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Liu H, Dang R, Zhang W, Hong J, Li X. SNARE proteins: Core engines of membrane fusion in cancer. Biochim Biophys Acta Rev Cancer 2024:189148. [PMID: 38960006 DOI: 10.1016/j.bbcan.2024.189148] [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: 02/29/2024] [Revised: 06/23/2024] [Accepted: 06/27/2024] [Indexed: 07/05/2024]
Abstract
Vesicles are loaded with a variety of cargoes, including membrane proteins, secreted proteins, signaling molecules, and various enzymes, etc. Not surprisingly, vesicle transport is essential for proper cellular life activities including growth, division, movement and cellular communication. Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) mediate membrane fusion of vesicles with their target compartments that is fundamental for cargo delivery. Recent studies have shown that multiple SNARE family members are aberrantly expressed in human cancers and actively contribute to malignant proliferation, invasion, metastasis, immune evasion and treatment resistance. Here, the localization and function of SNARE proteins in eukaryotic cells are firstly mapped. Then we summarize the expression and regulation of SNAREs in cancer, and describe their contribution to cancer progression and mechanisms, and finally we propose engineering botulinum toxin as a strategy to target SNAREs for cancer treatment.
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Affiliation(s)
- Hongyi Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China; Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, China
| | - Ruiyue Dang
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, China
| | - Wei Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China; Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, China
| | - Jidong Hong
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, China.
| | - Xuejun Li
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China; Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, China.
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2
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Morelli M, Lessi F, Franceschi S, Ferri G, Giacomarra M, Menicagli M, Gambacciani C, Pieri F, Pasqualetti F, Montemurro N, Aretini P, Santonocito OS, Di Stefano AL, Mazzanti CM. Exploring Regorafenib Responsiveness and Uncovering Molecular Mechanisms in Recurrent Glioblastoma Tumors through Longitudinal In Vitro Sampling. Cells 2024; 13:487. [PMID: 38534332 PMCID: PMC10968984 DOI: 10.3390/cells13060487] [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: 02/07/2024] [Revised: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 03/28/2024] Open
Abstract
Glioblastoma, a deadly brain tumor, shows limited response to standard therapies like temozolomide (TMZ). Recent findings from the REGOMA trial underscore a significant survival improvement offered by Regorafenib (REGO) in recurrent glioblastoma. Our study aimed to propose a 3D ex vivo drug response precision medicine approach to investigate recurrent glioblastoma sensitivity to REGO and elucidate the underlying molecular mechanisms involved in tumor resistance or responsiveness to treatment. Three-dimensional glioblastoma organoids (GB-EXPs) obtained from 18 patients' resected recurrent glioblastoma tumors were treated with TMZ and REGO. Drug responses were evaluated using NAD(P)H FLIM, stratifying tumors as responders (Resp) or non-responders (NRs). Whole-exome sequencing was performed on 16 tissue samples, and whole-transcriptome analysis on 13 GB-EXPs treated and untreated. We found 35% (n = 9) and 77% (n = 20) of tumors responded to TMZ and REGO, respectively, with no instances of TMZ-Resp being REGO-NRs. Exome analysis revealed a unique mutational profile in REGO-Resp tumors compared to NR tumors. Transcriptome analysis identified distinct expression patterns in Resp and NR tumors, impacting Rho GTPase and NOTCH signaling, known to be involved in drug response. In conclusion, recurrent glioblastoma tumors were more responsive to REGO compared to TMZ treatment. Importantly, our approach enables a comprehensive longitudinal exploration of the molecular changes induced by treatment, unveiling promising biomarkers indicative of drug response.
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Affiliation(s)
- Mariangela Morelli
- Fondazione Pisana per la Scienza, San Giuliano Terme, 56017 Pisa, Italy; (F.L.); (S.F.); (M.G.); (C.M.M.)
| | - Francesca Lessi
- Fondazione Pisana per la Scienza, San Giuliano Terme, 56017 Pisa, Italy; (F.L.); (S.F.); (M.G.); (C.M.M.)
| | - Sara Franceschi
- Fondazione Pisana per la Scienza, San Giuliano Terme, 56017 Pisa, Italy; (F.L.); (S.F.); (M.G.); (C.M.M.)
| | - Gianmarco Ferri
- Fondazione Pisana per la Scienza, San Giuliano Terme, 56017 Pisa, Italy; (F.L.); (S.F.); (M.G.); (C.M.M.)
| | - Manuel Giacomarra
- Fondazione Pisana per la Scienza, San Giuliano Terme, 56017 Pisa, Italy; (F.L.); (S.F.); (M.G.); (C.M.M.)
| | - Michele Menicagli
- Fondazione Pisana per la Scienza, San Giuliano Terme, 56017 Pisa, Italy; (F.L.); (S.F.); (M.G.); (C.M.M.)
| | - Carlo Gambacciani
- Neurosurgical Department of Spedali Riuniti di Livorno, 57124 Livorno, Italy (O.S.S.)
| | - Francesco Pieri
- Neurosurgical Department of Spedali Riuniti di Livorno, 57124 Livorno, Italy (O.S.S.)
| | - Francesco Pasqualetti
- Radiotherapy Department, Azienda Ospedaliera Universitaria Pisana, 56126 Pisa, Italy
| | - Nicola Montemurro
- Department of Neurosurgery, Azienda Ospedaliera Universitaria Pisana, 56126 Pisa, Italy;
| | - Paolo Aretini
- Fondazione Pisana per la Scienza, San Giuliano Terme, 56017 Pisa, Italy; (F.L.); (S.F.); (M.G.); (C.M.M.)
| | | | - Anna Luisa Di Stefano
- Neurosurgical Department of Spedali Riuniti di Livorno, 57124 Livorno, Italy (O.S.S.)
| | - Chiara Maria Mazzanti
- Fondazione Pisana per la Scienza, San Giuliano Terme, 56017 Pisa, Italy; (F.L.); (S.F.); (M.G.); (C.M.M.)
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3
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Mitiushkina NV, Tiurin VI, Anuskina AA, Bordovskaya NA, Shestakova AD, Martianov AS, Bubnov MG, Shishkina AS, Semina MV, Romanko AA, Kuligina ES, Imyanitov EN. Molecular Analysis of Biliary Tract Cancers with the Custom 3' RACE-Based NGS Panel. Diagnostics (Basel) 2023; 13:3168. [PMID: 37891989 PMCID: PMC10605186 DOI: 10.3390/diagnostics13203168] [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: 09/02/2023] [Revised: 10/05/2023] [Accepted: 10/08/2023] [Indexed: 10/29/2023] Open
Abstract
The technique 3' rapid amplification of cDNA ends (3' RACE) allows for detection of translocations with unknown gene partners located at the 3' end of the chimeric transcript. We composed a 3' RACE-based RNA sequencing panel for the analysis of FGFR1-4 gene rearrangements, detection of activating mutations located within FGFR1-4, IDH1/2, ERBB2 (HER2), KRAS, NRAS, BRAF, and PIK3CA genes, and measurement of the expression of ERBB2, PD-L1, and FGFR1-4 transcripts. This NGS panel was utilized for the molecular profiling of 168 biliary tract carcinomas (BTCs), including 83 intrahepatic cholangiocarcinomas (iCCAs), 44 extrahepatic cholangiocarcinomas (eCCAs), and 41 gallbladder adenocarcinomas (GBAs). The NGS failure rate was 3/168 (1.8%). iCCAs, but not other categories of BTCs, were characterized by frequent FGFR2 alterations (17/82, 20.7%) and IDH1/2 mutations (23/82, 28%). Other potentially druggable events included ERBB2 amplifications or mutations (7/165, 4.2% of all successfully analyzed BTCs) and BRAF p.V600E mutations (3/165, 1.8%). In addition to NGS, we analyzed microsatellite instability (MSI) using the standard five markers and revealed this event in 3/158 (1.9%) BTCs. There were no instances of ALK, ROS1, RET, and NTRK1-3 gene rearrangements or MET exon 14 skipping mutations. Parallel analysis of 47 iCCA samples with the Illumina TruSight Tumor 170 kit confirmed good performance of our NGS panel. In conclusion, targeted RNA sequencing coupled with the 3' RACE technology is an efficient tool for the molecular diagnostics of BTCs.
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Affiliation(s)
- Natalia V. Mitiushkina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St. Petersburg, Russia; (N.V.M.); (N.A.B.); (A.S.S.); (M.V.S.); (A.A.R.); (E.S.K.)
| | - Vladislav I. Tiurin
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St. Petersburg, Russia; (N.V.M.); (N.A.B.); (A.S.S.); (M.V.S.); (A.A.R.); (E.S.K.)
| | - Aleksandra A. Anuskina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St. Petersburg, Russia; (N.V.M.); (N.A.B.); (A.S.S.); (M.V.S.); (A.A.R.); (E.S.K.)
| | - Natalia A. Bordovskaya
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St. Petersburg, Russia; (N.V.M.); (N.A.B.); (A.S.S.); (M.V.S.); (A.A.R.); (E.S.K.)
| | - Anna D. Shestakova
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St. Petersburg, Russia; (N.V.M.); (N.A.B.); (A.S.S.); (M.V.S.); (A.A.R.); (E.S.K.)
| | - Aleksandr S. Martianov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St. Petersburg, Russia; (N.V.M.); (N.A.B.); (A.S.S.); (M.V.S.); (A.A.R.); (E.S.K.)
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, 194100 St. Petersburg, Russia
| | - Mikhail G. Bubnov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St. Petersburg, Russia; (N.V.M.); (N.A.B.); (A.S.S.); (M.V.S.); (A.A.R.); (E.S.K.)
| | - Anna S. Shishkina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St. Petersburg, Russia; (N.V.M.); (N.A.B.); (A.S.S.); (M.V.S.); (A.A.R.); (E.S.K.)
| | - Maria V. Semina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St. Petersburg, Russia; (N.V.M.); (N.A.B.); (A.S.S.); (M.V.S.); (A.A.R.); (E.S.K.)
| | - Aleksandr A. Romanko
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St. Petersburg, Russia; (N.V.M.); (N.A.B.); (A.S.S.); (M.V.S.); (A.A.R.); (E.S.K.)
| | - Ekaterina S. Kuligina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St. Petersburg, Russia; (N.V.M.); (N.A.B.); (A.S.S.); (M.V.S.); (A.A.R.); (E.S.K.)
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, 194100 St. Petersburg, Russia
| | - Evgeny N. Imyanitov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St. Petersburg, Russia; (N.V.M.); (N.A.B.); (A.S.S.); (M.V.S.); (A.A.R.); (E.S.K.)
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, 194100 St. Petersburg, Russia
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4
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Qi D, Li J, Quarles CC, Fonkem E, Wu E. Assessment and prediction of glioblastoma therapy response: challenges and opportunities. Brain 2023; 146:1281-1298. [PMID: 36445396 PMCID: PMC10319779 DOI: 10.1093/brain/awac450] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 11/03/2022] [Accepted: 11/10/2022] [Indexed: 11/30/2022] Open
Abstract
Glioblastoma is the most aggressive type of primary adult brain tumour. The median survival of patients with glioblastoma remains approximately 15 months, and the 5-year survival rate is <10%. Current treatment options are limited, and the standard of care has remained relatively constant since 2011. Over the last decade, a range of different treatment regimens have been investigated with very limited success. Tumour recurrence is almost inevitable with the current treatment strategies, as glioblastoma tumours are highly heterogeneous and invasive. Additionally, another challenging issue facing patients with glioblastoma is how to distinguish between tumour progression and treatment effects, especially when relying on routine diagnostic imaging techniques in the clinic. The specificity of routine imaging for identifying tumour progression early or in a timely manner is poor due to the appearance similarity of post-treatment effects. Here, we concisely describe the current status and challenges in the assessment and early prediction of therapy response and the early detection of tumour progression or recurrence. We also summarize and discuss studies of advanced approaches such as quantitative imaging, liquid biomarker discovery and machine intelligence that hold exceptional potential to aid in the therapy monitoring of this malignancy and early prediction of therapy response, which may decisively transform the conventional detection methods in the era of precision medicine.
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Affiliation(s)
- Dan Qi
- Department of Neurosurgery and Neuroscience Institute, Baylor Scott & White Health, Temple, TX 76502, USA
| | - Jing Li
- School of Industrial and Systems Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - C Chad Quarles
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Ekokobe Fonkem
- Department of Neurosurgery and Neuroscience Institute, Baylor Scott & White Health, Temple, TX 76502, USA
- Department of Medical Education, School of Medicine, Texas A&M University, Bryan, TX 77807, USA
| | - Erxi Wu
- Department of Neurosurgery and Neuroscience Institute, Baylor Scott & White Health, Temple, TX 76502, USA
- Department of Medical Education, School of Medicine, Texas A&M University, Bryan, TX 77807, USA
- Department of Pharmaceutical Sciences, Irma Lerma Rangel School of Pharmacy, Texas A&M University, College Station, TX 77843, USA
- Department of Oncology and LIVESTRONG Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA
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5
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Qi D, Geng Y, Cardenas J, Gu J, Yi SS, Huang JH, Fonkem E, Wu E. Transcriptomic analyses of patient peripheral blood with hemoglobin depletion reveal glioblastoma biomarkers. NPJ Genom Med 2023; 8:2. [PMID: 36697401 PMCID: PMC9877004 DOI: 10.1038/s41525-022-00348-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 12/21/2022] [Indexed: 01/26/2023] Open
Abstract
Peripheral blood is gaining prominence as a noninvasive alternative to tissue biopsy to develop biomarkers for glioblastoma (GBM); however, widely utilized blood-based biomarkers in clinical settings have not yet been identified due to the lack of a robust detection approach. Here, we describe the application of globin reduction in RNA sequencing of whole blood (i.e., WBGR) and perform transcriptomic analysis to identify GBM-associated transcriptomic changes. By using WBGR, we improved the detection sensitivity of informatic reads and identified differential gene expression in GBM blood. By analyzing tumor tissues, we identified transcriptomic traits of GBM blood. Further functional enrichment analyses retained the most changed genes in GBM. Subsequent validation elicited a 10-gene panel covering mRNA, long noncoding RNA, and microRNA (i.e., GBM-Dx panel) that has translational potential to aid in the early detection or clinical management of GBM. Here, we report an integrated approach, WBGR, with comprehensive analytic capacity for blood-based marker identification.
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Affiliation(s)
- Dan Qi
- Department of Neurosurgery and Neuroscience Institute, Baylor Scott & White Health, Temple, TX, 76508, USA
| | - Yiqun Geng
- Department of Neurosurgery and Neuroscience Institute, Baylor Scott & White Health, Temple, TX, 76508, USA
- Laboratory of Molecular Pathology, Shantou University Medical College, 515041, Shantou, China
| | - Jacob Cardenas
- Baylor Scott & White Research Institute, Dallas, TX, 75204, USA
| | - Jinghua Gu
- Baylor Scott & White Research Institute, Dallas, TX, 75204, USA
| | - S Stephen Yi
- Institute for Cellular and Molecular Biology (ICMB), College of Natural Sciences, The University of Texas at Austin, Austin, TX, 78712, USA
- Oden Institute for Computational Engineering and Sciences (ICES), The University of Texas at Austin, Austin, TX, 78712, USA
- Department of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
- Department of Oncology, LIVESTRONG Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Jason H Huang
- Department of Neurosurgery and Neuroscience Institute, Baylor Scott & White Health, Temple, TX, 76508, USA.
- Texas A & M University School of Medicine, Temple, TX, 76508, USA.
| | - Ekokobe Fonkem
- Department of Neurosurgery and Neuroscience Institute, Baylor Scott & White Health, Temple, TX, 76508, USA.
- Texas A & M University School of Medicine, Temple, TX, 76508, USA.
| | - Erxi Wu
- Department of Neurosurgery and Neuroscience Institute, Baylor Scott & White Health, Temple, TX, 76508, USA.
- Department of Oncology, LIVESTRONG Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, 78712, USA.
- Texas A & M University School of Medicine, Temple, TX, 76508, USA.
- Texas A & M University School of Pharmacy, College Station, TX, 77843, USA.
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Vermeirssen V, Deleu J, Morlion A, Everaert C, De Wilde J, Anckaert J, Durinck K, Nuytens J, Rishfi M, Speleman F, Van Droogenbroeck H, Verniers K, Baietti M, Albersen M, Leucci E, Post E, Best M, Van Maerken T, De Wilde B, Vandesompele J, Decock A. Whole transcriptome profiling of liquid biopsies from tumour xenografted mouse models enables specific monitoring of tumour-derived extracellular RNA. NAR Cancer 2022; 4:zcac037. [DOI: 10.1093/narcan/zcac037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 09/23/2022] [Accepted: 11/18/2022] [Indexed: 11/29/2022] Open
Abstract
Abstract
While cell-free DNA (cfDNA) is widely being investigated, free circulating RNA (extracellular RNA, exRNA) has the potential to improve cancer therapy response monitoring and detection due to its dynamic nature. However, it remains unclear in which blood subcompartment tumour-derived exRNAs primarily reside. We developed a host-xenograft deconvolution framework, exRNAxeno, with mapping strategies to either a combined human-mouse reference genome or both species genomes in parallel, applicable to exRNA sequencing data from liquid biopsies of human xenograft mouse models. The tool enables to distinguish (human) tumoural RNA from (murine) host RNA, to specifically analyse tumour-derived exRNA. We applied the combined pipeline to total exRNA sequencing data from 95 blood-derived liquid biopsy samples from 30 mice, xenografted with 11 different tumours. Tumoural exRNA concentrations are not determined by plasma platelet levels, while host exRNA concentrations increase with platelet content. Furthermore, a large variability in exRNA abundance and transcript content across individual mice is observed. The tumoural gene detectability in plasma is largely correlated with the RNA expression levels in the tumour tissue or cell line. These findings unravel new aspects of tumour-derived exRNA biology in xenograft models and open new avenues to further investigate the role of exRNA in cancer.
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Affiliation(s)
- Vanessa Vermeirssen
- Lab for Computational Biology, Integromics and Gene Regulation (CBIGR), Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
- Department of Biomedical Molecular Biology, Ghent University , 9000, Ghent , Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
| | - Jill Deleu
- OncoRNALab, Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
| | - Annelien Morlion
- OncoRNALab, Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
| | - Celine Everaert
- OncoRNALab, Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
| | - Jilke De Wilde
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
- Department of Pathology, Ghent University Hospital , 9000, Ghent , Belgium
| | - Jasper Anckaert
- OncoRNALab, Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
| | - Kaat Durinck
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
- Pediatric Precision Oncology Lab (PPOL), Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
| | - Justine Nuytens
- OncoRNALab, Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
| | - Muhammad Rishfi
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
- Pediatric Precision Oncology Lab (PPOL), Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
| | - Frank Speleman
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
- Pediatric Precision Oncology Lab (PPOL), Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
| | - Hanne Van Droogenbroeck
- OncoRNALab, Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
| | - Kimberly Verniers
- OncoRNALab, Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
| | - Maria Francesca Baietti
- Laboratory for RNA Cancer Biology, Department of Oncology , KU Leuven, 3000, Leuven , Belgium
- TRACE, Leuven Cancer Institute , KU Leuven, 3000, Leuven, Belgium
| | - Maarten Albersen
- Department of Development and Regeneration, Laboratory of Experimental Urology, KU Leuven, Department of Urology, University Hospitals Leuven , 3000, Leuven , Belgium
| | - Eleonora Leucci
- Laboratory for RNA Cancer Biology, Department of Oncology , KU Leuven, 3000, Leuven , Belgium
- TRACE, Leuven Cancer Institute , KU Leuven, 3000, Leuven, Belgium
| | - Edward Post
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Department of Neurosurgery , Boelelaan 1117, 1081 HV, Amsterdam , the Netherlands
- Cancer Center Amsterdam, Brain Tumor Center and Liquid Biopsy Center , 1081 HV, Amsterdam , the Netherlands
| | - Myron G Best
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Department of Neurosurgery , Boelelaan 1117, 1081 HV, Amsterdam , the Netherlands
- Cancer Center Amsterdam, Brain Tumor Center and Liquid Biopsy Center , 1081 HV, Amsterdam , the Netherlands
| | - Tom Van Maerken
- OncoRNALab, Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
- Department of Laboratory Medicine , AZ Groeninge, 8500, Kortrijk , Belgium
| | - Bram De Wilde
- OncoRNALab, Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
- Department of Paediatric Haematology Oncology and Stem Cell Transplantation, Ghent University Hospital , 9000, Ghent , Belgium
| | - Jo Vandesompele
- OncoRNALab, Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
| | - Anneleen Decock
- OncoRNALab, Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
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Cucciniello L, Gerratana L, Puglisi F. Liquid Biopsy, an Everchanging Balance between Clinical Utility and Emerging Technologies. Cancers (Basel) 2022; 14:4277. [PMID: 36077819 PMCID: PMC9454764 DOI: 10.3390/cancers14174277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 08/29/2022] [Accepted: 08/31/2022] [Indexed: 11/17/2022] Open
Abstract
To date, tissue biopsy still represents the mainstay for tumor diagnosis and molecular characterization [...].
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Affiliation(s)
- Linda Cucciniello
- Department of Medicine (DAME), University of Udine, 33100 Udine, Italy
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Lorenzo Gerratana
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
| | - Fabio Puglisi
- Department of Medicine (DAME), University of Udine, 33100 Udine, Italy
- Department of Medical Oncology, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, 33081 Aviano, Italy
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8
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Tang F, Fan J, Zhang X, Zou Z, Xiao D, Li X. The Role of Vti1a in Biological Functions and Its Possible Role in Nervous System Disorders. Front Mol Neurosci 2022; 15:918664. [PMID: 35711736 PMCID: PMC9197314 DOI: 10.3389/fnmol.2022.918664] [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: 04/12/2022] [Accepted: 05/09/2022] [Indexed: 11/24/2022] Open
Abstract
Vesicle transport through interaction with t-SNAREs 1A (Vti1a), a member of the N-ethylmaleimide-sensitive factor attachment protein receptor protein family, is involved in cell signaling as a vesicular protein and mediates vesicle trafficking. Vti1a appears to have specific roles in neurons, primarily by regulating upstream neurosecretory events that mediate exocytotic proteins and the availability of secretory organelles, as well as regulating spontaneous synaptic transmission and postsynaptic efficacy to control neurosecretion. Vti1a also has essential roles in neural development, autophagy, and unconventional extracellular transport of neurons. Studies have shown that Vti1a dysfunction plays critical roles in pathological mechanisms of Hepatic encephalopathy by influencing spontaneous neurotransmission. It also may have an unknown role in amyotrophic lateral sclerosis. A VTI1A variant is associated with the risk of glioma, and the fusion product of the VTI1A gene and the adjacent TCF7L2 gene is involved in glioma development. This review summarizes Vti1a functions in neurons and highlights the role of Vti1a in the several nervous system disorders.
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Affiliation(s)
- Fajuan Tang
- Department of Emergency, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Jiali Fan
- Department of Emergency, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Xiaoyan Zhang
- Department of Emergency, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Zhuan Zou
- Department of Emergency, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Dongqiong Xiao
- Department of Emergency, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
- Dongqiong Xiao,
| | - Xihong Li
- Department of Emergency, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
- *Correspondence: Xihong Li,
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9
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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: 10] [Impact Index Per Article: 5.0] [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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10
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Panachan J, Rojsirikulchai N, Pongsakul N, Khowawisetsut L, Pongphitcha P, Siriboonpiputtana T, Chareonsirisuthigul T, Phornsarayuth P, Klinkulab N, Jinawath N, Chiangjong W, Anurathapan U, Pattanapanyasat K, Hongeng S, Chutipongtanate S. Extracellular Vesicle-Based Method for Detecting MYCN Amplification Status of Pediatric Neuroblastoma. Cancers (Basel) 2022; 14:cancers14112627. [PMID: 35681607 PMCID: PMC9179557 DOI: 10.3390/cancers14112627] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/17/2022] [Accepted: 05/20/2022] [Indexed: 01/02/2023] Open
Abstract
Simple Summary MYCN gene amplification, the strongest prognostic marker of aggressive neuroblastoma, is detected on invasive biopsy tissues. This study aimed to establish a less invasive method to detect MYCN status based on MYCN mRNA contents in large extracellular vesicles or microvesicles. MYCN mRNA-containing microvesicles were detectable in three distinct MYCN-amplified neuroblastoma cell lines but absent in three neuroblastoma cells with MYCN-non-amplification. The feasibility of this EV-based workflow was successfully demonstrated by using the simulated samples (prepared by pulsing neuroblastoma MVs into the normal human serum) and bone marrow plasma specimens obtained from nine patients at various disease stages. Taken together, this study established the novel EV-based method for detecting MYCN status in pediatric neuroblastoma. Abstract MYCN amplification is the strongest predictor of high-risk neuroblastoma (NB). The standard procedure to detect MYCN status requires invasive procedures. Extracellular vesicles (EVs) contain molecular signatures of originated cells, present in biofluids, and serve as an invaluable source for cancer liquid biopsies. This study aimed to establish an EV-based method to detect the MYCN status of NB. Two EV subtypes, i.e., microvesicles (MVs) and exosomes, were sequentially isolated from the culture supernatant by step-wise centrifugation, ultrafiltration, and size-exclusion chromatography. Quantitative RT-PCR was performed to detect MYCN mRNA. As a result, MYCN mRNA was detectable in the MVs, but not exosomes, of MYCN-amplified NB cells. MYCN mRNA-containing MVs (MYCN-MV) were successfully detected in three distinct MYCN-amplified NB cell lines but absent in three MYCN non-amplification cells. The simulated samples were prepared by pulsing MVs into human serum. MYCN–MV detection in the simulated samples showed a less interfering effect from the human blood matrix. Validation using clinical specimens (2 mL bone marrow plasma) obtained from patients at various disease stages showed a promising result. Five out of six specimens of MYCN-amplified patients showed positive results, while there were no false positives in four plasma samples of the MYCN non-amplification group. This study communicated a novel EV-based method for detecting the MYCN status of pediatric NB based on MYCN mRNA contents in MVs. Future studies should be pursued in a prospective cohort to determine its true diagnostic performance.
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Affiliation(s)
- Jirawan Panachan
- Department of Pediatrics, Division of Hematology and Oncology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (J.P.); (P.P.); (U.A.)
| | - Napat Rojsirikulchai
- Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
- Pediatric Translational Research Unit, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (N.P.); (W.C.)
| | - Nutkridta Pongsakul
- Pediatric Translational Research Unit, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (N.P.); (W.C.)
| | - Ladawan Khowawisetsut
- Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand;
| | - Pongpak Pongphitcha
- Department of Pediatrics, Division of Hematology and Oncology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (J.P.); (P.P.); (U.A.)
| | - Teerapong Siriboonpiputtana
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (T.S.); (T.C.); (P.P.); (N.K.)
| | - Takol Chareonsirisuthigul
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (T.S.); (T.C.); (P.P.); (N.K.)
| | - Pitichai Phornsarayuth
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (T.S.); (T.C.); (P.P.); (N.K.)
| | - Nisakorn Klinkulab
- Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (T.S.); (T.C.); (P.P.); (N.K.)
| | - Natini Jinawath
- Program in Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Bangkok 10700, Thailand;
| | - Wararat Chiangjong
- Pediatric Translational Research Unit, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (N.P.); (W.C.)
| | - Usanarat Anurathapan
- Department of Pediatrics, Division of Hematology and Oncology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (J.P.); (P.P.); (U.A.)
| | - Kovit Pattanapanyasat
- Center of Excellence for Microparticle and Exosome in Diseases, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand;
| | - Suradej Hongeng
- Department of Pediatrics, Division of Hematology and Oncology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (J.P.); (P.P.); (U.A.)
- Correspondence: (S.H.); or (S.C.)
| | - Somchai Chutipongtanate
- Pediatric Translational Research Unit, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (N.P.); (W.C.)
- Department of Environmental and Public Health Sciences, Division of Epidemiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
- Correspondence: (S.H.); or (S.C.)
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11
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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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12
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Firdous S, Abid R, Nawaz Z, Bukhari F, Anwer A, Cheng LL, Sadaf S. Dysregulated Alanine as a Potential Predictive Marker of Glioma-An Insight from Untargeted HRMAS-NMR and Machine Learning Data. Metabolites 2021; 11:metabo11080507. [PMID: 34436448 PMCID: PMC8402070 DOI: 10.3390/metabo11080507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 07/22/2021] [Accepted: 07/28/2021] [Indexed: 01/04/2023] Open
Abstract
Metabolic alterations play a crucial role in glioma development and progression and can be detected even before the appearance of the fatal phenotype. We have compared the circulating metabolic fingerprints of glioma patients versus healthy controls, for the first time, in a quest to identify a panel of small, dysregulated metabolites with potential to serve as a predictive and/or diagnostic marker in the clinical settings. High-resolution magic angle spinning nuclear magnetic resonance spectroscopy (HRMAS-NMR) was used for untargeted metabolomics and data acquisition followed by a machine learning (ML) approach for the analyses of large metabolic datasets. Cross-validation of ML predicted NMR spectral features was done by statistical methods (Wilcoxon-test) using JMP-pro16 software. Alanine was identified as the most critical metabolite with potential to detect glioma with precision of 1.0, recall of 0.96, and F1 measure of 0.98. The top 10 metabolites identified for glioma detection included alanine, glutamine, valine, methionine, N-acetylaspartate (NAA), γ-aminobutyric acid (GABA), serine, α-glucose, lactate, and arginine. We achieved 100% accuracy for the detection of glioma using ML algorithms, extra tree classifier, and random forest, and 98% accuracy with logistic regression. Classification of glioma in low and high grades was done with 86% accuracy using logistic regression model, and with 83% and 79% accuracy using extra tree classifier and random forest, respectively. The predictive accuracy of our ML model is superior to any of the previously reported algorithms, used in tissue- or liquid biopsy-based metabolic studies. The identified top metabolites can be targeted to develop early diagnostic methods as well as to plan personalized treatment strategies.
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Affiliation(s)
- Safia Firdous
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore 54590, Pakistan; (S.F.); (R.A.)
- Riphah College of Rehabilitation and Allied Health Sciences, Riphah International University, Lahore 54770, Pakistan
| | - Rizwan Abid
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore 54590, Pakistan; (S.F.); (R.A.)
| | - Zubair Nawaz
- Department of Data Science, Punjab University College of Information Technology, University of the Punjab, Lahore 54590, Pakistan; (Z.N.); (F.B.)
| | - Faisal Bukhari
- Department of Data Science, Punjab University College of Information Technology, University of the Punjab, Lahore 54590, Pakistan; (Z.N.); (F.B.)
| | - Ammar Anwer
- Punjab Institute of Neurosciences (PINS), Lahore General Hospital, Lahore 54000, Pakistan;
| | - Leo L. Cheng
- Departments of Radiology and Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA;
| | - Saima Sadaf
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore 54590, Pakistan; (S.F.); (R.A.)
- Correspondence:
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