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Akinlalu A, Flaten Z, Rasuleva K, Mia MS, Bauer A, Elamurugan S, Ejjigu N, Maity S, Arshad A, Wu M, Xia W, Fan J, Guo A, Mathew S, Sun D. Integrated proteomic profiling identifies amino acids selectively cytotoxic to pancreatic cancer cells. Innovation (N Y) 2024; 5:100626. [PMID: 38699777 PMCID: PMC11063643 DOI: 10.1016/j.xinn.2024.100626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 04/05/2024] [Indexed: 05/05/2024] Open
Abstract
Pancreatic adenocarcinoma (PDAC) is one of the most deadly cancers, characterized by extremely limited therapeutic options and a poor prognosis, as it is often diagnosed during late disease stages. Innovative and selective treatments are urgently needed, since current therapies have limited efficacy and significant side effects. Through proteomics analysis of extracellular vesicles, we discovered an imbalanced distribution of amino acids secreted by PDAC tumor cells. Our findings revealed that PDAC cells preferentially excrete proteins with certain preferential amino acids, including isoleucine and histidine, via extracellular vesicles. These amino acids are associated with disease progression and can be targeted to elicit selective toxicity to PDAC tumor cells. Both in vitro and in vivo experiments demonstrated that supplementation with these specific amino acids effectively eradicated PDAC cells. Mechanistically, we also identified XRN1 as a potential target for these amino acids. The high selectivity of this treatment method allows for specific targeting of tumor metabolism with very low toxicity to normal tissues. Furthermore, we found this treatment approach is easy-to-administer and with sustained tumor-killing effects. Together, our findings reveal that exocytosed amino acids may serve as therapeutic targets for designing treatments of intractable PDAC and potentially offer alternative treatments for other types of cancers.
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Affiliation(s)
- Alfred Akinlalu
- Department of Electrical and Computer Engineering, University of Denver, 2155 E Wesley Avenue, Denver, CO 80210, USA
| | - Zachariah Flaten
- Biomedical Engineering Program, North Dakota State University; 1401 Centennial Boulevard, Engineering Administration, Room 203, Fargo, ND 58102, USA
| | - Komila Rasuleva
- Biomedical Engineering Program, North Dakota State University; 1401 Centennial Boulevard, Engineering Administration, Room 203, Fargo, ND 58102, USA
| | - Md Saimon Mia
- Department of Pharmaceutical Sciences, School of Pharmacy, North Dakota State University, 1001 S. 1401 Albrecht Boulevard Sudro Hall, Fargo, ND 58102, USA
| | - Aaron Bauer
- Biomedical Engineering Program, North Dakota State University; 1401 Centennial Boulevard, Engineering Administration, Room 203, Fargo, ND 58102, USA
| | - Santhalingam Elamurugan
- Biomedical Engineering Program, North Dakota State University; 1401 Centennial Boulevard, Engineering Administration, Room 203, Fargo, ND 58102, USA
| | - Nega Ejjigu
- Biomedical Engineering Program, North Dakota State University; 1401 Centennial Boulevard, Engineering Administration, Room 203, Fargo, ND 58102, USA
| | - Sudipa Maity
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, LA 70112, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, LA 70112, USA
| | - Amara Arshad
- Materials and Nanotechnology Program, North Dakota State University, 1410 North 14th Avenue, CIE 201, Fargo, ND 58102, USA
| | - Min Wu
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
| | - Wenjie Xia
- Department of Aerospace Engineering, Iowa State University, Ames, IA 50011, USA
| | - Jia Fan
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, LA 70112, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Avenue, New Orleans, LA 70112, USA
| | - Ang Guo
- Department of Pharmaceutical Sciences, School of Pharmacy, North Dakota State University, 1001 S. 1401 Albrecht Boulevard Sudro Hall, Fargo, ND 58102, USA
| | - Sijo Mathew
- Department of Pharmaceutical Sciences, School of Pharmacy, North Dakota State University, 1001 S. 1401 Albrecht Boulevard Sudro Hall, Fargo, ND 58102, USA
| | - Dali Sun
- Department of Electrical and Computer Engineering, University of Denver, 2155 E Wesley Avenue, Denver, CO 80210, USA
- Knoebel Institute for Healthy Aging, University of Denver, 2155 E Wesley Avenue, Denver, CO 80210, USA
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Seo Y, Rhim J, Kim JH. RNA-binding proteins and exoribonucleases modulating miRNA in cancer: the enemy within. Exp Mol Med 2024; 56:1080-1106. [PMID: 38689093 PMCID: PMC11148060 DOI: 10.1038/s12276-024-01224-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 02/20/2024] [Accepted: 02/25/2024] [Indexed: 05/02/2024] Open
Abstract
Recent progress in the investigation of microRNA (miRNA) biogenesis and the miRNA processing machinery has revealed previously unknown roles of posttranscriptional regulation in gene expression. The molecular mechanistic interplay between miRNAs and their regulatory factors, RNA-binding proteins (RBPs) and exoribonucleases, has been revealed to play a critical role in tumorigenesis. Moreover, recent studies have shown that the proliferation of hepatocellular carcinoma (HCC)-causing hepatitis C virus (HCV) is also characterized by close crosstalk of a multitude of host RBPs and exoribonucleases with miR-122 and its RNA genome, suggesting the importance of the mechanistic interplay among these factors during the proliferation of HCV. This review primarily aims to comprehensively describe the well-established roles and discuss the recently discovered understanding of miRNA regulators, RBPs and exoribonucleases, in relation to various cancers and the proliferation of a representative cancer-causing RNA virus, HCV. These have also opened the door to the emerging potential for treating cancers as well as HCV infection by targeting miRNAs or their respective cellular modulators.
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Affiliation(s)
- Yoona Seo
- Cancer Molecular Biology Branch, Research Institute, National Cancer Center, Goyang, 10408, Korea
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, 10408, Korea
| | - Jiho Rhim
- Cancer Molecular Biology Branch, Research Institute, National Cancer Center, Goyang, 10408, Korea
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, 10408, Korea
| | - Jong Heon Kim
- Cancer Molecular Biology Branch, Research Institute, National Cancer Center, Goyang, 10408, Korea.
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, 10408, Korea.
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Zou T, Zhou M, Gupta A, Zhuang P, Fishbein AR, Wei HY, Capcha-Rodriguez D, Zhang Z, Cherniack AD, Meyerson M. XRN1 deletion induces PKR-dependent cell lethality in interferon-activated cancer cells. Cell Rep 2024; 43:113600. [PMID: 38261514 PMCID: PMC10989277 DOI: 10.1016/j.celrep.2023.113600] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 10/12/2023] [Accepted: 12/05/2023] [Indexed: 01/25/2024] Open
Abstract
Emerging data suggest that induction of viral mimicry responses through activation of double-stranded RNA (dsRNA) sensors in cancer cells is a promising therapeutic strategy. One approach to induce viral mimicry is to target molecular regulators of dsRNA sensing pathways. Here, we show that the exoribonuclease XRN1 is a negative regulator of the dsRNA sensor protein kinase R (PKR) in cancer cells with high interferon-stimulated gene expression. XRN1 deletion causes PKR pathway activation and consequent cancer cell lethality. Disruption of interferon signaling with the JAK1/2 inhibitor ruxolitinib can decrease cellular PKR levels and rescue sensitivity to XRN1 deletion. Conversely, interferon-β stimulation can increase PKR levels and induce sensitivity to XRN1 inactivation. Lastly, XRN1 deletion causes accumulation of endogenous complementary sense/anti-sense RNAs, which may represent candidate PKR ligands. Our data demonstrate how XRN1 regulates PKR and how this interaction creates a vulnerability in cancer cells with an activated interferon cell state.
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Affiliation(s)
- Tao Zou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Meng Zhou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Akansha Gupta
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Patrick Zhuang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Alyssa R Fishbein
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Hope Y Wei
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Diego Capcha-Rodriguez
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Zhouwei Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Andrew D Cherniack
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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Zhang L, Jiao K, Liu Y, Xu G, Yang Z, Xiang L, Chen Z, Xu C, Zuo Y, Wu Z, Zheng N, Zhang X, Xia Q, Liu Y. UBXN9 inhibits the RNA exosome function to promote T cell control of liver tumorigenesis. Hepatology 2023:01515467-990000000-00672. [PMID: 38051955 DOI: 10.1097/hep.0000000000000711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 11/27/2023] [Indexed: 12/07/2023]
Abstract
BACKGROUND AND AIMS Liver tumorigenesis encompasses oncogenic activation and self-adaptation of various biological processes in premalignant hepatocytes to circumvent the pressure of cellular stress and host immune control. Ubiquitin regulatory X domain-containing proteins (UBXNs) participate in the regulation of certain signaling pathways. However, whether UBXN proteins function in the development of liver cancer remains unclear. APPROACH AND RESULTS Here, we demonstrated that UBXN9 (Alveolar Soft Part Sarcoma Chromosomal Region Candidate Gene 1 Protein/Alveolar Soft Part Sarcoma Locus) expression was decreased in autochthonous oncogene-induced mouse liver tumors and ~47.7% of human HCCs, and associated with poor prognosis in patients with HCC. UBXN9 attenuated liver tumorigenesis induced by different oncogenic factors and tumor growth of transplanted liver tumor cells in immuno-competent mice. Mechanistically, UBXN9 significantly inhibited the function of the RNA exosome, resulting in increased expression of RLR-stimulatory RNAs and activation of the retinoic acid-inducible gene-I-IFN-Ι signaling in tumor cells, and hence potentiated T cell recruitment and immune control of tumor growth. Abrogation of the CD8 + T cell response or inhibition of tumor cell retinoic acid-inducible gene-I signaling efficiently counteracted the UBXN9-mediated suppression of liver tumor growth. CONCLUSIONS Our results reveal a modality in which UBXN9 promotes the stimulatory RNA-induced retinoic acid-inducible gene-I-interferon signaling that induces anti-tumor T cell response in liver tumorigenesis. Targeted manipulation of the UBXN9-RNA exosome circuit may have the potential to reinstate the immune control of liver tumor growth.
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Affiliation(s)
- Li Zhang
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiaotong University Shanghai, China
| | - Kun Jiao
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiaotong University Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yun Liu
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiaotong University Shanghai, China
| | - Guiqin Xu
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiaotong University Shanghai, China
| | - Zhaojuan Yang
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiaotong University Shanghai, China
| | - Lvzhu Xiang
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiaotong University Shanghai, China
| | - Zehong Chen
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiaotong University Shanghai, China
| | - Chen Xu
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiaotong University Shanghai, China
| | - You Zuo
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiaotong University Shanghai, China
| | - Zhibai Wu
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiaotong University Shanghai, China
| | - Ningqian Zheng
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiaotong University Shanghai, China
| | - Xiaoren Zhang
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Qiang Xia
- Department of Liver Surgery, Renji Hospital,School of Medicine, Shanghai Jiaotong University Shanghai, China
| | - Yongzhong Liu
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiaotong University Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Renji Hospital, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
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Zou T, Zhou M, Gupta A, Zhuang P, Fishbein AR, Wei HY, Zhang Z, Cherniack AD, Meyerson M. XRN1 deletion induces PKR-dependent cell lethality in interferon-activated cancer cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.01.551488. [PMID: 37577567 PMCID: PMC10418227 DOI: 10.1101/2023.08.01.551488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Emerging data suggest that induction of viral mimicry responses through activation of double-stranded RNA (dsRNA) sensors in cancer cells is a promising therapeutic strategy. One approach to induce viral mimicry is to target molecular regulators of dsRNA sensing pathways. Here, we show that the exoribonuclease XRN1 is a negative regulator of the dsRNA sensor protein kinase R (PKR) in cancer cells with high interferon-stimulated gene (ISG) expression. XRN1 deletion causes PKR activation and consequent cancer cell lethality. Disruption of interferon signaling with the JAK1/2 inhibitor ruxolitinib can decrease cellular PKR levels and rescue sensitivity to XRN1 deletion. Conversely, interferon-β stimulation can increase PKR levels and induce sensitivity to XRN1 inactivation. Lastly, XRN1 deletion causes accumulation of endogenous complementary sense/anti-sense RNAs, which may represent candidate PKR ligands. Our data demonstrate how XRN1 regulates PKR and nominate XRN1 as a potential therapeutic target in cancer cells with an activated interferon cell state.
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Affiliation(s)
- Tao Zou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Meng Zhou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Akansha Gupta
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Patrick Zhuang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Alyssa R. Fishbein
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Hope Y. Wei
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Zhouwei Zhang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Andrew D. Cherniack
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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