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Ramien C, Yusko EC, Engler JB, Gamradt S, Patas K, Schweingruber N, Willing A, Rosenkranz SC, Diemert A, Harrison A, Vignali M, Sanders C, Robins HS, Tolosa E, Heesen C, Arck PC, Scheffold A, Chan K, Emerson RO, Friese MA, Gold SM. T Cell Repertoire Dynamics during Pregnancy in Multiple Sclerosis. Cell Rep 2020; 29:810-815.e4. [PMID: 31644905 DOI: 10.1016/j.celrep.2019.09.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 05/31/2018] [Revised: 07/10/2019] [Accepted: 09/06/2019] [Indexed: 02/08/2023] Open
Abstract
Identifying T cell clones associated with human autoimmunity has remained challenging. Intriguingly, many autoimmune diseases, including multiple sclerosis (MS), show strongly diminished activity during pregnancy, providing a unique research paradigm to explore dynamics of immune repertoire changes during active and inactive disease. Here, we characterize immunomodulation at the single-clone level by sequencing the T cell repertoire in healthy women and female MS patients over the course of pregnancy. Clonality is significantly reduced from the first to third trimester in MS patients, indicating that the T cell repertoire becomes less dominated by expanded clones. However, only a few T cell clones are substantially modulated during pregnancy in each patient. Moreover, relapse-associated T cell clones identified in an individual patient contract during pregnancy and expand during a postpartum relapse. Our data provide evidence that profiling the T cell repertoire during pregnancy could serve as a tool to discover and track "private" T cell clones associated with disease activity in autoimmunity.
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Affiliation(s)
- Caren Ramien
- Institut für Neuroimmunologie und Multiple Sklerose (INIMS), Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Erik C Yusko
- Adaptive Biotechnologies Corp., 1551 Eastlake Ave. E., Seattle, WA 98102, USA
| | - Jan Broder Engler
- Institut für Neuroimmunologie und Multiple Sklerose (INIMS), Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Stefanie Gamradt
- Charité - Universitätsmedizin Berlin, Klinik für Psychiatrie und Medizinische Klinik m.S. Psychosomatik, Campus Benjamin Franklin, Hindenburgdamm 30, 12203 Berlin, Germany
| | - Kostas Patas
- Institut für Neuroimmunologie und Multiple Sklerose (INIMS), Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany; Laboratory for Biopathology and Immunology, Eginition University Hospital, 72-74 Vasilissis Sophias Ave., 11528 Athens, Greece
| | - Nils Schweingruber
- Institut für Neuroimmunologie und Multiple Sklerose (INIMS), Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany; Klinik für Neurologie, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Anne Willing
- Institut für Neuroimmunologie und Multiple Sklerose (INIMS), Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Sina Cathérine Rosenkranz
- Institut für Neuroimmunologie und Multiple Sklerose (INIMS), Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany; Klinik für Neurologie, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Anke Diemert
- Klinik für Geburtshilfe und Pränatalmedizin, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Anja Harrison
- Institut für Neuroimmunologie und Multiple Sklerose (INIMS), Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany; Department of Psychology, University of Central Lancashire, Preston, PR1 2HE Lancashire, UK
| | - Marissa Vignali
- Adaptive Biotechnologies Corp., 1551 Eastlake Ave. E., Seattle, WA 98102, USA
| | - Catherine Sanders
- Adaptive Biotechnologies Corp., 1551 Eastlake Ave. E., Seattle, WA 98102, USA
| | - Harlan S Robins
- Adaptive Biotechnologies Corp., 1551 Eastlake Ave. E., Seattle, WA 98102, USA; Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109-1024, USA
| | - Eva Tolosa
- Institut für Immunologie, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Christoph Heesen
- Institut für Neuroimmunologie und Multiple Sklerose (INIMS), Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany; Klinik für Neurologie, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Petra C Arck
- Labor für Experimentelle Feto-Maternale Medizin, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Alexander Scheffold
- Institut für Immunologie, Universitätsklinikum Schleswig-Holstein, Arnold Heller Str. 3, 24105 Kiel, Germany
| | - Kenneth Chan
- Adaptive Biotechnologies Corp., 1551 Eastlake Ave. E., Seattle, WA 98102, USA
| | - Ryan O Emerson
- Adaptive Biotechnologies Corp., 1551 Eastlake Ave. E., Seattle, WA 98102, USA
| | - Manuel A Friese
- Institut für Neuroimmunologie und Multiple Sklerose (INIMS), Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Stefan M Gold
- Institut für Neuroimmunologie und Multiple Sklerose (INIMS), Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany; Charité - Universitätsmedizin Berlin, Klinik für Psychiatrie und Medizinische Klinik m.S. Psychosomatik, Campus Benjamin Franklin, Hindenburgdamm 30, 12203 Berlin, Germany.
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Khunger A, Rytlewski JA, Fields P, Yusko EC, Tarhini AA. The impact of CTLA-4 blockade and interferon-α on clonality of T-cell repertoire in the tumor microenvironment and peripheral blood of metastatic melanoma patients. Oncoimmunology 2019; 8:e1652538. [PMID: 31646098 DOI: 10.1080/2162402x.2019.1652538] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [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: 03/28/2019] [Revised: 07/24/2019] [Accepted: 07/31/2019] [Indexed: 02/06/2023] Open
Abstract
Patients with metastatic melanoma were treated with tremelimumab and interferon-α (IFN) in a previously reported clinical trial [NCT00610857]. Responses were assessed by RECIST criteria as complete (CR) or partial (PR), stable disease (SD) or progressive disease (PD). In this study, T-cell receptor (TCR) beta-chain repertoire was immunosequenced in peripheral blood mononuclear cells (PBMC) specimens (N = 33) and tumor samples (N = 18) utilizing the immunoSEQ® Assay to determine repertoire clonality and T cell fractions at pre-treatment (tumor and PBMC), one month (PBMC) and 3 months (PBMC) time points and evaluate its association with clinical outcomes. In the pretreatment tumor microenvironment (TME), T cell clonality was significantly (p = .035) different and greater in patients who achieved disease control (CR, PR, SD) versus those with non-disease control (PD) as best response to treatment. Further, there was significantly (p = .001) increased TCR fraction in tissue of responders (CR, PR) versus non-responders (PD, SD). In examining T cell clonality in the circulation (PBMC), no significant associations were found in the pretreatment samples. However, early on-treatment (4 weeks) there was a significant decrease in T cell clonality that was associated with improved overall survival (p = .01) and progression-free survival (p = .04). In addition, analysis of temporal changes in tumor-infiltrating lymphocytes (TIL) and peripheral TCR repertoire revealed that responders had significantly higher clonal expansion of TIL in the circulation at 4 weeks than non-responders (p = .036). Our study provided interesting mechanistic data related to CTLA-4 Blockade and IFN and potential biomarkers of immunotherapeutic benefit.
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Affiliation(s)
- Arjun Khunger
- Department of Hematology and Oncology, Cleveland Clinic, Cleveland, OH, USA
| | | | | | | | - Ahmad A Tarhini
- Department of Cutaneous Oncology, Moffitt Comprehensive Cancer Center, Tampa, Florida, USA
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Rytlewski JA, Rubinstein MP, Delinger CE, Gibney B, Yusko EC, Sanders C, Wrangle JM, Lindsey K. Abstract 3175: Detection of tumor T-cell clones in mediastinal lymph nodes is associated with lower risk of tumor progression. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-3175] [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: The presence of tumor metastases in standard of care lymph node biopsies during surgical resection is used to help determine clinical prognosis. Given the importance of T cells in mediating anti-tumor responses, we sought to assess the clinical significance of T-Cell Receptor (TCR) usage in matched hilar and mediastinal lymph nodes from non-small cell lung cancer (NSCLC) patients.
Methods: TCR-Beta chains were quantified by the immunoSEQ® Assay (Adaptive Biotechnologies) in primary early-stage NSCLC tissue, matched hilar lymph nodes (proximal), and matched mediastinal lymph nodes (distal) for 27 patients, who were treated with surgical resection. Patients were selected such that half experienced recurrence and half remained recurrence-free over the 30+ months of patient follow-up.
Results: T-cell clonality in resected tumors is significantly correlated (Spearman’s Rho = 0.52, p = 0.0005) but poorly concordant (Pearson’s R2 = 0.14, p = 0.05) with hilar and mediastinal lymph node clonality. The clonality of hilar and mediastinal lymph nodes is both significantly correlated and moderately concordant (Spearman’s Rho = 0.7, p << 0.01; Pearson’s R2 = 0.44, p = 0.0001). 70-80% of top T-cell clones in tumors were detected in at least one lymph node, and the 100 most abundant tumor clones comprised a median 8.4% and 7.5% of the hilar and mediastinal lymph node repertoires of progression-free subjects, and 7.6% and 6.4% of subjects with tumor progression. Aside from the traditional lymphvascular invasion assessment by histopathology and PET SUVs, the abundance of the top 100 tumor clones and the fraction of top 100 tumor clones detected in the mediastinal lymph node were both independently predictive of early-stage NSCLC progression-free survival (Cox Likelihood p = 0.031 and 0.017, respectively). A 10% increase in the abundance of top 100 tumor clones was associated with a 2.3x increase in risk for progression, suggesting that greater tumor repertoire diversity is favorable in the surgical resection setting. In contrast, for every 10 tumor clones detected in the mediastinal lymph node, the risk of progression decreased by 0.32x, suggesting that increased T-cell trafficking between the tumor and more distant lymph nodes is a favorable prognostic biomarker.
Conclusion: The representation of top tumor T-cell clones is fairly similar in hilar and mediastinal lymph nodes. However, the detection of more top tumor clones in the mediastinal lymph nodes is strongly associated with less risk of progression after surgical tumor resection. This biomarker is likely a surrogate for more robust T-cell trafficking between the tumor and lymph circulation and may be a novel hallmark of better patient outcomes.
Disclaimers: For Research Use Only. Not for use in diagnostic procedures.
Citation Format: Julie A. Rytlewski, Mark P. Rubinstein, Chadrick E. Delinger, Barry Gibney, Erik C. Yusko, Catherine Sanders, John M. Wrangle, Kathryn Lindsey. Detection of tumor T-cell clones in mediastinal lymph nodes is associated with lower risk of tumor progression [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 3175.
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Affiliation(s)
| | | | | | - Barry Gibney
- 2Medical University of South Carolina, Charleston, SC
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Khunger A, Rytlewski J, Yusko EC, Tarhini AA. Clonal expansion of tumor infiltrating lymphocytes (TILs) in the peripheral blood of metastatic melanoma patients is significantly associated with response to CTLA4 blockade-based immunotherapy. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.2541] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
2541 Background: Patients with metastatic melanoma were treated on a clinical trial with tremelimumab and High Dose Interferon-Alfa (HDI) (Tarhini. J Clin Oncol. 2012). We previously reported that patients who achieved disease control and clinical response had significantly greater T-cell clonality (p = 0.0008) and T-cell fraction (p = 0.044) respectively in their pretreatment tumor biopsy samples (Tarhini. J Clin Oncol. 2017). In this study, we further characterize T-cell repertoire clonality and clonal expansion in the peripheral blood at different time points to evaluate the association between repertoire features and clinical response. Methods: Patients received tremelimumab 15 mg/kg I.V. every 12 weeks and HDI was given concurrently. Responses were assessed by RECIST as complete (CR) or partial (PR), stable disease (SD) or progression (PD). Peripheral blood mononuclear cells (PBMCs) from treated patients (N = 33) were obtained at baseline, day 29, and day 85 (following tremelimumab-HDI treatment); tumor samples at baseline were also obtained (N = 18). The T-cell receptor beta chain (TCRB) repertoire of PBMCs and tumor samples was immunosequenced using the immunoSEQ assay (Adaptive Biotechnologies), and repertoire clonality was assessed at baseline, day 29, and day 85. Differential abundance analysis was used to detect and quantify peripheral clonal expansion pre- versus post-treatment and identify the subset of peripheral clones also detected in the tumor repertoire. The Morisita Index of repertoire similarity was also calculated to compare global repertoire changes between pre- and post-treatment PBMC samples. Results: T-cell repertoire turnover, as measured by the Morisita Index, showed a trend towards responders (CR/PR) having greater turnover (lower Morisita Index) post-treatment than non-responders (SD/PD). Similarly, the total number of clones expanding in the peripheral repertoire varied over time within an individual (p = 0.034) but was not significantly affected by response to therapy (p = 0.275) or by on-treatment time point (p = 0.768). When the analysis was restricted to peripherally expanded clones that were also found in the tumor repertoire, responders had significantly more TILs expanded in the periphery at day 29 than non-responders (p = 0.036). Conclusions: Our analysis of the peripheral T-cell repertoire following treatment showed that detection of TILs in early peripheral clonal expansion correlates with response to therapy.
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Affiliation(s)
| | | | | | - Ahmad A. Tarhini
- Case Comprehensive Cancer Center/Cleveland Clinic Taussig Cancer Institute, Cleveland, OH
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Nordstrom JL, Muth J, Erskine CL, Sanders C, Yusko EC, Emerson RO, Lee MJ, Lee S, Trepel JB, Im SA, Bang YJ, Giaccone G, Bauer TM, Burris HA, Baughman JE, Rock EP, Moore PA, Bonvini E, Knutson KL. High frequency of HER2-specific immunity observed in patients (pts) with HER2+ cancers treated with margetuximab (M), an Fc-enhanced anti-HER2 monoclonal antibody (mAb). J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.1030] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
1030 Background: Previous studies have shown that 44-71% of trastuzumab (T)-treated pts develop HER2-specific immunity (Clin Cancer Res 2007, 13:5133; Cancer Res 2016, 76:3702; Breast Cancer Res 2018, 20:52). M is an Fc-engineered mAb that shares similar HER2 binding and antiproliferative activity as T. The Fc region of M has been engineered for increased affinity to the activating FcγRIIIA (CD16A) and lower binding to the inhibitory FcγRIIB (CD32B), attributes that may enhance the mAb’s immune function, such as antigen presentation. Methods: HER2+ cancer pts who progressed on prior therapy received M (0.1-6 mg/kg QW for 3 of every 4 weeks [N = 34]; or 10-18 mg/kg Q3W [N = 32]) in phase 1 trial NCT01148849. PBMC and plasma were collected pre-dose and 50 days post-dose for 46 pts and > 4 years for 3 pts on long-term treatment. Response to HER2 or control antigens (Ag) was assessed by IFNγ ELISpot and antibody (Ab) ELISA. In 14 pts, T-cell antigen receptor (TCR) repertoire was assessed by immunosequencing. Results: Following M treatment, mean frequencies of IFNγ-producing T cells specific for intra- or extracellular fragments of HER2 increased by 2.5 to 6-fold (p < 0.0027, paired t test). Most (95%) of subjects responded to ≥2 of 6 (median = 5) HER2 Ag. Mean HER2-specific Ab concentration increased by 19-54% (p < 0.0001), with all subjects responding to ≥2 (median = 5) of the 6 Ag. A small 1.6-fold increase in IFNγ response to control CMV/EBV/Flu (but not tetanus or cyclin D1) peptides was observed; no increase in Ab response to control Ag was noted. Subsets of HER2-specific T-cell and Ab responses persisted during long-term treatment. Median TCR clonality increased by 54% (p = 0.003), with an average of 125 unique clones expanding, while overall TCR diversity remained unchanged (p = 0.19). Conclusions: Treatment of HER2+ cancer with M was associated with enhanced HER2-specific T-cell and Ab responses together with increased TCR clonality, indicative of a more focused T-cell repertoire. The high frequency of HER2-specific immunity in M-treated patients ( > 95%) is consistent with its enhanced Fc region contributing to linkage of innate and adaptive immune responses.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Seock-Ah Im
- Seoul National University Hospital, Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Yung-Jue Bang
- Seoul National University College of Medicine, Seoul, South Korea
| | | | | | | | | | - Edwin P. Rock
- Otsuka Pharmaceutical Dev and Commercialization Inc, Rockville, MD
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Agdashian D, ElGindi M, Xie C, Sandhu M, Pratt D, Kleiner DE, Figg WD, Rytlewski JA, Sanders C, Yusko EC, Wood B, Venzon D, Brar G, Duffy AG, Greten TF, Korangy F. The effect of anti-CTLA4 treatment on peripheral and intra-tumoral T cells in patients with hepatocellular carcinoma. Cancer Immunol Immunother 2019; 68:599-608. [PMID: 30688989 PMCID: PMC6662600 DOI: 10.1007/s00262-019-02299-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [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: 06/28/2018] [Accepted: 01/06/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND Checkpoint inhibitors have recently been approved for the treatment of patients with hepatocellular carcinoma (HCC). However, biomarkers, which will help identify patients responding to therapy, are missing. We recently tested the combination of anti-CTLA4 treatment (tremelimumab) with loco-regional therapy in patients with HCC and reported a partial response rate of 26%. METHODS Here, we report updated survival analyses and results from our immune monitoring studies on peripheral blood mononuclear cells (PBMCs) and tumors from these patients. RESULTS Tremelimumab therapy increased CD4+-HLA-DR+, CD4+PD-1+, CD8+HLA-DR+, CD8+PD-1+, CD4+ICOS+ and CD8+ICOS+ T cells in the peripheral blood of the treated patients. Patients with higher CD4+PD1+ cell frequency at baseline were more likely to respond to tremelimumab therapy. PD-1 expression was increased on alpha fetal protein (AFP) and survivin-specific CD8 T cells upon tremelimumab treatment. An increase of tumor infiltrating CD3+ T cells were also seen in these patients. Immunosequencing of longitudinal PBMC showed that one cycle of tremelimumab significantly decreased peripheral clonality, while no additional effects were seen after loco-regional therapy. CONCLUSION In summary, we observed a clear activation of T cell responses in HCC patients treated with tremelimumab and identified potential biomarkers which will help identify patients responding to immunotherapy with anti-CTLA4.
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MESH Headings
- Adult
- Aged
- Antineoplastic Agents, Immunological/pharmacology
- Biomarkers
- CTLA-4 Antigen/antagonists & inhibitors
- Carcinoma, Hepatocellular/drug therapy
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/immunology
- Carcinoma, Hepatocellular/pathology
- Cell Line, Tumor
- Cytotoxicity, Immunologic
- Female
- Genes, T-Cell Receptor beta
- Humans
- Immunophenotyping
- Liver Neoplasms/drug therapy
- Liver Neoplasms/genetics
- Liver Neoplasms/immunology
- Liver Neoplasms/pathology
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
- Male
- Middle Aged
- Neoplasm Staging
- Pilot Projects
- T-Lymphocyte Subsets/immunology
- T-Lymphocyte Subsets/metabolism
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Affiliation(s)
- David Agdashian
- Gastrointestinal Malignancies Section, Thoracic and GI Oncology Branch, Center for Cancer Research, National Cancer Institute (NCI), National Institutes of Health (NIH), Building 10, Room 3B43, Bethesda, MD, 20892, USA
| | - Mei ElGindi
- Gastrointestinal Malignancies Section, Thoracic and GI Oncology Branch, Center for Cancer Research, National Cancer Institute (NCI), National Institutes of Health (NIH), Building 10, Room 3B43, Bethesda, MD, 20892, USA
| | - Changqing Xie
- Gastrointestinal Malignancies Section, Thoracic and GI Oncology Branch, Center for Cancer Research, National Cancer Institute (NCI), National Institutes of Health (NIH), Building 10, Room 3B43, Bethesda, MD, 20892, USA
| | - Milan Sandhu
- Gastrointestinal Malignancies Section, Thoracic and GI Oncology Branch, Center for Cancer Research, National Cancer Institute (NCI), National Institutes of Health (NIH), Building 10, Room 3B43, Bethesda, MD, 20892, USA
| | - Drew Pratt
- Laboratory of Pathology, Center for Cancer Research (CCR) National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - David E Kleiner
- Laboratory of Pathology, Center for Cancer Research (CCR) National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - William D Figg
- Clinical Pharmacology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | | | - Bradford Wood
- Center for Interventional Oncology, Radiology and Imaging Sciences and Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA
| | - David Venzon
- Biostatistics and Data Management Section, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gagandeep Brar
- Gastrointestinal Malignancies Section, Thoracic and GI Oncology Branch, Center for Cancer Research, National Cancer Institute (NCI), National Institutes of Health (NIH), Building 10, Room 3B43, Bethesda, MD, 20892, USA
| | - Austin G Duffy
- Gastrointestinal Malignancies Section, Thoracic and GI Oncology Branch, Center for Cancer Research, National Cancer Institute (NCI), National Institutes of Health (NIH), Building 10, Room 3B43, Bethesda, MD, 20892, USA
| | - Tim F Greten
- Gastrointestinal Malignancies Section, Thoracic and GI Oncology Branch, Center for Cancer Research, National Cancer Institute (NCI), National Institutes of Health (NIH), Building 10, Room 3B43, Bethesda, MD, 20892, USA.
- NCI CCR Liver Cancer Program, Bethesda, MD, USA.
| | - Firouzeh Korangy
- Gastrointestinal Malignancies Section, Thoracic and GI Oncology Branch, Center for Cancer Research, National Cancer Institute (NCI), National Institutes of Health (NIH), Building 10, Room 3B43, Bethesda, MD, 20892, USA
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Tarhini A, Lin Y, Lin H, Rahman Z, Vallabhaneni P, Mendiratta P, Pingpank JF, Holtzman MP, Yusko EC, Rytlewski JA, Rao UNM, Ferris RL, Kirkwood JM. Neoadjuvant ipilimumab (3 mg/kg or 10 mg/kg) and high dose IFN-α2b in locally/regionally advanced melanoma: safety, efficacy and impact on T-cell repertoire. J Immunother Cancer 2018; 6:112. [PMID: 30352626 PMCID: PMC6199801 DOI: 10.1186/s40425-018-0428-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [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: 07/31/2018] [Accepted: 10/10/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Neoadjuvant immunotherapy utilizing novel combinations has the potential to transform the standard of care for locally/regionally advanced melanoma. We hypothesized that neoadjuvant ipilimumab in combination with high dose IFNα2b (HDI) is safe and associated with durable pathologic complete responses (pCR). METHODS Patients with locally/regionally advanced melanoma were randomized to ipilimumab 3 or 10 mg/kg × 4 doses bracketing definitive surgery, then every 12 weeks × 4. HDI was given concurrently. We evaluated the safety and efficacy of the combination with ipilimumab 3 or 10 mg/kg. The impact on T-cell fraction and clonality were investigated in tumor and blood. RESULTS Thirty patients (age 37-76), 15 each at 3 and 10 mg/kg, 18 male and 12 female were treated. Considering immune related adverse events (irAEs) of interest, more grade 3/4 irAEs were seen with ipilimumab 10 mg/kg versus 3 mg/kg (p = 0.042). Among 28 evaluable patients, 11 relapsed, of whom 5 died. Median follow-up for 17 patients who have not relapsed was 32 months. The radiologic preoperative response rate was 36% (95% CI, 21-54); 4 patients at ipilimumab 3 mg/kg and 6 at 10 mg/kg and 2 (at 10 mg/kg) later relapsed. The pCR was 32% (95% CI, 18-51); 5 patients at ipilimumab 3 mg/kg and 4 at 10 mg/kg and one (at 3 mg/kg) had a late relapse. In patients with pCR, T-cell fraction was significantly higher when measured in primary melanoma tumors (p = 0.033). Higher tumor T-cell clonality in primary tumor and more so following neoadjuvant therapy was significantly associated with improved relapse free survival. CONCLUSIONS Neoadjuvant ipilimumab-HDI was relatively safe and exhibited promising tumor response rates with an associated measurable impact on T-cell fraction and clonality. Most pCRs were durable supporting the value of pCR as a primary endpoint in neoadjuvant immunotherapy trials. TRIAL REGISTRATION ClinicalTrials.gov, NCT01608594 . Registered 31 May 2012.
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Affiliation(s)
- Ahmad Tarhini
- UPMC Hillman Cancer Center, Pittsburgh, USA. .,Department of Hematology and Oncology, Cleveland Clinic Taussig Cancer Institute and Case Comprehensive Cancer Center, 9500 Euclid Ave CA6-157, Cleveland, OH, 44195, USA.
| | - Yan Lin
- UPMC Hillman Cancer Center, Pittsburgh, USA
| | - Huang Lin
- UPMC Hillman Cancer Center, Pittsburgh, USA
| | | | | | - Prateek Mendiratta
- Department of Hematology and Oncology, Cleveland Clinic Taussig Cancer Institute and Case Comprehensive Cancer Center, 9500 Euclid Ave CA6-157, Cleveland, OH, 44195, USA
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Hopkins AC, Yarchoan M, Durham JN, Yusko EC, Rytlewski JA, Robins HS, Laheru DA, Le DT, Lutz ER, Jaffee EM. T cell receptor repertoire features associated with survival in immunotherapy-treated pancreatic ductal adenocarcinoma. JCI Insight 2018; 3:122092. [PMID: 29997287 PMCID: PMC6124515 DOI: 10.1172/jci.insight.122092] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [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: 05/08/2018] [Accepted: 05/31/2018] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Immune checkpoint inhibitors provide significant clinical benefit to a subset of patients, but novel prognostic markers are needed to predict which patients will respond. This study was initiated to determine if features of patient T cell repertoires could provide insights into the mechanisms of immunotherapy, while also predicting outcomes. METHODS We examined T cell receptor (TCR) repertoires in peripheral blood of 25 metastatic pancreatic cancer patients treated with ipilimumab with or without GVAX (a pancreatic cancer vaccine), as well as peripheral blood and tumor biopsies from 32 patients treated with GVAX and mesothelin-expressing Listeria monocytogenes with or without nivolumab. Statistics from these repertoires were then tested for their association with clinical response and treatment group. RESULTS We demonstrate that, first, the majority of patients receiving these treatments experience a net diversification of their peripheral TCR repertoires. Second, patients receiving ipilimumab experienced larger changes in their repertoires, especially in combination with GVAX. Finally, both a low baseline clonality and a high number of expanded clones following treatment were associated with significantly longer survival in patients who received ipilimumab but not in patients receiving nivolumab. CONCLUSIONS We show that these therapies have measurably different effects on the peripheral repertoire, consistent with their mechanisms of action, and demonstrate the potential for TCR repertoire profiling to serve as a biomarker of clinical response in pancreatic cancer patients receiving immunotherapy. In addition, our results suggest testing sequential administration of anti-CTLA-4 and anti-PD-1 antibodies to achieve optimal therapeutic benefit. TRIAL REGISTRATION Samples used in this study were collected from the NCT00836407 and NCT02243371 clinical trials. FUNDING Research supported by a Stand Up To Cancer Lustgarten Foundation Pancreatic Cancer Convergence Dream Team Translational Research grant (SU2C-AACR-DT14-14). Stand Up To Cancer is a program of the Entertainment Industry Foundation administered by the American Association for Cancer Research (AACR). Additional clinical trial funding was provided by AACR-Pancreatic Cancer Action Network Research Acceleration Network grant (14-90-25-LE), NCI SPORE in GI Cancer (CA062924), Quick-Trials for Novel Cancer Therapies: Exploratory Grants (R21CA126058-01A2), and the US Food and Drug Administration (R01FD004819). Research collaboration and financial support were provided by Adaptive Biotechnologies.
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Affiliation(s)
- Alexander C. Hopkins
- Johns Hopkins University, Sidney Kimmel Cancer Center, Skip Viragh Center for Pancreas Cancer, The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Baltimore, Maryland, USA
| | - Mark Yarchoan
- Johns Hopkins University, Sidney Kimmel Cancer Center, Skip Viragh Center for Pancreas Cancer, The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Baltimore, Maryland, USA
| | - Jennifer N. Durham
- Johns Hopkins University, Sidney Kimmel Cancer Center, Skip Viragh Center for Pancreas Cancer, The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Baltimore, Maryland, USA
| | | | | | | | - Daniel A. Laheru
- Johns Hopkins University, Sidney Kimmel Cancer Center, Skip Viragh Center for Pancreas Cancer, The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Baltimore, Maryland, USA
| | - Dung T. Le
- Johns Hopkins University, Sidney Kimmel Cancer Center, Skip Viragh Center for Pancreas Cancer, The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Baltimore, Maryland, USA
| | - Eric R. Lutz
- Johns Hopkins University, Sidney Kimmel Cancer Center, Skip Viragh Center for Pancreas Cancer, The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Baltimore, Maryland, USA
| | - Elizabeth M. Jaffee
- Johns Hopkins University, Sidney Kimmel Cancer Center, Skip Viragh Center for Pancreas Cancer, The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Baltimore, Maryland, USA
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9
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Wrangle JM, Velcheti V, Patel MR, Garrett-Mayer E, Hill EG, Ravenel JG, Miller JS, Farhad M, Anderton K, Lindsey K, Taffaro-Neskey M, Sherman C, Suriano S, Swiderska-Syn M, Sion A, Harris J, Edwards AR, Rytlewski JA, Sanders CM, Yusko EC, Robinson MD, Krieg C, Redmond WL, Egan JO, Rhode PR, Jeng EK, Rock AD, Wong HC, Rubinstein MP. ALT-803, an IL-15 superagonist, in combination with nivolumab in patients with metastatic non-small cell lung cancer: a non-randomised, open-label, phase 1b trial. Lancet Oncol 2018; 19:694-704. [PMID: 29628312 DOI: 10.1016/s1470-2045(18)30148-7] [Citation(s) in RCA: 281] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 01/31/2018] [Accepted: 02/01/2018] [Indexed: 12/18/2022]
Abstract
BACKGROUND Immunotherapy with PD-1 or PD-L1 blockade fails to induce a response in about 80% of patients with unselected non-small cell lung cancer (NSCLC), and many of those who do initially respond then develop resistance to treatment. Agonists that target the shared interleukin-2 (IL-2) and IL-15Rβγ pathway have induced complete and durable responses in some cancers, but no studies have been done to assess the safety or efficacy of these agonists in combination with anti-PD-1 immunotherapy. We aimed to define the safety, tolerability, and activity of this drug combination in patients with NSCLC. METHODS In this non-randomised, open-label, phase 1b trial, we enrolled patients (aged ≥18 years) with previously treated histologically or cytologically confirmed stage IIIB or IV NSCLC from three academic hospitals in the USA. Key eligibility criteria included measurable disease, eligibility to receive anti-PD-1 immunotherapy, and an Eastern Cooperative Oncology Group performance status of 0 or 1. Patients received the anti-PD-1 monoclonal antibody nivolumab intravenously at 3 mg/kg (then 240 mg when US Food and Drug Administration [FDA]-approved dosing changed) every 14 days (either as new treatment or continued treatment at the time of disease progression) and the IL-15 superagonist ALT-803 subcutaneously once per week on weeks 1-5 of four 6-week cycles for 6 months. ALT-803 was administered at one of four escalating dose concentrations: 6, 10, 15, or 20 μg/kg. The primary endpoint was to define safety and tolerability and to establish a recommended phase 2 dose of ALT-803 in combination with nivolumab. Analyses were per-protocol and included any patients who received at least one dose of study treatment. This trial is registered with ClinicalTrials.gov, number NCT02523469; phase 2 enrolment of patients is ongoing. FINDINGS Between Jan 18, 2016, and June 28, 2017, 23 patients were enrolled and 21 were treated at four dose levels of ALT-803 in combination with nivolumab. Two patients did not receive treatment because of the development of inter-current illness during enrolment, one patient due to leucopenia and one patient due to pulmonary dysfunction. No dose-limiting toxicities were recorded and the maximum tolerated dose was not reached. The most common adverse events were injection-site reactions (in 19 [90%] of 21 patients) and flu-like symptoms (15 [71%]). The most common grade 3 adverse events, occurring in two patients each, were lymphocytopenia and fatigue. A grade 3 myocardial infarction occurred in one patient. No grade 4 or 5 adverse events were recorded. The recommended phase 2 dose of ALT-803 is 20 μg/kg given once per week subcutaneously in combination with 240 mg intravenous nivolumab every 2 weeks. INTERPRETATION ALT-803 in combination with nivolumab can be safely administered in an outpatient setting. The promising clinical activity observed with the addition of ALT-803 to the regimen of patients with PD-1 monoclonal antibody relapsed and refractory disease shows evidence of anti-tumour activity for a new class of agents in NSCLC. FUNDING Altor BioScience (a NantWorks company), National Institutes of Health, and Medical University of South Carolina Hollings Cancer Center.
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Affiliation(s)
- John M Wrangle
- Department of Medicine, Division of Hematology and Oncology, and Department of Surgery Medical University of South Carolina, Charleston, SC, USA
| | | | - Manish R Patel
- Department of Medicine, Division of Hematology, Oncology, and Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Elizabeth Garrett-Mayer
- Department of Medicine, Division of Hematology and Oncology, and Department of Surgery Medical University of South Carolina, Charleston, SC, USA
| | - Elizabeth G Hill
- Department of Medicine, Division of Hematology and Oncology, and Department of Surgery Medical University of South Carolina, Charleston, SC, USA
| | - James G Ravenel
- Department of Medicine, Division of Hematology and Oncology, and Department of Surgery Medical University of South Carolina, Charleston, SC, USA
| | - Jeffrey S Miller
- Department of Medicine, Division of Hematology, Oncology, and Transplantation, University of Minnesota, Minneapolis, MN, USA
| | | | - Kate Anderton
- Department of Medicine, Division of Hematology and Oncology, and Department of Surgery Medical University of South Carolina, Charleston, SC, USA
| | - Kathryn Lindsey
- Department of Medicine, Division of Hematology and Oncology, and Department of Surgery Medical University of South Carolina, Charleston, SC, USA
| | - Michele Taffaro-Neskey
- Department of Medicine, Division of Hematology and Oncology, and Department of Surgery Medical University of South Carolina, Charleston, SC, USA
| | - Carol Sherman
- Department of Medicine, Division of Hematology and Oncology, and Department of Surgery Medical University of South Carolina, Charleston, SC, USA
| | - Samantha Suriano
- Department of Medicine, Division of Hematology and Oncology, and Department of Surgery Medical University of South Carolina, Charleston, SC, USA
| | - Marzena Swiderska-Syn
- Department of Medicine, Division of Hematology and Oncology, and Department of Surgery Medical University of South Carolina, Charleston, SC, USA
| | - Amy Sion
- Department of Medicine, Division of Hematology and Oncology, and Department of Surgery Medical University of South Carolina, Charleston, SC, USA
| | - Joni Harris
- Department of Medicine, Division of Hematology and Oncology, and Department of Surgery Medical University of South Carolina, Charleston, SC, USA
| | - Andie R Edwards
- Department of Medicine, Division of Hematology and Oncology, and Department of Surgery Medical University of South Carolina, Charleston, SC, USA
| | | | | | | | - Mark D Robinson
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Carsten Krieg
- Department of Medicine, Division of Hematology and Oncology, and Department of Surgery Medical University of South Carolina, Charleston, SC, USA
| | | | | | | | | | | | | | - Mark P Rubinstein
- Department of Medicine, Division of Hematology and Oncology, and Department of Surgery Medical University of South Carolina, Charleston, SC, USA.
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10
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Dovedi SJ, Cheadle EJ, Popple AL, Poon E, Morrow M, Stewart R, Yusko EC, Sanders CM, Vignali M, Emerson RO, Robins HS, Wilkinson RW, Honeychurch J, Illidge TM. Fractionated Radiation Therapy Stimulates Antitumor Immunity Mediated by Both Resident and Infiltrating Polyclonal T-cell Populations when Combined with PD-1 Blockade. Clin Cancer Res 2017; 23:5514-5526. [PMID: 28533222 DOI: 10.1158/1078-0432.ccr-16-1673] [Citation(s) in RCA: 245] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 11/17/2016] [Accepted: 05/16/2017] [Indexed: 12/18/2022]
Abstract
Purpose: Radiotherapy is a highly effective anticancer treatment forming part of the standard of care for the majority of patients, but local and distal disease recurrence remains a major cause of mortality. Radiotherapy is known to enhance tumor immunogenicity; however, the contribution and mechanisms of radiotherapy-induced immune responses are unknown.Experimental Design: The impact of low-dose fractionated radiotherapy (5 × 2 Gy) alone and in combination with αPD-1 mAb on the tumor microenvironment was evaluated by flow cytometry and next-generation sequencing of the T-cell receptor (TCR) repertoire. A dual-tumor model was used, with fractionated radiotherapy delivered to a single tumor site to enable evaluation of the local and systemic response to treatment and ability to induce abscopal responses outside the radiation field.Results: We show that fractionated radiotherapy leads to T-cell infiltration at the irradiated site; however, the TCR landscape remains dominated by polyclonal expansion of preexisting T-cell clones. Adaptive resistance via the PD-1/PD-L1 pathway restricts the generation of systemic anticancer immunity following radiotherapy, which can be overcome through combination with αPD-1 mAb leading to improved local and distal tumor control. Moreover, we show that effective clearance of tumor following combination therapy is dependent on both T cells resident in the tumor at the time of radiotherapy and infiltrating T cells.Conclusions: These data provide evidence that radiotherapy can enhance T-cell trafficking to locally treated tumor sites and augment preexisting anticancer T-cell responses with the capacity to mediate regression of out-of-field tumor lesions when delivered in combination with αPD-1 mAb therapy. Clin Cancer Res; 23(18); 5514-26. ©2017 AACR.
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MESH Headings
- Animals
- Antineoplastic Agents, Hormonal/pharmacology
- Cell Line, Tumor
- Combined Modality Therapy
- Cytokines/metabolism
- Disease Models, Animal
- Humans
- Lymphocytes, Tumor-Infiltrating/drug effects
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
- Lymphocytes, Tumor-Infiltrating/radiation effects
- Mice
- Neoplasms/immunology
- Neoplasms/metabolism
- Neoplasms/pathology
- Neoplasms/therapy
- Programmed Cell Death 1 Receptor/antagonists & inhibitors
- Programmed Cell Death 1 Receptor/metabolism
- Radiotherapy
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- Survival Rate
- T-Lymphocyte Subsets/drug effects
- T-Lymphocyte Subsets/immunology
- T-Lymphocyte Subsets/metabolism
- T-Lymphocyte Subsets/radiation effects
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Simon J Dovedi
- Targeted Therapy Group, Division of Molecular and Clinical Cancer Sciences, Manchester Cancer Research Centre, Christie Hospital, Manchester Academic Health Sciences Centre, United Kingdom.
- MedImmune Ltd., Granta Park, Cambridge, United Kingdom
| | - Eleanor J Cheadle
- Targeted Therapy Group, Division of Molecular and Clinical Cancer Sciences, Manchester Cancer Research Centre, Christie Hospital, Manchester Academic Health Sciences Centre, United Kingdom
| | - Amy L Popple
- Targeted Therapy Group, Division of Molecular and Clinical Cancer Sciences, Manchester Cancer Research Centre, Christie Hospital, Manchester Academic Health Sciences Centre, United Kingdom
| | - Edmund Poon
- MedImmune Ltd., Granta Park, Cambridge, United Kingdom
| | | | - Ross Stewart
- MedImmune Ltd., Granta Park, Cambridge, United Kingdom
| | | | | | | | | | | | | | - Jamie Honeychurch
- Targeted Therapy Group, Division of Molecular and Clinical Cancer Sciences, Manchester Cancer Research Centre, Christie Hospital, Manchester Academic Health Sciences Centre, United Kingdom
| | - Timothy M Illidge
- Targeted Therapy Group, Division of Molecular and Clinical Cancer Sciences, Manchester Cancer Research Centre, Christie Hospital, Manchester Academic Health Sciences Centre, United Kingdom.
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11
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Reuben A, Gittelman R, Gao J, Zhang J, Yusko EC, Wu CJ, Emerson R, Zhang J, Tipton C, Li J, Quek K, Gopalakrishnan V, Chen R, Vence LM, Cascone T, Vignali M, Fujimoto J, Rodriguez-Canales J, Parra ER, Little LD, Gumbs C, Forget MA, Federico L, Haymaker C, Behrens C, Benzeno S, Bernatchez C, Sepesi B, Gibbons DL, Wargo JA, William WN, Swisher S, Heymach JV, Robins H, Lee JJ, Sharma P, Allison JP, Futreal PA, Wistuba II, Zhang J. TCR Repertoire Intratumor Heterogeneity in Localized Lung Adenocarcinomas: An Association with Predicted Neoantigen Heterogeneity and Postsurgical Recurrence. Cancer Discov 2017; 7:1088-1097. [PMID: 28733428 DOI: 10.1158/2159-8290.cd-17-0256] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 06/01/2017] [Accepted: 07/19/2017] [Indexed: 12/27/2022]
Abstract
Genomic intratumor heterogeneity (ITH) may be associated with postsurgical relapse of localized lung adenocarcinomas. Recently, mutations, through generation of neoantigens, were shown to alter tumor immunogenicity through T-cell responses. Here, we performed sequencing of the T-cell receptor (TCR) in 45 tumor regions from 11 localized lung adenocarcinomas and observed substantial intratumor differences in T-cell density and clonality with the majority of T-cell clones restricted to individual tumor regions. TCR ITH positively correlated with predicted neoantigen ITH, suggesting that spatial differences in the T-cell repertoire may be driven by distinct neoantigens in different tumor regions. Finally, a higher degree of TCR ITH was associated with an increased risk of postsurgical relapse and shorter disease-free survival, suggesting a potential clinical significance of T-cell repertoire heterogeneity.Significance: The present study provides insights into the ITH of the T-cell repertoire in localized lung adenocarcinomas and its potential biological and clinical impact. The results suggest that T-cell repertoire ITH may be tightly associated to genomic ITH and disease relapse. Cancer Discov; 7(10); 1088-97. ©2017 AACR.This article is highlighted in the In This Issue feature, p. 1047.
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Affiliation(s)
- Alexandre Reuben
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Jianjun Gao
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jiexin Zhang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Chang-Jiun Wu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Jun Li
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kelly Quek
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Runzhe Chen
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Luis M Vence
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Tina Cascone
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Junya Fujimoto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jaime Rodriguez-Canales
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Edwin R Parra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Latasha D Little
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Curtis Gumbs
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Marie-Andrée Forget
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lorenzo Federico
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Cara Haymaker
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Carmen Behrens
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Chantale Bernatchez
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Boris Sepesi
- Department of Thoracic Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Don L Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jennifer A Wargo
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - William N William
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Stephen Swisher
- Department of Thoracic Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Harlan Robins
- Adaptive Biotechnologies, Seattle, Washington.,Department of Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - J Jack Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Padmanee Sharma
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - James P Allison
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - P Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Jianjun Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas. .,Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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12
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Yusko EC, Bruhn BR, Eggenberger OM, Houghtaling J, Rollings RC, Walsh NC, Nandivada S, Pindrus M, Hall AR, Sept D, Li J, Kalonia DS, Mayer M. Real-time shape approximation and fingerprinting of single proteins using a nanopore. Nat Nanotechnol 2017; 12:360-367. [PMID: 27992411 DOI: 10.1038/nnano.2016.267] [Citation(s) in RCA: 290] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 11/03/2016] [Indexed: 05/18/2023]
Abstract
Established methods for characterizing proteins typically require physical or chemical modification steps or cannot be used to examine individual molecules in solution. Ionic current measurements through electrolyte-filled nanopores can characterize single native proteins in an aqueous environment, but currently offer only limited capabilities. Here we show that the zeptolitre sensing volume of bilayer-coated solid-state nanopores can be used to determine the approximate shape, volume, charge, rotational diffusion coefficient and dipole moment of individual proteins. To do this, we developed a theory for the quantitative understanding of modulations in ionic current that arise from the rotational dynamics of single proteins as they move through the electric field inside the nanopore. The approach allows us to measure the five parameters simultaneously, and we show that they can be used to identify, characterize and quantify proteins and protein complexes with potential implications for structural biology, proteomics, biomarker detection and routine protein analysis.
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Affiliation(s)
- Erik C Yusko
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Brandon R Bruhn
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Olivia M Eggenberger
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, CH-1700 Fribourg, Switzerland
| | - Jared Houghtaling
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, CH-1700 Fribourg, Switzerland
| | - Ryan C Rollings
- Department of Physics, University of Arkansas, Fayetteville, Arkansas 72701, USA
| | - Nathan C Walsh
- Department of Physics, University of Arkansas, Fayetteville, Arkansas 72701, USA
| | - Santoshi Nandivada
- Department of Physics, University of Arkansas, Fayetteville, Arkansas 72701, USA
| | - Mariya Pindrus
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Adam R Hall
- Department of Biomedical Engineering and Comprehensive Cancer Center, Wake Forest University School of Medicine, Winston Salem, North Carolina 27157, USA
| | - David Sept
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
- Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Jiali Li
- Department of Physics, University of Arkansas, Fayetteville, Arkansas 72701, USA
| | - Devendra S Kalonia
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Michael Mayer
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, CH-1700 Fribourg, Switzerland
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, USA
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13
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Fong KK, Sarangapani KK, Yusko EC, Riffle M, Llauró A, Graczyk B, Davis TN, Asbury CL. Direct measurement of the strength of microtubule attachment to yeast centrosomes. Mol Biol Cell 2017; 28:1853-1861. [PMID: 28331072 PMCID: PMC5541836 DOI: 10.1091/mbc.e17-01-0034] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [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: 01/17/2017] [Revised: 03/13/2017] [Accepted: 03/17/2017] [Indexed: 01/14/2023] Open
Abstract
Laser trapping is used to manipulate single attached microtubules in vitro. Direct mechanical measurement shows that attachment of microtubule minus ends to yeast spindle pole bodies is extraordinarily strong. Centrosomes, or spindle pole bodies (SPBs) in yeast, are vital mechanical hubs that maintain load-bearing attachments to microtubules during mitotic spindle assembly, spindle positioning, and chromosome segregation. However, the strength of microtubule-centrosome attachments is unknown, and the possibility that mechanical force might regulate centrosome function has scarcely been explored. To uncover how centrosomes sustain and regulate force, we purified SPBs from budding yeast and used laser trapping to manipulate single attached microtubules in vitro. Our experiments reveal that SPB–microtubule attachments are extraordinarily strong, rupturing at forces approximately fourfold higher than kinetochore attachments under identical loading conditions. Furthermore, removal of the calmodulin-binding site from the SPB component Spc110 weakens SPB–microtubule attachment in vitro and sensitizes cells to increased SPB stress in vivo. These observations show that calmodulin binding contributes to SPB mechanical integrity and suggest that its removal may cause pole delamination and mitotic failure when spindle forces are elevated. We propose that the very high strength of SPB–microtubule attachments may be important for spindle integrity in mitotic cells so that tensile forces generated at kinetochores do not cause microtubule detachment and delamination at SPBs.
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Affiliation(s)
- Kimberly K Fong
- Department of Biochemistry, University of Washington, Seattle, WA 98195
| | - Krishna K Sarangapani
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195
| | - Erik C Yusko
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195
| | - Michael Riffle
- Department of Biochemistry, University of Washington, Seattle, WA 98195
| | - Aida Llauró
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195
| | - Beth Graczyk
- Department of Biochemistry, University of Washington, Seattle, WA 98195
| | - Trisha N Davis
- Department of Biochemistry, University of Washington, Seattle, WA 98195
| | - Charles L Asbury
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195
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14
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Abstract
Cells sense biochemical, electrical, and mechanical cues in their environment that affect their differentiation and behavior. Unlike biochemical and electrical signals, mechanical signals can propagate without the diffusion of proteins or ions; instead, forces are transmitted through mechanically stiff structures, flowing, for example, through cytoskeletal elements such as microtubules or filamentous actin. The molecular details underlying how cells respond to force are only beginning to be understood. Here we review tools for probing force-sensitive proteins and highlight several examples in which forces are transmitted, routed, and sensed by proteins in cells. We suggest that local unfolding and tension-dependent removal of autoinhibitory domains are common features in force-sensitive proteins and that force-sensitive proteins may be commonplace wherever forces are transmitted between and within cells. Because mechanical forces are inherent in the cellular environment, force is a signal that cells must take advantage of to maintain homeostasis and carry out their functions.
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Affiliation(s)
- Erik C Yusko
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195-7290
| | - Charles L Asbury
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195-7290
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15
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Vinnakota A, Bruhn BR, Yusko EC, Mayer M. Single Molecule Characterization of Cholera Toxin and its Interaction with Gm1 Gangliosides Using Lipid-Coated Nanopores. Biophys J 2015. [DOI: 10.1016/j.bpj.2014.11.961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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16
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Majd S, Yusko EC, Yang J, Sept D, Mayer M. A model for the interfacial kinetics of phospholipase D activity on long-chain lipids. Biophys J 2014; 105:146-53. [PMID: 23823233 DOI: 10.1016/j.bpj.2013.05.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 05/02/2013] [Accepted: 05/06/2013] [Indexed: 11/26/2022] Open
Abstract
The membrane-active enzyme phospholipase D (PLD) catalyzes the hydrolysis of the phosphodiester bond in phospholipids and plays a critical role in cell signaling. This catalytic reaction proceeds on lipid-water interfaces and is an example of heterogeneous catalysis in biology. Recently we showed that planar lipid bilayers, a previously unexplored model membrane for these kinetic studies, can be used for monitoring interfacial catalytic reactions under well-defined experimental conditions with chemical and electrical access to both sides of the lipid membrane. Employing an assay that relies on the conductance of the pore-forming peptide gramicidin A to monitor PLD activity, the work presented here reveals the kinetics of hydrolysis of long-chain phosphatidylcholine lipids in situ. We have developed an extension of a basic kinetic model for interfacial catalysis that includes product activation and substrate depletion. This model describes the kinetic behavior very well and reveals two kinetic parameters, the specificity constant and the interfacial quality constant. This approach results in a simple and general model to account for product accumulation in interfacial enzyme kinetics.
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Affiliation(s)
- Sheereen Majd
- Department of Bioengineering, Pennsylvania State University, University Park, Pennsylvania, USA.
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Bruhn BR, Yusko EC, Eggenberger O, Rollings RC, Walsh NC, Pindrus M, Sept D, Li J, Kalonia DS, Mayer M. Characterizing Shape, Dipole Moment, and Rotation of Single Proteins in Nanopores. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.1253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Yusko EC, Bruhn BR, Rollings RC, Li J, Sept D, Mayer M. Nanopores with Fluid Walls for Determining the Shape, Dipole Moment, and Rotational Diffusion Coefficient of Non-Spherical Proteins. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.2888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Prangkio P, Yusko EC, Sept D, Yang J, Mayer M. Multivariate analyses of amyloid-beta oligomer populations indicate a connection between pore formation and cytotoxicity. PLoS One 2012; 7:e47261. [PMID: 23077580 PMCID: PMC3471831 DOI: 10.1371/journal.pone.0047261] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [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: 07/25/2012] [Accepted: 09/07/2012] [Indexed: 11/18/2022] Open
Abstract
Aggregates of amyloid-beta (Aβ) peptides are thought to be involved in the development of Alzheimer's disease because they can change synaptic plasticity and induce neuronal cell death by inflammation, oxidative damage, and transmembrane pore formation. Exactly which oligomeric species underlie these cytotoxic effects remains unclear. The work presented here established well-controlled aggregation conditions of Aβ₁₋₄₀ or Aβ₁₋₄₂ peptides over a 20-day period and characterized these preparations with regard to their β-sheet content, degree of fibril formation, relative abundance of various oligomer sizes, and propensity to induce membrane pore formation and cytotoxicity. Using this multivariate data set, a systematic and inherently unbiased partial least squares (PLS) approach showed that for both peptides the abundance of oligomers in the tetramer to 13-mer range contributed positively to both pore formation and cytotoxicity, while monomers, dimers, trimers, and the largest oligomers (>210 kDa) were negatively correlated to both phenomena. Multivariate PLS analysis is ideally suited to handle complex data sets and interdependent variables such as relative oligomer concentrations, making it possible to elucidate structure function relationships in complex mixtures. This approach, therefore, introduces an enabling tool to the field of amyloid research, in which it is often difficult to interpret the activity of individual species within a complex mixture of bioactive species.
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Affiliation(s)
- Panchika Prangkio
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
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Abstract
Determining the pathological role of amyloids in amyloid-associated diseases will require a method for characterizing the dynamic distributions in size and shape of amyloid oligomers with high resolution. Here, we explored the potential of resistive-pulse sensing through lipid bilayer-coated nanopores to measure the size of individual amyloid-β oligomers directly in solution and without chemical modification. This method classified individual amyloid-β aggregates as spherical oligomers, protofibrils, or mature fibers and made it possible to account for the large heterogeneity of amyloid-β aggregate sizes. The approach revealed the distribution of protofibrillar lengths (12- to 155 -mer) as well as the average cross-sectional area of protofibrils and fibers.
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Affiliation(s)
- Erik C. Yusko
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Panchika Prangkio
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - David Sept
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Ryan C. Rollings
- Department of Physics, University of Arkansas, Fayetteville, Arkansas, 72701, USA
| | - Jiali Li
- Department of Physics, University of Arkansas, Fayetteville, Arkansas, 72701, USA
| | - Michael Mayer
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
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Yusko EC, Petti AM, Prangkio P, Rollings RC, Li J, Yang J, Mayer M. Developing Nanopores with Fluid Walls for Improved, Single-Molecule Biosensors. Biophys J 2012. [DOI: 10.1016/j.bpj.2011.11.2349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Yusko EC, Johnson JM, Majd S, Prangkio P, Rollings RC, Li J, Yang J, Mayer M. Controlling protein translocation through nanopores with bio-inspired fluid walls. Nat Nanotechnol 2011; 6:253-60. [PMID: 21336266 PMCID: PMC3071889 DOI: 10.1038/nnano.2011.12] [Citation(s) in RCA: 471] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Accepted: 01/17/2011] [Indexed: 05/18/2023]
Abstract
Synthetic nanopores have been used to study individual biomolecules in high throughput, but their performance as sensors does not match that of biological ion channels. Challenges include control of nanopore diameters and surface chemistry, modification of the translocation times of single-molecule analytes through nanopores, and prevention of non-specific interactions with pore walls. Here, inspired by the olfactory sensilla of insect antennae, we show that coating nanopores with a fluid lipid bilayer tailors their surface chemistry and allows fine-tuning and dynamic variation of pore diameters in subnanometre increments. Incorporation of mobile ligands in the lipid bilayer conferred specificity and slowed the translocation of targeted proteins sufficiently to time-resolve translocation events of individual proteins. Lipid coatings also prevented pores from clogging, eliminated non-specific binding and enabled the translocation of amyloid-beta (Aβ) oligomers and fibrils. Through combined analysis of their translocation time, volume, charge, shape and ligand affinity, different proteins were identified.
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Affiliation(s)
- Erik C. Yusko
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jay M. Johnson
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sheereen Majd
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Panchika Prangkio
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ryan C. Rollings
- Department of Physics, University of Arkansas, Fayetteville, AR 72701, USA
| | - Jiali Li
- Department of Physics, University of Arkansas, Fayetteville, AR 72701, USA
| | - Jerry Yang
- Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093, USA
| | - Michael Mayer
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
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Yusko EC, Billeh YN, Mayer M. Current oscillations generated by precipitate formation in the mixing zone between two solutions inside a nanopore. J Phys Condens Matter 2010; 22:454127. [PMID: 21339613 DOI: 10.1088/0953-8984/22/45/454127] [Citation(s) in RCA: 2] [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] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Unlike biological protein pores in lipid membranes, nanopores fabricated in synthetic materials can withstand a wide range of environmental conditions including the presence of organic solvents. This capability expands the potential of synthetic nanopores to monitor chemical reactions occurring at the interface between solutions of organic and aqueous character. In this work, nanopores fabricated in borosilicate glass or silicon nitride connected a predominantly organic solvent to an aqueous solvent, thereby generating a mixing zone between these solutions inside the pore. This configuration was exploited to precipitate small organic molecules with low aqueous solubility inside the nanopores, and concomitantly, to monitor this precipitation by the decrease of the ionic conductance through the nanopores over time. Hence, this method provides a means to induce and investigate the formation of nanoprecipitates or nanoparticles. Interestingly, precipitates with a slight electric charge were cleared from the pore, causing the conductance of the pore to return to its original value. This process repeated, resulting in stable oscillations of the ionic current. Although such oscillations might be useful in fluidic logic circuits, few conditions capable of generating oscillations in ionic currents have been reported. The frequency and amplitude of oscillations could be tuned by changing the concentration of the precipitating molecule, the pH of the electrolyte, and the applied potential bias. In addition to generating oscillations, nanopores that separate two different solutions may be useful for monitoring and mediating chemical reactions in the mixing zone between two solutions.
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Affiliation(s)
- Erik C Yusko
- Department of Biomedical Engineering, University of Michigan, 1101 Beal Avenue, Lurie Biomedical Engineering Building, Room 2174, Ann Arbor, MI 48109-2110, USA
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Majd S, Yusko EC, Billeh YN, Macrae MX, Yang J, Mayer M. Applications of biological pores in nanomedicine, sensing, and nanoelectronics. Curr Opin Biotechnol 2010; 21:439-76. [PMID: 20561776 PMCID: PMC3121537 DOI: 10.1016/j.copbio.2010.05.002] [Citation(s) in RCA: 264] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2010] [Revised: 05/03/2010] [Accepted: 05/06/2010] [Indexed: 12/29/2022]
Abstract
Biological protein pores and pore-forming peptides can generate a pathway for the flux of ions and other charged or polar molecules across cellular membranes. In nature, these nanopores have diverse and essential functions that range from maintaining cell homeostasis and participating in cell signaling to activating or killing cells. The combination of the nanoscale dimensions and sophisticated - often regulated - functionality of these biological pores make them particularly attractive for the growing field of nanobiotechnology. Applications range from single-molecule sensing to drug delivery and targeted killing of malignant cells. Potential future applications may include the use of nanopores for single strand DNA sequencing and for generating bio-inspired, and possibly, biocompatible visual detection systems and batteries. This article reviews the current state of applications of pore-forming peptides and proteins in nanomedicine, sensing, and nanoelectronics.
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Affiliation(s)
- Sheereen Majd
- Department of Biomedical Engineering, University of Michigan, 1101 Beal Avenue, Ann Arbor, Michigan 48109-2110, USA
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Abstract
This paper introduces a strategy for generating ion current rectification through nano- and micropores. This method generates ion current rectification by electroosmotic-driven flow of liquids of varying viscosity (and hence varying conductance) into or out of the narrowest constriction of a pore. The magnitude of current rectification was described by a rectification factor, R(f), which is defined by the ratio of the current measured at a positive voltage divided by the current measured at a negative voltage. This method achieved rectification factors in the range of 5-15 using pores with diameters ranging from 10 nm to 2.2 microm. These R(f) values are similar to the rectification factors reported in other nanopore-based methods that did not employ segmented surface charges. Interestingly, this work showed that in cylindrical nanopores with diameters of 10 nm and a length of at least 275 nm, electroosmotic flow was present and could generate ion current rectification. Unlike previous methods for generating ion current rectification that require nanopores with diameters comparable to the Debye length, this work demonstrated ion current rectification in micropores with diameters 500 times larger than the Debye length. Thus this method extends the concept of fluidic diodes to the micropore range. Several experiments designed to alter or remove electroosmotic flow through the pore demonstrated that electroosmotic flow was required for the mode of ion current rectification reported here. Consequently, the magnitude of current rectification could be used to indicate the presence of electroosmotic flow and the breakdown of electroosmotic flow with decreasing ionic strength and hence increasing electric double layer overlap inside nanopores.
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Affiliation(s)
- Erik C Yusko
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, 48109-2110, USA
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Abstract
Phospholipases constitute a ubiquitous class of membrane-active enzymes that play a key role in cellular signaling, proliferation, and membrane trafficking. Aberrant phospholipase activity is implicated in a range of diseases including cancer, inflammation, and myocardial disease. Characterization of these enzymes is therefore important, both for improving the understanding of phospholipase catalysis and for accelerating pharmaceutical and biotechnological applications. This paper describes a novel approach to monitor, in situ and in real-time, the activity of phospholipase D (PLD) and phospholipase C (PLC) on planar lipid bilayers. This method is based on lipase-induced changes in the electrical charge of lipid bilayers and on the concomitant change in ion concentration near lipid membranes. The approach reports these changes in local ion concentration by a measurable change in the single channel ion conductance through pores of the ion channel-forming peptide gramicidin A. This enzyme assay takes advantage of the amplification characteristics of gramicidin pores to sense the activity of picomolar to nanomolar concentrations of membrane-active enzymes without requiring labeled substrates or products. The resulting method proceeds on lipid bilayers without the need for detergents, quantifies enzyme activity on native lipid substrates within minutes, and provides unique access to both leaflets of well-defined lipid bilayers; this method also makes it possible to generate planar lipid bilayers with transverse lipid asymmetry.
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Affiliation(s)
- Sheereen Majd
- Department of Chemical Engineering, University of Michigan, 1101 Beal Avenue, Ann Arbor, Michigan 48109-2110, USA
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28
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Abstract
We demonstrate rapid fabrication of submicrometer-diameter pores in borosilicate glass using femtosecond laser machining and subsequent wet-etch techniques. This approach allows direct and repeatable fabrication of high-quality pores with diameters of 400-800 nm. Such small pores coupled with the desirable electrical and chemical properties of glass enable sensitive resistive-pulse analysis to determine the size and concentration of macromolecules and nanoparticles. Plasma-enhanced chemical vapor deposition allows further reduction of pore diameters to below 300 nm.
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Affiliation(s)
- Ran An
- Department of Biomedical Engineering, University of Michigan, Michigan 48109, USA
- Center for Ultrafast Optical Science, University of Michigan, Michigan 48109, USA
| | - Jeffrey D. Uram
- Department of Biomedical Engineering, University of Michigan, Michigan 48109, USA
| | - Erik C. Yusko
- Department of Biomedical Engineering, University of Michigan, Michigan 48109, USA
| | - Kevin Ke
- Department of Biomedical Engineering, University of Michigan, Michigan 48109, USA
- Center for Ultrafast Optical Science, University of Michigan, Michigan 48109, USA
| | - Michael Mayer
- Department of Biomedical Engineering, University of Michigan, Michigan 48109, USA
- Department of Chemical Engineering, University of Michigan, Michigan 48109, USA
| | - Alan J. Hunt
- Department of Biomedical Engineering, University of Michigan, Michigan 48109, USA
- Center for Ultrafast Optical Science, University of Michigan, Michigan 48109, USA
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