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  • 1
    In: The Lancet, Elsevier BV, Vol. 401, No. 10387 ( 2023-05), p. 1499-1507
    Type of Medium: Online Resource
    ISSN: 0140-6736
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    Language: English
    Publisher: Elsevier BV
    Publication Date: 2023
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  • 2
    Online Resource
    Online Resource
    Wiley ; 2022
    In:  Functional Ecology Vol. 36, No. 12 ( 2022-12), p. 2943-2954
    In: Functional Ecology, Wiley, Vol. 36, No. 12 ( 2022-12), p. 2943-2954
    Abstract: Understanding the factors that control decomposition is critical for predicting how the carbon cycle will alter with global change. Until recently, the accepted paradigm was that climate primarily drives decomposition rates, and interactions among decomposers only control variation at finer scales. Although it is now understood that biotic agents can play an important role, we know less about the importance of species interactions with a lack of field experiments at a large scale. Predation is a key ecological interaction that could influence decomposition by directly or indirectly regulating the abundances of decomposer organisms, but a comprehensive understanding of the cascading effects that predation can have on decomposition, particularly at large scales, is missing. Here we report on an experiment where we suppressed the abundance of ants, which are major predators of termites, at a hectare scale in a natural African savanna and examined how this affected the decomposition of three common substrates (wood, grass and dung). Our study revealed that ants exert considerable top‐down control on decomposition via their predation of termites: decomposition of wood, grass and dung increased by 98%, 74% and 84% with ant suppression, respectively. Suppression of ants increased termite activity and consequently resulted in increased termite‐mediated decomposition. Remarkably, for all substrates, the suppression of ants nearly doubled decomposition by termites. Additionally, for grass and dung substrates, the dominant agent of decomposition switched from microbes to termites with ant suppression. Our study highlights the critical importance of considering species interactions in decomposition studies, particularly given declines in predatory species in the Anthropocene. Read the free Plain Language Summary for this article on the Journal blog.
    Type of Medium: Online Resource
    ISSN: 0269-8463 , 1365-2435
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2022
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  • 3
    In: Nature Biotechnology, Springer Science and Business Media LLC, Vol. 36, No. 8 ( 2018-9), p. 758-764
    Type of Medium: Online Resource
    ISSN: 1087-0156 , 1546-1696
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2018
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    detail.hit.zdb_id: 1311932-1
    SSG: 12
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  • 4
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2022
    In:  Proceedings of the National Academy of Sciences Vol. 119, No. 23 ( 2022-06-07)
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 119, No. 23 ( 2022-06-07)
    Abstract: Dynamic motions of enzymes occurring on a broad range of timescales play a pivotal role in all steps of the reaction pathway, including substrate binding, catalysis, and product release. However, it is unknown whether structural information related to conformational flexibility can be exploited for the directed evolution of enzymes with higher catalytic activity. Here, we show that mutagenesis of residues exclusively located at flexible regions distal to the active site of Homo sapiens kynureninase (HsKYNase) resulted in the isolation of a variant (BF-HsKYNase) in which the rate of the chemical step toward kynurenine was increased by 45-fold. Mechanistic pre–steady-state kinetic analysis of the wild type and the evolved enzyme shed light on the underlying effects of distal mutations ( 〉 10 Å from the active site) on the rate-limiting step of the catalytic cycle. Hydrogen-deuterium exchange coupled to mass spectrometry and molecular dynamics simulations revealed that the amino acid substitutions in BF-HsKYNase allosterically affect the flexibility of the pyridoxal-5′-phosphate (PLP) binding pocket, thereby impacting the rate of chemistry, presumably by altering the conformational ensemble and sampling states more favorable to the catalyzed reaction.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    RVK:
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2022
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  • 5
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 77, No. 13_Supplement ( 2017-07-01), p. 5570-5570
    Abstract: Checkpoint inhibitors have become the cornerstone for new innovation in immune-based oncology therapy. Several orthogonal immune pathways are currently being investigated to relieve suppression or boost activity of the innate and adaptive immune system. The IDO immune-metabolism pathway was recently clinically validated in melanoma in combination with checkpoint inhibition. This opens up a new approach to relieving suppressive mediators and lends credence to the tumor microenvironment containing small molecule metabolites that induce immune tolerance. Both indoleamine-pyrrole 2,3-dioxygenase 1 (IDO1) and Tryptophan 2,3-dioxygenase (TDO) enzymes metabolize tryptophan, forming Kynurenine which binds the aryl hydrocarbon receptor (AHR) in multiple innate and adaptive immune cell types causing a net immunosuppressive effect. Both enzymes are upregulated across many tumor types, however, only the IDO1 enzyme has thus far been addressed in the clinic with small molecule inhibitors. We have postulated that enzyme-mediated depletion of Kynurenine into safe and immunologically inert metabolites can alleviate tumor immunosuppression. We have cloned and characterized several bacterial Kynureninases (KYNase) which preferentially degrade Kynurenine with a & gt;1,000 higher kcat/KM as opposed to mammalian enzymes that cleave 3-OH Kynurenine. We show that PEGylated bacterial KYNases can deplete Kynurenine produced by IDO1+, TDO+ and IDO1/TDO+ dual positive human cancer cells whereas, the IDO1 inhibitor epacadostat or TDO inhibitor 680C91 only selectively inhibited Kyn production in IDO1+ or TDO+ cells respectively. In vivo, a single subcutaneous dose of KYNase in B16F10 tumor-bearing mice was able to deplete Kynurenine in both the plasma and tumors and increase effector T-cells in the tumor. KYNase demonstrated significant tumor growth inhibition and survival benefit either as a single agent or in combination with checkpoint inhibitors (anti-PD1 or anti-CTLA4) in B16F10, CT26 and 4T1 models. Interestingly, KYNase combined with anti-PD1, showed greater efficacy than epacadostat / anti-PD1 combination in CT26 tumor bearing mice. A pharmacologically optimized human KYNase is currently moving toward clinical development for the treatment of cancers where both IDO/TDO pathways play a significant immunosuppressive role through kynurenine production. Citation Format: Michelle Zhang, Everett Stone, Todd A. Triplett, Kendra Triplett, Candice Lamb, Christos S. Karamitros, John Blazek, George Georgiou, Mark G. Manfredi. A novel approach to targeting the IDO/TDO pathway through degradation of the immunosuppressive metabolite kynurenine [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5570. doi:10.1158/1538-7445.AM2017-5570
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2017
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  • 6
    Online Resource
    Online Resource
    American Association for Cancer Research (AACR) ; 2017
    In:  Cancer Research Vol. 77, No. 13_Supplement ( 2017-07-01), p. 5571-5571
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 77, No. 13_Supplement ( 2017-07-01), p. 5571-5571
    Abstract: Tryptophan oxidation and the ensuing production of Kynurenine (Kyn) and downstream products have been established to play an important role in immunosuppression within the tumor microenvironment (TME). The rate limiting step in Tryptophan oxidation is catalyzed by the IFN-γ inducible IDO-1 enzyme which is upregulated in numerous cancers and also, in some instances via the ectopic expression of TDO, which is normally expressed primarily in the liver. Currently, IDO-1 small molecule inhibitors in combination with checkpoint inhibitor antibodies are being evaluated in & gt;12 clinical trials. However, whether the immune-suppressive effects of Tryptophan catabolism results from its depletion in the TME, or from the accumulation of Kynurenine, is not known. To distinguish between the effects of Trp depletion and Kyn accumulation in the TME we used an engineered Kynureninase (KYNase) enzyme that selectively degrades Kyn into immunologically inert and non-toxic metabolites. Peritumoral injection of PEGylated KYNase completely depletes serum and tumor Kyn levels for up to 72 hrs, while leaving Trp concentrations in both compartments unaffected. In the IDO-1 expressing CT26 colon carcinoma model KYNase treatment as monotherapy resulted in 16% complete and durable responses, accompanied by long-term immunity to tumor re-challenge. KYNase had no effect on tumor growth in IDO-/- mice, nor in RAG-/- or in CD8+ T cell depleted mice. Analysis of the TME demonstrated KYNase treatment resulted in increased accumulation of CD8+ cells, with a greater proportion expressing Granzyme B, undergoing proliferation and permeating the tumor interior. This effect was specific to the TME, as no detectable changes to the immune compartment occurred in other organs examined, nor overt signs of autoimmunity and toxicity. The increase in CD8+ cells was consistent with in vitro data showing that elevated concentration of Kyn directly induces apoptosis of activated CD8+ T cells partially through IL-2 suppression. No changes to the Treg percentages and phenotypes in the TME were observed, indicating that the Treg compartment is not impacted by treatment with KYNase. Cytokine analysis of tumor digests revealed increased IL-2 concentrations, as well as IFNγ and IL-9, in tumors after KYNase treatment. Furthermore, ex vivo stimulation of TIL after KYNase treatment demonstrated that the increase in cytokines in the TME is not solely due to an increase in TIL, but also an increased effector cytokine capacity on a per cell basis. Administration of KYNase together with either αCTLA4 or αPD1 synergistically elicited complete and durable regression of multiple established tumor models. In summary, our data support the hypothesis that Kyn accumulation in the TME rather than Trp depletion is the dominant IDO-mediated immune suppressive mechanism, and that enzyme-mediated Kyn depletion is a promising cancer immunotherapeutic approach. Citation Format: Todd A. Triplett, Kendra Triplett, Everett Stone, Michelle Zhang, Mark Manfredi, Candice Lamb, Yuri Tanno, Lauren Ehrlich, George Georgiou. Immune-checkpoint inhibition via enzyme-mediated degradation of kynurenine [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5571. doi:10.1158/1538-7445.AM2017-5571
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2017
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  • 7
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 78, No. 13_Supplement ( 2018-07-01), p. 3757-3757
    Abstract: The tryptophan/kynurenine pathway has been clinically validated in several tumor types with small-molecule IDO1 inhibitors in combination with checkpoint inhibition. Indoleamine-pyrrole 2,3-dioxygenase 1 (IDO1) and tryptophan 2,3-dioxygenase 2 (TDO2) are upregulated in a number of tumor types, metabolizing tryptophan to form immunosuppressive kynurenine. We are developing Kynureninase (Kynase), a kynurenine depleting enzyme, to treat IDO1 and TDO2 positive tumors. The human Kynase has been successfully engineered to vastly increase catalytic activity and stability toward kynurenine over the wild type enzyme. In mice, Kynase achieved prolonged Kynurenine degradation (≥5 days) in plasma and tumor draining lymph node (TDLN), leading to anti-tumor activity as a single agent and in combination with check point inhibitors in mouse syngeneic tumor models. Kynase demonstrated superior tumor growth inhibition and survival benefit relative to a leading IDO1 inhibitor epacadostat in these models. The effects of Kynase on a number of immune cell types, both in vitro and in vivo, are being investigated. Human Kynase has also shown a favorable PK profile and kynurenine degradation in non-human primates, and Kynase variants are now moving toward development candidate selection for treatment of cancers where both IDO/TDO pathways play a significant immunosuppressive role. Citation Format: Silvia Coma, Jill Cavanaugh, James Nolan, Jeremy Tchaicha, Karen McGovern, Everett Stone, Candice Lamb, Christos Karamitros, John Blazek, Kendra Garrison, George Georgiou, Mark Manfredi, Xiaoyan Michelle Zhang. Targeting the IDO/TDO pathway through degradation of the immunosuppressive metabolite kynurenine [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3757.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
    RVK:
    RVK:
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2018
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  • 8
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 119, No. 28 ( 2022-07-12)
    Abstract: Chromophobe (Ch) renal cell carcinoma (RCC) arises from the intercalated cell in the distal nephron. There are no proven treatments for metastatic ChRCC. A distinguishing characteristic of ChRCC is strikingly high levels of reduced (GSH) and oxidized (GSSG) glutathione. Here, we demonstrate that ChRCC-derived cells exhibit higher sensitivity to ferroptotic inducers compared with clear-cell RCC. ChRCC-derived cells are critically dependent on cystine via the cystine/glutamate antiporter xCT to maintain high levels of glutathione, making them sensitive to inhibitors of cystine uptake and cyst(e)inase. Gamma-glutamyl transferase 1 (GGT1), a key enzyme in glutathione homeostasis, is markedly suppressed in ChRCC relative to normal kidney. Importantly, GGT1 overexpression inhibits the proliferation of ChRCC cells in vitro and in vivo, suppresses cystine uptake, and decreases levels of GSH and GSSG. Collectively, these data identify ferroptosis as a metabolic vulnerability in ChRCC, providing a potential avenue for targeted therapy for these distinctive tumors.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    RVK:
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2022
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    SSG: 12
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  • 9
    In: The Journal of Immunology, The American Association of Immunologists, Vol. 200, No. 1_Supplement ( 2018-05-01), p. 177.3-177.3
    Abstract: Cancer is the second leading cause of death in the US and, despite progress in treatment options, there is a critical need for novel treatments that specifically target cancerous cells. Our immune system routinely identifies potential cancer cells and eliminates them without the need for clinical intervention. However, to evade immune clearance, many cancers elevate tryptophan catabolism in the tumor microenvironment (TME) by upregulating the enzymes indoleamine 2, 3-dioxygenase (IDO) or, alternatively, tryptophan 2, 3- dioxygenase (TDO). This results in greater tryptophan turnover, accumulation of IDO/TDO product, kynurenine (L-kyn), and immune suppression in the TME. Whether the resulting immunosuppression arises from tryptophan depletion or L-kyn accumulation remains highly controversial. This work aims to (1) clarify L-kyn’s effect on T-cells and (2) whether its depletion can relieve tumor burden. Exposing T cells to L-kyn in vitro results in gene expression changes consistent with regulatory T-cell generation and the suppression of naïve T-cell proliferation; establishing L-kyn as a key therapeutic target for depletion to relieve TME immune suppression. Using a pharmacologically optimized kynureninase (KynU) enzyme, we tested L-kyn depletion therapy in murine cancers. KynU administration potently inhibits tumor growth, reduces L-kyn concentration, and results in a significant increase in the infiltration and proliferation of polyfunctional T-lymphocytes. Our ongoing study of KynU’s efficacy and L-kyn’s in vitro effects will illuminate details of L-kyn’s elusive mechanism of action, resolving critical mechanisms of tumor tolerance while creating a more innovative and effective cancer treatment strategy.
    Type of Medium: Online Resource
    ISSN: 0022-1767 , 1550-6606
    RVK:
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    Language: English
    Publisher: The American Association of Immunologists
    Publication Date: 2018
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  • 10
    In: Nature Catalysis, Springer Science and Business Media LLC, Vol. 5, No. 10 ( 2022-10-19), p. 952-967
    Type of Medium: Online Resource
    ISSN: 2520-1158
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2916779-6
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