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Stoecklein NH, Fluegen G, Guglielmi R, Neves RPL, Hackert T, Birgin E, Cieslik SA, Sudarsanam M, Driemel C, van Dalum G, Franken A, Niederacher D, Neubauer H, Fehm T, Rox JM, Böhme P, Häberle L, Göring W, Esposito I, Topp SA, Coumans FAW, Weitz J, Knoefel WT, Fischer JC, Bork U, Rahbari NN. Ultra-sensitive CTC-based liquid biopsy for pancreatic cancer enabled by large blood volume analysis. Mol Cancer 2023; 22:181. [PMID: 37957606 PMCID: PMC10641981 DOI: 10.1186/s12943-023-01880-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 10/10/2023] [Indexed: 11/15/2023] Open
Abstract
The limited sensitivity of circulating tumor cell (CTC) detection in pancreatic adenocarcinoma (PDAC) stems from their extremely low concentration in the whole circulating blood, necessitating enhanced detection methodologies. This study sought to amplify assay-sensitivity by employing diagnostic leukapheresis (DLA) to screen large blood volumes. Sixty patients were subjected to DLA, with a median processed blood volume of ~ 2.8 L and approximately 5% of the resulting DLA-product analyzed using CellSearch (CS). Notably, DLA significantly increased CS-CTC detection to 44% in M0-patients and 74% in M1-patients, yielding a 60-fold increase in CS-CTC enumeration. DLA also provided sufficient CS-CTCs for genomic profiling, thereby delivering additional genomic information compared to tissue biopsy samples. DLA CS-CTCs exhibited a pronounced negative prognostic impact on overall survival (OS), evidenced by a reduction in OS from 28.6 to 8.5 months (univariate: p = 0.002; multivariable: p = 0.043). Additionally, a marked enhancement in sensitivity was achieved (by around 3-4-times) compared to peripheral blood (PB) samples, with positive predictive values for OS being preserved at around 90%. Prognostic relevance of CS-CTCs in PDAC was further validated in PB-samples from 228 PDAC patients, consolidating the established association between CTC-presence and reduced OS (8.5 vs. 19.0 months, p < 0.001). In conclusion, DLA-derived CS-CTCs may serve as a viable tool for identifying high-risk PDAC-patients and aiding the optimization of multimodal treatment strategies. Moreover, DLA enables comprehensive diagnostic profiling by providing ample CTC material, reinforcing its utility as a reliable liquid-biopsy approach. This high-volume liquid-biopsy strategy presents a potential pathway for enhancing clinical management in this malignancy.
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Affiliation(s)
- Nikolas H Stoecklein
- General, Visceral and Pediatric Surgery, University Hospital and Medical Faculty of the Heinrich-Heine-University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany.
| | - Georg Fluegen
- General, Visceral and Pediatric Surgery, University Hospital and Medical Faculty of the Heinrich-Heine-University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Rosa Guglielmi
- General, Visceral and Pediatric Surgery, University Hospital and Medical Faculty of the Heinrich-Heine-University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Rui P L Neves
- General, Visceral and Pediatric Surgery, University Hospital and Medical Faculty of the Heinrich-Heine-University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Thilo Hackert
- Department of General, Visceral, and Transplantation Surgery, Heidelberg University Hospital, Im Neuenheimer Feld 420, 69120, Heidelberg, Germany
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
| | - Emrullah Birgin
- Department of Surgery, Medical Faculty Mannheim, University Hospital Mannheim, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany
| | - Stefan A Cieslik
- General, Visceral and Pediatric Surgery, University Hospital and Medical Faculty of the Heinrich-Heine-University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Monica Sudarsanam
- General, Visceral and Pediatric Surgery, University Hospital and Medical Faculty of the Heinrich-Heine-University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Christiane Driemel
- General, Visceral and Pediatric Surgery, University Hospital and Medical Faculty of the Heinrich-Heine-University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Guus van Dalum
- General, Visceral and Pediatric Surgery, University Hospital and Medical Faculty of the Heinrich-Heine-University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - André Franken
- Department of Obstetrics and Gynecology, University Hospital and Medical Faculty of the Heinrich-Heine-University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Dieter Niederacher
- Department of Obstetrics and Gynecology, University Hospital and Medical Faculty of the Heinrich-Heine-University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Hans Neubauer
- Department of Obstetrics and Gynecology, University Hospital and Medical Faculty of the Heinrich-Heine-University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Tanja Fehm
- Department of Obstetrics and Gynecology, University Hospital and Medical Faculty of the Heinrich-Heine-University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Jutta M Rox
- Department of Transplantation Diagnostics and Cell Therapeutics, University Hospital and Medical Faculty of the Heinrich-Heine-University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Petra Böhme
- Institute of Forensic Medicine Düsseldorf, University Hospital and Medical Faculty of the Heinrich-Heine-University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Lena Häberle
- Institute of Pathology, University Hospital and Medical Faculty of the Heinrich-Heine-University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Wolfgang Göring
- Institute of Pathology, University Hospital and Medical Faculty of the Heinrich-Heine-University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Irene Esposito
- Institute of Pathology, University Hospital and Medical Faculty of the Heinrich-Heine-University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Stefan A Topp
- General, Visceral and Pediatric Surgery, University Hospital and Medical Faculty of the Heinrich-Heine-University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Frank A W Coumans
- Decisive Science, Ertskade 10, 1019 BB, Amsterdam, The Netherlands
- Current Affiliation: Department for General and Visceral Surgery, University Hospital Ulm, Albert-Einstein-Allee 23, 89081, Ulm, Germany
| | - Jürgen Weitz
- General, Visceral and Pediatric Surgery, University Hospital and Medical Faculty of the Heinrich-Heine-University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Wolfram T Knoefel
- General, Visceral and Pediatric Surgery, University Hospital and Medical Faculty of the Heinrich-Heine-University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Johannes C Fischer
- Department of Transplantation Diagnostics and Cell Therapeutics, University Hospital and Medical Faculty of the Heinrich-Heine-University Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Ulrich Bork
- Department of Visceral, Thoracic and Vascular Surgery, University Hospital Carl Gustav Carus of the Technical University Dresden, Fetscherstr. 74, 01307, Dresden, Germany
| | - Nuh N Rahbari
- Department of Surgery, Medical Faculty Mannheim, University Hospital Mannheim, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany.
- Current Affiliation: Department for General and Visceral Surgery, University Hospital Ulm, Albert-Einstein-Allee 23, 89081, Ulm, Germany.
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Leu C, Bautista JF, Sudarsanam M, Niestroj LM, Stefanski A, Ferguson L, Daly MJ, Jehi L, Najm IM, Busch RM, Lal D. Neurological disorder-associated genetic variants in individuals with psychogenic nonepileptic seizures. Sci Rep 2020; 10:15205. [PMID: 32938993 PMCID: PMC7495430 DOI: 10.1038/s41598-020-72101-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 04/30/2020] [Accepted: 08/24/2020] [Indexed: 12/19/2022] Open
Abstract
Psychogenic nonepileptic seizures (PNES) are diagnosed in approximately 30% of patients referred to tertiary care epilepsy centers. Little is known about the molecular pathology of PNES, much less about possible underlying genetic factors. We generated whole-exome sequencing and whole-genome genotyping data to identify rare, pathogenic (P) or likely pathogenic (LP) variants in 102 individuals with PNES and 448 individuals with focal (FE) or generalized (GE) epilepsy. Variants were classified for all individuals based on the ACMG-AMP 2015 guidelines. For research purposes only, we considered genes associated with neurological or psychiatric disorders as candidate genes for PNES. We observe in this first genetic investigation of PNES that six (5.88%) individuals with PNES without coexistent epilepsy carry P/LP variants (deletions at 10q11.22-q11.23, 10q23.1-q23.2, distal 16p11.2, and 17p13.3, and nonsynonymous variants in NSD1 and GABRA5). Notably, the burden of P/LP variants among the individuals with PNES was similar and not significantly different to the burden observed in the individuals with FE (3.05%) or GE (1.82%) (PNES vs. FE vs. GE (3 × 2 χ2), P = 0.30; PNES vs. epilepsy (2 × 2 χ2), P = 0.14). The presence of variants in genes associated with monogenic forms of neurological and psychiatric disorders in individuals with PNES shows that genetic factors are likely to play a role in PNES or its comorbidities in a subset of individuals. Future large-scale genetic research studies are needed to further corroborate these interesting findings in PNES.
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Affiliation(s)
- Costin Leu
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA. .,Stanley Center for Psychiatric Research, Broad Institute of Harvard and M.I.T, Cambridge, MA, 02142, USA. .,Department of Clinical and Experimental Epilepsy, Institute of Neurology, University College London, Queen Square, London, WC1N 3BG, UK.
| | - Jocelyn F Bautista
- Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.,Department of Neurology, Neurological Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Monica Sudarsanam
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Lisa-Marie Niestroj
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, DE, 50931, USA
| | - Arthur Stefanski
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Lisa Ferguson
- Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.,Department of Neurology, Neurological Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.,Department of Psychiatry & Psychology, Neurological Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Mark J Daly
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and M.I.T, Cambridge, MA, 02142, USA.,Institute of Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Lara Jehi
- Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.,Department of Neurology, Neurological Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Imad M Najm
- Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.,Department of Neurology, Neurological Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Robyn M Busch
- Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.,Department of Neurology, Neurological Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.,Department of Psychiatry & Psychology, Neurological Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Dennis Lal
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA. .,Stanley Center for Psychiatric Research, Broad Institute of Harvard and M.I.T, Cambridge, MA, 02142, USA. .,Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, 44195, USA. .,Cologne Center for Genomics (CCG), University of Cologne, Cologne, DE, 50931, USA.
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Du J, Sudarsanam M, Pérez-Palma E, Ganna A, Francioli L, Iqbal S, Niestroj LM, Leu C, Weisburd B, Poterba T, Nürnberg P, Daly MJ, Palotie A, May P, Lal D. Variant Score Ranker-a web application for intuitive missense variant prioritization. Bioinformatics 2020; 35:4478-4479. [PMID: 31086968 DOI: 10.1093/bioinformatics/btz252] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 03/21/2019] [Accepted: 04/17/2019] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION The correct classification of missense variants as benign or pathogenic remains challenging. Pathogenic variants are expected to have higher deleterious prediction scores than benign variants in the same gene. However, most of the existing variant annotation tools do not reference the score range of benign population variants on gene level. RESULTS We present a web-application, Variant Score Ranker, which enables users to rapidly annotate variants and perform gene-specific variant score ranking on the population level. We also provide an intuitive example of how gene- and population-calibrated variant ranking scores can improve epilepsy variant prioritization. AVAILABILITY AND IMPLEMENTATION http://vsranker.broadinstitute.org. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Juanjiangmeng Du
- Cologne Center for Genomics, University of Cologne, University Hospital Cologne, Cologne, Germany
| | - Monica Sudarsanam
- Cologne Center for Genomics, University of Cologne, University Hospital Cologne, Cologne, Germany.,Genomic Medicine Institute, Lerner Research Institute Cleveland Clinic, Cleveland, OH, USA
| | - Eduardo Pérez-Palma
- Cologne Center for Genomics, University of Cologne, University Hospital Cologne, Cologne, Germany
| | - Andrea Ganna
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Laurent Francioli
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Sumaiya Iqbal
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Lisa-Marie Niestroj
- Cologne Center for Genomics, University of Cologne, University Hospital Cologne, Cologne, Germany
| | - Costin Leu
- Genomic Medicine Institute, Lerner Research Institute Cleveland Clinic, Cleveland, OH, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Institute of Neurology, University College London, London, UK
| | - Ben Weisburd
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Tim Poterba
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Peter Nürnberg
- Cologne Center for Genomics, University of Cologne, University Hospital Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Mark J Daly
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Aarno Palotie
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.,Psychiatric & Neurodevelopmental Genetics Unit, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA.,Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University Luxembourg, Esch-sur-Alzette 4365, Luxembourg
| | - Dennis Lal
- Cologne Center for Genomics, University of Cologne, University Hospital Cologne, Cologne, Germany.,Genomic Medicine Institute, Lerner Research Institute Cleveland Clinic, Cleveland, OH, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.,Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA
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Bäuml CA, Schmitz T, Paul George AA, Sudarsanam M, Hardes K, Steinmetzer T, Holle LA, Wolberg AS, Pötzsch B, Oldenburg J, Biswas A, Imhof D. Coagulation Factor XIIIa Inhibitor Tridegin: On the Role of Disulfide Bonds for Folding, Stability, and Function. J Med Chem 2019; 62:3513-3523. [PMID: 30852892 PMCID: PMC6650289 DOI: 10.1021/acs.jmedchem.8b01982] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Tridegin is a potent and specific 66mer peptide inhibitor of coagulation factor XIIIa with six cysteines involved in three disulfide bonds. Three of the 15 possible 3-disulfide-bonded isomers have been identified, which share a bridge between cysteines 19 and 25. We synthesized the three possible 2-disulfide-bonded analogues using a targeted protecting group strategy to investigate the impact of the C19-C25 bond on tridegin's folding, stability, and function. The FXIIIa inhibitory activity of the analogues was retained, which was shown by in vitro fluorogenic activity and whole blood clotting assays. Molecular dynamics simulations of wild-type tridegin and the analogues as well as molecular docking studies with FXIIIa were performed to elucidate the impact of the C19-C25 bond on conformational stability and binding mode. The strategy of selectively reducing disulfide bonds to facilitate large-scale synthesis, while retaining the functionality of disulfide-bonded peptides, has been demonstrated with our present study.
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Affiliation(s)
- Charlotte A. Bäuml
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Thomas Schmitz
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Ajay A. Paul George
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Monica Sudarsanam
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Kornelia Hardes
- Department of Pharmacy, Institute of Pharmaceutical Chemistry, Philipps University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Torsten Steinmetzer
- Department of Pharmacy, Institute of Pharmaceutical Chemistry, Philipps University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Lori A. Holle
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 819 Brinkhous-Bullitt Building, Chapel Hill, NC 27599, USA
| | - Alisa S. Wolberg
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 819 Brinkhous-Bullitt Building, Chapel Hill, NC 27599, USA
| | - Bernd Pötzsch
- Institute of Experimental Hematology and Transfusion Medicine, University Hospital Bonn, Sigmund-Freud-Str. 25, 53127 Bonn, Germany
| | - Johannes Oldenburg
- Institute of Experimental Hematology and Transfusion Medicine, University Hospital Bonn, Sigmund-Freud-Str. 25, 53127 Bonn, Germany
| | - Arijit Biswas
- Institute of Experimental Hematology and Transfusion Medicine, University Hospital Bonn, Sigmund-Freud-Str. 25, 53127 Bonn, Germany
| | - Diana Imhof
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
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