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  • 11
    Online Resource
    Online Resource
    Public Library of Science (PLoS) ; 2021
    In:  PLOS Computational Biology Vol. 17, No. 3 ( 2021-3-25), p. e1008814-
    In: PLOS Computational Biology, Public Library of Science (PLoS), Vol. 17, No. 3 ( 2021-3-25), p. e1008814-
    Abstract: Adaptive immune system uses T cell receptors (TCRs) to recognize pathogens and to consequently initiate immune responses. TCRs can be sequenced from individuals and methods analyzing the specificity of the TCRs can help us better understand individuals’ immune status in different disorders. For this task, we have developed TCRGP, a novel Gaussian process method that predicts if TCRs recognize specified epitopes. TCRGP can utilize the amino acid sequences of the complementarity determining regions (CDRs) from TCR α and TCR β chains and learn which CDRs are important in recognizing different epitopes. Our comprehensive evaluation with epitope-specific TCR sequencing data shows that TCRGP achieves on average higher prediction accuracy in terms of AUROC score than existing state-of-the-art methods in epitope-specificity predictions. We also propose a novel analysis approach for combined single-cell RNA and TCR αβ (scRNA+TCR αβ ) sequencing data by quantifying epitope-specific TCRs with TCRGP and identify HBV-epitope specific T cells and their transcriptomic states in hepatocellular carcinoma patients.
    Type of Medium: Online Resource
    ISSN: 1553-7358
    Language: English
    Publisher: Public Library of Science (PLoS)
    Publication Date: 2021
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  • 12
    In: PLOS ONE, Public Library of Science (PLoS), Vol. 17, No. 11 ( 2022-11-28), p. e0278245-
    Abstract: Somatic mutations have a central role in cancer, but there are also a few rare autoimmune diseases in which somatic mutations play a major role. We have recently shown that nonsynonymous somatic mutations with low allele fractions are preferentially detectable in CD8+ cells and that the STAT3 gene is a promising target for screening. Here, we analyzed somatic mutations in the STAT3 SH2 domain in peripheral blood CD8+ cells in a set of 94 multiple sclerosis (MS) patients and 99 matched controls. PCR amplicons targeting the exons 20 and 21 of STAT3 were prepared and sequenced using the Illumina MiSeq instrument with 2x300bp reads. We designed a novel variant calling method, optimized for large number of samples, high sequencing depth ( 〉 25,000x) and small target genomic area. Overall, we discovered 64 STAT3 somatic mutations in the 193 donors, of which 63 were non-synonymous and 77% have been previously reported in cancer or lymphoproliferative disease. The overall median variant allele fraction was 0.065% (range 0.007–1.2%), without significant difference between MS and controls (p = 0.82). There were 26 (28%) MS patients vs. 24 (24%) controls with mutations (p = 0.62). Two or more mutations were found in 9 MS patients vs. 2 controls (p = 0.03, p corr = 0.12). Carriership of mutations associated with older age and lower neutrophil counts. These results demonstrate that STAT3 SH2 domain is a hotspot for somatic mutations in CD8+ cells with a prevalence of 26% among the participants. There were no significant differences in the mutation prevalences between MS patients and controls. Further research is needed to elucidate the role of antigenic stimuli in the expansion of the mutant clones. Furthermore, the high discovered prevalence of STAT3 somatic mutations makes it feasible to analyze these mutations directly in tissue-infiltrating CD8+ cells in autoimmune diseases.
    Type of Medium: Online Resource
    ISSN: 1932-6203
    Language: English
    Publisher: Public Library of Science (PLoS)
    Publication Date: 2022
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  • 13
    In: Scientific Reports, Springer Science and Business Media LLC, Vol. 8, No. 1 ( 2018-02-07)
    Abstract: CD8 + T-cell expansions are the primary manifestation of T-cell large granular lymphocytic leukemia (T-LGLL), which is frequently accompanied by neutropenia and rheumatoid arthritis, and also occur as a secondary phenomenon in leukemia patients treated with dasatinib, notably in association with various drug-induced side-effects. However, the mechanisms that underlie the genesis and maintenance of expanded CD8 + T-cell receptor (TCR)-Vβ + populations in these patient groups have yet to be fully defined. In this study, we performed a comprehensive phenotypic and clonotypic assessment of expanded (TCR-Vβ + ) and residual (TCR-Vβ − ) CD8 + T-cell populations in T-LGLL and dasatinib-treated chronic myelogenous leukemia (CML) patients. The dominant CD8 + TCR-Vβ + expansions in T-LGLL patients were largely monoclonal and highly differentiated, whereas the dominant CD8 + TCR-Vβ + expansions in dasatinib-treated CML patients were oligoclonal or polyclonal, and displayed a broad range of memory phenotypes. These contrasting features suggest divergent roles for antigenic drive in the immunopathogenesis of primary versus dasatinib-associated CD8 + TCR-Vβ + expansions.
    Type of Medium: Online Resource
    ISSN: 2045-2322
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2018
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  • 14
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 72, No. 8_Supplement ( 2012-04-15), p. 5067-5067
    Abstract: Despite significant advances in characterizing the molecular genetics of AML, the clonal evolution of leukemic cells and the dynamic impact of genomic changes on the development of the disease and progression to drug resistance are not well understood. Here, we applied next-generation sequencing to quantify aberrant tumor subclones carrying specific mutant alleles of key cancer genes and developed a method to extract quantitative high-resolution copy number changes across the genome using exome sequencing data from matching cancer and normal DNA. Serial bone marrow (BM) samples collected from diagnosis to relapse to post-treatment drug resistance in a patient-centric manner made it possible to trace the clonal evolution of AML and to identify variants potentially involved in drug resistance. Exome sequencing from AML blast cells and normal skin biopsies was performed as part of the Finnish Hematology Registry and Biobanking (FHRB) effort. Consecutive paired samples from different patients revealed unique genetic patterns of clonal evolution and cancer progression in each patient. In a pre-resistant sample of one AML M5 patient, we identified four closely spaced insertions in the Wilm's Tumor (WT1) suppressor gene, none of which appear on the same sequence reads. This suggests the presence of multiple distinct leukemic subclones even before treatment resistance and underscores the strong selective advantage conferred by WT1 mutations. After relapse, one of the subclones was lost, and another one significantly increased suggesting that the relapse arose from the expansion of a pre-existing resistant subclone. In this patient, recurrent clones otherwise featured similar copy number changes and the same fusion genes as the primary diagnostic sample. In another AML patient developing recurrence an opposite pattern was observed: The relapsed, drug-resistant cells displayed an enormous increase of small microdeletions compared to the diagnostic, pre-treatment sample, while almost all sequence-level alterations in potential cancer genes were the same between the two samples. This suggests that a distinct type of DNA repair deficiency may have contributed to the drug resistant clone in this patient. Conclusions: Exome sequencing from paired samples of AML cells before and after relapse makes it possible to trace the clonal evolution of the disease and study the impact of therapy both at the level of sequence alterations of key cancer genes and simultaneously at the level of copy number changes inferred from exome sequence data. This analysis has highlighted multiple genomic patterns by which resistance may evolve in vivo during cancer treatment. Refined bioinformatic analysis and interpretation of exome-seq data provides a rich resource to identify genetic biomarkers of drug response and minimal residual disease. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5067. doi:1538-7445.AM2012-5067
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
    RVK:
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2012
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  • 15
    In: Clinical Cancer Research, American Association for Cancer Research (AACR), Vol. 23, No. 21 ( 2017-11-01), p. 6697-6707
    Abstract: Purpose: Dasatinib is a short-acting dual ABL/SRC family tyrosine kinase inhibitor (TKI), which is frequently used to treat chronic myeloid leukemia. Although very effective, patients taking dasatinib often display severe adverse effects, including pleural effusions and increased risk of bleeding primarily in the gastrointestinal tract. The actual causes of these side effects are currently undetermined. We hypothesize that endothelial cells (ECs) that line the inner walls of blood vessels and control the traffic to the underlying tissues might be involved. Experimental Design: The effects of TKIs on ECs were studied by various assays, such as real-time cell impedance measurements, live-cell microscopy, wound healing, Western blot, and an in vivo model. Results: Dasatinib uniquely causes a profound, dose-dependent disorganization of the EC monolayers. Dasatinib promoted the disassembly of cell–cell contacts, altered cell–matrix contacts, and further altered the wound healing. A key observation is that this effect is fully reversible after drug washout. In line with these in vitro observations, intraperitoneal administration of dasatinib to mice caused significant vascular leakage in the intestine. The underlying molecular mechanism of dasatinib-induced reorganization of the actin involves ROCK activation, which increases the amount of the phosphorylation of myosin light chain and consequently activates the non-muscle myosin II. Conclusions: Our data are consistent with a scenario in which dasatinib triggers a transient increase in vascular leakage that probably contributes to adverse effects such as bleeding diathesis and pleural effusions. Clin Cancer Res; 23(21); 6697–707. ©2017 AACR.
    Type of Medium: Online Resource
    ISSN: 1078-0432 , 1557-3265
    RVK:
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2017
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  • 16
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 81, No. 13_Supplement ( 2021-07-01), p. 1867-1867
    Abstract: Despite the success of immune checkpoint inhibitors in the clinic, they only benefit a fraction of patients. A theoretical strategy to increase efficacy would be to enhance such antibodies with Fc-mediated effector mechanisms. Current IgG1 antibodies are excellent activators of natural killer cells yet neglect a crucial effector population, neutrophils. Hence, we designed a cross-hybrid Fc-fusion peptide against PD-L1 able to elicit simultaneously effector mechanisms of an IgG1 but also IgA1, consequently activating neutrophils, in order to combine multiple effector mechanisms. Moreover, to prevent toxicities, these Fc-fusion peptides were cloned in oncolytic adenoviruses whose replication is restricted to the tumor. Our oncolytic adenoviruses were able to selectively infect tumor cells, secrete the cross-hybrid Fc-fusion peptides able to bind to PD-L1 and activate multiple immune components enhancing tumor cytotoxicity compared to FDA-approved immune checkpoint inhibitors. We validated this in various human and murine cancer cell lines and also renal cell carcinoma patient derived organoids from four patients. In conclusion, our cross-hybrid Fc-fusion peptides demonstrate that activating multiple immune effector populations increases tumor cytotoxicity potentially leading to improved clinical outcomes. Citation Format: Firas Hamdan, Erkko Ylösmäki, Jacopo Chiaro, Yvonne Giannoula, Maeve Long, Manlio Fusciello, Sara Feola, Beatriz Martins, Michaela Feodoroff, Gabriella Antignani, Otto Kari, Moon Hee Lee, Petrus Järvinen, Harry Nisen, Anna Kreutzman, Satu Mustjoki, Thomas G McWilliams, Mikaela Grönholm, Vincenzo Cerullo. Characterization in patient derived tumor organoids of novel oncolytic adenoviruses expressing enhanced cross-hybrid IgGA Fc PD-L1 inhibitors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1867.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
    RVK:
    RVK:
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2021
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  • 17
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 81, No. 13_Supplement ( 2021-07-01), p. 1488-1488
    Abstract: Molecular mimicry is known to be one of the leading mechanisms by which infectious agents may induce autoimmunity. However, whether a similar mechanism triggers anti-tumor immune response is unexplored, and the role of anti-viral T-cells infiltrating the tumor has remained anecdotal. To address this question, we first developed a bioinformatic tool to identify tumor peptides with high similarity to viral epitopes. Using peptides identified by this tool, we showed that, in mice, viral pre-existing immunity enhanced the efficacy of cancer immunotherapy via molecular mimicry. Specifically, when treated with a cancer vaccine consisting of peptides with a high degree of homology with specific viral peptides, the mice with induced pre-existing immunity to these viral peptides showed significantly better anti-tumor response.To understand whether this mechanism could partly explain immunotherapy-response in humans, we analyzed a cohort of melanoma patients undergoing PD1 treatment with high IgG titer for Cytomegalovirus (CMV). In this cohort of patients, we showed that high level of CMV-antibodies was associated with a prolonged progression free survival, and found that in some cases PBMCs could cross-react with both melanoma and CMV homologous peptides. Finally, T-cell TCR sequencing revealed expansion of the same CD8+ T-cell clones, when PBMCs were pulsed with tumor- or homologous viral peptides.In conclusion, we have demonstrated that pre-existing immunity and molecular mimicry could explain part of the response observed in immunotherapy. Most importantly, we have developed a tool able to identify tumor antigens and neoantigens based on their similarity to pathogen antigens, in order to exploit molecular mimicry and cross-reactive T-cells in cancer vaccine development. Citation Format: Jacopo Chiaro, Henna Kasanen, Thomas Whalley, Cristian Capasso, Sara Feola, Mikaela Grönholm, Firas Hamdan, Karita Peltonen, Micaela Hernberg, Siru Mäkelä, Hanna Karhapää, Paul Brown, Beatriz Martins, Manlio Fusciello, Erkko Ylösmäki, Anna Kreutzman, Satu Mustjoki, Barbara Szomolay, Vincenzo Cerullo. Viral molecular mimicry influences the antitumor immune response in murine and human melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1488.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
    RVK:
    RVK:
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2021
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  • 18
    In: Molecular Cancer Therapeutics, American Association for Cancer Research (AACR), Vol. 14, No. 5 ( 2015-05-01), p. 1181-1191
    Abstract: Immune escape mechanisms promote tumor progression and are hurdles of cancer immunotherapy. Removing immunosuppressive cells before treatment can enhance efficacy. Tyrosine kinase inhibitors (TKI) may be of interest to combine with immunotherapy, as it has been shown that the inhibitor sunitinib reduces myeloid suppressor cells in patients with renal cell carcinoma and dasatinib promotes expansion of natural killer–like lymphocytes in chronic myeloid leukemia (CML). In this study, the capacity of dasatinib and imatinib to reduce myeloid suppressor cells and to induce immunomodulation in vivo was investigated ex vivo. Samples from CML patients treated with imatinib (n = 18) or dasatinib (n = 14) within a Nordic clinical trial (clinicalTrials.gov identifier: NCT00852566) were investigated for the presence of CD11b+CD14−CD33+ myeloid cells and inhibitory molecules (arginase I, myeloperoxidase, IL10) as well as the presence of natural killer cells, T cells (naïve/memory), and stimulatory cytokines (IL12, IFNγ, MIG, IP10). Both imatinib and dasatinib decreased the presence of CD11b+CD14−CD33+ myeloid cells as well as the inhibitory molecules and the remaining myeloid suppressor cells had an increased CD40 expression. Monocytes also increased CD40 after therapy. Moreover, increased levels of CD40, IL12, natural killer cells, and experienced T cells were noted after TKI initiation. The presence of experienced T cells was correlated to a higher IFNγ and MIG plasma concentration. Taken together, the results demonstrate that both imatinib and dasatinib tilted the immunosuppressive CML tumor milieu towards promoting immune stimulation. Hence, imatinib and dasatinib may be of interest to combine with cancer immunotherapy. Mol Cancer Ther; 14(5); 1181–91. ©2015 AACR.
    Type of Medium: Online Resource
    ISSN: 1535-7163 , 1538-8514
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2015
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  • 19
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 74, No. 19_Supplement ( 2014-10-01), p. 2587-2587
    Abstract: Dasatinib, a tyrosine kinase inhibitor used in the treatment of chronic myeloid leukemia and acute lymphoblastic leukemia, has been shown to exert immunomodulatory effects in addition to direct oncokinase inhibition. Recently, we observed that dasatinib induces a rapid (within one hour after oral administration) and marked mobilization of lymphocytes (up to 8-fold increase in lymphocyte count), which closely follows the drug plasma concentration. In addition, in a subgroup of patients a clonal expansion of large granular lymphocytes occurs, which is correlated with good therapy response. As dasatinib-induced immunomodulatory effects are not leukemia specific, we aimed to exploit this activity to slow down or inhibit the growth of a syngeneic murine melanoma model and to characterize in detail the anti-tumor immune responses. Ovalbumin expressing murine melanoma cell line B16.OVA was grown under the skin of immunocompetent mice. The mice (n=6/group) were treated daily i.g. either with 30 mg/kg dasatinib or vehicle only. Blood was collected before tumor transplantation, before treatment, and on treatment days 4, 7 and 10. Tumor volumes were measured manually and specific growth rate was calculated based on the first and the last day of the treatment. In addition to white blood cell differential counts, immunophenotyping of blood and tumor homogenate was done by flow cytometry using antibodies against CD45.1, CD3, CD4, CD8b and NK1.1, and SIINFEKL-pentamer to detect B16.OVA-specific cells. To assess the functional properties of lymphocytes, we used antibodies against immune checkpoint inhibitors CTLA-4 and PD-1, and a degranulation marker CD107. On the 10th day of treatment, the tumor volumes were smaller in dasatinib group compared to control group, and there was a significant decrease in the tumor growth rate (0.06 vs. 0.18, p=0.01). Furthermore, dasatinib treated mice had increased proportion of CD8+ cells in the circulation (21% vs. 14%, p=0.04) and the CD4/CD8 ratio was significantly decreased (1.39 vs. 1.52, p= 0.04). During the tumor growth the mean CTLA-4 expression on CD8+ cells increased from 1.2% to 9% in the control group, whereas, in dasatinib group the increase was more modest (1.2% to 5.7%). Interestingly, 80% of tumor infiltrating CD8+ cells expressed PD1 antigen compared to & lt;5% of PD1 positive CD8+ cells in the peripheral blood suggesting lymphocyte anergy or exhaustion induced by tumor cells. To conclude, dasatinib treatment slowed down the tumor growth in B16.OVA mouse model, which could be associated with the immunomodulatory effects of dasatinib. However, combinatorial treatment regimens may be needed as dasatinib is not able to fully break the immune cell anergy induced by tumor cells. Citation Format: Can Hekim, Mette Ilander, Markus Vähä-Koskela, Paula Savola, Siri Tähtinen, Akseli Hemminki, Kimmo Porkka, Satu Mustjoki. Dasatinib-induced reduction of tumor growth is accompanied by the changes in the immune profile in melanoma B16.OVA mouse model. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2587. doi:10.1158/1538-7445.AM2014-2587
    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: 2014
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  • 20
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 80, No. 16_Supplement ( 2020-08-15), p. LB-108-LB-108
    Abstract: STAT5 is a member of the signal transducer and activator of transcription family of proteins and is widely recognized as an oncogenic master regulator of hematological malignancies. To date, therapeutic approaches to attenuate aberrant activity have focused on upstream kinase targets such as JAK2, Bcr-Abl, Flt3, and Flt3-ITD. To date, there is no STAT5-selective inhibitor in clinical development. More recently, PROTAC approaches have been deployed successfully against the STAT3 isoform and demonstrated efficacy and safety in preclinical models. We herein report the identification of a potent and selective, non-PROTAC, small molecule degrader of STAT5 protein, JPX-0750. Upon binding, JPX-0750 covalently and selectively binds to a cysteine residue on STAT5 via an electrophilic warhead, which induces profound destabilization of STAT5. The unfolding/destabilization effect can be observed via Western blot, isothermal denaturation of purified protein and HDX exchange. In a range of AML and TPLL cell lines exposure to JPX-750 at nM concentrations leads to a rapid and dose-dependant degradation of both phospho-STAT5 and total STAT5 with resultant IC50's between 80-200 nM. Washout experiments determined that exposure to JPX-0750 at 1 µM for 2-4 h is sufficient to degrade STAT5, inhibit downstream targets, and induce apoptosis. Moreover, in the same washout experiments, 50% STAT5 recovery post-washout required & gt;72 h suggesting a long pharmacodynamic effect. Against STAT3, degrading effects are observed later, 24 h post washout (6 h treatment), indicating that anti-STAT5 activity is more rapid in AML cells and in line with the inherent stability of each protein. No effect was observed on either STAT1 or pSTAT1 upon exposure to JPX-750. Importantly, compared to standard AML cell lines JPX-750 demonstrated similar low nM potency in 25/30 primary AML blasts and TPLL patient samples, including those with poor prognostic markers. JPX-750 exhibits a large therapeutic window for AML versus pooled human fibroblasts and hematopoietic stem cells (ca 100 fold). In a preclinical MV4;11 luciferase model, structurally related JPX-700, at 5 mg/kg (IP, qd) significantly reduced leukemic burden, suppressed tumour dissemination to both the lung and liver, and had no effect on body weight, organ histology or blood parameters. In summary, JPX-750 represents a new class of potent and selective small molecule degraders of STAT5 protein. Citation Format: Ji Sung Park, Gary Tin, Elvin D. de Araujo, Anna Orlova, Helena Sorger, Florian Grebien, Elizabeth Heyes, Mulu Geletu, Ruth Villalonga, Angel Sampedro, Abootaleb Sedighi, Marco Herling, Satu Mustjoki, Mohammad S. Eram, Siawash Ahmar, Richard Moriggl, Jeff A. O'Meara, John Proudfoot, Kay Noel, Dziyana Kraskouskaya, Roman Fleck, Patrick T. Gunning. A potent and selective small molecule degrader of STAT5 for the treatment of hematological malignancies [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr LB-108.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
    RVK:
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2020
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    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
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