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Moser T, Waldispuehl-Geigl J, Belic J, Perakis S, Weber S, Zhou Q, Sill H, Lax S, Kashofer K, Hoefler G, Schoellnast H, Bauernhofer T, Heitzer E, Geigl JB, Speicher MR. Abstract 4295: Early circulating tumor DNA dynamics as a real-time predictor of FOLFOX efficacy in advanced colorectal cancer patients. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-4295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: In recent years, various efforts have been made to identify biomarkers in metastatic colorectal cancer patients (mCRC), all with the goal of improving patients' outcomes, including maximizing therapeutic response and minimizing exposure to ineffective treatments. Nevertheless, there is still no valid biomarker for the early assessment of therapeutic efficacy in the patient management strategy. To address this issue, we aimed to describe the predictive value of circulating tumor DNA (ctDNA) on the efficacy of FOLFOX treatment in mCRC patients.
Patients and methods: A total of 11 patients with mCRC receiving FOLFOX therapy were included in this study. During the 48-hour FOLFOX cycle, we performed serial liquid biopsy-based ctDNA analysis before treatment start (T1) and at eight further time points (T2-T9). Among the 11 patients tested, all patients had detectable variants identified by either tumor tissue genotyping or baseline sample ctDNA sequencing for longitudinal analysis. We assessed genome-wide somatic copy number alterations (SCNAs) and highly sensitive sequencing approaches were utilized to monitor changes in the ctDNA mutant allele frequencies (mAFs) between baseline and on-treatment samples.
Results: We were able to clearly assess different mAF patterns across patients with either stable disease, partial response or progressive disease. However, we invariably observed an early and deep ctDNA mAF decrease in all patients, as comparing the baseline (T1) mAF levels with the mAFs at all time points revealed that the most significant ctDNA drop was 23 hours after treatment start, i.e. at time point T5 (p <0.005). In addition, we observed in patients with stable disease or partial response (n=8) not only a significant decline of mAFs between T5 (p=0.0391) but also at T9 (52 hours after treatment start; p=0.0156) compared to the baseline sample. Conversely, mAFs of patients with progressive disease increased again within the next 29 hours (T9) after the initial ctDNA drop at time point T5, leading to higher ctDNA levels at T9 than the baseline values prior to treatment start.
Conclusion: Our observations clearly demonstrated for the first time that ctDNA dynamics allow real-time, individualized evaluation of treatment response using two early time points, i.e. at T5 and T9. Therefore, our data suggest that sequential ctDNA analysis can contribute to an improved patient treatment strategy. Nevertheless, further studies are clearly required to validate this promising early on-treatment indicator of therapeutic efficacy for CRC patients.
Citation Format: Tina Moser, Julie Waldispuehl-Geigl, Jelena Belic, Samantha Perakis, Sabrina Weber, Qing Zhou, Heinz Sill, Sigurd Lax, Karl Kashofer, Gerald Hoefler, Helmut Schoellnast, Thomas Bauernhofer, Ellen Heitzer, Jochen B. Geigl, Michael R. Speicher. Early circulating tumor DNA dynamics as a real-time predictor of FOLFOX efficacy in advanced colorectal cancer patients [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4295.
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Affiliation(s)
- Tina Moser
- 1Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Julie Waldispuehl-Geigl
- 1Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Jelena Belic
- 1Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Samantha Perakis
- 1Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Sabrina Weber
- 1Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Qing Zhou
- 1Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Heinz Sill
- 2Department of Internal Medicine, Division of Hematology, Medical University of Graz, Graz, Austria
| | - Sigurd Lax
- 3Department of Pathology, General Hospital Graz II, Graz, Austria
| | - Karl Kashofer
- 4Institute of Pathology, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, Graz, Austria
| | - Gerald Hoefler
- 4Institute of Pathology, Diagnostic and Research Center for Molecular Biomedicine, Medical University of Graz, Graz, Austria
| | - Helmut Schoellnast
- 5Department of Radiology, Division of General Radiology, Medical University of Graz, Graz, Austria
| | - Thomas Bauernhofer
- 6Department of Internal Medicine Graz, Division of Oncology, Medical University of Graz, Graz, Austria
| | - Ellen Heitzer
- 1Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Jochen B. Geigl
- 1Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Michael R. Speicher
- 1Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
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Ulz P, Perakis S, Zhou Q, Moser T, Belic J, Lazzeri I, Wölfler A, Zebisch A, Gerger A, Pristauz G, Petru E, White B, Roberts CES, John JS, Schimek MG, Geigl JB, Bauernhofer T, Sill H, Bock C, Heitzer E, Speicher MR. Publisher Correction: Inference of transcription factor binding from cell-free DNA enables tumor subtype prediction and early detection. Nat Commun 2020; 11:1965. [PMID: 32313081 PMCID: PMC7170910 DOI: 10.1038/s41467-020-15799-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
- Peter Ulz
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Samantha Perakis
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Qing Zhou
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Tina Moser
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Jelena Belic
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Isaac Lazzeri
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Albert Wölfler
- Department of Internal Medicine, Division of Hematology, Medical University of Graz, Graz, Austria
| | - Armin Zebisch
- Department of Internal Medicine, Division of Hematology, Medical University of Graz, Graz, Austria
| | - Armin Gerger
- Department of Internal Medicine, Division of Oncology, Medical University of Graz, Graz, Austria
| | - Gunda Pristauz
- Department of Obstetrics and Gynecology, Medical University of Graz, Graz, Austria
| | - Edgar Petru
- Department of Obstetrics and Gynecology, Medical University of Graz, Graz, Austria
| | | | | | | | - Michael G Schimek
- Institute of Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria
| | - Jochen B Geigl
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Thomas Bauernhofer
- Department of Internal Medicine, Division of Oncology, Medical University of Graz, Graz, Austria
| | - Heinz Sill
- Department of Internal Medicine, Division of Hematology, Medical University of Graz, Graz, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria.,Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany
| | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria. .,BioTechMed-Graz, Graz, Austria. .,Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Graz, Austria.
| | - Michael R Speicher
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria. .,BioTechMed-Graz, Graz, Austria.
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3
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Smith CG, Moser T, Mouliere F, Field-Rayner J, Eldridge M, Riediger AL, Chandrananda D, Heider K, Wan JCM, Warren AY, Morris J, Hudecova I, Cooper WN, Mitchell TJ, Gale D, Ruiz-Valdepenas A, Klatte T, Ursprung S, Sala E, Riddick ACP, Aho TF, Armitage JN, Perakis S, Pichler M, Seles M, Wcislo G, Welsh SJ, Matakidou A, Eisen T, Massie CE, Rosenfeld N, Heitzer E, Stewart GD. Comprehensive characterization of cell-free tumor DNA in plasma and urine of patients with renal tumors. Genome Med 2020; 12:23. [PMID: 32111235 PMCID: PMC7048087 DOI: 10.1186/s13073-020-00723-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 02/10/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Cell-free tumor-derived DNA (ctDNA) allows non-invasive monitoring of cancers, but its utility in renal cell cancer (RCC) has not been established. METHODS Here, a combination of untargeted and targeted sequencing methods, applied to two independent cohorts of patients (n = 91) with various renal tumor subtypes, were used to determine ctDNA content in plasma and urine. RESULTS Our data revealed lower plasma ctDNA levels in RCC relative to other cancers of similar size and stage, with untargeted detection in 27.5% of patients from both cohorts. A sensitive personalized approach, applied to plasma and urine from select patients (n = 22) improved detection to ~ 50%, including in patients with early-stage disease and even benign lesions. Detection in plasma, but not urine, was more frequent amongst patients with larger tumors and in those patients with venous tumor thrombus. With data from one extensively characterized patient, we observed that plasma and, for the first time, urine ctDNA may better represent tumor heterogeneity than a single tissue biopsy. Furthermore, in a subset of patients (n = 16), longitudinal sampling revealed that ctDNA can track disease course and may pre-empt radiological identification of minimal residual disease or disease progression on systemic therapy. Additional datasets will be required to validate these findings. CONCLUSIONS These data highlight RCC as a ctDNA-low malignancy. The biological reasons for this are yet to be determined. Nonetheless, our findings indicate potential clinical utility in the management of patients with renal tumors, provided improvement in isolation and detection approaches.
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Affiliation(s)
- Christopher G Smith
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.
| | - Tina Moser
- Medical University of Graz, Diagnostic and Research Center for Molecular Biomedicine, Institute of Human Genetics, Graz, Austria
| | - Florent Mouliere
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081, HV, Amsterdam, The Netherlands
| | - Johanna Field-Rayner
- Cambridge Urology Translational Research and Clinical Trials Office, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Matthew Eldridge
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Anja L Riediger
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Dineika Chandrananda
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Katrin Heider
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Jonathan C M Wan
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Anne Y Warren
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - James Morris
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Irena Hudecova
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Wendy N Cooper
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Thomas J Mitchell
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Davina Gale
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Andrea Ruiz-Valdepenas
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Tobias Klatte
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
- Department of Urology, Royal Bournemouth Hospital, Bournemouth, UK
| | - Stephan Ursprung
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Department of Radiology, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Evis Sala
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Department of Radiology, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Antony C P Riddick
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Tevita F Aho
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - James N Armitage
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Samantha Perakis
- Medical University of Graz, Diagnostic and Research Center for Molecular Biomedicine, Institute of Human Genetics, Graz, Austria
| | - Martin Pichler
- Department of Internal Medicine Graz, Austria Division of Oncology, Medical University of Graz, Graz, Austria
| | - Maximilian Seles
- Department of Urology, Medical University of Graz, Graz, Austria
| | - Gabriel Wcislo
- Department of Oncology, Military Institute of Medicine, Warsaw, Poland
| | - Sarah J Welsh
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Athena Matakidou
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, CB2 0AA, UK
| | - Tim Eisen
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, CB2 0AA, UK
- Department of Oncology, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Charles E Massie
- Hutchison/MRC Research Centre, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Nitzan Rosenfeld
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Ellen Heitzer
- Medical University of Graz, Diagnostic and Research Center for Molecular Biomedicine, Institute of Human Genetics, Graz, Austria.
- Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Graz, Austria.
| | - Grant D Stewart
- Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK.
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK.
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4
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Ulz P, Perakis S, Zhou Q, Moser T, Belic J, Lazzeri I, Wölfler A, Zebisch A, Gerger A, Pristauz G, Petru E, White B, Roberts CES, John JS, Schimek MG, Geigl JB, Bauernhofer T, Sill H, Bock C, Heitzer E, Speicher MR. Inference of transcription factor binding from cell-free DNA enables tumor subtype prediction and early detection. Nat Commun 2019; 10:4666. [PMID: 31604930 PMCID: PMC6789008 DOI: 10.1038/s41467-019-12714-4] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 09/24/2019] [Indexed: 12/19/2022] Open
Abstract
Deregulation of transcription factors (TFs) is an important driver of tumorigenesis, but non-invasive assays for assessing transcription factor activity are lacking. Here we develop and validate a minimally invasive method for assessing TF activity based on cell-free DNA sequencing and nucleosome footprint analysis. We analyze whole genome sequencing data for >1,000 cell-free DNA samples from cancer patients and healthy controls using a bioinformatics pipeline developed by us that infers accessibility of TF binding sites from cell-free DNA fragmentation patterns. We observe patient-specific as well as tumor-specific patterns, including accurate prediction of tumor subtypes in prostate cancer, with important clinical implications for the management of patients. Furthermore, we show that cell-free DNA TF profiling is capable of detection of early-stage colorectal carcinomas. Our approach for mapping tumor-specific transcription factor binding in vivo based on blood samples makes a key part of the noncoding genome amenable to clinical analysis.
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Affiliation(s)
- Peter Ulz
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Samantha Perakis
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Qing Zhou
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Tina Moser
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Jelena Belic
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Isaac Lazzeri
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Albert Wölfler
- Department of Internal Medicine, Division of Hematology, Medical University of Graz, Graz, Austria
| | - Armin Zebisch
- Department of Internal Medicine, Division of Hematology, Medical University of Graz, Graz, Austria
| | - Armin Gerger
- Department of Internal Medicine, Division of Oncology, Medical University of Graz, Graz, Austria
| | - Gunda Pristauz
- Department of Obstetrics and Gynecology, Medical University of Graz, Graz, Austria
| | - Edgar Petru
- Department of Obstetrics and Gynecology, Medical University of Graz, Graz, Austria
| | | | | | | | - Michael G Schimek
- Institute of Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria
| | - Jochen B Geigl
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Thomas Bauernhofer
- Department of Internal Medicine, Division of Oncology, Medical University of Graz, Graz, Austria
| | - Heinz Sill
- Department of Internal Medicine, Division of Hematology, Medical University of Graz, Graz, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
- Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany
| | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria.
- BioTechMed-Graz, Graz, Austria.
- Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Graz, Austria.
| | - Michael R Speicher
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria.
- BioTechMed-Graz, Graz, Austria.
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5
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Moser T, Smith CG, Seles M, Wcislo G, Eldridge M, Perakis S, Mouliere F, Lazzeri I, Heider K, Warren A, Rosenfeld N, Stewart GD, Heitzer E. Abstract 1367: Comprehensive characterization of cell-free tumor DNA in plasma and urine of patients with renal tumors. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-1367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Renal cell carcinoma (RCC) represents a heterogenous disease in terms of histologic subtypes, prognosis and treatment response. Genetic heterogeneity offers a particular challenge to direct available targeted therapies that best match the patient. Profiling and monitoring of tumor-specific alterations from body fluids has been demonstrated as a valuable tool for many tumor types. Yet, the utility of circulating tumor DNA (ctDNA) in RCC has not been well established. To characterize the levels and composition of ctDNA in the plasma and urine we employed a broad range of targeted and untargeted methods to two independent cohorts of patients with renal tumors. We applied shallow Whole Genome Sequencing (sWGS) and modified Fast Aneuploidy Screen Test-Sequencing System (mFAST-SeqS) to 43 patients with metastatic RCCs. Using the mFAST-SeqS, ctDNA was detectable in only 2 out of 43 patients (4.7%). However, assessment of tumor fractions based on sWGS using the ichorCNA algorithm revealed 6 further patients with detectable amounts of ctDNA. In silico size selection of fragments < 150bp further improved the detection rate to 27% (12 out of 43 patients). This is consistent with previous reports that tumor-derived fragments are often smaller compared to cell-free DNA of normal cells and as such enrichment of smaller fragment increases the sensitivity. High-resolution mutation analysis of 10 recurrently mutated genes in RCC was performed using a QIASeq custom capture panel, enabling detection of tumor-specific mutations at baseline in 18% (8/43) of patients. Of these five had detectable tumor fractions as observed with ichorCNA. Furthermore, we had access to longitudinally obtained plasma samples for 37 of our 43 (86%) patients with a median follow-up period of 6 months (range, 0.4-19.2). The QIASeq panel was applied to follow-up patients of which mutations were identified at baseline. For most of these patients, ctDNA was elevated at treatment initiation but decreased with response. At the time of progression, or when a response could not be achieved, ctDNA increased or remained elevated. Plasma and urine samples were available for a second cohort (n=47) of patients with a wide range of renal tumors. Detection rates using both broad, untargeted sequencing methods and targeted, sensitive approaches were similarly low with 7/47 (14.9%) and 45.5% (10/22), respectively. Interrogation of those patients with detectable ctDNA revealed, for the first time, that urine ctDNA is capable of overcoming genetic heterogeneity and offers information that is complementary to that provided by plasma. Taken together, our data revealed that ctDNA levels are lower in RCC than other cancers of similar stage. Although, ctDNA can be detected in blood and urine of RCC patients and there is potential for clinical utility, improved isolation and detection methods are needed to achieve a broad patient coverage.
Citation Format: Tina Moser, Christopher G. Smith, Maximilian Seles, Gabriel Wcislo, Matthew Eldridge, Samantha Perakis, Florent Mouliere, Isaac Lazzeri, Katrin Heider, Anne Warren, Nitzan Rosenfeld, Grant D. Stewart, Ellen Heitzer. Comprehensive characterization of cell-free tumor DNA in plasma and urine of patients with renal tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1367.
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Affiliation(s)
- Tina Moser
- 1Medical University of Graz, Diagnostic and Research Center for Molecular Biomedicine, Graz, Austria
| | | | | | | | - Matthew Eldridge
- 2Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Samantha Perakis
- 1Medical University of Graz, Diagnostic and Research Center for Molecular Biomedicine, Graz, Austria
| | - Florent Mouliere
- 5Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Isaac Lazzeri
- 1Medical University of Graz, Diagnostic and Research Center for Molecular Biomedicine, Graz, Austria
| | - Katrin Heider
- 2Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Anne Warren
- 6Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Nitzan Rosenfeld
- 2Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Grant D. Stewart
- 6Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Ellen Heitzer
- 1Medical University of Graz, Diagnostic and Research Center for Molecular Biomedicine, Graz, Austria
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6
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Belic J, Graf R, Bauernhofer T, Cherkas Y, Ulz P, Waldispuehl‐Geigl J, Perakis S, Gormley M, Patel J, Li W, Geigl JB, Smirnov D, Heitzer E, Gross M, Speicher MR. Genomic alterations in plasma DNA from patients with metastasized prostate cancer receiving abiraterone or enzalutamide. Int J Cancer 2018; 143:1236-1248. [PMID: 29574703 PMCID: PMC6099279 DOI: 10.1002/ijc.31397] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 03/06/2018] [Accepted: 03/19/2018] [Indexed: 12/14/2022]
Abstract
In patients with metastatic castrate-resistant prostate cancer (mCRPC), circulating tumor DNA (ctDNA) analysis offers novel opportunities for the development of non-invasive biomarkers informative of treatment response with novel agents targeting the androgen-receptor (AR) pathway, such as abiraterone or enzalutamide. However, the relationship between ctDNA abundance, detectable somatic genomic alterations and clinical progression of mCRPC remains unexplored. Our study aimed to investigate changes in plasma DNA during disease progression and their associations with clinical variables in mCRPC patients. We analyzed ctDNA in two cohorts including 94 plasma samples from 25 treatment courses (23 patients) and 334 plasma samples from 125 patients, respectively. We conducted whole-genome sequencing (plasma-Seq) for genome-wide profiling of somatic copy number alterations and targeted sequencing of 31 prostate cancer-associated genes. The combination of plasma-Seq with targeted AR analyses identified prostate cancer-related genomic alterations in 16 of 25 (64%) treatment courses in the first cohort, in which we demonstrated that AR amplification does not always correlate with poor abiraterone and enzalutamide therapy outcome. As we observed a wide variability of ctDNA levels, we evaluated ctDNA levels and their association with clinical parameters and included the second, larger cohort for these analyses. Employing altogether 428 longitudinal plasma samples from 148 patients, we identified the presence of bone metastases, increased lactate dehydrogenase and prostate-specific antigen (PSA) as having the strongest association with high ctDNA levels. In summary, ctDNA alterations are observable in the majority of patients with mCRPC and may eventually be useful to guide clinical decision-making in this setting.
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Affiliation(s)
- Jelena Belic
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstraße 6A‐8010GrazAustria
| | - Ricarda Graf
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstraße 6A‐8010GrazAustria
| | - Thomas Bauernhofer
- Division of OncologyMedical University of Graz, Auenbruggerplatz 15A‐8036GrazAustria
| | - Yauheniya Cherkas
- Pharmaceutical Companies of Johnson & JohnsonJanssen Oncology Therapeutic Area, Janssen Research and Development, LLCSpring HousePA19477USA
| | - Peter Ulz
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstraße 6A‐8010GrazAustria
| | - Julie Waldispuehl‐Geigl
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstraße 6A‐8010GrazAustria
| | - Samantha Perakis
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstraße 6A‐8010GrazAustria
| | - Michael Gormley
- Pharmaceutical Companies of Johnson & JohnsonJanssen Oncology Therapeutic Area, Janssen Research and Development, LLCSpring HousePA19477USA
| | - Jaymala Patel
- Pharmaceutical Companies of Johnson & JohnsonJanssen Oncology Therapeutic Area, Janssen Research and Development, LLCSpring HousePA19477USA
| | - Weimin Li
- Pharmaceutical Companies of Johnson & JohnsonJanssen Oncology Therapeutic Area, Janssen Research and Development, LLCSpring HousePA19477USA
| | - Jochen B. Geigl
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstraße 6A‐8010GrazAustria
| | - Denis Smirnov
- Pharmaceutical Companies of Johnson & JohnsonJanssen Oncology Therapeutic Area, Janssen Research and Development, LLCSpring HousePA19477USA
| | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstraße 6A‐8010GrazAustria
| | - Mitchell Gross
- Lawrence J. Ellison Institute for Transformative Medicine of USC, USC Westside Cancer Center, University of Southern California, 9033 Wilshire Blvd, Suite 300Beverly HillsCA90211USA
| | - Michael R. Speicher
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstraße 6A‐8010GrazAustria
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8
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Moser T, Ulz P, Zhou Q, Perakis S, Geigl JB, Speicher MR, Heitzer E. Single-Stranded DNA Library Preparation Does Not Preferentially Enrich Circulating Tumor DNA. Clin Chem 2017; 63:1656-1659. [DOI: 10.1373/clinchem.2017.277988] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Tina Moser
- Institute of Human Genetics Medical University of Graz Graz, Austria
| | - Peter Ulz
- Institute of Human Genetics Medical University of Graz Graz, Austria
| | - Qing Zhou
- Institute of Human Genetics Medical University of Graz Graz, Austria
| | - Samantha Perakis
- Institute of Human Genetics Medical University of Graz Graz, Austria
| | - Jochen B Geigl
- Institute of Human Genetics Medical University of Graz Graz, Austria
| | - Michael R Speicher
- Institute of Human Genetics Medical University of Graz Graz, Austria
- BioTechMed-Graz, Austria
| | - Ellen Heitzer
- Institute of Human Genetics Medical University of Graz Graz, Austria
- BioTechMed-Graz, Austria
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Abstract
Characterizing and monitoring tumor genomes with blood samples could achieve significant improvements in precision medicine. As tumors shed parts of themselves into the circulation, analyses of circulating tumor cells, circulating tumor DNA, and tumor-derived exosomes, often referred to as "liquid biopsies", may enable tumor genome characterization by minimally invasive means. Indeed, multiple studies have described how molecular information about parent tumors can be extracted from these components. Here, we briefly summarize current technologies and then elaborate on emerging novel concepts that may further propel the field. We address normal and detectable mutation levels in the context of our current knowledge regarding the gradual accumulation of mutations during aging and in light of technological limitations. Finally, we discuss whether liquid biopsies are ready to be used in routine clinical practice.
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Affiliation(s)
- Samantha Perakis
- Institute of Human Genetics, Medical University of Graz, Harrachgasse 21/8, A-8010, Graz, Austria
| | - Michael R Speicher
- Institute of Human Genetics, Medical University of Graz, Harrachgasse 21/8, A-8010, Graz, Austria. .,BioTechMed, Graz, Austria.
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Graier T, Auer M, Heitzer E, Ulz P, Perakis S, Speicher M, Geigl J. Rapid single-cell copy-number aberration analysis using high-throughput sequencing. Eur J Cancer 2017. [DOI: 10.1016/s0959-8049(17)30159-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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11
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Abstract
The analysis of cell-free circulating tumor DNA (ctDNA) is a very promising tool and might revolutionize cancer care with respect to early detection, identification of minimal residual disease, assessment of treatment response, and monitoring tumor evolution. ctDNA analysis, often referred to as "liquid biopsy" offers what tissue biopsies cannot-a continuous monitoring of tumor-specific changes during the entire course of the disease. Owing to technological improvements, efforts for the establishment of preanalytical and analytical benchmark, and the inclusion of ctDNA analyses in clinical trial, an actual clinical implementation has come within easy reach. In this chapter, recent advances of the analysis of ctDNA are summarized starting from the discovery of cell-free DNA, to methodological approaches and the clinical applicability.
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Affiliation(s)
- Samantha Perakis
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Martina Auer
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Jelena Belic
- Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Ellen Heitzer
- Institute of Human Genetics, Medical University of Graz, Graz, Austria.
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Seles M, Hutterer GC, Kiesslich T, Pummer K, Berindan-Neagoe I, Perakis S, Schwarzenbacher D, Stotz M, Gerger A, Pichler M. Current Insights into Long Non-Coding RNAs in Renal Cell Carcinoma. Int J Mol Sci 2016; 17:573. [PMID: 27092491 PMCID: PMC4849029 DOI: 10.3390/ijms17040573] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 04/08/2016] [Accepted: 04/12/2016] [Indexed: 02/07/2023] Open
Abstract
Renal cell carcinoma (RCC) represents a deadly disease with rising mortality despite intensive therapeutic efforts. It comprises several subtypes in terms of distinct histopathological features and different clinical presentations. Long non-coding RNAs (lncRNAs) are non-protein-coding transcripts in the genome which vary in expression levels and length and perform diverse functions. They are involved in the inititation, evolution and progression of primary cancer, as well as in the development and spread of metastases. Recently, several lncRNAs were described in RCC. This review emphasises the rising importance of lncRNAs in RCC. Moreover, it provides an outlook on their therapeutic potential in the future.
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Affiliation(s)
- Maximilian Seles
- Department of Urology, Medical University of Graz, A-8036 Graz, Austria.
| | - Georg C Hutterer
- Department of Urology, Medical University of Graz, A-8036 Graz, Austria.
| | - Tobias Kiesslich
- Department of Internal Medicine I, Salzburger Landeskliniken (SALK), Paracelsus Medical University, A-5020 Salzburg, Austria.
- Laboratory for Tumour Biology and Experimental Therapies, Institute of Physiology and Pathophysiology, Paracelsus Medical University, A-5020 Salzburg, Austria.
| | - Karl Pummer
- Department of Urology, Medical University of Graz, A-8036 Graz, Austria.
| | - Ioana Berindan-Neagoe
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA.
- Research Center of Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 400337 Cluj-Napoca, Romania.
- Department of Experimental Pathology, The Oncology Institute Ion Chiricuta, 400015 Cluj-Napoca, Romania.
| | - Samantha Perakis
- Institute of Human Genetics, Medical University of Graz, A-8036 Graz, Austria.
| | - Daniela Schwarzenbacher
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, A-8036 Graz, Austria.
| | - Michael Stotz
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, A-8036 Graz, Austria.
| | - Armin Gerger
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, A-8036 Graz, Austria.
- Center for Biomarker Research in Medicine, Medical University of Graz, A-8036 Graz, Austria.
| | - Martin Pichler
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA.
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, A-8036 Graz, Austria.
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Ress AL, Stiegelbauer V, Schwarzenbacher D, Deutsch A, Perakis S, Ling H, Ivan C, Calin GA, Rinner B, Gerger A, Pichler M. Spinophilin expression determines cellular growth, cancer stemness and 5-flourouracil resistance in colorectal cancer. Oncotarget 2015; 5:8492-502. [PMID: 25261368 PMCID: PMC4226699 DOI: 10.18632/oncotarget.2329] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The putative tumor suppressor gene spinophilin has been involved in cancer progression in several types of cancer. In this study, we explored the prognostic value of spinophilin expression in 162 colon adenocarcinoma patients. In addition, we generated stably expressing spinophilin-directed shRNA CRC cell lines and studied the influence of spinophilin expression on cellular phenotypes and molecular interactions. We independently confirmed that low spinophilin expression levels are associated with poor prognosis in CRC patients (p = 0.038). A reduction of spinophilin levels in p53 wild-type HCT116 and p53-mutated Caco-2 cells led to increased cellular growth rates and anchorage-independent growth (p<0.05). At molecular level, reduced spinophilin levels increased the expression of the transcription factor E2F-1. In addition, we observed an increased formation of tumor spheres, increased number of CD133 positive cells and an increased resistance to 5-flourouracil (p<0.05). Finally, treatment with the de-methylating agent 5-aza-dC increased spinophilin expression in CRC cells (p<0.05), corroborated by a correlation of spinophilin expression and extent of methylated CpG sites in the gene promoter region (p<0.001). In conclusion, gain of aggressive biological properties of CRC cells including cellular growth, cancer stem cell features and 5-flourouracil resistance partly explains the role of spinophilin in CRC.
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Affiliation(s)
- Anna Lena Ress
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Austria. These authors contributed equally to this work
| | - Verena Stiegelbauer
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Austria. These authors contributed equally to this work
| | | | - Alexander Deutsch
- Division of Haematology, Department of Internal Medicine, Medical University of Graz, Austria
| | - Samantha Perakis
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Austria
| | - Hui Ling
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, TX, USA
| | - Cristina Ivan
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, TX, USA
| | - George Adrian Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, TX, USA. Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, TX, USA
| | - Beate Rinner
- Center for Medical Research, Medical University of Graz, Graz, Austria
| | - Armin Gerger
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Austria
| | - Martin Pichler
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Austria. Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, TX, USA
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14
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Stiegelbauer V, Ress A, Schwarzenbacher D, Deutsch A, Perakis S, Ling H, Ivan C, Calin G, Gerger A, Rinner B, Pichler M. P-219 The role of the putative tumor suppressor protein spinophilin in colorectal cancer. Ann Oncol 2015. [DOI: 10.1093/annonc/mdv233.216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Abstract
Colorectal cancer (CRC) is one of the most common types of human cancer with high cancer-related morbidity and mortality rates. The development and clinical validation of novel therapeutic avenues have improved the clinical outcome, but metastatic CRC still remains an incurable disease in most cases. The interest in discovering novel pathophysiological drivers in CRC is intensively ongoing and the search for novel biomarkers for early diagnosis, for patient's stratification for prognostic purposes or for predicting treatment response are warranted. microRNAs are small RNA molecules that regulate the expression of larger messenger RNA species by different mechanisms with the final consequence to provide a fine tuning tool for global gene expression patterns. First discovered in worms, around 15 years ago it became clear that microRNAs are also existing in humans and that they are widely involved in human carcinogenesis. Within the last years, tremendous progress in the understanding of microRNAs and their role in CRC carcinogenesis has been developed. In this book chapter, several examples of previously identified microRNAs and how they influence colorectal carcinogenesis will be discussed. The information starting at the underlying molecular mechanisms towards clinical applications will be depicted and an overview what great potential these small molecules might carry in future colorectal cancer medicine, will be discussed.
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Affiliation(s)
- Anna Lena Ress
- Division of Oncology, Medical University of Graz, Graz, Austria
| | | | - Martin Pichler
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Stiegelbauer V, Perakis S, Deutsch A, Ling H, Gerger A, Pichler M. MicroRNAs as novel predictive biomarkers and therapeutic targets in colorectal cancer. World J Gastroenterol 2014; 20:11727-11735. [PMID: 25206276 PMCID: PMC4155362 DOI: 10.3748/wjg.v20.i33.11727] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 04/04/2014] [Accepted: 06/05/2014] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is the third most common cancer in western countries. Despite significant improvement in available treatment options, CRC still remains the second leading cause of cancer-related death. Traditionally, 5-fluorouracil has been used as the main chemotherapy drug for treatment of metastatic CRC (mCRC). However, during the last two decades more effective chemotherapeutic agents such as oxaliplatin, irinotecan and the monoclonal antibodies cetuximab, panitumumab and bevacizumab have been used in clinical practice. More recently, the therapeutic armamentarium has been supplemented by the monoclonal antibodies bevacizumab, cetuximab and panitumumab as well as the protein-trap aflibercept and the small molecule multi-kinase inhibitor regorafenib. One of the major problems for the management of CRC is the inherent or acquired resistance to therapeutic approaches. The discovery of microRNAs (miRNAs), a class of small, endogenous, non-coding, single-stranded RNAs that play a role as post-transcriptional regulators, has added new dimensions to the diagnosis and treatment of cancer. Because miRNAs are important regulators of carcinogenesis, progression, invasion, angiogenesis and metastases in CRC, they might serve as potential predictive and prognostic factors and even as therapeutic targets themselves. Several miRNAs are already known to be dysregulated in CRCs and have been linked to biological processes involved in tumor progression and response to anti-cancer therapies. This review summarizes current therapeutic approaches for treating CRC and highlights the role of miRNAs as novel predictive biomarkers and potential drug targets in CRC patients.
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Pitroda SP, Zhou T, Sweis RF, Filippo M, Labay E, Beckett MA, Mauceri HJ, Liang H, Darga TE, Perakis S, Khan SA, Sutton HG, Zhang W, Khodarev NN, Garcia JGN, Weichselbaum RR. Tumor endothelial inflammation predicts clinical outcome in diverse human cancers. PLoS One 2012; 7:e46104. [PMID: 23056240 PMCID: PMC3464251 DOI: 10.1371/journal.pone.0046104] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Accepted: 08/28/2012] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Vascular endothelial cells contribute to the pathogenesis of numerous human diseases by actively regulating the stromal inflammatory response; however, little is known regarding the role of endothelial inflammation in the growth of human tumors and its influence on the prognosis of human cancers. METHODS Using an experimental model of tumor necrosis factor-alpha (TNF-α)-mediated inflammation, we characterized inflammatory gene expression in immunopurified tumor-associated endothelial cells. These genes formed the basis of a multivariate molecular predictor of overall survival that was trained and validated in four types of human cancer. RESULTS We report that expression of experimentally derived tumor endothelial genes distinguished pathologic tissue specimens from normal controls in several human diseases associated with chronic inflammation. We trained these genes in human cancer datasets and defined a six-gene inflammatory signature that predicted significantly reduced overall survival in breast cancer, colon cancer, lung cancer, and glioma. This endothelial-derived signature predicted outcome independently of, but cooperatively with, standard clinical and pathological prognostic factors. Consistent with these findings, conditioned culture media from human endothelial cells stimulated by pro-inflammatory cytokines accelerated the growth of human colon and breast tumors in immunodeficient mice as compared with conditioned media from untreated endothelial cells. CONCLUSIONS This study provides the first prognostic cancer gene signature derived from an experimental model of tumor-associated endothelial inflammation. These findings support the notion that activation of inflammatory pathways in non-malignant tumor-infiltrating endothelial cells contributes to tumor growth and progression in multiple human cancers. Importantly, these results identify endothelial-derived factors that could serve as potential targets for therapy in diverse human cancers.
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Affiliation(s)
- Sean P Pitroda
- Department of Radiation and Cellular Oncology, The University of Chicago, Chicago, Illinois, United States of America
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Xing RH, Lussier YA, Salama JK, Khodarev NN, Huang Y, Zhang Q, Khan SA, Yang X, Hasselle MD, Darga TE, Malik R, Fan H, Perakis S, Filippo M, Corbin K, Lee Y, Posner MC, Chmura SJ, Hellman S, Weichselbaum RR. Abstract 3405: MicroRNA expression characterizes oligometastasis(es). Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-3405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Cancer staging and treatment presumes a division into localized or metastatic disease. We proposed an intermediate state defined by β5 cumulative metastasis(es), termed oligometastases. In contrast to widespread polymetastases, oligometastatic patients may benefit from metastasis-directed local treatments. However, many patients who initially present with oligometastases progress to polymetastases. Predictors of progression could improve patient selection for metastasis-directed therapy. Methods: Here, we identified patterns of microRNA expression of tumor samples from oligometastatic patients treated with high-dose radiotherapy. Results: Patients who failed to develop polymetastases are characterized by unique prioritized features of a microRNA classifier that includes the microRNA-200 family. We created an oligometastatic-polymetastatic xenograft model in which the patient-derived microRNAs discriminated between the two metastatic outcomes. MicroRNA-200c enhancement in an oligometastatic cell line resulted in polymetastatic progression. Conclusions: These results demonstrate a biological basis for oligometastases and a potential for using microRNA expression to identify patients most likely to remain oligometastatic after metastasis-directed treatment.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3405. doi:1538-7445.AM2012-3405
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Gutt R, Liauw S, Beckett M, Liang H, Perakis S, Filippo M, Pitroda S, Darga T, Khodarev N, Weichselbaum R. Statin Therapy for Prostate Cancer: Understudied and Underutilized. Int J Radiat Oncol Biol Phys 2011. [DOI: 10.1016/j.ijrobp.2011.06.1226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Khodarev N, Pitroda S, Sood R, Khan S, Filippo M, Gutt R, Perakis S, Darga T, Malik R, Pederson A, Weichselbaum R. Abstract 573: Ionizing radiation activates IFN signaling in tumor cells. Cancer Res 2011. [DOI: 10.1158/1538-7445.am2011-573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Ionizing radiation (IR) uses multiple pathways to mediate killing in tumor cells. We found that fractionated irradiation leads to the constitutive overexpression of Interferon Stimulated Genes (ISGs) which are controlled by Signal Transducer and Activator of Transcription 1 (Stat1). Stat1 mediated IFN signal transduction and at the same time was involved in the production of Type I and Type II IFNs. IR-induced ISGs represent the following groups: 1) mitochondrial-related genes with pro- and anti-apoptotic functions, 2) cell cycle control and regulators of transcription, 3) protein modification and degradation, 4) cytoplasmic sensors of nucleic acids, and 5) anti-viral defense. Fractionated or single-dose IR induced the IFN pathway mediated by activation of Stat1 in breast, colon, prostate and head and neck tumor xenografts. Depletion of tumor-derived IFNs led to the suppression of IR response indicating that IFN production/signaling is a component of anti-tumor IR action. Cell-autonomous experiments indicated that tumor cells up-regulate Stat1 and ISGs and produce IFNα in response to single dose IR (3Gy). Up-regulated Stat1 in irradiated tumor cells was not phosphorylated at Tyr701 position compared to Stat1 activation following interferon stimulation. In a syngeneic tumor model of B16F1, IR-induced activation of IFN signaling in tumors (assessed both by up-regulation of the Stat1-dependent pathway and induction of Type I and Type II IFNs) was dependent on TNFα signaling in the host and was impaired in TNFR1,2-/- mice. We therefore conclude that IR induces IFN signaling in tumor cells as a component of the cytotoxic response. This interferon induction depends on TNFα signaling in host cells.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 573. doi:10.1158/1538-7445.AM2011-573
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Khodarev NN, Pitroda SP, Wakim BT, Golden DW, Beckett MA, Mauceri HJ, Sutton HG, Perakis S, Malik R, Wietholt C, Pelizzari C, Chen CT, Weichselbaum RR. Abstract 44: STAT1-dependent expression of genes and proteins involved in energy metabolism links tumor growth and radioresistance to the Warburg effect and predicts poor prognosis in cancer patients. Cancer Res 2010. [DOI: 10.1158/1538-7445.am10-44] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Signal Transducer and Activator of Transcription 1 (STAT1) has traditionally been regarded as a transmitter of interferon signaling and a pro-apoptotic tumor suppressor. Recent data have identified new functions of STAT1 associated with tumorigenesis and resistance to genotoxic stress, including ionizing radiation (IR) and chemotherapy. To investigate the mechanisms contributing to the tumorigenic functions of STAT1, we performed a combined transcriptomic-proteomic expressional analysis of tumor xenografts with stable Stat1 knock-down (KD) relative to tumors with wild type (wt) Stat1. We also compared previously described SCC61 and nu61 isologous tumors, where SCC61 is radiosensitive and nu61 is radioresistant counterparts with different expression of IFN/Stat1 pathway. Transcriptional profiling was based on Affymetrix Human GeneChip® Gene 1.0 ST microarrays. Proteomes were determined from the MS/MS data by searching against the human subset of the UniProt database. Knockdown of STAT1 led to significant growth suppression in untreated tumors and radiosensitization of irradiated tumors. These changes were accompanied by alterations in the expression of genes and proteins of glycolysis/gluconeogenesis (GG), the citrate cycle (CC), and oxidative phosphorylation (OP). Of these pathways, GG had the most concordant changes in gene and protein expression and demonstrated a STAT1-dependent expression of genes and proteins consistent with tumor-specific glycolysis. IR drastically suppressed the GG pathway in STAT1 KD tumors without significant change in STAT1 WT tumors. Using 18F-FDG-PET we observed significantly higher glucose uptake in nu61 compared to SCC61 post-irradiation (6Gy). The STAT1 and glycolytic pathways were co-expressed in human breast tumors, and expression of STAT1-linked glycolytic genes was highly predictive of poor prognosis. Our results identify a previously uncharacterized function of STAT1 in tumors: expressional regulation of genes and enzymes involved in glycolysis, the citrate cycle, and mitochondrial oxidative phosphorylation, with predominant regulation of glycolysis. STAT1-dependent transcriptional and translational regulation of glycolysis suggests a potential role for STAT1 as a transcriptional modulator of genes responsible for the Warburg effect.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 44.
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