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Lynch AR, Bradford S, Zhou AS, Oxendine K, Henderson L, Horner VL, Weaver BA, Burkard ME. A survey of chromosomal instability measures across mechanistic models. Proc Natl Acad Sci U S A 2024; 121:e2309621121. [PMID: 38588415 PMCID: PMC11032477 DOI: 10.1073/pnas.2309621121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 01/25/2024] [Indexed: 04/10/2024] Open
Abstract
Chromosomal instability (CIN) is the persistent reshuffling of cancer karyotypes via chromosome mis-segregation during cell division. In cancer, CIN exists at varying levels that have differential effects on tumor progression. However, mis-segregation rates remain challenging to assess in human cancer despite an array of available measures. We evaluated measures of CIN by comparing quantitative methods using specific, inducible phenotypic CIN models of chromosome bridges, pseudobipolar spindles, multipolar spindles, and polar chromosomes. For each, we measured CIN fixed and timelapse fluorescence microscopy, chromosome spreads, six-centromere FISH, bulk transcriptomics, and single-cell DNA sequencing (scDNAseq). As expected, microscopy of tumor cells in live and fixed samples significantly correlated (R = 0.72; P < 0.001) and sensitively detect CIN. Cytogenetics approaches include chromosome spreads and 6-centromere FISH, which also significantly correlate (R = 0.76; P < 0.001) but had limited sensitivity for lower rates of CIN. Bulk genomic DNA signatures and bulk transcriptomic scores, CIN70 and HET70, did not detect CIN. By contrast, scDNAseq detects CIN with high sensitivity, and significantly correlates with imaging methods (R = 0.82; P < 0.001). In summary, single-cell methods such as imaging, cytogenetics, and scDNAseq can measure CIN, with the latter being the most comprehensive method accessible to clinical samples. To facilitate the comparison of CIN rates between phenotypes and methods, we propose a standardized unit of CIN: Mis-segregations per Diploid Division. This systematic analysis of common CIN measures highlights the superiority of single-cell methods and provides guidance for measuring CIN in the clinical setting.
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Affiliation(s)
- Andrew R. Lynch
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, WI53705
- McArdle Laboratory for Cancer Research, University of Wisconsin–Madison, Madison, WI53705
| | - Shermineh Bradford
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, WI53705
- McArdle Laboratory for Cancer Research, University of Wisconsin–Madison, Madison, WI53705
| | - Amber S. Zhou
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, WI53705
- McArdle Laboratory for Cancer Research, University of Wisconsin–Madison, Madison, WI53705
| | - Kim Oxendine
- Cytogenetic and Molecular Genetic Services Laboratory, Wisconsin State Laboratory of Hygiene, University of Wisconsin–Madison, Madison, WI53706
| | - Les Henderson
- Cytogenetic and Molecular Genetic Services Laboratory, Wisconsin State Laboratory of Hygiene, University of Wisconsin–Madison, Madison, WI53706
| | - Vanessa L. Horner
- Cytogenetic and Molecular Genetic Services Laboratory, Wisconsin State Laboratory of Hygiene, University of Wisconsin–Madison, Madison, WI53706
| | - Beth A. Weaver
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, WI53705
- McArdle Laboratory for Cancer Research, University of Wisconsin–Madison, Madison, WI53705
- Department of Cell and Regenerative Biology, University of Wisconsin–Madison, Madison, WI53705
| | - Mark E. Burkard
- Carbone Cancer Center, University of Wisconsin–Madison, Madison, WI53705
- McArdle Laboratory for Cancer Research, University of Wisconsin–Madison, Madison, WI53705
- Division of Hematology Oncology and Palliative Care, Department of Medicine University of Wisconsin–Madison, Madison, WI53705
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Zhou AS, Tucker JB, Scribano CM, Lynch AR, Carlsen CL, Pop-Vicas ST, Pattaswamy SM, Burkard ME, Weaver BA. Diverse microtubule-targeted anticancer agents kill cells by inducing chromosome missegregation on multipolar spindles. PLoS Biol 2023; 21:e3002339. [PMID: 37883329 PMCID: PMC10602348 DOI: 10.1371/journal.pbio.3002339] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 09/18/2023] [Indexed: 10/28/2023] Open
Abstract
Microtubule-targeted agents are commonly used for cancer treatment, though many patients do not benefit. Microtubule-targeted drugs were assumed to elicit anticancer activity via mitotic arrest because they cause cell death following mitotic arrest in cell culture. However, we recently demonstrated that intratumoral paclitaxel concentrations are insufficient to induce mitotic arrest and rather induce chromosomal instability (CIN) via multipolar mitotic spindles. Here, we show in metastatic breast cancer and relevant human cellular models that this mechanism is conserved among clinically useful microtubule poisons. While multipolar divisions typically produce inviable progeny, multipolar spindles can be focused into near-normal bipolar spindles at any stage of mitosis. Using a novel method to quantify the rate of CIN, we demonstrate that cell death positively correlates with net loss of DNA. Spindle focusing decreases CIN and causes resistance to diverse microtubule poisons, which can be counteracted by addition of a drug that increases CIN without affecting spindle polarity. These results demonstrate conserved mechanisms of action and resistance for diverse microtubule-targeted agents. Trial registration: clinicaltrials.gov, NCT03393741.
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Affiliation(s)
- Amber S. Zhou
- Molecular and Cellular Pharmacology Graduate Training Program, University of Wisconsin, Madison, Wisconsin, United States of America
| | - John B. Tucker
- Cancer Biology Graduate Training Program, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Christina M. Scribano
- Molecular and Cellular Pharmacology Graduate Training Program, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Andrew R. Lynch
- Cellular and Molecular Pathology Graduate Training Program, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Caleb L. Carlsen
- Cellular and Molecular Biology Graduate Training Program, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Sophia T. Pop-Vicas
- Department of Cell and Regenerative Biology, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Srishrika M. Pattaswamy
- Department of Cell and Regenerative Biology, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Mark E. Burkard
- Department of Medicine, University of Wisconsin, Madison, Wisconsin, United States of America
- Department of Oncology/McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, Wisconsin, United States of America
- Carbone Cancer Center, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Beth A. Weaver
- Department of Cell and Regenerative Biology, University of Wisconsin, Madison, Wisconsin, United States of America
- Department of Oncology/McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, Wisconsin, United States of America
- Carbone Cancer Center, University of Wisconsin, Madison, Wisconsin, United States of America
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3
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Lynch AR, Bradford S, Zhou AS, Oxendine K, Henderson L, Horner VL, Weaver BA, Burkard ME. A survey of CIN measures across mechanistic models. bioRxiv 2023:2023.06.15.544840. [PMID: 37398147 PMCID: PMC10312700 DOI: 10.1101/2023.06.15.544840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Chromosomal instability (CIN) is the persistent reshuffling of cancer karyotypes via chromosome mis-segregation during cell division. In cancer, CIN exists at varying levels that have differential effects on tumor progression. However, mis-segregation rates remain challenging to assess in human cancer despite an array of available measures. We evaluated measures of CIN by comparing quantitative methods using specific, inducible phenotypic CIN models of chromosome bridges, pseudobipolar spindles, multipolar spindles, and polar chromosomes. For each, we measured CIN fixed and timelapse fluorescence microscopy, chromosome spreads, 6-centromere FISH, bulk transcriptomics, and single cell DNA sequencing (scDNAseq). As expected, microscopy of tumor cells in live and fixed samples correlated well (R=0.77; p<0.01) and sensitively detect CIN. Cytogenetics approaches include chromosome spreads and 6-centromere FISH, which also correlate well (R=0.77; p<0.01) but had limited sensitivity for lower rates of CIN. Bulk genomic DNA signatures and bulk transcriptomic scores, CIN70 and HET70, did not detect CIN. By contrast, single-cell DNA sequencing (scDNAseq) detects CIN with high sensitivity, and correlates very well with imaging methods (R=0.83; p<0.01). In summary, single-cell methods such as imaging, cytogenetics, and scDNAseq can measure CIN, with the latter being the most comprehensive method accessible to clinical samples. To facilitate comparison of CIN rates between phenotypes and methods, we propose a standardized unit of CIN: Mis-segregations per Diploid Division (MDD). This systematic analysis of common CIN measures highlights the superiority of single-cell methods and provides guidance for measuring CIN in the clinical setting.
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Affiliation(s)
- Andrew R. Lynch
- Carbone Cancer Center, University of Wisconsin – Madison, Madison, WI, USA
- McArdle Laboratory for Cancer Research, University of Wisconsin – Madison, Madison, WI, USA
| | - Shermineh Bradford
- Carbone Cancer Center, University of Wisconsin – Madison, Madison, WI, USA
- McArdle Laboratory for Cancer Research, University of Wisconsin – Madison, Madison, WI, USA
| | - Amber S. Zhou
- Carbone Cancer Center, University of Wisconsin – Madison, Madison, WI, USA
- McArdle Laboratory for Cancer Research, University of Wisconsin – Madison, Madison, WI, USA
| | - Kim Oxendine
- Wisconsin State Laboratory of Hygiene, University of Wisconsin – Madison, Madison, WI, USA
| | - Les Henderson
- Wisconsin State Laboratory of Hygiene, University of Wisconsin – Madison, Madison, WI, USA
| | - Vanessa L. Horner
- Wisconsin State Laboratory of Hygiene, University of Wisconsin – Madison, Madison, WI, USA
| | - Beth A. Weaver
- Carbone Cancer Center, University of Wisconsin – Madison, Madison, WI, USA
- McArdle Laboratory for Cancer Research, University of Wisconsin – Madison, Madison, WI, USA
- Department of Cell and Regenerative Biology, University of Wisconsin – Madison, Madison, WI, USA
| | - Mark E. Burkard
- Carbone Cancer Center, University of Wisconsin – Madison, Madison, WI, USA
- McArdle Laboratory for Cancer Research, University of Wisconsin – Madison, Madison, WI, USA
- Division of Hematology Oncology and Palliative Care, Department of Medicine, University of Wisconsin – Madison, Madison, WI, USA
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Lynch AR, Arp NL, Zhou AS, Weaver BA, Burkard ME. Quantifying chromosomal instability from intratumoral karyotype diversity using agent-based modeling and Bayesian inference. eLife 2022; 11:e69799. [PMID: 35380536 PMCID: PMC9054132 DOI: 10.7554/elife.69799] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 04/01/2022] [Indexed: 12/03/2022] Open
Abstract
Chromosomal instability (CIN)-persistent chromosome gain or loss through abnormal mitotic segregation-is a hallmark of cancer that drives aneuploidy. Intrinsic chromosome mis-segregation rate, a measure of CIN, can inform prognosis and is a promising biomarker for response to anti-microtubule agents. However, existing methodologies to measure this rate are labor intensive, indirect, and confounded by selection against aneuploid cells, which reduces observable diversity. We developed a framework to measure CIN, accounting for karyotype selection, using simulations with various levels of CIN and models of selection. To identify the model parameters that best fit karyotype data from single-cell sequencing, we used approximate Bayesian computation to infer mis-segregation rates and karyotype selection. Experimental validation confirmed the extensive chromosome mis-segregation rates caused by the chemotherapy paclitaxel (18.5 ± 0.5/division). Extending this approach to clinical samples revealed that inferred rates fell within direct observations of cancer cell lines. This work provides the necessary framework to quantify CIN in human tumors and develop it as a predictive biomarker.
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Affiliation(s)
- Andrew R Lynch
- Carbone Cancer Center, University of Wisconsin-MadisonMadisonUnited States
- McArdle Laboratory for Cancer Research, University of Wisconsin-MadisonMadisonUnited States
| | - Nicholas L Arp
- Carbone Cancer Center, University of Wisconsin-MadisonMadisonUnited States
| | - Amber S Zhou
- Carbone Cancer Center, University of Wisconsin-MadisonMadisonUnited States
- McArdle Laboratory for Cancer Research, University of Wisconsin-MadisonMadisonUnited States
| | - Beth A Weaver
- Carbone Cancer Center, University of Wisconsin-MadisonMadisonUnited States
- McArdle Laboratory for Cancer Research, University of Wisconsin-MadisonMadisonUnited States
- Department of Cell and Regenerative Biology, University of WisconsinMadisonUnited States
| | - Mark E Burkard
- Carbone Cancer Center, University of Wisconsin-MadisonMadisonUnited States
- McArdle Laboratory for Cancer Research, University of Wisconsin-MadisonMadisonUnited States
- Division of Hematology Medical Oncology and Palliative Care, Department of Medicine University of WisconsinMadisonUnited States
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Scribano CM, Wan J, Esbona K, Tucker JB, Lasek A, Zhou AS, Zasadil LM, Molini R, Fitzgerald J, Lager AM, Laffin JJ, Correia-Staudt K, Wisinski KB, Tevaarwerk AJ, O’Regan R, McGregor SM, Fowler AM, Chappell RJ, Bugni TS, Burkard ME, Weaver BA. Chromosomal instability sensitizes patient breast tumors to multipolar divisions induced by paclitaxel. Sci Transl Med 2021; 13:eabd4811. [PMID: 34516829 PMCID: PMC8612166 DOI: 10.1126/scitranslmed.abd4811] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [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] [Indexed: 12/20/2022]
Abstract
Paclitaxel (Taxol) is a cornerstone of cancer treatment. However, its mechanism of cytotoxicity is incompletely understood and not all patients benefit from treatment. We show that patients with breast cancer did not accumulate sufficient intratumoral paclitaxel to induce mitotic arrest in tumor cells. Instead, clinically relevant concentrations induced multipolar mitotic spindle formation. However, the extent of early multipolarity did not predict patient response. Whereas multipolar divisions frequently led to cell death, multipolar spindles focused into bipolar spindles before division at variable frequency, and maintaining multipolarity throughout mitosis was critical to induce the high rates of chromosomal instability necessary for paclitaxel to elicit cell death. Increasing multipolar divisions in paclitaxel resulted in improved cytotoxicity. Conversely, decreasing paclitaxel-induced multipolar divisions reduced paclitaxel efficacy. Moreover, we found that preexisting chromosomal instability sensitized breast cancer cells to paclitaxel. Both genetic and pharmacological methods of inducing chromosomal instability were sufficient to increase paclitaxel efficacy. In patients, the amount of pretreatment chromosomal instability directly correlated with taxane response in metastatic breast cancer such that patients with a higher rate of preexisting chromosomal instability showed improved response to taxanes. Together, these results support the use of baseline rates of chromosomal instability as a predictive biomarker for paclitaxel response. Furthermore, they suggest that agents that increase chromosomal instability or maintain multipolar spindles throughout mitosis will improve the clinical utility of paclitaxel.
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Affiliation(s)
- Christina M. Scribano
- Molecular and Cellular Pharmacology Graduate Training Program, University of Wisconsin, Madison, WI 53705, USA
| | - Jun Wan
- Physiology Graduate Training Program, University of Wisconsin, Madison, WI 53705, USA
| | - Karla Esbona
- Department of Medicine, University of Wisconsin, Madison, WI 53705, USA
| | - John B. Tucker
- Cancer Biology Graduate Training Program, University of Wisconsin, Madison, WI 53705, USA
| | - Amber Lasek
- Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI 53705, USA
| | - Amber S. Zhou
- Molecular and Cellular Pharmacology Graduate Training Program, University of Wisconsin, Madison, WI 53705, USA
| | - Lauren M. Zasadil
- Molecular and Cellular Pharmacology Graduate Training Program, University of Wisconsin, Madison, WI 53705, USA
| | - Ryan Molini
- Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI 53705, USA
| | - Jonathan Fitzgerald
- Molecular and Cellular Pharmacology Graduate Training Program, University of Wisconsin, Madison, WI 53705, USA
| | - Angela M. Lager
- Wisconsin State Laboratory of Hygiene, Madison, WI 53705, USA
| | | | | | - Kari B. Wisinski
- Department of Medicine, University of Wisconsin, Madison, WI 53705, USA
| | | | - Ruth O’Regan
- Department of Medicine, University of Wisconsin, Madison, WI 53705, USA
| | - Stephanie M. McGregor
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI 53705, USA
| | - Amy M. Fowler
- Department of Radiology, University of Wisconsin, Madison, WI 53792, USA
- Department of Medical Physics, University of Wisconsin, Madison, WI 53705, USA
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | | | - Tim S. Bugni
- School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA
| | - Mark E. Burkard
- Department of Medicine, University of Wisconsin, Madison, WI 53705, USA
- Department of Oncology/McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, WI 53705, USA
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Beth A. Weaver
- Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI 53705, USA
- Department of Oncology/McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, WI 53705, USA
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53705, USA
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6
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Gardner MR, Fellinger CH, Kattenhorn LM, Davis-Gardner ME, Weber JA, Alfant B, Zhou AS, Prasad NR, Kondur HR, Newton WA, Weisgrau KL, Rakasz EG, Lifson JD, Gao G, Schultz-Darken N, Farzan M. AAV-delivered eCD4-Ig protects rhesus macaques from high-dose SIVmac239 challenges. Sci Transl Med 2020; 11:11/502/eaau5409. [PMID: 31341061 DOI: 10.1126/scitranslmed.aau5409] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 02/09/2019] [Accepted: 05/31/2019] [Indexed: 12/17/2022]
Abstract
A number of simian and simian human immunodeficiency viruses (SIV and SHIV, respectively) have been used to assess the efficacy of HIV-1 vaccine strategies. Among these, SIVmac239 is considered among the most stringent because, unlike SHIV models, its full genome has coevolved in its macaque host and its tier 3 envelope glycoprotein (Env) is exceptionally hard to neutralize. Here, we investigated the ability of eCD4-Ig, an antibody-like entry inhibitor that emulates the HIV-1 and SIV receptor and coreceptor, to prevent SIVmac239 infection. We show that rh-eCD4-IgI39N expressed by recombinant adeno-associated virus (AAV) vectors afforded four rhesus macaques complete protection from high-dose SIVmac239 challenges that infected all eight control macaques. However, rh-eCD4-IgI39N-expressing macaques eventually succumbed to serial escalating challenge doses that were 2, 8, 16, and 32 times the challenge doses that infected the control animals. Despite receiving greater challenge doses, these macaques had significantly lower peak and postpeak viral loads than the control group. Virus isolated from three of four macaques showed evidence of strong immune pressure from rh-eCD4-IgI39N, with mutations located in the CD4-binding site, which, in one case, exploited a point-mutation difference between rh-eCD4-IgI39N and rhesus CD4. Other escape pathways associated with clear fitness costs to the virus. Our data report effective protection of rhesus macaques from SIVmac239.
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Affiliation(s)
- Matthew R Gardner
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA.
| | - Christoph H Fellinger
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Lisa M Kattenhorn
- Department of Microbiology and Immunobiology, Harvard Medical School, New England Primate Research Center, Southborough, MA 01772, USA
| | - Meredith E Davis-Gardner
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Jesse A Weber
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Barnett Alfant
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Amber S Zhou
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Neha R Prasad
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Hema R Kondur
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Wendy A Newton
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53715 USA
| | - Kimberly L Weisgrau
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53715 USA
| | - Eva G Rakasz
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53715 USA
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA.,Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Nancy Schultz-Darken
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53715 USA
| | - Michael Farzan
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA.
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Fellinger CH, Gardner MR, Weber JA, Alfant B, Zhou AS, Farzan M. eCD4-Ig Limits HIV-1 Escape More Effectively than CD4-Ig or a Broadly Neutralizing Antibody. J Virol 2019; 93:e00443-19. [PMID: 31068428 PMCID: PMC6600210 DOI: 10.1128/jvi.00443-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 04/23/2019] [Indexed: 01/30/2023] Open
Abstract
The engineered antibody-like entry inhibitor eCD4-Ig neutralizes every human immunodeficiency virus type 1 (HIV-1), HIV-2, and simian immunodeficiency virus isolate it has been tested against. The exceptional breadth of eCD4-Ig derives from its ability to closely and simultaneously emulate the HIV-1 receptor CD4 and coreceptors, either CCR5 or CXCR4. Here we investigated whether viral escape from eCD4-Ig is more difficult than that from CD4-Ig or the CD4-binding site antibody NIH45-46. We observed that a viral swarm selected with high concentrations of eCD4-Ig was increasingly resistant to but did not fully escape from eCD4-Ig. In contrast, viruses selected under the same conditions with CD4-Ig or NIH45-46 fully escaped from those inhibitors. eCD4-Ig-resistant viruses acquired unique changes in the V2 apex, V3, V4, and CD4-binding regions of the HIV-1 envelope glycoprotein (Env). Most of the alterations did not directly affect neutralization by eCD4-Ig or neutralizing antibodies. However, alteration of Q428 to an arginine or lysine resulted in markedly greater resistance to eCD4-Ig and CD4-Ig, with correspondingly dramatic losses in infectivity and greater sensitivity to a V3 antibody and to serum from an infected individual. Compensatory mutations in the V3 loop (N301D) and in the V2 apex (K171E) partially restored viral fitness without affecting serum or eCD4-Ig sensitivity. Collectively, these data suggest that multiple mutations will be necessary to fully escape eCD4-Ig without loss of viral fitness.IMPORTANCE HIV-1 broadly neutralizing antibodies (bNAbs) and engineered antibody-like inhibitors have been compared for their breadths, potencies, and in vivo half-lives. However, a key limitation in the use of antibodies to treat an established HIV-1 infection is the rapid emergence of fully resistant viruses. Entry inhibitors of similar breadths and potencies can differ in the ease with which viral escape variants arise. Here we show that HIV-1 escape from the potent and exceptionally broad entry inhibitor eCD4-Ig is more difficult than that from CD4-Ig or the bNAb NIH45-46. Indeed, full escape was not observed under conditions under which escape from CD4-Ig or NIH45-46 was readily detected. Moreover, viruses that were partially resistant to eCD4-Ig were markedly less infective and more sensitive to antibodies in the serum of an infected person. These data suggest that eCD4-Ig will be more difficult to escape and that even partial escape will likely extract a high fitness cost.
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Affiliation(s)
- Christoph H Fellinger
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Matthew R Gardner
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Jesse A Weber
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Barnett Alfant
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Amber S Zhou
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
| | - Michael Farzan
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida, USA
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8
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Gardner MR, Fetzer I, Kattenhorn LM, Davis-Gardner ME, Zhou AS, Alfant B, Weber JA, Kondur HR, Martinez-Navio JM, Fuchs SP, Desrosiers RC, Gao G, Lifson JD, Farzan M. Anti-drug Antibody Responses Impair Prophylaxis Mediated by AAV-Delivered HIV-1 Broadly Neutralizing Antibodies. Mol Ther 2019; 27:650-660. [PMID: 30704961 PMCID: PMC6403482 DOI: 10.1016/j.ymthe.2019.01.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [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: 08/19/2018] [Revised: 01/04/2019] [Accepted: 01/08/2019] [Indexed: 11/12/2022] Open
Abstract
Adeno-associated virus (AAV) delivery of potent and broadly neutralizing antibodies (bNAbs is a promising approach for the prevention of HIV-1 infection. The immunoglobulin G (IgG)1 subtype is usually selected for this application, because it efficiently mediates antibody effector functions and has a somewhat longer half-life. However, the use of IgG1-Fc has been associated with the generation of anti-drug antibodies (ADAs) that correlate with loss of antibody expression. In contrast, we have shown that expression of the antibody-like molecule eCD4-Ig bearing a rhesus IgG2-Fc domain showed reduced immunogenicity and completely protected rhesus macaques from simian-HIV (SHIV)-AD8 challenges. To directly compare the performance of the IgG1-Fc and the IgG2-Fc domains in a prophylactic setting, we compared AAV1 expression of rhesus IgG1 and IgG2 forms of four anti-HIV bNAbs: 3BNC117, NIH45-46, 10-1074, and PGT121. Interestingly, IgG2-isotyped bNAbs elicited significantly lower ADA than their IgG1 counterparts. We also observed significant protection from two SHIV-AD8 challenges in macaques expressing IgG2-isotyped bNAbs, but not from those expressing IgG1. Our data suggest that monoclonal antibodies isotyped with IgG2-Fc domains are less immunogenic than their IgG1 counterparts, and they highlight ADAs as a key barrier to the use of AAV1-expressed bNAbs.
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Affiliation(s)
- Matthew R Gardner
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA.
| | - Ina Fetzer
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Lisa M Kattenhorn
- Department of Microbiology and Immunobiology, Harvard Medical School, New England Primate Research Center, Southborough, MA 01772, USA
| | - Meredith E Davis-Gardner
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Amber S Zhou
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Barnett Alfant
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Jesse A Weber
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Hema R Kondur
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Jose M Martinez-Navio
- Department of Pathology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Sebastian P Fuchs
- Department of Pathology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Ronald C Desrosiers
- Department of Pathology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Guangping Gao
- The Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, MA 01605, USA; Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Michael Farzan
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
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Yang E, Gardner MR, Zhou AS, Farzan M, Arvin AM, Oliver SL. HIV-1 inhibitory properties of eCD4-Igmim2 determined using an Env-mediated membrane fusion assay. PLoS One 2018; 13:e0206365. [PMID: 30359435 PMCID: PMC6201953 DOI: 10.1371/journal.pone.0206365] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Accepted: 10/11/2018] [Indexed: 11/19/2022] Open
Abstract
Human Immunodeficiency Virus-1 (HIV-1) entry is dependent on the envelope glycoprotein (Env) that is present on the virion and facilitates fusion between the envelope and the cellular membrane. The protein consists of two subunits, gp120 and gp41, with the former required for binding the CD4 receptor and either the CXCR4 or CCR5 coreceptor, and the latter for mediating fusion. The requirement of fusion for infection has made Env an attractive target for HIV therapy development and led to the FDA approval of enfuvirtide, a fusion inhibitor. Continued development of entry inhibitors is warranted because enfuvirtide resistant HIV-1 strains have emerged. In this study, a novel HIV-1 fusion assay was validated using neutralizing antibodies and then used to investigate the mechanism of action of eCD4-Igmim2, an HIV-1 inhibitor proposed to cooperatively bind the CD4 binding site and the sulfotyrosine-binding pocket of gp120. Greater reduction in fusion levels was observed with eCD4-Igmim2 in the fusion assay than all of the gp120 antibodies evaluated. Lab adapted isolates, HIV-1HXB2 and HIV-1YU2, were sensitive to eCD4-Igmim2 in the fusion assay, while primary isolates, HIV-1BG505 and HIV-1ZM651 were resistant. These results correlated with greater IC50 values for primary isolates compared to the lab adapted isolates observed in a virus neutralization assay. Analysis of gp120 models identified differences in the V1 and V2 domains that are associated with eCD4-Igmim2 sensitivity. This study highlights the use of a fusion assay to identify key areas for improving the potency of eCD4-Igmim2.
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Affiliation(s)
- Edward Yang
- Departments of Pediatrics and Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
| | - Matthew R. Gardner
- Department of Infectious Diseases, The Scripps Research Institute, Jupiter, Florida, United States of America
| | - Amber S. Zhou
- Department of Infectious Diseases, The Scripps Research Institute, Jupiter, Florida, United States of America
| | - Michael Farzan
- Department of Infectious Diseases, The Scripps Research Institute, Jupiter, Florida, United States of America
| | - Ann M. Arvin
- Departments of Pediatrics and Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Stefan L. Oliver
- Departments of Pediatrics and Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, United States of America
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Bhatnagar S, Soni MS, Wrighton LS, Hebert AS, Zhou AS, Paul PK, Gregg T, Rabaglia ME, Keller MP, Coon JJ, Attie AD. Phosphorylation and degradation of tomosyn-2 de-represses insulin secretion. J Biol Chem 2014; 289:25276-86. [PMID: 25002582 DOI: 10.1074/jbc.m114.575985] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The abundance and functional activity of proteins involved in the formation of the SNARE complex are tightly regulated for efficient exocytosis. Tomosyn proteins are negative regulators of exocytosis. Tomosyn causes an attenuation of insulin secretion by limiting the formation of the SNARE complex. We hypothesized that glucose-dependent stimulation of insulin secretion from β-cells must involve reversing the inhibitory action of tomosyn. Here, we show that glucose increases tomosyn protein turnover. Within 1 h of exposure to 15 mM glucose, ~50% of tomosyn was degraded. The degradation of tomosyn in response to high glucose was blocked by inhibitors of the proteasomal pathway. Using (32)P labeling and mass spectrometry, we showed that tomosyn-2 is phosphorylated in response to high glucose, phorbol esters, and analogs of cAMP, all key insulin secretagogues. We identified 11 phosphorylation sites in tomosyn-2. Site-directed mutagenesis was used to generate phosphomimetic (Ser → Asp) and loss-of-function (Ser → Ala) mutants. The Ser → Asp mutant had enhanced protein turnover compared with the Ser → Ala mutant and wild type tomosyn-2. Additionally, the Ser → Asp tomosyn-2 mutant was ineffective at inhibiting insulin secretion. Using a proteomic screen for tomosyn-2-binding proteins, we identified Hrd-1, an E3-ubiquitin ligase. We showed that tomosyn-2 ubiquitination is increased by Hrd-1, and knockdown of Hrd-1 by short hairpin RNA resulted in increased abundance in tomosyn-2 protein levels. Taken together, our results reveal a mechanism by which enhanced phosphorylation of a negative regulator of secretion, tomosyn-2, in response to insulin secretagogues targets it to degradation by the Hrd-1 E3-ubiquitin ligase.
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Affiliation(s)
| | | | | | - Alexander S Hebert
- Chemistry and Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin 53706
| | | | | | | | | | | | - Joshua J Coon
- Chemistry and Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin 53706
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Xue AN, Cai QY, Wang SQ, Zhou AS, Li WX, Fu P, Chen XS. Antioxidant status in persons with and without senile lens changes. Biomed Environ Sci 1996; 9:144-148. [PMID: 8886325] [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] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Biochemical evidence on lens culture suggests that antioxidant nutrients can protect lens against peroxidation caused by radiation. A case-control study was carried out on 262 middle aged (45-54) and aged (55-64) subjects. The relationship between biochemical markers of antioxidant status and senile lens changes (including cataract) was examined in 131 subjects with senile lens changes and 131 control subjects with clear lens. Antioxidant status was measured using plasma and erythrocyte glutathione peroxidase, erythrocyte superoxide dismutase and catalase activity and plasma levels of vitamin E and vitamin A. Subjects were grouped by age and sex. The results were as follows: (1) The subjects with lens changes tended to have lower plasma levels of vitamin E and vitamin A, lower activity of several antioxidant enzymes and higher level of MDA. (2) The subjects with senile lens changes had significantly lower erythrocyte glutathione peroxidase level. (3) In the middle-aged group, subjects with senile lens changes were observed to have lower erythrocyte and plasma glutathione peroxidase level than those without senile lens changes. The results suggest that appropriate amount of antioxidant nutrients might be expected to prevent or retard the process of lens changes.
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Affiliation(s)
- A N Xue
- Department of Geriatric Nutrition, Institute of Nutrition and Food Hygiene, Beijing, China
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