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Babayan A, Vassilian A, Poladyan A, Trchounian K. Role of the Escherichia coli FocA and FocB formate channels in controlling proton/potassium fluxes and hydrogen production during osmotic stress in energy-limited, stationary phase fermenting cells. Biochimie 2024; 221:91-98. [PMID: 38307245 DOI: 10.1016/j.biochi.2024.01.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/12/2024] [Accepted: 01/30/2024] [Indexed: 02/04/2024]
Abstract
Escherichia coli FocA and FocB formate channels export formate or import it for further disproportionation by the formate hydrogenlyase (FHL) complex to H2 and CO2. Here, we show that under pH and osmotic stress FocA and FocB play important roles in regulating proton and potassium fluxes and couple this with H2 production in stationary-phase cells. Using whole-cell assays with glucose as electron donor, a focB mutant showed a 50 % decrease in VH2, while N'N'-dicyclohexylcarbodiimide (DCCD) treatment of osmotically stressed cells underlined the role of FOF1 ATPase in H2 production. At pH 7.5 and under osmotic stress FocB contributed to the proton flux but not to the potassium flux. At pH 5.5 both formate channels contributed to the proton and potassium fluxes. Particulalry, a focA mutant had 40 % lower potassium flux whereas the proton flux increased approximately two-fold. Moreover, at pH 5.5H2 production was totally inhibited by DCCD in the focA mutant. Taken together, our results suggest that depending on external pH, the formate channels play an important role in osmoregulation by helping to balance proton/potassium fluxes and H2 production, and thus assist the proton FOF1-ATPase in maintenance of ion gradients in fermenting stationary-phase cells.
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Affiliation(s)
- A Babayan
- Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, 0025, Yerevan, Armenia; Research Institute of Biology, Yerevan State University, 0025, Yerevan, Armenia
| | - A Vassilian
- Research Institute of Biology, Yerevan State University, 0025, Yerevan, Armenia.
| | - A Poladyan
- Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, 0025, Yerevan, Armenia; Research Institute of Biology, Yerevan State University, 0025, Yerevan, Armenia.
| | - K Trchounian
- Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, 0025, Yerevan, Armenia; Research Institute of Biology, Yerevan State University, 0025, Yerevan, Armenia; Microbial Biotechnologies and Biofuel Innovation Center, Yerevan State University, 0025, Yerevan, Armenia.
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Rusetsky Y, Meytel I, Mokoyan Z, Fisenko A, Babayan A, Malyavina U. Smell Status in Children Infected with SARS-CoV-2. Laryngoscope 2021; 131:E2475-E2480. [PMID: 33443298 PMCID: PMC8013292 DOI: 10.1002/lary.29403] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/29/2020] [Accepted: 01/06/2021] [Indexed: 12/17/2022]
Abstract
OBJECTIVES/HYPOTHESIS This study aimed to evaluate the olfactory status in children with laboratory confirmed SARS-CoV-2 using subjective and psychophysical methods. STUDY DESIGN Prospective clinical cross-sectional study. METHODS This is a prospective clinical cross-sectional study of 79 children with COVID-19. The 21st item of SNOT-22 questionnaire and odor identification test were used for smell assessment. Children were examined twice during the hospitalization, and a telephone survey was conducted 60 days after hospital discharge. RESULTS Immediately after confirmation of COVID-19, smell impairment was detected in 86.1% of children by means of the Identification test and in 68.4% of children by means of the survey (P = .010). After 5 days survey revealed a statistically significant decrease in the number of patients with hyposmia (41 out of 79, 51.9%). On the first visit, the mean Identification test score corresponded to "hyposmia" (9.5 ± 2.7), while on the second visit, the average value was 13.1 ± 1.9, which corresponded to "normosmia." According to the telephone survey, recovery of the olfactory function occurred within 10 days in 37 of 52 patients (71.2%), 11 to 29 days - in 12 children (23.1%), and later than 30 days - in three cases (5.7%). CONCLUSIONS In the pediatric population, olfactory dysfunction is an early and common symptom of COVID-19. There is a trend to quick recovery of olfactory function in children with COVID-19. The overwhelming majority of patients (94.3%) had no subjective olfactory complaints by the end of the first month. LEVEL OF EVIDENCE 4 Laryngoscope, 131:E2475-E2480, 2021.
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Affiliation(s)
- Yury Rusetsky
- Otorhinolaryngological surgical department with a group of head and neck diseases, National Medical Research Center of Children's Health, Moscow, Russia.,Department of ear, nose and throat diseases, Central State Medical Academy, Moscow, Russia
| | - Irina Meytel
- Otorhinolaryngological surgical department with a group of head and neck diseases, National Medical Research Center of Children's Health, Moscow, Russia
| | - Zhanna Mokoyan
- Department of ear, nose and throat diseases, I.M.Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Andrey Fisenko
- Otorhinolaryngological surgical department with a group of head and neck diseases, National Medical Research Center of Children's Health, Moscow, Russia
| | - Anna Babayan
- Otorhinolaryngological surgical department with a group of head and neck diseases, National Medical Research Center of Children's Health, Moscow, Russia
| | - Ulyana Malyavina
- Otorhinolaryngological surgical department with a group of head and neck diseases, National Medical Research Center of Children's Health, Moscow, Russia
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Lampignano R, Neumann MHD, Weber S, Kloten V, Herdean A, Voss T, Groelz D, Babayan A, Tibbesma M, Schlumpberger M, Chemi F, Rothwell DG, Wikman H, Galizzi JP, Riise Bergheim I, Russnes H, Mussolin B, Bonin S, Voigt C, Musa H, Pinzani P, Lianidou E, Brady G, Speicher MR, Pantel K, Betsou F, Schuuring E, Kubista M, Ammerlaan W, Sprenger-Haussels M, Schlange T, Heitzer E. Multicenter Evaluation of Circulating Cell-Free DNA Extraction and Downstream Analyses for the Development of Standardized (Pre)analytical Work Flows. Clin Chem 2020; 66:149-160. [PMID: 31628139 DOI: 10.1373/clinchem.2019.306837] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 08/05/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND In cancer patients, circulating cell-free DNA (ccfDNA) can contain tumor-derived DNA (ctDNA), which enables noninvasive diagnosis, real-time monitoring, and treatment susceptibility testing. However, ctDNA fractions are highly variable, which challenges downstream applications. Therefore, established preanalytical work flows in combination with cost-efficient and reproducible reference materials for ccfDNA analyses are crucial for analytical validity and subsequently for clinical decision-making. METHODS We describe the efforts of the Innovative Medicines Initiative consortium CANCER-ID (http://www.cancer-id.eu) for comparing different technologies for ccfDNA purification, quantification, and characterization in a multicenter setting. To this end, in-house generated mononucleosomal DNA (mnDNA) from lung cancer cell lines carrying known TP53 mutations was spiked in pools of plasma from healthy donors generated from 2 different blood collection tubes (BCTs). ccfDNA extraction was performed at 15 partner sites according to their respective routine practice. Downstream analysis of ccfDNA with respect to recovery, integrity, and mutation analysis was performed centralized at 4 different sites. RESULTS We demonstrate suitability of mnDNA as a surrogate for ccfDNA as a process quality control from nucleic acid extraction to mutation detection. Although automated extraction protocols and quantitative PCR-based quantification methods yielded the most consistent and precise results, some kits preferentially recovered spiked mnDNA over endogenous ccfDNA. Mutated TP53 fragments derived from mnDNA were consistently detected using both next-generation sequencing-based deep sequencing and droplet digital PCR independently of BCT. CONCLUSIONS This comprehensive multicenter comparison of ccfDNA preanalytical and analytical work flows is an important contribution to establishing evidence-based guidelines for clinically feasible (pre)analytical work flows.
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Affiliation(s)
| | | | - Sabrina Weber
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria.,Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Graz, Austria
| | - Vera Kloten
- Bayer AG, Biomarker Research, Wuppertal, Germany
| | | | | | | | - Anna Babayan
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marco Tibbesma
- University of Groningen, University Medical Center of Groningen, Groningen, the Netherlands
| | | | - Francesca Chemi
- CR-UK Manchester Institute, University of Manchester, Manchester, UK
| | | | - Harriet Wikman
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Inger Riise Bergheim
- Department of Cancer Genetics, Institute of Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Hege Russnes
- Department of Cancer Genetics, Institute of Cancer Research, Oslo University Hospital, Oslo, Norway
| | | | - Serena Bonin
- University of Trieste, DSM-Cattinara Hospital, Trieste, Italy
| | | | - Hanny Musa
- Boehringer-Ingelheim, Ingelheim am Rhein, Germany
| | | | | | - Ged Brady
- CR-UK Manchester Institute, University of Manchester, Manchester, UK
| | - Michael R Speicher
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Klaus Pantel
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Fay Betsou
- Integrated BioBank of Luxembourg, Dudelange, Luxembourg
| | - Ed Schuuring
- University of Groningen, University Medical Center of Groningen, Groningen, the Netherlands
| | | | - Wim Ammerlaan
- Integrated BioBank of Luxembourg, Dudelange, Luxembourg
| | | | | | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria.,Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Graz, Austria
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Provencher E, Remmel M, Hauch S, Otte M, Ullius A, Groelz D, Babayan A. Abstract PR11: Multimodal analysis of circulating tumor cell RNA, circulating cell-free DNA, and genomic DNA from a single blood sample collected into a PAXgene Blood ccfDNA Tube*. Clin Cancer Res 2020. [DOI: 10.1158/1557-3265.liqbiop20-pr11] [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: High demand for liquid biopsy tests in cancer research increases the need for combined approaches that allow multimodal testing from a limited blood volume. Although crosslinking-based fixatives allow for efficient preservation of the circulating cell-free DNA (ccfDNA) profile in whole blood, analysis of mRNA from circulating tumor cells (CTCs) is hampered. Currently, there are no blood collection tubes available that allow RNA analysis from CTCs after prolonged (>48 hours) storage. In this research study, we present a newly developed combined workflow for blood stabilization and subsequent analysis of CTC RNA, ccfDNA, and gDNA after prolonged (≥72 hours) storage.
Methods: To establish the multimodal workflow, blood was collected from healthy donors into PAXgene Blood ccfDNA Tubes*, aliquoted and manually spiked with 20 individual LNCaP95 cells/5 mL blood as a CTC model or 20 µL PBS as a control. Blood samples were spiked and stored at 2–8°C for 3, 24, 48, and 72 hours before processing. CTCs were enriched and detected using the AdnaTest ProstateCancerPanel AR-V7† (QIAGEN). The plasma and cellular fraction of the CTC-depleted blood was then used to extract ccfDNA and gDNA, respectively. As a control for ccfDNA and gDNA yield measurements, plasma and the cellular fraction were also generated from whole samples (not CTC-depleted) spiked with 20 LNCaP95 cells/5 mL. The resulting multimodal workflow was tested: 1) in comparison to Streck Cell-Free DNA BCT; 2) to assess the impact of room temperature.
Results: Tumor cells spiked into PAXgene Blood ccfDNA Tubes could be enriched and detected at experimental time points 3, 24, 48, and 72 hours after spiking with 100% test sensitivity within 24 hours storage and 91% test sensitivity after 72 hours storage at 2–8°C. In unspiked samples, the PAXgene stabilization solution did not cause false positive signals at any experimental time point. Yields of ccfDNA and gDNA were not statistically significantly affected by CTC capture (p>0.05). RNA from spiked tumor cells was detected in blood samples collected and stored in Streck Cell-Free DNA BCTs for 3 hours, but not at later time points. Storage of PAXgene stabilization solution-treated samples at room temperature is feasible, with 100% test sensitivity for CTC detection within 24 hours storage (similar to storage at 2–8°C) and 80% after 72 hours storage.
Conclusions: Blood collected into PAXgene Blood ccfDNA Tubes and stored for up to 72 hours at 2–8°C or at room temperature can be used for multimodal analysis of CTC RNA, ccfDNA, and gDNA from a single blood sample.
*For research use only. Not for use in diagnostic procedures.
†For molecular biology applications. Not intended for the diagnosis, prevention, or treatment of a disease.
This abstract is also being presented as Poster B18.
Citation Format: Eric Provencher, Maike Remmel, Siegfried Hauch, Michael Otte, Andrea Ullius, Daniel Groelz, Anna Babayan. Multimodal analysis of circulating tumor cell RNA, circulating cell-free DNA, and genomic DNA from a single blood sample collected into a PAXgene Blood ccfDNA Tube* [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr PR11.
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Babayan A, Neumann MHD, Herdean A, Shaffer JM, Janning M, Kobus F, Loges S, Di Pasquale F, Kubista M, Schlumpberger M, Lampignano R, Krahn T, Schlange T, Sprenger-Haussels M, Pantel K, Kloten V. Multicenter Evaluation of Independent High-Throughput and RT-qPCR Technologies for the Development of Analytical Workflows for Circulating miRNA Analysis. Cancers (Basel) 2020; 12:cancers12051166. [PMID: 32380788 PMCID: PMC7281602 DOI: 10.3390/cancers12051166] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/01/2020] [Accepted: 05/02/2020] [Indexed: 01/08/2023] Open
Abstract
Background: Among emerging circulating biomarkers, miRNA has the potential to detect lung cancer and follow the course of the disease. However, miRNA analysis deserves further standardization before implementation into clinical trials or practice. Here, we performed international ring experiments to explore (pre)-analytical factors relevant to the outcome of miRNA blood tests in the context of the EU network CANCER-ID. Methods: Cell-free (cfmiRNA) and extracellular vesicle-derived miRNA (EVmiRNA) were extracted using the miRNeasy Serum/Plasma Advanced, and the ExoRNeasy Maxi kit, respectively, in a plasma cohort of 27 NSCLC patients and 20 healthy individuals. Extracted miRNA was investigated using small RNA sequencing and hybridization platforms. Validation of the identified miRNA candidates was performed using quantitative PCR. Results: We demonstrate the highest read counts in healthy individuals and NSCLC patients using QIAseq. Moreover, QIAseq showed 15.9% and 162.9% more cfmiRNA and EVmiRNA miRNA counts, respectively, in NSCLC patients compared to healthy control samples. However, a systematic comparison of selected miRNAs revealed little agreement between high-throughput platforms, thus some miRNAs are detected with one technology, but not with the other. Adding to this, 35% (9 of 26) of selected miRNAs in the cfmiRNA and 42% (11 of 26) in the EVmiRNA fraction were differentially expressed by at least one qPCR platform; about half of the miRNAs (54%) were concordant for both platforms. Conclusions: Changing of (pre)-analytical methods of miRNA analysis has a significant impact on blood test results and is therefore a major confounding factor. In addition, to confirm miRNA biomarker candidates screening studies should be followed by targeted validation using an independent platform or technology.
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Affiliation(s)
- Anna Babayan
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (A.B.); (M.J.); (F.K.); (S.L.); (K.P.)
| | | | - Andrei Herdean
- TATAA Biocenter AB, 411 03 Gothenburg, Sweden; (A.H.); (M.K.)
| | | | - Melanie Janning
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (A.B.); (M.J.); (F.K.); (S.L.); (K.P.)
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Franca Kobus
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (A.B.); (M.J.); (F.K.); (S.L.); (K.P.)
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Sonja Loges
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (A.B.); (M.J.); (F.K.); (S.L.); (K.P.)
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- Division of Personalized Medical Oncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Personalized Oncology, University Hospital Mannheim, 68167 Mannheim, Germany
| | | | - Mikael Kubista
- TATAA Biocenter AB, 411 03 Gothenburg, Sweden; (A.H.); (M.K.)
| | | | - Rita Lampignano
- Bayer AG, Pharmaceutical Division, Precision Medicine Markers, 42096 Wuppertal, Germany; (R.L.); (T.K.); (T.S.)
| | - Thomas Krahn
- Bayer AG, Pharmaceutical Division, Precision Medicine Markers, 42096 Wuppertal, Germany; (R.L.); (T.K.); (T.S.)
| | - Thomas Schlange
- Bayer AG, Pharmaceutical Division, Precision Medicine Markers, 42096 Wuppertal, Germany; (R.L.); (T.K.); (T.S.)
| | | | - Klaus Pantel
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (A.B.); (M.J.); (F.K.); (S.L.); (K.P.)
| | - Vera Kloten
- Bayer AG, Pharmaceutical Division, Precision Medicine Markers, 42096 Wuppertal, Germany; (R.L.); (T.K.); (T.S.)
- Correspondence:
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Liu H, Koch C, Haller A, Joosse SA, Kumar R, Vellekoop MJ, Horst LJ, Keller L, Babayan A, Failla AV, Jensen J, Peine S, Keplinger F, Fuchs H, Pantel K, Hirtz M. Evaluation of Microfluidic Ceiling Designs for the Capture of Circulating Tumor Cells on a Microarray Platform. ACTA ACUST UNITED AC 2019; 4:e1900162. [DOI: 10.1002/adbi.201900162] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 11/26/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Hui‐Yu Liu
- Institute of Nanotechnology (INT) and Karlsruhe Nano Micro Facility (KNMF)Karlsruhe Institute of Technology (KIT) 76344 Eggenstein‐Leopoldshafen Germany
| | - Claudia Koch
- Department of Tumor BiologyUniversity Medical Center Hamburg‐Eppendorf 20246 Hamburg Germany
| | - Anna Haller
- Institute of Sensor and Actuator SystemsTU Wien 1040 Vienna Austria
| | - Simon A. Joosse
- Department of Tumor BiologyUniversity Medical Center Hamburg‐Eppendorf 20246 Hamburg Germany
| | - Ravi Kumar
- Institute of Nanotechnology (INT) and Karlsruhe Nano Micro Facility (KNMF)Karlsruhe Institute of Technology (KIT) 76344 Eggenstein‐Leopoldshafen Germany
| | - Michael J. Vellekoop
- Institute for MicrosensorsMicroactuators and Microsystems (IMSAS)Microsystems Center Bremen MCBUniversity of Bremen 28359 Bremen Germany
| | - Ludwig J. Horst
- Department of Tumor BiologyUniversity Medical Center Hamburg‐Eppendorf 20246 Hamburg Germany
| | - Laura Keller
- Department of Tumor BiologyUniversity Medical Center Hamburg‐Eppendorf 20246 Hamburg Germany
| | - Anna Babayan
- Department of Tumor BiologyUniversity Medical Center Hamburg‐Eppendorf 20246 Hamburg Germany
| | - Antonio Virgilio Failla
- Microscopy Imaging Facility (UMIF)University Medical Center Hamburg‐Eppendorf 20246 Hamburg Germany
| | - Jana Jensen
- Department of Tumor BiologyUniversity Medical Center Hamburg‐Eppendorf 20246 Hamburg Germany
| | - Sven Peine
- Department of Transfusion MedicineUniversity Medical Center Hamburg‐Eppendorf 20246 Hamburg Germany
| | - Franz Keplinger
- Institute of Sensor and Actuator SystemsTU Wien 1040 Vienna Austria
| | - Harald Fuchs
- Institute of Nanotechnology (INT) and Karlsruhe Nano Micro Facility (KNMF)Karlsruhe Institute of Technology (KIT) 76344 Eggenstein‐Leopoldshafen Germany
- Physical Institute and Center for Nanotechnology (CeNTech)University of Münster 48149 Münster Germany
| | - Klaus Pantel
- Department of Tumor BiologyUniversity Medical Center Hamburg‐Eppendorf 20246 Hamburg Germany
| | - Michael Hirtz
- Institute of Nanotechnology (INT) and Karlsruhe Nano Micro Facility (KNMF)Karlsruhe Institute of Technology (KIT) 76344 Eggenstein‐Leopoldshafen Germany
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Lampignano R, Neumann M, Kloten V, Kessler N, Babayan A, Keller L, Stevic I, Pantel K, Krahn T, Schlange T. Abstract 3985: Dynamic changes of tumor-derived extracellular vesicles and related RNAs in blood samples of NSCLC patients. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-3985] [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
Liquid biopsy is defined as molecular analysis of rare cells or cell-free nucleic acids circulating in blood or in other biofluids. The concept of liquid biopsy aims at closely monitoring the status of a disease or treatment efficacy in a simple, fast, cost efficient way and at any point in time with minimal risk and burden for the patient. It has been suggested that the most reproducible approach to investigate “liquid” mRNAs would be to focus on cell-free extracellular vesicle (EV)-transcripts rather than on circulating cell-free mRNAs, as the former are well protected from degradation and therefore more stable. However, the volumes of available blood samples can be limiting for molecular analysis and rare cells as well as cell-free nucleic acids are normally present in low abundance. Therefore, detection of rare events or quantification of limited material requires robust, highly sensitive technologies like droplet digital PCR (ddPCR).
In this pilot study, we investigated the absolute expression of 10 EV-transcripts typically involved in cancer development and chemotherapy resistance in longitudinal serum samples of 13 non-small cell lung cancer (NSCLC) patients (age range 37-76 years) treated with cisplatin at the Department of Inner Medicine II, University of Ulm, between May 2011 and August 2012.
Blood samples were collected at baseline, after 3-6 months and after 9-12 months of chemotherapy from patients showing objective clinical response. Then, EV-RNAs were isolated by sequentially processing obtained serum samples with miRCURY® exosome kit and miRNeasy kit (both Qiagen, Hilden, Germany). Afterwards, the status of selected EV-transcripts was investigated via ddPCR (Biorad, Milan, Italy).
After start of chemotherapy, we observed a downregulation of at least 2-fold of the following potentially cancer-related EV-transcripts : PTEN, ERBB2, FOSL1, IL-8, MET, RPS27A, SF3B1 and of the following housekeeping EV-mRNAs: ACTB, HIST1H3H and HSPA1A, in all patients. Interestingly, in none of patients' samples, the expression of EV-AKT1 and of EV-PD-L1 transcripts could be detected.
Our preliminary results demonstrates significant dynamic changes of cancer-related EV-mRNA expression in serum samples of NSCLC patients during cisplatin treatment, thus suggesting a potential overall decrease of EVs in response to chemotherapy. Moreover, despite the small amounts of mRNA in extracellular vesicles from patient blood, using ddPCR differential mRNA levels could be determined in patient serum and expand the scope of biomarker analysis of EVs.
This work is supported by IMI JU & EFPIA (grand no. 115749, CANCER-ID). Samples from patients and healthy volunteers, respectively, were collected under signed informed consent.
Citation Format: Rita Lampignano, Martin Neumann, Vera Kloten, Nina Kessler, Anna Babayan, Laura Keller, Ines Stevic, Klaus Pantel, Thomas Krahn, Thomas Schlange, for the IMI CANCER-ID consortium. Dynamic changes of tumor-derived extracellular vesicles and related RNAs in blood samples of NSCLC patients [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 3985.
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Affiliation(s)
| | | | | | | | | | - Laura Keller
- 3University Cancer Center Hamburg/Eppendorf, Hamburg, Germany
| | - Ines Stevic
- 3University Cancer Center Hamburg/Eppendorf, Hamburg, Germany
| | - Klaus Pantel
- 3University Cancer Center Hamburg/Eppendorf, Hamburg, Germany
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Ricklefs FL, Maire CL, Reimer R, Dührsen L, Kolbe K, Holz M, Schneider E, Rissiek A, Babayan A, Hille C, Pantel K, Krasemann S, Glatzel M, Heiland DH, Flitsch J, Martens T, Schmidt NO, Peine S, Breakefield XO, Lawler S, Chiocca EA, Fehse B, Giebel B, Görgens A, Westphal M, Lamszus K. Imaging flow cytometry facilitates multiparametric characterization of extracellular vesicles in malignant brain tumours. J Extracell Vesicles 2019; 8:1588555. [PMID: 30949309 PMCID: PMC6442086 DOI: 10.1080/20013078.2019.1588555] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 02/15/2019] [Accepted: 02/21/2019] [Indexed: 01/08/2023] Open
Abstract
Cells release heterogeneous nano-sized vesicles either as exosomes, being derived from endosomal compartments, or through budding from the plasma membrane as so-called microvesicles, commonly referred to as extracellular vesicles (EVs). EVs are known for their important roles in mammalian physiology and disease pathogenesis and provide a potential biomarker source in cancer patients. EVs are generally often analysed in bulk using Western blotting or by bead-based flow-cytometry or, with limited parameters, through nanoparticle tracking analysis. Due to their small size, single EV analysis is technically highly challenging. Here we demonstrate imaging flow cytometry (IFCM) to be a robust, multiparametric technique that allows analysis of single EVs and the discrimination of distinct EV subpopulations. We used IFCM to analyse the tetraspanin (CD9, CD63, CD81) surface profiles on EVs from human and murine cell cultures as well as plasma samples. The presence of EV subpopulations with specific tetraspanin profiles suggests that EV-mediated cellular responses are tightly regulated and dependent on cell environment. We further demonstrate that EVs with double positive tetraspanin expression (CD63+/CD81+) are enriched in cancer cell lines and patient plasma samples. In addition, we used IFCM to detect tumour-specific GFP-labelled EVs in the blood of mice bearing syngeneic intracerebral gliomas, indicating that this technique allows unprecedented disease modelling. In summary, our study highlights the heterogeneous and adaptable nature of EVs according to their marker profile and demonstrates that IFCM facilitates multiparametric phenotyping of EVs not only in vitro but also in patient plasma at a single EV level, with the potential for future functional studies and clinically relevant applications. Abbreviation: EDTA = ethylenediamine tetraacetic acid.
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Affiliation(s)
- Franz L. Ricklefs
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Cecile L. Maire
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Rudolph Reimer
- Leibnitz Institute for Experimental Virology, Heinrich-Pette-Institut, Hamburg, Germany
| | - Lasse Dührsen
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katharina Kolbe
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mareike Holz
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Enja Schneider
- Institute for Diagnostics and Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anne Rissiek
- Institute for Diagnostics and Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anna Babayan
- Department for Tumour Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Claudia Hille
- Department for Tumour Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Klaus Pantel
- Department for Tumour Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Susanne Krasemann
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Markus Glatzel
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Dieter Henrik Heiland
- Department of Neurosurgery, Medical Center University of Freiburg, Freiburg, Germany
| | - Jörg Flitsch
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tobias Martens
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nils Ole Schmidt
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sven Peine
- Institute of Transfusion Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Xandra O. Breakefield
- Molecular Neurogenetics Unit, Massachusetts General Hospital-East, Harvard Medical School, Boston, USA
| | - Sean Lawler
- Harvey Cushing Neurooncology Laboratories, Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, USA
| | - E. Antonio. Chiocca
- Harvey Cushing Neurooncology Laboratories, Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, USA
| | - Boris Fehse
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, Hamburg, Gemany
| | - Bernd Giebel
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - André Görgens
- Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institutet, Stockholm, Sweden
- Evox Therapeutics Limited, Oxford, UK
| | - Manfred Westphal
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katrin Lamszus
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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9
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Kumral D, Schaare HL, Beyer F, Reinelt J, Uhlig M, Liem F, Lampe L, Babayan A, Reiter A, Erbey M, Roebbig J, Loeffler M, Schroeter ML, Husser D, Witte AV, Villringer A, Gaebler M. The age-dependent relationship between resting heart rate variability and functional brain connectivity. Neuroimage 2018; 185:521-533. [PMID: 30312808 DOI: 10.1016/j.neuroimage.2018.10.027] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 10/05/2018] [Accepted: 10/09/2018] [Indexed: 12/30/2022] Open
Abstract
Resting heart rate variability (HRV), an index of parasympathetic cardioregulation and an individual trait marker related to mental and physical health, decreases with age. Previous studies have associated resting HRV with structural and functional properties of the brain - mainly in cortical midline and limbic structures. We hypothesized that aging affects the relationship between resting HRV and brain structure and function. In 388 healthy subjects of three age groups (140 younger: 26.0 ± 4.2 years, 119 middle-aged: 46.3 ± 6.2 years, 129 older: 66.9 ± 4.7 years), gray matter volume (GMV, voxel-based morphometry) and resting state functional connectivity (eigenvector centrality mapping and exploratory seed-based functional connectivity) were related to resting HRV, measured as the root mean square of successive differences (RMSSD). Confirming previous findings, resting HRV decreased with age. For HRV-related GMV, there were no statistically significant differences between the age groups, nor similarities across all age groups. In whole-brain functional connectivity analyses, we found an age-dependent association between resting HRV and eigenvector centrality in the bilateral ventromedial prefrontal cortex (vmPFC), driven by the younger adults. Across all age groups, HRV was positively correlated with network centrality in the bilateral posterior cingulate cortex. Seed-based functional connectivity analysis using the vmPFC cluster revealed an HRV-related cortico-cerebellar network in younger but not in middle-aged or older adults. Our results indicate that the decrease of HRV with age is accompanied by changes in functional connectivity along the cortical midline. This extends our knowledge of brain-body interactions and their changes over the lifespan.
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Affiliation(s)
- D Kumral
- Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany; MindBrainBody Institute at the Berlin School of Mind and Brain, Humboldt-Universitaet zu Berlin, Berlin, Germany.
| | - H L Schaare
- Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany; International Max Planck Research School NeuroCom, Leipzig, Germany
| | - F Beyer
- Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany; Subproject A1, Collaborative Research Centre 1052 "Obesity Mechanisms", University of Leipzig, Leipzig, Germany
| | - J Reinelt
- Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - M Uhlig
- Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany; International Max Planck Research School NeuroCom, Leipzig, Germany
| | - F Liem
- Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - L Lampe
- Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - A Babayan
- Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - A Reiter
- Lifespan Developmental Neuroscience, Technical University of Dresden, Dresden, Germany; Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - M Erbey
- MindBrainBody Institute at the Berlin School of Mind and Brain, Humboldt-Universitaet zu Berlin, Berlin, Germany
| | - J Roebbig
- Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - M Loeffler
- LIFE - Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - M L Schroeter
- Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany; LIFE - Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany; Department of Cognitive Neurology, University of Leipzig, Leipzig, Germany
| | - D Husser
- Department of Electrophysiology, Leipzig Heart Centre, University of Leipzig, Leipzig, Germany
| | - A V Witte
- Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - A Villringer
- Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany; MindBrainBody Institute at the Berlin School of Mind and Brain, Humboldt-Universitaet zu Berlin, Berlin, Germany; Subproject A1, Collaborative Research Centre 1052 "Obesity Mechanisms", University of Leipzig, Leipzig, Germany; LIFE - Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany; Center for Stroke Research Berlin, Charité - Universitaetsmedizin Berlin, Berlin, Germany
| | - M Gaebler
- Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany; MindBrainBody Institute at the Berlin School of Mind and Brain, Humboldt-Universitaet zu Berlin, Berlin, Germany; LIFE - Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
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10
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Joosse SA, Souche FR, Babayan A, Gasch C, Kerkhoven RM, Ramos J, Fabre JM, Riethdorf S, König A, Wikman H, Alix-Panabières C, Pantel K. Chromosomal Aberrations Associated with Sequential Steps of the Metastatic Cascade in Colorectal Cancer Patients. Clin Chem 2018; 64:1505-1512. [PMID: 30030273 DOI: 10.1373/clinchem.2018.289819] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 07/02/2018] [Indexed: 02/02/2023]
Abstract
BACKGROUND Genomic information can help to identify colorectal tumors with high and low metastatic potential, thereby improving prediction of benefit of local and/or systemic treatment. Here we investigated chromosomal aberrations in relation to the different stages of the metastatic cascade: dissemination of tumor cells into the mesenteric vein, metastatic outgrowth in the liver, intravasation of the peripheral blood circulation, and development of further distant metastasis. METHODS Peripheral and mesenteric blood from colorectal cancer patients (n = 72) were investigated for circulating tumor cells, and DNA extracted from their primary tumors was subjected to array comparative genomic hybridization profiling. The results were validated with an independent set of primary colorectal tumors (n = 53) by quantitative reverse transcription PCR. RESULTS Mesenteric intravasation and liver metastasis were correlated with losses of chromosomes 16p (72%), 16q (27%), and 19 (54%), gain along 1q31 (45%) and 20q (60%), tumor cell infiltration into the peripheral blood circulation, and further distant metastasis with gain of chromosome 8q (59%) and 12 (47%, P < 0.01). Chromosome 12 gain was associated with poor overall survival in the initial (2.8 vs >7 years) and validation cohort (3.3 vs >6 years). The prospective study presented here is a hypothesis-generating study and confirmation with larger cohorts is required. CONCLUSIONS This is the first study that investigated colorectal cancer in its different stages of metastasis in correlation with copy number changes of the primary tumor. This information might be helpful to identify patients with limited metastatic spread who may profit from liver metastasis resection and may lead to the discovery of new therapeutic targets.Microarray data have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE82228.
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Affiliation(s)
- Simon A Joosse
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - François-Régis Souche
- Department of Digestive Surgery, University Medical Center Montpellier, Montpellier, France
| | - Anna Babayan
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christin Gasch
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ron M Kerkhoven
- Genomics Core Facility, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Jeanne Ramos
- Laboratory of Pathology, University Medical Center Montpellier, Montpellier, France
| | - Jean-Michel Fabre
- Department of Digestive Surgery, University Medical Center Montpellier, Montpellier, France
| | - Sabine Riethdorf
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Alexandra König
- Department of General, Visceral, and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Harriet Wikman
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Catherine Alix-Panabières
- Laboratory of Rare Human Circulating Cells, Department of Pathology and Oncobiology, University Medical Centre Montpellier, University of Montpellier EA2415 - Help for personalized Decision: Methodological Aspects, Montpellier, France
| | - Klaus Pantel
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany;
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11
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Abstract
Progress in sensitive analytical approaches has opened new avenues for the detection of cells or products such as circulating cell-free DNA released by tumors. These ‘liquid biopsies’ are being explored in clinical trials for early cancer detection, prediction of recurrent disease, and assessment of therapeutic resistance mechanisms.
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Affiliation(s)
- Anna Babayan
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany.
| | - Klaus Pantel
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany.
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12
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Schütze A, Vogeley C, Gorges T, Twarock S, Butschan J, Babayan A, Klein D, Knauer SK, Metzen E, Müller V, Jendrossek V, Pantel K, Milde-Langosch K, Fischer JW, Röck K. RHAMM splice variants confer radiosensitivity in human breast cancer cell lines. Oncotarget 2017; 7:21428-40. [PMID: 26870892 PMCID: PMC5008296 DOI: 10.18632/oncotarget.7258] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 01/20/2016] [Indexed: 11/25/2022] Open
Abstract
Biomarkers for prognosis in radiotherapy-treated breast cancer patients are urgently needed and important to stratify patients for adjuvant therapies. Recently, a role of the receptor of hyaluronan-mediated motility (RHAMM) has been suggested for tumor progression. Our aim was (i) to investigate the prognostic value of RHAMM in breast cancer and (ii) to unravel its potential function in the radiosusceptibility of breast cancer cells. We demonstrate that RHAMM mRNA expression in breast cancer biopsies is inversely correlated with tumor grade and overall survival. Radiosusceptibility in vitro was evaluated by sub-G1 analysis (apoptosis) and determination of the proliferation rate. The potential role of RHAMM was addressed by short interfering RNAs against RHAMM and its splice variants. High expression of RHAMMv1/v2 in p53 wild type cells (MCF-7) induced cellular apoptosis in response to ionizing radiation. In comparison, in p53 mutated cells (MDA-MB-231) RHAMMv1/v2 was expressed sparsely resulting in resistance towards irradiation induced apoptosis. Proliferation capacity was not altered by ionizing radiation in both cell lines. Importantly, pharmacological inhibition of the major ligand of RHAMM, hyaluronan, sensitized both cell lines towards radiation induced cell death. Based on the present data, we conclude that the detection of RHAMM splice variants in correlation with the p53 mutation status could help to predict the susceptibility of breast cancer cells to radiotherapy. Additionally, our studies raise the possibility that the response to radiotherapy in selected cohorts may be improved by pharmaceutical strategies against RHAMM and its ligand hyaluronan.
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Affiliation(s)
- Alexandra Schütze
- Institut für Pharmakologie und Klinische Pharmakologie, Universitätsklinikum der Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Christian Vogeley
- Institut für Pharmakologie und Klinische Pharmakologie, Universitätsklinikum der Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Tobias Gorges
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sören Twarock
- Institut für Pharmakologie und Klinische Pharmakologie, Universitätsklinikum der Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Jonas Butschan
- Institut für Pharmakologie und Klinische Pharmakologie, Universitätsklinikum der Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Anna Babayan
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Diana Klein
- Institute of Cell Biology (Cancer Research), University Hospital, University of Duisburg-Essen, Essen, Germany
| | - Shirley K Knauer
- Institute for Molecular Biology II, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Eric Metzen
- Institute of Physiology, Faculty of Medicine, University Duisburg-Essen, Essen, Germany
| | - Volkmar Müller
- Department of Gynecology, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Verena Jendrossek
- Institute of Cell Biology (Cancer Research), University Hospital, University of Duisburg-Essen, Essen, Germany
| | - Klaus Pantel
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Karin Milde-Langosch
- Department of Gynecology, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Jens W Fischer
- Institut für Pharmakologie und Klinische Pharmakologie, Universitätsklinikum der Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Katharina Röck
- Institut für Pharmakologie und Klinische Pharmakologie, Universitätsklinikum der Heinrich-Heine-Universität, Düsseldorf, Germany
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13
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Joosse SA, Babayan A, Prieske K, Indenbirken D, Alawi M, Burandt EC, Grundhoff A, Müller V, Pantel K. Abstract 2421: Circulating tumor cells reveal the genetic evolution of metastatic breast cancer. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-2421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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. Anti-cancer treatment failure is caused by the genetic and phenotypic heterogeneous properties of the disease. Early dissemination of circulating tumor cells (CTCs) into the blood circulation of cancer patients allows for parallel genetic evolution of the primary tumor and metastases. This study investigated the genomic make-up of CTCs originating from metastasis as a so called “liquid biopsy” and compared these with the different clones of the archived autologous primary tumor on single cell level.
METHODS. From two breast cancer patients, individual CTCs were isolated from blood using Ficoll density gradient followed by micromanipulation of keratin positive cells. Single cells from archived primary breast tumors from the same patients were captured by laser microdissection. DNA was isolated and amplified by whole genome amplification and copy number alterations (CNA) were obtained by shallow, whole genome next generations sequencing (NGS).
RESULTS. From the first breast cancer patient, the genomes from 50 single cells from the primary tumor were sequenced. An unsupervised phylogenetic cluster analysis based on CNA revealed five distinct subclones that displayed increasing chromosomal instability from the first to the last cluster. Using support vector machine (SVM) learning, the CNA profiles of 42 CTCs were residing mostly to the first three clones with few chromosomal aberrations, whereas only one CTC resided to the fourth clone and none to the last with many chromosomal aberrations. The tumor from a second breast cancer patient displayed the presence of three genetically distinct clones with increasing chromosomal instability after sequencing 11 single cells. CTCs (n = 12) from this patient at metastatic disease were classified to the last branch using SVM, however with low probability. After repeating unsupervised clustering on the genomes of the primary tumor tissue and CTCs, a fourth branch was formed with CTCs only.
CONCLUSION. Our results suggest that therapy resistant metastases in breast cancer patients can originate from tumor clones from early stages of tumor evolution and may genetically still be similar (patient 1). On the other hand, further genetic progression may also take place (patient 2) after which the genetic landscape of the metastasis does not resemble the primary tumor anymore. These results underline the importance of “liquid biopsy” in the diagnosis of metastatic cancer.
Citation Format: Simon A. Joosse, Anna Babayan, Katharina Prieske, Daniela Indenbirken, Malik Alawi, Eike C. Burandt, Adam Grundhoff, Volkmar Müller, Klaus Pantel. Circulating tumor cells reveal the genetic evolution of metastatic breast cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2421.
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Affiliation(s)
- Simon A. Joosse
- 1University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anna Babayan
- 1University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | | | - Malik Alawi
- 1University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Eike C. Burandt
- 1University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Adam Grundhoff
- 2Heinrich-Pette-Institute for Experimental Virology, Hamburg, Germany
| | - Volkmar Müller
- 1University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Klaus Pantel
- 1University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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14
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Babayan A, Hannemann J, Spötter J, Müller V, Pantel K, Joosse SA. Heterogeneity of estrogen receptor expression in circulating tumor cells from metastatic breast cancer patients. PLoS One 2013; 8:e75038. [PMID: 24058649 PMCID: PMC3776726 DOI: 10.1371/journal.pone.0075038] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 08/06/2013] [Indexed: 02/07/2023] Open
Abstract
Background Endocrine treatment is the most preferable systemic treatment in metastatic breast cancer patients that have had an estrogen receptor (ER) positive primary tumor or metastatic lesions, however, approximately 20% of these patients do not benefit from the therapy and demonstrate further metastatic progress. One reason for failure of endocrine therapy might be the heterogeneity of ER expression in tumor cells spreading from the primary tumor to distant sites which is reflected in detectable circulating tumor cells (CTCs). Methods A sensitive and specific staining protocol for ER, keratin 8/18/19, CD45 was established. Peripheral blood from 35 metastatic breast cancer patients with ER-positive primary tumors was tested for the presence of CTCs. Keratin 8/18/19 and DAPI positive but CD45 negative cells were classified as CTCs and evaluated for ER staining. Subsequently, eight individual CTCs from four index patients (2 CTCs per patient) were isolated and underwent whole genome amplification and ESR1 gene mutation analysis. Results CTCs were detected in blood of 16 from 35 analyzed patients (46%), with a median of 3 CTCs/7.5 ml. In total, ER-negative CTCs were detected in 11/16 (69%) of the CTC positive cases, including blood samples with only ER-negative CTCs (19%) and samples with both ER-positive and ER-negative CTCs (50%). No correlation was found between the intensity and/or percentage of ER staining in the primary tumor with the number and ER status of CTCs of the same patient. ESR1 gene mutations were not found. Conclusion CTCs frequently lack ER expression in metastatic breast cancer patients with ER-positive primary tumors and show a considerable intra-patient heterogeneity, which may reflect a mechanism to escape endocrine therapy. Provided single cell analysis did not support a role of ESR1 mutations in this process.
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Affiliation(s)
- Anna Babayan
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Juliane Hannemann
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julia Spötter
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Volkmar Müller
- Department of Gynecology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Klaus Pantel
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- * E-mail: (SAJ); (KP)
| | - Simon A. Joosse
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- * E-mail: (SAJ); (KP)
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15
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Abstract
The purpose of this study was to assess the epidemiology and some of the possible risk factors causing oral cleft in Tehran. The study was a 7-year retrospective study from March 1998 to March 2005. Twenty-five live births with cleft lip and/or palate (CL+/-P) were born between 20 March 1998 and 20 March 2005 from the total of 11,651 live births in a maternity hospital in Tehran. After recognizing the child as a cleft patient, previous and following children born were recognized as a noncleft sample. Cleft and noncleft samples were compared for variables such as gender, mother's age, parity, consanguineous marriage and infant's weight, and then analyzed with Chi-square. The overall incidence was 2.14 per 1000 live births. CL+ P is more prevalent, which was 52% and the least incidence was for "only cleft lip'' patients, which was 12%. This study reveals that the incidence of oral clefts in Tehran is higher than many other countries. Consanguineous marriage and low birth weight in cleft group were significant statistically from those of noncleft group.
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Affiliation(s)
- A Jamilian
- Orthodontic Department, Islamic Azad University, Tehran, Iran.
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16
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Spandorfer S, Babayan A, Davis O, Rosenwaks Z, Witkin S. A G→A polymorphism at position +331 in the progesterone receptor (PR) gene is strongly associated with oocyte donation (OD) outcome. Fertil Steril 2007. [DOI: 10.1016/j.fertnstert.2007.07.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Akopians A, Babayan A, Basbaum A, Phelps P. [P181]: The Reelin signaling pathway contributes to positioning and nociceptive processing in the dorsal spinal cord. Int J Dev Neurosci 2006. [DOI: 10.1016/j.ijdevneu.2006.09.241] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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18
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Axt R, Boos R, Babayan A, Ertan K, Schmidt W. [Effect of hypertensive pregnancy complications on neonatal outcome of growth retarded fetuses]. Z Geburtshilfe Neonatol 2000; 204:49-54. [PMID: 10798264 DOI: 10.1055/s-2000-10196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
OBJECTIVE To determine the effect of hypertensive disorders in pregnancy on the neonatal outcome of growth restricted fetuses. There is conflicting data on the effect of hypertension during pregnancy on the incidence of neonatal respiratory distress syndrome (RDS) and intraventricular hemorrhage. Some studies report a lower incidence of RDS and intraventricular hemorrhage in infants of hypertensive mothers, whereas other studies report a similar or higher incidence in infants born to hypertensive mothers. STUDY DESIGN We performed a retrospective analysis of 220 growth restricted fetuses born between January 1, 1996 to July 1, 1997 at the Department of Obstetrics and Gynecology of the University-Hospital at Homburg/Saar. Data were obtained by review of the medical records. Growth restricted infants born to preeclamptic women or women with HELLP syndrome were compared to growth restricted fetuses born to mothers without hypertensive disorders. RESULTS Growth restricted fetuses born to hypertensive mothers had a significant lower birth weight (p < 0.05). The incidence of RDS in children born to hypertensive mothers was significantly higher (p < 0.05, p < 0.01) and they stayed significantly longer in the neonatal intensive care unit (p < 0.01). In contrast to infants born to mothers with HELLP syndrome (n = 7) there was no difference in the incidence of intraventricular hemorrhage, infection, sepsis, necrotizing enterocolitis or cardiac complications (arrhythmia, insufficiency) in case of preeclampsia (n = 68). The perinatal mortality of infants born to hypertensive mothers was significantly higher (p < 0.05, p < 0.01). CONCLUSION This study does not support the contention that hypertensive disorders in pregnancy have a beneficial effect on the postnatal course of IUGR infants.
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Affiliation(s)
- R Axt
- Universitäts-Frauenklinik und Poliklinik mit Hebammenlehranstalt Homburg/Saar
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