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Bowers RM, Gonzalez-Pena V, Wardhani K, Goudeau D, Blow MJ, Udwary D, Klein D, Vill AC, Brito IL, Woyke T, Malmstrom R, Gawad C. scMicrobe PTA: Near Complete Genomes from Single Bacterial Cells. bioRxiv 2024:2024.01.30.577819. [PMID: 38352480 PMCID: PMC10862798 DOI: 10.1101/2024.01.30.577819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Microbial genomes produced by single-cell amplification are largely incomplete. Here, we show that primary template amplification (PTA), a novel single-cell amplification technique, generated nearly complete genomes from three bacterial isolate species. Furthermore, taxonomically diverse genomes recovered from aquatic and soil microbiomes using PTA had a median completeness of 81%, whereas genomes from standard amplification approaches were usually <30% complete. PTA-derived genomes also included more associated viruses and biosynthetic gene clusters.
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Affiliation(s)
- Robert M Bowers
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Kartika Wardhani
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Danielle Goudeau
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Matthew James Blow
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Daniel Udwary
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David Klein
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | | | | | - Tanja Woyke
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Rex Malmstrom
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Charles Gawad
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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Pilheden M, Ahlgren L, Hyrenius-Wittsten A, Gonzalez-Pena V, Sturesson H, Hansen Marquart HV, Lausen B, Castor A, Pronk CJ, Barbany G, Pokrovskaja Tamm K, Fogelstrand L, Lohi O, Norén-Nyström U, Asklin J, Chen Y, Song G, Walsh M, Ma J, Zhang J, Saal LH, Gawad C, Hagström-Andersson AK. Duplex Sequencing Uncovers Recurrent Low-frequency Cancer-associated Mutations in Infant and Childhood KMT2A-rearranged Acute Leukemia. Hemasphere 2022; 6:e785. [PMID: 36204688 PMCID: PMC9529062 DOI: 10.1097/hs9.0000000000000785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 08/30/2022] [Indexed: 11/26/2022] Open
Abstract
Infant acute lymphoblastic leukemia (ALL) with KMT2A-gene rearrangements (KMT2A-r) have few mutations and a poor prognosis. To uncover mutations that are below the detection of standard next-generation sequencing (NGS), a combination of targeted duplex sequencing and NGS was applied on 20 infants and 7 children with KMT2A-r ALL, 5 longitudinal and 6 paired relapse samples. Of identified nonsynonymous mutations, 87 had been previously implicated in cancer and targeted genes recurrently altered in KMT2A-r leukemia and included mutations in KRAS, NRAS, FLT3, TP53, PIK3CA, PAX5, PIK3R1, and PTPN11, with infants having fewer such mutations. Of identified cancer-associated mutations, 62% were below the resolution of standard NGS. Only 33 of 87 mutations exceeded 2% of cellular prevalence and most-targeted PI3K/RAS genes (31/33) and typically KRAS/NRAS. Five patients only had low-frequency PI3K/RAS mutations without a higher-frequency signaling mutation. Further, drug-resistant clones with FLT3 D835H or NRAS G13D/G12S mutations that comprised only 0.06% to 0.34% of diagnostic cells, expanded at relapse. Finally, in longitudinal samples, the relapse clone persisted as a minor subclone from diagnosis and through treatment before expanding during the last month of disease. Together, we demonstrate that infant and childhood KMT2A-r ALL harbor low-frequency cancer-associated mutations, implying a vast subclonal genetic landscape.
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Affiliation(s)
- Mattias Pilheden
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Louise Ahlgren
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Axel Hyrenius-Wittsten
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Veronica Gonzalez-Pena
- Division of Pediatric Hematology/Oncology, Stanford University, School of Medicine, Stanford, CA, USA
| | - Helena Sturesson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | | | - Birgitte Lausen
- Department of Paediatrics and Adolescent Medicine, Rigshospitalet, University of Copenhagen, Denmark
| | - Anders Castor
- Childhood Cancer Center, Skane University Hospital, Lund, Sweden
| | | | - Gisela Barbany
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | | | - Linda Fogelstrand
- Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Sweden
| | - Olli Lohi
- Tampere Center for Child, Adolescent and Maternal Health Research and Tays Cancer Center, Tampere University and Tampere University Hospital, Tampere, Finland
| | | | | | | | - Guangchun Song
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Michael Walsh
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Jing Ma
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Lao H. Saal
- SAGA Diagnostics, Lund, Sweden
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Charles Gawad
- Division of Pediatric Hematology/Oncology, Stanford University, School of Medicine, Stanford, CA, USA
| | - Anna K. Hagström-Andersson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Center for Translational Genomics, Lund University, Lund, Sweden
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3
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Barsan V, Xia Y, Klein D, Gonzalez-Pena V, Youssef S, Inaba Y, Mahmud O, Natarajan S, Agarwal V, Pang Y, Autry R, Pui CH, Inaba H, Evans W, Gawad C. Simultaneous monitoring of disease and microbe dynamics through plasma DNA sequencing in pediatric patients with acute lymphoblastic leukemia. Sci Adv 2022; 8:eabj1360. [PMID: 35442732 PMCID: PMC9020671 DOI: 10.1126/sciadv.abj1360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 01/19/2022] [Indexed: 05/09/2023]
Abstract
Treatment of acute lymphoblastic leukemia (ALL) necessitates continuous risk assessment of leukemic disease burden and infections that arise in the setting of immunosuppression. This study was performed to assess the feasibility of a hybrid capture next-generation sequencing panel to longitudinally measure molecular leukemic disease clearance and microbial species abundance in 20 pediatric patients with ALL throughout induction chemotherapy. This proof of concept helps establish a technical and conceptual framework that we anticipate will be expanded and applied to additional patients with leukemia, as well as extended to additional cancer types. Molecular monitoring can help accelerate the attainment of insights into the temporal biology of host-microbe-leukemia interactions, including how those changes correlate with and alter anticancer therapy efficacy. We also anticipate that fewer invasive bone marrow examinations will be required, as these methods improve with standardization and are validated for clinical use.
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Affiliation(s)
- Valentin Barsan
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Yuntao Xia
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - David Klein
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Veronica Gonzalez-Pena
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94304, USA
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Sarah Youssef
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Yuki Inaba
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Ousman Mahmud
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Sivaraman Natarajan
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Vibhu Agarwal
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Yakun Pang
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94304, USA
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Robert Autry
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Ching-Hon Pui
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Hiroto Inaba
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - William Evans
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Charles Gawad
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94304, USA
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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4
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Goggin KP, Gonzalez-Pena V, Inaba Y, Allison KJ, Hong DK, Ahmed AA, Hollemon D, Natarajan S, Mahmud O, Kuenzinger W, Youssef S, Brenner A, Maron G, Choi J, Rubnitz JE, Sun Y, Tang L, Wolf J, Gawad C. Evaluation of Plasma Microbial Cell-Free DNA Sequencing to Predict Bloodstream Infection in Pediatric Patients With Relapsed or Refractory Cancer. JAMA Oncol 2020; 6:552-556. [PMID: 31855231 PMCID: PMC6990667 DOI: 10.1001/jamaoncol.2019.4120] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Question Might plasma microbial cell-free DNA sequencing (mcfDNA-seq) predict bloodstream infection (BSI) in immunocompromised patients days before the onset of attributable symptoms? Findings This pilot cohort study included 47 pediatric patients with relapsed or refractory cancer. The causative pathogen was identified by mcfDNA-seq in the 3 days before onset of BSI in 12 of 16 episodes; of 33 negative control samples collected from the same patient population, mcfDNA-seq was negative in 27 and identified no common pathogens in 30. Meaning In patients with imminent BSI, it appears that mcfDNA-seq can identify clinically relevant pathogens days before onset of attributable symptoms. Importance Bloodstream infection (BSI) is a common, life-threatening complication of treatment for cancer. Predicting BSI before onset of clinical symptoms would enable preemptive therapy, but there is no reliable screening test. Objective To estimate sensitivity and specificity of plasma microbial cell-free DNA sequencing (mcfDNA-seq) for predicting BSI in patients at high risk of life-threatening infection. Design, Setting, and Participants A prospective pilot cohort study of mcfDNA-seq for predicting BSI in pediatric patients (<25 years of age) with relapsed or refractory cancers at St Jude Children’s Research Hospital, a specialist quaternary pediatric hematology-oncology referral center. Remnant clinical blood samples were collected during chemotherapy and hematopoietic cell transplantation. Samples collected during the 7 days before and at onset of BSI episodes, along with negative control samples from study participants, underwent blinded testing using a mcfDNA-seq test in a Clinical Laboratory Improvement Amendments/College of American Pathologists–approved laboratory. Main Outcomes and Measures The primary outcomes were sensitivity of mcfDNA-seq for detecting a BSI pathogen during the 3 days before BSI onset and specificity of mcfDNA-seq in the absence of fever or infection in the preceding or subsequent 7 days. Results Between August 9, 2017, and June 4, 2018, 47 participants (27 [57%] male; median age [IQR], 10 [5-14] years) were enrolled; 19 BSI episodes occurred in 12 participants, and predictive samples were available for 16 episodes, including 15 bacterial BSI episodes. In the 3 days before the onset of infection, predictive sensitivity of mcfDNA-seq was 75% for all BSIs (12 of 16; 95% CI, 51%-90%) and 80% (12 of 15; 95% CI, 55%-93%) for bacterial BSIs. The specificity of mcfDNA-seq, evaluated on 33 negative control samples from enrolled participants, was 82% (27 of 33; 95% CI, 66%-91%) for any bacterial or fungal organism and 91% (30 of 33; 95% CI, 76%-97%) for any common BSI pathogen, and the concentration of pathogen DNA was lower in control than predictive samples. Conclusions and Relevance A clinically relevant pathogen can be identified by mcfDNA-seq days before the onset of BSI in a majority of episodes, potentially enabling preemptive treatment. Clinical application appears feasible pending further study. Trial Registration ClinicalTrials.gov identifier: NCT03226158
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Affiliation(s)
- Kathryn P Goggin
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee
| | | | - Yuki Inaba
- Department of Oncology, St Jude Children's Research Hospital, Memphis, Tennessee
| | - Kim J Allison
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee
| | | | | | | | - Sivaraman Natarajan
- Department of Oncology, St Jude Children's Research Hospital, Memphis, Tennessee
| | - Ousman Mahmud
- Department of Oncology, St Jude Children's Research Hospital, Memphis, Tennessee
| | - William Kuenzinger
- Department of Oncology, St Jude Children's Research Hospital, Memphis, Tennessee
| | - Sarah Youssef
- Department of Oncology, St Jude Children's Research Hospital, Memphis, Tennessee
| | - Abigail Brenner
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee
| | - Gabriela Maron
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee
| | - John Choi
- Department of Pathology, St Jude Children's Research Hospital, Memphis, Tennessee
| | - Jeffrey E Rubnitz
- Department of Oncology, St Jude Children's Research Hospital, Memphis, Tennessee.,Department of Pediatrics, The University of Tennessee Health Science Center, Memphis
| | - Yilun Sun
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, Tennessee
| | - Li Tang
- Department of Biostatistics, St Jude Children's Research Hospital, Memphis, Tennessee
| | - Joshua Wolf
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee.,Department of Pediatrics, The University of Tennessee Health Science Center, Memphis.,Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Charles Gawad
- Department of Oncology, St Jude Children's Research Hospital, Memphis, Tennessee.,Department of Pediatrics, The University of Tennessee Health Science Center, Memphis.,Department of Computational Biology, St Jude Children's Research Hospital, Memphis, Tennessee
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Abstract
Single-cell genome sequencing can detect low-frequency genetic alterations present in complex tissues. However, the experimental procedures are technically challenging. This includes dissociation of the tissue, isolation of single cells, whole-genome amplification, sequencing library preparation, and an optional target enrichment. Here we describe how to perform each of these processes to obtain high-quality single-cell genome sequencing data.
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Affiliation(s)
- Veronica Gonzalez-Pena
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles Gawad
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA.
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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6
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Goggin K, Inaba Y, Gonzalez-Pena V, Allison KJ, Chan KL, Hollemon D, Ahmed A, Hong D, Maron G, Hayden R, Choi J, Rubnitz J, Gawad C, Wolf J. 1756. Prediction of Bloodstream Infection Prior to Onset of Symptoms by Plasma Metagenomic Sequencing in Pediatric Patients With Relapsed or Refractory Malignancy (PREDSEQ). Open Forum Infect Dis 2018. [PMCID: PMC6253069 DOI: 10.1093/ofid/ofy209.141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Background Patients undergoing treatment for relapsed or refractory malignancies are at high risk of life-threatening bloodstream infection (BSI). A predictive screening test for BSI might allow pre-emptive therapy, but no validated test is currently available. We tested the hypothesis that plasma metagenomic next generation pathogen sequencing (NGS) would predict BSI before the onset of attributable symptoms. Methods We enrolled 31 pediatric patients receiving for treatment relapsed or refractory malignancy in an IRB-approved prospective cohort study (PREDSEQ) of predictive sequencing. Episodes of febrile neutropenia or documented infection were collected prospectively from the medical record. BSI was defined according to NHSN criteria. Control Samples were defined as samples collected ≥7 clear days before or after any fever or documented infection. Residual clinical samples were stored for NGS; after filtering human sequences, reads were aligned to a curated pathogen database, and organisms above a predefined threshold were reported (Karius Inc., Redwood City, CA). Only bacteria and fungi were included in this analysis. Results A total of 11 BSI episodes occurred in 9 participants (Table 1) during the study period. Predictive sensitivity of NGS in the 2 days before onset of infection (n = 9) was 78% (95% CI 45–94%), and diagnostic sensitivity on the day of infection (n = 11) was 82% (95% CI 52–95%). Specificity of NGS for development of fever or infection within 7 days (n = 16) was 81% (95% CI 57–93%). NGS was positive up to 6 days prior to onset of BSI. In samples collected before or during documented infections, NGS also identified additional bacteria and fungi that were not detected by standard clinical testing. Conclusion Plasma NGS shows promise for the detection of BSI prior to onset of symptoms in high-risk patients. Disclosures K. Goggin, Karius Inc.: Investigator, Research support. K. L. Chan, Karius Inc.: Employee, Salary. D. Hollemon, Karius Inc.: Employee, Salary. A. Ahmed, Karius, Inc.: Employee, Salary. D. Hong, Karius, Inc.: Employee, Salary. R. Hayden, Roche Molecular: Scientific Advisor, Consulting fee. Abbott Molecular: Scientific Advisor, Consulting fee. Quidel: Scientific Advisor, Consulting fee. C. Gawad, Karius Inc.: Investigator, Research support. J. Wolf, Karius Inc.: Investigator, Research support.
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Affiliation(s)
- Kathryn Goggin
- St. Jude Children’s Research Hospital, Memphis, Tennessee
| | - Yuki Inaba
- St. Jude Children’s Research Hospital, Memphis, Tennessee
| | | | - Kim J Allison
- St. Jude Children’s Research Hospital, Memphis, Tennessee
| | | | | | | | | | - Gabriela Maron
- St. Jude Children’s Research Hospital, Memphis, Tennessee
| | - Randall Hayden
- St. Jude Children’s Research Hospital, Memphis, Tennessee
| | - John Choi
- St. Jude Children’s Research Hospital, Memphis, Tennessee
| | | | - Charles Gawad
- St. Jude Children’s Research Hospital, Memphis, Tennessee
| | - Joshua Wolf
- St. Jude Children’s Research Hospital, Memphis, Tennessee
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Easton J, Gonzalez-Pena V, Yergeau D, Ma X, Gawad C. Genome-wide segregation of single nucleotide and structural variants into single cancer cells. BMC Genomics 2017; 18:906. [PMID: 29178827 PMCID: PMC5702214 DOI: 10.1186/s12864-017-4286-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [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: 05/08/2017] [Accepted: 11/08/2017] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Single-cell genome sequencing provides high-resolution details of the clonal genomic modifications that occur during cancer initiation, progression, and ongoing evolution as patients undergo treatment. One limitation of current single-cell sequencing strategies is a suboptimal capacity to detect all classes of single-nucleotide and structural variants in the same cells. RESULTS Here we present a new approach for determining comprehensive variant profiles of single cells using a microfluidic amplicon-based strategy to detect structural variant breakpoint sequences instead of using relative read depth to infer copy number changes. This method can reconstruct the clonal architecture and mutational history of a malignancy using all classes and sizes of somatic variants, providing more complete details of the temporal changes in mutational classes and processes that led to the development of a malignant neoplasm. Using this approach, we interrogated cells from a patient with leukemia, determining that processes producing structural variation preceded single nucleotide changes in the development of that malignancy. CONCLUSIONS All classes and sizes of genomic variants can be efficiently detected in single cancer cells using our new method, enabling the ordering of distinct classes of mutations during tumor evolution.
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Affiliation(s)
- John Easton
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | | | - Donald Yergeau
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.,Buffalo Institute for Genomics and Data Analytics, University at Buffalo, Buffalo, NY, 14260, USA.,Present address: Buffalo Institute for Genomics and Data Analytics CBLS, 701 Ellicott St, Buffalo, NY, 14203, USA
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Charles Gawad
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA. .,Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA. .,Present address: MS 1260, Room IA6042, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
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Luo P, Tsang TC, He X, Gonzalez-Pena V, Jaramillo M, Takeuchi C, Harris DT. Novel amplifier expression vectors producing higher levels of IL-2 led to slower tumor growth and longer survival in vivo. DNA Cell Biol 2006; 24:595-604. [PMID: 16153160 DOI: 10.1089/dna.2005.24.595] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Sufficient levels of gene expression are required for effective gene therapy. One of the major obstacles in gene therapy is the low transgene expression obtained from currently available vector systems. To address this issue, we employed a transcriptional amplifier strategy in a single construct to enhance transgene expression. In the amplifier vectors (pHi-1 and pHi-2), the strong CMV promoter was used to drive a transcriptional factor, Tat, which could transactivate a second promoter (HIV1 LTR or HIV2 LTR) located in the same construct driving the gene of interest. Using the human interleukin-2 (IL-2) cytokine gene, our data showed that the pHi-1/2 amplifier vectors could produce significantly higher IL-2 levels in human lung cancer cells (A549) and breast cancer cells (MCF-7) than that obtained by directly using the CMV promoter alone. Injection of pHi-2-IL-2-modified Lewis Lung (LL/2) tumor clones led to significantly slower tumor growth and longer survival in mice compared to those injected with either CMV promoter driven IL-2 clones or the parental tumor cells. Our results demonstrated that the transcriptional amplifier-based expression cassettes could be very useful in applications where high levels of gene expression are difficult to achieve.
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Affiliation(s)
- P Luo
- Gene Therapy Group, Department of Microbiology and Immunology, University of Arizona, Tucson, 85724, USA.
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