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Luo X, Li J, Huang G, Xie F, He Z, Zeng X, Tian H, Liu Y, Fu W, Yang X. Metal-Graphene Hybrid Terahertz Metasurfaces for Circulating Tumor DNA Detection Based on Dual Signal Amplification. ACS Sens 2024. [PMID: 38602840 DOI: 10.1021/acssensors.4c00168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
Terahertz (THz) spectroscopy has impressive capability for label-free biosensing, but its utility in clinical laboratories is rarely reported due to often unsatisfactory detection performances. Here, we fabricated metal-graphene hybrid THz metasurfaces (MSs) for the sensitive and enzyme-free detection of circulating tumor DNA (ctDNA) in pancreatic cancer plasma samples. The feasibility and mechanism of the enhanced effects of a graphene bridge across the MS and amplified by gold nanoparticles (AuNPs) were investigated experimentally and theoretically. The AuNPs serve to boost charge injection in the graphene film and result in producing a remarkable change in the graded transmissivity index to THz radiation of the MS resonators. Assay design utilizes this feature and a cascade hybridization chain reaction initiated on magnetic beads in the presence of target ctDNA to achieve dual signal amplification (chemical and optical). In addition to demonstrating subfemtomolar detection sensitivity and single-nucleotide mismatch selectivity, the proposed method showed remarkable capability to discriminate between pancreatic cancer patients and healthy individuals by recognizing and quantifying targeted ctDNAs. The introduction of graphene to the metasurface produces an improved sensitivity of 2 orders of magnitude for ctDNA detection. This is the first study to report the combined application of graphene and AuNPs in biosensing by THz spectroscopic resonators and provides a combined identification scheme to detect and discriminate different biological analytes, including nucleic acids, proteins, and various biomarkers.
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Affiliation(s)
- Xizi Luo
- Department of Laboratory Medicine, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Jining Li
- Institute of Laser and Optoelectronics, School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin 300072, China
| | - Guorong Huang
- Department of Laboratory Medicine, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Fengxin Xie
- Department of Laboratory Medicine, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Zhe He
- Department of Laboratory Medicine, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Xiaojun Zeng
- Department of Laboratory Medicine, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Huiyan Tian
- Department of Laboratory Medicine, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Yu Liu
- Department of Laboratory Medicine, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Weiling Fu
- Department of Laboratory Medicine, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Xiang Yang
- Department of Laboratory Medicine, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing 400038, China
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Fu X, Luo Z, Deng Y, LaFramboise W, Bartlett D, Schwartz R. Marker selection strategies for circulating tumor DNA guided by phylogenetic inference. bioRxiv 2024:2024.03.21.585352. [PMID: 38586041 PMCID: PMC10996527 DOI: 10.1101/2024.03.21.585352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Motivation Blood-based profiling of tumor DNA ("liquid biopsy") has offered great prospects for non-invasive early cancer diagnosis, treatment monitoring, and clinical guidance, but require further advances in computational methods to become a robust quantitative assay of tumor clonal evolution. We propose new methods to better characterize tumor clonal dynamics from circulating tumor DNA (ctDNA), through application to two specific questions: 1) How to apply longitudinal ctDNA data to refine phylogeny models of clonal evolution, and 2) how to quantify changes in clonal frequencies that may be indicative of treatment response or tumor progression. We pose these questions through a probabilistic framework for optimally identifying maximum likelihood markers and applying them to characterizing clonal evolution. Results We first estimate a distribution over plausible clonal lineage models, using bootstrap samples over pre-treatment tissue-based sequence data. We then refine these lineage models and the clonal frequencies they imply over successive longitudinal samples. We use the resulting framework for modeling and refining tree distributions to pose a set of optimization problems to select ctDNA markers to maximize measures of utility capturing ability to solve the two questions of reducing uncertain in phylogeny models or quantifying clonal frequencies given the models. We tested our methods on synthetic data and showed them to be effective at refining distributions of tree models and clonal frequencies so as to minimize measures of tree distance relative to the ground truth. Application of the tree refinement methods to real tumor data further demonstrated their effectiveness in refining a clonal lineage model and assessing its clonal frequencies. The work shows the power of computational methods to improve marker selection, clonal lineage reconstruction, and clonal dynamics profiling for more precise and quantitative assays of tumor progression. Availability https://github.com/CMUSchwartzLab/Mase-phi.git. Contact russells@andrew.cmu.edu.
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Affiliation(s)
- Xuecong Fu
- Department of Biological Sciences, Carnegie Mellon University, 5000 Forbes Avenue, 15217, Pittsburgh, PA, USA
| | - Zhicheng Luo
- Department of Biological Sciences, Carnegie Mellon University, 5000 Forbes Avenue, 15217, Pittsburgh, PA, USA
| | - Yueqian Deng
- Ray and Stephanie Lane Computational Biology Department, Carnegie Mellon University, 5000 Forbes Avenue, 15217, Pittsburgh, PA, USA
| | - William LaFramboise
- Allegheny Health Network Cancer Institute, Allegheny Health Network, 320 East North Avenue, 15212, Pittsburgh, PA, USA
| | - David Bartlett
- Allegheny Health Network Cancer Institute, Allegheny Health Network, 320 East North Avenue, 15212, Pittsburgh, PA, USA
| | - Russell Schwartz
- Department of Biological Sciences, Carnegie Mellon University, 5000 Forbes Avenue, 15217, Pittsburgh, PA, USA
- Ray and Stephanie Lane Computational Biology Department, Carnegie Mellon University, 5000 Forbes Avenue, 15217, Pittsburgh, PA, USA
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Ben-Ami R, Wang QL, Zhang J, Supplee JG, Fahrmann JF, Lehmann-Werman R, Brais LK, Nowak J, Yuan C, Loftus M, Babic A, Irajizad E, Davidi T, Zick A, Hubert A, Neiman D, Piyanzin S, Gal-Rosenberg O, Horn A, Shemer R, Glaser B, Boos N, Jajoo K, Lee L, Clancy TE, Rubinson DA, Ng K, Chabot JA, Kastrinos F, Kluger M, Aguirre AJ, Jänne PA, Bardeesy N, Stanger B, O'Hara MH, Till J, Maitra A, Carpenter EL, Bullock AJ, Genkinger J, Hanash SM, Paweletz CP, Dor Y, Wolpin BM. Protein biomarkers and alternatively methylated cell-free DNA detect early stage pancreatic cancer. Gut 2024; 73:639-648. [PMID: 38123998 PMCID: PMC10958271 DOI: 10.1136/gutjnl-2023-331074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/26/2023] [Indexed: 12/23/2023]
Abstract
OBJECTIVE Pancreatic ductal adenocarcinoma (PDAC) is commonly diagnosed at an advanced stage. Liquid biopsy approaches may facilitate detection of early stage PDAC when curative treatments can be employed. DESIGN To assess circulating marker discrimination in training, testing and validation patient cohorts (total n=426 patients), plasma markers were measured among PDAC cases and patients with chronic pancreatitis, colorectal cancer (CRC), and healthy controls. Using CA19-9 as an anchor marker, measurements were made of two protein markers (TIMP1, LRG1) and cell-free DNA (cfDNA) pancreas-specific methylation at 9 loci encompassing 61 CpG sites. RESULTS Comparative methylome analysis identified nine loci that were differentially methylated in exocrine pancreas DNA. In the training set (n=124 patients), cfDNA methylation markers distinguished PDAC from healthy and CRC controls. In the testing set of 86 early stage PDAC and 86 matched healthy controls, CA19-9 had an area under the receiver operating characteristic curve (AUC) of 0.88 (95% CI 0.83 to 0.94), which was increased by adding TIMP1 (AUC 0.92; 95% CI 0.88 to 0.96; p=0.06), LRG1 (AUC 0.92; 95% CI 0.88 to 0.96; p=0.02) or exocrine pancreas-specific cfDNA methylation markers at nine loci (AUC 0.92; 95% CI 0.88 to 0.96; p=0.02). In the validation set of 40 early stage PDAC and 40 matched healthy controls, a combined panel including CA19-9, TIMP1 and a 9-loci cfDNA methylation panel had greater discrimination (AUC 0.86, 95% CI 0.77 to 0.95) than CA19-9 alone (AUC 0.82; 95% CI 0.72 to 0.92). CONCLUSION A combined panel of circulating markers including proteins and methylated cfDNA increased discrimination compared with CA19-9 alone for early stage PDAC.
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Affiliation(s)
- Roni Ben-Ami
- Department of Developmental Biology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Qiao-Li Wang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Jinming Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Julianna G Supplee
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Johannes F Fahrmann
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Roni Lehmann-Werman
- Department of Developmental Biology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Lauren K Brais
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Jonathan Nowak
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Chen Yuan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Maureen Loftus
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Ana Babic
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Ehsan Irajizad
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Tal Davidi
- Sharett Institute of Oncology, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | - Aviad Zick
- Sharett Institute of Oncology, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | - Ayala Hubert
- Sharett Institute of Oncology, Hebrew University-Hadassah Medical Center, Jerusalem, Israel
| | - Daniel Neiman
- Department of Developmental Biology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sheina Piyanzin
- Department of Developmental Biology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ofer Gal-Rosenberg
- Department of Developmental Biology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Amit Horn
- Department of Developmental Biology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ruth Shemer
- Department of Developmental Biology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Benjamin Glaser
- Department of Developmental Biology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Endocrinology and Metabolism, Hadassah Medical Center, Jerusalem, Israel
| | - Natalia Boos
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Kunal Jajoo
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Linda Lee
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Thomas E Clancy
- Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Douglas A Rubinson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Kimmie Ng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - John A Chabot
- Department of Surgery, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, USA
| | - Fay Kastrinos
- Division of Digestive and Liver Diseases, Columbia University Irving Medical Cancer and the Vagelos College of Physicians and Surgeons, New York, New York, USA
| | - Michael Kluger
- Department of Surgery, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, USA
| | - Andrew J Aguirre
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Pasi A Jänne
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Nabeel Bardeesy
- Massachusetts General Hospital Cancer Center, Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Ben Stanger
- Department of Medicine, Division of Gastroenterology, Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Mark H O'Hara
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jacob Till
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Anirban Maitra
- Department of Pathology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas, USA
| | - Erica L Carpenter
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Andrea J Bullock
- Division of Hematology and Oncology, Beth-Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA
| | - Jeanine Genkinger
- Department of epidemiology, Mailman school of public health, Columbia university, New York, New York, USA
- Herbert Irving Comprehensive Cancer Center, Columbia university Irving Medical Center, New York, New York, USA
| | - Samir M Hanash
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Cloud P Paweletz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Yuval Dor
- Department of Developmental Biology and Cancer Research, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Brian M Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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Singh S, Raucci A, Cimmino W, Cinti S. Paper-Based Analytical Devices for Cancer Liquid Biopsy. Anal Chem 2024; 96:3698-3706. [PMID: 38377543 DOI: 10.1021/acs.analchem.3c04478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Liquid biopsies have caused a significant revolution in cancer diagnosis, and the use of point of care (PoC) platforms has the potential to bring liquid biopsy-based cancer detection closer to patients. These platforms provide rapid and on-site analysis by reducing the time between sample collection and results output. The aim of this tutorial content is to provide readers an in-depth understanding regarding the choice of the ideal sensing platform suitable for specific cancer-related biomarkers.
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Affiliation(s)
- Sima Singh
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy
| | - Ada Raucci
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy
| | - Wanda Cimmino
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy
| | - Stefano Cinti
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131 Naples, Italy
- BAT Center- Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology, University of Napoli Federico II, 80055 Naples, Italy
- Bioelectronics Task Force at University of Naples Federico II, Via Cinthia 21, 80126 Naples, Italy
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5
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Sacino AN, Chen H, Sahgal A, Bettegowda C, Rhines LD, Maralani P, Redmond KJ. Stereotactic body radiation therapy for spinal metastases: A new standard of care. Neuro Oncol 2024; 26:S76-S87. [PMID: 38437670 PMCID: PMC10911798 DOI: 10.1093/neuonc/noad225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024] Open
Abstract
Advancements in systemic therapies for patients with metastatic cancer have improved overall survival and, hence, the number of patients living with spinal metastases. As a result, the need for more versatile and personalized treatments for spinal metastases to optimize long-term pain and local control has become increasingly important. Stereotactic body radiation therapy (SBRT) has been developed to meet this need by providing precise and conformal delivery of ablative high-dose-per-fraction radiation in few fractions while minimizing risk of toxicity. Additionally, advances in minimally invasive surgical techniques have also greatly improved care for patients with epidural disease and/or unstable spines, which may then be combined with SBRT for durable local control. In this review, we highlight the indications and controversies of SBRT along with new surgical techniques for the treatment of spinal metastases.
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Affiliation(s)
- Amanda N Sacino
- Department of Neurosurgery, John Hopkins University, Baltimore, Maryland, USA
| | - Hanbo Chen
- Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Ontario, Canada
| | - Arjun Sahgal
- Department of Radiation Oncology, Odette Cancer Centre, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Ontario, Canada
| | - Chetan Bettegowda
- Department of Neurosurgery, John Hopkins University, Baltimore, Maryland, USA
| | - Laurence D Rhines
- Department of Neurosurgery, MD Anderson Cancer Center, Houston, Texas, USA
| | - Pejman Maralani
- Department of Medical Imaging, Sunnybrook Health Sciences Centre, University of Toronto, Toronto, Ontario, Canada
| | - Kristin J Redmond
- Department of Radiation and Molecular Oncology, John Hopkins University, Baltimore, Maryland, USA
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Gines G, Espada R, Dramé-Maigné A, Baccouche A, Larrouy N, Rondelez Y. Functional analysis of single enzymes combining programmable molecular circuits with droplet-based microfluidics. Nat Nanotechnol 2024:10.1038/s41565-024-01617-1. [PMID: 38409552 DOI: 10.1038/s41565-024-01617-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 01/22/2024] [Indexed: 02/28/2024]
Abstract
The analysis of proteins at the single-molecule level reveals heterogeneous behaviours that are masked in ensemble-averaged techniques. The digital quantification of enzymes traditionally involves the observation and counting of single molecules partitioned into microcompartments via the conversion of a profluorescent substrate. This strategy, based on linear signal amplification, is limited to a few enzymes with sufficiently high turnover rate. Here we show that combining the sensitivity of an exponential molecular amplifier with the modularity of DNA-enzyme circuits and droplet readout makes it possible to specifically detect, at the single-molecule level, virtually any D(R)NA-related enzymatic activity. This strategy, denoted digital PUMA (Programmable Ultrasensitive Molecular Amplifier), is validated for more than a dozen different enzymes, including many with slow catalytic rate, and down to the extreme limit of apparent single turnover for Streptococcus pyogenes Cas9. Digital counting uniquely yields absolute molar quantification and reveals a large fraction of inactive catalysts in all tested commercial preparations. By monitoring the amplification reaction from single enzyme molecules in real time, we also extract the distribution of activity among the catalyst population, revealing alternative inactivation pathways under various stresses. Our approach dramatically expands the number of enzymes that can benefit from quantification and functional analysis at single-molecule resolution. We anticipate digital PUMA will serve as a versatile framework for accurate enzyme quantification in diagnosis or biotechnological applications. These digital assays may also be utilized to study the origin of protein functional heterogeneity.
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Affiliation(s)
- Guillaume Gines
- Laboratoire Gulliver, UMR7083 CNRS/ESPCI Paris-PSL Research University, Paris, France.
| | - Rocίo Espada
- Laboratoire Gulliver, UMR7083 CNRS/ESPCI Paris-PSL Research University, Paris, France
| | - Adèle Dramé-Maigné
- Laboratoire Gulliver, UMR7083 CNRS/ESPCI Paris-PSL Research University, Paris, France
| | - Alexandre Baccouche
- LIMMS, IRL 2820 CNRS-Institute of Industrial Science, The University of Tokyo, Tokyo, Japan
| | - Nicolas Larrouy
- Laboratoire Gulliver, UMR7083 CNRS/ESPCI Paris-PSL Research University, Paris, France
| | - Yannick Rondelez
- Laboratoire Gulliver, UMR7083 CNRS/ESPCI Paris-PSL Research University, Paris, France
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7
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Rachman T, Bartlett D, LaFramboise W, Wagner P, Schwartz R, Carja O. Modeling the Effect of Spatial Structure on Solid Tumor Evolution and Circulating Tumor DNA Composition. Cancers (Basel) 2024; 16:844. [PMID: 38473206 PMCID: PMC10930890 DOI: 10.3390/cancers16050844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 03/14/2024] Open
Abstract
Circulating tumor DNA (ctDNA) monitoring, while sufficiently advanced to reflect tumor evolution in real time and inform cancer diagnosis, treatment, and prognosis, mainly relies on DNA that originates from cell death via apoptosis or necrosis. In solid tumors, chemotherapy and immune infiltration can induce spatially variable rates of cell death, with the potential to bias and distort the clonal composition of ctDNA. Using a stochastic evolutionary model of boundary-driven growth, we study how elevated cell death on the edge of a tumor can simultaneously impact driver mutation accumulation and the representation of tumor clones and mutation detectability in ctDNA. We describe conditions in which invasive clones are over-represented in ctDNA, clonal diversity can appear elevated in the blood, and spatial bias in shedding can inflate subclonal variant allele frequencies (VAFs). Additionally, we find that tumors that are mostly quiescent can display similar biases but are far less detectable, and the extent of perceptible spatial bias strongly depends on sequence detection limits. Overall, we show that spatially structured shedding might cause liquid biopsies to provide highly biased profiles of tumor state. While this may enable more sensitive detection of expanding clones, it could also increase the risk of targeting a subclonal variant for treatment. Our results indicate that the effects and clinical consequences of spatially variable cell death on ctDNA composition present an important area for future work.
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Affiliation(s)
- Thomas Rachman
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Joint Carnegie Mellon University-University of Pittsburgh Ph.D. Program in Computational Biology, Pittsburgh, PA 15213, USA
| | - David Bartlett
- Allegheny Cancer Institute, Allegheny Health Network, Pittsburgh, PA 15224, USA
| | - William LaFramboise
- Allegheny Cancer Institute, Allegheny Health Network, Pittsburgh, PA 15224, USA
| | - Patrick Wagner
- Allegheny Cancer Institute, Allegheny Health Network, Pittsburgh, PA 15224, USA
| | - Russell Schwartz
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Oana Carja
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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8
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Wang Z, Liu M, Lin H, Zhu G, Dong Z, Wu N, Fan Y, Xu G, Chang L, Wang Y. An Ion Concentration Polarization Microplatform for Efficient Enrichment and Analysis of ctDNA. ACS Nano 2024; 18:2872-2884. [PMID: 38236597 DOI: 10.1021/acsnano.3c07137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Strategies for rapid, effective nucleic acid processing hold tremendous significance to the clinical analysis of circulating tumor DNA (ctDNA), a family of important markers indicating tumorigenesis and metastasis. However, traditional techniques remain challenging to achieve efficient DNA enrichment, further bringing about complicated operation and limited detection sensitivity. Here, we developed an ion concentration polarization microplatform that enabled highly rapid, efficient enrichment and purification of ctDNA from a variety of clinical samples, including serum, urine, and feces. The platform demonstrated efficiently separating and enriching ctDNA within 30 s, with a 100-fold improvement over traditional methods. Integrating an on-chip isothermal amplification module, the platform further achieved 100-fold enhanced sensitivity in ctDNA detection, which significantly eliminated false-negative results in the serum or urine samples due to the low abundance of ctDNA. Such a simple-designed platform offers a user-friendly yet powerful diagnosis technique with a wide applicability, ranging from early tumor diagnosis to infection screening.
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Affiliation(s)
- Zhiying Wang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
| | - Ming Liu
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
| | - Haocheng Lin
- Department of Urology, Peking University Third Hospital, Beijing, 100191, China
| | - Guiying Zhu
- School of Biomedical Engineering/Med-X, Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Zaizai Dong
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
- School of Engineering Medicine, Beihang University, Beijing 100083, China
| | - Nan Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Yubo Fan
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
- School of Engineering Medicine, Beihang University, Beijing 100083, China
| | - Gaolian Xu
- School of Biomedical Engineering/Med-X, Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- Shanghai Sci-Tech InnoCenter for Infection & Immunity, Shanghai, 200000, China
| | - Lingqian Chang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
| | - Yang Wang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
- School of Engineering Medicine, Beihang University, Beijing 100083, China
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9
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Greene MP, Vassy JL. Helping patients understand multi-cancer early detection tests: a scoping review. Per Med 2024. [PMID: 38269535 DOI: 10.2217/pme-2023-0090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
Multi-cancer early detection tests are emerging as a revolutionary technology for the early detection of dozens of cancers from a single blood sample, including cancers without proven screening methods. However, they also come with challenges, including false-positive and false-negative results. To help patients make informed decisions, patient education materials are crucial. A review of available materials reveals that, while some materials provide understandable and actionable information, most lack a balanced presentation of the current benefits and risks of multi-cancer early detection testing. The dynamic nature of this field necessitates continuous updates to educational materials, incorporating current evidence and uncertainties.
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Affiliation(s)
| | - Jason L Vassy
- Harvard Medical School, Boston, 02115 MA, USA
- Veterans Affairs Boston Healthcare System, Boston, 02130 MA, USA
- Brigham and Women's Hospital, Boston, 02115 MA, USA
- Precision Population Health, Ariadne Labs, Boston, 02215 MA, USA
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10
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Yang L, Gu X, Liu J, Wu L, Qin Y. Functionalized nanomaterials-based electrochemiluminescent biosensors and their application in cancer biomarkers detection. Talanta 2024; 267:125237. [PMID: 37757698 DOI: 10.1016/j.talanta.2023.125237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 09/29/2023]
Abstract
To detect a range of trace biomarkers associated with human diseases, researchers have been focusing on developing biosensors that possess high sensitivity and specificity. Electrochemiluminescence (ECL) biosensors have emerged as a prominent research tool in recent years, owing to their potential superiority in low background signal, high sensitivity, straightforward instrumentation, and ease of operation. Functional nanomaterials (FNMs) exhibit distinct advantages in optimizing electrical conductivity, increasing reaction rate, and expanding specific surface area due to their small size effect, quantum size effect, and surface and interface effects, which can significantly improve the stability, reproducibility, and sensitivity of the biosensors. Thereby, various nanomaterials (NMs) with excellent properties have been developed to construct efficient ECL biosensors. This review provides a detailed summary and discussion of FNMs-based ECL biosensors and their applications in cancer biomarkers detection.
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Affiliation(s)
- Luxia Yang
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China
| | - Xijuan Gu
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China
| | - Jinxia Liu
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China.
| | - Li Wu
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China.
| | - Yuling Qin
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China.
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11
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Najafi S, Majidpoor J, Mortezaee K. Liquid biopsy in colorectal cancer. Clin Chim Acta 2024; 553:117674. [PMID: 38007059 DOI: 10.1016/j.cca.2023.117674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 11/27/2023]
Abstract
Liquid biopsy refers to a set of pathological samples retrieved from non-solid sources, such as blood, cerebrospinal fluid, urine, and saliva through non-invasive or minimally invasive approaches. In the recent decades, an increasing number of studies have focused on clinical applications and improving technological investigation of liquid biopsy biosources for diagnostic goals particularly in cancer. Materials extracted from these sources and used for medical evaluations include cells like circulating tumor cells (CTCs), tumor-educated platelets (TEPs), cell-free nucleic acids released by cells, such as circulating tumor DNA (ctDNA), cell-free DNA (cfDNA), cell-free RNA (cfRNA), and exosomes. Playing significant roles in the pathogenesis of human malignancies, analysis of these sources can provide easier access to genetic and transcriptomic information of the cancer tissue even better than the conventional tissue biopsy. Notably, they can represent the inter- and intra-tumoral heterogeneity and accordingly, liquid biopsies demonstrate strengths for improving diagnosis in early detection and screening, monitoring and follow-up after therapies, and personalization of therapeutical strategies in various types of human malignancies. In this review, we aim to discuss the roles, functions, and analysis approaches of liquid biopsy sources and their clinical implications in human malignancies with a focus on colorectal cancer.
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Affiliation(s)
- Sajad Najafi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Jamal Majidpoor
- Department of Anatomy, School of Medicine, Infectious Diseases Research Center, Gonabad University of Medical Sciences, Gonabad, Iran
| | - Keywan Mortezaee
- Department of Anatomy, School of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran.
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12
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Wu L, Ye C, Yao Q, Li Q, Zhang C, Li Y. The role of serum acylcarnitine profiling for the detection of multiple solid tumors in humans. Heliyon 2024; 10:e23867. [PMID: 38205321 PMCID: PMC10776988 DOI: 10.1016/j.heliyon.2023.e23867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 11/28/2023] [Accepted: 12/14/2023] [Indexed: 01/12/2024] Open
Abstract
Metabolic reprogramming is an essential hallmark of cancer. Several studies have reported the dysregulation of acylcarnitine (ACar) metabolism in tumor cells, suggesting that changes in the blood ACar may be related to tumor growth. Accordingly, this study aimed to understand the alteration of serum ACar profiles in various solid tumors and explore the potential of differential serum ACars as diagnostic biomarkers. A series of 69 relatively abundant ACars were identified via untargeted analysis. Then, targeted metabolomics was used to describe the metabolic alterations in ACars between normal controls and patients with six types of solid tumors. The results suggested that changes in ACars correlated with their carbon chain length and saturation. The six tumor types had highly similar ACar metabolic profiles, indicating similar fatty acid oxidation (FAO) metabolic pathways. Moreover, the receiver operating curve analysis of differential ACars showed that 16 ACars (C8-C14) had high diagnostic capability towards the studied solid tumors. Specifically, the area under the curve of ACar 10:2 isomer2 and ACar 12:2 isomer2 was greater than 0.95. In conclusion, the marked decrease in the levels of medium- and long-chain ACars (C8-C18) in the six solid tumors suggests that they may have similar FAO-based metabolic pathways, which could afford a common target for cancer therapy. Additionally, 16 ACars (C8-C14) were identified as potential biomarkers for diagnosing six types of solid tumors.
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Affiliation(s)
| | | | | | - Qianqian Li
- Department of Research, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi Zhuang Autonomous Region, China
| | - Chunyan Zhang
- Department of Research, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi Zhuang Autonomous Region, China
| | - Yuandong Li
- Department of Research, Guangxi Medical University Cancer Hospital, Nanning, 530021, Guangxi Zhuang Autonomous Region, China
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13
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Weber DG, Casjens S, Wichert K, Lehnert M, Taeger D, Rihs HP, Brüning T, Johnen G. Tasks and Experiences of the Prospective, Longitudinal, Multicenter MoMar (Molecular Markers) Study for the Early Detection of Mesothelioma in Individuals Formerly Exposed to Asbestos Using Liquid Biopsies. Cancers (Basel) 2023; 15:5896. [PMID: 38136442 PMCID: PMC10742125 DOI: 10.3390/cancers15245896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/07/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
Mesothelioma is an aggressive cancer, strongly associated with prior exposure to asbestos. Commonly, tumors are detected at late stages of the disease. Detection at early stages might be meaningful, because therapies might be more effective when the tumor burden is relatively low and the tumor has not spread to distant sites. Circulating biomarkers in blood might be a promising tool to improve the early detection of mesothelioma, but for screening in asymptomatic subjects, candidate biomarkers need to be validated in appropriate studies. This study was conducted to assess the performance of biomarkers in liquid biopsies to detect mesothelioma at early stages. Over a period of 10 years, 2769 volunteers formerly exposed to asbestos were annually examined and liquid biopsies were collected. A follow-up was completed 17 months after the last blood collection. The article provides a detailed overview of our lessons learned and experiences of conducting a prospective, longitudinal, multicenter study. The existing cohort of individuals at risk is highly suitable for the validation of blood-based biomarkers for the early detection of mesothelioma as well as lung cancer.
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Affiliation(s)
- Daniel Gilbert Weber
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance (IPA), Ruhr University Bochum, 44801 Bochum, Germany
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14
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Zhao Y, Chen Y, Wan Q, Xiao C, Guo Z, Du X, Hu Y, Zheng A, Cao Z. Identification of SAA1 as a novel metastasis marker in ovarian cancer and development of a graphene-based detection platform for early assessment. J Cancer Res Clin Oncol 2023; 149:16391-16406. [PMID: 37707574 DOI: 10.1007/s00432-023-05296-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 08/14/2023] [Indexed: 09/15/2023]
Abstract
BACKGROUND Ovarian cancer (OC) is a prevalent gynecological malignancy with the highest mortality rate, which generally diagnosed at late stages due to the lack of effective early screening methods and the nonspecific symptoms. Hence, here we aim to identify new metastasis markers and develop a novel detection method with the characteristics of high sensitivity, rapid detection, high specificity, and low cost when compared with other conventional detection technologies. METHODS Blood from OC patients with or without metastasis were collected and analyzed by 4D Label free LC - MS/MS. Surgically resect samples from OC patients were collected for Single cell RNA sequencing (sc-RNA seq). Short hairpin RNA (shRNA) was used to silence SAA1 expression in SKOV3 and ID8 to verify the relationship between endogenous SAA1 and tumor invasion or metastasis. The functional graphene chips prepared by covalent binding were used for SAA1 detection. RESULTS In our study, we identified Serum Amyloid A1 (SAA1) as a hematological marker of OC metastasis by comprehensive analysis of proteins in plasma from OC patients with or without metastasis using 4D Label free LC - MS/MS and gene expression patterns from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Further validation using tumor tissues and plasma from human OC and mouse OC model confirmed the correlation between SAA1 and tumor metastasis. Importantly, sc-RNA seq of human OC samples revealed that SAA1 was specifically expressed in tumor cells and upregulated in the metastasis group. The functional role of SAA1 in metastasis was demonstrated through experiments in vitro and in vivo. Based on these findings, we designed and investigated a graphene-based platform for SAA1 detection to predict the risk of metastasis of OC patients. CONCLUSION Our study suggests that SAA1 is a biomarker of OC metastasis, and we have developed a rapid and highly sensitive platform using graphene chips to detection of plasma SAA1 for the early assessment of metastasis in OC patients.
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Affiliation(s)
- Yilin Zhao
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, No.17 Section 3, Renmin South Road, Chengdu, 610041, People's Republic of China
| | - Yao Chen
- Department of Breast Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Qi Wan
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, No.17 Section 3, Renmin South Road, Chengdu, 610041, People's Republic of China
- Department of Gynecology and Obstetrics, West China Second Hospital, Sichuan University, Chengdu, 610041, China
| | - Chengju Xiao
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, No.17 Section 3, Renmin South Road, Chengdu, 610041, People's Republic of China
| | - Zhiqing Guo
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, No.17 Section 3, Renmin South Road, Chengdu, 610041, People's Republic of China
| | - Xinjie Du
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, No.17 Section 3, Renmin South Road, Chengdu, 610041, People's Republic of China
| | - Yan Hu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, No.17 Section 3, Renmin South Road, Chengdu, 610041, People's Republic of China.
| | - Ai Zheng
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, No.17 Section 3, Renmin South Road, Chengdu, 610041, People's Republic of China.
- Department of Gynecology and Obstetrics, West China Second Hospital, Sichuan University, Chengdu, 610041, China.
| | - Zhongwei Cao
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, No.17 Section 3, Renmin South Road, Chengdu, 610041, People's Republic of China.
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Myers RE, Hallman MH, Shimada A, DiCarlo M, Davis K, Leach WT, Jackson H, Indictor A, Chambers CV. Primary Care Patient Interest in Multi-Cancer Early Detection for Cancer Screening. J Pers Med 2023; 13:1613. [PMID: 38003928 PMCID: PMC10671850 DOI: 10.3390/jpm13111613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/27/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Multi-cancer early detection (MCED) tests are being developed, but little is known about patient receptivity to their use for cancer screening. The current study assessed patient interest in such testing. Our team conducted a prospective, observational study among primary care patients in a large, urban health system. They were asked to complete a telephone survey that briefly described a new blood test in development to identify multiple types of cancer, but was not currently recommended or covered by insurance. The survey included items to assess respondent background characteristics, perceptions about MCED testing, and interest in having such an MCED test. We also used multivariable analyses to identify factors associated with patient interest in test use. In 2023, we surveyed 159 (32%) of 500 identified patients. Among respondents, 125 (79%) reported a high level of interest in having an MCED test. Interest was not associated with personal background characteristics, but was positively associated with the following expectations: testing would be recommended for cancer screening, be convenient, and be effective in finding early-stage disease (OR = 11.70, 95% CI: 4.02, 34.04, p < 0.001). Research is needed to assess patient interest and actual uptake when detailed information on testing is presented in routine care.
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Affiliation(s)
- Ronald E. Myers
- Division of Population Science, Department of Medical Oncology, Thomas Jefferson University, Philadelphia, PA 19107, USA (M.D.); (H.J.); (A.I.)
| | - Mie H. Hallman
- Division of Population Science, Department of Medical Oncology, Thomas Jefferson University, Philadelphia, PA 19107, USA (M.D.); (H.J.); (A.I.)
| | - Ayako Shimada
- Division of Biostatistics, Department of Pharmacology, Physiology, and Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA;
| | - Melissa DiCarlo
- Division of Population Science, Department of Medical Oncology, Thomas Jefferson University, Philadelphia, PA 19107, USA (M.D.); (H.J.); (A.I.)
| | - Kaitlyn Davis
- Department of Family and Community Medicine, Thomas Jefferson University, Philadelphia, PA 19107, USA; (K.D.); (W.T.L.); (C.V.C.)
| | - William T. Leach
- Department of Family and Community Medicine, Thomas Jefferson University, Philadelphia, PA 19107, USA; (K.D.); (W.T.L.); (C.V.C.)
| | - Hattie Jackson
- Division of Population Science, Department of Medical Oncology, Thomas Jefferson University, Philadelphia, PA 19107, USA (M.D.); (H.J.); (A.I.)
| | - Amanda Indictor
- Division of Population Science, Department of Medical Oncology, Thomas Jefferson University, Philadelphia, PA 19107, USA (M.D.); (H.J.); (A.I.)
| | - Christopher V. Chambers
- Department of Family and Community Medicine, Thomas Jefferson University, Philadelphia, PA 19107, USA; (K.D.); (W.T.L.); (C.V.C.)
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Rachman T, Bartlett D, Laframboise W, Wagner P, Schwartz R, Carja O. Modeling the effect of spatial structure on solid tumor evolution and ctDNA composition. bioRxiv 2023:2023.11.10.566658. [PMID: 37986965 PMCID: PMC10659436 DOI: 10.1101/2023.11.10.566658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Circulating tumor DNA (ctDNA) monitoring, while sufficiently advanced to reflect tumor evolution in real time and inform on cancer diagnosis, treatment, and prognosis, mainly relies on DNA that originates from cell death via apoptosis or necrosis. In solid tumors, chemotherapy and immune infiltration can induce spatially variable rates of cell death, with the potential to bias and distort the clonal composition of ctDNA. Using a stochastic evolutionary model of boundary-driven growth, we study how elevated cell death on the edge of a tumor can simultaneously impact driver mutation accumulation and the representation of tumor clones and mutation detectability in ctDNA. We describe conditions in which invasive clones end up over-represented in ctDNA, clonal diversity can appear elevated in the blood, and spatial bias in shedding can inflate subclonal variant allele frequencies (VAFs). Additionally, we find that tumors that are mostly quiescent can display similar biases, but are far less detectable, and the extent of perceptible spatial bias strongly depends on sequence detection limits. Overall, we show that spatially structured shedding might cause liquid biopsies to provide highly biased profiles of tumor state. While this may enable more sensitive detection of expanding clones, it could also increase the risk of targeting a subclonal variant for treatment. Our results indicate that the effects and clinical consequences of spatially variable cell death on ctDNA composition present an important area for future work.
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Affiliation(s)
- Thomas Rachman
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
- Joint Carnegie Mellon University-University of Pittsburgh Ph.D. Program in Computational Biology
| | - David Bartlett
- Allegheny Cancer Institute, Allegheny Health Network, Pittsburgh PA
| | | | - Patrick Wagner
- Allegheny Cancer Institute, Allegheny Health Network, Pittsburgh PA
| | - Russell Schwartz
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Oana Carja
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
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17
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Parida P, Baburaj G, Rao M, Lewis S, Damerla RR. Circulating cell-free DNA as a diagnostic and prognostic marker for cervical cancer. Int J Gynecol Cancer 2023:ijgc-2023-004873. [PMID: 37949487 DOI: 10.1136/ijgc-2023-004873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023] Open
Abstract
Circulating cell-free DNA (cfDNA) is a promising tool for liquid biopsy-based tests. cfDNA has been reported to help in the diagnosis, quantification of minimal residual disease, prognosis, and identification of mutations conferring resistance in various types of cancers. Cervical cancer is the fourth most common cancer among women worldwide. High-risk human papillomavirus (hr-HPV) infections have been associated with almost all cervical cancers. Lack of HPV vaccines in national vaccination programs and irregular screening strategies in nations with low or moderate levels of human development index have led to cervical cancer becoming the second leading cause of cancer mortality in women. As HPV integration and overexpression of E6/E7 oncoprotein are crucial steps in the development of cancer, HPV cfDNA could potentially be used as a specific biomarker for the detection of cervical cancer. Many studies have used HPV cfDNA and other gene mutations or mRNA expression profiles for diagnosis and disease surveillance in patients with cervical cancer at various stages of disease progression. In this review we present an overview of different studies discussing the utility of cfDNA in cervical cancer and summarize the evidence supporting its potential use in diagnosis and treatment monitoring.
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Affiliation(s)
- Preetiparna Parida
- Department of Medical Genetics, Kasturba Medical College Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Gayathri Baburaj
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Mahadev Rao
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Shirley Lewis
- Department of Radiotherapy and Oncology, Kasturba Medical College Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Rama Rao Damerla
- Department of Medical Genetics, Kasturba Medical College Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
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Pancrazzi A, Bloise F, Moncada A, Perticucci R, Vecchietti S, Pompili F, Ricciarini F, Lenzi S, Gatteschi C, Giusti S, Rosito MP, Del Buono S, Belardi P, Bruni A, Borri F, Campione A, Laurini L, Occhini R, Presenti L, Viticchi V, Rossi M, Bardi S, D'Urso A, Dei S, Venezia D, Scala R, Bengala C, Decarli NL, Carnevali A, Milandri C, Ognibene A. BL-MOL-AR Project, Preliminary Results about Liquid Biopsy: Molecular Approach Experience and Research Activity in Oncological Settings. Glob Med Genet 2023; 10:172-187. [PMID: 37457625 PMCID: PMC10348843 DOI: 10.1055/s-0043-1771193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023] Open
Abstract
Background Liquid biopsy is mainly used to identify tumor cells in pulmonary neoplasms. It is more often used in research than in clinical practice. The BL-MOL-AR study aims to investigate the efficacy of next-generation sequencing (NGS) and clinical interpretation of the circulating free DNA (cfDNA) levels. This study reports the preliminary results from the first samples analyzed from patients affected by various neoplasms: lung, intestinal, mammary, gastric, biliary, and cutaneous. Methods The Biopsia Liquida-Molecolare-Arezzo study aims to enroll cancer patients affected by various malignancies, including pulmonary, intestinal, advanced urothelial, biliary, breast, cutaneous, and gastric malignancies. Thirty-nine patients were included in this preliminary report. At time zero, a liquid biopsy is executed, and two types of NGS panels are performed, comprising 17 genes in panel 1, which is already used in the routine tissue setting, and 52 genes in panel 2. From the 7th month after enrollment, 10 sequential liquid biopsies are performed up to the 17th month. The variant allele frequency (%) and cfDNA levels (ng/mL) are measured in every plasmatic sample. Results The NGS results obtained by different panels are similar even though the number of mutations is more concordant for lung pathologies. There are no significant differences in the actionability levels of the identified variants. Most of the molecular profiles of liquid biopsies reflect tissue data. Conclusions Preliminary data from this study confirm the need to clarify the limitations and potential of liquid biopsy beyond the lung setting. Overall, parameters related to cfDNA levels and variant allele frequency could provide important indications for prognosis and disease monitoring.
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Affiliation(s)
- Alessandro Pancrazzi
- Laboratory Medicine Department, Clinical and Molecular Pathology Sector, San Donato Hospital, Arezzo, Italy
| | - Francesco Bloise
- Oncology Department, Unit of Medical Oncology, San Donato Hospital, Arezzo, Italy
| | - Alice Moncada
- Laboratory Medicine Department, Clinical and Molecular Pathology Sector, San Donato Hospital, Arezzo, Italy
| | - Roberta Perticucci
- Laboratory Medicine Department, Clinical and Molecular Pathology Sector, San Donato Hospital, Arezzo, Italy
| | - Stefania Vecchietti
- Laboratory Medicine Department, Clinical and Molecular Pathology Sector, San Donato Hospital, Arezzo, Italy
| | - Francesca Pompili
- Laboratory Medicine Department, Clinical and Molecular Pathology Sector, San Donato Hospital, Arezzo, Italy
| | - Francesca Ricciarini
- Laboratory Medicine Department, Clinical and Molecular Pathology Sector, San Donato Hospital, Arezzo, Italy
| | - Silvia Lenzi
- Laboratory Medicine Department, Clinical and Molecular Pathology Sector, San Donato Hospital, Arezzo, Italy
| | - Cristina Gatteschi
- Laboratory Medicine Department, Clinical and Molecular Pathology Sector, San Donato Hospital, Arezzo, Italy
| | - Sabrina Giusti
- Oncology Department, Unit of Medical Oncology, San Donato Hospital, Arezzo, Italy
| | - Maria Pia Rosito
- Oncology Department, Unit of Medical Oncology, San Donato Hospital, Arezzo, Italy
| | - Sabrina Del Buono
- Oncology Department, Unit of Medical Oncology, San Donato Hospital, Arezzo, Italy
| | - Paola Belardi
- Oncology Department, Unit of Medical Oncology, San Donato Hospital, Arezzo, Italy
| | - Alessandra Bruni
- Oncology Department, Pathological Anatomy Laboratory, San Donato Hospital, Italy
| | - Filippo Borri
- Oncology Department, Pathological Anatomy Laboratory, San Donato Hospital, Italy
| | - Andrea Campione
- Oncology Department, Pathological Anatomy Laboratory, San Donato Hospital, Italy
| | - Lorella Laurini
- Oncology Department, Pathological Anatomy Laboratory, San Donato Hospital, Italy
| | - Rossella Occhini
- Oncology Department, Pathological Anatomy Laboratory, San Donato Hospital, Italy
| | - Loretta Presenti
- Oncology Department, Pathological Anatomy Laboratory, San Donato Hospital, Italy
| | - Viviana Viticchi
- Oncology Department, Pathological Anatomy Laboratory, San Donato Hospital, Italy
| | - Maja Rossi
- Laboratory Medicine Department, Clinical and Molecular Pathology Sector, Misericordia Hospital, Grosseto, Italy
| | - Sara Bardi
- Laboratory Medicine Department, Clinical and Molecular Pathology Sector, Misericordia Hospital, Grosseto, Italy
| | - Antonio D'Urso
- General Management, Local Health Unit South-East Tuscany, Tuscany, Italy
| | - Simona Dei
- General Management, Local Health Unit South-East Tuscany, Tuscany, Italy
| | - Duccio Venezia
- Diagnostic Imaging Department, Radiology Unit, San Donato Hospital, Arezzo, Italy
| | - Raffaele Scala
- Cardio Thoracic Neuro Vascular Department, Pneumology Unit, San Donato Hospital, Arezzo, Italy
| | - Carmelo Bengala
- Oncology Department, Unit of Medical Oncology, Misericordia Hospital, Grosseto, Italy
| | - Nicola Libertà Decarli
- Oncology Department, Pathological Anatomy Laboratory, Misericordia Hospital, Grosseto, Italy
| | - Andrea Carnevali
- Oncology Department, Pathological Anatomy Laboratory, San Donato Hospital, Italy
| | - Carlo Milandri
- Oncology Department, Unit of Medical Oncology, San Donato Hospital, Arezzo, Italy
| | - Agostino Ognibene
- Laboratory Medicine Department, Clinical and Molecular Pathology Sector, San Donato Hospital, Arezzo, Italy
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19
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Karimi F, Azadbakht O, Veisi A, Sabaghan M, Owjfard M, Kharazinejad E, Dinarvand N. Liquid biopsy in ovarian cancer: advantages and limitations for prognosis and diagnosis. Med Oncol 2023; 40:265. [PMID: 37561363 DOI: 10.1007/s12032-023-02128-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 07/17/2023] [Indexed: 08/11/2023]
Abstract
Ovarian cancer (OC) is a highly fatal gynecologic malignancy, often diagnosed at an advanced stage which presents significant challenges for disease management. The clinical application of conventional tissue biopsy methods and serological biomarkers has limitations for the diagnosis and prognosis of OC patients. Liquid biopsy is a novel sampling method that involves analyzing distinctive tumor elements secreted into the peripheral blood. Growing evidence suggests that liquid biopsy methods such as circulating tumor cells, cell-free RNA, circulating tumor DNA, exosomes, and tumor-educated platelets may improve early prognosis and diagnosis of OC, leading to enhanced therapeutic management of the disease. This study reviewed the evidence demonstrating the utility of liquid biopsy components in OC prognosis and diagnosis, and evaluated the current advantages and limitations of these methods. Additionally, the existing obstacles and crucial topics for future studies utilizing liquid biopsy in OC patients were discussed.
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Affiliation(s)
- Farzaneh Karimi
- Department of Physiology, Behbahan Faculty of Medical Sciences, Behbahan, Iran.
| | - Omid Azadbakht
- Department of Radiology Technology, Behbahan Faculty of Medical Sciences, Behbahan, Iran
| | - Ali Veisi
- Department of Physiology, Behbahan Faculty of Medical Sciences, Behbahan, Iran
| | - Mohammad Sabaghan
- Department of Parasitology, Behbahan Faculty of Medical Sciences, Behbahan, Iran
| | - Maryam Owjfard
- Clinical Neurology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Shiraz University of Applied Science and Technology (UAST), Shiraz, Iran
| | | | - Negar Dinarvand
- Hyperlipidemia Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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20
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Pattiya Arachchillage KGG, Chandra S, Williams A, Piscitelli P, Pham J, Castillo A, Florence L, Rangan S, Artes Vivancos JM. Electrical detection of RNA cancer biomarkers at the single-molecule level. Sci Rep 2023; 13:12428. [PMID: 37528139 PMCID: PMC10393997 DOI: 10.1038/s41598-023-39450-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 07/25/2023] [Indexed: 08/03/2023] Open
Abstract
Cancer is a significant healthcare issue, and early screening methods based on biomarker analysis in liquid biopsies are promising avenues to reduce mortality rates. Electrical detection of nucleic acids at the single molecule level could enable these applications. We examine the electrical detection of RNA cancer biomarkers (KRAS mutants G12C and G12V) as a single-molecule proof-of-concept electrical biosensor for cancer screening applications. We show that the electrical conductance is highly sensitive to the sequence, allowing discrimination of the mutants from a wild-type KRAS sequence differing in just one base. In addition to this high specificity, our results also show that these biosensors are sensitive down to an individual molecule with a high signal-to-noise ratio. These results pave the way for future miniaturized single-molecule electrical biosensors that could be groundbreaking for cancer screening and other applications.
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Affiliation(s)
| | - Subrata Chandra
- Department of Chemistry, University of Massachusetts Lowell, Lowell, MA, 01854, USA
| | - Ajoke Williams
- Department of Chemistry, University of Massachusetts Lowell, Lowell, MA, 01854, USA
| | - Patrick Piscitelli
- Department of Chemistry, University of Massachusetts Lowell, Lowell, MA, 01854, USA
| | - Jennifer Pham
- Department of Chemistry, University of Massachusetts Lowell, Lowell, MA, 01854, USA
| | - Aderlyn Castillo
- Department of Chemistry, University of Massachusetts Lowell, Lowell, MA, 01854, USA
| | - Lily Florence
- Department of Chemistry, University of Massachusetts Lowell, Lowell, MA, 01854, USA
| | - Srijith Rangan
- Department of Chemistry, University of Massachusetts Lowell, Lowell, MA, 01854, USA
| | - Juan M Artes Vivancos
- Department of Chemistry, University of Massachusetts Lowell, Lowell, MA, 01854, USA.
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21
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Trosman JR, Weldon CB, Kurian AW, Pasquinelli MM, Kircher SM, Martin N, Douglas MP, Phillips KA. Perspectives of private payers on multicancer early-detection tests: informing research, implementation, and policy. Health Aff Sch 2023; 1:qxad005. [PMID: 38756840 PMCID: PMC10986216 DOI: 10.1093/haschl/qxad005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 03/08/2023] [Indexed: 05/18/2024]
Abstract
Emerging blood-based multicancer early-detection (MCED) tests may redefine cancer screening, reduce mortality, and address health disparities if their benefit is demonstrated. U.S. payers' coverage policies will impact MCED test adoption and access; thus, their perspectives must be understood. We examined views, coverage barriers, and evidentiary needs for MCED from 19 private payers collectively covering 150 000 000 enrollees. Most saw an MCED test's potential merit for cancers without current screening (84%), but fewer saw its merit for cancers with existing screening (37%). The largest coverage barriers were inclusion of cancers without demonstrated benefits of early diagnosis (73%), a high false-negative rate (53%), and lack of care protocols for MCED-detected but unconfirmed cancers (53%). The majority (58%) would not require mortality evidence and would accept surrogate endpoints. Most payers (64%) would accept rigorous real-world evidence in the absence of a large randomized controlled trial. The majority (74%) did not expect MCED to reduce disparities due to potential harm from overtreatment resulting from an MCED and barriers to downstream care. Payers' perspectives and evidentiary needs may inform MCED test developers, researchers producing evidence, and health systems framing MCED screening programs. Private payers should be stakeholders of a national MCED policy and equity agenda.
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Affiliation(s)
- Julia R Trosman
- UCSF Center for Translational and Policy Research on Precision Medicine (TRANSPERS), San Francisco, CA 94143, United States
- Department of Clinical Pharmacy, University of California San Francisco, San Francisco, CA 94143, United States
- Center for Business Models in Healthcare, Glencoe, IL 60022, United States
| | - Christine B Weldon
- UCSF Center for Translational and Policy Research on Precision Medicine (TRANSPERS), San Francisco, CA 94143, United States
- Center for Business Models in Healthcare, Glencoe, IL 60022, United States
| | | | | | - Sheetal M Kircher
- Northwestern University Feinberg School of Medicine, Chicago, IL 60611, United States
| | - Nikki Martin
- LUNGevity Foundation, Bethesda, MD 20814, United States
| | - Michael P Douglas
- UCSF Center for Translational and Policy Research on Precision Medicine (TRANSPERS), San Francisco, CA 94143, United States
- Department of Clinical Pharmacy, University of California San Francisco, San Francisco, CA 94143, United States
| | - Kathryn A Phillips
- UCSF Center for Translational and Policy Research on Precision Medicine (TRANSPERS), San Francisco, CA 94143, United States
- Department of Clinical Pharmacy, University of California San Francisco, San Francisco, CA 94143, United States
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22
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Abstract
Glioma is one of the most common malignant primary brain tumours in adults, of which, glioblastoma is the most prevalent and malignant entity. Glioma is often diagnosed at a later stage of disease progression, which means it is associated with significant mortality and morbidity. Therefore, there is a need for earlier diagnosis of these tumours, which would require sensitive and specific biomarkers. These biomarkers could better predict glioma onset to improve diagnosis and therapeutic options for patients. While liquid biopsies could provide a cheap and non-invasive test to improve the earlier detection of glioma, there is little known on pre-diagnostic biomarkers which predate disease detection. In this review, we examine the evidence in the literature for pre-diagnostic biomarkers in glioma, including metabolomics and proteomics. We also consider the limitations of these approaches and future research directions of pre-diagnostic biomarkers for glioma.
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Affiliation(s)
- Lily J. Andrews
- Medical Research Council (MRC) Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, United Kingdom
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- Cancer Research Integrative Cancer Epidemiology Programme, University of Bristol, Bristol, United Kingdom
| | - Philippa Davies
- Medical Research Council (MRC) Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, United Kingdom
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- Cancer Research Integrative Cancer Epidemiology Programme, University of Bristol, Bristol, United Kingdom
| | - Christopher Herbert
- Bristol Haematology and Oncology Centre, University Hospitals Bristol National Health Service (NHS) Foundation Trust, Bristol, United Kingdom
| | - Kathreena M. Kurian
- Medical Research Council (MRC) Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, United Kingdom
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
- Cancer Research Integrative Cancer Epidemiology Programme, University of Bristol, Bristol, United Kingdom
- Brain Tumour Research Centre, Bristol Medical School, University of Bristol, Bristol, United Kingdom
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23
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Kim ES, Scharpf RB, Garcia-Closas M, Visvanathan K, Velculescu VE, Chatterjee N. Potential utility of risk stratification for multicancer screening with liquid biopsy tests. NPJ Precis Oncol 2023; 7:39. [PMID: 37087533 PMCID: PMC10122653 DOI: 10.1038/s41698-023-00377-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/30/2023] [Indexed: 04/24/2023] Open
Abstract
Our proof-of-concept study reveals the potential of risk stratification by the combined effects of age, polygenic risk scores (PRS), and non-genetic risk factors in increasing the risk-benefit balance of rapidly emerging non-invasive multicancer early detection (MCED) liquid biopsy tests. We develop and validate sex-specific pan-cancer risk scores (PCRSs), defined by the combination of body mass index, smoking, family history of cancers, and cancer-specific polygenic risk scores (PRSs), to predict the absolute risk of developing at least one of the many common cancer types. We demonstrate the added value of PRSs in improving the predictive performance of the risk factors only model and project the positive and negative predictive values for two promising multicancer screening tests across risk strata defined by age and PCRS.
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Affiliation(s)
- Elle S Kim
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Robert B Scharpf
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Montserrat Garcia-Closas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute of Health, 9609 Medical Center Drive 7E-342, Rockville, MD, 20850, USA
| | - Kala Visvanathan
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Victor E Velculescu
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Nilanjan Chatterjee
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA.
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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24
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Wang W, Zhu X, Zhang X, Lei C, Zeng Z, Lan X, Cui W, Wang F, Xu S, Zhou J, Wu X, Deng H, Li X, Fan J, Ding Y, Huang Z, Liang L. Recurrence risk assessment for stage III colorectal cancer based on five methylation biomarkers in plasma cell-free DNA. J Pathol 2023; 259:376-387. [PMID: 36573552 DOI: 10.1002/path.6047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 11/20/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022]
Abstract
For stage III colorectal cancer (CRC) patients with a high risk of recurrence, intensified adjuvant chemotherapy can improve overall survival. We aimed to develop a circulating tumor DNA (ctDNA) methylation marker model for predicting the relapse risk of stage III CRC patients. Differentially methylated markers identified between 53 normal mucosa samples and 165 CRC tissue samples, as well as between plasma samples from 75 stage I/II (early-stage) CRC patients and 55 stage IV (late-stage) CRC patients, were analyzed using Student's t-tests. The overlapping methylation markers shared by plasma and tissue samples were used to establish a methylation marker model to evaluate the tumor burden in the peripheral blood of CRC patients using the random forest method. This model was verified in the validation cohort (n = 44) and then applied to predict recurrence risk in 50 stage III CRC patients and monitor the clinical disease course in serial samples from four CRC patients. We built a five-marker-based ctDNA methylation model that had high sensitivity (84.21%) and specificity (84%) in identifying late-stage CRC in a validation cohort containing 24 stage I/II CRC patients and 20 stage IV CRC patients. The model achieved high sensitivity (87.5%) and specificity (94.12%) in predicting tumor relapse in an independent cohort of 50 stage III CRC patients and could be an independent recurrence risk factor for stage III patients [Hazard ratio (HR), 60.4; 95% confidence interval (CI): 7.68-397; p = 9.73e-5]. Analysis of serial blood samples of CRC showed that the model could monitor disease relapse earlier than imaging examination and serum carcinoembryonic antigen (CEA) and so may provide an opportunity for the early adjustment of therapeutic strategies. Moreover, the model could potentially monitor the clinical course and treatment response dynamically. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Wei Wang
- Department of Pathology, Nanfang Hospital and Basic Medical College, Southern Medical University, Guangzhou, PR China.,Department of Pathology, General Hospital of Southern Theater Command, People's Liberation Army of China, Guangzhou, PR China
| | - Xiaohui Zhu
- Department of Pathology, Nanfang Hospital and Basic Medical College, Southern Medical University, Guangzhou, PR China.,Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, PR China
| | - Xuecong Zhang
- Department of Bioinformatics, School of Basic Medicine, Southern Medical University, Guangzhou, PR China
| | - Chengyong Lei
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, PR China
| | - Zhicheng Zeng
- Department of Pathology, Nanfang Hospital and Basic Medical College, Southern Medical University, Guangzhou, PR China.,Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, PR China
| | - Xiaoliang Lan
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, PR China
| | - Wenzhi Cui
- Department of Pathology, General Hospital of Southern Theater Command, People's Liberation Army of China, Guangzhou, PR China
| | - Feifei Wang
- Department of Pathology, Nanfang Hospital and Basic Medical College, Southern Medical University, Guangzhou, PR China.,Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, PR China
| | - Shaowan Xu
- Department of Pathology, Nanfang Hospital and Basic Medical College, Southern Medical University, Guangzhou, PR China.,Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, PR China
| | - Juan Zhou
- Department of Oncology, General Hospital of Southern Theater Command, People's Liberation Army of China, Guangzhou, PR China
| | - Xuehui Wu
- Department of Pathology, Nanfang Hospital and Basic Medical College, Southern Medical University, Guangzhou, PR China.,Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, PR China
| | - Haijun Deng
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, PR China
| | - Xia Li
- AnchorDx Medical Co., Ltd., Guangzhou, PR China
| | - Jianbing Fan
- Department of Pathology, Nanfang Hospital and Basic Medical College, Southern Medical University, Guangzhou, PR China.,AnchorDx Medical Co., Ltd., Guangzhou, PR China
| | - Yanqing Ding
- Department of Pathology, Nanfang Hospital and Basic Medical College, Southern Medical University, Guangzhou, PR China.,Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, PR China
| | - Zhongxi Huang
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, PR China
| | - Li Liang
- Department of Pathology, Nanfang Hospital and Basic Medical College, Southern Medical University, Guangzhou, PR China.,Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, PR China
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25
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Mazzitelli C, Santini D, Corradini AG, Zamagni C, Trerè D, Montanaro L, Taffurelli M. Liquid Biopsy in the Management of Breast Cancer Patients: Where Are We Now and Where Are We Going. Diagnostics (Basel) 2023; 13:diagnostics13071241. [PMID: 37046459 PMCID: PMC10092978 DOI: 10.3390/diagnostics13071241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/17/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
Liquid biopsy (LB) is an emerging diagnostic tool that analyzes biomarkers in the blood (and possibly in other body fluids) to provide information about tumor genetics and response to therapy. This review article provides an overview of LB applications in human cancer with a focus on breast cancer patients. LB methods include circulating tumor cells and cell-free tumor products, such as circulating tumor DNA. LB has shown potential in detecting cancer at an early stage, monitoring tumor progression and recurrence, and predicting patient response to therapy. Several studies have demonstrated its clinical utility in breast cancer patients. However, there are limitations to LB, including the lack of standardized assays and the need for further validation. Future potential applications of LB include identifying the minimal residual disease, early detection of recurrence, and monitoring treatment response in various cancer types. LB represents a promising non-invasive diagnostic tool with potential applications in breast cancer diagnosis, treatment, and management. Further research is necessary to fully understand its clinical utility and overcome its current limitations.
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26
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Manoochehri M, Borhani N, Gerhäuser C, Assenov Y, Schönung M, Hielscher T, Christensen BC, Lee MK, Gröne HJ, Lipka DB, Brüning T, Brauch H, Ko YD, Hamann U. DNA methylation biomarkers for noninvasive detection of triple-negative breast cancer using liquid biopsy. Int J Cancer 2023; 152:1025-1035. [PMID: 36305646 DOI: 10.1002/ijc.34337] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 09/06/2022] [Accepted: 09/20/2022] [Indexed: 01/06/2023]
Abstract
Noninvasive detection of aberrant DNA methylation could provide invaluable biomarkers for earlier detection of triple-negative breast cancer (TNBC) which could help clinicians with easier and more efficient treatment options. We evaluated genome-wide DNA methylation data derived from TNBC and normal breast tissues, peripheral blood of TNBC cases and controls and reference samples of sorted blood and mammary cells. Differentially methylated regions (DMRs) between TNBC and normal breast tissues were stringently selected, verified and externally validated. A machine-learning algorithm was applied to select the top DMRs, which then were evaluated on plasma-derived circulating cell-free DNA (cfDNA) samples of TNBC patients and healthy controls. We identified 23 DMRs accounting for the methylation profile of blood cells and reference mammary cells and then selected six top DMRs for cfDNA analysis. We quantified un-/methylated copies of these DMRs by droplet digital PCR analysis in a plasma test set from TNBC patients and healthy controls and confirmed our findings obtained on tissues. Differential cfDNA methylation was confirmed in an independent validation set of plasma samples. A methylation score combining signatures of the top three DMRs overlapping with the SPAG6, LINC10606 and TBCD/ZNF750 genes had the best capability to discriminate TNBC patients from controls (AUC = 0.78 in the test set and AUC = 0.74 in validation set). Our findings demonstrate the usefulness of cfDNA-based methylation signatures as noninvasive liquid biopsy markers for the diagnosis of TNBC.
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Affiliation(s)
- Mehdi Manoochehri
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of In Vitro Diagnostics, Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Stuttgart, Germany
| | - Nasim Borhani
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Clarissa Gerhäuser
- Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Yassen Assenov
- Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Maximilian Schönung
- Section Translational Cancer Epigenomics, Translational Medical Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Thomas Hielscher
- Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire, USA
| | - Min Kyung Lee
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire, USA
| | | | - Daniel B Lipka
- Section Translational Cancer Epigenomics, Translational Medical Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Thomas Brüning
- Institute for Prevention & Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr University Bochum (IPA), Bochum, Germany
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,iFIT Cluster of Excellence, University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Tübingen, Germany
| | - Yon-Dschun Ko
- Department of Internal Medicine, Evangelische Kliniken Bonn gGmbH, Johanniter Krankenhaus, Bonn, Germany
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
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27
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Kim SI, Hwangbo S, Dan K, Kim HS, Chung HH, Kim JW, Park NH, Song YS, Han D, Lee M. Proteomic Discovery of Plasma Protein Biomarkers and Development of Models Predicting Prognosis of High-Grade Serous Ovarian Carcinoma. Mol Cell Proteomics 2023; 22:100502. [PMID: 36669591 PMCID: PMC9972571 DOI: 10.1016/j.mcpro.2023.100502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 12/27/2022] [Accepted: 01/11/2023] [Indexed: 01/19/2023] Open
Abstract
Ovarian cancer is one of the most lethal female cancers. For accurate prognosis prediction, this study aimed to investigate novel, blood-based prognostic biomarkers for high-grade serous ovarian carcinoma (HGSOC) using mass spectrometry-based proteomics methods. We conducted label-free liquid chromatography-tandem mass spectrometry using frozen plasma samples obtained from patients with newly diagnosed HGSOC (n = 20). Based on progression-free survival (PFS), the samples were divided into two groups: good (PFS ≥18 months) and poor prognosis groups (PFS <18 months). Proteomic profiles were compared between the two groups. Referring to proteomics data that we previously obtained using frozen cancer tissues from chemotherapy-naïve patients with HGSOC, overlapping protein biomarkers were selected as candidate biomarkers. Biomarkers were validated using an independent set of HGSOC plasma samples (n = 202) via enzyme-linked immunosorbent assay (ELISA). To construct models predicting the 18-month PFS rate, we performed stepwise selection based on the area under the receiver operating characteristic curve (AUC) with 5-fold cross-validation. Analysis of differentially expressed proteins in plasma samples revealed that 35 and 61 proteins were upregulated in the good and poor prognosis groups, respectively. Through hierarchical clustering and bioinformatic analyses, GSN, VCAN, SND1, SIGLEC14, CD163, and PRMT1 were selected as candidate biomarkers and were subjected to ELISA. In multivariate analysis, plasma GSN was identified as an independent poor prognostic biomarker for PFS (adjusted hazard ratio, 1.556; 95% confidence interval, 1.073-2.256; p = 0.020). By combining clinical factors and ELISA results, we constructed several models to predict the 18-month PFS rate. A model consisting of four predictors (FIGO stage, residual tumor after surgery, and plasma levels of GSN and VCAN) showed the best predictive performance (mean validated AUC, 0.779). The newly developed model was converted to a nomogram for clinical use. Our study results provided insights into protein biomarkers, which might offer clues for developing therapeutic targets.
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Affiliation(s)
- Se Ik Kim
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Suhyun Hwangbo
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Kisoon Dan
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Hee Seung Kim
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hyun Hoon Chung
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jae-Weon Kim
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Noh Hyun Park
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yong-Sang Song
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Dohyun Han
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea; Transdisciplinary Department of Medicine and Advanced Technology, Seoul National University Hospital, Seoul, Republic of Korea.
| | - Maria Lee
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul, Republic of Korea; Department of Obstetrics and Gynecology, Seoul National University Hospital, Seoul, Republic of Korea.
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28
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McCloskey D, Semeere A, Ayanga R, Laker-Oketta M, Lukande R, Semakadde M, Kanyesigye M, Wenger M, LeBoit P, McCalmont T, Maurer T, Gardner A, Boza J, Cesarman E, Martin J, Erickson D. LAMP-enabled diagnosis of Kaposi's sarcoma for sub-Saharan Africa. Sci Adv 2023; 9:eadc8913. [PMID: 36638178 DOI: 10.1126/sciadv.adc8913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Kaposi's sarcoma (KS) is an endothelial cancer caused by the Kaposi's sarcoma-associated herpesvirus (KSHV) and is one of the most common cancers in sub-Saharan Africa. In limited-resource settings, traditional pathology infrastructure is often insufficient for timely diagnosis, leading to frequent diagnoses at advanced-stage disease where survival is poor. In this study, we investigate molecular diagnosis of KS performed in a point-of-care device to circumvent the limited infrastructure for traditional diagnosis. Using 506 mucocutaneous biopsies collected from patients at three HIV clinics in Uganda, we achieved 97% sensitivity, 92% specificity, and 96% accuracy compared to gold standard U.S.-based pathology. The results presented in this manuscript show that LAMP-based quantification of KSHV DNA extracted from KS-suspected biopsies has the potential to serve as a successful diagnostic for the disease and that diagnosis may be accurately achieved using a point-of-care device, reducing the barriers to obtaining KS diagnosis while increasing diagnostic accuracy.
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Affiliation(s)
- Duncan McCloskey
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14850, USA
| | - Aggrey Semeere
- Infectious Diseases Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Racheal Ayanga
- Infectious Diseases Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Miriam Laker-Oketta
- Infectious Diseases Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Robert Lukande
- Pathology Department, Makerere University College of Health Sciences, Kampala, Uganda
| | | | - Micheal Kanyesigye
- Immune Suppression Syndrome Clinic, Mbarara Regional Referral Hospital, Mbarara, Uganda
| | - Megan Wenger
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Philip LeBoit
- Pathology and Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Timothy McCalmont
- Pathology and Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
- Golden State Dermatology Dermatopathology, Walnut Creek, CA 94598, USA
| | - Toby Maurer
- Department of Dermatology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Andrea Gardner
- Pathology and Laboratory Medicine, Weill Cornell Medical College; New York, NY, 10021, USA
| | - Juan Boza
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14850, USA
| | - Ethel Cesarman
- Pathology and Laboratory Medicine, Weill Cornell Medical College; New York, NY, 10021, USA
| | - Jeffrey Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - David Erickson
- Sibley School of Mechanical and Aerospace Engineering, Cornell University; Ithaca, NY, 14850, USA
- Division of Nutritional Science, Cornell University, Ithaca, NY 14850, USA
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29
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Bhattacharjee B, Syeda AF, Rynjah D, Hussain SM, Chandra Bora S, Pegu P, Sahu RK, Khan J. Pharmacological impact of microRNAs in head and neck squamous cell carcinoma: Prevailing insights on molecular pathways, diagnosis, and nanomedicine treatment. Front Pharmacol 2023; 14:1174330. [PMID: 37205904 PMCID: PMC10188950 DOI: 10.3389/fphar.2023.1174330] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 04/11/2023] [Indexed: 05/21/2023] Open
Abstract
Head and neck squamous cell carcinoma is a disease that most commonly produce tumours from the lining of the epithelial cells of the lips, larynx, nasopharynx, mouth, or oro-pharynx. It is one of the most deadly forms of cancer. About one to two percent of all neo-plasm-related deaths are attributed to head and neck squamous cell carcinoma, which is responsible for about six percent of all cancers. MicroRNAs play a critical role in cell proliferation, differentiation, tumorigenesis, stress response, triggering apoptosis, and other physiological process. MicroRNAs regulate gene expression and provide new diagnostic, prognostic, and therapeutic options for head and neck squamous cell carcinoma. In this work, the role of molecular signaling pathways related to head and neck squamous cell carcinoma is emphasized. We also provide an overview of MicroRNA downregulation and overexpression and its role as a diagnostic and prognostic marker in head and neck squamous cell carcinoma. In recent years, MicroRNA nano-based therapies for head and neck squamous cell carcinoma have been explored. In addition, nanotechnology-based alternatives have been discussed as a promising strategy in exploring therapeutic paradigms aimed at improving the efficacy of conventional cytotoxic chemotherapeutic agents against head and neck squamous cell carcinoma and attenuating their cytotoxicity. This article also provides information on ongoing and recently completed clinical trials for therapies based on nanotechnology.
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Affiliation(s)
| | - Ayesha Farhana Syeda
- Department of Pharmaceutics, Unaiza College of Pharmacy, Qassim University, Unaizah, Saudi Arabia
- *Correspondence: Ayesha Farhana Syeda, ; Ram Kumar Sahu, ; Jiyauddin Khan,
| | | | - Shalam M. Hussain
- Department of Clinical Pharmacy, College of Nursing and Health Sciences, Al-Rayyan Medical College, Madinah, Saudi Arabia
| | | | - Padmanath Pegu
- Girijananda Chowdhury Institute of Pharmaceutical Science, Tezpur, India
| | - Ram Kumar Sahu
- Department of Pharmaceutical Sciences, Hemvati Nandan Bahuguna Garhwal University (A Central University), Chauras Campus, Tehri Garhwal, Uttarakhand, India
- *Correspondence: Ayesha Farhana Syeda, ; Ram Kumar Sahu, ; Jiyauddin Khan,
| | - Jiyauddin Khan
- School of Pharmacy, Management and Science University, Shah Alam, Malaysia
- *Correspondence: Ayesha Farhana Syeda, ; Ram Kumar Sahu, ; Jiyauddin Khan,
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30
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Davis KV, Hallman MH, DiCarlo M, Wambua SM, Jaffe RL, Welsh AW, Kerber C, Yang H, Chambers CV, Myers RE. Factors Likely to Affect the Uptake of Genomic Approaches to Cancer Screening in Primary Care: A Scoping Review. J Pers Med 2022; 12:jpm12122044. [PMID: 36556264 PMCID: PMC9785136 DOI: 10.3390/jpm12122044] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/02/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
Genomic tests are being developed for use in cancer screening. As most screening is offered in primary care settings, primary care provider and patient perceptions of such tests are likely to affect uptake. We conducted a scoping review to synthesize information on factors likely to affect patient and provider use of biospecimen collection and analysis for cancer screening, methods referred to as liquid biopsy or multi-cancer early detection (MCED) testing when used to detect multiple cancers. We ultimately identified 7 articles for review and analyzed them for major themes. None reported on primary care provider perspectives. Six articles focused on patient perceptions about testing for a single cancer (colorectal), and 1 reported on patient views related to testing for multiple cancers. Factors favoring this type of testing included its non-invasiveness, and the perceived safety, convenience, and effectiveness of testing. There is a dearth of information in the literature on primary care provider perceptions about liquid biopsy and MCED testing. The limited information on patient perceptions suggests that they are receptive to such tests. Research on primary care provider and patient test-related knowledge, attitudes, and behavior is needed to guide future implementation in primary care settings.
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Affiliation(s)
- Kaitlyn V. Davis
- Department of Family and Community Medicine, Thomas Jefferson University, 1015 Walnut St., Philadelphia, PA 19107, USA
| | - Mie H. Hallman
- Department of Medical Oncology, Thomas Jefferson University, 834 Chestnut St., The Franklin Building, Suite 314, Philadelphia, PA 19107, USA
| | - Melissa DiCarlo
- Department of Medical Oncology, Thomas Jefferson University, 834 Chestnut St., The Franklin Building, Suite 314, Philadelphia, PA 19107, USA
| | - Sophie M. Wambua
- Department of Family and Community Medicine, Thomas Jefferson University, 1015 Walnut St., Philadelphia, PA 19107, USA
| | - Rachel L. Jaffe
- Department of Medical Oncology, Thomas Jefferson University, 834 Chestnut St., The Franklin Building, Suite 314, Philadelphia, PA 19107, USA
| | - Allison W. Welsh
- Exact Sciences Corporation, 5505 Endeavor Lane, Madison, WI 53719, USA
| | - Cameron Kerber
- Exact Sciences Corporation, 5505 Endeavor Lane, Madison, WI 53719, USA
| | - Hushan Yang
- Department of Medical Oncology, Thomas Jefferson University, 834 Chestnut St., The Franklin Building, Suite 314, Philadelphia, PA 19107, USA
| | - Christopher V. Chambers
- Department of Family and Community Medicine, Thomas Jefferson University, 1015 Walnut St., Philadelphia, PA 19107, USA
| | - Ronald E. Myers
- Department of Medical Oncology, Thomas Jefferson University, 834 Chestnut St., The Franklin Building, Suite 314, Philadelphia, PA 19107, USA
- Correspondence: ; Tel.: +1-215-503-4085
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31
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Yin Z, Shi R, Xia X, Li L, Yang Y, Li S, Xu J, Xu Y, Cai X, Wang S, Liu Z, Peng T, Peng Y, Wang H, Ye M, Liu Y, Chen Z, Tan W. An Implantable Magnetic Vascular Scaffold for Circulating Tumor Cell Removal In Vivo. Adv Mater 2022; 34:e2207870. [PMID: 36271719 DOI: 10.1002/adma.202207870] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/11/2022] [Indexed: 06/16/2023]
Abstract
An integrated trapped device (ITD) capable of removal of circulating tumor cells (CTCs) can assuage or even prevent metastasis. However, adhesion repertoires are ordinarily neglected in the design of ITDs, possibly leading to the omission of highly metastatic CTC and treatment failure. Here a vascular-like ITD with adhesive sites and wireless magnetothermal response to remove highly metastatic CTC in vivo is presented. Such a vascular-like ITD comprises circumferential well-aligned fibers and artificial adhesion repertoires and is optimized for magnetothermal integration. Continuous and repeated capture in a dynamic environment increases capture efficiency over time. Meanwhile, the heat generation of the ITD leads to the capture of CTC death owing to cell heat sensitivity. Furthermore, the constructed bioinspired ultrastructure of the ITD prevents vascular blockage and induces potential vascular regeneration. Overall, this work defines an extendable strategy for constructing adhesion repertoires against intravascular shear forces, provides a vascular-like ITD for reducing CTC counts, and is expected to alleviate the risk of cancer recurrence.
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Affiliation(s)
- Zhiwei Yin
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, 410082, China
| | - Rui Shi
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, 410082, China
| | - Xin Xia
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, 410082, China
| | - Ling Li
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, 410082, China
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Yanxia Yang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, 410082, China
| | - Shengkai Li
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, 410082, China
| | - Jieqiong Xu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, 410082, China
| | - Yiting Xu
- Key Laboratory of Theoretical Organic Chemistry and Function Molecule, Ministry of Education, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, 411201, China
| | - Xinqi Cai
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, 410082, China
| | - Shen Wang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, 410082, China
| | - Zhangkun Liu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, 410082, China
| | - Tianhuan Peng
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, 410082, China
| | - Ying Peng
- NHC Key Laboratory of Birth Defect for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, 410008, China
| | - Hua Wang
- Pediatric Research Institute, Hunan Children's Hospital, Changsha, 410007, China
| | - Mao Ye
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, 410082, China
| | - Yanlan Liu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, 410082, China
| | - Zhuo Chen
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, 410082, China
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
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Wu X, Iliuk AB, Tao WA. Translational proteomics and phosphoproteomics: Tissue to extracellular vesicles. Adv Clin Chem 2023; 112:119-53. [PMID: 36642482 DOI: 10.1016/bs.acc.2022.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We are currently experiencing a rapidly developing era in terms of translational and clinical medical sciences. The relatively mature state of nucleic acid examination has significantly improved our understanding of disease mechanism and therapeutic potential of personalized treatment, but misses a large portion of phenotypic disease information. Proteins, in particular phosphorylation events that regulates many cellular functions, could provide real-time information for disease onset, progression and treatment efficacy. The technical advances in liquid chromatography and mass spectrometry have realized large-scale and unbiased proteome and phosphoproteome analyses with disease relevant samples such as tissues. However, tissue biopsy still has multiple shortcomings, such as invasiveness of sample collection, potential health risk for patients, difficulty in protein preservation and extreme heterogeneity. Recently, extracellular vesicles (EVs) have offered a great promise as a unique source of protein biomarkers for non-invasive liquid biopsy. Membranous EVs provide stable preservation of internal proteins and especially labile phosphoproteins, which is essential for effective routine biomarker detection. To aid efficient EV proteomic and phosphoproteomic analyses, recent developments showcase clinically-friendly EV techniques, facilitating diagnostic and therapeutic applications. Ultimately, we envision that with streamlined sample preparation from tissues and EVs proteomics and phosphoproteomics analysis will become routine in clinical settings.
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McCloskey D, Erickson D. Rapid nucleic acid extraction from skin biopsies using a point-of-care device. Lab Chip 2022; 22:3229-3235. [PMID: 35861177 PMCID: PMC9399003 DOI: 10.1039/d2lc00457g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Sample processing is often the rate-limiting step for point-of-care nucleic acid testing, especially for large, robust tissues such as skin biopsies, which can be used to diagnose a variety of dermatological diseases. Extraction of nucleic acids from these samples often relies on lengthy enzymatic digestions, increasing the time to result and reducing the potential impact of rapid molecular diagnostic approaches. To address this, we have developed BLENDER, a device for rapid nucleic acid extraction from tissue biopsies that combines bead-beating homogenization with simultaneous sample heating for enzymatic lysis. Our device can produce a complete DNA yield from a 3 mm cylindrical skin biopsy with only a 15 minute extraction compared to 4 hours when using a commercially available extraction protocol. Decreasing sample-processing time for tissue biopsies could reduce time-to-result for downstream analysis, enabling faster point-of-care diagnosis of solid cancers in limited resource settings.
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Affiliation(s)
- Duncan McCloskey
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - David Erickson
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY, USA.
- Division of Nutritional Science, Cornell University, Ithaca, NY, USA
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34
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Sierra-Agudelo J, Rodriguez-Trujillo R, Samitier J. Microfluidics for the Isolation and Detection of Circulating Tumor Cells. Adv Exp Med Biol 2022; 1379:389-412. [PMID: 35761001 DOI: 10.1007/978-3-031-04039-9_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nowadays, liquid biopsy represents one of the most promising techniques for early diagnosis, monitoring, and therapy screening of cancer. This novel methodology includes, among other techniques, the isolation, capture, and analysis of circulating tumor cells (CTCs). Nonetheless, the identification of CTC from whole blood is challenging due to their extremely low concentration (1-100 per ml of whole blood), and traditional methods result insufficient in terms of purity, recovery, throughput and/or viability of the processed sample. In this context, the development of microfluidic devices for detecting and isolating CTCs offers a wide range of new opportunities due to their excellent properties for cell manipulation and the advantages to integrate and bring different laboratory processes into the microscale improving the sensitivity, portability, reducing cost and time. This chapter explores current and recent microfluidic approaches that have been developed for the analysis and detection of CTCs, which involve cell capture methods based on affinity binding and label-free methods and detection based on electrical, chemical, and optical sensors. All the exposed technologies seek to overcome the limitations of commercial systems for the analysis and isolation of CTCs, as well as to provide extended analysis that will allow the development of novel and more efficient diagnostic tools.
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Affiliation(s)
- Jessica Sierra-Agudelo
- Nanobioengineering Group, Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Romen Rodriguez-Trujillo
- Nanobioengineering Group, Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. .,Department of Electronics and Biomedical Engineering, University of Barcelona, Barcelona, Spain.
| | - Josep Samitier
- Nanobioengineering Group, Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Department of Electronics and Biomedical Engineering, University of Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain
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35
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Miserocchi G, Spadazzi C, Calpona S, De Rosa F, Usai A, De Vita A, Liverani C, Cocchi C, Vanni S, Calabrese C, Bassi M, De Luca G, Meccariello G, Ibrahim T, Schiavone M, Mercatali L. Precision Medicine in Head and Neck Cancers: Genomic and Preclinical Approaches. J Pers Med 2022; 12:854. [PMID: 35743639 DOI: 10.3390/jpm12060854] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/11/2022] [Accepted: 05/19/2022] [Indexed: 02/07/2023] Open
Abstract
Head and neck cancers (HNCs) represent the sixth most widespread malignancy worldwide. Surgery, radiotherapy, chemotherapeutic and immunotherapeutic drugs represent the main clinical approaches for HNC patients. Moreover, HNCs are characterised by an elevated mutational load; however, specific genetic mutations or biomarkers have not yet been found. In this scenario, personalised medicine is showing its efficacy. To study the reliability and the effects of personalised treatments, preclinical research can take advantage of next-generation sequencing and innovative technologies that have been developed to obtain genomic and multi-omic profiles to drive personalised treatments. The crosstalk between malignant and healthy components, as well as interactions with extracellular matrices, are important features which are responsible for treatment failure. Preclinical research has constantly implemented in vitro and in vivo models to mimic the natural tumour microenvironment. Among them, 3D systems have been developed to reproduce the tumour mass architecture, such as biomimetic scaffolds and organoids. In addition, in vivo models have been changed over the last decades to overcome problems such as animal management complexity and time-consuming experiments. In this review, we will explore the new approaches aimed to improve preclinical tools to study and apply precision medicine as a therapeutic option for patients affected by HNCs.
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36
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Rehman AU, Khan P, Maurya SK, Siddiqui JA, Santamaria-Barria JA, Batra SK, Nasser MW. Liquid biopsies to occult brain metastasis. Mol Cancer 2022; 21:113. [PMID: 35538484 PMCID: PMC9088117 DOI: 10.1186/s12943-022-01577-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 04/19/2022] [Indexed: 02/08/2023] Open
Abstract
Brain metastasis (BrM) is a major problem associated with cancer-related mortality, and currently, no specific biomarkers are available in clinical settings for early detection. Liquid biopsy is widely accepted as a non-invasive method for diagnosing cancer and other diseases. We have reviewed the evidence that shows how the molecular alterations are involved in BrM, majorly from breast cancer (BC), lung cancer (LC), and melanoma, with an inception in how they can be employed for biomarker development. We discussed genetic and epigenetic changes that influence cancer cells to breach the blood-brain barrier (BBB) and help to establish metastatic lesions in the uniquely distinct brain microenvironment. Keeping abreast with the recent breakthroughs in the context of various biomolecules detections and identifications, the circulating tumor cells (CTC), cell-free nucleotides, non-coding RNAs, secretory proteins, and metabolites can be pursued in human body fluids such as blood, serum, cerebrospinal fluid (CSF), and urine to obtain potential candidates for biomarker development. The liquid biopsy-based biomarkers can overlay with current imaging techniques to amplify the signal viable for improving the early detection and treatments of occult BrM.
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Affiliation(s)
- Asad Ur Rehman
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68108, USA
| | - Parvez Khan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68108, USA
| | - Shailendra Kumar Maurya
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68108, USA
| | - Jawed A Siddiqui
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68108, USA.,Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68108, USA
| | | | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68108, USA.,Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68108, USA.,Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE-68198, USA
| | - Mohd Wasim Nasser
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68108, USA. .,Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68108, USA.
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37
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Ferguson S, Yang KS, Zelga P, Liss AS, Carlson JCT, del Castillo CF, Weissleder R. Single-EV analysis (sEVA) of mutated proteins allows detection of stage 1 pancreatic cancer. Sci Adv 2022; 8:eabm3453. [PMID: 35452280 PMCID: PMC9032977 DOI: 10.1126/sciadv.abm3453] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 03/07/2022] [Indexed: 05/02/2023]
Abstract
Tumor cell-derived extracellular vesicles (EVs) are being explored as circulating biomarkers, but it is unclear whether bulk measurements will allow early cancer detection. We hypothesized that a single-EV analysis (sEVA) technique could potentially improve diagnostic accuracy. Using pancreatic cancer (PDAC), we analyzed the composition of putative cancer markers in 11 model lines. In parental PDAC cells positive for KRASmut and/or P53mut proteins, only ~40% of EVs were also positive. In a blinded study involving 16 patients with surgically proven stage 1 PDAC, KRASmut and P53mut protein was detectable at much lower levels, generally in <0.1% of vesicles. These vesicles were detectable by the new sEVA approach in 15 of the 16 patients. Using a modeling approach, we estimate that the current PDAC detection limit is at ~0.1-cm3 tumor volume, below clinical imaging capabilities. These findings establish the potential for sEVA for early cancer detection.
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Affiliation(s)
- Scott Ferguson
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114, USA
| | - Katherine S. Yang
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114, USA
| | - Piotr Zelga
- Department of Surgery, Massachusetts General Hospital, 32 Fruit St, Boston, MA 02114, USA
| | - Andrew S. Liss
- Department of Surgery, Massachusetts General Hospital, 32 Fruit St, Boston, MA 02114, USA
| | - Jonathan C. T. Carlson
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Carlos Fernandez del Castillo
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114, USA
- Department of Surgery, Massachusetts General Hospital, 32 Fruit St, Boston, MA 02114, USA
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114, USA
- Department of Systems Biology, Harvard Medical School, 200 Longwood Ave, Boston, MA 02115, USA
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Barsan V, Xia Y, Klein D, Gonzalez-Pena V, Youssef S, Inaba Y, Mahmud O, Natarajan S, Agarwal V, Pang Y, Autry R, Pui CH, Inaba H, Evans W, Gawad C. Simultaneous monitoring of disease and microbe dynamics through plasma DNA sequencing in pediatric patients with acute lymphoblastic leukemia. Sci Adv 2022; 8:eabj1360. [PMID: 35442732 PMCID: PMC9020671 DOI: 10.1126/sciadv.abj1360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 01/19/2022] [Indexed: 05/09/2023]
Abstract
Treatment of acute lymphoblastic leukemia (ALL) necessitates continuous risk assessment of leukemic disease burden and infections that arise in the setting of immunosuppression. This study was performed to assess the feasibility of a hybrid capture next-generation sequencing panel to longitudinally measure molecular leukemic disease clearance and microbial species abundance in 20 pediatric patients with ALL throughout induction chemotherapy. This proof of concept helps establish a technical and conceptual framework that we anticipate will be expanded and applied to additional patients with leukemia, as well as extended to additional cancer types. Molecular monitoring can help accelerate the attainment of insights into the temporal biology of host-microbe-leukemia interactions, including how those changes correlate with and alter anticancer therapy efficacy. We also anticipate that fewer invasive bone marrow examinations will be required, as these methods improve with standardization and are validated for clinical use.
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Affiliation(s)
- Valentin Barsan
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Yuntao Xia
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - David Klein
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Veronica Gonzalez-Pena
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94304, USA
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Sarah Youssef
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Yuki Inaba
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Ousman Mahmud
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Sivaraman Natarajan
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Vibhu Agarwal
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Yakun Pang
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94304, USA
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Robert Autry
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Hiroto Inaba
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - William Evans
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Charles Gawad
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94304, USA
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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Maher GJ, Fisher RA, Kaur B, Aguiar X, Aravind P, Cedeno N, Clark J, Damon D, Ghorani E, Januszewski A, Kalofonou F, Murphy R, Roy R, Sarwar N, Openshaw MR, Seckl MJ. Sensitive screening of single nucleotide polymorphisms in cell free DNA for diagnosis of gestational tumours. NPJ Genom Med 2022; 7:26. [PMID: 35396509 DOI: 10.1038/s41525-022-00297-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 03/04/2022] [Indexed: 11/24/2022] Open
Abstract
Tumours expressing human chorionic gonadotropin (hCG), the majority of which are difficult to biopsy due to their vascularity, have disparate prognoses depending on their origin. As optimal management relies on accurate diagnosis, we aimed to develop a sensitive cell free DNA (cfDNA) assay to non-invasively distinguish between cases of gestational and non-gestational origin. Deep error-corrected Illumina sequencing of 195 common single nucleotide polymorphisms (SNPs) in cfDNA and matched genomic DNA from 36 patients with hCG-secreting tumours (serum hCG 5 to 3,042,881 IU/L) and 7 controls with normal hCG levels (≤4 IU/L) was performed. cfDNA from confirmed gestational tumours with hCG levels ranging from 1497 to 700,855 IU/L had multiple (n ≥ 12) ‘non-host’ alleles (i.e. alleles of paternal origin). In such cases the non-host fraction of cfDNA ranged from 0.3 to 40.4% and correlated with serum hCG levels. At lower hCG levels the ability to detect non-host cfDNA was variable, with the detection limit dependent on the type of causative pregnancy. Patients with non-gestational tumours were identifiable by the absence of non-host cfDNA, with copy number alterations detectable in the majority of cases. Following validation in a larger cohort, our sensitive assay will enable clinicians to better inform patients, for whom biopsy is inappropriate, of their prognosis and provide optimum management.
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Tulukcuoglu Guneri ET, Lakis E, Hajji I, Martin E, Champ J, Rampanou A, Pierga J, Viovy J, Proudhon C, Bidard F, Descroix S. Deciphering HER2-HER3 Dimerization at the Single CTC Level: A Microfluidic Approach. Cancers (Basel) 2022; 14:1890. [PMID: 35454795 PMCID: PMC9026778 DOI: 10.3390/cancers14081890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 03/31/2022] [Accepted: 04/03/2022] [Indexed: 02/01/2023] Open
Abstract
Simple Summary Among these different biomarkers, circulating tumor cells have proven to be of high interest for different types of cancer and in particular for breast cancer. Here we focus our attention on a breast cancer subtype referred as HER2-positive breast cancer, this cancer being associated with an amplification of HER2 protein at the plasma membrane of cancer cells. Combined with therapies targeting the HER2 protein, HER2-HER3 dimerization blockade further improves a patient’s outcome. In this work, we propose a new approach to CTC characterization by on-chip integrating proximity ligation assay, so that we can quantify the HER2-HER3 dimerization event at the level of single CTC. Abstract Microfluidics has provided clinicians with new technologies to detect and analyze circulating tumor biomarkers in order to further improve their understanding of disease mechanism, as well as to improve patient management. Among these different biomarkers, circulating tumor cells have proven to be of high interest for different types of cancer and in particular for breast cancer. Here we focus our attention on a breast cancer subtype referred as HER2-positive breast cancer, this cancer being associated with an amplification of HER2 protein at the plasma membrane of cancer cells. Combined with therapies targeting the HER2 protein, HER2-HER3 dimerization blockade further improves a patient’s outcome. In this work, we propose a new approach to CTC characterization by on-chip integrating proximity ligation assay, so that we can quantify the HER2-HER3 dimerization event at the level of single CTC. To achieve this, we developed a microfluidic approach combining both CTC capture, identification and HER2-HER3 status quantification by Proximity Ligation Assay (PLA). We first optimized and demonstrated the potential of the on-chip quantification of HER2-HER3 dimerization using cancer cell lines with various levels of HER2 overexpression and validated its clinical potential with a patient’s sample treated or not with HER2-targeted therapy.
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De Alwis R, Hansson J, Lindgren D, Schoch S, Tejera A, Scholtz B, Elfving P, Möller C, Nilsson H, Johansson M, Axelson H. Size‑based isolation and detection of renal carcinoma cells from whole blood. Mol Clin Oncol 2022; 16:101. [PMID: 35463211 PMCID: PMC9022084 DOI: 10.3892/mco.2022.2534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 02/18/2022] [Indexed: 11/25/2022] Open
Abstract
Renal cell carcinoma (RCC) is a tumour type with an indolent growth pattern and rather vague symptoms. The present study developed a platform for liquid biopsy of RCC based upon the isolation of circulating tumour cells (CTCs). Founded on the observation that RCC tumour cells are considerably larger than leucocytes, the present study employed a microfluidics-based system for isolation of RCC CTCs from whole blood. Using this system, it was revealed that 66% of spiked-in RCC tumour cells could be retrieved using this approach. Furthermore, it was demonstrated that these cells could be molecularly detected with digital PCR using RCC-specific genes down to one tumour cell, whilst avoiding detection in samples lacking tumour cells. Finally, subtype specific transcripts were identified to distinguish the different subtypes of RCC, which were then validated in patient tumours. The present study established a novel workflow for the isolation of RCC CTCs from whole blood, with the potential to detect these cells irrespective of subtype.
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Affiliation(s)
- Roger De Alwis
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, 223 81 Lund, Sweden
| | - Jennifer Hansson
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, 223 81 Lund, Sweden
| | - David Lindgren
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, 223 81 Lund, Sweden
| | - Sarah Schoch
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, 223 81 Lund, Sweden
| | - Alexander Tejera
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, 223 81 Lund, Sweden
| | - Bianca Scholtz
- Department of Urology, Skåne University Hospital, 214 28 Malmö, Sweden
| | - Peter Elfving
- Department of Urology, Skåne University Hospital, 214 28 Malmö, Sweden
| | - Christina Möller
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, 223 81 Lund, Sweden
| | - Helén Nilsson
- Center for Molecular Pathology, Department of Translational Medicine, Skåne University Hospital, 214 28 Malmö, Sweden
| | - Martin Johansson
- Center for Molecular Pathology, Department of Translational Medicine, Skåne University Hospital, 214 28 Malmö, Sweden
| | - Håkan Axelson
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, 223 81 Lund, Sweden
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Pedersen SK, Musher BL, LaPointe LC, Tuck MK, Symonds EL, Loayza N, Young GP. Detection of recurrent colorectal cancer with high specificity using a reporting threshold for circulating tumor DNA methylated in BCAT1 and IKZF1. Cancer 2022; 128:1921-1928. [PMID: 35290664 DOI: 10.1002/cncr.34159] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 01/18/2022] [Accepted: 02/03/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND A blood assay measuring methylated BCAT1 and IKZF1 can detect recurrent colorectal cancer (CRC) with high sensitivity but suboptimal specificity. This study aimed to establish an upper reference limit (URL) of these biomarkers in a reference population without CRC, apply that threshold to detecting clinical recurrence in patients who had undergone definitive therapy for CRC, and compare the performance of the biomarkers with carcinoembryonic antigen (CEA). METHODS The level of methylation was reported as the aggregate methylated BCAT1 and IKZF1 expressed as a percentage of total plasma DNA. A reference population of patients confirmed to have no colorectal neoplasia (n = 857) was used to determine the URL. Test accuracy for clinical recurrence was determined in a post-treatment surveillance population (n = 549; 77 recurrence cases). RESULTS A methylation level of 0.07%, corresponding to the 98th percentile in the reference population, was set as the URL. In the surveillance population, 60 patients had methylation levels above 0.07%, and 81.7% of these had recurrence. In comparison with no minimum threshold being applied, assay sensitivity with a URL of 0.07% yielded similar sensitivity (63.6% [CI, 51.9%-74.3%] vs 64.9% [CI, 53.8%-74.7%]; P = .87) and higher specificity (97.7% [CI, 95.9%-98.8%] vs 91.3% [CI, 88.4%-93.5%]; P < .001). The BCAT1/IKZF1 test was 2.5-fold more sensitive than CEA for detecting recurrences considered amenable to surgery with curative intent (50.0% vs 20.8%; P = .016). CONCLUSIONS Applying a threshold for positivity to the methylated BCAT1/IKZF1 blood assay improved the specificity for CRC recurrence without compromising sensitivity. Both the sensitivity and the specificity were superior to those of CEA.
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Affiliation(s)
- Susanne K Pedersen
- Cancer Research, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Bedford Park, South Australia, Australia.,Clinical Genomics, Inc, Bridgewater, New Jersey
| | - Benjamin L Musher
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Lawrence C LaPointe
- Cancer Research, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Bedford Park, South Australia, Australia.,Clinical Genomics, Inc, Bridgewater, New Jersey
| | | | - Erin L Symonds
- Cancer Research, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Bedford Park, South Australia, Australia.,Bowel Health Service, Flinders Medical Centre, Bedford Park, South Australia, Australia
| | | | - Graeme P Young
- Cancer Research, Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, Bedford Park, South Australia, Australia
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Deverka PA, Douglas MP, Phillips KA. Multicancer Screening Tests: Anticipating And Addressing Considerations For Payer Coverage And Patient Access. Health Aff (Millwood) 2022; 41:383-389. [PMID: 35254936 DOI: 10.1377/hlthaff.2021.01316] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
There is a tremendous public health need to identify potentially lethal cancers at earlier stages, when there is a greater chance for improved survival. Although in the US there are currently screening recommendations for only five cancers (breast, colorectal, cervical, lung, and prostate), new tests can screen for up to fifty cancers simultaneously based on a simple blood draw. However, these multicancer screening tests (also called "liquid biopsy" tests) will also present challenges to payers because of intrinsic features of the tests and the complexity of payer coverage assessments for screening tests. We describe these considerations while also offering potential solutions that can inform payers' decision making if these tests prove to be beneficial.
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Affiliation(s)
- Patricia A Deverka
- Patricia A. Deverka , University of California San Francisco, San Francisco, California
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44
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Gilson P, Merlin JL, Harlé A. Deciphering Tumour Heterogeneity: From Tissue to Liquid Biopsy. Cancers (Basel) 2022; 14:1384. [PMID: 35326534 DOI: 10.3390/cancers14061384] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/04/2022] [Accepted: 03/05/2022] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Most malignant tumours are highly heterogeneous at molecular and phenotypic levels. Tumour variability poses challenges for the management of patients, as it arises between patients and even evolves in space and time within a single patient. Currently, treatment-decision making usually relies on the molecular characteristics of a limited tumour tissue sample at the time of diagnosis or disease progression but does not take into account the complexity of the bulk tumours and their constant evolution over time. In this review, we explore the extent of tumour heterogeneity and report the mechanisms that promote and sustain this diversity in cancers. We summarise the clinical strikes of tumour diversity in the management of patients with cancer. Finally, we discuss the current material and technological approaches that are relevant to adequately appreciate tumour heterogeneity. Abstract Human solid malignancies harbour a heterogeneous set of cells with distinct genotypes and phenotypes. This heterogeneity is installed at multiple levels. A biological diversity is commonly observed between tumours from different patients (inter-tumour heterogeneity) and cannot be fully captured by the current consensus molecular classifications for specific cancers. To extend the complexity in cancer, there are substantial differences from cell to cell within an individual tumour (intra-tumour heterogeneity, ITH) and the features of cancer cells evolve in space and time. Currently, treatment-decision making usually relies on the molecular characteristics of a limited tumour tissue sample at the time of diagnosis or disease progression but does not take into account the complexity of the bulk tumours and their constant evolution over time. In this review, we explore the extent of tumour heterogeneity with an emphasis on ITH and report the mechanisms that promote and sustain this diversity in cancers. We summarise the clinical strikes of ITH in the management of patients with cancer. Finally, we discuss the current material and technological approaches that are relevant to adequately appreciate ITH.
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Adams E, Sepich-Poore GD, Miller-Montgomery S, Knight R. Using All Our Genomes: Blood-based Liquid Biopsies for the Early Detection of Cancer. View (Beijing) 2022; 3:20200118. [PMID: 35872970 PMCID: PMC9307139 DOI: 10.1002/viw.20200118] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 10/22/2021] [Indexed: 02/02/2023] Open
Abstract
The pursuit of highly sensitive and specific cancer diagnostics based on cell-free (cf) nucleic acids isolated from minimally invasive liquid biopsies has been an area of intense research and commercial effort for at least two decades. Most of these tests detect cancer-specific mutations or epigenetic modifications on circulating DNA derived from tumor cells (ctDNA). Although recent FDA approvals of both single and multi-analyte liquid biopsy companion diagnostic assays are proof of the tremendous progress made in this domain, using ctDNA for the diagnosis of early-stage (stage I/II) cancers remains challenging due to several factors, such as low mutational allele frequency in circulation, overlapping profiles in genomic alterations among diverse cancers, and clonal hematopoiesis. This review discusses these analytical challenges, interim solutions, and the opportunity to complement ctDNA diagnostics with microbiome-aware analyses that may mitigate several existing ctDNA assay limitations.
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Affiliation(s)
| | - Gregory D Sepich-Poore
- Micronoma, Inc., San Diego, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | | | - Rob Knight
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
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Iliuk AB. Purification and Phosphoproteomic Analysis of Plasma-Derived Extracellular Vesicles. Methods Mol Biol 2022; 2504:147-56. [PMID: 35467285 DOI: 10.1007/978-1-0716-2341-1_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A successful phosphoproteomics analysis of extracellular vesicles (EVs) requires a unique approach, fine-tuned to address the challenges that have plagued plasma-based biomarker discovery. Here, I detail a procedure, which combines EVtrap-based high-recovery EV isolation, phase-transfer surfactant method for protein extraction, and PolyMAC-based enrichment of phosphopeptides. The combination of these methods provides a highly effective strategy for EV-based phosphoproteome analysis and leads to the discovery of novel phospho-markers previously undetectable.
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47
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Whitlock JH, Soelter TM, Williams AS, Hardigan AA, Lasseigne BN. Liquid biopsies in epilepsy: biomarkers for etiology, diagnosis, prognosis, and therapeutics. Hum Cell 2022; 35:15-22. [PMID: 34694568 PMCID: PMC8732818 DOI: 10.1007/s13577-021-00624-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 09/29/2021] [Indexed: 01/19/2023]
Abstract
Epilepsy is one of the most common diseases of the central nervous system, impacting nearly 50 million people around the world. Heterogeneous in nature, epilepsy presents in children and adults alike. Currently, surgery is one treatment approach that can completely cure epilepsy. However, not all individuals are eligible for surgical procedures or have successful outcomes. In addition to surgical approaches, antiepileptic drugs (AEDs) have also allowed individuals with epilepsy to achieve freedom from seizures. Others have found treatment through nonpharmacologic approaches such as vagus nerve stimulation, or responsive neurostimulation. Difficulty in accessing samples of human brain tissue along with advances in sequencing technology have driven researchers to investigate sampling liquid biopsies in blood, serum, plasma, and cerebrospinal fluid within the context of epilepsy. Liquid biopsies provide minimal or non-invasive sample collection approaches and can be assayed relatively easily across multiple time points, unlike tissue-based sampling. Various efforts have investigated circulating nucleic acids from these samples including microRNAs, cell-free DNA, transfer RNAs, and long non-coding RNAs. Here, we review nucleic acid-based liquid biopsies in epilepsy to improve understanding of etiology, diagnosis, prediction, and therapeutic monitoring.
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Affiliation(s)
- Jordan H Whitlock
- Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Tabea M Soelter
- Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Avery S Williams
- Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Andrew A Hardigan
- Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Brittany N Lasseigne
- Cell, Developmental and Integrative Biology, The University of Alabama at Birmingham, Birmingham, AL, USA.
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48
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Affiliation(s)
- Elaine R Mardis
- Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA.
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49
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Abstract
Circular RNA (circRNA) is a novel class of single-stranded RNAs with a closed loop structure. The majority of circRNAs are formed by a back-splicing process in pre-mRNA splicing. Their expression is dynamically regulated and shows spatiotemporal patterns among cell types, tissues and developmental stages. CircRNAs have important biological functions in many physiological processes, and their aberrant expression is implicated in many human diseases. Due to their high stability, circRNAs are becoming promising biomarkers in many human diseases, such as cardiovascular diseases, autoimmune diseases and human cancers. In this review, we focus on the translational potential of using human blood circRNAs as liquid biopsy biomarkers for human diseases. We highlight their abundant expression, essential biological functions and significant correlations to human diseases in various components of peripheral blood, including whole blood, blood cells and extracellular vesicles. In addition, we summarize the current knowledge of blood circRNA biomarkers for disease diagnosis or prognosis.
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Affiliation(s)
- Guoxia Wen
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Tong Zhou
- Department of Physiology and Cell Biology, Reno School of Medicine, University of Nevada, Reno, NV, 89557, USA.
| | - Wanjun Gu
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, 210096, China.
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50
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Zhang Y, Wang Y, Su X, Wang P, Lin W. The Value of Circulating Circular RNA in Cancer Diagnosis, Monitoring, Prognosis, and Guiding Treatment. Front Oncol 2021; 11:736546. [PMID: 34722285 PMCID: PMC8551378 DOI: 10.3389/fonc.2021.736546] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/23/2021] [Indexed: 12/31/2022] Open
Abstract
Liquid biopsy includes non-invasive analysis of circulating tumor-derived substances. It is a novel, innovative cancer screening tool that overcomes the limitations of current invasive tissue examinations in precision oncology. Circular RNA (circRNA) is a recent, novel, and attractive liquid biomarker showing stability, abundance, and high specificity in various diseases, especially in human cancers. This review focused on the emerging potential of human circRNA in body fluids as the liquid biopsy biomarkers for cancers and the methods used to detect the circRNA expression and summarized the construction of circRNA biomarkers in body fluids for treating human cancers and their limitations before they become part of routine clinical medicine. Furthermore, the future opportunities and challenges of translating circRNAs in liquid biopsy into clinical practices were explored.
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Affiliation(s)
- Yunjing Zhang
- Department of Nephrology, The Fourth Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Jinhua, China
| | - Ying Wang
- Department of Nephrology, The Fourth Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Jinhua, China
| | - Xinwan Su
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ping Wang
- Department of Urology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Weiqiang Lin
- Department of Nephrology, The Fourth Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Jinhua, China
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