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Lall R, Evans M, Seo Y, Niknejad A, Anwar M. Dosimetry Reconstruction in Radiopharmaceutical Therapy Using a Sparse Network of External γ-Sensors. Int J Radiat Oncol Biol Phys 2023; 117:S30-S31. [PMID: 37784473 DOI: 10.1016/j.ijrobp.2023.06.293] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Radiopharmaceutical therapy (RPT) has demonstrated promise in the treatment of neuroendocrine and prostate cancer. Due to the highly varied biodistribution and non-homogeneity of total integrated dose across cancer patients, a system for real-time dosimetry based on continuous measurement is desirable to deliver sufficient dose for tumor ablation while preventing toxicity from off-target uptake by organs at risk (OAR). Single time point imaging (mostly SPECT)-based dosimetry offers a snapshot of the body-wide dose distribution at a given time point, but even single SPECT imaging is generally limited in availability, often leading to significant inaccuracies in estimating total integrated dose. Therefore, accurate personalized dosimetry in RPT is an unmet need and requires continuous dosimetry measurements of tumors and OARs across multiple half-lives of the therapeutic radiopharmaceutical. Using a priori knowledge of tumor and OAR locations from pretherapy imaging, we have developed a novel algorithm that utilizes a network of custom uncollimated, optical fiber-based γ-counting probes to isolate the real-time in vivo tumor and OAR uptake in 177Lu-PSMA-617 and 225Ac-MACROPA-YS5 therapy. MATERIALS/METHODS The proposed system was successfully validated in athymic mice models bearing varying numbers of tumors from two human prostate cancer cell lines (PC3-pip, PC3-flu). Uncollimated γ counts using the developed probes were acquired outside of the mice for 10 minutes, starting at 0 hr, 6 hrs, 12 hrs, 24 hrs, and 48 hrs after the injection of 177Lu-PSMA-617. The percent injected activity per mL of tissue (%IA/mL) of each tumor and OAR was reconstructed at every time point and compared to the %IA/mL extracted from SPECT/CT immediately after the recording. RESULTS The developed system's %IA/mL reconstruction in PC3-pip tumors, PC3-flu tumors, kidneys, and bladders is highly correlative with the %IA/mL extracted from state-of-art in vivo dosimetry techniques, with %IA/mL ranging from 0.1% to 160% assuming a 29.6 MBq 177Lu-PSMA-617 administration. The least squares linear regression fit between the reconstructed activity and the activity measured from SPECT/CT is given by Estimated %IA/mL = 0.91 x SPECT %IA/mL, with an R2 of 0.991, and Pearson's r of 0.9975. There is a nearly 1:1 mapping between the proposed model and SPECT/CT. CONCLUSION A novel dose reconstruction algorithm for personalized dosimetry in RPT that utilizes a sparse set of external γ-counters and a priori knowledge of tumor and OAR locations was developed and validated in in vivo human prostate cancer murine models. The proposed system enables continuous dosimetry measurements of multiple tumors and OAR noninvasively, with high accessibility, high temporal resolution, and across multiple classes of ɑ and β-based RPT. Similar experiments using 225Ac-MACROPA-YS5 are ongoing and additional results will be reported.
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Affiliation(s)
- R Lall
- University of California, Berkeley, Berkeley, CA
| | - M Evans
- University of California, San Francisco, San Francisco, CA
| | - Y Seo
- University of California, San Francisco, San Francisco, CA
| | - A Niknejad
- University of California, Berkeley, Berkeley, CA
| | - M Anwar
- University of California, San Francisco, San Francisco, CA
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Fabrizio JJ, Rollins J, Bazinet CW, Wegener S, Koziy I, Daniel R, Lombardo V, Pryce D, Bharrat K, Innabi E, Villanobos M, Mendoza G, Ferrara E, Rodway S, Vicioso M, Siracusa V, Dailey E, Pronovost J, Innabi S, Patel V, DeSouza N, Quaranto D, Niknejad A. Tubulin-binding cofactor E-like (TBCEL), the protein product of the mulet gene, is required in the germline for the regulation of inter-flagellar microtubule dynamics during spermatid individualization. Biol Open 2020; 9:bio049080. [PMID: 32033965 PMCID: PMC7055396 DOI: 10.1242/bio.049080] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 01/22/2020] [Indexed: 11/14/2022] Open
Abstract
Individual sperm cells are resolved from a syncytium during late step of spermiogenesis known as individualization, which is accomplished by an Individualization Complex (IC) composed of 64 investment cones. mulet encodes Tubulin-binding cofactor E-like (TBCEL), suggesting a role for microtubule dynamics in individualization. Indeed, a population of ∼100 cytoplasmic microtubules fails to disappear in mulet mutant testes during spermatogenesis. This persistence, detected using epi-fluorescence and electron microscopy, suggests that removal of these microtubules by TBCEL is a prerequisite for individualization. Immunofluorescence reveals TBCEL expression in elongated spermatid cysts. In addition, testes from mulet mutant males were rescued to wild type using tubulin-Gal4 to drive TBCEL expression, indicating that the mutant phenotype is caused by the lack of TBCEL. Finally, RNAi driven by bam-GAL4 successfully phenocopied mulet, confirming that mulet is required in the germline for individualization. We propose a model in which the cytoplasmic microtubules serve as alternate tracks for investment cones in mulet mutant testes.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- James J Fabrizio
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Janet Rollins
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | | | - Stephanie Wegener
- Leibniz Institute for Neurobiology Magdeburg, Department Genetics of Learning and Memory, 39118 Magdeburg, Germany
| | - Iryna Koziy
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Rachel Daniel
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Vincent Lombardo
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Dwaine Pryce
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Kavita Bharrat
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Elissa Innabi
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Marielle Villanobos
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Gabriela Mendoza
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Elisa Ferrara
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Stephanie Rodway
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Matthew Vicioso
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Victoria Siracusa
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Erin Dailey
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Justin Pronovost
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Simon Innabi
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Vrutant Patel
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Nicole DeSouza
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Danielle Quaranto
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Amir Niknejad
- Department of Mathematics, College of Mt St Vincent, Bronx, NY 10471, USA
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Lähnemann D, Köster J, Szczurek E, McCarthy DJ, Hicks SC, Robinson MD, Vallejos CA, Campbell KR, Beerenwinkel N, Mahfouz A, Pinello L, Skums P, Stamatakis A, Attolini CSO, Aparicio S, Baaijens J, Balvert M, Barbanson BD, Cappuccio A, Corleone G, Dutilh BE, Florescu M, Guryev V, Holmer R, Jahn K, Lobo TJ, Keizer EM, Khatri I, Kielbasa SM, Korbel JO, Kozlov AM, Kuo TH, Lelieveldt BP, Mandoiu II, Marioni JC, Marschall T, Mölder F, Niknejad A, Rączkowska A, Reinders M, Ridder JD, Saliba AE, Somarakis A, Stegle O, Theis FJ, Yang H, Zelikovsky A, McHardy AC, Raphael BJ, Shah SP, Schönhuth A. Eleven grand challenges in single-cell data science. Genome Biol 2020; 21:31. [PMID: 32033589 PMCID: PMC7007675 DOI: 10.1186/s13059-020-1926-6] [Citation(s) in RCA: 534] [Impact Index Per Article: 133.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 01/02/2020] [Indexed: 02/08/2023] Open
Abstract
The recent boom in microfluidics and combinatorial indexing strategies, combined with low sequencing costs, has empowered single-cell sequencing technology. Thousands-or even millions-of cells analyzed in a single experiment amount to a data revolution in single-cell biology and pose unique data science problems. Here, we outline eleven challenges that will be central to bringing this emerging field of single-cell data science forward. For each challenge, we highlight motivating research questions, review prior work, and formulate open problems. This compendium is for established researchers, newcomers, and students alike, highlighting interesting and rewarding problems for the coming years.
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Affiliation(s)
- David Lähnemann
- Algorithms for Reproducible Bioinformatics, Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Department of Paediatric Oncology, Haematology and Immunology, Medical Faculty, Heinrich Heine University, University Hospital, Düsseldorf, Germany
- Computational Biology of Infection Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Johannes Köster
- Algorithms for Reproducible Bioinformatics, Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, USA
| | - Ewa Szczurek
- Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warszawa, Poland
| | - Davis J. McCarthy
- Bioinformatics and Cellular Genomics, St Vincent’s Institute of Medical Research, Fitzroy, Australia
- Melbourne Integrative Genomics, School of BioSciences–School of Mathematics & Statistics, Faculty of Science, University of Melbourne, Melbourne, Australia
| | - Stephanie C. Hicks
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD USA
| | - Mark D. Robinson
- Institute of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zürich, Zürich, Switzerland
| | - Catalina A. Vallejos
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
- The Alan Turing Institute, British Library, London, UK
| | - Kieran R. Campbell
- Department of Statistics, University of British Columbia, Vancouver, Canada
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, Canada
- Data Science Institute, University of British Columbia, Vancouver, Canada
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Ahmed Mahfouz
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
- Delft Bioinformatics Lab, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, The Netherlands
| | - Luca Pinello
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital Research Institute, Charlestown, USA
- Department of Pathology, Harvard Medical School, Boston, USA
- Broad Institute of Harvard and MIT, Cambridge, MA USA
| | - Pavel Skums
- Department of Computer Science, Georgia State University, Atlanta, USA
| | - Alexandros Stamatakis
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | | | - Samuel Aparicio
- Department of Molecular Oncology, BC Cancer Agency, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Jasmijn Baaijens
- Life Sciences and Health, Centrum Wiskunde & Informatica, Amsterdam, The Netherlands
| | - Marleen Balvert
- Life Sciences and Health, Centrum Wiskunde & Informatica, Amsterdam, The Netherlands
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht, The Netherlands
| | - Buys de Barbanson
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
- Quantitative biology, Hubrecht Institute, Utrecht, The Netherlands
| | - Antonio Cappuccio
- Institute for Advanced Study, University of Amsterdam, Amsterdam, The Netherlands
| | - Giacomo Corleone
- Department of Surgery and Cancer, The Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, UK
| | - Bas E. Dutilh
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht, The Netherlands
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Maria Florescu
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
- Quantitative biology, Hubrecht Institute, Utrecht, The Netherlands
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Rens Holmer
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Katharina Jahn
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Thamar Jessurun Lobo
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Emma M. Keizer
- Biometris, Wageningen University & Research, Wageningen, The Netherlands
| | - Indu Khatri
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
| | - Szymon M. Kielbasa
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Jan O. Korbel
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Alexey M. Kozlov
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Tzu-Hao Kuo
- Computational Biology of Infection Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Boudewijn P.F. Lelieveldt
- PRB lab, Delft University of Technology, Delft, The Netherlands
- Division of Image Processing, Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ion I. Mandoiu
- Computer Science & Engineering Department, University of Connecticut, Storrs, USA
| | - John C. Marioni
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Tobias Marschall
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
- Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Felix Mölder
- Algorithms for Reproducible Bioinformatics, Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Amir Niknejad
- Computation molecular design, Zuse Institute Berlin, Berlin, Germany
- Mathematics Department, Mount Saint Vincent, New York, USA
| | - Alicja Rączkowska
- Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warszawa, Poland
| | - Marcel Reinders
- Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands
- Delft Bioinformatics Lab, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, The Netherlands
| | - Jeroen de Ridder
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Antoine-Emmanuel Saliba
- Helmholtz Institute for RNA-based Infection Research, Helmholtz-Center for Infection Research, Würzburg, Germany
| | - Antonios Somarakis
- Division of Image Processing, Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Oliver Stegle
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center–DKFZ, Heidelberg, Germany
| | - Fabian J. Theis
- Institute of Computational Biology, Helmholtz Zentrum München–German Research Center for Environmental Health, Neuherberg, Germany
| | - Huan Yang
- Division of Drug Discovery and Safety, Leiden Academic Center for Drug Research–LACDR–Leiden University, Leiden, The Netherlands
| | - Alex Zelikovsky
- Department of Computer Science, Georgia State University, Atlanta, USA
- The Laboratory of Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Alice C. McHardy
- Computational Biology of Infection Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Sohrab P. Shah
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Alexander Schönhuth
- Life Sciences and Health, Centrum Wiskunde & Informatica, Amsterdam, The Netherlands
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht, The Netherlands
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