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  • 1
    In: Journal of Proteome Research, American Chemical Society (ACS), Vol. 20, No. 6 ( 2021-06-04), p. 3134-3149
    Type of Medium: Online Resource
    ISSN: 1535-3893 , 1535-3907
    Language: English
    Publisher: American Chemical Society (ACS)
    Publication Date: 2021
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  • 2
    In: Blood, American Society of Hematology, Vol. 134, No. Supplement_1 ( 2019-11-13), p. 5534-5534
    Abstract: Introduction The use of proteasome inhibitors (PIs), such as bortezomib (BTZ), in multiple myeloma (MM) has markedly increased the survival of newly diagnosed patients. Although advancements in therapeutic regimens in the past decade have improved prognosis, we lack knowledge of the mechanisms that lead to drug resistance. To assess the contributors to BTZ-resistance, we integrated steady-state metabolomics, proteomics and gene expression from two naïve and BTZ-resistant cell line models. In addition, gene expression associated with ex vivo PI resistance has been analyzed. Potential predictive biomarkers of PI-resistance and novel targets for combination therapy will be investigated. Methods Parental cell lines, RPMI 8226 and U266, were acquired from ATCC. 8226-B25 and U266-PSR (kind gift from Dr. S. Grant) BTZ-resistant derivatives were selected from their respective parental naïve cell lines by chronic drug exposure. Untargeted metabolomics, activity-based protein profiling (ABPP), and expression proteomics data were acquired using liquid chromatography-mass spectrometry. Gene expression profiles of both cell lines and ex vivo patient specimens were derived from RNAseq. Metabolomics and proteomics data were normalized with iterative rank order normalization. Significantly different genes, proteins, and metabolites were integrated for pathway mapping and identification of biomarkers for PI resistance. Results Consistent with previous findings, kynurenine, a product of tryptophan catabolism, is significantly altered in both of our cell line models. In the 8226 and 8226-B25 pair, PI resistance was associated with increased kynurenine and positively correlated with TDO2 and IDO1 overexpression consistent with published literature (Li et al. Nature Medicine, 2019, 25, 850-60). As expected, PSMB2, a subunit of the proteasome, is overexpressed and has a higher activity in both 8226-B25 and U266-PSR in the ABPP and expression proteomics, and higher expression in 8226-B25 RNAseq data. PSMB2 is also overexpressed and significant in the RNAseq patient data, increasingly from newly diagnosed/pre-treatment to early relapse (p-value 2E-4) and late relapse (p-value 0.0052). In addition, CD38 is an enzyme responsible for conversion of NAD+ to nicotinamide and ADP-ribose. It has increased expression in MM cells and is significantly downregulated in ABPP (log2 ratio -4.25, p-value 2E-13), expression proteomics (log2 ratio -2.5), and RNAseq (log2 ratio -2.6, p-value 5E-6) in the 8226-B25 BTZ-resistant cells. In the steady-state metabolomics of the 8226-B25 cells, ADP-ribose (log2 ratio 4.11, p-value 2E-5) is the most upregulated known metabolite. This change suggests a downstream result of resistance within this interaction and a potential biomarker of PI resistance. However, gene expression of CD38 in patient samples was relatively unchanged. CD38 was not detected in the U266-PSR proteomics or RNAseq data and ADP-ribose (log2 ratio -0.63, p-value 0.06) was not significantly altered, suggesting a different mechanism of resistance in this cell line. Conclusions Though common mechanisms of PI resistance were identified, our data clearly show that BTZ-resistance arises by heterogeneous means in the two cell line models, promoting the need for biomarkers that can determine resistance and predict response in individual patients (or cohorts). Decreased expression of CD38 in 8226-B25 could elucidate mechanisms of PI resistance and immune response evasion strategies of MM cells. Further investigation of CD38 expression as a BTZ-resistance biomarker could lead to improving combination therapies with monoclonal antibodies, such as daratumumab, and PIs in newly diagnosed MM patients by predicting response prior to treatment. Further examination of ADP-ribose metabolism may lead to the mechanism of synergy between PARP inhibitors and proteasome inhibitors. Ultimately, we plan to integrate and utilize these multi-omics approaches in patient specimens and improve MM patient care by identifying PI resistance biomarkers to predict patient response. Disclosures Shain: Adaptive Biotechnologies: Consultancy; Janssen: Membership on an entity's Board of Directors or advisory committees; AbbVie: Research Funding; Celgene: Membership on an entity's Board of Directors or advisory committees; Sanofi Genzyme: Membership on an entity's Board of Directors or advisory committees; Takeda: Membership on an entity's Board of Directors or advisory committees; Amgen: Membership on an entity's Board of Directors or advisory committees; Bristol-Myers Squibb: Membership on an entity's Board of Directors or advisory committees.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2019
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  • 3
    In: Blood, American Society of Hematology, Vol. 132, No. Supplement 1 ( 2018-11-29), p. 5619-5619
    Abstract: Although advancements in therapeutic regimens for treating multiple myeloma (MM) have prolonged patient survival, the disease remains incurable. Several classes of drugs have contributed to these improvements, such as proteasome inhibitors, immunomodulators, deacetylase inhibitors, monoclonal antibodies, and alkylating agents including melphalan. An expanded arsenal of diverse chemotherapy targets has improved patient care significantly, yet we still lack sufficient knowledge of how cellular metabolism and drug processing can contribute to drug resistance. To address this issue, we utilize cell line models to simulate naïve and drug resistant states, which identify drug modifications, endogenous metabolites, proteins, and acute metabolic profile alterations associated with therapeutic escape. Here, we specifically focus on melphalan; an alkylating agent that forms DNA interstrand crosslinks, inhibits cell division, and leads to cell death through apoptosis (Povirk & Shuker. Mutat. Res. 1994, 318, 205). Melphalan remains a critical component of high dose therapy in the context of stem cell transplant and induction therapy in transplant ineligible patients outside the US. Ineffectiveness of alkylating agents remains a critical problem and serves as an excellent model for investigation of cellular metabolism and its contribution to drug resistance. Two parental MM cell lines (8226 & U266) were obtained from ATCC and resistant derivatives of each cell line (8226-LR5 & U266-LR6) were selected after chronic drug exposure. To assess mechanisms of melphalan resistance, we use liquid chromatography-mass spectrometry-based metabolomics and proteomics approaches, including studies of drug metabolism, untargeted metabolomics, and activity based protein profiling (ABPP). Drug metabolism monitors the intracellular and extracellular drug modifications over a 24-hour period after acute treatment. Untargeted metabolomics is used to compare the steady state endogenous intracellular metabolites of naïve and drug resistant cells. Differences in endogenous metabolites between naïve and drug resistant cell lines are also examined in the acute treatment dataset. ABPP utilizes desthiobiotinylating probes to enrich for ATP-utilizing enzymes, which are identified and quantified to enable comparison. We initially compared acute melphalan treatment in drug naive and resistant isogenic cell line pairs. Predictably, melphalan was converted into monohydroxylated and dihydroxylated metabolites more quickly in cells than in media controls. Differences in the formation of these metabolites between the naïve and resistant cell lines were not observed. The untargeted metabolomics data indicated in the 8226-LR5 model, glutathione and xanthine levels are elevated, while guanine is suppressed relative to naive cells. ABPP demonstrated changes in several enzymes related to purine and glutathione metabolism (Figure 1). Interestingly, the U266/U266-LR6 cell line models exhibit higher baseline levels of glutathione when compared with 8226/8226-LR5, indicating heterogeneous means of drug resistance. Alterations in arginine biosynthesis and nicotinate/nicotinamide metabolism are observed in the untargeted metabolomics and ABPP of U266/U266-LR6. Common pathways (e.g. purine biosynthesis) are altered in both models, although the changes involve different molecules. In examining two models of acquired melphalan resistance, we demonstrate frank differences in metabolic pathways associated with steady state and acute drug response. These data demonstrate the potential heterogeneity in drug resistance mechanisms and the need for more biomarkers to personalize treatment. Ongoing studies involve introduction of enzyme inhibitors in targeted pathways and supplementation of metabolites to validate their role in resistance. Furthermore, we will examine expression of these metabolic pathways associated with ex vivo melphalan resistance in a cohort of over 100 patient samples with paired RNA sequencing. The long term goals are to elucidate mechanisms of therapeutic response, identify biomarkers of metabolism in melphalan resistance, enhance drug efficacy, predict personalized patient treatment, and improve overall MM patient care. Disclosures No relevant conflicts of interest to declare.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2018
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  • 4
    In: Indian Heart Journal, Elsevier BV, Vol. 70, No. 6 ( 2018-11), p. 828-835
    Type of Medium: Online Resource
    ISSN: 0019-4832
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2018
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  • 5
    In: JCI Insight, American Society for Clinical Investigation, Vol. 8, No. 18 ( 2023-9-22)
    Type of Medium: Online Resource
    ISSN: 2379-3708
    Language: English
    Publisher: American Society for Clinical Investigation
    Publication Date: 2023
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  • 6
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 74, No. 19_Supplement ( 2014-10-01), p. 1610-1610
    Abstract: Melanoma is the deadliest form of skin cancer with the worst prognosis in patients with metastasis to distant sites such as brain, liver and bone. Studies have shown that MAPK reactivation is a key signaling event leading to BRAF inhibitor resistance. As such, clinical investigations are now underway to evaluate the efficacy of combining frontline BRAF plus MEK inhibitors. Though this approach appears to have meaningful clinical benefit, there are a number of patients who do not respond to therapy, or who through unknown mechanisms, succumb to refractory disease. In order to identify the dynamic changes that drive MAPK inhibitor resistance, we have developed a systems level approach combining mass spectrometry based phosphoproteomic and bioinformatics methodologies. Based on significant changes in tyrosine, threonine and serine phosphorylation events between naive and vemurafenib resistant melanoma cell lines, we have mapped a resistance interactome of ∼550 nodes. This resistance network was significantly enriched for pathways associated with metastatic disease where changes in network connectivity resulted in the appearance of new signaling hubs such as EGFR, EphA2, EphB4, STAT3, FAK1 and HDAC1. The clinical relevance of these findings was demonstrated in a retrospective study showing that 65% of BRAFV600E patients on vemurafenib therapy developed metastases at new sites, with 25% of these new metastases involving the brain. Consistent with our bioinformatics prediction, resistant lines had greater metastatic potential as seen by increased migration and invasion across matrigel and endothelial cell barriers. Extending our findings to a panel of BRAF and BRAF plus MEK inhibitor resistant cell lines, we found compelling evidence that EphA2 is essential for maintaining a resistance phenotype. This phenotype was associated with AKT activation and uncoupled Eph-ephrin signaling resulting in S897 phosphorylation and overexpression of EphA2. In vivo analysis of matched primary and metastatic tumors from vemurafenib resistant xenografts showed that EphA2 expression is increased in metastatic but not primary lesions. Importantly, analysis of clinical specimens from melanoma patients undergoing or failing vemurafenib therapy confirmed that EphA2 receptor expression is significantly upregulated in metastatic but not primary tumors. Functionally, EphA2 S897 phosphorylation was increased at the tumor leading edge of metastatic lesions while absent in primary lesions. Our results show that MAPK resistant melanomas can adaptively rewire their signaling leading to a more malignant phenotype and that through proteomics based approaches we can reliably identify resistance pathways that will translate into rational therapeutic strategies for disseminated disease. Citation Format: Kim H. T. Paraiso, Meghna Das Thakur, Jobin K. John, Bin Fang, John M. Koomen, Inna V. Fedorenko, Hensin Tsao, Keith T. Flaherty, Jane L. Messina, Elena M. Pasquale, Alejandro Villagra, John M. Kirkwood, Friedegund Meier, Sarah Sloot, Geoffrey T. Gibney, Darrin Stuart, Hussein Tawbi, Keiran S.M. Smalley. MAPK inhibitor resistance leads to ligand-independent Ephrin A2 receptor signaling and the formation of new melanoma metastases. [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 1610. doi:10.1158/1538-7445.AM2014-1610
    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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  • 7
    In: Cancer Discovery, American Association for Cancer Research (AACR), Vol. 5, No. 3 ( 2015-03-01), p. 264-273
    Abstract: Many patients with BRAF inhibitor resistance can develop disease at new sites, suggesting that drug-induced selection pressure drives metastasis. Here, we used mass spectrometry–based phosphoproteomic screening to uncover ligand-independent EPHA2 signaling as an adaptation to BRAF inhibitor therapy that led to the adoption of a metastatic phenotype. The EPHA2-mediated invasion was AKT-dependent and readily reversible upon removal of the drug as well as through PI3K and AKT inhibition. In xenograft models, BRAF inhibition led to the development of EPHA2-positive metastases. A retrospective analysis of patients with melanoma on BRAF inhibitor therapy showed that 68% of those failing therapy develop metastases at new disease sites, compared with 35% of patients on dacarbazine. Further IHC staining of melanoma specimens taken from patients on BRAF inhibitor therapy as well as metastatic samples taken from patients failing therapy showed increased EPHA2 staining. We suggest that inhibition of ligand-independent EPHA2 signaling may limit metastases associated with BRAF inhibitor therapy. Significance: This study provides evidence that BRAF inhibition promotes the adoption of a reversible, therapy-driven metastatic phenotype in melanoma. The cotargeting of ligand-independent EPHA2 signaling and BRAF may be one strategy to prevent the development of therapy-mediated disease at new sites. Cancer Discov; 5(3); 264–73. ©2014 AACR. See related article by Miao et al., p. 274 This article is highlighted in the In This Issue feature, p. 213
    Type of Medium: Online Resource
    ISSN: 2159-8274 , 2159-8290
    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2015
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  • 8
    In: Blood, American Society of Hematology, Vol. 134, No. Supplement_1 ( 2019-11-13), p. 5537-5537
    Abstract: Multiple Myeloma (MM) remains an incurable malignancy, despite the advent of several new therapeutic agents, including immunomodulatory drugs (IMiDs, e.g., Lenalidomide (Len)) and proteasome inhibitors (PIs, e.g., Bortezomib (Btz)). Accordingly, there is an urgent need to identify new targetable vulnerabilities for MM patients. We developed an ex vivo 384-well platform that allows one to define drug sensitivities of primary patient CD138+ MM cells in the context of a reconstructed tumor microenvironment (TME), including allogeneic bone marrow stromal cells, extracellular matrix and MM patient serum. Using this platform and activity-based proteomic profiling (ABPP), we identified shared signaling pathways induced by the interactions of MM with stromal cells and integrated these data with screens performed using a bank of protein kinase inhibitors (PKI) and current anti-MM therapeutics. These analyses revealed that the serine/threonine kinases casein kinase-1δ (CK1δ) and CK1ε as high priority targets for MM. Indeed, a highly selective and potent dual inhibitor of CK1δ/CK1ε coined SR-3029 is the most potent PKI versus MM. Further, our studies revealed SR-3029 has potent activity in 138/153 primary patient MM specimens tested thus far, including quad and penta-refractory MM. Analysis of RNAseq data of over 600 Moffitt Cancer Center (MCC) MM patients revealed that patients with high expression of CK1ε had worse survival outcomes while no survival difference was seen with CK1δ expression. Importantly, using the established 5TGM1/Kal-Ridge (C57B6/KaLwRijHsd) syngeneic mouse model of multiple myeloma, we show that tumors derived from 5TGM1 MM cells, which rapidly die following exposure to SR-3029 ex vivo, are also sensitive to CK1δ/CK1ε inhibition in vivo, where SR-3029 treatment reduced tumor burden and significantly improved survival. Similar results were observed using NSG immune compromised animals inoculated with human MM1.S multiple myeloma cells (both flank and tail vein models), where SR-3029 treated animals had reduced tumor burden and extended survival. Analysis of RNAseq on patients' samples (on stroma) treated ex vivo with SR-3029 revealed CK1δ/CK1ε inhibition suppressed multiple metabolic pathways (oxidative phosphorylation, glycolysis, xenobiotic metabolism). Interestingly, analyses of MCC MM patient RNAseq data revealed upregulation of the genes identified in these metabolic pathways as patients progress from pre-treatment to relapse, and that patient MM samples that were resistant to CK1δ/CK1ε inhibition had an upregulation of some of these metabolic genes. Functional studies are being performed to define the mechanism(s) by which CK1δ/CK1ε inhibition disables MM metabolism. Collectively, these findings establish CK1ε and/or CK1δ as attractive targets for anti-myeloma therapy that are required to sustain MM metabolism. Disclosures Dai: M2Gen: Employment. Shain:Bristol-Myers Squibb: Membership on an entity's Board of Directors or advisory committees; Takeda: Membership on an entity's Board of Directors or advisory committees; Sanofi Genzyme: Membership on an entity's Board of Directors or advisory committees; AbbVie: Research Funding; Janssen: Membership on an entity's Board of Directors or advisory committees; Adaptive Biotechnologies: Consultancy; Amgen: Membership on an entity's Board of Directors or advisory committees; Celgene: Membership on an entity's Board of Directors or advisory committees.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2019
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  • 9
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 80, No. 16_Supplement ( 2020-08-15), p. CT056-CT056
    Abstract: Study Objectives: A hallmark of tumor infiltrating lymphocytes (TIL) in melanoma is the potential for a complete response (CR) which can last for decades. This long-lived effect is attributed to persistence of memory T cells. However, clinical efficacy in metastatic non-small cell lung cancer (mNSCLC) has not previously been reported. We launched a phase I trial with the objective to evaluate the safety and efficacy in mNSCLC after evidence of progression on nivolumab. Methodology: Full eligibility criteria is described in trial registry (NCT03215810). Patients were required to have mNSCLC with at least 1 RECIST measurable lesion and also 1 lesion safely accessible for excisional biopsy, usually a supraclavicular lymph node or pleural nodule. This histologically confirmed metastasis was resected and TIL cultured. Autologously reactive cultures were pooled and cryopreserved. TIL was successfully expanded in 95% of patients, to a median dose of 103 billion CD3+ cells. Patients received nivolumab for 4 cycles with two serial CT scans. Patients with tumor enlargement or new lesions proceeded to lymphodepletion cyclophosphamide/fludarabine (Cy/Flu), TIL, and attenuated IL-2. After first CT scan, patients resumed nivolumab for up to 11 doses to augment TIL persistence. Results: Of 32 patients screened, 20 were eligible and enrolled. Median age 54 yrs (range 38 - 75), median PD-L1 proportion score 6%, median estimated TMB 5 mut/MB, 20% EGFR-mutant. The majority had bulky disease with mean sum of target lesion diameters of 7.0 cm. Of 20 enrolled, 13 had evidence of progression on nivolumab and received subsequent Cy/Flu/TIL/IL-2. Two more are progressing on nivolumab and set to receive TIL within next 2 months. Common non-hematologic adverse events (AEs) of the Cy/Flu/TIL/IL2 regimen included hypoalbuminemia (92%), hypophosphatemia (85%), nausea (77%), hyponatremia (69%), diarrhea (62%), the majority of these AEs resolving by Day +10 post-TIL. Initial tumor regression occurred in most patients at their first post-TIL CT scan, with the median best overall change in sum of target lesion diameters of -38% (range +20 to -100). Median time-on-trial post-TIL is 1.4 years. Two patients have achieved durable CRs which are still ongoing almost 1 year post-TIL. One is a never-smoker with EGFREx19 mutation and PD-L1 1%. Three additional patients were able to maintain a clinical remission by local ablative therapy of an isolated new lesion performed 6 to 17 months post-TIL. Persistence of the infused TCR-Vβ clonotypes at post-infusion timepoints was associated with clinical benefit. Neoantigen-specific T cells were detected in the TIL and post-TIL peripheral blood. Conclusions: TIL has manageable toxicity and capacity to achieve durable remission in mNSCLC after nivolumab treatment. TIL may be a promising option for fit mNSCLC patients. Citation Format: Ben Creelan, Chao Wang, Jamie Teer, Eric Toloza, John Mullinax, Jiqiang Yao, John Koomen, Sungjune Kim, Alberto Chiappori, James Saller, Leighann Montoya, Ana Marie Landin, Tawee Tanvetyanon, Bin Fang, Zachary Thompson, Xiaoping Yu, Andreas Saltos, Dung-Tsa Chen, Jose Conejo-Garcia, Eric Haura, Scott Antonia. Durable complete responses to adoptive cell transfer using tumor infiltrating lymphocytes (TIL) in non-small cell lung cancer (NSCLC): A phase I trial [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 CT056.
    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: 2020
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  • 10
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 82, No. 7 ( 2022-04-01), p. 1234-1250
    Abstract: MYC family oncoproteins are regulators of metabolic reprogramming that sustains cancer cell anabolism. Normal cells adapt to nutrient-limiting conditions by activating autophagy, which is required for amino acid (AA) homeostasis. Here we report that the autophagy pathway is suppressed by Myc in normal B cells, in premalignant and neoplastic B cells of Eμ-Myc transgenic mice, and in human MYC-driven Burkitt lymphoma. Myc suppresses autophagy by antagonizing the expression and function of transcription factor EB (TFEB), a master regulator of autophagy. Mechanisms that sustained AA pools in MYC-expressing B cells include coordinated induction of the proteasome and increases in AA transport. Reactivation of the autophagy-lysosomal pathway by TFEB disabled the malignant state by disrupting mitochondrial functions, proteasome activity, AA transport, and AA and nucleotide metabolism, leading to metabolic anergy, growth arrest, and apoptosis. This phenotype provides therapeutic opportunities to disable MYC-driven malignancies, including AA restriction and treatment with proteasome inhibitors. Significance: MYC suppresses TFEB and autophagy and controls amino acid homeostasis by upregulating amino acid transport and the proteasome, and reactivation of TFEB disables the metabolism of MYC-driven tumors.
    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: 2022
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