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Conca V, Ciracì P, Boccaccio C, Minelli A, Antoniotti C, Cremolini C. Waiting for the "liquid revolution" in the adjuvant treatment of colon cancer patients: a review of ongoing trials. Cancer Treat Rev 2024; 126:102735. [PMID: 38613871 DOI: 10.1016/j.ctrv.2024.102735] [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: 12/01/2023] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 04/15/2024]
Abstract
Since colon cancer has a high rate of shedding of tumour fragments into the blood, several research efforts are now focused on the investigation of the minimal residual disease through the detection of ctDNA to tailor the adjuvant therapy of colon cancer patients and optimize its cost/effectiveness balance. The negative prognostic impact of detectable ctDNA in patients' blood after radical surgery for colon cancer is well established. Several clinical trials adopting heterogeneous designs and techniques are now ongoing to translate promises into daily practice by answering five general questions: i) is a ctDNA-guided decision making efficacious in the post-operative management of colon cancer patients? ii) are de-escalation strategies possible in ctDNA-negative cases? iii) are escalation strategies useful to improve the prognosis of ctDNA-positive patients? iv) when MRD is identified at the end of the adjuvant chemotherapy, is another post-adjuvant systemic therapy efficacious? v) can we exploit ctDNA technologies in the follow up of colon cancer patients? This review focuses on currently ongoing trials and how their results may affect the ctDNA "liquid revolution" of early colon cancer.
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Affiliation(s)
- V Conca
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy; Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - P Ciracì
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy; Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - C Boccaccio
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy; Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - A Minelli
- Division of Medical Oncology, Policlinico Universitario Campus Bio-Medico, Rome, Italy
| | - C Antoniotti
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy; Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - C Cremolini
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy; Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy.
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Huang T, Zhao Y, Jiang G, Yang Z. tsRNA: A Promising Biomarker in Breast Cancer. J Cancer 2024; 15:2613-2626. [PMID: 38577588 PMCID: PMC10988313 DOI: 10.7150/jca.93531] [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: 12/23/2023] [Accepted: 02/29/2024] [Indexed: 04/06/2024] Open
Abstract
tRNA-derived small RNAs (tsRNAs) are a novel class of non-coding small RNAs, generated from specific cleavage sites of tRNA or pre-tRNA. tsRNAs can directly participate in RNA silencing, transcription, translation, and other processes. Their dysregulation is closely related to the occurrence and development of various cancers. Breast cancer is one of the most common and fastest-growing malignant tumors in humans. tsRNAs have been found to be dysregulated in breast cancer, serving as a new target for exploring the pathogenesis of breast cancer. They are also considered new tumor markers, providing a basis for diagnosis and treatment. This article reviews the generation, classification, mechanism of action, function of tsRNAs, and their biological effects and related mechanisms in breast cancer, in the hope of providing a new direction for the diagnosis and treatment of breast cancer.
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Affiliation(s)
- Ting Huang
- Department of Thyroid and Breast Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Yuexin Zhao
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Guoqin Jiang
- Department of Thyroid and Breast Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Zhixue Yang
- Department of Thyroid and Breast Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
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Sharma D, Singh A, Wilson C, Swaroop P, Kumar S, Yadav DK, Jain V, Agarwala S, Husain M, Sharawat SK. Exosomal long non-coding RNA MALAT1: a candidate of liquid biopsy in monitoring of Wilms' tumor. Pediatr Surg Int 2024; 40:57. [PMID: 38353772 DOI: 10.1007/s00383-023-05626-4] [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] [Accepted: 12/26/2023] [Indexed: 02/16/2024]
Abstract
PURPOSE Wilms' tumor (WT) is a rare kidney cancer that primarily affects children. Exosomes are extracellular vesicles that cargo nucleic acids, proteins,etc. for cellular communication. Long non-coding RNAs (lncRNAs) have utility as biomarkers for cancer diagnosis, prognosis, and disease monitoring. We hypothesize that expression of lncRNA, metastasis-associated lung adenocarcinoma transcript-1(MALAT1), is dysregulated and possibly trafficked within exosomes to influence the tissue microenvironment for metastasis and recurrence of WT. METHODS We investigated the expression of MALAT1 in thirty WT samples by qPCR. Exosomes were isolated using a precipitated and affinity-binding-based kit, and characterized using TEM, NTA, and DLS. RESULTS Mean number of exosomes was 9.01×108/mL in primary culture, 1.64×108/mL in urine, and 4.65×108/plasma:400µl. Average yield of total RNA was 1.28µg (primary-culture supernatant:1ml), 1.47µg (Urine:1ml), 1.65µg (Plasma:400 µL). We quantified MALAT1 in exosomes derived from these sources in patients of WT. Expression of MALAT1 was significantly downregulated (p=0.008) in WT samples. CONCLUSION This is the first study that demonstrated the presence of lncRNA MALAT1 in various invasive and non-invasive samples of patients with WT(primary tissue culture, urine, and plasma samples).
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Affiliation(s)
- Diwakar Sharma
- Virology and Oncology Lab, Department of Biotechnology, Jamia Millia Islamia, New Delhi, India
- Department of Medical Oncology, All India Institute of Medical Sciences, New Delhi, India
| | - Apoorv Singh
- Department of Paediatric Surgery, All India Institute of Medical Sciences, New Delhi, India
| | - Christine Wilson
- Department of Medical Oncology, All India Institute of Medical Sciences, New Delhi, India
| | - Priyanka Swaroop
- Department of Paediatric Surgery, All India Institute of Medical Sciences, New Delhi, India
| | - Sachin Kumar
- Department of Medical Oncology, All India Institute of Medical Sciences, New Delhi, India
| | - Devendra K Yadav
- Department of Paediatric Surgery, All India Institute of Medical Sciences, New Delhi, India
| | - Vishesh Jain
- Department of Paediatric Surgery, All India Institute of Medical Sciences, New Delhi, India
| | - Sandeep Agarwala
- Department of Paediatric Surgery, All India Institute of Medical Sciences, New Delhi, India
| | - Mohammad Husain
- Virology and Oncology Lab, Department of Biotechnology, Jamia Millia Islamia, New Delhi, India.
| | - Surender K Sharawat
- Department of Medical Oncology, All India Institute of Medical Sciences, New Delhi, India.
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Di Santo R, Niccolini B, Romanò S, Vaccaro M, Di Giacinto F, De Spirito M, Ciasca G. Advancements in Mid-Infrared spectroscopy of extracellular vesicles. Spectrochim Acta A Mol Biomol Spectrosc 2024; 305:123346. [PMID: 37774583 DOI: 10.1016/j.saa.2023.123346] [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] [Received: 01/09/2023] [Revised: 08/07/2023] [Accepted: 09/02/2023] [Indexed: 10/01/2023]
Abstract
Extracellular vesicles (EVs) are lipid vesicles secreted by all cells into the extracellular space and act as nanosized biological messengers among cells. They carry a specific molecular cargo, composed of lipids, proteins, nucleic acids, and carbohydrates, which reflects the state of their parent cells. Due to their remarkable structural and compositional heterogeneity, characterizing EVs, particularly from a biochemical perspective, presents complex challenges. In this context, mid-infrared (IR) spectroscopy is emerging as a valuable tool, providing researchers with a comprehensive and label-free spectral fingerprint of EVs in terms of their specific molecular content. This review aims to provide an up-to-date critical overview of the major advancements in mid-IR spectroscopy of extracellular vesicles, encompassing both fundamental and applied research achievements. We also systematically emphasize the new possibilities offered by the integration of emerging cutting-edge IR technologies, such as tip-enhanced and surface-enhanced spectroscopy approaches, along with the growing use of machine learning for data analysis and spectral interpretation. Additionally, to assist researchers in navigating this intricate subject, our manuscript includes a wide and detailed collection of the spectral peaks that have been assigned to EV molecular constituents up to now in the literature.
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Affiliation(s)
- Riccardo Di Santo
- Dipartimento di Neuroscienze, Sezione di Fisica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; Fondazione Policlinico Universitario "A. Gemelli" IRCCS, 00168 Rome, Italy.
| | - Benedetta Niccolini
- Dipartimento di Neuroscienze, Sezione di Fisica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Sabrina Romanò
- Dipartimento di Neuroscienze, Sezione di Fisica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Maria Vaccaro
- Fondazione Policlinico Universitario "A. Gemelli" IRCCS, 00168 Rome, Italy
| | - Flavio Di Giacinto
- Dipartimento di Neuroscienze, Sezione di Fisica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; Fondazione Policlinico Universitario "A. Gemelli" IRCCS, 00168 Rome, Italy
| | - Marco De Spirito
- Dipartimento di Neuroscienze, Sezione di Fisica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; Fondazione Policlinico Universitario "A. Gemelli" IRCCS, 00168 Rome, Italy
| | - Gabriele Ciasca
- Dipartimento di Neuroscienze, Sezione di Fisica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; Fondazione Policlinico Universitario "A. Gemelli" IRCCS, 00168 Rome, Italy
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Moro G, Fratte CD, Normanno N, Polo F, Cinti S. Point-of-Care Testing for the Detection of MicroRNAs: Towards Liquid Biopsy on a Chip. Angew Chem Int Ed Engl 2023; 62:e202309135. [PMID: 37672490 DOI: 10.1002/anie.202309135] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 06/28/2023] [Revised: 08/23/2023] [Accepted: 09/06/2023] [Indexed: 09/08/2023]
Abstract
Point-of-care (PoC) testing is revolutionizing the healthcare sector improving patient care in daily hospital practice and allowing reaching even remote geographical areas. In the frame of cancer management, the design and validation of PoC enabling the non-invasive, rapid detection of cancer markers is urgently required to implement liquid biopsy in clinical practice. Therefore, focusing on stable blood-based markers with high-specificity, such as microRNAs, is of crucial importance. In this work, we highlight the potential impact of circulating microRNAs detection on cancer management and the crucial role of PoC testing devices, especially for low-income countries. A detailed discussion about the challenges that should be faced to promote the technological transfer and clinical use of these tools has been added, to provide the readers with a complete overview of potentialities and current limitations.
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Affiliation(s)
- Giulia Moro
- Department of Pharmacy, University of Naples Federico II, Via Montesano 9, 80131, Naples, Italy
| | - Chiara Dalle Fratte
- Department of Medical Biotechnology and Translational Medicine, Postgraduate School of Clinical Pharmacology and Toxicology, University of Milan "Statale", Via Vanvitelli 32, 20133, Milan, Italy
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori (IRCCS), Fondazione Pascale, Via Mariano Semmola, 53, 80131, Naples, Italy
| | - Federico Polo
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172, Venice, Italy
- European Centre for Living Technology (ECLT), Ca' Foscari University of Venice Ca' Bottacin, 30124, Venice, Italy
| | - Stefano Cinti
- Department of Pharmacy, University of Naples Federico II, Via Montesano 9, 80131, Naples, Italy
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Patil-Takbhate BR, Suryawanshi PV, Tripathy S, Khopkar-Kale P. Liquid Biopsy: A New Torchbearer in the Ever-Evolving Landscape of Breast Cancer Diagnosis. Asian Pac J Cancer Prev 2023; 24:4009. [PMID: 38156831 PMCID: PMC10909094 DOI: 10.31557/apjcp.2023.24.12.4009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 12/17/2023] [Indexed: 01/03/2024] Open
Affiliation(s)
| | - Poonam Vishal Suryawanshi
- Dr. D Y Patil Medical College Hospital and Research Centre Pune India Dr. D Y Patil Vidyapeeth Pune India
| | - Srikanth Tripathy
- Dr. D Y Patil Medical College Hospital and Research Centre Pune India Dr. D Y Patil Vidyapeeth Pune India
| | - Priyanka Khopkar-Kale
- Dr. D Y Patil Medical College Hospital and Research Centre Pune India Dr. D Y Patil Vidyapeeth Pune India
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Foster JB, Koptyra MP, Bagley SJ. Recent Developments in Blood Biomarkers in Neuro-oncology. Curr Neurol Neurosci Rep 2023; 23:857-867. [PMID: 37943477 DOI: 10.1007/s11910-023-01321-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2023] [Indexed: 11/10/2023]
Abstract
PURPOSE OF REVIEW Given the invasive and high-risk nature of brain surgery, the need for non-invasive biomarkers obtained from the peripheral blood is greatest in tumors of the central nervous system (CNS). In this comprehensive review, we highlight recent advances in blood biomarker development for adult and pediatric brain tumors. RECENT FINDINGS We summarize recent blood biomarker development for CNS tumors across multiple key analytes, including peripheral blood mononuclear cells, cell-free DNA, cell-free RNA, proteomics, circulating tumor cells, and tumor-educated platelets. We also discuss methods for enhancing blood biomarker detection through transient opening of the blood-brain barrier. Although blood-based biomarkers are not yet used in routine neuro-oncology practice, this field is advancing rapidly and holds great promise for improved and non-invasive management of patients with brain tumors. Prospective and adequately powered studies are needed to confirm the clinical utility of any blood biomarker prior to widespread clinical implementation.
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Affiliation(s)
- Jessica B Foster
- Division of Oncology, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mateusz P Koptyra
- Center for Data-Driven Discovery in Biomedicine (D3b), Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Stephen J Bagley
- Division of Hematology/Oncology, Hospital of the University of Pennsylvania, Perelman School of Medicine, University of Pennsylvania, 10th Floor Perelman Center, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA.
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Swarup N, Cheng J, Choi I, Heo YJ, Kordi M, Aziz M, Arora A, Li F, Chia D, Wei F, Elashoff D, Zhang L, Kim S, Kim Y, Wong DTW. Multi-faceted attributes of salivary cell-free DNA as liquid biopsy biomarkers for gastric cancer detection. Biomark Res 2023; 11:90. [PMID: 37817261 PMCID: PMC10566128 DOI: 10.1186/s40364-023-00524-2] [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: 07/09/2023] [Accepted: 09/12/2023] [Indexed: 10/12/2023] Open
Abstract
BACKGROUND Recent advances in circulating cell-free DNA (cfDNA) analysis from biofluids have opened new avenues for liquid biopsy (LB). However, current cfDNA LB assays are limited by the availability of existing information on established genotypes associated with tumor tissues. Certain cancers present with a limited list of established mutated cfDNA biomarkers, and thus, nonmutated cfDNA characteristics along with alternative biofluids are needed to broaden the available cfDNA targets for cancer detection. Saliva is an intriguing and accessible biofluid that has yet to be fully explored for its clinical utility for cancer detection. METHODS In this report, we employed a low-coverage single stranded (ss) library NGS pipeline "Broad-Range cell-free DNA-Seq" (BRcfDNA-Seq) using saliva to comprehensively investigate the characteristics of salivary cfDNA (ScfDNA). The identification of cfDNA features has been made possible by applying novel cfDNA processing techniques that permit the incorporation of ultrashort, ss, and jagged DNA fragments. As a proof of concept using 10 gastric cancer (GC) and 10 noncancer samples, we examined whether ScfDNA characteristics, including fragmentomics, end motif profiles, microbial contribution, and human chromosomal mapping, could differentiate between these two groups. RESULTS Individual and integrative analysis of these ScfDNA features demonstrated significant differences between the two cohorts, suggesting that disease state may affect the ScfDNA population by altering nuclear cleavage or the profile of contributory organism cfDNA to total ScfDNA. We report that principal component analysis integration of several aspects of salivary cell-free DNA fragmentomic profiles, genomic element profiles, end-motif sequence patterns, and distinct oral microbiome populations can differentiate the two populations with a p value of < 0.0001 (PC1). CONCLUSION These novel features of ScfDNA characteristics could be clinically useful for improving saliva-based LB detection and the eventual monitoring of local or systemic diseases.
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Affiliation(s)
- Neeti Swarup
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Jordan Cheng
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Irene Choi
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - You Jeong Heo
- The Samsung Advanced Institute for Health Sciences & Technology (SAIHST), Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06355, Republic of Korea
| | - Misagh Kordi
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Mohammad Aziz
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Akanksha Arora
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Indraprastha Institute of Information Technology (IIIT), Delhi, India
| | - Feng Li
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - David Chia
- Indraprastha Institute of Information Technology (IIIT), Delhi, India
| | - Fang Wei
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - David Elashoff
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Liying Zhang
- Indraprastha Institute of Information Technology (IIIT), Delhi, India
| | - Sung Kim
- Department of Medicine, Biostatistics and Computational Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 06355, South Korea
| | - Yong Kim
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
| | - David T W Wong
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
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Dhoundiyal S, Alam PDMA. Advancements in Biotechnology and Stem Cell Therapies for Breast Cancer Patients. Curr Stem Cell Res Ther 2023:CSCR-EPUB-134844. [PMID: 37815191 DOI: 10.2174/011574888x268109230924233850] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/09/2023] [Accepted: 08/18/2023] [Indexed: 10/11/2023]
Abstract
This comprehensive review article examines the integration of biotechnology and stem cell therapy in breast cancer diagnosis and treatment. It discusses the use of biotechnological tools such as liquid biopsies, genomic profiling, and imaging technologies for accurate diagnosis and monitoring of treatment response. Stem cell-based approaches, their role in modeling breast cancer progression, and their potential for breast reconstruction post-mastectomy are explored. The review highlights the importance of personalized treatment strategies that combine biotechnological tools and stem cell therapies. Ethical considerations, challenges in clinical translation, and regulatory frameworks are also addressed. The article concludes by emphasizing the potential of integrating biotechnology and stem cell therapy to improve breast cancer outcomes, highlighting the need for continued research and collaboration in this field.
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Paturu R, Lingaiah R, Kumari N, Singh S, Krishnani N, Srivastava S, Siddiqui SH, Nath A. Non-Small Cell Lung Cancer: Targetable Variants in Concurrent Tissue and Liquid Biopsy Testing in a North Indian Cohort. Asian Pac J Cancer Prev 2023; 24:3467-3475. [PMID: 37898852 PMCID: PMC10770664 DOI: 10.31557/apjcp.2023.24.10.3467] [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: 04/16/2023] [Accepted: 10/11/2023] [Indexed: 10/30/2023] Open
Abstract
OBJECTIVES Testing for EGFR, ALK, ROS1 and MET alterations in paired tissue and plasma samples of treatment-naïve patients of NSCLC and correlating their status with overall survival. MATERIALS AND METHODS One hundred treatment-naïve patients were recruited after obtaining informed consent. Ten ml of blood was collected within a period of two weeks from histological diagnosis, prior to the start of any treatment. DNA & RNA extraction was done from formalin-fixed paraffin embedded (FFPE) tissue and total cell-free nucleic acid extraction was done from plasma samples. EGFR mutation, ALK, ROS1 and MET rearrangements were tested by ARMS (Amplification Refractory Mutation System) PCR. All statistical analyses were conducted in R version 4.1.1. RESULTS A total of 61 cases showed molecular alterations in tissue samples which included EGFR mutations (47), ALK rearrangements (12), ROS1 fusion (2). MET alteration was not detected. Forty-three cases showed EGFR mutations in plasma, 26 of which were concurrently positive in tissue. Concordance observed was 62%. ALK-EML4 rearrangement, ROS1 fusion and MET were not detected in plasma samples. Sensitivity and specificity for detection of EGFR mutation in plasma were 55.3% and 67.9% respectively. Univariate Cox regression analysis showed a positive association between EGFR mutation in tissue and overall survival (HR = 0.4; 95% CI: 0.2-0.7; p = 0.003) and improved overall survival in those who received targeted therapy (HR = 0.29; 95% CI: 0.1-0.8; p = 0.02). CONCLUSION Concurrent testing in tissue and liquid biopsy in NSCLC increased the detection of EGFR mutations (47% to 64%). This has substantial implications in deciding treatment and administration targeted therapy and the consequent overall survival.
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Affiliation(s)
- Radha Paturu
- Department of Pathology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India.
| | - Raghavendra Lingaiah
- Department of Pathology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India.
| | - Niraj Kumari
- Department of Pathology & Lab Medicine, AIIMS Raebareli, Raebareli, Uttar Pradesh, India.
| | - Shalini Singh
- Department of Radiotherapy, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India.
| | - Narendra Krishnani
- Department of Pathology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India.
| | - Shreya Srivastava
- Department of Pathology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India.
| | - Saima Haleem Siddiqui
- Department of Pathology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India.
| | - Alok Nath
- Department of Pulmonary Medicine, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India.
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Liang PS, Zaman A, Kaminsky A, Cui Y, Castillo G, Tenner CT, Sherman SE, Dominitz JA. Blood Test Increases Colorectal Cancer Screening in Persons Who Declined Colonoscopy and Fecal Immunochemical Test: A Randomized Controlled Trial. Clin Gastroenterol Hepatol 2023; 21:2951-2957.e2. [PMID: 37037262 PMCID: PMC10523873 DOI: 10.1016/j.cgh.2023.03.036] [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: 11/06/2022] [Revised: 03/21/2023] [Accepted: 03/29/2023] [Indexed: 04/12/2023]
Abstract
BACKGROUND & AIMS The septin 9 blood test is indicated for colorectal cancer screening in individuals who decline first-line tests, but participation in this context is unclear. We conducted a randomized controlled trial to compare reoffering colonoscopy and fecal immunochemical test (FIT) alone versus also offering the blood test among individuals who declined colonoscopy and FIT. METHODS Screen-eligible Veterans aged 50-75 years who declined colonoscopy and FIT within the previous 6 months were randomized to letter and telephone outreach to reoffer screening with colonoscopy/FIT only (control), or additionally offering the blood test as a second-line option (intervention). The primary outcome was completion of any screening test within 6 months. The secondary outcome was completion of a full screening strategy within 6 months, including colonoscopy for those with a positive noninvasive test. RESULTS Of 359 participants who completed follow-up, 9.6% in the control group and 17.1% in the intervention group completed any screening (7.5% difference; P = .035). Uptake of colonoscopy and FIT was similar in the 2 groups. The full screening strategy was completed in 9.0% and 14.9% in the control and intervention groups, respectively (5.9% difference; P = .084). CONCLUSIONS Among individuals who previously declined colonoscopy and FIT, offering a blood test as a secondary option increased screening by 7.5% without decreasing uptake of first-line screening options. However, completion of a full screening strategy did not increase. These findings indicate that a blood test is a promising method to improve colorectal cancer screening, but obtaining a timely colonoscopy after a positive noninvasive test remains a challenge (ClincialTrials.gov number, NCT03598166).
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Affiliation(s)
- Peter S Liang
- Department of Medicine, VA New York Harbor Health Care System, New York, New York; Department of Medicine, NYU Langone Health, New York, New York.
| | - Anika Zaman
- Department of Medicine, VA New York Harbor Health Care System, New York, New York; Department of Medicine, NYU Langone Health, New York, New York
| | - Anne Kaminsky
- Department of Medicine, VA New York Harbor Health Care System, New York, New York
| | - Yongyan Cui
- Department of Medicine, NYU Langone Health, New York, New York
| | | | - Craig T Tenner
- Department of Medicine, VA New York Harbor Health Care System, New York, New York; Department of Medicine, NYU Langone Health, New York, New York
| | - Scott E Sherman
- Department of Medicine, VA New York Harbor Health Care System, New York, New York; Department of Medicine, NYU Langone Health, New York, New York
| | - Jason A Dominitz
- Department of Medicine, VA Puget Sound Health Care System, Seattle, Washington; Department of Medicine, University of Washington School of Medicine, Seattle, Washington
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Chamba C, Mawalla W. The future of lymphoma diagnosis, prognosis, and treatment monitoring in countries with limited access to pathology services. Semin Hematol 2023; 60:215-219. [PMID: 37596119 DOI: 10.1053/j.seminhematol.2023.07.004] [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: 05/31/2023] [Revised: 07/17/2023] [Accepted: 07/24/2023] [Indexed: 08/20/2023]
Abstract
The world is moving towards precision medicine for cancer. This movement goes hand in hand with the development of newer advanced technologies for early, precise diagnosis of cancer and personalized treatment plans with fewer adverse effects for the patient. Liquid biopsy is one such advancement. At the same time, it has the advantage of minimal invasion and avoids serial invasive biopsies. In countries with limited access to pathology services, such as sub-Saharan Africa, liquid biopsy may provide an opportunity for early detection and prognostication of lymphoma. We discuss the current diagnostic modalities for lymphoma, highlighting the existing challenges with tissue biopsy, and how feasible it is for countries with limited pathology resources to leverage advancements made in the clinical application of liquid biopsy to improve lymphoma care.
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Affiliation(s)
- Clara Chamba
- Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania.
| | - William Mawalla
- Department of Hematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
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Voss JK, Ebner DW, Burger KN, Mahoney DW, Devens ME, Lowrie KL, Kisiel JB. Multitarget Stool DNA Testing Has High Positive Predictive Value for Colorectal Neoplasia on the Second Round of Testing. Clin Gastroenterol Hepatol 2023; 21:2399-2406. [PMID: 36621751 PMCID: PMC10323033 DOI: 10.1016/j.cgh.2022.12.026] [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: 07/06/2022] [Revised: 11/08/2022] [Accepted: 12/11/2022] [Indexed: 01/10/2023]
Abstract
BACKGROUND & AIMS Multitarget stool DNA (mt-sDNA) testing is a stool-based screening test for colorectal cancer (CRC). In a single instance of testing, the pivotal Food and Drug Administration-approval study (NCT01397747) found that 16% of mt-sDNA tests were positive, and the positive predictive value (PPV) for CRC or advanced precursor lesions (APL) was 27.3%. We aimed to examine real-world longitudinal performance by determining the test-positive rate and PPV of mt-sDNA on the second round of testing. METHODS Colonoscopy and pathology reports were reviewed retrospectively for patients with a negative mt-sDNA on the first round of screening and a positive mt-sDNA on the second round. The test-positivity rate and PPV for CRC, APL, and any colorectal neoplasia were calculated for the second mt-sDNA and compared with baseline PPVs from a previously published cohort of patients from our institution who tested positive on the first round of screening. RESULTS A total of 2758 patients completed a second test at a median of 3.2 years after the first test. Of these, 422 (15%) had a positive second mt-sDNA. The PPV was 0.25% for CRC, 24% for APL, and 67% for any colorectal neoplasia. There was no significant difference in PPV on the second mt-sDNA test compared with the first round (24% vs 28% for APL; P = .12). CONCLUSIONS mt-sDNA test positive rate and PPV were similar between the first and second rounds of screening. These observations confirm the utility of a second round of mt-sDNA screening and may inform estimates of mt-sDNA effectiveness for CRC screening.
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Affiliation(s)
- Jordan K Voss
- Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota
| | - Derek W Ebner
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Keli N Burger
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Douglas W Mahoney
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Mary E Devens
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Kari L Lowrie
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - John B Kisiel
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota.
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Swarup N, Cheng J, Choi I, Heo YJ, Kordi M, Li F, Aziz M, Chia D, Wei F, Elashoff D, Zhang L, Kim S, Kim Y, Wong DT. Multi-Faceted Attributes of Salivary Cell-free DNA as Liquid Biopsy Biomarkers for Gastric Cancer Detection. Res Sq 2023:rs.3.rs-3154388. [PMID: 37503289 PMCID: PMC10371094 DOI: 10.21203/rs.3.rs-3154388/v1] [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: 07/29/2023]
Abstract
Background Recent advances in circulating cell-free DNA (cfDNA) analysis from biofluids have opened new avenues for liquid biopsy (LB). However, current cfDNA LB assays are limited by the availability of existing information on established genotypes associated with tumor tissues. Certain cancers present with a limited list of established mutated cfDNA biomarkers, and thus, nonmutated cfDNA characteristics along with alternative biofluids are needed to broaden the available cfDNA targets for cancer detection. Saliva is an intriguing and accessible biofluid that has yet to be fully explored for its clinical utility for cancer detection. Methods In this report, we employed a low-coverage single stranded (ss) library NGS pipeline "Broad-Range cell-free DNA-Seq" (BRcfDNA-Seq) using saliva to comprehensively investigate the characteristics of salivary cfDNA (ScfDNA). The identification of cfDNA features has been made possible by applying novel cfDNA processing techniques that permit the incorporation of ultrashort, ss, and jagged DNA fragments. As a proof of concept using 10 gastric cancer (GC) and 10 noncancer samples, we examined whether ScfDNA characteristics, including fragmentomics, end motif profiles, microbial contribution, and human chromosomal mapping, could differentiate between these two groups. Results Individual and integrative analysis of these ScfDNA features demonstrated significant differences between the two cohorts, suggesting that disease state may affect the ScfDNA population by altering nuclear cleavage or the profile of contributory organism cfDNA to total ScfDNA. We report that principal component analysis integration of several aspects of salivary cell-free DNA fragmentomic profiles, genomic element profiles, end-motif sequence patterns, and distinct oral microbiome populations can differentiate the two populations with a p value of < 0.0001 (PC1). Conclusion These novel features of ScfDNA characteristics could be clinically useful for improving saliva-based LB detection and the eventual monitoring of local or systemic diseases.
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Affiliation(s)
- Neeti Swarup
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Jordan Cheng
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Irene Choi
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - You Jeong Heo
- The Samsung Advanced Institute for Health Sciences & Technology (SAIHST), Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06355, Republic of Korea
| | - Misagh Kordi
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Feng Li
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Mohammad Aziz
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - David Chia
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Fang Wei
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - David Elashoff
- Department of Medicine, Biostatistics and Computational Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Liying Zhang
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Sung Kim
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06355, South Korea
| | - Yong Kim
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - David T.W. Wong
- School of Dentistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
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Wehrle CJ, Raj R, Aykun N, Orabi D, Estfan B, Kamath S, Krishnamurthi S, Fujiki M, Hashimoto K, Quintini C, Kwon DCH, Diago-Uso T, Sasaki K, Aucejo FN. Liquid Biopsy by ctDNA in Liver Transplantation for Colorectal Cancer Liver Metastasis. J Gastrointest Surg 2023; 27:1498-1509. [PMID: 37273078 DOI: 10.1007/s11605-023-05723-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/20/2023] [Indexed: 06/06/2023]
Abstract
INTRODUCTION Colorectal cancer is a leading cause of cancer-related death worldwide. Metastatic liver disease develops in 50% of cases and drives patient outcomes. Although the ideal treatment for colorectal cancer liver metastases (CRLM) is resection, only a third of patients are suitable for this approach. Reports of liver transplantation in selected patients with unresectable CRLM have shown encouraging results compared to conventional forms of therapy. No study to date has examined the utility of liquid biopsy circulating tumor DNA (ctDNA) for evaluation of residual disease in this cohort of patients. We report a small series of liver transplantation in patients with CRLM in whom ctDNA was assessed peri-operatively. METHODS Five patients underwent liver transplantation for unresectable CRLM or liver failure following CRLM treatment from 2018 to 2022. Clinical data, cross-sectional imaging, and serum biomarkers including peri-operative ctDNA were reviewed from electronic medical records. RESULTS All patients are alive without radiologic evidence of disease at time of this publication. Median time of follow-up was 32 months (IQR 6.6-40 months). ctDNA was assessed before (4 patients) and after transplant (6 patients). One patient experienced a pulmonary recurrence that was resected, for whom pre-recurrence ctDNA was not available; the remaining patients have not experienced recurrence. Four patients are without evidence of ctDNA following transplant, and two demonstrate persistent ctDNA positivity post-transplant. Three of four patients with positive pre-transplant ctDNA remain ctDNA-negative post-transplant. CONCLUSIONS Liver transplantation for liver-confined unresectable CRLM is emerging as a valid surgical option in selected patients. The significance of liquid biopsy in this population remains elusive due to lack of data. The clearance of ctDNA after transplant in these patients with metastatic disease and despite their immunosuppression is notable. The significance and usefulness of liquid biopsy in patient selection, surveillance, and as an indication for treatment warrant further investigation.
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Affiliation(s)
- Chase J Wehrle
- Digestive Diseases and Surgery Institute, Department of Hepato-Pancreato-Biliary/Liver Transplant Surgery, Cleveland Clinic Foundation, Cleveland, OH, USA.
| | - Roma Raj
- Digestive Diseases and Surgery Institute, Department of Hepato-Pancreato-Biliary/Liver Transplant Surgery, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Nihal Aykun
- Digestive Diseases and Surgery Institute, Department of Hepato-Pancreato-Biliary/Liver Transplant Surgery, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Danny Orabi
- Digestive Diseases and Surgery Institute, Department of Hepato-Pancreato-Biliary/Liver Transplant Surgery, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Bassam Estfan
- Department of Hematology and Oncology, Cleveland Clinic Foundation, Taussig Cancer Institute, Cleveland, OH, USA
| | - Suneel Kamath
- Department of Hematology and Oncology, Cleveland Clinic Foundation, Taussig Cancer Institute, Cleveland, OH, USA
| | - Smitha Krishnamurthi
- Department of Hematology and Oncology, Cleveland Clinic Foundation, Taussig Cancer Institute, Cleveland, OH, USA
| | - Masato Fujiki
- Digestive Diseases and Surgery Institute, Department of Hepato-Pancreato-Biliary/Liver Transplant Surgery, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Koji Hashimoto
- Digestive Diseases and Surgery Institute, Department of Hepato-Pancreato-Biliary/Liver Transplant Surgery, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Cristiano Quintini
- Digestive Diseases and Surgery Institute, Department of Hepato-Pancreato-Biliary/Liver Transplant Surgery, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - David Choon Hyuck Kwon
- Digestive Diseases and Surgery Institute, Department of Hepato-Pancreato-Biliary/Liver Transplant Surgery, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Teresa Diago-Uso
- Digestive Diseases and Surgery Institute, Department of Hepato-Pancreato-Biliary/Liver Transplant Surgery, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Kazunari Sasaki
- Department of Surgery - Abdominal Transplantation, Stanford Hospital and Clinics, Palo Alto, CA, 94035, USA
| | - Federico N Aucejo
- Digestive Diseases and Surgery Institute, Department of Hepato-Pancreato-Biliary/Liver Transplant Surgery, Cleveland Clinic Foundation, Cleveland, OH, USA
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Haan D, Bergamaschi A, Friedl V, Guler GD, Ning Y, Reggiardo R, Kesling M, Collins M, Gibb B, Hazen K, Bates S, Antoine M, Fraire C, Lopez V, Malta R, Nabiyouni M, Nguyen A, Phillips T, Riviere M, Leighton A, Ellison C, McCarthy E, Scott A, Gigliotti L, Nilson E, Sheard J, Peters M, Bethel K, Chowdhury S, Volkmuth W, Levy S. Epigenomic Blood-Based Early Detection of Pancreatic Cancer Employing Cell-Free DNA. Clin Gastroenterol Hepatol 2023; 21:1802-1809.e6. [PMID: 36967102 DOI: 10.1016/j.cgh.2023.03.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 03/05/2023] [Accepted: 03/16/2023] [Indexed: 04/25/2023]
Abstract
BACKGROUND & AIMS Early detection of pancreatic cancer (PaC) can drastically improve survival rates. Approximately 25% of subjects with PaC have type 2 diabetes diagnosed within 3 years prior to the PaC diagnosis, suggesting that subjects with type 2 diabetes are at high risk of occult PaC. We have developed an early-detection PaC test, based on changes in 5-hydroxymethylcytosine (5hmC) signals in cell-free DNA from plasma. METHODS Blood was collected from 132 subjects with PaC and 528 noncancer subjects to generate epigenomic and genomic feature sets yielding a predictive PaC signal algorithm. The algorithm was validated in a blinded cohort composed of 102 subjects with PaC, 2048 noncancer subjects, and 1524 subjects with non-PaCs. RESULTS 5hmC differential profiling and additional genomic features enabled the development of a machine learning algorithm capable of distinguishing subjects with PaC from noncancer subjects with high specificity and sensitivity. The algorithm was validated with a sensitivity for early-stage (stage I/II) PaC of 68.3% (95% confidence interval [CI], 51.9%-81.9%) and an overall specificity of 96.9% (95% CI, 96.1%-97.7%). CONCLUSIONS The PaC detection test showed robust early-stage detection of PaC signal in the studied cohorts with varying type 2 diabetes status. This assay merits further clinical validation for the early detection of PaC in high-risk individuals.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Bill Gibb
- ClearNote Health, San Mateo, California
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17
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Hosseinpour Z, Rezaei Tavirani M, Akbari ME. Stage Analysis of Breast Cancer Metabolomics: A System Biology Approach. Asian Pac J Cancer Prev 2023; 24:1571-1582. [PMID: 37247276 PMCID: PMC10495889 DOI: 10.31557/apjcp.2023.24.5.1571] [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: 10/02/2022] [Accepted: 05/12/2023] [Indexed: 05/31/2023] Open
Abstract
BACKGROUND Breast cancer (BC) is the most common malignancy in women worldwide. Altered miRNA profile can disturb the metabolic homeostatic via regulation of gene expression in BC. METHODS In the present study to evaluate which miRNA, regulate metabolic pathways according to their stage, we performed comprehensive analysis of BC expression (mRNA and miRNA) of a set of patients by comparing samples of solid tumor tissue and adjacent tissue. The mRNA and miRNA data of breast cancer were downloaded from the cancer genome database (TCGA) using TCGAbiolinks package. Differentially expressed (mRNAs and miRNAs) was determined by DESeq2 package and predict valid miRNA-mRNA pairs using multiMiR package. All analyses were performed using the R software. Compound-reaction-enzyme-gene network was constructed using the Metscape a plugin for Cytoscape software. Then, core subnetwork computed by CentiScaPe, another plugin for Cytoscape. RESULTS In Stage I, hsa-miR-592, hsa-miR-449a and hsa-miR-1269a targeted HS3ST4, ACSL1 and USP9Y genes respectively. In stage II, hsa-miR-3662, Hsa-miR-429, and hsa-miR-1269a targeted GYS2, HAS3, ASPA, TRHDE, USP44, GDA, DGAT2, and USP9Y genes. In stage III, hsa-miR-3662 targeted TRHDE, GYS2, DPYS, HAS3, NMNAT2, ASPA genes. In stage IV, hsa-miR-429, has-miR-23c, and hsa-miR-449a targeted genes GDA, DGAT2, PDK4, ALDH1A2, ENPP2, and KL. Those miRNAs and their targets were identified as the discriminative elements for the four stages of breast cancer. CONCLUSION The most notable differences between BC and normal tissue in four stages involved multiple pathways and metabolites include: carbohydrate metabolism (e.g., Amylose, N-acetyl-D-glucosamin, beta-D-Glucuronoside, ""g""-CEHC-glucuronide, ""a""-CEHC-glucuronide, Heparan-glucosamine, 5,6-Dihydrouracil, 5,6-Dihydrothymine), branch-chain amino acid metabolism (e.g., N-Acetyl-L-aspartate, N-Formyl-L-aspartate, N`-acetyl-L-asparagine), Retinal metabolism (e.g., Retinal, 9-`cis`-retinal, 13-`cis`-retinal) and (FAD, NAD) as central coenzymes of metabolism. Set of crucial microRNAs and targeted genes plus the related metabolites were introduced for four stages of BC that can be consider for therapeutic and diagnostic purposes in the different stages of disease.
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Affiliation(s)
- Zahra Hosseinpour
- Cancer Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mostafa Rezaei Tavirani
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mohammad Esmaeil Akbari
- Surgical Oncology, Cancer Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Lambert T, Tasoulas J, Flores M, Sheth S, Patel SN. Circulating tumor HPV DNA as an alternative method to determine HPV status in oropharyngeal squamous cell carcinoma. Oral Oncol 2023; 140:106361. [PMID: 36965412 DOI: 10.1016/j.oraloncology.2023.106361] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 03/27/2023]
Abstract
Human Papilloma Virus (HPV) testing is mandatory for all newly diagnosed oropharyngeal squamous cell carcinoma (OPSCC) due to its importance for prognostication and aiding in treatment decision making. Fine needle aspiration (FNA) is a widely used and accepted diagnostic tool for OPSCC. Although FNA can accurately determine histological diagnosis, results are often indeterminate or lack insufficient samples for HPV testing. For samples with an indeterminant FNA, we propose an alternate method for determining HPV status using circulating tumor tissue modified HPV DNA (ctHPVDNA). We report three cases that confirmed HPV status using ctHPVDNA following an indeterminate FNA. If validated, this non-invasive assay could prevent the need for repeat FNAs or operative biopsies for the sole purpose of determining HPV status.
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Affiliation(s)
- Todd Lambert
- Department of Otolaryngology/Head and Neck Surgery, University of North Carolina School of Medicine, Chapel Hill, NC, United States
| | - Jason Tasoulas
- Department of Otolaryngology/Head and Neck Surgery, University of North Carolina School of Medicine, Chapel Hill, NC, United States
| | - Melissa Flores
- Division of Hematology/Oncology, University of North Carolina School of Medicine, Chapel Hill, NC, United States
| | - Siddharth Sheth
- Division of Hematology/Oncology, University of North Carolina School of Medicine, Chapel Hill, NC, United States.
| | - Samip N Patel
- Department of Otolaryngology/Head and Neck Surgery, University of North Carolina School of Medicine, Chapel Hill, NC, United States; Department of Otolaryngology/Head and Neck Surgery, Mayo Clinic, Jacksonville, FL, United States
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Bates M, Mohamed BM, Ward MP, Kelly TE, O'Connor R, Malone V, Brooks R, Brooks D, Selemidis S, Martin C, O'Toole S, O'Leary JJ. Circulating tumour cells: The Good, the Bad and the Ugly. Biochim Biophys Acta Rev Cancer 2023; 1878:188863. [PMID: 36796527 DOI: 10.1016/j.bbcan.2023.188863] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 01/06/2023] [Accepted: 01/21/2023] [Indexed: 02/17/2023]
Abstract
This review is an overview of the current knowledge regarding circulating tumour cells (CTCs), which are potentially the most lethal type of cancer cell, and may be a key component of the metastatic cascade. The clinical utility of CTCs (the "Good"), includes their diagnostic, prognostic, and therapeutic potential. Conversely, their complex biology (the "Bad"), including the existence of CD45+/EpCAM+ CTCs, adds insult to injury regarding their isolation and identification, which in turn hampers their clinical translation. CTCs are capable of forming microemboli composed of both non-discrete phenotypic populations such as mesenchymal CTCs and homotypic and heterotypic clusters which are poised to interact with other cells in the circulation, including immune cells and platelets, which may increase their malignant potential. These microemboli (the "Ugly") represent a prognostically important CTC subset, however, phenotypic EMT/MET gradients bring additional complexities to an already challenging situation.
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Affiliation(s)
- Mark Bates
- Department of Histopathology, Trinity College Dublin, Dublin 2, Ireland; Emer Casey Molecular Pathology Research Laboratory, Coombe Women & Infants University Hospital, Dublin 8, Ireland; Trinity St James's Cancer Institute, Dublin 8, Ireland.
| | - Bashir M Mohamed
- Department of Histopathology, Trinity College Dublin, Dublin 2, Ireland; Emer Casey Molecular Pathology Research Laboratory, Coombe Women & Infants University Hospital, Dublin 8, Ireland; Trinity St James's Cancer Institute, Dublin 8, Ireland
| | - Mark P Ward
- Department of Histopathology, Trinity College Dublin, Dublin 2, Ireland; Emer Casey Molecular Pathology Research Laboratory, Coombe Women & Infants University Hospital, Dublin 8, Ireland; Trinity St James's Cancer Institute, Dublin 8, Ireland
| | - Tanya E Kelly
- Department of Histopathology, Trinity College Dublin, Dublin 2, Ireland; Emer Casey Molecular Pathology Research Laboratory, Coombe Women & Infants University Hospital, Dublin 8, Ireland; Trinity St James's Cancer Institute, Dublin 8, Ireland
| | - Roisin O'Connor
- Department of Histopathology, Trinity College Dublin, Dublin 2, Ireland; Emer Casey Molecular Pathology Research Laboratory, Coombe Women & Infants University Hospital, Dublin 8, Ireland; Trinity St James's Cancer Institute, Dublin 8, Ireland; Department of Pathology, Coombe Women & Infants University Hospital, Dublin 8, Ireland
| | - Victoria Malone
- Department of Histopathology, Trinity College Dublin, Dublin 2, Ireland; Emer Casey Molecular Pathology Research Laboratory, Coombe Women & Infants University Hospital, Dublin 8, Ireland; Trinity St James's Cancer Institute, Dublin 8, Ireland; Department of Pathology, Coombe Women & Infants University Hospital, Dublin 8, Ireland
| | - Robert Brooks
- Cancer Research Institute, University of South Australia, Adelaide, SA 5001, Australia
| | - Doug Brooks
- Department of Histopathology, Trinity College Dublin, Dublin 2, Ireland; Trinity St James's Cancer Institute, Dublin 8, Ireland; Cancer Research Institute, University of South Australia, Adelaide, SA 5001, Australia
| | - Stavros Selemidis
- School of Health and Biomedical Sciences, Royal Melbourne Institute of Technology, Bundoora, VIC 3083, Australia
| | - Cara Martin
- Department of Histopathology, Trinity College Dublin, Dublin 2, Ireland; Emer Casey Molecular Pathology Research Laboratory, Coombe Women & Infants University Hospital, Dublin 8, Ireland; Trinity St James's Cancer Institute, Dublin 8, Ireland; Department of Pathology, Coombe Women & Infants University Hospital, Dublin 8, Ireland
| | - Sharon O'Toole
- Department of Histopathology, Trinity College Dublin, Dublin 2, Ireland; Emer Casey Molecular Pathology Research Laboratory, Coombe Women & Infants University Hospital, Dublin 8, Ireland; Trinity St James's Cancer Institute, Dublin 8, Ireland; Department of Obstetrics and Gynaecology, Trinity College Dublin, Dublin 2, Ireland
| | - John J O'Leary
- Department of Histopathology, Trinity College Dublin, Dublin 2, Ireland; Emer Casey Molecular Pathology Research Laboratory, Coombe Women & Infants University Hospital, Dublin 8, Ireland; Trinity St James's Cancer Institute, Dublin 8, Ireland; Department of Pathology, Coombe Women & Infants University Hospital, Dublin 8, Ireland
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Srivastava P, Mishra S, Agarwal A, Pandey A, Husain N. Circulating microRNAs in gallbladder cancer: Is serum assay of diagnostic value? Pathol Res Pract 2023; 242:154320. [PMID: 36682281 DOI: 10.1016/j.prp.2023.154320] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/10/2022] [Accepted: 01/16/2023] [Indexed: 01/18/2023]
Abstract
The microRNAs (miRNAs) in circulation could serve as biomarkers for cancer detection. Gallbladder carcinoma (GBC) is mostly asymptomatic; therefore, using microRNAs (miRNAs) as an early diagnostic biomarker could be a valuable tool. We aimed to identify the tumor-associated miR-1, miR130, miR-146, miR-182, and miR-21expression in serum as a biomarker for early detection of GBC and identify their possible diagnostic role. The study group comprised of paired serum and tissue samples from 34 GBC, 19 cholecystitis (CC), 21 normal controls (uninflamed gall bladder), and additional 29 serum-only samples of GBC. Total RNA was isolated using a commercially available RNA isolation kit (Applied Biosystem, USA) and reverse transcribed using Advanced Taqman MicroRNA reverse transcription kit. The relative expression of miRNAs was analyzed using Quantitative real-time polymerase chain reaction. The diagnostic potential of these miRNAs was assessed by ROC analysis. In paired samples, the trend towards up and down regulation for miR-182, miR-21, miR-1, miR-130, and miR-146 was similar in both tissue and sera of GBC. The expression pattern of serum miR-1, miR130, and miR-146 gradually decreased from normal control (NC) to CC to GBC, while miR-21 and miR-182 gradually increased from NC to CC to GBC. The miR-1, miR-121, miR-182, and miR-146 significantly differed between CC vs. early stage and early stage vs. NC. Among these miRNAs, the sensitivity of miR-1 (85.71 %) was the highest, and the specificity of miR-21 was the highest (92.73 %). The combined sensitivity for miRNAs ranged from 73.13 % (CI: 60.90-83.24 %) to 98.63 % (CI: 89.0-99.61 %); however, the specificity was lower. In stage I&II vs. III&IV discrimination, the diagnostic sensitivity of miR-1 was highest (89.36 %, CI: 76.90-96.45). The two miRNAs, in combination, increase the diagnostic sensitivity. Circulating serum miRNAs may provide a new approach for clinical application. Panels of specific circulating miRNA, which require further validation, could be potential non-invasive diagnostic biomarkers for GBC in combination with abnormal radio diagnostic scans.
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21
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Nakamura K, Hernández G, Sharma GG, Wada Y, Banwait JK, González N, Perea J, Balaguer F, Takamaru H, Saito Y, Toiyama Y, Kodera Y, Boland CR, Bujanda L, Quintero E, Goel A. A Liquid Biopsy Signature for the Detection of Patients With Early-Onset Colorectal Cancer. Gastroenterology 2022; 163:1242-1251.e2. [PMID: 35850198 PMCID: PMC9613521 DOI: 10.1053/j.gastro.2022.06.089] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/18/2022] [Accepted: 06/27/2022] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS Early-onset colorectal cancer (EOCRC) is a distinct clinical and molecular entity with poor survival outcomes compared with late-onset CRC. Although the incidence of EOCRC is rising, current CRC screening strategies have several limitations in diagnostic performance for EOCRC. In view of this clinical challenge, novel and robust biomarkers for detection of EOCRC are necessary. The aim of this study was to develop a circulating micro RNA (miRNA) signature for the diagnosis of patients with EOCRC. METHODS A systematic discovery approach by analyzing a large, publicly available, noncoding RNA expression profiling dataset (GSE115513) was used. A panel of miRNAs was identified, which was subsequently validated in blood samples from patients with EOCRC in 2 independent cohorts (n = 149) compared with controls (n = 110) and pre/postoperative plasma specimens (n = 22) using quantitative reverse-transcription polymerase chain reaction assays. RESULTS In the discovery phase, 4 miRNAs were found to be expressed in blood samples. A combination signature of these 4 miRNAs (miR-193a-5p, miR-210, miR-513a-5p, and miR-628-3p) yielded an area under the curve of 0.92 (95% confidence interval, 0.85-0.96) for identification of EOCRC in the training cohort. The miRNA panel performance was then confirmed in an independent validation cohort (area under the curve, 0.88; 95% confidence interval, 0.82-0.93). Moreover, the miRNA panel robustly identified patients with early-stage EOCRC (P < .001). The decreased expression of miRNAs in postsurgery plasma specimens indicated their tumor specificity. CONCLUSIONS Our novel miRNA signature for the diagnosis of EOCRC has the potential to identify patients with EOCRC with high accuracy for clinical application in the noninvasive diagnosis of EOCRC.
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Affiliation(s)
- Kota Nakamura
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, Monrovia, California; Department of Surgery, Nara Medical University, Nara, Japan
| | - Goretti Hernández
- Center for Gastrointestinal Research, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas; Gastroenterology Department, Hospital Universitario de Canarias, Instituto Universitario de Tecnologías Biomédicas (ITB) and Centro de Investigación Biomédica de Canarias (CIBICAN), Departamento de Medicina Interna, Universidad de La Laguna, Santa Cruz de Tenerife, Tenerife, Spain
| | - Geeta G Sharma
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, Monrovia, California
| | - Yuma Wada
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, Monrovia, California; Center for Gastrointestinal Research, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas
| | - Jasjit K Banwait
- Center for Gastrointestinal Research, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas
| | - Natalia González
- Gastroenterology Department, Hospital Universitario de Canarias, Instituto Universitario de Tecnologías Biomédicas (ITB) and Centro de Investigación Biomédica de Canarias (CIBICAN), Departamento de Medicina Interna, Universidad de La Laguna, Santa Cruz de Tenerife, Tenerife, Spain
| | - Jose Perea
- Department of Surgery, Fundación Jiménez Díaz University Hospital, Madrid, Spain; Fundación Jiménez Díaz University Hospital Health Research Institute, Madrid, Spain
| | - Francesc Balaguer
- Gastroenterology Department, Hospital Clinic de Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | | | - Yutaka Saito
- Endoscopy Division, National Cancer Center Hospital, Tokyo, Japan
| | - Yuji Toiyama
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Mie University Graduate School of Medicine, Mie, Japan
| | - Yasuhiro Kodera
- Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - C Richard Boland
- Division of Gastroenterology, School of Medicine, University of California San Diego, La Jolla, California
| | - Luis Bujanda
- Gastroenterology Department, Instituto Biodonostia, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Universidad del País Vasco (UPV/EHU), San Sebastián, Spain
| | - Enrique Quintero
- Gastroenterology Department, Hospital Universitario de Canarias, Instituto Universitario de Tecnologías Biomédicas (ITB) and Centro de Investigación Biomédica de Canarias (CIBICAN), Departamento de Medicina Interna, Universidad de La Laguna, Santa Cruz de Tenerife, Tenerife, Spain
| | - Ajay Goel
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, Monrovia, California; Center for Gastrointestinal Research, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas; City of Hope Comprehensive Cancer Center, Duarte, California.
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22
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Nakamura K, Zhu Z, Roy S, Jun E, Han H, Munoz RM, Nishiwada S, Sharma G, Cridebring D, Zenhausern F, Kim S, Roe DJ, Darabi S, Han IW, Evans DB, Yamada S, Demeure MJ, Becerra C, Celinski SA, Borazanci E, Tsai S, Kodera Y, Park JO, Bolton JS, Wang X, Kim SC, Von Hoff D, Goel A. An Exosome-based Transcriptomic Signature for Noninvasive, Early Detection of Patients With Pancreatic Ductal Adenocarcinoma: A Multicenter Cohort Study. Gastroenterology 2022; 163:1252-1266.e2. [PMID: 35850192 PMCID: PMC9613527 DOI: 10.1053/j.gastro.2022.06.090] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/18/2022] [Accepted: 06/25/2022] [Indexed: 12/25/2022]
Abstract
BACKGROUND & AIMS Pancreatic ductal adenocarcinoma (PDAC) incidence is rising worldwide, and most patients present with an unresectable disease at initial diagnosis. Measurement of carbohydrate antigen 19-9 (CA19-9) levels lacks adequate sensitivity and specificity for early detection; hence, there is an unmet need to develop alternate molecular diagnostic biomarkers for PDAC. Emerging evidence suggests that tumor-derived exosomal cargo, particularly micro RNAs (miRNAs), offer an attractive platform for the development of cancer-specific biomarkers. Herein, genomewide profiling in blood specimens was performed to develop an exosome-based transcriptomic signature for noninvasive and early detection of PDAC. METHODS Small RNA sequencing was undertaken in a cohort of 44 patients with an early-stage PDAC and 57 nondisease controls. Using machine-learning algorithms, a panel of cell-free (cf) and exosomal (exo) miRNAs were prioritized that discriminated patients with PDAC from control subjects. Subsequently, the performance of the biomarkers was trained and validated in independent cohorts (n = 191) using quantitative reverse transcription polymerase chain reaction (qRT-PCR) assays. RESULTS The sequencing analysis initially identified a panel of 30 overexpressed miRNAs in PDAC. Subsequently using qRT-PCR assays, the panel was reduced to 13 markers (5 cf- and 8 exo-miRNAs), which successfully identified patients with all stages of PDAC (area under the curve [AUC] = 0.98 training cohort; AUC = 0.93 validation cohort); but more importantly, was equally robust for the identification of early-stage PDAC (stages I and II; AUC = 0.93). Furthermore, this transcriptomic signature successfully identified CA19-9 negative cases (<37 U/mL; AUC = 0.96), when analyzed in combination with CA19-9 levels, significantly improved the overall diagnostic accuracy (AUC = 0.99 vs AUC = 0.86 for CA19-9 alone). CONCLUSIONS In this study, an exosome-based liquid biopsy signature for the noninvasive and robust detection of patients with PDAC was developed.
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Affiliation(s)
- Kota Nakamura
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, Monrovia, California
| | - Zhongxu Zhu
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, Monrovia, California; Department of Surgery, The Chinese University of Hong Kong. Prince of Wales Hospital, Shatin, N.T., Hong Kong, SAR, China; Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China
| | - Souvick Roy
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, Monrovia, California
| | - Eunsung Jun
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Ulsan University College of Medicine and Asan Medical Center, Seoul, Korea
| | - Haiyong Han
- The Translational Genomics Research Institute, Phoenix, Arizona
| | - Ruben M Munoz
- The Translational Genomics Research Institute, Phoenix, Arizona
| | - Satoshi Nishiwada
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, Monrovia, California
| | - Geeta Sharma
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, Monrovia, California
| | | | - Frederic Zenhausern
- Center for Applied NanoBioscience and Medicine, University of Arizona College of Medicine-Phoenix, Phoenix, Arizona
| | - Seungchan Kim
- Department of Electrical and Computer Engineering, Roy G. Perry College of Engineering, Prairie View A&M University, Prairie View, Texas
| | - Denise J Roe
- Department of Epidemiology and Biostatistics, The University of Arizona, Tucson, Arizona
| | - Sourat Darabi
- Hoag Family Center Institute, Newport Beach, California
| | - In-Woong Han
- Division of Hepato-Biliary Pancreatic Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Douglas B Evans
- Department of Surgery, The Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Suguru Yamada
- Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Michael J Demeure
- The Translational Genomics Research Institute, Phoenix, Arizona; Hoag Family Center Institute, Newport Beach, California
| | - Carlos Becerra
- Baylor Scott and White Research Institute, Baylor University Medical Center, Dallas, Texas
| | - Scott A Celinski
- Baylor Scott and White Research Institute, Baylor University Medical Center, Dallas, Texas
| | | | - Susan Tsai
- Department of Surgery, The Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Yasuhiro Kodera
- Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Joon Oh Park
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - John S Bolton
- Department of Surgery, Ochsner Clinic Foundation, New Orleans, Louisiana
| | - Xin Wang
- Department of Surgery, The Chinese University of Hong Kong. Prince of Wales Hospital, Shatin, N.T., Hong Kong, SAR, China.
| | - Song Cheol Kim
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, Ulsan University College of Medicine and Asan Medical Center, Seoul, Korea.
| | - Daniel Von Hoff
- The Translational Genomics Research Institute, Phoenix, Arizona.
| | - Ajay Goel
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, Monrovia, California; City of Hope Comprehensive Cancer Center, Duarte, California.
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23
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Berchuck JE, Facchinetti F, DiToro DF, Baiev I, Majeed U, Reyes S, Chen C, Zhang K, Sharman R, Junior PLSU, Maurer J, Shroff RT, Pritchard CC, Wu MJ, Catenacci DVT, Javle M, Friboulet L, Hollebecque A, Bardeesy N, Zhu AX, Lennerz JK, Tan B, Borad M, Parikh AR, Kiedrowski LA, Kelley RK, Mody K, Juric D, Goyal L. The Clinical Landscape of Cell-Free DNA Alterations in 1,671 Patients with Advanced Biliary Tract Cancer. Ann Oncol 2022; 33:1269-1283. [PMID: 36089135 DOI: 10.1016/j.annonc.2022.09.150] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [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: 08/09/2022] [Revised: 08/18/2022] [Accepted: 09/01/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Targeted therapies have transformed clinical management of advanced biliary tract cancer (BTC). Cell-free DNA (cfDNA) analysis is an attractive approach for cancer genomic profiling that overcomes many limitations of traditional tissue-based analysis. We examined cfDNA as a tool to inform clinical management of patients with advanced BTC and generate novel insights into BTC tumor biology. PATIENTS AND METHODS We analyzed next-generation sequencing data of 2,068 cfDNA samples from 1,671 patients with advanced BTC generated with Guardant360. We performed clinical annotation on a multi-institutional subset (n=225) to assess intra-patient cfDNA-tumor concordance and the association of cfDNA variant allele fraction (VAF) with clinical outcomes. RESULTS Genetic alterations were detected in cfDNA in 84% of patients, with targetable alterations detected in 44% of patients. FGFR2 fusions, IDH1 mutations, and BRAF V600E were clonal in majority of cases, affirming these targetable alterations as early driver events in BTC. Concordance between cfDNA and tissue for mutation detection was high for IDH1 mutations (87%) and BRAF V600E (100%), and low for FGFR2 fusions (18%). cfDNA analysis uncovered novel putative mechanisms of resistance to targeted therapies, including mutation of the cysteine residue (FGFR2 C492F) to which covalent FGFR inhibitors bind. High pre-treatment cfDNA VAF associated with poor prognosis and shorter response to chemotherapy and targeted therapy. Finally, we report the frequency of promising targets in advanced BTC currently under investigation in other advanced solid tumors, including KRAS G12C (1.0%), KRAS G12D (5.1%), PIK3CA mutations (6.8%), and ERBB2 amplifications (4.9%). CONCLUSIONS These findings from the largest and most comprehensive study to date of cfDNA from patients with advanced BTC highlight the utility of cfDNA analysis in current management of this disease. Characterization of oncogenic drivers and mechanisms of therapeutic resistance in this study will inform drug development efforts to reduce mortality for patients with BTC.
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Affiliation(s)
- Jacob E Berchuck
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Francesco Facchinetti
- Université Paris-Saclay, Institut Gustave Roussy, Inserm U981, Biomarqueurs Prédictifs et Nouvelles Stratégies Thérapeutiques en Oncologie, Villejuif, France
| | - Daniel F DiToro
- Center for Integrated Diagnostics, Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, MA
| | - Islam Baiev
- Department of Medicine, Mass General Cancer Center, Harvard Medical School, Boston, MA
| | - Umair Majeed
- Division of Hematology/Oncology, Mayo Clinic, Jacksonville, FL
| | | | - Christopher Chen
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Palo Alto, CA
| | - Karen Zhang
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Reya Sharman
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ
| | | | - Jordan Maurer
- Department of Medicine, Mass General Cancer Center, Harvard Medical School, Boston, MA
| | - Rachna T Shroff
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ
| | - Colin C Pritchard
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Meng-Ju Wu
- Department of Medicine, Mass General Cancer Center, Harvard Medical School, Boston, MA
| | | | - Milind Javle
- Division of Cancer Medicine, Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Luc Friboulet
- Université Paris-Saclay, Institut Gustave Roussy, Inserm U981, Biomarqueurs Prédictifs et Nouvelles Stratégies Thérapeutiques en Oncologie, Villejuif, France
| | - Antoine Hollebecque
- Université Paris-Saclay, Institut Gustave Roussy, Inserm U981, Biomarqueurs Prédictifs et Nouvelles Stratégies Thérapeutiques en Oncologie, Villejuif, France
| | - Nabeel Bardeesy
- Department of Medicine, Mass General Cancer Center, Harvard Medical School, Boston, MA
| | - Andrew X Zhu
- Jiahui International Cancer Center, Jihaui Health, Shanghai, China; I-Mab Biopharma, Shanghai, China
| | - Jochen K Lennerz
- Center for Integrated Diagnostics, Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, MA
| | - Benjamin Tan
- Department of Medicine, Washington University, St. Louis, MO
| | - Mitesh Borad
- Division of Hematology/Oncology, Mayo Clinic, Scottsdale, AZ
| | - Aparna R Parikh
- Department of Medicine, Mass General Cancer Center, Harvard Medical School, Boston, MA
| | | | - Robin Kate Kelley
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Kabir Mody
- Division of Hematology/Oncology, Mayo Clinic, Jacksonville, FL
| | - Dejan Juric
- Department of Medicine, Mass General Cancer Center, Harvard Medical School, Boston, MA
| | - Lipika Goyal
- Department of Medicine, Mass General Cancer Center, Harvard Medical School, Boston, MA.
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24
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Henriksen TV, Reinert T, Rasmussen MH, Demuth C, Løve US, Madsen AH, Gotschalck KA, Iversen LH, Andersen CL. Comparing single-target and multi-target approaches for postoperative circulating tumor DNA detection in stage II-III colorectal cancer patients. Mol Oncol 2022; 16:3654-3665. [PMID: 35895438 PMCID: PMC9580876 DOI: 10.1002/1878-0261.13294] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 05/10/2022] [Revised: 07/08/2022] [Accepted: 07/26/2022] [Indexed: 11/09/2022] Open
Abstract
Circulating tumour DNA (ctDNA) detection for postoperative risk stratification in cancer patients has great clinical potential. However, low ctDNA abundances complicates detection. Multitarget (MT) detection strategies have been developed to increase sensitivity. Yet, empirical evidence supporting performance gains of MT vs. single‐target (ST) strategies in a postoperative setting is limited. We compared ctDNA detection in 379 paired plasma samples from 112 stage II–III colorectal cancer patients by ST digital PCR and MT sequencing of 16 patient‐specific variants. The strategies exhibited good concordance (90%, Cohen's Kappa 0.79), with highly correlated ctDNA quantifications (Pearson r = 0.985). A difference was observed in ctDNA detection preoperatively (ST 72/92, MT 88/92). However, no difference was observed immediately after surgery in recurrence (ST 11/22, MT 10/22) or nonrecurrence (both 2/34) patients. In serial samples, detection was similar within recurrence (ST 13/16, MT 14/16) and nonrecurrence (ST 3/49, MT 1/49) patients. Both approaches yielded similar lead times to standard‐of‐care radiology (ST 4.0 months, MT 4.1 months). Our findings do not support significant performance gains of the MT strategy over the ST strategy for postoperative ctDNA detection.
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Affiliation(s)
- Tenna Vesterman Henriksen
- Department of Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens, Boulevard 99, DK-8200, Aarhus N, Denmark.,Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, DK-8200, Aarhus N, Denmark
| | - Thomas Reinert
- Department of Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens, Boulevard 99, DK-8200, Aarhus N, Denmark.,Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, DK-8200, Aarhus N, Denmark
| | - Mads Heilskov Rasmussen
- Department of Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens, Boulevard 99, DK-8200, Aarhus N, Denmark.,Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, DK-8200, Aarhus N, Denmark
| | - Christina Demuth
- Department of Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens, Boulevard 99, DK-8200, Aarhus N, Denmark.,Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, DK-8200, Aarhus N, Denmark
| | - Uffe Schou Løve
- Department of Surgery, Regional Hospital Viborg, Banevejen 7C, DK-8800, Viborg, Denmark
| | - Anders Husted Madsen
- Department of Surgery, Regional Hospital Herning, Hospitalsparken 15, DK-7400, Herning, Denmark
| | | | - Lene Hjerrild Iversen
- Department of Surgery, Aarhus University Hospital, Palle Juul-Jensens, Boulevard 35, DK-8200, Aarhus N, Denmark
| | - Claus Lindbjerg Andersen
- Department of Molecular Medicine, Aarhus University Hospital, Palle Juul-Jensens, Boulevard 99, DK-8200, Aarhus N, Denmark.,Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, DK-8200, Aarhus N, Denmark
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25
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Fackler MJ, Tulac S, Venkatesan N, Aslam AJ, de Guzman T, Mercado-Rodriguez C, Cope LM, Downs BM, Vali AH, Ding W, Lehman J, Denbow R, Reynolds J, Buckley ME, Visvanathan K, Umbricht CB, Wolff AC, Stearns V, Bates M, Lai EW, Sukumar S. Development of an automated liquid biopsy assay for methylated markers in advanced breast cancer. Cancer Res Commun 2022; 2:391-401. [PMID: 36046124 PMCID: PMC9426415 DOI: 10.1158/2767-9764.crc-22-0133] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/03/2022] [Accepted: 05/03/2022] [Indexed: 11/16/2022]
Abstract
Current molecular liquid biopsy assays to detect recurrence or monitor response to treatment require sophisticated technology, highly trained personnel, and a turnaround time of weeks. We describe the development and technical validation of an automated Liquid Biopsy for Breast Cancer Methylation (LBx-BCM) prototype, a DNA methylation detection cartridge assay that is simple to perform and quantitatively detects nine methylated markers within 4.5 h. LBx-BCM demonstrated high interassay reproducibility when analyzing exogenous methylated DNA (75-300 DNA copies) spiked into plasma (Coefficient of Variation, CV = 7.1 - 10.9%) and serum (CV = 19.1 - 36.1%). It also demonstrated high interuser reproducibility (Spearman r = 0.887, P < 0.0001) when samples of metastatic breast cancer (MBC, N = 11) and normal control (N = 4) were evaluated independently by two users. Analyses of interplatform reproducibility indicated very high concordance between LBx-BCM and the reference assay, cMethDNA, among 66 paired plasma samples (MBC N = 40, controls N = 26; Spearman r = 0.891; 95% CI = 0.825 - 0.933, P< 0.0001). LBx-BCM achieved a ROC AUC = 0.909 (95% CI = 0.836 - 0.982), 83% sensitivity and 92% specificity; cMethDNA achieved a ROC AUC = 0.896 (95% CI = 0.817 - 0.974), 83% sensitivity and 92% specificity in test set samples. The automated LBx-BCM cartridge prototype is fast, with performance levels equivalent to the highly sensitive, manual cMethDNA method. Future prospective clinical studies will evaluate LBx-BCM detection sensitivity and its ability to monitor therapeutic response during treatment for advanced breast cancer.
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Affiliation(s)
- Mary Jo Fackler
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | | | | | | | | | - Leslie M. Cope
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Bradley M. Downs
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Abdul Hussain Vali
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Wanjun Ding
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, Hubei, P.R. China
| | - Jennifer Lehman
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Rita Denbow
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jeffrey Reynolds
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Morgan E. Buckley
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kala Visvanathan
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | | | - Antonio C. Wolff
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Vered Stearns
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | | | - Saraswati Sukumar
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
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26
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Kahroba H, Samadi N, Mostafazadeh M, Hejazi MS, Sadeghi MR, Hashemzadeh S, Eftekhar Sadat AT, Karimi A. Evaluating the presence of deregulated tumoral onco-microRNAs in serum-derived exosomes of gastric cancer patients as noninvasive diagnostic biomarkers. Bioimpacts 2022; 12:127-138. [PMID: 35411299 PMCID: PMC8905585 DOI: 10.34172/bi.2021.22178] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 02/20/2021] [Accepted: 02/27/2021] [Indexed: 12/14/2022]
Abstract
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Introduction: Exosomal microRNAs (miRNAs) are emerging diagnostic biomarkers for different types of cancers. We aim to detect gastric cancer (GC)-specific miRNAs in serum exosomes with diagnostic potential.
Methods: A pair of 43 tumor and tumor-adjacent tissue biopsies obtained from GC patients, also 5 mL peripheral blood (following 12h fasting) were collected from the same patients and healthy controls (HCs). QIAGEN miRCURY LNA miRNA Focus PCR Panel applied to screen differentially expressed onco-miRNAs. The candidate miRNAs with the highest fold changes proceeded for validation by qRT-PCR in individuals.
Results: We identified that exosomal miR-10a-5p, miR-19b-3p, miR-215-5p, and miR-18a-5p were significantly upregulated in GC patient’s exosomes in contrast to HCs exosomes, Roc curve analysis indicated area under the ROC curve (AUC) of 0.801, 0.721, 0.780 and 0.736 respectively. The Roc curve analysis for the combined signature of four exosomal miRNAs indicated AUC of 0.813. Also, Spearman's correlation coefficients indicated that the miRNA expression is highly correlated between tumor and exosome.
Conclusion: Herein, we specifically identified four miRNAs in serum exosomes of GC patients for a diagnostic purpose which are directly associated with tumoral miRNA expression profile.
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Affiliation(s)
- Houman Kahroba
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.,Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nasser Samadi
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.,Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Biochemistry, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mostafa Mostafazadeh
- Department of Biochemistry, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohamad Saied Hejazi
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.,Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Reza Sadeghi
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.,Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Shahryar Hashemzadeh
- Liver and Gastrointestinal Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Amir Taher Eftekhar Sadat
- Department of General and Vascular Surgery, Imam Reza Educational Hospital, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Abbas Karimi
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
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Chalasani NP, Porter K, Bhattacharya A, Book AJ, Neis BM, Xiong KM, Ramasubramanian TS, Edwards DK, Chen I, Johnson S, Roberts LR, Kisiel JB, Reddy KR, Singal AG, Olson MC, Bruinsma JJ. Validation of a Novel Multitarget Blood Test Shows High Sensitivity to Detect Early Stage Hepatocellular Carcinoma. Clin Gastroenterol Hepatol 2022; 20:173-182.e7. [PMID: 34391922 DOI: 10.1016/j.cgh.2021.08.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/23/2021] [Accepted: 08/09/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS Hepatocellular carcinoma (HCC) is a leading cause of cancer-related death worldwide. Although biannual ultrasound surveillance with or without α-fetoprotein (AFP) testing is recommended for at-risk patients, sensitivity for early stage HCC, for which potentially curative treatments exist, is suboptimal. We conducted studies to establish the multitarget HCC blood test (mt-HBT) algorithm and cut-off values and to validate test performance in patients with chronic liver disease. METHODS Algorithm development and clinical validation studies were conducted with participants in an international, multicenter, case-control study. Study subjects had underlying cirrhosis or chronic hepatitis B virus; HCC cases were diagnosed per the American Association for the Study of Liver Diseases criteria and controls were matched for age and liver disease etiology. Whole blood and serum were shipped to a central laboratory and processed while blinded to case/control status. An algorithm was developed for the mt-HBT, which incorporates methylation biomarkers (HOXA1, TSPYL5, and B3GALT6), AFP, and sex. RESULTS In algorithm development, with 136 HCC cases (60% early stage) and 404 controls, the mt-HBT showed 72% sensitivity for early stage HCC at 88% specificity. Test performance was validated in an independent cohort of 156 HCC cases (50% early stage) and 245 controls, showing 88% overall sensitivity, 82% early stage sensitivity, and 87% specificity. Early stage sensitivity in clinical validation was significantly higher than AFP at 20 ng/mL or greater (40%; P < .0001) and GALAD (gender, age, Lens culinaris agglutinin-reactive AFP, AFP, and des-γ-carboxy-prothrombin score) of -0.63 or greater (71%; P = .03), although AFP and GALAD at these cut-off values had higher specificities (100% and 93%, respectively). CONCLUSIONS The mt-HBT may significantly improve early stage HCC detection for patients undergoing HCC surveillance, a critical step to increasing curative treatment opportunities and reducing mortality. ClinicalTrials.gov number NCT03628651.
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Affiliation(s)
- Naga P Chalasani
- Division of Gastroenterology and Hepatology, Indiana University School of Medicine, Indianapolis, Indiana.
| | - Kyle Porter
- Exact Sciences Corporation, Madison, Wisconsin
| | | | - Adam J Book
- Exact Sciences Development Corporation, Madison, Wisconsin
| | - Brenda M Neis
- Exact Sciences Development Corporation, Madison, Wisconsin
| | - Kong M Xiong
- Exact Sciences Development Corporation, Madison, Wisconsin
| | | | | | - Irene Chen
- Exact Sciences Corporation, Madison, Wisconsin
| | | | - Lewis R Roberts
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - John B Kisiel
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - K Rajender Reddy
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Amit G Singal
- Division of Digestive and Liver Diseases, University of Texas Southwestern Medical Center, Dallas, Texas
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Howard J, Goh CY, Gorzel KW, Higgins M, McCann A. The potential role of cofilin-1 in promoting triple negative breast cancer (TNBC) metastasis via the extracellular vesicles (EVs). Transl Oncol 2022; 15:101247. [PMID: 34678587 PMCID: PMC8529549 DOI: 10.1016/j.tranon.2021.101247] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [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: 05/26/2021] [Revised: 09/25/2021] [Accepted: 10/12/2021] [Indexed: 02/09/2023] Open
Abstract
Triple negative breast cancer (TNBC) is an aggressive cancer, particularly prone to metastasis and is associated with poor survival outcomes. The key to unravelling the aggressiveness of TNBC lies in decoding the mechanism by which it metastasises. Cofilin-1 is a well-studied member of the cofilin family, involved in actin depolymerisation. Studies have described the diverse roles of cofilin-1 including cell motility, apoptosis and lipid metabolism. Levels of cofilin-1 have been shown to be increased in many different types of malignant cells, with increased cofilin-1 protein levels associated with poor prognosis in patients with TNBC. Extracellular vesicles (EVs) are microvesicles typically around 100 nm in size, found in all biological fluids examined to date (Lötvall et al., 2014). Proteomic studies on extracellular vesicles (EVs) have shown that cofilin-1 is amongst the most frequently detected. Moreover, decreased levels of cofilin-1 potentially inhibit the release of EVs from cells. Additionally, Cofilin-1 is essential for the maturation of EVs and may also play a key role in the establishment of the pre-metastatic niche, thus promoting tumour cell migration. Further work into the exact mechanism by which cofilin-1 advances TNBC metastasis, may potentially prevent disease progression and improve outcomes for patients with TNBC.
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Affiliation(s)
- Jane Howard
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland; UCD School of Medicine, College of Health and Agricultural Sciences (CHAS), University College Dublin, Belfield, Dublin 4, Ireland.
| | - Chia Yin Goh
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland; UCD School of Medicine, College of Health and Agricultural Sciences (CHAS), University College Dublin, Belfield, Dublin 4, Ireland
| | - Karolina Weiner Gorzel
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland; St Vincent's University Hospital (SVUH), Elm Park, Dublin 4, Ireland
| | - Michaela Higgins
- St Vincent's University Hospital (SVUH), Elm Park, Dublin 4, Ireland
| | - Amanda McCann
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland; UCD School of Medicine, College of Health and Agricultural Sciences (CHAS), University College Dublin, Belfield, Dublin 4, Ireland
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Rapier-Sharman N, Clancy J, Pickett BE. Joint Secondary Transcriptomic Analysis of Non-Hodgkin's B-Cell Lymphomas Predicts Reliance on Pathways Associated with the Extracellular Matrix and Robust Diagnostic Biomarkers. J Bioinform Syst Biol 2022; 5:119-135. [PMID: 36873459 PMCID: PMC9980876 DOI: 10.26502/jbsb.5107040] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Approximately 450,000 cases of Non-Hodgkin's lymphoma are annually diagnosed worldwide, resulting in ~240,000 deaths. An augmented understanding of the common mechanisms of pathology among larger numbers of B-cell Non-Hodgkin's Lymphoma (BCNHL) patients is sorely needed. We consequently performed a large joint secondary transcriptomic analysis of the available BCNHL RNA-sequencing projects from GEO, consisting of 322 relevant samples across ten distinct public studies, to find common underlying mechanisms and biomarkers across multiple BCNHL subtypes and patient subpopulations; limitations may include lack of diversity in certain ethnicities and age groups and limited clinical subtype diversity due to sample availability. We found ~10,400 significant differentially expressed genes (FDR-adjusted p-value < 0.05) and 33 significantly modulated pathways (Bonferroni-adjusted p-value < 0.05) when comparing BCNHL samples to non-diseased B-cell samples. Our findings included a significant class of proteoglycans not previously associated with lymphomas as well as significant modulation of genes that code for extracellular matrix-associated proteins. Our drug repurposing analysis predicted new candidates for repurposed drugs including ocriplasmin and collagenase. We also used a machine learning approach to identify robust BCNHL biomarkers that include YES1, FERMT2, and FAM98B, which have not previously been associated with BCNHL in the literature, but together provide ~99.9% combined specificity and sensitivity for differentiating lymphoma cells from healthy B-cells based on measurement of transcript expression levels in B-cells. This analysis supports past findings and validates existing knowledge while providing novel insights into the inner workings and mechanisms of transformed B-cell lymphomas that could give rise to improved diagnostics and/or therapeutics.
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Affiliation(s)
- Naomi Rapier-Sharman
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Jeffrey Clancy
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Brett E Pickett
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
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Chalasani NP, Ramasubramanian TS, Bhattacharya A, Olson MC, Edwards V DK, Roberts LR, Kisiel JB, Reddy KR, Lidgard GP, Johnson SC, Bruinsma JJ. A Novel Blood-Based Panel of Methylated DNA and Protein Markers for Detection of Early-Stage Hepatocellular Carcinoma. Clin Gastroenterol Hepatol 2021; 19:2597-2605.e4. [PMID: 32889146 DOI: 10.1016/j.cgh.2020.08.065] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/31/2020] [Accepted: 08/27/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS Hepatocellular carcinoma (HCC) can be treated effectively if detected at an early stage. Recommended surveillance strategies for at-risk patients include ultrasound with or without α-fetoprotein (AFP), but their sensitivity is suboptimal. We sought to develop a novel, blood-based biomarker panel with improved sensitivity for early-stage HCC detection. METHODS In a multicenter, case-control study, we collected blood specimens from patients with HCC and age-matched controls with underlying liver disease but without HCC. Ten previously reported methylated DNA markers (MDMs) associated with HCC, methylated B3GALT6 (reference DNA marker), and 3 candidate proteins, including AFP, were assayed and analyzed by a logistic regression algorithm to predict HCC cases. The accuracy of the multi-target HCC panel was compared with that of other blood-based biomarkers for HCC detection. RESULTS The study included 135 HCC cases and 302 controls. We identified a multi-target HCC panel of 3 MDMs (HOXA1, EMX1, and TSPYL5), B3GALT6 and 2 protein markers (AFP and AFP-L3) with a higher sensitivity (71%, 95% CI: 60-81%) at 90% specificity for early-stage HCC than the GALAD score (41%, 95% CI: 30-53%) or AFP ≥7.32 ng/mL (45%, 95% CI: 33-57%). The AUC for the multi-target HCC panel for detecting any stage HCC was 0.92 compared with 0.87 for the GALAD score and 0.81 for AFP alone. The panel performed equally well in important subgroups based on liver disease etiology, presence of cirrhosis, or sex. CONCLUSIONS We developed a novel, blood-based biomarker panel that demonstrates high sensitivity for early-stage HCC. These data support the potential for liquid biopsy detection of early-stage HCC to clinically benefit at-risk patients. This study was registered on ClinicalTrials.gov (NCT03628651).
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Affiliation(s)
- Naga P Chalasani
- Division of Gastroenterology and Hepatology, Indiana University School of Medicine, Indianapolis, Indiana.
| | | | | | | | | | - Lewis R Roberts
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - John B Kisiel
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - K Rajender Reddy
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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D'Cruz A, Dechamma PN, Saldanha M, Maben S, Shetty P, Chakraborty A. Non-Invasive Saliva-based Detection of Gene Mutations in Oral Cancer Patients by Oral Rub and Rinse Technique. Asian Pac J Cancer Prev 2021; 22:3287-3291. [PMID: 34711005 PMCID: PMC8858228 DOI: 10.31557/apjcp.2021.22.10.3287] [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: 06/02/2021] [Indexed: 11/30/2022] Open
Abstract
Background: Oral Squamous Cell Carcinoma (OSCC) is the most widely reported cancer worldwide. Liquid biopsy, a method that relies on identification of tumor-associated cells and/or cell free nucleic acids from body fluids is becoming increasingly popular in cancer diagnostics. The aim of the study was to evaluate the feasibility of Oral Rub and Rinse (ORR) technique in determining the genetic changes in common biomarkers of oral cancer such as TP53 using DNA obtained from saliva of oral cancer patients. Methods: A total of 15 oral cancer patients were recruited in the study and pre-surgical saliva samples were collected using the ORR technique. Tissue samples included in the study were obtained during the surgical excision of the cancerous oral lesion. Genomic DNA was isolated from the salivary cell plug and the tissues and the TP53 gene was amplified by PCR. The PCR products of all the exons of TP53 (Exons 2 to 11) were electrophoresed on agarose gel, purified and sequenced by Sanger method. The obtained sequences were compared with the reference sequence of TP53 gene. Statistical analysis used: Descriptive statistics were used and reported as frequency and percentage. Results: Capillary sequencing of TP53 gene from tissue DNA revealed the presence of codon 72 c.215C>G (p.Pro72Arg) polymorphism in 10 patients (67%) and a heterozygous mutation at codon 172 c.514 G>T (p.Val172Phe) in 2 patients (13%). Among the 10 samples that showed codon 72 polymorphism, matched salivary DNA was available for 6 samples and 4 out of these showed same genetic change at codon 72. Similarly, of the 3 samples that showed codon 172 mutation, matched salivary DNA was available for 1 sample and the mutation status was identical. Conclusion: The results suggest a potential for clinical applications of ORR technique as an alternative to invasive tissue biopsy for detection of genetic changes in candidate biomarkers in oral cancer.
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Affiliation(s)
- Audrey D'Cruz
- Nitte (Deemed to be University), AB Shetty Memorial Institute of Dental Sciences, Department of Public Health Dentistry, Mangaluru, Karnataka, India
| | - Pandyanda Nanjappa Dechamma
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Molecular Genetics and Cancer, Mangaluru, Karnataka, India
| | - Marina Saldanha
- Nitte (Deemed to be University), KS Hegde Medical Academy, Department of Otorhinolaryngology, Mangaluru, Karnataka, India
| | - Sahana Maben
- Nitte (Deemed to be University), AB Shetty Memorial Institute of Dental Sciences, Department of Public Health Dentistry, Mangaluru, Karnataka, India
| | - Pushparaja Shetty
- Nitte (Deemed to be University), AB Shetty Memorial Institute of Dental Sciences, Department of Public Health Dentistry, Mangaluru, Karnataka, India
| | - Anirban Chakraborty
- Nitte (Deemed to be University), Nitte University Centre for Science Education and Research (NUCSER), Division of Molecular Genetics and Cancer, Mangaluru, Karnataka, India
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ANDREOLLA ELTON, FERNANDES MARCOBERNARDOCURY, LIMA CARLAORMUNDOGONÇALVESXIMENES, SARAIVA AUGUSTOCARLOSMACIEL. ANALYSIS OF TISSUE BIOPSY AND JOINT ASPIRATION IN THE DIAGNOSIS OF PERIPROSTHETIC HIP INFECTIONS: CROSS-SECTIONAL STUDY. Acta Ortop Bras 2021; 29:242-245. [PMID: 34629946 PMCID: PMC8478434 DOI: 10.1590/1413-785220212905241752] [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] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/09/2020] [Indexed: 11/30/2022]
Abstract
Objective: To evaluate sensitivity, specificity, accuracy, positive predictive value, and negative predictive value of preoperative joint aspiration (PJA) and periarticular tissue percutaneous biopsy (PTPB), as well as their combination, in the diagnosis of infection after total hip arthroplasty. Methods: This cross-sectional study (Level of Evidence II) was conducted with prospective data on 29 patients submitted to PJA with PTPB at the National Institute of Orthopedics and Traumatology from September 2015 to January 2016. Specimens obtained during the procedures underwent microbiological analyses, and the results were compared with those obtained in subsequent revision arthroplasty surgeries. Results: PJA, PTPB, and their combination reached values of 78%, 73%, 89% for sensitivity, respectively; 72%, 90%, 94% for specificity; and 76%, 80%, 90% for accuracy. Conclusions: PJA combined with PTPB was sensitive, specific, and effective in diagnosing periprosthetic hip infection.Level of Evidence II, Prospective Cross-Sectional Study
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Mohanty A, Mohanty SK, Rout S, Pani C. Liquid Biopsy, the hype vs. hope in molecular and clinical oncology. Semin Oncol 2021; 48:259-267. [PMID: 34384614 DOI: 10.1053/j.seminoncol.2021.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 05/28/2021] [Accepted: 06/28/2021] [Indexed: 12/12/2022]
Abstract
The molecular landscape of tumors has been traditionally established using a biopsy or resection specimens. These modalities result in sampling bias that offer only a single snapshot of tumor heterogeneity. Over the last decade intensive research towards alleviating such a bias and obtaining an integral yet accurate portrait of the tumors, evolved to the use of established molecular and genetic analysis using blood and several other body fluids, such as urine, saliva, and pleural effusions as liquid biopsies. Genomic profiling of the circulating markers including circulating cell-free tumor DNA (ctDNA), circulating tumor cells (CTCs) or even RNA, proteins, and lipids constituting exosomes, have facilitated the diligent monitoring of response to treatment, allowed one to follow the emergence of drug resistance, and enumerate minimal residual disease. The prevalence of tumor educated platelets (TEPs) and our understanding of how tumor cells influence platelets are beginning to unearth TEPs as a potentially dynamic component of liquid biopsies. Here, we review the biology, methodology, approaches, and clinical applications of biomarkers used to assess liquid biopsies. The current review addresses recent technological advances and different forms of liquid biopsy along with upcoming challenges and how they can be integrated to get the best possible tumor-derived genetic information that can be leveraged to more precise therapies for patient as liquid biopsies become increasingly routine in clinical practice.
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Affiliation(s)
- Abhishek Mohanty
- Rajiv Gandhi Cancer Institute and Research Centre, New Delhi, India.
| | - Sambit K Mohanty
- Advanced Medical Research Institute, Bhubaneswar, Odisha, India; CORE Diagnostics, Gurgaon, Haryana, India
| | - Sipra Rout
- Christian Medical College, Vellore, Tamil Nadu, India
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de Kock R, Borne BVD, Soud MY, Belderbos H, Stege G, de Saegher M, van Dongen-Schrover C, Genet S, Brunsveld L, Scharnhorst V, Deiman B. Circulating biomarkers for monitoring therapy response and detection of disease progression in lung cancer patients. Cancer Treat Res Commun 2021; 28:100410. [PMID: 34107412 DOI: 10.1016/j.ctarc.2021.100410] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/17/2021] [Accepted: 05/20/2021] [Indexed: 01/27/2023]
Abstract
Liquid biopsies have become of interest as minimally invasive ways to monitor treatment response in lung cancer patients. Circulating tumor DNA (ctDNA) and protein biomarkers are evaluated for their added value in monitoring therapy response and early detection of disease progression. Plasma and serum samples of non-small cell or small cell lung cancer patients were analyzed for driver mutations in ctDNA (EGFR, KRAS or BRAF) using droplet digital PCR and protein biomarkers (CA125, CEA, CA15.3, Cyfra 21-1, HE4, NSE, proGRP and SCCA) using electrochemiluminescence immunoassays. Biomarker concentration changes were compared with the outcome of CT-scans during therapy. The median difference of the concentration of ctDNA, CA125 and Cyfra21-1 was significantly lower in patients with partial response (PR) compared to patients with progressive disease (PD) on the first evaluation CT-scan (P<0.001, P=0.042 and P=0.020, respectively). A substantial agreement between ctDNA or CA125 response and radiographic response was observed (k=0.692 and k=0.792, respectively). The median difference of the concentration of ctDNA and Cyfra21-1 was also significantly lower in PR patients compared to PD patients at the last CT-scan during therapy (P<0.001 and P=0.026, respectively). An almost perfect agreement between ctDNA and radiographic response (k=0.827) and a moderate agreement between Cyfra21-1 response and radiographic response was observed (k=0.553). Serial testing of the concentration of ctDNA, Cyfra21-1, and possibly CA125 could be a useful added tool for monitoring therapy response and early detection of disease progression in lung cancer patients.
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Mahmood N, Mushtaq S, Jamal Q, Hanif M, Akhlaq H, Rehman DES, Awan R. Potential Utility of Cell Free High Mobility Group AT-hook 2 (HMGA2) as a Prognostic Biomarker in Liquid Biopsies of Oral Squamous Cell Carcinoma. Asian Pac J Cancer Prev 2021; 22:407-412. [PMID: 33639654 PMCID: PMC8190352 DOI: 10.31557/apjcp.2021.22.2.407] [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: 09/07/2020] [Indexed: 12/24/2022] Open
Abstract
Background: Locoregional spread is a frequent finding in oral cancer which dictates poor prognosis. HMGA2 expression has been linked to malignant traits of oral cancer in tissue biopsies however, data on HMGA2 expression in liquid biopsies in oral cancer is sparse. Purpose of this study was to explore prognostic relevance of HMGA2 in liquid biopsies of oral cancer patients. Patients and Methods: After obtaining approval from Institutional Review Board of Ziauddin University and informed written consent from study subjects, expression of circulating HMGA2 was evaluated in 96 OSCC cases and 100 age and sex matched controls via real time PCR using specific set of primers. We further analyzed relationship of various sociodemographic and clinicopathological variables with HMGA2expression and explored its prognostic potential. Results: Expression was seen in 22 (23%) cases. A higher expression was observed among subjects with local invasion (52.6% vs 47.4 %), distant metastasis (71.4% vs 28.6%) and tumor recurrence (57.1% vs 42.9%) p <0.05. Subjects having HMGA2 expression had a poor survival compared to HMGA2 negative (13.6% vs 35.4%), p <0.05. Conclusion: Circulating HMGA2 reflects presence of local invasion and distant metastasis and dictates poor prognosis in OSCC. It may contribute in categorizing high risk patients using a minimally invasive technique who are likely to benefit from targeted therapy.
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Affiliation(s)
| | - Shamim Mushtaq
- Biochemsitry, Director Postgraduate Ziauddin University, Pakistan
| | | | - Muhammad Hanif
- Karachi Institute of Radiotherapy and Nuclear Medicine, Pakistan
| | | | | | - Rashid Awan
- Internal, Medicine, Chinniot General Hospital, Pakistan
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Castellano JJ, Canals J, Han B, Díaz T, Monzo M, Navarro A. LncRNA Quantification from Extracellular Vesicles Isolated from Blood Plasma or Conditioned Media. Methods Mol Biol 2021; 2348:285-304. [PMID: 34160815 DOI: 10.1007/978-1-0716-1581-2_20] [Citation(s) in RCA: 3] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
During the last years, the study of extracellular vesicles (EVs) and its cargo has gained interest in the scientific media. EVs have been found in all biofluids and it is postulated that all cells are capable to secrete a wide variety of these vesicles, which play a key role in different cell-to-cell communication processes as well as in the microenvironment modulation. In the EV cargo, DNA, protein, and RNA molecules can be found, including long noncoding RNAs (lncRNAs). Several authors consider the study of EV lncRNAs an ideal source of biomarkers due to the easy sampling of EVs in different biofluids and the high specificity of the lncRNA expression pattern.In the present chapter, a detailed explanation of the EV isolation workflow followed by RNA isolation and lncRNA gene expression study is provided for two sample sources: blood plasma and cell culture conditioned media. EVs from both plasma samples and cell cultured media are isolated using sequential ultracentrifugation method (UC), which has been reported as one of the best methods available to date in terms of purity. UC is followed by RNA extraction based on the combination of phenol/guanidine-based lysis of samples with silica-membrane-based purification of total RNA. LncRNA quantification is performed by qRT-PCR. This chapter includes detailed discussion on lncRNA quantification using hydrolysis probes, recommended housekeeping genes and evaluation of methods for comparing lncRNA levels between EVs and its parental cells. In summary, we describe here the main steps for a successful isolation of the EVs-lncRNA cargo, paying attention to how overcome the different challenges found in the experimental procedure and in the data analysis of lncRNA expression from this source.
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Affiliation(s)
- Joan J Castellano
- Molecular Oncology and Embryology Laboratory, Human Anatomy Unit, Faculty of Medicine and Health Sciences, University of Barcelona, IDIBAPS, Barcelona, Spain
| | - Jordi Canals
- Molecular Oncology and Embryology Laboratory, Human Anatomy Unit, Faculty of Medicine and Health Sciences, University of Barcelona, IDIBAPS, Barcelona, Spain
| | - Bing Han
- Molecular Oncology and Embryology Laboratory, Human Anatomy Unit, Faculty of Medicine and Health Sciences, University of Barcelona, IDIBAPS, Barcelona, Spain
| | - Tania Díaz
- Molecular Oncology and Embryology Laboratory, Human Anatomy Unit, Faculty of Medicine and Health Sciences, University of Barcelona, IDIBAPS, Barcelona, Spain
| | - Mariano Monzo
- Molecular Oncology and Embryology Laboratory, Human Anatomy Unit, Faculty of Medicine and Health Sciences, University of Barcelona, IDIBAPS, Barcelona, Spain.,Thoracic Oncology Unit, Hospital Clinic, Barcelona, Spain
| | - Alfons Navarro
- Molecular Oncology and Embryology Laboratory, Human Anatomy Unit, Faculty of Medicine and Health Sciences, University of Barcelona, IDIBAPS, Barcelona, Spain. .,Thoracic Oncology Unit, Hospital Clinic, Barcelona, Spain.
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Abstract
Since the inception of silicon nanowires (SINWs)-based biosensors in 2001, SINWs employed in various detection schemes have routinely demonstrated label-free, real-time, sub femtomolar detection of both protein and nucleic acid analytes. This has allowed SiNW-based biosensors to integrate into the field of cancer detection and cancer monitoring and thus have the potential to be a paradigm shift in how cancer biomarkers are detected and monitored. Combining this with several promising fields such as liquid biopsies and targeted oncology, SiNW based biosensors represents an opportunity for cancer monitoring and treatment to be a more dynamic process. Such advances provide clinicians with more information on the molecular landscape of cancer patients which can better inform cancer treatment guidelines.
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Affiliation(s)
- Rasheid Smith
- Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, University of Iowa, Iowa City, IA, 52242
| | - Sean M Geary
- Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, University of Iowa, Iowa City, IA, 52242
| | - Aliasger K Salem
- Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, University of Iowa, Iowa City, IA, 52242
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Howard J, Wyse C, Argyle D, Quinn C, Kelly P, McCann A. Exosomes as Biomarkers of Human and Feline Mammary Tumours; A Comparative Medicine Approach to Unravelling the Aggressiveness of TNBC. Biochim Biophys Acta Rev Cancer 2020; 1874:188431. [PMID: 32950643 DOI: 10.1016/j.bbcan.2020.188431] [Citation(s) in RCA: 4] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 09/07/2020] [Accepted: 09/08/2020] [Indexed: 02/07/2023]
Abstract
Comparative oncology is defined as the discipline that integrates naturally occurring cancers seen in veterinary medicine, into more general studies of cancer biology and therapy in humans, including the study of cancer-pathogenesis and new cancer treatments. While experimental studies in mice and rodents offer several advantages, including a wealth of genetic information, reduced variation and short generation intervals, their relevance in cancer biology is somewhat limited. Toward this end, as the biomedical research community works to make the promise of precision medicine a reality, more efficient animal cohort studies are critical. Like humans, companion animals such as cats and dogs living in family homes, are exposed to environmental factors that may influence the development of disease. Furthermore, it has been shown that the basic biochemical and physiological processes of companion animals more closely resemble humans compared to rodents. Research has demonstrated that female domestic cats (Felis catus) may represent a comparative model for investigation of mammary carcinogenesis, and in particular, Triple Negative Breast Cancer (TNBC). TNBC is a subtype of breast cancer that typically lacks the expression of the oestrogen receptor (ER), progesterone receptor (PR), and does not overexpress the human epidermal growth factor receptor 2 (HER2). An exciting and rapidly expanding area in cancer biology is the study of exosomes. Exosomes are nanoparticles released from cells and have been found in biological fluids of humans, domestic cats and dogs. In addition to their role as biomarkers, exosomes are implicated in the pathogenesis of certain diseases, including cancer. This review explores the current understanding of exosome biology in human TNBC, and of the potential benefits of comparative research in naturally-occurring mammary tumours in companion animals.
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Affiliation(s)
- Jane Howard
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland; UCD School of Medicine, College of Health and Agricultural Sciences, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Cathy Wyse
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - David Argyle
- The Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK
| | - Cecily Quinn
- UCD School of Medicine, College of Health and Agricultural Sciences, University College Dublin, Belfield, Dublin 4, Ireland; Department of Histopathology, St. Vincent's University Hospital (SVUH), Elm Park, Dublin 4, Ireland
| | - Pamela Kelly
- UCD School of Veterinary Medicine, College of Health and Agricultural Sciences, University College Dublin, Belfield, Dublin 4, Ireland
| | - Amanda McCann
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland; UCD School of Medicine, College of Health and Agricultural Sciences, University College Dublin, Belfield, Dublin 4, Ireland
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Jayaraj R, Kumaraswamy C, Raymond G, Ravishankar Ram M, Govind SK, Chandramoorthy HC, Shaw P. Diagnostic implications of miRNAs in Liquid Biopsy for Oral Squamous Cell Carcinoma (OSCC): Clinical validity and interpretation. Oral Oncol 2020; 109:104634. [PMID: 32171663 DOI: 10.1016/j.oraloncology.2020.104634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 03/05/2020] [Indexed: 10/24/2022]
Affiliation(s)
- Rama Jayaraj
- Department of Artificial Intelligence, Nanjing University of Information Science and Technology (NUIST), Jiangsu, China; Theme Lead -Health Profession and Society - Advanced Studies, Northern Territory Medical Program (NTMP), College of Medicine and Public Health, Flinders University, CDU Campus, Ellengowan Drive, Darwin, Northern Territory 0909, Australia.
| | - Chellan Kumaraswamy
- School of Public Health, The University of Adelaide, North Terrace Campus, Adelaide, SA 5005, Australia
| | - Greg Raymond
- Flinders University Northern Territory Medical Program, CDU Campus, Ellengowan Drive, Darwin, Northern Territory 0909, Australia.
| | - M Ravishankar Ram
- Department of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia.
| | - Suresh Kumar Govind
- Department of Parasitology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia.
| | - Harish C Chandramoorthy
- Department of Microbiology and Clinical Parasitology, College of Medicine, King Khalid University, PO. Box # 641, 61421 Abha, Saudi Arabia.
| | - Peter Shaw
- Department of Artificial Intelligence, Nanjing University of Information Science and Technology (NUIST), Jiangsu, China.
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Abstract
PURPOSE OF REVIEW Although liquid biopsies hold significant promise in the management of patients with cancer, peripheral blood analyses remain dependent on the degree of tumor burden with prohibitively low yields until the cancer is widely metastatic. Multiple lines of evidence support a dynamic, spatiotemporal localization of circulating tumor cells (CTCs) supporting specific targeting of vascular compartments, such as the portal vein. This review discusses the literature evaluating the possibility of portal venous blood as a new, potentially higher yield liquid biopsy and the current devices and techniques for endoscopic ultrasound (EUS)-guided portal venous sampling for CTC detection. RECENT FINDINGS Two recent studies in pancreatic cancer have demonstrated that portal venous blood can be safely sampled via EUS and consistently yields significantly higher CTC counts compared with matched peripheral blood. EUS-acquired samples can be used for molecular testing, clinical prognostication, and drug sensitivity analyses. Portal venous CTCs are identified in higher quantity relative to peripheral blood and can be safely obtained via EUS. Further studies are required to demonstrate the clinical utility of EUS-guided portal venous tumor material enrichment and analysis; however, obtaining EUS-guided "liquid biopsies" appears to merit significant consideration for procedural adoption.
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Affiliation(s)
- Christopher G Chapman
- Center for Endoscopic Research and Therapeutics (CERT), The University of Chicago Medicine and Biological Sciences, 5700 S Maryland Ave. MC 8043, Chicago, IL, 60637, USA
| | - Irving Waxman
- Center for Endoscopic Research and Therapeutics (CERT), The University of Chicago Medicine and Biological Sciences, 5700 S Maryland Ave. MC 8043, Chicago, IL, 60637, USA.
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Abstract
Cancer is the second leading cause of death in developed countries, making it a global public health problem. In this scenario, early detection is the key to successful treatment. Tissue biopsy, the current gold standard for cancer diagnosis, offers reliable results, but it is feasible only when the mass becomes detectable. On the other hand liquid biopsy, a promising experimental system, not yet implemented within clinical practice, allows early detection as its functioning relies on the analysis of body fluids. Yet, its results are less reliable if compared to those of tissue biopsy as, for instance, false positives and false negatives might occur. Despite technical features, the tradeoff between a reliable diagnosis available at a later time and a potentially less reliable diagnosis available at an early stage poses significant ethical challenges in the clinical scenario which involve, among other aspects, informed consent, communication, and patient-physician encounter.
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Affiliation(s)
- Chiara Mannelli
- Candiolo Cancer Institute, FPO-IRCCS, Strada Provinciale 142 KM 3.950, 10060, Candiolo, (TO), Italy.
- Italian Ministry of Health, Viale G. Ribotta, 5, 00144, Roma, Italy.
- Department of Philosophy and Educational Sciences, University of Turin, Via Verdi, 8, 10124, Torino, Italy.
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Nunes SP, Diniz F, Moreira-Barbosa C, Constâncio V, Silva AV, Oliveira J, Soares M, Paulino S, Cunha AL, Rodrigues J, Antunes L, Henrique R, Jerónimo C. Subtyping Lung Cancer Using DNA Methylation in Liquid Biopsies. J Clin Med. 2019;8. [PMID: 31546933 DOI: 10.3390/jcm8091500] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 09/15/2019] [Accepted: 09/17/2019] [Indexed: 12/24/2022] Open
Abstract
Background: Lung cancer (LCa) is the most frequently diagnosed and lethal cancer worldwide. Histopathological subtyping, which has important therapeutic and prognostic implications, requires material collection through invasive procedures, which might be insufficient to enable definitive diagnosis. Aberrant DNA methylation is an early event in carcinogenesis, detectable in circulating cell-free DNA (ccfDNA). Herein, we aimed to assess methylation of selected genes in ccfDNA from LCa patients and determine its accuracy for tumor subtyping. Methods: Methylation levels of APC, HOXA9, RARβ2, and RASSF1A were assessed in three independent study groups (study group #1: 152 tissue samples; study group #2: 129 plasma samples; study group #3: 28 benign lesions of lung) using quantitative methylation-specific PCR. Associations between gene promoter methylation levels and LCa subtypes were evaluated using non-parametric tests. Receiver operating characteristic (ROC) curve analysis was performed. Results: In study group #2, HOXA9 and RASSF1A displayed higher methylation levels in small-cell lung cancer (SCLC) than in non-small-cell lung cancer (NSCLC). HOXA9 displayed high sensitivity (63.8%), whereas RASSF1A disclosed high specificity (96.2%) for SCLC detection in ccfDNA. Furthermore, HOXA9 methylation levels showed to be higher in squamous cell carcinoma in comparison with adenocarcinoma in study group #1. Conclusions: Methylation level assessments in ccfDNA may provide a minimally invasive procedure for LCa subtyping, complementing standard diagnostic procedures.
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Sutton TL, Walker BS, Wong MH. Circulating Hybrid Cells Join the Fray of Circulating Cellular Biomarkers. Cell Mol Gastroenterol Hepatol 2019; 8:595-607. [PMID: 31319228 DOI: 10.1016/j.jcmgh.2019.07.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 07/03/2019] [Accepted: 07/05/2019] [Indexed: 12/11/2022]
Abstract
Gastrointestinal cancers account for more cancer-related deaths than any other organ system, owing in part to difficulties in early detection, treatment response assessment, and post-treatment surveillance. Circulating biomarkers hold the promise for noninvasive liquid biopsy platforms to overcome these obstacles. Although tumors shed detectable levels of degraded genetic material and cellular debris into peripheral blood, identifying reproducible and clinically relevant information from these analytes (eg, cell-free nucleotides, exosomes, proteins) has proven difficult. Cell-based circulating biomarkers also present challenges, but have multiple advantages including allowing for a more comprehensive tumor analysis, and communicating the risk of metastatic spread. Circulating tumor cells have dominated the cancer cell biomarker field with robust evidence in extraintestinal cancers; however, establishing their clinical utility beyond that of prognostication in colorectal and pancreatic cancers has remained elusive. Recently identified novel populations of tumor-derived cells bring renewed potential to this area of investigation. Cancer-associated macrophage-like cells, immune cells with phagocytosed tumor material, also show utility in prognostication and assessing treatment responsiveness. In addition, circulating hybrid cells are the result of tumor-macrophage fusion, with mounting evidence for a role in the metastatic cascade. Because of their relative abundance in circulation, circulating hybrid cells have great potential as a liquid biomarker for early detection, prognostication, and surveillance. In all, the power of the cell reaches beyond enumeration by providing a cellular source of tumor DNA, RNA, and protein, which can be harnessed to impact overall survival.
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Affiliation(s)
- Wai Kei Jacky Lam
- a Department of Chemical Pathology , The Chinese University of Hong Kong, Prince of Wales Hospital , Hong Kong SAR, China.,b Li Ka Shing Institute of Health Sciences , The Chinese University of Hong Kong , Hong Kong SAR, China.,c State Key Laboratory of Translational Oncology , The Chinese University of Hong Kong , Hong Kong SAR, China
| | - Kwan Chee Allen Chan
- a Department of Chemical Pathology , The Chinese University of Hong Kong, Prince of Wales Hospital , Hong Kong SAR, China.,b Li Ka Shing Institute of Health Sciences , The Chinese University of Hong Kong , Hong Kong SAR, China.,c State Key Laboratory of Translational Oncology , The Chinese University of Hong Kong , Hong Kong SAR, China
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Abstract
Treatment of advanced hepatocellular carcinoma remains unsatisfying and so far only prognostic biomarkers like α-fetoprotein have been established. No clear predictive biomarker is currently available for standard of care therapies, including targeted therapies like sorafenib. Novel therapeutic options like immune checkpoint inhibitors may pose new challenges to identification and validation of such markers. Currently, PD-L1 expression via immunohistochemistry and tumor mutational burden via next-generation sequencing are explored as predictive biomarkers for these novel treatments. Limited tissue availability due to lack of biopsies still restricts the use of tissue based approaches. Novel methods exploring circulating or cell free nucleic acids (DNA, RNA or miRNA-containing exosomes) could provide a new opportunity to establish predictive biomarkers. Epigenetic profiling and next-generation sequencing approaches from liquid biopsies are under development. Sample size, etiologic and geographical background need to be carefully addressed in such studies to achieve meaningful results that could be translated into clinical practice. Proteomics, metabolomics and molecular imaging are further emerging technologies.
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Affiliation(s)
- Matthias Ocker
- Department of Translational Medicine Oncology, Bayer AG, Berlin 13353, Germany
- Charité University Medicine Berlin, Berlin 10117, Germany
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Santarpia M, Funel N, Ali A, Giovannetti E. Liquid biopsies to optimize therapeutic efficacy in unresponsive lung cancer patients. Expert Opin Drug Metab Toxicol 2018; 14:761-763. [PMID: 29933706 DOI: 10.1080/17425255.2018.1491965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Mariacarmela Santarpia
- a Medical Oncology Unit, Department of Human Pathology , University of Messina , Messina , Italy
| | - Niccola Funel
- b Institute of Nanoscience and Nanotechnology , CNR-Nano , Pisa , Italy.,c Cancer Pharmacology Lab, AIRC Start-Up Unit , University of Pisa , Pisa , Italy
| | - Asif Ali
- d Institute of Basic Medical Sciences , Khyber Medical University , Peshawar , Pakistan
| | - Elisa Giovannetti
- b Institute of Nanoscience and Nanotechnology , CNR-Nano , Pisa , Italy.,c Cancer Pharmacology Lab, AIRC Start-Up Unit , University of Pisa , Pisa , Italy.,e Lab. Medical Oncology, Department Medical oncology , VUmc, Cancer Center Amsterdam , Amsterdam , The Netherlands
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Zhang L, Beasley S, Prigozhina NL, Higgins R, Ikeda S, Lee FY, Marrinucci D, Jia S. Detection and Characterization of Circulating Tumour Cells in Multiple Myeloma. J Circ Biomark 2016; 5:10. [PMID: 28936258 PMCID: PMC5548310 DOI: 10.5772/64124] [Citation(s) in RCA: 12] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 05/06/2016] [Indexed: 12/15/2022] Open
Abstract
Multiple myeloma (MM) remains an incurable disease despite recent therapeutic improvements. The ability to detect and characterize MM circulating tumour cells (CTCs) in peripheral blood provides an alternative to replace or augment invasive bone marrow (BM) biopsies with a simple blood draw, providing real-time, clinically relevant information leading to improved disease management and therapy selection. Here we have developed and qualified an enrichment-free, cell-based immunofluorescence MM CTC assay that utilizes an automated digital pathology algorithm to distinguish MM CTCs from white blood cells (WBCs) on the basis of CD138 and CD45 expression levels, as well as a number of morphological parameters. These MM CTCs were further characterized for expression of phospho-ribosomal protein S6 (pS6) as a readout for PI3K/AKT pathway activation. Clinical feasibility of the assay was established by testing blood samples from a small cohort of patients, where we detected populations of both CD138pos and CD138neg MM CTCs. In this study, we developed an immunofluorescent cell-based assay to detect and characterize CTCs in MM.
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Affiliation(s)
- Liangxuan Zhang
- Departments of Oncology Biomarker Development, Genentech Inc, South San Francisco, CA, USA
| | | | | | | | - Shoji Ikeda
- Departments of Oncology Biomarker Development, Genentech Inc, South San Francisco, CA, USA
| | | | | | - Shidong Jia
- Departments of Oncology Biomarker Development, Genentech Inc, South San Francisco, CA, USA
- Predicine Inc, Hayward, CA, USA
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Werner SL, Graf RP, Landers M, Valenta DT, Schroeder M, Greene SB, Bales N, Dittamore R, Marrinucci D. Analytical Validation and Capabilities of the Epic CTC Platform: Enrichment-Free Circulating Tumour Cell Detection and Characterization. J Circ Biomark 2015; 4:3. [PMID: 28936239 PMCID: PMC5572988 DOI: 10.5772/60725] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 04/20/2015] [Indexed: 12/21/2022] Open
Abstract
The Epic Platform was developed for the unbiased detection and molecular characterization of circulating tumour cells (CTCs). Here, we report assay performance data, including accuracy, linearity, specificity and intra/inter-assay precision of CTC enumeration in healthy donor (HD) blood samples spiked with varying concentrations of cancer cell line controls (CLCs). Additionally, we demonstrate clinical feasibility for CTC detection in a small cohort of metastatic castrate-resistant prostate cancer (mCRPC) patients. The Epic Platform demonstrated accuracy, linearity and sensitivity for the enumeration of all CLC concentrations tested. Furthermore, we established the precision between multiple operators and slide staining batches and assay specificity showing zero CTCs detected in 18 healthy donor samples. In a clinical feasibility study, at least one traditional CTC/mL (CK+, CD45-, and intact nuclei) was detected in 89 % of 44 mCRPC samples, whereas 100 % of samples had CTCs enumerated if additional CTC subpopulations (CK-/CD45- and CK+ apoptotic CTCs) were included in the analysis. In addition to presenting Epic Platform's performance with respect to CTC enumeration, we provide examples of its integrated downstream capabilities, including protein biomarker expression and downstream genomic analyses at single cell resolution.
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