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Abstract
ABSTRACT The advent of high-throughput technologies has enabled the analysis of minute amounts of tumor-derived material purified from body fluids, termed "liquid biopsies." Prostate cancer (PCa) management, like in many other cancer types, has benefited from liquid biopsies at several stages of the disease. Although initially describing circulating tumor cells in blood, the term "liquid biopsy" has come to more prominently include cell-free, circulating tumor DNA, as well as RNA, proteins, and other molecules. They provide tumor molecular information representing the entire, often-heterogeneous disease, relatively noninvasively and longitudinally. Blood has been the main liquid biopsy specimen in PCa, and urine has also proven beneficial. Technological advances have allowed clinical implementation of some liquid biopsies in PCa, in disease monitoring and precision oncology. This narrative review introduces the main types of blood-based PCa liquid biopsies focusing on advances in the past 5 years. Clinical adoption of liquid biopsies to detect and monitor the evolving PCa tumor biology promises to deepen our understanding of the disease and improve patient outcomes.
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Affiliation(s)
- Andi K. Cani
- Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Simpa S. Salami
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
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Meriranta L, Pitkänen E, Leppä S. Blood has never been thicker: Cell-free DNA fragmentomics in the liquid biopsy toolbox of B-cell lymphomas. Semin Hematol 2023; 60:132-141. [PMID: 37455222 DOI: 10.1053/j.seminhematol.2023.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/30/2023] [Accepted: 06/24/2023] [Indexed: 07/18/2023]
Abstract
Liquid biopsies utilizing plasma circulating tumor DNA (ctDNA) are anticipated to revolutionize decision-making in cancer care. In the field of lymphomas, ctDNA-based blood tests represent the forefront of clinically applicable tools to harness decades of genomic research for disease profiling, quantification, and detection. More recently, the discovery of nonrandom fragmentation patterns in cell-free DNA (cfDNA) has opened another avenue of liquid biopsy research beyond mutational interrogation of ctDNA. Through examination of structural features, nucleotide content, and genomic distribution of massive numbers of plasma cfDNA molecules, the study of fragmentomics aims at identifying new tools that augment existing ctDNA-based analyses and discover new ways to profile cancer from blood tests. Indeed, the characterization of aberrant lymphoma ctDNA fragment patterns and harnessing them with powerful machine-learning techniques are expected to unleash the potential of nonmutant molecules for liquid biopsy purposes. In this article, we review cfDNA fragmentomics as an emerging approach in the ctDNA research of B-cell lymphomas. We summarize the biology behind the formation of cfDNA fragment patterns and discuss the preanalytical and technical limitations faced with current methodologies. Then we go through the advances in the field of lymphomas and envision what other noninvasive tools based on fragment characteristics could be explored. Last, we place fragmentomics as one of the facets of ctDNA analyses in emerging multiview and multiomics liquid biopsies. We pay attention to the unknowns in the field of cfDNA fragmentation biology that warrant further mechanistic investigation to provide rational background for the development of these precision oncology tools and understanding of their limitations.
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Affiliation(s)
- Leo Meriranta
- Applied Tumor Genomics, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Department of Oncology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland.
| | - Esa Pitkänen
- Applied Tumor Genomics, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland; Institute for Molecular Medicine Finland (FIMM), HILIFE, Helsinki, Finland
| | - Sirpa Leppä
- Applied Tumor Genomics, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Department of Oncology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland.
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Kravitz CJ, Yan Q, Nguyen DX. Epigenetic markers and therapeutic targets for metastasis. Cancer Metastasis Rev 2023; 42:427-443. [PMID: 37286865 PMCID: PMC10595046 DOI: 10.1007/s10555-023-10109-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 05/19/2023] [Indexed: 06/09/2023]
Abstract
The last few years have seen an increasing number of discoveries which collectively demonstrate that histone and DNA modifying enzyme modulate different stages of metastasis. Moreover, epigenomic alterations can now be measured at multiple scales of analysis and are detectable in human tumors or liquid biopsies. Malignant cell clones with a proclivity for relapse in certain organs may arise in the primary tumor as a consequence of epigenomic alterations which cause a loss in lineage integrity. These alterations may occur due to genetic aberrations acquired during tumor progression or concomitant to therapeutic response. Moreover, evolution of the stroma can also alter the epigenome of cancer cells. In this review, we highlight current knowledge with a particular emphasis on leveraging chromatin and DNA modifying mechanisms as biomarkers of disseminated disease and as therapeutic targets to treat metastatic cancers.
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Affiliation(s)
- Carolyn J Kravitz
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA.
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, 06520, USA.
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, 06520, USA.
- Yale Center for Immuno-Oncology, Yale School of Medicine, New Haven, CT, 06520, USA.
| | - Don X Nguyen
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA.
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, 06520, USA.
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, 06520, USA.
- Department of Internal Medicine (Section of Medical Oncology), Yale School of Medicine, New Haven, CT, 06520, USA.
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Herberts C, Wyatt AW, Nguyen PL, Cheng HH. Genetic and Genomic Testing for Prostate Cancer: Beyond DNA Repair. Am Soc Clin Oncol Educ Book 2023; 43:e390384. [PMID: 37207301 DOI: 10.1200/edbk_390384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Significant progress has been made in genetic and genomic testing for prostate cancer across the disease spectrum. Molecular profiling is increasingly relevant for routine clinical management, fueled in part by advancements in testing technology and integration of biomarkers into clinical trials. In metastatic prostate cancer, defects in DNA damage response genes are now established predictors of benefit to US Food and Drug Administration-approved poly (ADP-ribose) polymerase inhibitors and immune checkpoint inhibitors, and trials are actively investigating these and other targeted treatment strategies in earlier disease states. Excitingly, opportunities for molecularly informed management beyond DNA damage response genes are also maturing. Germline genetic variants (eg, BRCA2 or MSH2/6) and polygenic germline risk scores are being investigated to inform cancer screening and active surveillance in at-risk carriers. RNA expression tests have recently gained traction in localized prostate cancer, enabling patient risk stratification and tailored treatment intensification via radiotherapy and/or androgen deprivation therapy for localized or salvage treatment. Finally, emerging minimally invasive circulating tumor DNA technology promises to enhance biomarker testing in advanced disease pending additional methodological and clinical validation. Collectively, genetic and genomic tests are rapidly becoming indispensable tools for informing the optimal clinical management of prostate cancer.
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Affiliation(s)
- Cameron Herberts
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alexander W Wyatt
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Paul L Nguyen
- Harvard Medical School, Dana-Farber/Brigham and Women's Cancer Center, Boston, MA
| | - Heather H Cheng
- University of Washington, Fred Hutchinson Cancer Center, Seattle, WA
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Obinata D, Hashimoto S, Uchida H, Nakahara K, Yoshizawa T, Mochida J, Yamaguchi K, Takahashi S. Clinical characteristics of patients with metastatic castration-resistant prostate cancer after treatment with combined androgen blockade. BMC Urol 2023; 23:74. [PMID: 37118708 PMCID: PMC10148407 DOI: 10.1186/s12894-023-01233-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 04/02/2023] [Indexed: 04/30/2023] Open
Abstract
BACKGROUND Although the second-generation androgen receptor inhibitors and taxanes have recently been recommended for the initial treatment of metastatic prostate cancer, bicalutamide and flutamide are still used in a large number of cases. Therefore, it is important to elucidate the clinical characteristics of these treated CRPC cases and their sensitivity to the currently used therapeutic agents. We aimed to examine the outcomes of metastatic castration-resistant prostate cancer following combined androgen blockade as initial therapy at our institution. METHODS Ninety-four patients who developed metastatic castration-resistant prostate cancer after hormonal treatment with combined nonsteroidal androgen receptor antagonists and continuous androgen deprivation therapy between January 2015 and December 2020 were included. The presence of visceral metastases, duration of efficacy of each treatment, and overall survival after castration-resistant prostate cancer were evaluated. RESULTS Patients with a longer duration of castration-resistant prostate cancer tended to have a longer response duration to subsequent enzalutamide administration (p = 0.003). Patients who achieved a 90% reduction in prostate-specific antigen levels with enzalutamide had a significantly better castration-resistant prostate cancer prognosis (p = 0.002). Meanwhile, those with visceral metastases at the time of castration-resistant prostate cancer diagnosis had a significantly poorer prognosis (p < 0.001). A positive correlation was observed between the treatment efficacy of abiraterone and taxanes for castration-resistant prostate cancer. CONCLUSION The study provides scientific evidence to support that patients with longer time to castration-resistant prostate cancer are more sensitive to enzalutamide, and the use of abiraterone between docetaxel and cabazitaxel has favorable prognostic impact. These findings provide instrumental evidence that can enable better treatment selection for prostate cancer patients.
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Affiliation(s)
- Daisuke Obinata
- Department of Urology, Nihon University School of Medicine, 30-1, Oyaguchikamicho, Itabashi-Ku, Tokyo, 173-8610, Japan
| | - Sho Hashimoto
- Department of Urology, Nihon University School of Medicine, 30-1, Oyaguchikamicho, Itabashi-Ku, Tokyo, 173-8610, Japan
| | - Hideaki Uchida
- Department of Urology, Nihon University School of Medicine, 30-1, Oyaguchikamicho, Itabashi-Ku, Tokyo, 173-8610, Japan
| | - Ken Nakahara
- Department of Urology, Nihon University School of Medicine, 30-1, Oyaguchikamicho, Itabashi-Ku, Tokyo, 173-8610, Japan
| | - Tsuyoshi Yoshizawa
- Department of Urology, Nihon University School of Medicine, 30-1, Oyaguchikamicho, Itabashi-Ku, Tokyo, 173-8610, Japan
| | - Junichi Mochida
- Department of Urology, Nihon University School of Medicine, 30-1, Oyaguchikamicho, Itabashi-Ku, Tokyo, 173-8610, Japan
| | - Kenya Yamaguchi
- Department of Urology, Nihon University School of Medicine, 30-1, Oyaguchikamicho, Itabashi-Ku, Tokyo, 173-8610, Japan.
| | - Satoru Takahashi
- Department of Urology, Nihon University School of Medicine, 30-1, Oyaguchikamicho, Itabashi-Ku, Tokyo, 173-8610, Japan
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Abbosh C, Frankell AM, Harrison T, Kisistok J, Garnett A, Johnson L, Veeriah S, Moreau M, Chesh A, Chaunzwa TL, Weiss J, Schroeder MR, Ward S, Grigoriadis K, Shahpurwalla A, Litchfield K, Puttick C, Biswas D, Karasaki T, Black JRM, Martínez-Ruiz C, Bakir MA, Pich O, Watkins TBK, Lim EL, Huebner A, Moore DA, Godin-Heymann N, L'Hernault A, Bye H, Odell A, Roberts P, Gomes F, Patel AJ, Manzano E, Hiley CT, Carey N, Riley J, Cook DE, Hodgson D, Stetson D, Barrett JC, Kortlever RM, Evan GI, Hackshaw A, Daber RD, Shaw JA, Aerts HJWL, Licon A, Stahl J, Jamal-Hanjani M, Birkbak NJ, McGranahan N, Swanton C. Tracking early lung cancer metastatic dissemination in TRACERx using ctDNA. Nature 2023; 616:553-562. [PMID: 37055640 PMCID: PMC7614605 DOI: 10.1038/s41586-023-05776-4] [Citation(s) in RCA: 67] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 01/30/2023] [Indexed: 04/15/2023]
Abstract
Circulating tumour DNA (ctDNA) can be used to detect and profile residual tumour cells persisting after curative intent therapy1. The study of large patient cohorts incorporating longitudinal plasma sampling and extended follow-up is required to determine the role of ctDNA as a phylogenetic biomarker of relapse in early-stage non-small-cell lung cancer (NSCLC). Here we developed ctDNA methods tracking a median of 200 mutations identified in resected NSCLC tissue across 1,069 plasma samples collected from 197 patients enrolled in the TRACERx study2. A lack of preoperative ctDNA detection distinguished biologically indolent lung adenocarcinoma with good clinical outcome. Postoperative plasma analyses were interpreted within the context of standard-of-care radiological surveillance and administration of cytotoxic adjuvant therapy. Landmark analyses of plasma samples collected within 120 days after surgery revealed ctDNA detection in 25% of patients, including 49% of all patients who experienced clinical relapse; 3 to 6 monthly ctDNA surveillance identified impending disease relapse in an additional 20% of landmark-negative patients. We developed a bioinformatic tool (ECLIPSE) for non-invasive tracking of subclonal architecture at low ctDNA levels. ECLIPSE identified patients with polyclonal metastatic dissemination, which was associated with a poor clinical outcome. By measuring subclone cancer cell fractions in preoperative plasma, we found that subclones seeding future metastases were significantly more expanded compared with non-metastatic subclones. Our findings will support (neo)adjuvant trial advances and provide insights into the process of metastatic dissemination using low-ctDNA-level liquid biopsy.
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Affiliation(s)
- Christopher Abbosh
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
| | - Alexander M Frankell
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | | | - Judit Kisistok
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | | | | | - Selvaraju Veeriah
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | | | | | - Tafadzwa L Chaunzwa
- Artificial Intelligence in Medicine (AIM) Program, Mass General Brigham, Harvard Medical School, Boston, MA, USA
- Department of Radiation Oncology, Brigham and Women's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Jakob Weiss
- Artificial Intelligence in Medicine (AIM) Program, Mass General Brigham, Harvard Medical School, Boston, MA, USA
- Department of Radiation Oncology, Brigham and Women's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Radiology, Freiburg University Hospital, Freiburg, Germany
| | | | - Sophia Ward
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Advanced Sequencing Facility, The Francis Crick Institute, London, UK
| | - Kristiana Grigoriadis
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | | | - Kevin Litchfield
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, UK
| | - Clare Puttick
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Dhruva Biswas
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | - Takahiro Karasaki
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
| | - James R M Black
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Carlos Martínez-Ruiz
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Maise Al Bakir
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Oriol Pich
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Thomas B K Watkins
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Emilia L Lim
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Ariana Huebner
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - David A Moore
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Department of Cellular Pathology, University College London Hospitals, London, UK
| | | | | | | | | | | | - Fabio Gomes
- The Christie NHS Foundation Trust, Manchester, UK
| | - Akshay J Patel
- University Hospital Birmingham NHS Foundation Trust, Birmingham, UK
| | - Elizabeth Manzano
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Crispin T Hiley
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Nicolas Carey
- Cancer Research Centre, University of Leicester, Leicester, UK
| | - Joan Riley
- Cancer Research Centre, University of Leicester, Leicester, UK
| | - Daniel E Cook
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | | | | | | | | | - Gerard I Evan
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Allan Hackshaw
- Cancer Research UK & UCL Cancer Trials Centre, London, UK
| | | | - Jacqui A Shaw
- Cancer Research Centre, University of Leicester, Leicester, UK
| | - Hugo J W L Aerts
- Artificial Intelligence in Medicine (AIM) Program, Mass General Brigham, Harvard Medical School, Boston, MA, USA
- Department of Radiation Oncology, Brigham and Women's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Radiology and Nuclear Medicine, CARIM & GROW, Maastricht University, Maastricht, The Netherlands
| | | | | | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
- Department of Oncology, University College London Hospitals, London, UK
| | - Nicolai J Birkbak
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
- Department of Oncology, University College London Hospitals, London, UK.
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Li C, Baj A, Sowalsky AG. One toolkit to bring them all, and in silico analyze them. CLINICAL AND TRANSLATIONAL DISCOVERY 2023; 3:e194. [PMID: 37220531 PMCID: PMC10201993 DOI: 10.1002/ctd2.194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Affiliation(s)
- Chennan Li
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Anna Baj
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Adam G Sowalsky
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
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Revealing influencing factors on global waste distribution via deep-learning based dumpsite detection from satellite imagery. Nat Commun 2023; 14:1444. [PMID: 36922495 PMCID: PMC10015540 DOI: 10.1038/s41467-023-37136-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 03/01/2023] [Indexed: 03/17/2023] Open
Abstract
With the advancement of global civilisation, monitoring and managing dumpsites have become essential parts of environmental governance in various countries. Dumpsite locations are difficult to obtain in a timely manner by local government agencies and environmental groups. The World Bank shows that governments need to spend massive labour and economic costs to collect illegal dumpsites to implement management. Here we show that applying novel deep convolutional networks to high-resolution satellite images can provide an effective, efficient, and low-cost method to detect dumpsites. In sampled areas of 28 cities around the world, our model detects nearly 1000 dumpsites that appeared around 2021. This approach reduces the investigation time by more than 96.8% compared with the manual method. With this novel and powerful methodology, it is now capable of analysing the relationship between dumpsites and various social attributes on a global scale, temporally and spatially.
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Vandekerkhove G. BRCA Reversion Mutations in Metastatic Castration-Resistant Prostate Cancer. Eur Urol 2023; 83:210-211. [PMID: 36273936 DOI: 10.1016/j.eururo.2022.09.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 09/28/2022] [Indexed: 11/04/2022]
Affiliation(s)
- Gillian Vandekerkhove
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, Canada; Department of Medical Oncology, BC Cancer, Vancouver, Canada.
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60
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Fang P, Ji X, Zhao X, Yan-Do R, Wan Y, Wang Y, Zhang Y, Shi P. Self-Healing Electronics for Prognostic Monitoring of Methylated Circulating Tumor DNAs. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2207282. [PMID: 36412926 DOI: 10.1002/adma.202207282] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 11/09/2022] [Indexed: 06/16/2023]
Abstract
Methylated circulating DNAs (ctDNAs) have recently been reported as a promising biomarker for early cancer diagnostics, but limited tools are currently available for continuous and dynamic profiling of ctDNAs and their methylation levels, especially when such assays need to be conducted in point-of-care (POC) scenarios. Here, a self-healing bioelectronic patch (iMethy) is developed that combines transdermal interstitial fluid (ISF) extraction and field effect transistor-based (FET-based) biosensing for dynamic monitoring of methylated ctDNAs as a prognostic approach for cancer risk management. The projection micro-stereolithography-based 3D patterning of an Eutectic Gallium-Indium (EGaIn) circuit with an unprecedented 10 µm resolution enables the construction of self-healing EGaIn microfluidic circuits that remain conductive under 100% strain and self-healing under severe destruction. In combination with continuous transdermal ISF sampling of methylated ctDNAs, iMethy can detect ctDNAs as low as 10-16 m in cellular models and is capable of phenotypic analysis of tumor growth in rodent animals. As the first demonstration of a wearable device for real-time in vivo analysis of disease-indicative biomarkers, this proof-of-concept study well demonstrated the potential of the iMethy platform for cancer risk management based on dynamic transdermal surveillance of methylated ctDNAs via a painless and self-administrable procedure.
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Affiliation(s)
- Peilin Fang
- Department of Biomedical Engineering, The City University of Hong Kong, Kowloon, Hong Kong SAR, 999077, China
- Department of Otolaryngology Head and Neck Surgery, Beijing Tong Ren Hospital, Capital Medical University, Beijing, 100730, China
- Beijing Key Laboratory of Nasal Diseases, Beijing Institute of Otolaryngology, Beijing, 100005, China
| | - Xianglin Ji
- Department of Biomedical Engineering, The City University of Hong Kong, Kowloon, Hong Kong SAR, 999077, China
- Hong Kong Centre for Cerebro-Cardiovascular Health Engineering, Hong Kong Science Park, Shatin, Hong Kong SAR, 999077, China
| | - Xi Zhao
- Department of Biomedical Engineering, The City University of Hong Kong, Kowloon, Hong Kong SAR, 999077, China
- Hong Kong Centre for Cerebro-Cardiovascular Health Engineering, Hong Kong Science Park, Shatin, Hong Kong SAR, 999077, China
| | - Richard Yan-Do
- Department of Biomedical Engineering, The City University of Hong Kong, Kowloon, Hong Kong SAR, 999077, China
- Hong Kong Centre for Cerebro-Cardiovascular Health Engineering, Hong Kong Science Park, Shatin, Hong Kong SAR, 999077, China
| | - Youyang Wan
- Department of Biomedical Engineering, The City University of Hong Kong, Kowloon, Hong Kong SAR, 999077, China
| | - Ying Wang
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China
| | - Yuanting Zhang
- Department of Biomedical Engineering, The City University of Hong Kong, Kowloon, Hong Kong SAR, 999077, China
- Hong Kong Centre for Cerebro-Cardiovascular Health Engineering, Hong Kong Science Park, Shatin, Hong Kong SAR, 999077, China
| | - Peng Shi
- Department of Biomedical Engineering, The City University of Hong Kong, Kowloon, Hong Kong SAR, 999077, China
- Hong Kong Centre for Cerebro-Cardiovascular Health Engineering, Hong Kong Science Park, Shatin, Hong Kong SAR, 999077, China
- Center of Super-Diamond and Advanced Films (COSDAF), The City University of Hong Kong, Kowloon, Hong Kong SAR, 999077, China
- Shenzhen Research Institute, The City University of Hong Kong, Shenzhen, 518000, China
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Miyahira AK, Hawley JE, Adelaiye-Ogala R, Calais J, Nappi L, Parikh R, Seibert TM, Wasmuth EV, Wei XX, Pienta KJ, Soule HR. Exploring new frontiers in prostate cancer research: Report from the 2022 Coffey-Holden prostate cancer academy meeting. Prostate 2023; 83:207-226. [PMID: 36443902 DOI: 10.1002/pros.24461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 11/02/2022] [Indexed: 12/03/2022]
Abstract
INTRODUCTION The 2022 Coffey-Holden Prostate Cancer Academy (CHPCA) Meeting, "Exploring New Frontiers in Prostate Cancer Research," was held from June 23 to 26, 2022, at the University of California, Los Angeles, Luskin Conference Center, in Los Angeles, CA. METHODS The CHPCA Meeting is an annual discussion-oriented scientific conference organized by the Prostate Cancer Foundation, that focuses on emerging and next-step topics deemed critical for making the next major advances in prostate cancer research and clinical care. The 2022 CHPCA Meeting included 35 talks over 10 sessions and was attended by 73 academic investigators. RESULTS Major topic areas discussed at the meeting included: prostate cancer diversity and disparities, the impact of social determinants on research and patient outcomes, leveraging real-world and retrospective data, development of artificial intelligence biomarkers, androgen receptor (AR) signaling biology and new strategies for targeting AR, features of homologous recombination deficient prostate cancer, and future directions in immunotherapy and nuclear theranostics. DISCUSSION This article summarizes the scientific presentations from the 2022 CHPCA Meeting, with the goal that dissemination of this knowledge will contribute to furthering global prostate cancer research efforts.
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Affiliation(s)
| | - Jessica E Hawley
- Department of Medicine, Division of Medical Oncology, University of Washington, Seattle, Washington, USA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Remi Adelaiye-Ogala
- Department of Medicine, Division of Hematology and Oncology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York, USA
- Department of Pharmacology and Toxicology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York, USA
| | - Jeremie Calais
- Department of Molecular and Medical Pharmacology, Ahmanson Translational Imaging Division, University of California, Los Angeles, Los Angeles, California, USA
| | - Lucia Nappi
- Department of Urologic Sciences, Vancouver Prostate Centre, University of British Columbia, British Columbia, Canada
- Department of Medical Oncology, BC Cancer, British Columbia, Canada
| | - Ravi Parikh
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Medical Ethics and Health Policy, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, Pennsylvania, USA
| | - Tyler M Seibert
- Department of Radiation Medicine and Applied Sciences, University of California San Diego, La Jolla, California, USA
- Department of Radiology, University of California San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
- Research Service, VA San Diego Healthcare System, San Diego, California, USA
| | - Elizabeth V Wasmuth
- Department of Biochemistry and Structural Biology, University of Texas Health at San Antonio, San Antonio, Texas, USA
| | - Xiao X Wei
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Kenneth J Pienta
- The James Buchanan Brady Urological Institute, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Howard R Soule
- Prostate Cancer Foundation, Santa Monica, California, USA
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Madueke I, Lee RJ, Miyamoto DT. Circulating Tumor Cells and Circulating Tumor DNA in Urologic Cancers. Urol Clin North Am 2023; 50:109-114. [DOI: 10.1016/j.ucl.2022.09.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Raith F, O’Donovan DH, Lemos C, Politz O, Haendler B. Addressing the Reciprocal Crosstalk between the AR and the PI3K/AKT/mTOR Signaling Pathways for Prostate Cancer Treatment. Int J Mol Sci 2023; 24:ijms24032289. [PMID: 36768610 PMCID: PMC9917236 DOI: 10.3390/ijms24032289] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/17/2023] [Accepted: 01/20/2023] [Indexed: 01/27/2023] Open
Abstract
The reduction in androgen synthesis and the blockade of the androgen receptor (AR) function by chemical castration and AR signaling inhibitors represent the main treatment lines for the initial stages of prostate cancer. Unfortunately, resistance mechanisms ultimately develop due to alterations in the AR pathway, such as gene amplification or mutations, and also the emergence of alternative pathways that render the tumor less or, more rarely, completely independent of androgen activation. An essential oncogenic axis activated in prostate cancer is the phosphatidylinositol-3-kinase (PI3K)/AKT/mammalian target of rapamycin (mTOR) pathway, as evidenced by the frequent alterations of the negative regulator phosphatase and tensin homolog (PTEN) and by the activating mutations in PI3K subunits. Additionally, crosstalk and reciprocal feedback loops between androgen signaling and the PI3K/AKT/mTOR signaling cascade that activate pro-survival signals and play an essential role in disease recurrence and progression have been evidenced. Inhibitors addressing different players of the PI3K/AKT/mTOR pathway have been evaluated in the clinic. Only a limited benefit has been reported in prostate cancer up to now due to the associated side effects, so novel combination approaches and biomarkers predictive of patient response are urgently needed. Here, we reviewed recent data on the crosstalk between AR signaling and the PI3K/AKT/mTOR pathway, the selective inhibitors identified, and the most advanced clinical studies, with a focus on combination treatments. A deeper understanding of the complex molecular mechanisms involved in disease progression and treatment resistance is essential to further guide therapeutic approaches with improved outcomes.
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Affiliation(s)
- Fabio Raith
- Research & Development, Pharmaceuticals, Bayer AG, Müllerstr. 178, 13353 Berlin, Germany
| | - Daniel H. O’Donovan
- Research & Development, Pharmaceuticals, Bayer AG, Müllerstr. 178, 13353 Berlin, Germany
| | - Clara Lemos
- Bayer Research and Innovation Center, Bayer US LLC, 238 Main Street, Cambridge, MA 02142, USA
| | - Oliver Politz
- Research & Development, Pharmaceuticals, Bayer AG, Müllerstr. 178, 13353 Berlin, Germany
| | - Bernard Haendler
- Research & Development, Pharmaceuticals, Bayer AG, Müllerstr. 178, 13353 Berlin, Germany
- Correspondence: ; Tel.: +49-30-2215-41198
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Raina K, Forbes CD, Stronk R, Rappi JP, Eastman KJ, Gerritz SW, Yu X, Li H, Bhardwaj A, Forgione M, Hundt A, King MP, Posner ZM, Denny A, McGovern A, Puleo DE, Garvin E, Chenard R, Zaware N, Mousseau JJ, Macaluso J, Martin M, Bassoli K, Jones K, Garcia M, Howard K, Smith LM, Chen JM, De Leon CA, Hines J, Kayser-Bricker KJ, Crews CM. Regulated Induced Proximity Targeting Chimeras (RIPTACs): a Novel Heterobifunctional Small Molecule Therapeutic Strategy for Killing Cancer Cells Selectively. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.01.522436. [PMID: 36711980 PMCID: PMC9881854 DOI: 10.1101/2023.01.01.522436] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
While specific cell signaling pathway inhibitors have yielded great success in oncology, directly triggering cancer cell death is one of the great drug discovery challenges facing biomedical research in the era of precision oncology. Attempts to eradicate cancer cells expressing unique target proteins, such as antibody-drug conjugates (ADCs), T-cell engaging therapies, and radiopharmaceuticals have been successful in the clinic, but they are limited by the number of targets given the inability to target intracellular proteins. More recently, heterobifunctional small molecules such as Proteolysis Targeting Chimera (PROTACs) have paved the way for protein proximity inducing therapeutic modalities. Here, we describe a proof-of-concept study using novel heterobifunctional small molecules called Regulated Induced Proximity Targeting Chimeras or RIPTACs, which elicit a stable ternary complex between a target protein selectively expressed in cancer tissue and a pan-expressed protein essential for cell survival. The resulting cooperative protein:protein interaction (PPI) abrogates the function of the essential protein, thus leading to cell death selectively in cells expressing the target protein. This approach not only opens new target space by leveraging differentially expressed intracellular proteins but also has the advantage of not requiring the target to be a driver of disease. Thus, RIPTACs can address non-target mechanisms of resistance given that cell killing is driven by inactivation of the essential protein. Using the HaloTag7-FKBP model system as a target protein, we describe RIPTACs that incorporate a covalent or non-covalent target ligand connected via a linker to effector ligands such as JQ1 (BRD4), BI2536 (PLK1), or multi-CDK inhibitors such as TMX3013 or dinaciclib. We show that these RIPTACs exhibit positive co-operativity, accumulate selectively in cells expressing HaloTag7-FKBP, form stable target:RIPTAC:effector trimers in cells, and induce an anti-proliferative response in target-expressing cells. We propose that RIPTACs are a novel heterobifunctional therapeutic modality to treat cancers that are known to selectively express a specific intracellular protein.
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Affiliation(s)
- Kanak Raina
- co-corresponding authors
- Halda Therapeutics OpCo Inc, New Haven CT USA
| | | | | | | | | | | | - Xinheng Yu
- Halda Therapeutics OpCo Inc, New Haven CT USA
| | - Hao Li
- Halda Therapeutics OpCo Inc, New Haven CT USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Kelli Jones
- Halda Therapeutics OpCo Inc, New Haven CT USA
| | | | | | | | | | - Cesar A De Leon
- Department of Molecular, Cellular, & Developmental Biology, Yale University New Haven CT USA
| | - John Hines
- Department of Molecular, Cellular, & Developmental Biology, Yale University New Haven CT USA
| | | | - Craig M Crews
- co-corresponding authors
- Department of Molecular, Cellular, & Developmental Biology, Yale University New Haven CT USA
- Department of Pharmacology, Yale University New Haven CT USA
- Department of Chemistry, Yale University New Haven CT USA
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Nguyen AT, Liu CTS, Kamrava M. A "scoping" review of prostate brachytherapy and immune responses. Brachytherapy 2023; 22:21-29. [PMID: 36437221 DOI: 10.1016/j.brachy.2022.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 10/21/2022] [Indexed: 11/27/2022]
Abstract
PURPOSE Whether prostate brachytherapy (BT) results in opportunistic biological changes that can improve clinical outcomes is not well studied. We sought to investigate the impact of prostate BT on the immune system. MATERIALS AND METHODS A scoping review was performed using PubMed/Scopus for papers published between 2011-2021. Search terms were "brachytherapy" AND "immune" AND "prostate". A total of 81 records were identified and 6 were selected for further review. RESULTS 2 low-dose-rate BT papers (n=68) evaluated changes in the peripheral blood following I-125 monotherapy. Both showed significant increases in peripheral CD3+ and CD4+ T cells post-BT. One also demonstrated significant increases in Treg subsets up to 150 days post-BT. 4 high-dose-rate (HDR) studies (n=37) were identified, and all were done in combination with EBRT. The largest study (n=24) showed a single 10 Gy fraction of HDR converted 80% of "cold" tumors into an "intermediate" or "hot" state, based on a tumor inflammation signature when comparing a pre-BT biopsy to one prior to a second HDR fraction. CONCLUSION Prostate BT can invoke an immune activating phenotype; however, changes in immunosuppressive cells are also seen. Additional data is needed to understand how to promote synergy between BT and the immune system.
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Affiliation(s)
- Anthony T Nguyen
- Department of Radiation Oncology, Cedars-Sinai Medical Center, Los Angeles, CA; Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | | | - Mitchell Kamrava
- Department of Radiation Oncology, Cedars-Sinai Medical Center, Los Angeles, CA; Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA.
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The Novel Prognostic Index Model of Combining Circulating Tumor DNA and PINK-E Predicts the Clinical Outcomes for Newly Diagnosed Extranodal NK/T-cell Lymphoma. Hemasphere 2022; 7:e822. [PMID: 36570690 PMCID: PMC9771254 DOI: 10.1097/hs9.0000000000000822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/21/2022] [Indexed: 12/27/2022] Open
Abstract
Extranodal NK/T-cell lymphoma (ENKTL) is a highly aggressive and heterogeneous disease with poor clinical outcome. Our previous work had demonstrated that circulating tumor DNA (ctDNA) analyses were feasible in ENKTL, and dynamic tracing of ctDNA could be used to monitor the disease status. However, the prognostic value of ctDNA in ENKTL has not been fully investigated. Patients with newly diagnosed ENKTL from February 2017 to December 2021 (n = 70) were enrolled. The pretreatment ctDNA concentration (hGE/mL) was measured. The prognostic value of ctDNA, international prognostic index (IPI), Korean prognostic index (KPI), PINK-E, and the combination of PINK-E and ctDNA (PINK-EC) were investigated in our cohort. The IPI and PINK-E risk categories had a significant difference in progression-free survival (PFS) and overall survival (OS) between the low-risk and intermediate-risk groups. The KPI risk category had a difference in PFS and OS between the intermediate-risk and high-risk groups. Furthermore, integrating ctDNA into the PINK-E model could overcome the shortcomings of other prognostic models, which could significantly distinguish the different-risk groups. Overall, our results demonstrated that PINK-EC showed a superior prognostic prediction value and stability compared with IPI, KPI, and PINK-E. The integration of molecular features of the tumor into classic risk categories might better characterize a high-risk group where novel treatment approaches are most needed.
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Akhoundova D, Feng FY, Pritchard CC, Rubin MA. Molecular Genetics of Prostate Cancer and Role of Genomic Testing. Surg Pathol Clin 2022; 15:617-628. [PMID: 36344179 DOI: 10.1016/j.path.2022.08.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Prostate cancer (PCa) is characterized by profound genomic heterogeneity. Recent advances in personalized treatment entail an increasing need of genomic profiling. For localized PCa, gene expression assays can support clinical decisions regarding active surveillance and adjuvant treatment. In metastatic PCa, homologous recombination deficiency, microsatellite instability-high (MSI-H), and CDK12 deficiency constitute main actionable alterations. Alterations in DNA repair genes confer variable sensitivities to poly(ADP-ribose)polymerase inhibitors, and the use of genomic instability assays as predictive biomarker is still incipient. MSI can be assessed by immunohistochemistry To date there is a lack of consensus as to testing standards.
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Affiliation(s)
- Dilara Akhoundova
- Department for BioMedical Research, University of Bern, Murtenstrasse 24, Bern 3008, Switzerland; Department of Medical Oncology, Inselspital, University Hospital of Bern, Bern 3010, Switzerland
| | - Felix Y Feng
- Department of Radiation Oncology, University of California, 1600 Divisadero Street, Suite H-1031, San Francisco, CA 94115, USA
| | - Colin C Pritchard
- Department of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific St Seattle, WA 98195-7110, USA
| | - Mark A Rubin
- Department for BioMedical Research, University of Bern, Murtenstrasse 24, Bern 3008, Switzerland; Bern Center for Precision Medicine, Inselspital, University Hospital of Bern, Bern, 3008, Switzerland.
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Kwan EM, Wyatt AW, Chi KN. Towards clinical implementation of circulating tumor DNA in metastatic prostate cancer: Opportunities for integration and pitfalls to interpretation. Front Oncol 2022; 12:1054497. [PMID: 36439451 PMCID: PMC9685669 DOI: 10.3389/fonc.2022.1054497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 10/25/2022] [Indexed: 08/13/2023] Open
Abstract
Plasma circulating tumor DNA (ctDNA) represents short fragments of tumor-derived DNA released into the bloodstream primarily from cancer cells undergoing apoptosis. In metastatic castration-resistant prostate cancer (mCRPC), characterizing genomic alterations in ctDNA identifies mutations, copy number alterations, and structural rearrangements with predictive and prognostic biomarker utility. These associations with clinical outcomes have resulted in ctDNA increasingly incorporated into routine clinical care. In this review, we summarize current and emerging applications for ctDNA analysis in metastatic prostate cancer, including outcome prediction, treatment selection, and characterization of treatment resistance. We also discuss potential pitfalls with interpreting ctDNA findings, namely false negatives arising from low tumor content and optimal assay design, including correction for clonal hematopoiesis of indeterminate potential and germline variants. Understanding the influence of these limitations on interpretation of ctDNA results is necessary to overcome barriers to clinical implementation. Nevertheless, as assay availability and technology continue to improve, recognizing both opportunities and shortcomings of ctDNA analysis will retain relevance with informing the implementation of precision-oncology initiatives for metastatic prostate cancer.
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Affiliation(s)
- Edmond M. Kwan
- Vancouver Prostate Centre, Department of Urologic Sciences, The University of British Columbia, Vancouver, BC, Canada
- BC Cancer, Vancouver Centre, Vancouver, BC, Canada
| | - Alexander W. Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, The University of British Columbia, Vancouver, BC, Canada
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Kim N. Chi
- Vancouver Prostate Centre, Department of Urologic Sciences, The University of British Columbia, Vancouver, BC, Canada
- BC Cancer, Vancouver Centre, Vancouver, BC, Canada
- Department of Medicine, The University of British Columbia, Vancouver, BC, Canada
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Accidentals of the DNA Symphony. Cancer Res 2022; 82:3880-3881. [DOI: 10.1158/0008-5472.can-22-2750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 09/06/2022] [Indexed: 11/07/2022]
Abstract
Abstract
Cancer epigenome profiling such as DNA methylation (5mC) and DNA hydroxymethylation (5hmC) is emerging as a sensitive approach for cancer detection and risk stratification. 5mC modification has been widely described in many cancer types including prostate cancer; however, the 5hmC landscape is yet to be explored. In this issue of Cancer Research, Sjöström and colleagues have comprehensively incorporated genomic, transcriptomic, and epigenomic, including 5hmC, data to interrogate the molecular evolution of prostate cancer.
See related article by Sjöström et al., p. 3888
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Takeda DY, Sowalsky AG. Unpacking circulating tumor DNA lends insight into prostate cancer biology and the clonal dynamics of metastasis. Cancer Cell 2022; 40:1086-1088. [PMID: 36179684 DOI: 10.1016/j.ccell.2022.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Prostate cancer (PCa) frequently metastasizes to bone, and analyses of DNA from bone biopsies are exceptionally challenging. A recent report in Nature demonstrates that whole-genome sequencing (WGS) of circulating tumor DNA (ctDNA) from patients with metastatic PCa can inform on the subclonal composition of metastatic disease and infer patterns of gene expression.
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Affiliation(s)
- David Y Takeda
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA
| | - Adam G Sowalsky
- Laboratory of Genitourinary Cancer Pathogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA.
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71
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Logothetis C, Pilié P. Putting Precision Medicine in Prostate Cancer into Practice: Are We There Yet? Eur Urol 2022. [DOI: 10.1016/j.eururo.2022.09.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Huang J, Du M, Soupir A, Wang L, Tan W, Kalari KR, Kilari D, Park J, Huang CC, Kohli M, Wang L. Plasma Copy Number Alteration-Based Prognostic and Predictive Multi-Gene Risk Score in Metastatic Castration-Resistant Prostate Cancer. Cancers (Basel) 2022; 14:4714. [PMID: 36230636 PMCID: PMC9562906 DOI: 10.3390/cancers14194714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/17/2022] [Accepted: 09/23/2022] [Indexed: 11/17/2022] Open
Abstract
Prostate cancer (PCa) accounted for more than 34,000 deaths in US males [...].
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Affiliation(s)
- Jinyong Huang
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Meijun Du
- Department of the Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Alex Soupir
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Liewei Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Winston Tan
- Department of Hematology and Oncology, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Krishna R. Kalari
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA
| | - Deepak Kilari
- Department of Oncology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jong Park
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Chiang-Ching Huang
- Joseph J. Zilber School of Public Health, University of Wisconsin Milwaukee, Milwaukee, WI 53205, USA
| | - Manish Kohli
- Division of Oncology, Department of Medicine, University of Utah Huntsman Cancer Center, Salt Lake City, UT 84112, USA
| | - Liang Wang
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
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Liu Z, Han Y, Dang Q, Xu H, Zhang Y, Duo M, Lv J, Li H, Kong Y, Han X. Roles of circulating tumor DNA in PD-1/PD-L1 immune checkpoint Inhibitors: Current evidence and future directions. Int Immunopharmacol 2022; 111:109173. [PMID: 35998502 DOI: 10.1016/j.intimp.2022.109173] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/11/2022] [Accepted: 08/14/2022] [Indexed: 12/18/2022]
Abstract
Circulating tumor DNA (ctDNA) sequencing holds considerable promise for early diagnosis and detection of surveillance and minimal residual disease. Blood ctDNA monitors specific cancers by detecting the alterations found in cancer cells, such as apoptosis and necrosis. Due to the short half-life, ctDNA reflects the actual burden of other treatments on tumors. In addition, ctDNA might be preferable to monitor tumor development and treatment compared with invasive tissue biopsy. ctDNA-based liquid biopsy brings remarkable strength to targeted therapy and precision medicine. Notably, multiple ctDNA analysis platforms have been broadly applied in clinical immunotherapy. Through targeted sequencing, early variations in ctDNA could predict response to immune checkpoint inhibitor (ICI). Several studies have demonstrated a correlation between ctDNA kinetics and anti-PD1 antibodies. The need for further research and development remains, although this biomarker holds significant prospects for early cancer detection. This review focuses on describing the basis of ctDNA and its current utilities in oncology and immunotherapy, either for clinical management or early detection, highlighting its advantages and inherent limitations.
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Affiliation(s)
- Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China; Interventional Institute of Zhengzhou University, Zhengzhou, Henan 450052, China; Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, Henan 450052, China.
| | - Yilin Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Qin Dang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Hui Xu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Yuyuan Zhang
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Mengjie Duo
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Jinxiang Lv
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Huanyun Li
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Ying Kong
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China; Interventional Institute of Zhengzhou University, Zhengzhou, Henan 450052, China; Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, Henan 450052, China.
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