adip G. Bhargav
- Department of Neurological Surgery, University of Kansas Medical Center, Kansas City, KS, United States
| | - Joseph S. Domino
- Department of Neurological Surgery, University of Kansas Medical Center, Kansas City, KS, United States
| | - Anthony M. Alvarado
- Department of Neurological Surgery, Rush University Medical Center, Chicago, IL, United States
| | - Chad A. Tuchek
- Department of Neurological Surgery, University of Kansas Medical Center, Kansas City, KS, United States
| | - David Akhavan
- Department of Radiation Oncology, University of Kansas Medical Center, Kansas City, KS, United States
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, United States
- Bioengineering Program, University of Kansas Medical Center, Kansas City, KS, United States
| | - Paul J. Camarata
- Department of Neurological Surgery, University of Kansas Medical Center, Kansas City, KS, United States
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Yuan J, Xu L, Chien CY, Yang Y, Yue Y, Fadera S, Stark AH, Schwetye KE, Nazeri A, Desai R, Athiraman U, Chaudhuri AA, Chen H, Leuthardt EC. First-in-human prospective trial of sonobiopsy in glioblastoma patients using neuronavigation-guided focused ultrasound. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.17.23287378. [PMID: 36993173 PMCID: PMC10055591 DOI: 10.1101/2023.03.17.23287378] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Sonobiopsy is an emerging technology that combines focused ultrasound (FUS) with microbubbles to enrich circulating brain disease-specific biomarkers for noninvasive molecular diagnosis of brain diseases. Here, we report the first-in-human prospective trial of sonobiopsy in glioblastoma patients to evaluate its feasibility and safety in enriching circulating tumor biomarkers. A nimble FUS device integrated with a clinical neuronavigation system was used to perform sonobiopsy following an established clinical workflow for neuronavigation. Analysis of blood samples collected before and after FUS sonication showed enhanced plasma circulating tumor biomarker levels. Histological analysis of surgically resected tumors confirmed the safety of the procedure. Transcriptome analysis of sonicated and unsonicated tumor tissues found that FUS sonication modulated cell physical structure-related genes but evoked minimal inflammatory response. These feasibility and safety data support the continued investigation of sonobiopsy for noninvasive molecular diagnosis of brain diseases.
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Otsuji R, Fujioka Y, Hata N, Kuga D, Sangatsuda Y, Takigawa K, Funakoshi Y, Sako A, Yamamoto H, Nakamizo A, Mizoguchi M, Yoshimoto K. Liquid biopsy with multiplex ligation-dependent probe amplification targeting cell-free tumor DNA in cerebrospinal fluid from patients with adult diffuse glioma. Neurooncol Adv 2023; 5:vdac178. [PMID: 36875626 PMCID: PMC9977236 DOI: 10.1093/noajnl/vdac178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Background Copy number alterations (CNAs) are common in diffuse gliomas and have been shown to have diagnostic significance. While liquid biopsy for diffuse glioma has been widely investigated, techniques for detecting CNAs are currently limited to methods such as next-generation sequencing. Multiplex ligation-dependent probe amplification (MLPA) is an established method for copy number analysis in pre-specified loci. In this study, we investigated whether CNAs could be detected by MLPA using patients' cerebrospinal fluid (CSF). Methods Twenty-five cases of adult diffuse glioma with CNAs were selected. Cell-free DNA (cfDNA) was extracted from the CSF, and DNA sizes and concentrations were recorded. Twelve samples, which had appropriate DNA sizes and concentrations, were subsequently used for analysis. Results MLPA could be successfully performed in all 12 cases, and the detected CNAs were concordant with those detected using tumor tissues. Cases with epidermal growth factor receptor (EGFR) amplification, combination of gain of chromosome 7 and loss of chromosome 10, platelet-derived growth factor receptor alpha amplification, cyclin-dependent kinase 4 amplification, and cyclin-dependent kinase inhibitor 2A (CDKN2A) homozygous deletion were clearly distinguished from those with normal copy numbers. Moreover, EGFR variant III was accurately detected based on CNA. Conclusions Thus, our results demonstrate that copy number analysis can be successfully performed by MLPA of cfDNA extracted from the CSF of patients with diffuse glioma.
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Affiliation(s)
- Ryosuke Otsuji
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yutaka Fujioka
- Corresponding Author: Yutaka Fujioka, Department of Neurosurgery, Graduate School of Medical Science, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan ()
| | - Nobuhiro Hata
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Daisuke Kuga
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yuhei Sangatsuda
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kosuke Takigawa
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yusuke Funakoshi
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Aki Sako
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Hidetaka Yamamoto
- Department of Pathology, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Akira Nakamizo
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Masahiro Mizoguchi
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Koji Yoshimoto
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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Bauman MM, Bouchal SM, Monie DD, Aibaidula A(Z, Singh R, Parney IF. Strategies, considerations, and recent advancements in the development of liquid biopsy for glioblastoma: a step towards individualized medicine in glioblastoma. Neurosurg Focus 2022; 53:E14. [PMID: 36455271 PMCID: PMC9879623 DOI: 10.3171/2022.9.focus22430] [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: 07/31/2022] [Accepted: 09/19/2022] [Indexed: 12/03/2022]
Abstract
OBJECTIVE Glioblastoma (GBM) is a devasting primary brain tumor with less than a 5% 5-year survival. Treatment response assessment can be challenging because of inflammatory pseudoprogression that mimics true tumor progression clinically and on imaging. Developing additional noninvasive assays is critical. In this article, the authors review various biomarkers that could be used in developing liquid biopsies for GBM, along with strengths, limitations, and future applications. In addition, they present a potential liquid biopsy design based on the use of an extracellular vesicle-based liquid biopsy targeting nonneoplastic extracellular vesicles. METHODS The authors conducted a current literature review of liquid biopsy in GBM by searching the PubMed, Scopus, and Google Scholar databases. Articles were assessed for type of biomarker, isolation methodology, analytical techniques, and clinical relevance. RESULTS Recent work has shown that liquid biopsies of plasma, blood, and/or CSF hold promise as noninvasive clinical tools that can be used to diagnose recurrence, assess treatment response, and predict patient outcomes in GBM. Liquid biopsy in GBM has focused primarily on extracellular vesicles, cell-free tumor nucleic acids, and whole-cell isolates as focal biomarkers. GBM tumor signatures have been generated via analysis of tumor gene mutations, unique RNA expression, and metabolic and proteomic alterations. Liquid biopsies capture tumor heterogeneity, identifying alterations in GBM tumors that may be undetectable via surgical biopsy specimens. Finally, biomarker burden can be used to assess treatment response and recurrence in GBM. CONCLUSIONS Liquid biopsy offers a promising avenue for monitoring treatment response and recurrence in GBM without invasive procedures. Although additional steps must be taken to bring liquid biopsy into the clinic, proof-of-principle studies and isolation methodologies are promising. Ultimately, CSF and/or plasma-based liquid biopsy is likely to be a powerful tool in the neurosurgeon's arsenal in the near future for the treatment and management of GBM patients.
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Affiliation(s)
- Megan M.J. Bauman
- Mayo Clinic Alix School of Medicine, Rochester, Minnesota, USA,Department of Neurological Surgery, Rochester, Minnesota, USA
| | - Samantha M. Bouchal
- Mayo Clinic Alix School of Medicine, Rochester, Minnesota, USA,Department of Neurological Surgery, Rochester, Minnesota, USA
| | - Dileep D. Monie
- Mayo Clinic Alix School of Medicine, Rochester, Minnesota, USA,Department of Neurological Surgery, Rochester, Minnesota, USA
| | - Abudumijiti (Zack) Aibaidula
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | - Rohin Singh
- Mayo Clinic Alix School of Medicine, Phoenix, Arizona, USA
| | - Ian F. Parney
- Department of Neurological Surgery, Rochester, Minnesota, USA
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Stankunaite R, Marshall LV, Carceller F, Chesler L, Hubank M, George SL. Liquid biopsy for children with central nervous system tumours: Clinical integration and technical considerations. Front Pediatr 2022; 10:957944. [PMID: 36467471 PMCID: PMC9709284 DOI: 10.3389/fped.2022.957944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 10/28/2022] [Indexed: 11/18/2022] Open
Abstract
Circulating cell-free DNA (cfDNA) analysis has the potential to revolutionise the care of patients with cancer and is already moving towards standard of care in some adult malignancies. Evidence for the utility of cfDNA analysis in paediatric cancer patients is also accumulating. In this review we discuss the limitations of blood-based assays in patients with brain tumours and describe the evidence supporting cerebrospinal fluid (CSF) cfDNA analysis. We make recommendations for CSF cfDNA processing to aid the standardisation and technical validation of future assays. We discuss the considerations for interpretation of cfDNA analysis and highlight promising future directions. Overall, cfDNA profiling shows great potential as an adjunct to the analysis of biopsy tissue in paediatric cancer patients, with the potential to provide a genetic molecular profile of the tumour when tissue biopsy is not feasible. However, to fully realise the potential of cfDNA analysis for children with brain tumours larger prospective studies incorporating serial CSF sampling are required.
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Affiliation(s)
- Reda Stankunaite
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
- Clinical Genomics, Royal Marsden NHS Foundation Trust, London, United Kingdom
- Evolutionary Genomics and Modelling, Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | - Lynley V. Marshall
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
- Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Fernando Carceller
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
- Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Louis Chesler
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
- Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Michael Hubank
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
- Clinical Genomics, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Sally L. George
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
- Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
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Abstract
There have been significant strides toward understanding the molecular landscape of brain cancer. These advances have been focused on analyses of the tumor microenvironment and have recently expanded to include liquid biopsies to identify molecular biomarkers noninvasively. Moving from tissue to liquid-based analyses of molecular biomarkers has been challenging and currently, there are no approved noninvasive tests that are clinically useful. However, the emerging field of molecular liquid biopsy assay development in the neuro-oncology space has great potential to revolutionize the detection and monitoring of patients with brain cancer.
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Affiliation(s)
- Dimitrios Mathios
- Department of Neurosurgery, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine , Baltimore, Maryland , USA
| | - Jillian Phallen
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine , Baltimore, Maryland , USA
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Batool SM, Hsia T, Khanna SK, Gamblin AS, Rosenfeld Y, You DG, Carter BS, Balaj L. Decoding vesicle-based precision oncology in gliomas. Neurooncol Adv 2022; 4:ii53-ii60. [PMID: 36380860 PMCID: PMC9650467 DOI: 10.1093/noajnl/vdac035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Extracellular vesicles (EVs) represent a valuable tool in liquid biopsy with tremendous clinical potential in diagnosis, prognosis, and therapeutic monitoring of gliomas. Compared to tissue biopsy, EV-based liquid biopsy is a low-cost, minimally invasive method that can provide information on tumor dynamics before, during, and after treatment. Tumor-derived EVs circulating in biofluids carry a complex cargo of molecular biomarkers, including DNA, RNA, and proteins, which can be indicative of tumor growth and progression. Here, we briefly review current commercial and noncommercial methods for the isolation, quantification, and biochemical characterization of plasma EVs from patients with glioma, touching on whole EV analysis, mutation detection techniques, and genomic and proteomic profiling. We review notable advantages and disadvantages of plasma EV isolation and analytical methods, and we conclude with a discussion on clinical translational opportunities and key challenges associated with the future implementation of EV-based liquid biopsy for glioma treatment.
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Affiliation(s)
| | | | - Sirena K Khanna
- Department of Neurosurgery, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Austin S Gamblin
- Department of Neurosurgery, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Yulia Rosenfeld
- Department of Neurosurgery, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Dong Gil You
- Department of Neurosurgery, Massachusetts General Hospital, Boston, Massachusetts, USA
| | | | - Leonora Balaj
- Corresponding Author: Leonora Balaj, PhD, Department of Neurosurgery, Massachusetts General Hospital, 185 Cambridge St., Boston, MA 02114, USA ()
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Friedman JS, Hertz CAJ, Karajannis MA, Miller AM. Tapping into the genome: the role of CSF ctDNA liquid biopsy in glioma. Neurooncol Adv 2022; 4:ii33-ii40. [PMID: 36380863 PMCID: PMC9650472 DOI: 10.1093/noajnl/vdac034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Liquid biopsy has emerged as a novel noninvasive tool in cancer diagnostics. While significant strides have been made in other malignancies using liquid biopsy for diagnosis, disease monitoring, and treatment selection, development of these assays has been more challenging for brain tumors. Recently, research in primary and metastatic brain tumors has begun to harness the potential utility of liquid biopsy-particularly using circulating tumor DNA (ctDNA). Initial studies to identify ctDNA in plasma of brain tumor patients have shown feasibility, but the yield of ctDNA is far below that for other malignancies. Attention has therefore turned to the cerebrospinal fluid (CSF) as a more robust source of ctDNA. This review discusses the unique considerations in liquid biopsy for glioma and places them in the context of the work to date. We address the utility of CSF liquid biopsy for diagnosis, longitudinal monitoring, tracking tumor evolution, clinical trial eligibility, and prognostication. We discuss the differences in assay requirements for each clinical application to best optimize factors such as efficacy, cost, and speed. Ultimately, CSF liquid biopsy has the potential to transform how we manage primary brain tumor patients.
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Affiliation(s)
- Joshua S Friedman
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Charli Ann J Hertz
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Matthias A Karajannis
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Alexandra M Miller
- Corresponding Author: Alexandra M. Miller, MD, PhD, Department of Neurology and Pediatrics, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York NY 10065, USA ()
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Abstract
Noninvasive molecular profiling of tumors using plasma-based next-generation sequencing (NGS) is increasingly used to aid in diagnosis, treatment selection, and disease monitoring in oncology. In patients with glioma, however, the plasma cell-free DNA (cfDNA) tumor fraction, defined as the fractional proportion of circulating tumor-derived DNA (ctDNA) relative to total cfDNA, is especially low, in large part due to the blood-brain barrier. As a result, commercial plasma-based NGS assays, designed to screen for a small number of actionable genomic alterations, are not sensitive enough to guide the management of patients with glioma. As this has been long recognized in neuro-oncology, significant research efforts have been undertaken to improve the sensitivity of plasma ctDNA detection in patients with glioma and to understand the biology and clinical relevance of non-tumor-derived cfDNA, which makes up most of the total cfDNA pool. Here, we review key recent advances in the field of plasma cfDNA analysis in patients with glioma, including (1) the prognostic impact of pre-treatment and on-treatment total plasma cfDNA concentrations, (2) use of tumor-guided sequencing approaches to improve the sensitivity of ctDNA detection in the plasma, and (3) the emergence of plasma cfDNA methylomics for detection and discrimination of glioma from other primary intracranial tumors.
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Affiliation(s)
- Erica L Carpenter
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Stephen J Bagley
- Corresponding Author: Stephen J. Bagley, MD, MSCE, Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA 19104, USA ()
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Abstract
Over the last decade, molecular markers have become an integral part in the management of Central Nervous System (CNS) tumors. Somatic mutations that identify and prognosticate tumors are also detected in the bio-fluids especially the serum and CSF; the sampling of which is known as liquid biopsy (LB). These tumor-derived biomarkers include plasma circulating tumor cells (CTCs), cell-free DNA (cf/ctDNAs), circulating cell-free microRNAs (cfmiRNAs), circulating extracellular vesicles, or exosomes (EVs), proteins, and tumor educated platelets. Established in the management of other malignancies, liquid biopsy is becoming an important tool in the management of CNS tumors as well. This review presents a snapshot of the current state of LB research its potential and the possible pitfalls.
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Affiliation(s)
- Amitava Ray
- Senior Consultant Neurosurgeon, Department of Neurosciences, Apollo Health City and Apollo Secunderabad, Hyderabad 500089, Telangana, India
| | - Tarang K Vohra
- Consultant Neurosurgeon, Department of Neurosciences, Apollo Health City, Hyderabad 500089, Telangana, India
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Dhinakaran AK, Ganesh S, Haldavnekar R, Tan B, Das S, Venkatakrishnan K. Holistic Analysis of Glioblastoma Stem Cell DNA Using Nanoengineered Plasmonic Metasensor for Glioblastoma Diagnosis. SMALL METHODS 2022; 6:e2200547. [PMID: 35908161 DOI: 10.1002/smtd.202200547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/27/2022] [Indexed: 06/15/2023]
Abstract
The clinical relevance of liquid biopsy for glioblastoma (GBM) remains undetermined due to practical and biological limitations such as absence of a reliable GBM-specific biomarker, trace levels in circulation due to the blood-brain-barrier, and lack of a sensitive method to detect the trace levels of biomarkers. It is hypothesized that GBM stem cell (GSC)-associated cell free DNA can function as reliable biomarker for GBM because it accounts for tumor heterogeneity and provide accurate molecular information about the cancer. An integrative methodology is used for GBM diagnosis by utilizing the sub-single molecular sensitivity of nanoengineered plasmonic metasensors for real-time genomic profiling of GSC DNA. The nanoengineered metasensors can detect the rare circulating GSC-DNA accurately from just 5 µL of blood and the test can be performed in under 10 min. Analysis of clinical serum samples from GBM patients and healthy volunteers demonstrates that the technology yielded an accurate classification of GBM in an independent validation cohort (accuracy 98.3%, specificity 100%). The methodology detects GBM-signatures from the patient blood rapidly within the half-life period of cfDNA in circulation, non-invasively and amplification-free with a high diagnostic accuracy. With clinical validation, this methodology can evolve as a clinically viable diagnostic tool for fatal and hard-to-detect cancer like GBM.
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Affiliation(s)
- Ashok Kumar Dhinakaran
- Institute for Biomedical Engineering, Science and Technology (I BEST), Partnership between Ryerson University and St. Michael's Hospital, Toronto, Ontario, M5B 1W8, Canada
- Ultrashort Laser Nanomanufacturing Research Facility, Department of Mechanical and Industrial Engineering, Ryerson University, Toronto, ON M5B 2K3, Canada
- Nano-Bio Interface facility, Department of Mechanical and Industrial Engineering, Ryerson University, Toronto, ON, M5B 2K3, Canada
| | - Swarna Ganesh
- Institute for Biomedical Engineering, Science and Technology (I BEST), Partnership between Ryerson University and St. Michael's Hospital, Toronto, Ontario, M5B 1W8, Canada
- Ultrashort Laser Nanomanufacturing Research Facility, Department of Mechanical and Industrial Engineering, Ryerson University, Toronto, ON M5B 2K3, Canada
- Nano-Bio Interface facility, Department of Mechanical and Industrial Engineering, Ryerson University, Toronto, ON, M5B 2K3, Canada
| | - Rupa Haldavnekar
- Institute for Biomedical Engineering, Science and Technology (I BEST), Partnership between Ryerson University and St. Michael's Hospital, Toronto, Ontario, M5B 1W8, Canada
- Ultrashort Laser Nanomanufacturing Research Facility, Department of Mechanical and Industrial Engineering, Ryerson University, Toronto, ON M5B 2K3, Canada
- Nano-Bio Interface facility, Department of Mechanical and Industrial Engineering, Ryerson University, Toronto, ON, M5B 2K3, Canada
| | - Bo Tan
- Nano-Bio Interface facility, Department of Mechanical and Industrial Engineering, Ryerson University, Toronto, ON, M5B 2K3, Canada
- Keenan Research Center for Biomedical Science, Unity Health Toronto, Toronto, Ontario, M5B 1W8, Canada
- Nanocharacterization Laboratory, Department of Aerospace Engineering, Ryerson University, Toronto, Ontario, M5B 2K3, Canada
| | - Sunit Das
- Department of Surgery, Division of Neurosurgery, University of Toronto, Toronto, M5B1W8, Canada
| | - Krishnan Venkatakrishnan
- Ultrashort Laser Nanomanufacturing Research Facility, Department of Mechanical and Industrial Engineering, Ryerson University, Toronto, ON M5B 2K3, Canada
- Nano-Bio Interface facility, Department of Mechanical and Industrial Engineering, Ryerson University, Toronto, ON, M5B 2K3, Canada
- Keenan Research Center for Biomedical Science, Unity Health Toronto, Toronto, Ontario, M5B 1W8, Canada
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Batool SM, Muralidharan K, Hsia T, Falotico S, Gamblin AS, Rosenfeld YB, Khanna SK, Balaj L, Carter BS. Highly sensitive EGFRvIII detection in circulating extracellular vesicle RNA of glioma patients. Clin Cancer Res 2022; 28:4070-4082. [PMID: 35849415 DOI: 10.1158/1078-0432.ccr-22-0444] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 05/01/2022] [Accepted: 07/14/2022] [Indexed: 11/16/2022]
Abstract
PURPOSE Liquid biopsy offers an attractive platform for non-invasive tumor diagnosis, prognostication and prediction of glioblastoma clinical outcomes. Prior studies report that 30-50% of GBM lesions characterized by EGFR amplification also harbor the EGFRvIII mutation. EXPERIMENTAL DESIGN A novel digital droplet PCR (ddPCR) assay for high GC content amplicons was developed and optimized for sensitive detection of EGFRvIII in tumor tissue and circulating extracellular vesicle RNA (EV RNA) isolated from the plasma of glioma patients. RESULTS Our optimized qPCR assay detected EGFRvIII mRNA in 81% (95% CI, 68% - 94%) of EGFR amplified glioma tumor tissue, indicating a higher than previously reported prevalence of EGFRvIII in glioma. Using the optimized ddPCR assay in discovery and blinded validation cohorts, we detected EGFRvIII mutation in 73% (95% CI, 64% - 82%) of patients with a specificity of 98% (95% CI, 87% - 100%), compared with qPCR tumor tissue analysis. Additionally, upon longitudinal monitoring in 4 patients, we report detection of EGFRvIII in the plasma of patients with different clinical outcomes, rising with tumor progression, and decreasing in response to treatment. CONCLUSION This study demonstrates the feasibility of detecting EGFRvIII mutation in plasma using a highly sensitive and specific ddPCR assay. We also show a higher than previously reported EGFRvIII prevalence in glioma tumor tissue. Several features of the assay are favorable for clinical implementation for detection and monitoring of EGFRvIII positive tumors.
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Affiliation(s)
| | | | - Tiffaney Hsia
- Massachusetts General Hospital, Boston, MA, United States
| | | | | | | | | | - Leonora Balaj
- Massachusetts General Hospital, Boston, United States
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Yekula A, Tracz J, Rincon-Torroella J, Azad T, Bettegowda C. Single-Cell RNA Sequencing of Cerebrospinal Fluid as an Advanced Form of Liquid Biopsy for Neurological Disorders. Brain Sci 2022; 12:brainsci12070812. [PMID: 35884620 PMCID: PMC9313114 DOI: 10.3390/brainsci12070812] [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: 05/27/2022] [Revised: 06/17/2022] [Accepted: 06/18/2022] [Indexed: 11/16/2022] Open
Abstract
Diagnosis and longitudinal monitoring of neurological diseases are limited by the poor specificity and limited resolution of currently available techniques. Analysis of circulating cells in cerebrospinal fluid (CSF) has emerged as a promising strategy for the diagnosis, molecular characterization, and monitoring of neurological disease. In comparison to bulk sequencing analysis, single-cell sequencing studies can provide novel insights into rare cell populations and uncover heterogeneity in gene expression at a single-cell resolution, which has several implications for understanding disease pathology and treatment. Parallel development of standardized biofluid collection protocols, pre-processing strategies, reliable single-cell isolation strategies, downstream genomic analysis, and robust computational analysis is paramount for comprehensive single-cell sequencing analysis. Here we perform a comprehensive review of studies focusing on single-cell sequencing of cells in the CSF of patients with oncological or non-oncological diseases of the central nervous system.
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Affiliation(s)
- Anudeep Yekula
- Department of Surgery, Yale School of Medicine, New Haven, CT 06510, USA;
| | - Jovanna Tracz
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; (J.T.); (J.R.-T.); (T.A.)
| | - Jordina Rincon-Torroella
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; (J.T.); (J.R.-T.); (T.A.)
| | - Tej Azad
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; (J.T.); (J.R.-T.); (T.A.)
| | - Chetan Bettegowda
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; (J.T.); (J.R.-T.); (T.A.)
- Correspondence:
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Shrivastava R, Gandhi P, Gothalwal R. The road-map for establishment of a prognostic molecular marker panel in glioma using liquid biopsy: current status and future directions. Clin Transl Oncol 2022; 24:1702-1714. [PMID: 35653004 DOI: 10.1007/s12094-022-02833-8] [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: 02/28/2022] [Accepted: 04/02/2022] [Indexed: 11/24/2022]
Abstract
Gliomas are primary intracranial tumors with defined molecular markers available for precise diagnosis. The prognosis of glioma is bleak as there is an overlook of the dynamic crosstalk between tumor cells and components of the microenvironment. Herein, different phases of gliomagenesis are presented with reference to the role and involvement of secreted proteomic markers at various stages of tumor initiation and development. The secreted markers of inflammatory response, namely interleukin-6, tumor necrosis factor-α, interferon-ϒ, and kynurenine, proliferation markers human telomerase reverse transcriptase and microtubule-associated-protein-Tau, and stemness marker human-mobility-group-AThook-1 are involved in glial tumor initiation and growth. Further, hypoxia and angiogenic factors, heat-shock-protein-70, endothelial-growth-factor-receptor-1 and vascular endothelial growth factor play a major role in promoting vascularization and tumor volume expansion. Eventually, molecules such as matrix-metalloprotease-7 and intercellular adhesion molecule-1 contribute to the degradation and remodeling of the extracellular matrix, ultimately leading to glioma progression. Our study delineates the roadmap to develop and evaluate a non-invasive panel of secreted biomarkers using liquid biopsy for precisely evaluating disease progression, to accomplish a clinical translation.
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Affiliation(s)
- Richa Shrivastava
- Department of Research, Bhopal Memorial Hospital and Research Centre, Raisen Bypass Road, Bhopal, M.P., 462038, India
| | - Puneet Gandhi
- Department of Research, Bhopal Memorial Hospital and Research Centre, Raisen Bypass Road, Bhopal, M.P., 462038, India.
| | - Ragini Gothalwal
- Department of Biotechnology, Barkatullah University, Bhopal, M.P., 462026, India
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Balana C, Castañer S, Carrato C, Moran T, Lopez-Paradís A, Domenech M, Hernandez A, Puig J. Preoperative Diagnosis and Molecular Characterization of Gliomas With Liquid Biopsy and Radiogenomics. Front Neurol 2022; 13:865171. [PMID: 35693015 PMCID: PMC9177999 DOI: 10.3389/fneur.2022.865171] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 05/05/2022] [Indexed: 12/13/2022] Open
Abstract
Gliomas are a heterogenous group of central nervous system tumors with different outcomes and different therapeutic needs. Glioblastoma, the most common subtype in adults, has a very poor prognosis and disabling consequences. The World Health Organization (WHO) classification specifies that the typing and grading of gliomas should include molecular markers. The molecular characterization of gliomas has implications for prognosis, treatment planning, and prediction of treatment response. At present, gliomas are diagnosed via tumor resection or biopsy, which are always invasive and frequently risky methods. In recent years, however, substantial advances have been made in developing different methods for the molecular characterization of tumors through the analysis of products shed in body fluids. Known as liquid biopsies, these analyses can potentially provide diagnostic and prognostic information, guidance on choice of treatment, and real-time information on tumor status. In addition, magnetic resonance imaging (MRI) is another good source of tumor data; radiomics and radiogenomics can link the imaging phenotypes to gene expression patterns and provide insights to tumor biology and underlying molecular signatures. Machine and deep learning and computational techniques can also use quantitative imaging features to non-invasively detect genetic mutations. The key molecular information obtained with liquid biopsies and radiogenomics can be useful not only in the diagnosis of gliomas but can also help predict response to specific treatments and provide guidelines for personalized medicine. In this article, we review the available data on the molecular characterization of gliomas using the non-invasive methods of liquid biopsy and MRI and suggest that these tools could be used in the future for the preoperative diagnosis of gliomas.
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Affiliation(s)
- Carmen Balana
- Medical Oncology Service, Institut Català d'Oncologia Badalona (ICO), Badalona Applied Research Group in Oncology (B-ARGO Group), Institut Investigació Germans Trias i Pujol (IGTP), Barcelona, Spain
- *Correspondence: Carmen Balana
| | - Sara Castañer
- Diagnostic Imaging Institute (IDI), Hospital Universitari Germans Trias I Pujol, Institut Investigació Germans Trias i Pujol (IGTP), Barcelona, Spain
| | - Cristina Carrato
- Department of Pathology, Hospital Universitari Germans Trias I Pujol, Institut Investigació Germans Trias i Pujol (IGTP), Barcelona, Spain
| | - Teresa Moran
- Medical Oncology Service, Institut Català d'Oncologia Badalona (ICO), Badalona Applied Research Group in Oncology (B-ARGO Group), Institut Investigació Germans Trias i Pujol (IGTP), Barcelona, Spain
| | - Assumpció Lopez-Paradís
- Medical Oncology Service, Institut Català d'Oncologia Badalona (ICO), Badalona Applied Research Group in Oncology (B-ARGO Group), Institut Investigació Germans Trias i Pujol (IGTP), Barcelona, Spain
| | - Marta Domenech
- Medical Oncology Service, Institut Català d'Oncologia Badalona (ICO), Badalona Applied Research Group in Oncology (B-ARGO Group), Institut Investigació Germans Trias i Pujol (IGTP), Barcelona, Spain
| | - Ainhoa Hernandez
- Medical Oncology Service, Institut Català d'Oncologia Badalona (ICO), Badalona Applied Research Group in Oncology (B-ARGO Group), Institut Investigació Germans Trias i Pujol (IGTP), Barcelona, Spain
| | - Josep Puig
- Department of Radiology IDI [Girona Biomedical Research Institute] IDIBGI, Hospital Universitari Dr Josep Trueta, Girona, Spain
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
- Comparative Medicine and Bioimage of Catalonia, Institut Investigació Germans Trias i Pujol (IGTP), Barcelona, Spain
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Liquid biopsy: early and accurate diagnosis of brain tumor. J Cancer Res Clin Oncol 2022; 148:2347-2373. [PMID: 35451698 DOI: 10.1007/s00432-022-04011-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 04/01/2022] [Indexed: 12/15/2022]
Abstract
Noninvasive examination is an emerging area in the field of neuro-oncology. Liquid biopsy captures the landscape of genomic alterations of brain tumors and revolutionizes the traditional diagnosis approaches. Rapidly changing sequencing technologies and more affordable prices put the screws on more application of liquid biopsy in clinical settings. In the past few years, extensive application of liquid biopsy has been seen throughout the whole diagnosis and treatment process of brain tumors, including early and accurate detection, characterization and dynamic monitoring. Here, we summarized and compared the most advanced techniques and target molecules or macrostructures related to brain tumor liquid biopsy. We further reviewed and emphasized recent progression in different clinical settings for brain tumors in blood and CSF. The preferred protocol, potential novel biomarkers and future development are discussed in the last part.
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Wolter M, Felsberg J, Malzkorn B, Kaulich K, Reifenberger G. Droplet digital PCR-based analyses for robust, rapid, and sensitive molecular diagnostics of gliomas. Acta Neuropathol Commun 2022; 10:42. [PMID: 35361262 PMCID: PMC8973808 DOI: 10.1186/s40478-022-01335-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/20/2022] [Indexed: 11/10/2022] Open
Abstract
Classification of gliomas involves the combination of histological features with molecular biomarkers to establish an integrated histomolecular diagnosis. Here, we report on the application and validation of a set of molecular assays for glioma diagnostics based on digital PCR technology using the QX200™ Droplet Digital™ PCR (ddPCR) system. The investigated ddPCR-based assays enable the detection of diagnostically relevant glioma-associated mutations in the IDH1, IDH2, H3-3A, BRAF, and PRKCA genes, as well as in the TERT promoter. In addition, ddPCR-based assays assessing diagnostically relevant copy number alterations were studied, including 1p/19q codeletion, gain of chromosome 7 and loss of chromosome 10 (+ 7/-10), EGFR amplification, duplication of the BRAF locus, and CDKN2A homozygous deletion. Results obtained by ddPCR were validated by other methods, including immunohistochemistry, Sanger sequencing, pyrosequencing, microsatellite analyses for loss of heterozygosity, as well as real-time PCR- or microarray-based copy number assays. Particular strengths of the ddPCR approach are (1) its high analytical sensitivity allowing for reliable detection of mutations even with low mutant allele frequencies, (2) its quantitative determination of mutant allele frequencies and copy number changes, and (3) its rapid generation of results within a single day. Thus, in line with other recent studies our findings support ddPCR analysis as a valuable approach for molecular glioma diagnostics in a fast, quantitative and highly sensitive manner.
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Hasanau T, Pisarev E, Kisil O, Nonoguchi N, Le Calvez-Kelm F, Zvereva M. Detection of TERT Promoter Mutations as a Prognostic Biomarker in Gliomas: Methodology, Prospects, and Advances. Biomedicines 2022; 10:728. [PMID: 35327529 PMCID: PMC8945783 DOI: 10.3390/biomedicines10030728] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/13/2022] [Accepted: 03/17/2022] [Indexed: 11/16/2022] Open
Abstract
This article reviews the existing approaches to determining the TERT promoter mutational status in patients with various tumoral diseases of the central nervous system. The operational characteristics of the most common methods and their transferability in medical practice for the selection or monitoring of personalized treatments based on the TERT status and other related molecular biomarkers in patients with the most common tumors, such as glioblastoma, oligodendroglioma, and astrocytoma, are compared. The inclusion of new molecular markers in the course of CNS clinical management requires their rapid and reliable assessment. Availability of molecular evaluation of gliomas facilitates timely decisions regarding patient follow-up with the selection of the most appropriate treatment protocols. Significant progress in the inclusion of molecular biomarkers for their subsequent clinical application has been made since 2016 when the WHO CNS classification first used molecular markers to classify gliomas. In this review, we consider the methodological approaches used to determine mutations in the promoter region of the TERT gene in tumors of the central nervous system. In addition to classical molecular genetical methods, other methods for determining TERT mutations based on mass spectrometry, magnetic resonance imaging, next-generation sequencing, and nanopore sequencing are reviewed with an assessment of advantages and disadvantages. Beyond that, noninvasive diagnostic methods based on the determination of the mutational status of the TERT promoter are discussed.
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Affiliation(s)
- Tsimur Hasanau
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Eduard Pisarev
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia;
- Chair of Chemistry of Natural Compounds, Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Olga Kisil
- Gause Institute of New Antibiotics, 119021 Moscow, Russia;
| | - Naosuke Nonoguchi
- Department of Neurosurgery, Osaka Medical and Pharmaceutical University, Takatsuki 569-8686, Japan;
| | - Florence Le Calvez-Kelm
- Genomic Epidemiology Branch, International Agency for Research on Cancer (IARC), 69372 Lyon, France;
| | - Maria Zvereva
- Chair of Chemistry of Natural Compounds, Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
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Kang SY, Kim DG, Kim H, Cho YA, Ha SY, Kwon GY, Jang KT, Kim KM. Direct comparison of the next-generation sequencing and iTERT PCR methods for the diagnosis of TERT hotspot mutations in advanced solid cancers. BMC Med Genomics 2022; 15:25. [PMID: 35135543 PMCID: PMC8827275 DOI: 10.1186/s12920-022-01175-2] [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: 08/03/2021] [Accepted: 02/02/2022] [Indexed: 01/12/2023] Open
Abstract
Background Mutations in the telomerase reverse transcriptase (TERT) promoter region have been proposed as novel mechanisms for the transcriptional activation of telomerase. Two recurrent mutations in the TERT promoter, C228T and C250T, are prognostic biomarkers. Herein, we directly compared the commercially available iTERT PCR kit with NGS-based deep sequencing to validate the NGS results and determine the analytical sensitivity of the PCR kit.
Methods Of the 2032 advanced solid tumors diagnosed using the TruSight Oncology 500 NGS test, mutations in the TERT promoter region were detected in 103 cases, with 79 cases of C228T, 22 cases of C250T, and 2 cases of C228A hotspot mutations. TERT promoter mutations were detected from 31 urinary bladder, 19 pancreato-biliary, 22 hepatic, 12 malignant melanoma, and 12 other tumor samples. Results In all 103 TERT-mutated cases detected using NGS, the same DNA samples were also tested with the iTERT PCR/Sanger sequencing. PCR successfully verified the presence of the same mutations in all cases with 100% agreement. The average read depth of the TERT promoter region was 320.4, which was significantly lower than that of the other genes (mean, 743.5). Interestingly, NGS read depth was significantly higher at C250 compared to C228 (p < 0.001). Conclusions The NGS test results were validated by a PCR test and iTERT PCR/Sanger sequencing is sensitive for the identification of the TERT promoter mutations.
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Affiliation(s)
- So Young Kang
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, #81, Irwon-ro, Gangnam-Gu, Seoul, 06351, Korea
| | - Deok Geun Kim
- Department of Clinical Genomic Center, Samsung Medical Center, Seoul, Korea.,Department of Digital Health, Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University, Seoul, Korea
| | - Hyunjin Kim
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, #81, Irwon-ro, Gangnam-Gu, Seoul, 06351, Korea.,Center of Companion Diagnostics, Samsung Medical Center, Seoul, Republic of Korea
| | - Yoon Ah Cho
- Department of Pathology, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Republic of Korea
| | - Sang Yun Ha
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, #81, Irwon-ro, Gangnam-Gu, Seoul, 06351, Korea
| | - Ghee Young Kwon
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, #81, Irwon-ro, Gangnam-Gu, Seoul, 06351, Korea
| | - Kee-Taek Jang
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, #81, Irwon-ro, Gangnam-Gu, Seoul, 06351, Korea.
| | - Kyoung-Mee Kim
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, #81, Irwon-ro, Gangnam-Gu, Seoul, 06351, Korea. .,Department of Clinical Genomic Center, Samsung Medical Center, Seoul, Korea. .,Center of Companion Diagnostics, Samsung Medical Center, Seoul, Republic of Korea.
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Mair R, Mouliere F. Cell-free DNA technologies for the analysis of brain cancer. Br J Cancer 2022; 126:371-378. [PMID: 34811503 PMCID: PMC8811068 DOI: 10.1038/s41416-021-01594-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 09/07/2021] [Accepted: 10/06/2021] [Indexed: 11/08/2022] Open
Abstract
Survival for glioma patients has shown minimal improvement over the past 20 years. The ability to detect and monitor gliomas relies primarily upon imaging technologies that lack sensitivity and specificity, especially during the post-surgical treatment phase. Treatment-response monitoring with an effective liquid-biopsy paradigm may also provide the most facile clinical scenario for liquid-biopsy integration into brain-tumour care. Conceptually, liquid biopsy is advantageous when compared with both tissue sampling (less invasive) and imaging (more sensitive and specific), but is hampered by technical and biological problems. These problems predominantly relate to low concentrations of tumour-derived DNA in the bloodstream of glioma patients. In this review, we highlight methods by which the neuro-oncological scientific and clinical communities have attempted to circumvent this limitation. The use of novel biological, technological and computational approaches will be explored. The utility of alternate bio-fluids, tumour-guided sequencing, epigenomic and fragmentomic methods may eventually be leveraged to provide the biological and technological means to unlock a wide range of clinical applications for liquid biopsy in glioma.
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Affiliation(s)
- Richard Mair
- Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE, Cambridge, UK.
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, CB2 0RE, Cambridge, UK.
- Division of Neurosurgery, Department of Clinical Neurosciences, University of Cambridge, CB2 0QQ, Cambridge, UK.
| | - Florent Mouliere
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Centre Amsterdam, 1081 HV, Amsterdam, The Netherlands.
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Wang Y, Chen Y, Li C, Xiao Z, Yuan H, Zhang Y, Pang D, Tang X, Li M, Ouyang H. TERT Promoter Revertant Mutation Inhibits Melanoma Growth through Intrinsic Apoptosis. BIOLOGY 2022; 11:biology11010141. [PMID: 35053139 PMCID: PMC8773187 DOI: 10.3390/biology11010141] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/08/2022] [Accepted: 01/12/2022] [Indexed: 12/15/2022]
Abstract
Simple Summary TERT -146 C>T frequently occurs in many cancer cells. Research targeting the telomerase reverse transcriptase (TERT) promoter contributes to a better understanding of cancer development and treatment. Many conventional cancer treatments aim to develop new drugs targeting TERT. Here, for TERT -146 we converted T to C. The proliferation, migration and invasion of melanoma cells in vitro, and the growth of the tumor in vivo were inhibited. Moreover, the downregulated protein expression of B-cell lymphoma 2 (Bcl-2) indicated that the TERT promoter revertant mutation abrogated the inhibitory effect of mutant TERT on apoptosis. These data elucidated the relationship between the TERT promoter revertant mutations and apoptosis for the first time, and also implied that TERT -146 may be a causal mutation of melanoma. This study provides a new insight into the TERT promoter revertant mutations and apoptosis. The TERT promoter provides preliminary validation of the potential tumor treatment. Abstract Human telomerase is a specialized DNA polymerase whose catalytic core includes both TERT and human telomerase RNA (hTR). Telomerase in humans, which is silent in most somatic cells, is activated to maintain the telomere length (TEL) in various types of cancer cells, including melanoma. In the vast majority of tumor cells, the TERT promoter is mutated to promote proliferation and inhibit apoptosis. Here, we exploited NG-ABEmax to revert TERT -146 T to -146 C in melanoma, and successfully obtained TERT promoter revertant mutant cells. These TERT revertant mutant cells exhibited significant growth inhibition both in vitro and in vivo. Moreover, A375−146C/C cells exhibited telomere shortening and the downregulation of TERT at both the transcription and protein levels, and migration and invasion were inhibited. In addition, TERT promoter revertant mutation abrogated the inhibitory effect of mutant TERT on apoptosis via B-cell lymphoma 2 (Bcl-2), ultimately leading to cell death. Collectively, the results of our work demonstrate that reverting mutations in the TERT promoter is a potential therapeutic option for melanoma.
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Affiliation(s)
- Yanbing Wang
- Key Laboratory for Zoonoses Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun 130062, China; (Y.W.); (Y.C.); (Z.X.); (H.Y.); (Y.Z.); (D.P.); (X.T.)
| | - Yiwu Chen
- Key Laboratory for Zoonoses Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun 130062, China; (Y.W.); (Y.C.); (Z.X.); (H.Y.); (Y.Z.); (D.P.); (X.T.)
| | - Chang Li
- College of Plant Sciences, Jilin University, Changchun 130062, China;
| | - Zhiwei Xiao
- Key Laboratory for Zoonoses Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun 130062, China; (Y.W.); (Y.C.); (Z.X.); (H.Y.); (Y.Z.); (D.P.); (X.T.)
| | - Hongming Yuan
- Key Laboratory for Zoonoses Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun 130062, China; (Y.W.); (Y.C.); (Z.X.); (H.Y.); (Y.Z.); (D.P.); (X.T.)
| | - Yuanzhu Zhang
- Key Laboratory for Zoonoses Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun 130062, China; (Y.W.); (Y.C.); (Z.X.); (H.Y.); (Y.Z.); (D.P.); (X.T.)
| | - Daxin Pang
- Key Laboratory for Zoonoses Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun 130062, China; (Y.W.); (Y.C.); (Z.X.); (H.Y.); (Y.Z.); (D.P.); (X.T.)
- Chongqing Research Institute, Jilin University, Chongqing 401123, China
- Chongqing Jitang Biotechnology Research Institute, Chongqing 401123, China
| | - Xiaochun Tang
- Key Laboratory for Zoonoses Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun 130062, China; (Y.W.); (Y.C.); (Z.X.); (H.Y.); (Y.Z.); (D.P.); (X.T.)
- Chongqing Research Institute, Jilin University, Chongqing 401123, China
- Chongqing Jitang Biotechnology Research Institute, Chongqing 401123, China
| | - Mengjing Li
- Key Laboratory for Zoonoses Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun 130062, China; (Y.W.); (Y.C.); (Z.X.); (H.Y.); (Y.Z.); (D.P.); (X.T.)
- Chongqing Research Institute, Jilin University, Chongqing 401123, China
- Chongqing Jitang Biotechnology Research Institute, Chongqing 401123, China
- Correspondence: (M.L.); (H.O.); Tel.: +86-0431-87836175 (H.O.)
| | - Hongsheng Ouyang
- Key Laboratory for Zoonoses Research, Ministry of Education, College of Animal Sciences, Jilin University, Changchun 130062, China; (Y.W.); (Y.C.); (Z.X.); (H.Y.); (Y.Z.); (D.P.); (X.T.)
- Chongqing Research Institute, Jilin University, Chongqing 401123, China
- Chongqing Jitang Biotechnology Research Institute, Chongqing 401123, China
- Correspondence: (M.L.); (H.O.); Tel.: +86-0431-87836175 (H.O.)
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Pacia CP, Yuan J, Yue Y, Xu L, Nazeri A, Desai R, Gach HM, Wang X, Talcott MR, Chaudhuri AA, Dunn GP, Leuthardt EC, Chen H. Sonobiopsy for minimally invasive, spatiotemporally-controlled, and sensitive detection of glioblastoma-derived circulating tumor DNA. Am J Cancer Res 2022; 12:362-378. [PMID: 34987650 PMCID: PMC8690937 DOI: 10.7150/thno.65597] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 10/06/2021] [Indexed: 12/12/2022] Open
Abstract
Though surgical biopsies provide direct access to tissue for genomic characterization of brain cancer, they are invasive and pose significant clinical risks. Brain cancer management via blood-based liquid biopsies is a minimally invasive alternative; however, the blood-brain barrier (BBB) restricts the release of brain tumor-derived molecular biomarkers necessary for sensitive diagnosis. Methods: A mouse glioblastoma multiforme (GBM) model was used to demonstrate the capability of focused ultrasound (FUS)-enabled liquid biopsy (sonobiopsy) to improve the diagnostic sensitivity of brain tumor-specific genetic mutations compared with conventional blood-based liquid biopsy. Furthermore, a pig GBM model was developed to characterize the translational implications of sonobiopsy in humans. Magnetic resonance imaging (MRI)-guided FUS sonication was performed in mice and pigs to locally enhance the BBB permeability of the GBM tumor. Contrast-enhanced T1-weighted MR images were acquired to evaluate the BBB permeability change. Blood was collected immediately after FUS sonication. Droplet digital PCR was used to quantify the levels of brain tumor-specific genetic mutations in the circulating tumor DNA (ctDNA). Histological staining was performed to evaluate the potential for off-target tissue damage by sonobiopsy. Results: Sonobiopsy improved the detection sensitivity of EGFRvIII from 7.14% to 64.71% and TERT C228T from 14.29% to 45.83% in the mouse GBM model. It also improved the diagnostic sensitivity of EGFRvIII from 28.57% to 100% and TERT C228T from 42.86% to 71.43% in the porcine GBM model. Conclusion: Sonobiopsy disrupts the BBB at the spatially-targeted brain location, releases tumor-derived DNA into the blood circulation, and enables timely collection of ctDNA. Converging evidence from both mouse and pig GBM models strongly supports the clinical translation of sonobiopsy for the minimally invasive, spatiotemporally-controlled, and sensitive molecular characterization of brain cancer.
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Soffietti R, Bettegowda C, Mellinghoff IK, Warren KE, Ahluwalia MS, De Groot JF, Galanis E, Gilbert MR, Jaeckle KA, Le Rhun E, Rudà R, Seoane J, Thon N, Umemura Y, Weller M, van den Bent MJ, Vogelbaum MA, Chang SM, Wen PY. Liquid biopsy in gliomas: A RANO review and proposals for clinical applications. Neuro Oncol 2022; 24:855-871. [PMID: 34999836 PMCID: PMC9159432 DOI: 10.1093/neuonc/noac004] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND There is an extensive literature highlighting the utility of blood-based liquid biopsies in several extracranial tumors for diagnosis and monitoring. METHODS The RANO (Response Assessment in Neuro-Oncology) group developed a multidisciplinary international Task Force to review the English literature on liquid biopsy in gliomas focusing on the most frequently used techniques, that is circulating tumor DNA, circulating tumor cells, and extracellular vesicles in blood and CSF. RESULTS ctDNA has a higher sensitivity and capacity to represent the spatial and temporal heterogeneity in comparison to circulating tumor cells. Exosomes have the advantages to cross an intact blood-brain barrier and carry also RNA, miRNA, and proteins. Several clinical applications of liquid biopsies are suggested: to establish a diagnosis when tissue is not available, monitor the residual disease after surgery, distinguish progression from pseudoprogression, and predict the outcome. CONCLUSIONS There is a need for standardization of biofluid collection, choice of an analyte, and detection strategies along with rigorous testing in future clinical trials to validate findings and enable entry into clinical practice.
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Affiliation(s)
- Riccardo Soffietti
- Corresponding Author: Riccardo Soffietti, MD, Division of Neuro-Oncology, Department of Neuroscience, University and City of Health and Science Hospital, Via Cherasco 15, 10126 Turin, Italy ()
| | | | | | | | - Manmeet S Ahluwalia
- Brain Tumor and Neuro-Oncology Center, Cleveland Clinic, Cleveland, Ohio, USA
| | - John F De Groot
- Department of Neuro-Oncology, University of Texas, MD Anderson Cancer Center Houston, Houston, Texas, USA
| | - Evanthia Galanis
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | - Mark R Gilbert
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Kurt A Jaeckle
- Department of Neurology, Mayo Clinic Florida, Jacksonville, Florida, USA
| | - Emilie Le Rhun
- Departments of Neurology & Neurosurgery, Clinical Neuroscience Center, University Hospital and University of Zurich, Zurich, Switzerland
| | - Roberta Rudà
- Department of Neurology, Castelfranco Veneto/Treviso Hospital and Division of Neuro-Oncology, Department of Neuroscience, University of Turin, Turin, Italy
| | - Joan Seoane
- Vall d’Hebron Institute of Oncology (VHIO) University Hospital, Universitat Autònoma de Barcelona, ICREA,CIBERONC, Barcelona, Spain
| | - Niklas Thon
- Division of Neuro-Oncology, Department of Neurosurgery, Ludwig Maximilians University School of Medicine, Munich, Germany
| | - Yoshie Umemura
- Division of Neuro-Oncology, Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA
| | - Michael Weller
- Department of Neurology, Clinical Neuroscience Center, University Hospital and University of Zurich, Zurich, Switzerland
| | - Martin J van den Bent
- Department of Neurology, Brain Tumor Center at Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | - Susan M Chang
- Division of Neuro-Oncology, University of California San Francisco, San Francisco, California, USA
| | - Patrick Y Wen
- Center for Neuro-Oncology, Dana-Farber/Brigham and Women’s Cancer Center, Harvard Medical School, Boston, Massachusetts, USA
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Clarner P, Lau SK, Chowdhury T, Guilmette E, Trapa P, Lo SC, Shen S. Development of a one-step RT-ddPCR method to determine the expression and potency of AAV vectors. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2021; 23:68-77. [PMID: 34589555 PMCID: PMC8449018 DOI: 10.1016/j.omtm.2021.05.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/07/2021] [Indexed: 12/11/2022]
Abstract
Robust assays to quantify adeno-associated virus (AAV) vector expression and potency are essential for gene therapy development. These assays inform the efficacy, safety, and pharmacodynamic profiles of AAV development candidates. Additionally, for gene downregulation strategies such as RNAi, knockdown of endogenous genes reflects the mechanism of action of such development candidates. Therefore, a method to quantify target mRNA repression is necessary for measuring vector potency both in vitro and in vivo. Here, we report the development of a one-step reverse-transcription droplet digital PCR (RT-ddPCR) method to analyze expression of AAV vectors and the potency of AAV-RNAi vectors. This one-step RT-ddPCR method simplifies the workflow, allows for duplexing reactions, and enables absolute quantification of transcripts without standard materials. With a gene augmentation vector, we demonstrate the application of RT-ddPCR in quantifying vector expression in vitro and in non-human primate (NHP) samples. This novel method is demonstrated to be precise and linear within the range of 0.05–25 ng of RNA input. Using an AAV-RNAi vector, we further demonstrate the utility of this RT-ddPCR method in quantifying potency. Orthogonal potency assays, including ELISA and functional readout, correlate well with RT-ddPCR results. Therefore, one-step RT-ddPCR can be implemented in the analytical and pharmacological characterization of AAV vectors.
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Fontanilles M, Sanson M, Touat M. Liquid biopsy in neuro-oncology: are we finally there? Ann Oncol 2021; 32:1472-1474. [PMID: 34815016 DOI: 10.1016/j.annonc.2021.10.215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 11/30/2022] Open
Affiliation(s)
- M Fontanilles
- Cancer Centre Henri Becquerel, Département d'oncologie médicale, Rouen, France; Normandie Université, Rouen University Hospital, UNIROUEN, IRON group, Normandy Centre for Genomic and Personalized Medicine, Inserm U1245, Rouen, France
| | - M Sanson
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie 2-Mazarin, Paris, France
| | - M Touat
- Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie 2-Mazarin, Paris, France.
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Bouzidi A, Labreche K, Baron M, Veyri M, Denis JA, Touat M, Sanson M, Davi F, Guillerm E, Jouannet S, Charlotte F, Bielle F, Choquet S, Boëlle PY, Cadranel J, Leblond V, Autran B, Lacorte JM, Spano JP, Coulet F. Low-Coverage Whole Genome Sequencing of Cell-Free DNA From Immunosuppressed Cancer Patients Enables Tumor Fraction Determination and Reveals Relevant Copy Number Alterations. Front Cell Dev Biol 2021; 9:661272. [PMID: 34710202 PMCID: PMC8369887 DOI: 10.3389/fcell.2021.661272] [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: 01/30/2021] [Accepted: 06/18/2021] [Indexed: 11/13/2022] Open
Abstract
Cell-free DNA (cfDNA) analysis is a minimally invasive method that can be used to detect genomic abnormalities by directly testing a blood sample. This method is particularly useful for immunosuppressed patients, who are at high risk of complications from tissue biopsy. The cfDNA tumor fraction (TF) varies greatly across cancer type and between patients. Thus, the detection of molecular alterations is highly dependent on the circulating TF. In our study, we aimed to calculate the TF and characterize the copy number aberration (CNA) profile of cfDNA from patients with rare malignancies occurring in immunosuppressed environments or immune-privileged sites. To accomplish this, we recruited 36 patients: 19 patients with non-Hodgkin lymphoma (NHL) who were either human immunodeficiency virus (HIV)-positive or organ transplant recipients, 5 HIV-positive lung cancer patients, and 12 patients with glioma. cfDNA was extracted from the patients' plasma and sequenced using low-coverage whole genome sequencing (LC-WGS). The cfDNA TF was then calculated using the ichorCNA bioinformatic algorithm, based on the CNA profile. In parallel, we performed whole exome sequencing of patient tumor tissue and cfDNA samples with detectable TFs. We detected a cfDNA TF in 29% of immune-suppressed patients (one patient with lung cancer and six with systemic NHL), with a TF range from 8 to 70%. In these patients, the events detected in the CNA profile of cfDNA are well-known events associated with NHL and lung cancer. Moreover, cfDNA CNA profile correlated with the CNA profile of matched tumor tissue. No tumor-derived cfDNA was detected in the glioma patients. Our study shows that tumor genetic content is detectable in cfDNA from immunosuppressed patients with advanced NHL or lung cancer. LC-WGS is a time- and cost-effective method that can help select an appropriate strategy for performing extensive molecular analysis of cfDNA. This technique also enables characterization of CNAs in cfDNA when sufficient tumor content is available. Hence, this approach can be used to collect useful molecular information that is relevant to patient care.
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Affiliation(s)
- Amira Bouzidi
- Sorbonne University, INSERM, Research Unit on Cardiovascular and Metabolic Disease UMR ICAN, Department of Endocrine Biochemistry and Oncology, AP-HP, Hôpital Pitié Salpêtrière, Paris, France
| | - Karim Labreche
- Sorbonne University, INSERM, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Marine Baron
- Sorbonne University, Center for Immunology and Infectious Diseases (CIMI-Paris), Department of Hematology, APHP, Hôpital Pitié Salpêtrière, Paris, France
| | - Marianne Veyri
- Sorbonne University, INSERM, Pierre Louis Institute of Epidemiology and Public Health, Theravir Team, Medical Oncology, AP-HP, Hôpital Pitié Salpêtrière, Paris, France
| | - Jérôme Alexandre Denis
- Sorbonne University, INSERM, Saint-Antoine Research Center, Cancer Biology and Therapeutics, CRSA, Department of Endocrine Biochemistry and Oncology, AP-HP, Hôpital Pitié Salpêtrière, Paris, France
| | - Mehdi Touat
- Sorbonne University, INSERM, CNRS, Brain and Spine Institute, ICM, Department of Neurology 2-Mazarin, AP-HP, Hôpital Pitié Salpêtrière, Paris, France
| | - Marc Sanson
- Sorbonne University, INSERM, CNRS, Brain and Spine Institute, ICM, Department of Neurology 2-Mazarin, AP-HP, Hôpital Pitié Salpêtrière, Paris, France
| | - Frédéric Davi
- Sorbonne University, INSERM, Centre de Recherche des Cordeliers, Department of Biological Hematology, AP-HP, Hôpital Pitié Salpêtrière, Paris, France
| | - Erell Guillerm
- Sorbonne University, INSERM, Saint-Antoine Research Center, Microsatellites Instability and Cancer, CRSA, Genetics Department, AP-HP, Hôpital Pitié Salpêtrière, Paris, France
| | - Stéphanie Jouannet
- Sorbonne University, Neurosurgery Department, AP-HP, Hôpital Pitié Salpêtrière, Paris, France
| | - Frédéric Charlotte
- Sorbonne University, Anatomy and Pathologic Cytology, AP-HP, Hôpital Pitié Salpêtrière, Paris, France
| | - Franck Bielle
- Sorbonne University, Neuropathology Department, AP-HP, Hôpital Pitié Salpêtrière, Paris, France
| | - Sylvain Choquet
- Sorbonne University, Center for Immunology and Infectious Diseases (CIMI-Paris), Department of Hematology, APHP, Hôpital Pitié Salpêtrière, Paris, France
| | - Pierre-Yves Boëlle
- Sorbonne University, INSERM, Pierre Louis Institute of Epidemiology and Public Health, Paris, France
| | - Jacques Cadranel
- Sorbonne University, Chest Department and Thoracic Oncology, GRC 04, Theranoscan, AP-HP, Hôpital Tenon, Paris, France
| | - Véronique Leblond
- Sorbonne University, Center for Immunology and Infectious Diseases (CIMI-Paris), Department of Hematology, APHP, Hôpital Pitié Salpêtrière, Paris, France
| | - Brigitte Autran
- Sorbonne University, INSERM, CNRS, Center for Immunology and Infectious Diseases (CIMI-Paris), AP-HP, Pitié-Salpêtrière Hospital, Paris, France
| | - Jean-Marc Lacorte
- Sorbonne University, INSERM, Research Unit on Cardiovascular and Metabolic Disease UMR ICAN, Department of Endocrine Biochemistry and Oncology, AP-HP, Hôpital Pitié Salpêtrière, Paris, France
| | - Jean-Philippe Spano
- Sorbonne University, INSERM, Research Unit on Cardiovascular and Metabolic Disease UMR ICAN, Department of Endocrine Biochemistry and Oncology, AP-HP, Hôpital Pitié Salpêtrière, Paris, France
| | - Florence Coulet
- Sorbonne University, INSERM, Research Unit on Cardiovascular and Metabolic Disease UMR ICAN, Department of Endocrine Biochemistry and Oncology, AP-HP, Hôpital Pitié Salpêtrière, Paris, France
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