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Hong L, Yue H, Cai D, DeHart A, Toloza-Alvarez G, Du L, Zhou X, Fan X, Huang H, Chen S, Rahaman SO, Zhuang J, Li W. Thymidine Phosphorylase Promotes the Formation of Abdominal Aortic Aneurysm in Mice Fed a Western Diet. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.27.582208. [PMID: 38464026 PMCID: PMC10925194 DOI: 10.1101/2024.02.27.582208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Aims The precise molecular drivers of abdominal aortic aneurysm (AAA) remain unclear. Thymidine phosphorylase (TYMP) contributes to increased platelet activation, thrombosis, and inflammation, all of which are key factors in AAA development. Additionally, TYMP suppresses the proliferation of vascular smooth muscle cells (VSMCs), which are central to the development and progression of AAA. We hypothesize that TYMP plays a key role in AAA development. Methods and Results We conducted a histological study using human AAA samples and normal abdominal aortas, revealing heightened levels of TYMP in human AAA vessel walls. To validate this observation, we utilized an Ang II perfusion-induced AAA model in wild-type C57BL/6J (WT) and Tymp-/- mice, feeding them a Western diet (TD.88137) starting from 4 weeks of age. We found that Tymp-/- mice were protected from Ang II perfusion-induced AAA formation. Furthermore, by using TYMP-expressing VSMCs as well as primarily cultured VSMCs from WT and Tymp-/- mice, we elucidated the essential role of TYMP in regulating MMP2 expression and activation. TYMP deficiency or inhibition by tipiracil, a selective TYMP inhibitor, led to reduced MMP2 production, release, and activation in VSMCs. Additionally, TYMP was found to promote pro-inflammatory cytokine expression systemically, and its absence attenuates TNF-α-stimulated activation of MMP2 and AKT. By co-culturing VSMCs and platelets, we observed that TYMP-deficient platelets had a reduced inhibitory effect on VSMC proliferation compared to WT platelets. Moreover, TYMP appeared to enhance the expression of activated TGFβ1 in cultured VSMCs in vitro and in human AAA vessel walls in vivo. TYMP also boosted the activation of thrombospondin-1 type 1 repeat domain-enhanced TGFβ1 signaling, resulting in increased connective tissue growth factor production. Conclusion Our findings collectively demonstrated that TYMP serves as a novel regulatory force in vascular biology, exerting influence over VSMC functionality and inflammatory responses that promote the development of AAA.
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Affiliation(s)
- Liang Hong
- Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine at Marshall University, Huntington, WV
| | - Hong Yue
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine at Marshall University, Huntington, WV
| | - Dunpeng Cai
- Department of Surgery, University of Missouri School of Medicine, Columbia, MO
| | - Autumn DeHart
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine at Marshall University, Huntington, WV
| | - Gretel Toloza-Alvarez
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine at Marshall University, Huntington, WV
| | - Lili Du
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine at Marshall University, Huntington, WV
| | - Xianwu Zhou
- Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xiaoping Fan
- Department of Cardiovascular Surgery, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Huanlei Huang
- Department of Cardiovascular Surgery, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Shiyou Chen
- Department of Surgery, University of Missouri School of Medicine, Columbia, MO
- The Research Service, Harry S. Truman Memorial Veterans Hospital, Columbia, MO
| | - Shaik O. Rahaman
- University of Maryland, Department of Nutrition and Food Science, College Park, MD
| | - Jian Zhuang
- Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Wei Li
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine at Marshall University, Huntington, WV
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Kmiotek-Wasylewska K, Łabędź-Masłowska A, Bobis-Wozowicz S, Karnas E, Noga S, Sekuła-Stryjewska M, Woźnicka O, Madeja Z, Dawn B, Zuba-Surma EK. Induced pluripotent stem cell-derived extracellular vesicles enriched with miR-126 induce proangiogenic properties and promote repair of ischemic tissue. FASEB J 2024; 38:e23415. [PMID: 38243682 DOI: 10.1096/fj.202301836r] [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: 09/08/2023] [Revised: 12/15/2023] [Accepted: 12/27/2023] [Indexed: 01/21/2024]
Abstract
Emerging evidence suggests that stem cell-derived extracellular vesicles (EVs) may induce pro-regenerative effects in ischemic tissues by delivering bioactive molecules, including microRNAs. Recent studies have also shown pro-regenerative benefits of EVs derived from induced pluripotent stem (iPS) cells. However, the underlying mechanisms of EV benefits and the role of their transferred regulatory molecules remain incompletely understood. Accordingly, we investigated the effects of human iPS-derived EVs (iPS-EVs) enriched in proangiogenic miR-126 (iPS-miR-126-EVs) on functional properties of human endothelial cells (ECs) in vitro. We also examined the outcomes following EV injection in a murine model of limb ischemia in vivo. EVs were isolated from conditioned media from cultures of unmodified and genetically modified human iPS cells overexpressing miR-126. The iPS-miR-126-EVs were enriched in miR-126 when compared with control iPS-EVs and effectively transferred miR-126 along with other miRNAs to recipient ECs improving their functional properties essential for ischemic tissue repair, including proliferation, metabolic activity, cell survival, migration, and angiogenic potential. Injection of iPS-miR-126-EVs in vivo in a murine model of acute limb ischemia promoted angiogenesis, increased perfusion, and enhanced functional recovery. These observations corresponded with elevated expression of genes for several proangiogenic factors in ischemic tissues following iPS-miR-126-EV transplantation. These results indicate that innate pro-regenerative properties of iPS-EVs may be further enhanced by altering their molecular composition via controlled genetic modifications. Such iPS-EVs overexpressing selected microRNAs, including miR-126, may represent a novel acellular tool for therapy of ischemic tissues in vivo.
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Affiliation(s)
- Katarzyna Kmiotek-Wasylewska
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Cell Biology, Jagiellonian University, Kraków, Poland
| | - Anna Łabędź-Masłowska
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Cell Biology, Jagiellonian University, Kraków, Poland
| | - Sylwia Bobis-Wozowicz
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Cell Biology, Jagiellonian University, Kraków, Poland
| | - Elżbieta Karnas
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Cell Biology, Jagiellonian University, Kraków, Poland
| | - Sylwia Noga
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Cell Biology, Jagiellonian University, Kraków, Poland
- Malopolska Centre of Biotechnology, Laboratory of Stem Cell Biotechnology, Jagiellonian University, Kraków, Poland
| | - Małgorzata Sekuła-Stryjewska
- Malopolska Centre of Biotechnology, Laboratory of Stem Cell Biotechnology, Jagiellonian University, Kraków, Poland
| | - Olga Woźnicka
- Faculty of Biology, Institute of Zoology and Biomedical Research, Department of Cell Biology and Imaging, Jagiellonian University, Kraków, Poland
| | - Zbigniew Madeja
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Cell Biology, Jagiellonian University, Kraków, Poland
| | - Buddhadeb Dawn
- Department of Internal Medicine, Kirk Kerkorian School of Medicine, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | - Ewa K Zuba-Surma
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Cell Biology, Jagiellonian University, Kraków, Poland
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Montero-Calle A, Jiménez de Ocaña S, Benavente-Naranjo R, Rejas-González R, Bartolomé RA, Martínez-Useros J, Sanz R, Dziaková J, Fernández-Aceñero MJ, Mendiola M, Casal JI, Peláez-García A, Barderas R. Functional Proteomics Characterization of the Role of SPRYD7 in Colorectal Cancer Progression and Metastasis. Cells 2023; 12:2548. [PMID: 37947626 PMCID: PMC10648221 DOI: 10.3390/cells12212548] [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: 07/04/2023] [Revised: 10/12/2023] [Accepted: 10/24/2023] [Indexed: 11/12/2023] Open
Abstract
SPRY domain-containing protein 7 (SPRYD7) is a barely known protein identified via spatial proteomics as being upregulated in highly metastatic-to-liver KM12SM colorectal cancer (CRC) cells in comparison to its isogenic poorly metastatic KM12C CRC cells. Here, we aimed to analyze SPRYD7's role in CRC via functional proteomics. Through immunohistochemistry, the overexpression of SPRYD7 was observed to be associated with the poor survival of CRC patients and with an aggressive and metastatic phenotype. Stable SPRYD7 overexpression was performed in KM12C and SW480 poorly metastatic CRC cells and in their isogenic highly metastatic-to-liver-KM12SM-and-to-lymph-nodes SW620 CRC cells, respectively. Upon upregulation of SPRYD7, in vitro and in vivo functional assays confirmed a key role of SPRYD7 in the invasion and migration of CRC cells and in liver homing and tumor growth. Additionally, transient siRNA SPRYD7 silencing allowed us to confirm in vitro functional results. Furthermore, SPRYD7 was observed as an inductor of angiogenesis. In addition, the dysregulated SPRYD7-associated proteome and SPRYD7 interactors were elucidated via 10-plex TMT quantitative proteins, immunoproteomics, and bioinformatics. After WB validation, the biological pathways associated with the stable overexpression of SPRYD7 were visualized. In conclusion, it was demonstrated here that SPRYD7 is a novel protein associated with CRC progression and metastasis. Thus, SPRYD7 and its interactors might be of relevance in identifying novel therapeutic targets for advanced CRC.
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Affiliation(s)
- Ana Montero-Calle
- Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, 28220 Madrid, Spain; (S.J.d.O.); (R.B.-N.); (R.R.-G.)
| | - Sofía Jiménez de Ocaña
- Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, 28220 Madrid, Spain; (S.J.d.O.); (R.B.-N.); (R.R.-G.)
| | - Ruth Benavente-Naranjo
- Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, 28220 Madrid, Spain; (S.J.d.O.); (R.B.-N.); (R.R.-G.)
| | - Raquel Rejas-González
- Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, 28220 Madrid, Spain; (S.J.d.O.); (R.B.-N.); (R.R.-G.)
| | - Rubén A. Bartolomé
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain;
| | - Javier Martínez-Useros
- Translational Oncology Division, OncoHealth Institute, Health Research Institute-University Hospital Fundación Jiménez Díaz-Universidad Autónoma de Madrid, 28040 Madrid, Spain;
| | - Rodrigo Sanz
- Surgical Digestive Department, Hospital Universitario Clínico San Carlos, 28040 Madrid, Spain; (R.S.); (J.D.)
| | - Jana Dziaková
- Surgical Digestive Department, Hospital Universitario Clínico San Carlos, 28040 Madrid, Spain; (R.S.); (J.D.)
| | | | - Marta Mendiola
- Molecular Pathology and Therapeutic Targets Group, La Paz University Hospital (IdiPAZ), 28046 Madrid, Spain; (M.M.); (A.P.-G.)
| | - José Ignacio Casal
- Centro de Investigaciones Biológicas Margarita Salas, CSIC, 28040 Madrid, Spain;
| | - Alberto Peláez-García
- Molecular Pathology and Therapeutic Targets Group, La Paz University Hospital (IdiPAZ), 28046 Madrid, Spain; (M.M.); (A.P.-G.)
| | - Rodrigo Barderas
- Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, 28220 Madrid, Spain; (S.J.d.O.); (R.B.-N.); (R.R.-G.)
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Du J, Zhang C, Liu F, Liu X, Wang D, Zhao D, Shui G, Zhao Y, Yan C. Distinctive metabolic remodeling in TYMP deficiency beyond mitochondrial dysfunction. J Mol Med (Berl) 2023; 101:1237-1253. [PMID: 37603049 DOI: 10.1007/s00109-023-02358-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 07/09/2023] [Accepted: 08/14/2023] [Indexed: 08/22/2023]
Abstract
Mitochondrial neurogastrointestinal encephalomyopathy (MNGIE) is caused by mutations in the TYMP gene, which encodes thymidine phosphorylase (TP). As a cytosolic metabolic enzyme, TP defects affect biological processes that are thought to not be limited to the abnormal replication of mitochondrial DNA. This study aimed to elucidate the characteristic metabolic alterations and associated homeostatic regulation caused by TYMP deficiency. The pathogenicity of novel TYMP variants was evaluated in terms of clinical features, genetic analysis, and structural instability. We analyzed plasma samples from three patients with MNGIE; three patients with m.3243A > G mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes (MELAS); and four healthy controls (HC) using both targeted and untargeted metabolomics techniques. Transcriptomics analysis and bioenergetic studies were performed on skin fibroblasts from participants in these three groups. A TYMP overexpression experiment was conducted to rescue the observed changes. Compared with controls, specific alterations in nucleosides, bile acids, and steroid metabolites were identified in the plasma of MNGIE patients. Comparable mitochondrial dysfunction was present in fibroblasts from patients with TYMP deficiency and in those from patients with the m.3243A > G mutation. Distinctively decreased sterol regulatory element binding protein (SREBP) regulated cholesterol metabolism and fatty acid (FA) biosynthesis as well as reduced FA degradation were revealed in fibroblasts with TYMP deficiency. The restoration of thymidine phosphorylase activity rescued the observed changes in MNGIE fibroblasts. Our findings indicated that more widespread metabolic disturbance may be caused by TYMP deficiency in addition to mitochondrial dysfunction, which expands our knowledge of the biochemical outcome of TYMP deficiency. KEY MESSAGES: Distinct metabolic profiles in patients with TYMP deficiency compared to those with m.3243A > G mutation. TYMP deficiency leads to a global disruption of nucleoside metabolism. Cholesterol and fatty acid metabolism are inhibited in individuals with MNGIE. TYMP is functionally related to SREBP-regulated pathways. Potential metabolite biomarkers that could be valuable clinical tools to improve the diagnosis of MNGIE.
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Affiliation(s)
- Jixiang Du
- Department of Neurology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Chao Zhang
- Key Laboratory of Experimental Teratology, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Fuchen Liu
- Department of Neurology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Xihan Liu
- Key Laboratory of Experimental Teratology, Ministry of Education, Department of Cell Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Dongdong Wang
- Department of Neurology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Dandan Zhao
- Department of Neurology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Guanghou Shui
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of the Chinese Academy of Sciences, Beijing, 101408, China
| | - Yuying Zhao
- Department of Neurology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Chuanzhu Yan
- Department of Neurology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China.
- Qingdao Key Lab of Mitochondrial Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Qingdao, 266103, China.
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van der List ACJ, Litjens NHR, Brouwer RWW, Klepper M, den Dekker AT, van Ijcken WFJ, Betjes MGH. Single-Cell RNA Sequencing of Donor-Reactive T Cells Reveals Role of Apoptosis in Donor-Specific Hyporesponsiveness of Kidney Transplant Recipients. Int J Mol Sci 2023; 24:14463. [PMID: 37833911 PMCID: PMC10572284 DOI: 10.3390/ijms241914463] [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: 08/21/2023] [Revised: 09/12/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023] Open
Abstract
After kidney transplantation (KT), donor-specific hyporesponsiveness (DSH) of recipient T cells develops over time. Recently, apoptosis was identified as a possible underlying mechanism. In this study, both transcriptomic profiles and complete V(D)J variable regions of TR transcripts from individual alloreactive T cells of kidney transplant recipients were determined with single-cell RNA sequencing. Alloreactive T cells were identified by CD137 expression after stimulation of peripheral blood mononuclear cells obtained from KT recipients (N = 7) prior to and 3-5 years after transplantation with cells of their donor or a third party control. The alloreactive T cells were sorted, sequenced and the transcriptome and T cell receptor profiles were analyzed using unsupervised clustering. Alloreactive T cells retain a highly polyclonal T Cell Receptor Alpha/Beta repertoire over time. Post transplantation, donor-reactive CD4+ T cells had a specific downregulation of genes involved in T cell cytokine-mediated pathways and apoptosis. The CD8+ donor-reactive T cell profile did not change significantly over time. Single-cell expression profiling shows that activated and pro-apoptotic donor-reactive CD4+ T cell clones are preferentially lost after transplantation in stable kidney transplant recipients.
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Affiliation(s)
- Amy C. J. van der List
- Erasmus MC Transplant Institute, Department of Internal Medicine, University Medical Center, 3015 CN Rotterdam, The Netherlands; (A.C.J.v.d.L.); (N.H.R.L.); (M.K.)
| | - Nicolle H. R. Litjens
- Erasmus MC Transplant Institute, Department of Internal Medicine, University Medical Center, 3015 CN Rotterdam, The Netherlands; (A.C.J.v.d.L.); (N.H.R.L.); (M.K.)
| | - Rutger W. W. Brouwer
- Erasmus MC Center for Biomics, University Medical Center, 3015 CN Rotterdam, The Netherlands; (R.W.W.B.); (A.T.d.D.); (W.F.J.v.I.)
| | - Mariska Klepper
- Erasmus MC Transplant Institute, Department of Internal Medicine, University Medical Center, 3015 CN Rotterdam, The Netherlands; (A.C.J.v.d.L.); (N.H.R.L.); (M.K.)
| | - Alexander T. den Dekker
- Erasmus MC Center for Biomics, University Medical Center, 3015 CN Rotterdam, The Netherlands; (R.W.W.B.); (A.T.d.D.); (W.F.J.v.I.)
| | - Wilfred F. J. van Ijcken
- Erasmus MC Center for Biomics, University Medical Center, 3015 CN Rotterdam, The Netherlands; (R.W.W.B.); (A.T.d.D.); (W.F.J.v.I.)
| | - Michiel G. H. Betjes
- Erasmus MC Transplant Institute, Department of Internal Medicine, University Medical Center, 3015 CN Rotterdam, The Netherlands; (A.C.J.v.d.L.); (N.H.R.L.); (M.K.)
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Warfield BM, Reigan P. Multifunctional role of thymidine phosphorylase in cancer: (Trends in Cancer, 8:6 p:482-493, 2022). Trends Cancer 2023:S2405-8033(23)00100-0. [PMID: 37355411 DOI: 10.1016/j.trecan.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2023]
Affiliation(s)
- Becka M Warfield
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, 12850 East Montview Boulevard, V20-2102, Aurora, CO, 80045, USA
| | - Philip Reigan
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, 12850 East Montview Boulevard, V20-2102, Aurora, CO, 80045, USA..
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Roytenberg R, García-Sastre A, Li W. Vaccine-induced immune thrombotic thrombocytopenia: what do we know hitherto? Front Med (Lausanne) 2023; 10:1155727. [PMID: 37261122 PMCID: PMC10227460 DOI: 10.3389/fmed.2023.1155727] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/28/2023] [Indexed: 06/02/2023] Open
Abstract
Vaccine-induced immune thrombotic thrombocytopenia (VITT), also known as thrombosis with thrombocytopenia syndrome, is a catastrophic and life-threatening reaction to coronavirus disease 2019 (COVID-19) vaccines, which occurs disproportionately in response to vaccination with non-replicating adenovirus vector (AV) vaccines. The mechanism of VITT is not well defined and it has not been resolved why cases of VITT are predominated by vaccination with AV vaccines. However, virtually all VITT patients have positive platelet-activating anti-platelet factor 4 (PF4) antibody titers. Subsequently, platelets are activated and depleted in an Fcγ-receptor IIa (FcγRIIa or CD32a)-dependent manner, but it is not clear why or how the anti-PF4 response is mounted. This review describes the pathogenesis of VITT and provides insight into possible mechanisms that prompt the formation of a PF4/polyanion complex, which drives VITT pathology, as an amalgam of current experimental data or hypotheses.
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Affiliation(s)
- Renat Roytenberg
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine at Marshall University, Huntington, WV, United States
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Wei Li
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine at Marshall University, Huntington, WV, United States
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Du L, Yue H, Rorabaugh BR, Li OQY, DeHart AR, Toloza‐Alvarez G, Hong L, Denvir J, Thompson E, Li W. Thymidine Phosphorylase Deficiency or Inhibition Preserves Cardiac Function in Mice With Acute Myocardial Infarction. J Am Heart Assoc 2023; 12:e028023. [PMID: 36974758 PMCID: PMC10122909 DOI: 10.1161/jaha.122.028023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 02/22/2023] [Indexed: 03/29/2023]
Abstract
Background Ischemic cardiovascular disease is the leading cause of death worldwide. Current pharmacologic therapy has multiple limitations, and patients remain symptomatic despite maximal medical therapies. Deficiency or inhibition of thymidine phosphorylase (TYMP) in mice reduces thrombosis, suggesting that TYMP could be a novel therapeutic target for patients with acute myocardial infarction (AMI). Methods and Results A mouse AMI model was established by ligation of the left anterior descending coronary artery in C57BL/6J wild-type and TYMP-deficient (Tymp-/-) mice. Cardiac function was monitored by echocardiography or Langendorff assay. TYMP-deficient hearts had lower baseline contractility. However, cardiac function, systolic left ventricle anterior wall thickness, and diastolic wall strain were significantly greater 4 weeks after AMI compared with wild-type hearts. TYMP deficiency reduced microthrombus formation after AMI. TYMP deficiency did not affect angiogenesis in either normal or infarcted myocardium but increased arteriogenesis post-AMI. TYMP deficiency enhanced the mobilization of bone marrow stem cells and promoted mesenchymal stem cell (MSC) proliferation, migration, and resistance to inflammation and hypoxia. TYMP deficiency increased the number of larger MSCs and decreased matrix metalloproteinase-2 expression, resulting in a high homing capability. TYMP deficiency induced constitutive AKT phosphorylation in MSCs but reduced expression of genes associated with retinoid-interferon-induced mortality-19, a molecule that enhances cell death. Inhibition of TYMP with its selective inhibitor, tipiracil, phenocopied TYMP deficiency, improved post-AMI cardiac function and systolic left ventricle anterior wall thickness, attenuated diastolic stiffness, and reduced infarct size. Conclusions This study demonstrated that TYMP plays an adverse role after AMI. Targeting TYMP may be a novel therapy for patients with AMI.
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Affiliation(s)
- Lili Du
- Department of Biomedical SciencesJoan C. Edwards School of Medicine at Marshall UniversityHuntingtonWVUSA
- Department of PathophysiologyCollege of Basic Medical Science, China Medical UniversityShenyangLiaoningChina
| | - Hong Yue
- Department of Biomedical SciencesJoan C. Edwards School of Medicine at Marshall UniversityHuntingtonWVUSA
| | - Boyd R. Rorabaugh
- Department of Biomedical SciencesJoan C. Edwards School of Medicine at Marshall UniversityHuntingtonWVUSA
- Department of Pharmaceutical SciencesSchool of Pharmacy at Marshall UniversityHuntingtonWVUSA
| | - Oliver Q. Y. Li
- Department of Biomedical SciencesJoan C. Edwards School of Medicine at Marshall UniversityHuntingtonWVUSA
| | - Autumn R. DeHart
- Department of Biomedical SciencesJoan C. Edwards School of Medicine at Marshall UniversityHuntingtonWVUSA
| | - Gretel Toloza‐Alvarez
- Department of Biomedical SciencesJoan C. Edwards School of Medicine at Marshall UniversityHuntingtonWVUSA
| | - Liang Hong
- Department of Biomedical SciencesJoan C. Edwards School of Medicine at Marshall UniversityHuntingtonWVUSA
| | - James Denvir
- Department of Biomedical SciencesJoan C. Edwards School of Medicine at Marshall UniversityHuntingtonWVUSA
| | - Ellen Thompson
- Department of MedicineJoan C. Edwards School of Medicine at Marshall UniversityHuntingtonWVUSA
| | - Wei Li
- Department of Biomedical SciencesJoan C. Edwards School of Medicine at Marshall UniversityHuntingtonWVUSA
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9
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Chen SA, Zhang JP, Wang N, Chen J. Identifying TYMP as an Immune Prognostic Marker in Clear Cell Renal Cell Carcinoma. Technol Cancer Res Treat 2023; 22:15330338231194555. [PMID: 38043946 PMCID: PMC10695089 DOI: 10.1177/15330338231194555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 07/07/2023] [Accepted: 07/27/2023] [Indexed: 12/05/2023] Open
Abstract
BACKGROUND In clear cell renal cell carcinoma (ccRCC), only some patients can benefit from immunotherapy therapy, and it is urgent to find immune-related molecular markers and targets. METHODS Thymidine phosphorylase (TYMP) expression level and predictive value in pan-cancers were analyzed using TIMER, GEPIA2, and The Human Protein Atlas. We obtained ccRCC tissues to verify the differential expression of TYMP and confirmed the biological function in vitro. Subsequently, Gene Ontology, Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA) are used to explore the potential mechanism of TYMP. Finally, TIMER was used to analyze the infiltration levels and prognostic value of different immune cells. RESULTS TYMP is upregulated in various cancers, including ccRCC, and there is a certain degree of causality between high expression and poor prognosis in ccRCC. It was confirmed that TYMP knockdown could suppress cell aggressiveness, and cause cell death. Differential analysis showed that 55 differential genes were upregulated in the high-expression groups of TYMP. KEGG and GSEA analyses suggested that TYMP was linked to immune cell invasion, fatty acid metabolism, and P53 signaling pathway. Further investigation revealed that the expression level of TYMP linked positively to T-cell follicular helper and Tregs, but negatively with mast cell activation. Finally, a Nomogram was established on the base of expression level of TYMP and the clinical characteristics of ccRCC patients to predict prognosis. CONCLUSIONS Patient survival is poor and immune cell infiltration is abnormal when TYMP is highly expressed in ccRCC, suggesting that ccRCC patients could benefit from using TYMP as a molecular diagnostic and therapeutic target.
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Affiliation(s)
- Shao-An Chen
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Jun-Peng Zhang
- Department of Medical Ultrasound, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Ning Wang
- Department of Radiology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Ji Chen
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
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10
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di Meo NA, Lasorsa F, Rutigliano M, Loizzo D, Ferro M, Stella A, Bizzoca C, Vincenti L, Pandolfo SD, Autorino R, Crocetto F, Montanari E, Spilotros M, Battaglia M, Ditonno P, Lucarelli G. Renal Cell Carcinoma as a Metabolic Disease: An Update on Main Pathways, Potential Biomarkers, and Therapeutic Targets. Int J Mol Sci 2022; 23:ijms232214360. [PMID: 36430837 PMCID: PMC9698586 DOI: 10.3390/ijms232214360] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 11/22/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most frequent histological kidney cancer subtype. Over the last decade, significant progress has been made in identifying the genetic and metabolic alterations driving ccRCC development. In particular, an integrated approach using transcriptomics, metabolomics, and lipidomics has led to a better understanding of ccRCC as a metabolic disease. The metabolic profiling of this cancer could help define and predict its behavior in terms of aggressiveness, prognosis, and therapeutic responsiveness, and would be an innovative strategy for choosing the optimal therapy for a specific patient. This review article describes the current state-of-the-art in research on ccRCC metabolic pathways and potential therapeutic applications. In addition, the clinical implication of pharmacometabolomic intervention is analyzed, which represents a new field for novel stage-related and patient-tailored strategies according to the specific susceptibility to new classes of drugs.
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Affiliation(s)
- Nicola Antonio di Meo
- Urology, Andrology and Kidney Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Francesco Lasorsa
- Urology, Andrology and Kidney Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Monica Rutigliano
- Urology, Andrology and Kidney Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Davide Loizzo
- Urology, Andrology and Kidney Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Matteo Ferro
- Division of Urology, European Institute of Oncology, IRCCS, 20141 Milan, Italy
| | - Alessandro Stella
- Laboratory of Human Genetics, Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Cinzia Bizzoca
- Division of General Surgery, Polyclinic Hospital, 70124 Bari, Italy
| | | | | | | | - Felice Crocetto
- Department of Neurosciences, Reproductive Sciences and Odontostomatology, University of Naples “Federico II”, 80131 Naples, Italy
| | - Emanuele Montanari
- Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy
| | - Marco Spilotros
- Urology, Andrology and Kidney Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Michele Battaglia
- Urology, Andrology and Kidney Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Pasquale Ditonno
- Urology, Andrology and Kidney Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Giuseppe Lucarelli
- Urology, Andrology and Kidney Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari “Aldo Moro”, 70124 Bari, Italy
- Correspondence: or
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Paladhi A, Daripa S, Mondal I, Hira SK. Targeting thymidine phosphorylase alleviates resistance to dendritic cell immunotherapy in colorectal cancer and promotes antitumor immunity. Front Immunol 2022; 13:988071. [PMID: 36090972 PMCID: PMC9449540 DOI: 10.3389/fimmu.2022.988071] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/08/2022] [Indexed: 11/22/2022] Open
Abstract
T-cell exhaustion plays a pivotal role in the resistance of microsatellite-stable colorectal cancer (CRC) to immunotherapy. Identifying and targeting T-cell exhaustion-activating mechanisms is a promising strategy to augment the effects of immunotherapy. Here, we found that thymidine phosphorylase (TYMP) plays a decisive role in inducing systemic T-cell exhaustion and abrogating the efficacy of dendritic cell (DC) therapy in a CRC model. Targeting TYMP with tipiracil hydrochloride (TPI) induces immunological cell death (ICD). The combined effects of TPI and imiquimod-activated DCs turn CT26 tumors into immunologically ‘hot’ tumors by inducing ICD in vivo. High-dimensional cytometry analysis revealed T-cell and IFN-γ dependency on the therapeutic outcome. In addition, chemoimmunotherapy converts intratumoral Treg cells into Th1 effector cells and eliminates tumor-associated macrophages, resulting in higher cytotoxic T lymphocyte infiltration and activation. This effect is also associated with the downregulation of PD-L1 expression in tumors, leading to the prevention of T-cell exhaustion. Thus, cooperative and cognitive interactions between dendritic cells and immunogenic cell death induced by therapy with TPI promote the immune response and tumoricidal activities against microsatellite stable colorectal cancer. Our results support TYMP targeting to improve the effects of DC immunotherapy and outcomes in CRC.
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Affiliation(s)
- Ankush Paladhi
- Cellular Immunology Laboratory, Department of Zoology, The University of Burdwan, Purba Bardhaman, India
| | - Samrat Daripa
- Cellular Immunology Laboratory, Department of Zoology, The University of Burdwan, Purba Bardhaman, India
| | - Indrani Mondal
- Department of Hematology, Nil Ratan Sircar (NRS) Medical College and Hospital, Kolkata, India
| | - Sumit Kumar Hira
- Cellular Immunology Laboratory, Department of Zoology, The University of Burdwan, Purba Bardhaman, India
- *Correspondence: Sumit Kumar Hira,
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12
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Domingo-Relloso A, Makhani K, Riffo-Campos AL, Tellez-Plaza M, Klein KO, Subedi P, Zhao J, Moon KA, Bozack AK, Haack K, Goessler W, Umans JG, Best LG, Zhang Y, Herreros-Martinez M, Glabonjat RA, Schilling K, Galvez-Fernandez M, Kent JW, Sanchez TR, Taylor KD, Craig Johnson W, Durda P, Tracy RP, Rotter JI, Rich SS, Berg DVD, Kasela S, Lappalainen T, Vasan RS, Joehanes R, Howard BV, Levy D, Lohman K, Liu Y, Daniele Fallin M, Cole SA, Mann KK, Navas-Acien A. Arsenic Exposure, Blood DNA Methylation, and Cardiovascular Disease. Circ Res 2022; 131:e51-e69. [PMID: 35658476 PMCID: PMC10203287 DOI: 10.1161/circresaha.122.320991] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 05/18/2022] [Indexed: 02/03/2023]
Abstract
BACKGROUND Epigenetic dysregulation has been proposed as a key mechanism for arsenic-related cardiovascular disease (CVD). We evaluated differentially methylated positions (DMPs) as potential mediators on the association between arsenic and CVD. METHODS Blood DNA methylation was measured in 2321 participants (mean age 56.2, 58.6% women) of the Strong Heart Study, a prospective cohort of American Indians. Urinary arsenic species were measured using high-performance liquid chromatography coupled to inductively coupled plasma mass spectrometry. We identified DMPs that are potential mediators between arsenic and CVD. In a cross-species analysis, we compared those DMPs with differential liver DNA methylation following early-life arsenic exposure in the apoE knockout (apoE-/-) mouse model of atherosclerosis. RESULTS A total of 20 and 13 DMPs were potential mediators for CVD incidence and mortality, respectively, several of them annotated to genes related to diabetes. Eleven of these DMPs were similarly associated with incident CVD in 3 diverse prospective cohorts (Framingham Heart Study, Women's Health Initiative, and Multi-Ethnic Study of Atherosclerosis). In the mouse model, differentially methylated regions in 20 of those genes and DMPs in 10 genes were associated with arsenic. CONCLUSIONS Differential DNA methylation might be part of the biological link between arsenic and CVD. The gene functions suggest that diabetes might represent a relevant mechanism for arsenic-related cardiovascular risk in populations with a high burden of diabetes.
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Affiliation(s)
- Arce Domingo-Relloso
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA
- Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Carlos III Health Institute, Madrid, Spain
- Department of Statistics and Operations Research, University of Valencia, Spain
| | - Kiran Makhani
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Angela L. Riffo-Campos
- Millennium Nucleus on Sociomedicine (SocioMed) and Vicerrectoría Académica, Universidad de La Frontera, Temuco, Chile
- Department of Computer Science, ETSE, University of Valencia, Valencia, Spain
| | - Maria Tellez-Plaza
- Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Carlos III Health Institute, Madrid, Spain
| | - Kathleen Oros Klein
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Pooja Subedi
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, FL, USA
| | - Jinying Zhao
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, FL, USA
| | - Katherine A. Moon
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Anne K. Bozack
- Department of Environmental Health Sciences, School of Public Health, University of California, Berkeley, USA
| | - Karin Haack
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Walter Goessler
- Institute of Chemistry - Analytical Chemistry for Health and Environment, University of Graz, Austria
| | | | - Lyle G. Best
- Missouri Breaks Industries and Research Inc., Eagle Butte, SD, USA
| | - Ying Zhang
- Department of Biostatistics and Epidemiology, The University of Oklahoma Health Sciences Center, OK, USA
| | | | - Ronald A. Glabonjat
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Kathrin Schilling
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Marta Galvez-Fernandez
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA
- Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Carlos III Health Institute, Madrid, Spain
| | - Jack W. Kent
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Tiffany R Sanchez
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - W. Craig Johnson
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Peter Durda
- Department of Pathology Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Russell P. Tracy
- Department of Pathology Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Stephen S. Rich
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - David Van Den Berg
- Department of Population and Public Health Sciences, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | - Silva Kasela
- New York Genome Center, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Tuuli Lappalainen
- New York Genome Center, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Ramachandran S Vasan
- National Heart, Lung, and Blood Institute’s and Boston University’s Framingham Heart Study, Framingham, MA; Sections of Preventive Medicine and Epidemiology and Cardiovascular Medicine, Department of Medicine, department of Epidemiology, Boston University Schools of medicine and Public health, Boston, MA, USA
| | - Roby Joehanes
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
- Framingham Heart Study, Framingham, MA
| | | | - Daniel Levy
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
- Framingham Heart Study, Framingham, MA
| | - Kurt Lohman
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Yongmei Liu
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - M Daniele Fallin
- Departments of Mental Health and Epidemiology, Johns Hopkins University, Baltimore, MD, USA
| | - Shelley A. Cole
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Koren K. Mann
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Ana Navas-Acien
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA
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13
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van Dieken A, Staecker H, Schmitt H, Harre J, Pich A, Roßberg W, Lenarz T, Durisin M, Warnecke A. Bioinformatic Analysis of the Perilymph Proteome to Generate a Human Protein Atlas. Front Cell Dev Biol 2022; 10:847157. [PMID: 35573665 PMCID: PMC9096870 DOI: 10.3389/fcell.2022.847157] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 04/04/2022] [Indexed: 11/16/2022] Open
Abstract
The high complexity of the cellular architecture of the human inner ear and the inaccessibility for tissue biopsy hampers cellular and molecular analysis of inner ear disease. Sampling and analysis of perilymph may present an opportunity for improved diagnostics and understanding of human inner ear pathology. Analysis of the perilymph proteome from patients undergoing cochlear implantation was carried out revealing a multitude of proteins and patterns of protein composition that may enable characterisation of patients into subgroups. Based on existing data and databases, single proteins that are not present in the blood circulation were related to cells within the cochlea to allow prediction of which cells contribute to the individual perilymph proteome of the patients. Based on the results, we propose a human atlas of the cochlea. Finally, druggable targets within the perilymph proteome were identified. Understanding and modulating the human perilymph proteome will enable novel avenues to improve diagnosis and treatment of inner ear diseases.
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Affiliation(s)
- Alina van Dieken
- Department of Otolaryngology, Hannover Medical School, Hannover, Germany
| | - Hinrich Staecker
- Department of Otolaryngology, Head and Neck, Surgery, University of Kansas School of Medicine, Kansas City, KS, United States
| | - Heike Schmitt
- Department of Otolaryngology, Hannover Medical School, Hannover, Germany
| | - Jennifer Harre
- Department of Otolaryngology, Hannover Medical School, Hannover, Germany
| | - Andreas Pich
- Core Facility Proteomics, Hannover Medical School, Hannover, Germany
| | - Willi Roßberg
- Department of Otolaryngology, Hannover Medical School, Hannover, Germany
| | - Thomas Lenarz
- Department of Otolaryngology, Hannover Medical School, Hannover, Germany
| | - Martin Durisin
- Department of Otolaryngology, Hannover Medical School, Hannover, Germany
| | - Athanasia Warnecke
- Department of Otolaryngology, Hannover Medical School, Hannover, Germany
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14
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Sun Z, Tao W, Guo X, Jing C, Zhang M, Wang Z, Kong F, Suo N, Jiang S, Wang H. Construction of a Lactate-Related Prognostic Signature for Predicting Prognosis, Tumor Microenvironment, and Immune Response in Kidney Renal Clear Cell Carcinoma. Front Immunol 2022; 13:818984. [PMID: 35250999 PMCID: PMC8892380 DOI: 10.3389/fimmu.2022.818984] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 01/18/2022] [Indexed: 12/31/2022] Open
Abstract
Kidney renal clear cell carcinoma (KIRC) is one of the most prevalent primary malignancies with high heterogeneity in the urological system. Growing evidence implies that lactate is a significant carbon source for cell metabolism and plays a vital role in tumor development, maintenance, and therapeutic response. However, the global influence of lactate-related genes (LRGs) on prognostic significance, tumor microenvironment characteristics, and therapeutic response has not been comprehensively elucidated in patients with KIRC. In the present study, we collected RNA sequencing and clinical data of KIRC from The Cancer Genome Atlas (TCGA), E-MTAB-1980, and GSE22541 cohorts. Unsupervised clustering of 17 differentially expressed LRG profiles divided the samples into three clusters with distinct immune characteristics. Three genes (FBP1, HADH, and TYMP) were then identified to construct a lactate-related prognostic signature (LRPS) using the least absolute shrinkage and selection operator (LASSO) and Cox regression analyses. The novel signature exhibited excellent robustness and predictive ability for the overall survival of patients. In addition, the constructed nomogram based on the LRPS-based risk scores and clinical factors (age, gender, tumor grade, and stage) showed a robust predictive performance. Furthermore, patients classified by risk scores had distinguishable immune status, tumor mutation burden, response to immunotherapy, and sensitivity to drugs. In conclusion, we developed an LRPS for KIRC that was closely related to the immune landscape and therapeutic response. This LRPS may guide clinicians to make more precise and personalized treatment decisions for KIRC patients.
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Affiliation(s)
- Zhuolun Sun
- Department of Urology, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Wen Tao
- Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xudong Guo
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Changying Jing
- Institute of Diabetes and Regeneration, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Mingxiao Zhang
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Zhenqing Wang
- Department of Urology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Feng Kong
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Ning Suo
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Shaobo Jiang
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Hanbo Wang
- Department of Urology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
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15
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Najem H, Ott M, Kassab C, Rao A, Rao G, Marisetty A, Sonabend AM, Horbinski C, Verhaak R, Shankar A, Krishnan SN, Varn FS, Arrieta VA, Gupta P, Ferguson SD, Huse JT, Fuller GN, Long JP, Winkowski DE, Freiberg BA, James CD, Platanias LC, Lesniak MS, Burks JK, Heimberger AB. Central nervous system immune interactome is function of cancer lineage, tumor microenvironment and STAT3 expression. JCI Insight 2022; 7:157612. [PMID: 35316217 PMCID: PMC9090258 DOI: 10.1172/jci.insight.157612] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/18/2022] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Immune cell profiling of primary and metastatic CNS tumors has been focused on the tumor, not the tumor microenvironment (TME), or has been analyzed via biopsies. METHODS En bloc resections of gliomas (n = 10) and lung metastases (n = 10) were analyzed via tissue segmentation and high-dimension Opal 7-color multiplex imaging. Single-cell RNA analyses were used to infer immune cell functionality. RESULTS Within gliomas, T cells were localized in the infiltrating edge and perivascular space of tumors, while residing mostly in the stroma of metastatic tumors. CD163+ macrophages were evident throughout the TME of metastatic tumors, whereas in gliomas, CD68+, CD11c+CD68+, and CD11c+CD68+CD163+ cell subtypes were commonly observed. In lung metastases, T cells interacted with CD163+ macrophages as dyads and clusters at the brain-tumor interface and within the tumor itself and as clusters within the necrotic core. In contrast, gliomas typically lacked dyad and cluster interactions, except for T cell CD68+ cell dyads within the tumor. Analysis of transcriptomic data in glioblastomas revealed that innate immune cells expressed both proinflammatory and immunosuppressive gene signatures. CONCLUSION Our results show that immunosuppressive macrophages are abundant within the TME and that the immune cell interactome between cancer lineages is distinct. Further, these data provide information for evaluating the role of different immune cell populations in brain tumor growth and therapeutic responses. FUNDING This study was supported by the NIH (NS120547), a Developmental research project award (P50CA221747), ReMission Alliance, institutional funding from Northwestern University and the Lurie Comprehensive Cancer Center, and gifts from the Mosky family and Perry McKay. Performed in the Flow Cytometry & Cellular Imaging Core Facility at MD Anderson Cancer Center, this study received support in part from the NIH (CA016672) and the National Cancer Institute (NCI) Research Specialist award 1 (R50 CA243707). Additional support was provided by CCSG Bioinformatics Shared Resource 5 (P30 CA046592), a gift from Agilent Technologies, a Research Scholar Grant from the American Cancer Society (RSG-16-005-01), a Precision Health Investigator Award from University of Michigan (U-M) Precision Health, the NCI (R37-CA214955), startup institutional research funds from U-M, and a Biomedical Informatics & Data Science Training Grant (T32GM141746).
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Affiliation(s)
- Hinda Najem
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, United States of America
| | - Martina Ott
- Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | - Cynthia Kassab
- Department of General Surgery, University of Texas Galveston, Galveston, United States of America
| | - Arvind Rao
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, United States of America
| | - Ganesh Rao
- Department of Neurosurgery, Baylor College of Medicine, Houston, United States of America
| | - Anantha Marisetty
- Department of Neurosurgery, Baylor College of Medicine, Houston, United States of America
| | - Adam M Sonabend
- Department of Neurological Surgery, Feinberg School of Medicine Northwestern University, Chicago, United States of America
| | - Craig Horbinski
- Department of Neurological Surgery, Feinberg School of Medicine Northwestern University, Chicago, United States of America
| | - Roel Verhaak
- The Jackson Laboratory, Farmington, United States of America
| | - Anand Shankar
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, United States of America
| | - Santhoshi N Krishnan
- Department of Electrical and Computer Engineering, Rice University, Houston, United States of America
| | | | - Víctor A Arrieta
- Department of Neurological Surgery, Feinberg School of Medicine Northwestern University, Chicago, United States of America
| | - Pravesh Gupta
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, United States of America
| | - Sherise D Ferguson
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, United States of America
| | - Jason T Huse
- Department of Neuropathology, The University of Texas MD Anderson Cancer Center, Houston, United States of America
| | - Gregory N Fuller
- Department of Neuropathology, The University of Texas MD Anderson Cancer Center, Houston, United States of America
| | - James P Long
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, United States of America
| | | | | | - C David James
- Department of Neurological Surgery, Feinberg School of Medicine Northwestern University, Chicago, United States of America
| | - Leonidas C Platanias
- Department of Neurological Surgery, Feinberg School of Medicine Northwestern University, Chicago, United States of America
| | - Maciej S Lesniak
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, United States of America
| | - Jared K Burks
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, United States of America
| | - Amy B Heimberger
- Department of Neurological Surgery, Feinberg School of Medicine Northwestern University, Chicago, United States of America
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16
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Identifying Potential New Gene Expression-Based Biomarkers in the Peripheral Blood Mononuclear Cells of Hepatitis B-Related Hepatocellular Carcinoma. Can J Gastroenterol Hepatol 2022; 2022:9541600. [PMID: 35265561 PMCID: PMC8901362 DOI: 10.1155/2022/9541600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/13/2021] [Accepted: 01/22/2022] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVE The analysis of the gene expression of peripheral blood mononuclear cells (PBMCs) is important to clarify the pathogenesis of hepatocellular carcinoma (HCC) and the detection of suitable biomarkers. The purpose of this investigation was to use RNA-sequencing to screen the appropriate differentially expressed genes (DEGs) in the PBMCs for the HCC. METHODS The comprehensive transcriptome of extracted RNA of PBMC (n = 20) from patients with chronic hepatitis B (CHB), liver cirrhosis, and early stage of HCC (5 samples per group) was carried out using RNA-sequencing. All raw RNA-sequencing data analyses were performed using conventional RNA-sequencing analysis tools. Next, gene ontology (GO) analyses were carried out to elucidate the biological processes of DEGs. Finally, relative transcript abundance of selected DEGs was verified using qRT-PCR on additional validation groups. RESULTS Specifically, 13, 1262, and 1450 DEGs were identified for CHB, liver cirrhosis, and HCC, when compared with the healthy controls. GO enrichment analysis indicated that HCC is closely related to the immune response. Seven DEGs (TYMP, TYROBP, CD14, TGFBI, LILRA2, GNLY, and GZMB) were common to HCC, cirrhosis, and CHB when compared to healthy controls. The data revealed that the expressions of these 7 DEGs were consistent with those from the RNA-sequencing results. Also, the expressions of 7 representative genes that had higher sensitivity were obtained by receiver operating characteristic analysis, which indicated their important diagnostic accuracy for HBV-HCC. CONCLUSION This study provides us with new horizons into the biological process and potential prospective clinical diagnosis and prognosis of HCC in the near future.
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The Proteome of Antibody-Mediated Rejection: From Glomerulitis to Transplant Glomerulopathy. Biomedicines 2022; 10:biomedicines10030569. [PMID: 35327371 PMCID: PMC8945687 DOI: 10.3390/biomedicines10030569] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 01/11/2023] Open
Abstract
Antibody-mediated rejection (ABMR) is the leading cause of allograft failure in kidney transplantation. Its histological hallmark is represented by lesions of glomerulitis i.e., inflammatory cells within glomeruli. Current therapies for ABMR fail to prevent chronic allograft damage i.e., transplant glomerulopathy, leading to allograft loss. We used laser microdissection of glomeruli from formalin-fixed allograft biopsies combined with mass spectrometry-based proteomics to describe the proteome modification of 11 active and 10 chronic active ABMR cases compared to 8 stable graft controls. Of 1335 detected proteins, 77 were deregulated in glomerulitis compared to stable grafts, particularly involved in cellular stress mediated by interferons type I and II, leukocyte activation and microcirculation remodeling. Three proteins extracted from this protein profile, TYMP, WARS1 and GBP1, showed a consistent overexpression by immunohistochemistry in glomerular endothelial cells that may represent relevant markers of endothelial stress during active ABMR. In transplant glomerulopathy, 137 proteins were deregulated, which favor a complement-mediated mechanism, wound healing processes through coagulation activation and ultimately a remodeling of the glomerular extracellular matrix, as observed by light microscopy. This study brings novel information on glomerular proteomics of ABMR in kidney transplantation, and highlights potential targets of diagnostic and therapeutic interest.
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Platelet-Derived Drug Targets and Biomarkers of Ischemic Stroke-The First Dynamic Human LC-MS Proteomic Study. J Clin Med 2022; 11:jcm11051198. [PMID: 35268287 PMCID: PMC8911047 DOI: 10.3390/jcm11051198] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/15/2022] [Accepted: 02/21/2022] [Indexed: 12/15/2022] Open
Abstract
(1) Objective: The aim of this dynamic LC-MS (liquid chromatography and mass spectrometry) human platelet proteomic study was to identify the potential proteins candidates for biomarkers of acute ischemic stroke (AIS), their changes during the acute phase of stroke and to define potential novel drug targets. (2) Methods: A total of 32 patients (18–80 years old) were investigated that presented symptoms of AIS lasting less than 24 h from the onset, confirmed by neurological examination and/or new cerebral ischemia visualized in the CT (computed-tomography) scans. The analysis of platelet proteome was performed using LC-MS at baseline, and then on the third and seventh day from the onset of symptoms. The control group was demographically matched without any clinical signs of acute brain injury. (3) Results: The differences between platelets, at 24 h after first symptoms of stroke subjects and the control group included: β-amyloid A4 and amyloid-like protein 2, coactosin-like protein, thymidine phosphorylase 4 (TYMP-4), interferon regulatory factor 7 (IRF7), vitamin K-dependent protein S, histone proteins (H2A type 1 and 1-A, H2A types 2B and J, H2Av, -z, and -x), and platelet basic protein. The dynamic changes in the platelet protein concentration involved thrombospondin-1, thrombospondin-2, filamin A, B, and C. (4) Conclusions: This is the first human dynamic LC-MS proteomic study that differentiates platelet proteome in the acute phase of ischemic stroke in time series and compares the results with healthy controls. Identified proteins may be considered as future markers of ischemic stroke or therapeutic drug targets. Thymidine phosphorylase 4 (TYMP-4) holds promise as an interesting drug target in the management or prevention of ischemic stroke.
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Turek-Jakubowska A, Dębski J, Jakubowski M, Szahidewicz-Krupska E, Gawryś J, Gawryś K, Janus A, Trocha M, Doroszko A. New Candidates for Biomarkers and Drug Targets of Ischemic Stroke-A First Dynamic LC-MS Human Serum Proteomic Study. J Clin Med 2022; 11:jcm11020339. [PMID: 35054033 PMCID: PMC8780942 DOI: 10.3390/jcm11020339] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/06/2022] [Accepted: 01/10/2022] [Indexed: 01/27/2023] Open
Abstract
(1) Background: The aim of this dynamic-LC/MS-human-serum-proteomic-study was to identify potential proteins-candidates for biomarkers of acute ischemic stroke, their changes during acute phase of stroke and to define potential novel drug-targets. (2) Methods: A total of 32 patients (29–80 years) with acute ischemic stroke were enrolled to the study. The control group constituted 29 demographically-matched volunteers. Subjects with stroke presented clinical symptoms lasting no longer than 24 h, confirmed by neurological-examination and/or new cerebral ischemia visualized in the CT scans (computed tomography). The analysis of plasma proteome was performed using LC-MS (liquid chromatography–mass spectrometry). (3) Results: Ten proteins with significantly different serum concentrations between groups volunteers were: complement-factor-B, apolipoprotein-A-I, fibronectin, alpha-2-HS-glycoprotein, alpha-1B-glycoprotein, heat-shock-cognate-71kDa protein/heat-shock-related-70kDa-protein-2, thymidine phosphorylase-2, cytoplasmic-tryptophan-tRNA-ligase, ficolin-2, beta-Ala-His-dipeptidase. (4) Conclusions: This is the first dynamic LC-MS study performed on a clinical model which differentiates serum proteome of patients in acute phase of ischemic stroke in time series and compares to control group. Listed proteins should be considered as risk factors, markers of ischemic stroke or potential therapeutic targets. Further clinical validation might define their exact role in differential diagnostics, monitoring the course of the ischemic stroke or specifying them as novel drug targets.
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Affiliation(s)
| | - Janusz Dębski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warszawa, Poland;
| | - Maciej Jakubowski
- Lower Silesian Centre for Lung Diseases, Grabiszyńska 105, 53-439 Wroclaw, Poland;
| | - Ewa Szahidewicz-Krupska
- Department of Internal Medicine, Hypertension and Clinical Oncology, Wroclaw Medical University, Borowska 213, 50-556 Wroclaw, Poland; (E.S.-K.); (J.G.); (A.J.)
| | - Jakub Gawryś
- Department of Internal Medicine, Hypertension and Clinical Oncology, Wroclaw Medical University, Borowska 213, 50-556 Wroclaw, Poland; (E.S.-K.); (J.G.); (A.J.)
| | - Karolina Gawryś
- Department of Neurology, 4th Military Hospital, Weigla 5, 50-556 Wroclaw, Poland; (A.T.-J.); (K.G.)
| | - Agnieszka Janus
- Department of Internal Medicine, Hypertension and Clinical Oncology, Wroclaw Medical University, Borowska 213, 50-556 Wroclaw, Poland; (E.S.-K.); (J.G.); (A.J.)
| | - Małgorzata Trocha
- Department of Pharmacology, Faculty of Medicine, Wroclaw Medical University, Mikulicz-Radecki 2, 50-349 Wroclaw, Poland;
| | - Adrian Doroszko
- Department of Internal Medicine, Hypertension and Clinical Oncology, Wroclaw Medical University, Borowska 213, 50-556 Wroclaw, Poland; (E.S.-K.); (J.G.); (A.J.)
- Correspondence: ; Tel.: +48-71-736-4000
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20
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Gu Y, Guo Y, Gao N, Fang Y, Xu C, Hu G, Guo M, Ma Y, Zhang Y, Zhou J, Luo Y, Zhang H, Wen Q, Qiao H. The proteomic characterization of the peritumor microenvironment in human hepatocellular carcinoma. Oncogene 2022; 41:2480-2491. [PMID: 35314790 PMCID: PMC9033583 DOI: 10.1038/s41388-022-02264-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 02/17/2022] [Accepted: 02/23/2022] [Indexed: 01/29/2023]
Abstract
The tumor microenvironment (TME) was usually studied in tumor tissue and in relation to only tumor progression, with little involved in occurrence, recurrence and metastasis of tumor. Thus, a new concept "peritumor microenvironment (PME)" was proposed in the proteomic characterization of peritumor liver tissues in human hepatocellular carcinoma (HCC). The PME for occurrence (PME-O) and progression (PME-P) were almost totally different at proteome composition and function. Proteins for occurrence and progression rarely overlapped and crossed. Immunity played a central role in PME-O, whereas inflammation, angiogenesis and metabolism were critical in PME-P. Proteome profiling identified three PME subtypes with different features of HCC. Thymidine phosphorylase (TYMP) was validated as an antiangiogenic target in an orthotopic HCC mouse model. Overall, the proteomic characterization of the PME revealed that the entire processes of HCC occurrence and progression differ substantially. These findings could enable advances in cancer biology, diagnostics and therapeutics.
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Affiliation(s)
- Yuhan Gu
- grid.207374.50000 0001 2189 3846Institute of Clinical Pharmacology, Zhengzhou University, Zhengzhou, China
| | - Yuanyuan Guo
- grid.207374.50000 0001 2189 3846Institute of Clinical Pharmacology, Zhengzhou University, Zhengzhou, China ,grid.412633.10000 0004 1799 0733Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Na Gao
- grid.207374.50000 0001 2189 3846Institute of Clinical Pharmacology, Zhengzhou University, Zhengzhou, China
| | - Yan Fang
- grid.207374.50000 0001 2189 3846Institute of Clinical Pharmacology, Zhengzhou University, Zhengzhou, China
| | - Chen Xu
- grid.207374.50000 0001 2189 3846Institute of Clinical Pharmacology, Zhengzhou University, Zhengzhou, China
| | - Guiming Hu
- grid.207374.50000 0001 2189 3846Institute of Clinical Pharmacology, Zhengzhou University, Zhengzhou, China
| | - Mengxue Guo
- grid.207374.50000 0001 2189 3846Institute of Clinical Pharmacology, Zhengzhou University, Zhengzhou, China
| | - Yaxing Ma
- grid.207374.50000 0001 2189 3846Institute of Clinical Pharmacology, Zhengzhou University, Zhengzhou, China
| | - Yunfei Zhang
- grid.414008.90000 0004 1799 4638Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, China
| | - Jun Zhou
- grid.414011.10000 0004 1808 090XAffiliated People’s Hospital of Zhengzhou University, Zhengzhou, China
| | - Yanlin Luo
- grid.414008.90000 0004 1799 4638Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, China
| | - Haifeng Zhang
- grid.207374.50000 0001 2189 3846Institute of Clinical Pharmacology, Zhengzhou University, Zhengzhou, China
| | - Qiang Wen
- grid.207374.50000 0001 2189 3846Institute of Clinical Pharmacology, Zhengzhou University, Zhengzhou, China
| | - Hailing Qiao
- grid.207374.50000 0001 2189 3846Institute of Clinical Pharmacology, Zhengzhou University, Zhengzhou, China
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21
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Matsumae G, Shimizu T, Tian Y, Takahashi D, Ebata T, Alhasan H, Yokota S, Kadoya K, Terkawi MA, Iwasaki N. Targeting thymidine phosphorylase as a potential therapy for bone loss associated with periprosthetic osteolysis. Bioeng Transl Med 2021; 6:e10232. [PMID: 34589604 PMCID: PMC8459589 DOI: 10.1002/btm2.10232] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 12/19/2022] Open
Abstract
Macrophages are generally thought to play a key role in the pathogenesis of aseptic loosening through initiating periprosthetic inflammation and pathological bone resorption. The aim of this study was to identify macrophage-derived factors that promote osteoclast differentiation and periprosthetic bone destruction. To achieve this, we examined the effects of 12 macrophage-derived factors that were identified by RNA-seq analysis of stimulated macrophages on osteoclast differentiation. Surprisingly, thymidine phosphorylase (TYMP) was found to trigger significant number of osteoclasts that exhibited resorbing activities on dentine slices. Functionally, TYMP knockdown reduced the number of osteoclasts in macrophages that had been stimulated with polyethylene debris. TYMP were detected in serum and synovial tissues of patients that had been diagnosed with aseptic loosening. Moreover, the administration of TYMP onto calvariae of mice induced pathological bone resorption that was accompanied by an excessive infiltration of inflammatory cells and osteoclasts. The RNA-seq for TYMP-induced-osteoclasts was then performed in an effort to understand action mode of TYMP. TYMP stimulation appeared to activate the tyrosine kinase FYN signaling associated with osteoclast formation. Oral administration of saracatinib, a FYN kinase inhibitor, significantly suppressed formation of bone osteolytic lesions in a polyethylene debris-induced osteolysis model. Our findings highlight a novel molecular target for therapeutic intervention in periprosthetic osteolysis.
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Affiliation(s)
- Gen Matsumae
- Department of Orthopedic Surgery, Faculty of Medicine and Graduate School of MedicineHokkaido UniversitySapporoJapan
| | - Tomohiro Shimizu
- Department of Orthopedic Surgery, Faculty of Medicine and Graduate School of MedicineHokkaido UniversitySapporoJapan
| | - Yuan Tian
- Department of Orthopedic Surgery, Faculty of Medicine and Graduate School of MedicineHokkaido UniversitySapporoJapan
| | - Daisuke Takahashi
- Department of Orthopedic Surgery, Faculty of Medicine and Graduate School of MedicineHokkaido UniversitySapporoJapan
| | - Taku Ebata
- Department of Orthopedic Surgery, Faculty of Medicine and Graduate School of MedicineHokkaido UniversitySapporoJapan
| | - Hend Alhasan
- Department of Orthopedic Surgery, Faculty of Medicine and Graduate School of MedicineHokkaido UniversitySapporoJapan
| | - Shunichi Yokota
- Department of Orthopedic Surgery, Faculty of Medicine and Graduate School of MedicineHokkaido UniversitySapporoJapan
| | - Ken Kadoya
- Department of Orthopedic Surgery, Faculty of Medicine and Graduate School of MedicineHokkaido UniversitySapporoJapan
| | - Mohamad Alaa Terkawi
- Department of Orthopedic Surgery, Faculty of Medicine and Graduate School of MedicineHokkaido UniversitySapporoJapan
- Global Institution for Collaborative Research and Education (GI‐CoRE), Frontier Research Center for Advanced Material and Life Science Bldg No 2. Hokkaido UniversitySapporoJapan
| | - Norimasa Iwasaki
- Department of Orthopedic Surgery, Faculty of Medicine and Graduate School of MedicineHokkaido UniversitySapporoJapan
- Global Institution for Collaborative Research and Education (GI‐CoRE), Frontier Research Center for Advanced Material and Life Science Bldg No 2. Hokkaido UniversitySapporoJapan
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22
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Azwar S, Seow HF, Abdullah M, Faisal Jabar M, Mohtarrudin N. Recent Updates on Mechanisms of Resistance to 5-Fluorouracil and Reversal Strategies in Colon Cancer Treatment. BIOLOGY 2021; 10:854. [PMID: 34571731 PMCID: PMC8466833 DOI: 10.3390/biology10090854] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/04/2020] [Accepted: 08/11/2020] [Indexed: 02/06/2023]
Abstract
5-Fluorouracil (5-FU) plus leucovorin (LV) remain as the mainstay standard adjuvant chemotherapy treatment for early stage colon cancer, and the preferred first-line option for metastatic colon cancer patients in combination with oxaliplatin in FOLFOX, or irinotecan in FOLFIRI regimens. Despite treatment success to a certain extent, the incidence of chemotherapy failure attributed to chemotherapy resistance is still reported in many patients. This resistance, which can be defined by tumor tolerance against chemotherapy, either intrinsic or acquired, is primarily driven by the dysregulation of various components in distinct pathways. In recent years, it has been established that the incidence of 5-FU resistance, akin to multidrug resistance, can be attributed to the alterations in drug transport, evasion of apoptosis, changes in the cell cycle and DNA-damage repair machinery, regulation of autophagy, epithelial-to-mesenchymal transition, cancer stem cell involvement, tumor microenvironment interactions, miRNA dysregulations, epigenetic alterations, as well as redox imbalances. Certain resistance mechanisms that are 5-FU-specific have also been ascertained to include the upregulation of thymidylate synthase, dihydropyrimidine dehydrogenase, methylenetetrahydrofolate reductase, and the downregulation of thymidine phosphorylase. Indeed, the successful modulation of these mechanisms have been the game plan of numerous studies that had employed small molecule inhibitors, plant-based small molecules, and non-coding RNA regulators to effectively reverse 5-FU resistance in colon cancer cells. It is hoped that these studies would provide fundamental knowledge to further our understanding prior developing novel drugs in the near future that would synergistically work with 5-FU to potentiate its antitumor effects and improve the patient's overall survival.
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Affiliation(s)
- Shamin Azwar
- Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia; (S.A.); (H.F.S.); (M.A.)
| | - Heng Fong Seow
- Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia; (S.A.); (H.F.S.); (M.A.)
| | - Maha Abdullah
- Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia; (S.A.); (H.F.S.); (M.A.)
| | - Mohd Faisal Jabar
- Department of Surgery, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia;
| | - Norhafizah Mohtarrudin
- Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia; (S.A.); (H.F.S.); (M.A.)
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23
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Benfatto S, Serçin Ö, Dejure FR, Abdollahi A, Zenke FT, Mardin BR. Uncovering cancer vulnerabilities by machine learning prediction of synthetic lethality. Mol Cancer 2021; 20:111. [PMID: 34454516 PMCID: PMC8401190 DOI: 10.1186/s12943-021-01405-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 08/10/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Synthetic lethality describes a genetic interaction between two perturbations, leading to cell death, whereas neither event alone has a significant effect on cell viability. This concept can be exploited to specifically target tumor cells. CRISPR viability screens have been widely employed to identify cancer vulnerabilities. However, an approach to systematically infer genetic interactions from viability screens is missing. METHODS Here we describe PAn-canceR Inferred Synthetic lethalities (PARIS), a machine learning approach to identify cancer vulnerabilities. PARIS predicts synthetic lethal (SL) interactions by combining CRISPR viability screens with genomics and transcriptomics data across hundreds of cancer cell lines profiled within the Cancer Dependency Map. RESULTS Using PARIS, we predicted 15 high confidence SL interactions within 549 DNA damage repair (DDR) genes. We show experimental validation of an SL interaction between the tumor suppressor CDKN2A, thymidine phosphorylase (TYMP) and the thymidylate synthase (TYMS), which may allow stratifying patients for treatment with TYMS inhibitors. Using genome-wide mapping of SL interactions for DDR genes, we unraveled a dependency between the aldehyde dehydrogenase ALDH2 and the BRCA-interacting protein BRIP1. Our results suggest BRIP1 as a potential therapeutic target in ~ 30% of all tumors, which express low levels of ALDH2. CONCLUSIONS PARIS is an unbiased, scalable and easy to adapt platform to identify SL interactions that should aid in improving cancer therapy with increased availability of cancer genomics data.
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Affiliation(s)
- Salvatore Benfatto
- BioMed X Institute (GmbH), Im Neuenheimer Feld 583, 69120, Heidelberg, Germany
| | - Özdemirhan Serçin
- BioMed X Institute (GmbH), Im Neuenheimer Feld 583, 69120, Heidelberg, Germany
| | - Francesca R Dejure
- BioMed X Institute (GmbH), Im Neuenheimer Feld 583, 69120, Heidelberg, Germany
| | - Amir Abdollahi
- Division of Molecular and Translational Radiation Oncology, National Centre for Tumour Diseases (NCT), Heidelberg University Hospital, 69120, Heidelberg, Germany
| | - Frank T Zenke
- Translational Innovation Platform Oncology & Immuno-Oncology, Merck KGaA, Frankfurter Str. 250, 64293, Darmstadt, Germany
| | - Balca R Mardin
- BioMed X Institute (GmbH), Im Neuenheimer Feld 583, 69120, Heidelberg, Germany.
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24
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Kaspar F, Wolff DS, Neubauer P, Kurreck A, Arcus VL. pH-Independent Heat Capacity Changes during Phosphorolysis Catalyzed by the Pyrimidine Nucleoside Phosphorylase from Geobacillus thermoglucosidasius. Biochemistry 2021; 60:1573-1577. [PMID: 33955225 DOI: 10.1021/acs.biochem.1c00156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Enzyme-catalyzed reactions sometimes display curvature in their Eyring plots in the absence of denaturation, indicative of a change in activation heat capacity. However, the effects of pH and (de)protonation on this phenomenon have remained unexplored. Herein, we report a kinetic characterization of the thermophilic pyrimidine nucleoside phosphorylase from Geobacillus thermoglucosidasius across a two-dimensional working space covering 35 °C and 3 pH units with two substrates displaying different pKa values. Our analysis revealed the presence of a measurable activation heat capacity change ΔCp⧧ in this reaction system, which showed no significant dependence on medium pH or substrate charge. Our results further describe the remarkable effects of a single halide substitution that has a minor influence on ΔCp⧧ but conveys a significant kinetic effect by decreasing the activation enthalpy, causing a >10-fold rate increase. Collectively, our results present an important piece in the understanding of enzymatic systems across multidimensional working spaces where the choice of reaction conditions can affect the rate, affinity, and thermodynamic phenomena independently of one another.
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Affiliation(s)
- Felix Kaspar
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany.,BioNukleo GmbH, Ackerstraße 76, D-13355 Berlin, Germany
| | - Darian S Wolff
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Anke Kurreck
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Straße des 17. Juni 135, D-10623 Berlin, Germany.,BioNukleo GmbH, Ackerstraße 76, D-13355 Berlin, Germany
| | - Vickery L Arcus
- Te Aka Ma̅tuatua-School of Science, Te Whare Wa̅nanga o Waikato-University of Waikato, Hamilton 3240, New Zealand
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25
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Li W, Yue H. Thymidine Phosphorylase Is Increased in COVID-19 Patients in an Acuity-Dependent Manner. Front Med (Lausanne) 2021; 8:653773. [PMID: 33829029 PMCID: PMC8019714 DOI: 10.3389/fmed.2021.653773] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/01/2021] [Indexed: 12/23/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-COV-2), is a human respiratory disease. Hitherto, there is no effective treatment has been established. Patients with cardiovascular or diabetes comorbidities are a high-risk cohort. COVID-19 is accompanied by excessive systemic thrombotic events, but the mechanism is not yet known. Recent studies have indicated that thymidine phosphorylase (TYMP) plays an important role in platelet activation, thrombosis, and TYMP expression is increased in diabetic patients. By using data provided by the MGH (Massachusetts General Hospital) Emergency Department COVID-19 Cohort with Olink Proteomics, here we show that plasma TYMP level is correlated with the COVID-19 associated thrombotic event, inflammation, and organ damage, as evidenced by the positive correlations with plasma D-dimer, CRP (C reactive protein), and LDH (lactate dehydrogenase), as well as Interferons (IFN). Plasma TYMP is also positively correlated with COVID-19 patients who had respiratory symptoms. TYMP thus could be an acuity marker for COVID-19 diagnosis. Targeting TYMP with tipiracil, a selective TYMP inhibitor, which has been approved by the Food and Drug Administration for clinical use, could be a novel effective medicine for COVID-19.
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Affiliation(s)
- Wei Li
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine of Marshall University, Huntington, WV, United States
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26
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Belcher A, Zulfiker AHM, Li OQ, Yue H, Gupta AS, Li W. Targeting Thymidine Phosphorylase With Tipiracil Hydrochloride Attenuates Thrombosis Without Increasing Risk of Bleeding in Mice. Arterioscler Thromb Vasc Biol 2021; 41:668-682. [PMID: 33297751 PMCID: PMC8105268 DOI: 10.1161/atvbaha.120.315109] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Current antiplatelet medications increase the risk of bleeding, which leads to a clear clinical need in developing novel mechanism-based antiplatelet drugs. TYMP (Thymidine phosphorylase), a cytoplasm protein that is highly expressed in platelets, facilitates multiple agonist-induced platelet activation, and enhances thrombosis. Tipiracil hydrochloride (TPI), a selective TYMP inhibitor, has been approved by the Food and Drug Administration for clinical use. We tested the hypothesis that TPI is a safe antithrombotic medication. Approach and Results: By coexpression of TYMP and Lyn, GST (glutathione S-transferase) tagged Lyn-SH3 domain or Lyn-SH2 domain, we showed the direct evidence that TYMP binds to Lyn through both SH3 and SH2 domains, and TPI diminished the binding. TYMP deficiency significantly inhibits thrombosis in vivo in both sexes. Pretreatment of platelets with TPI rapidly inhibited collagen- and ADP-induced platelet aggregation. Under either normal or hyperlipidemic conditions, treating wild-type mice with TPI via intraperitoneal injection, intravenous injection, or gavage feeding dramatically inhibited thrombosis without inducing significant bleeding. Even at high doses, TPI has a lower bleeding side effect compared with aspirin and clopidogrel. Intravenous delivery of TPI alone or combined with tissue plasminogen activator dramatically inhibited thrombosis. Dual administration of a very low dose of aspirin and TPI, which had no antithrombotic effects when used alone, significantly inhibited thrombosis without disturbing hemostasis. CONCLUSIONS This study demonstrated that inhibition of TYMP, a cytoplasmic protein, attenuated multiple signaling pathways that mediate platelet activation, aggregation, and thrombosis. TPI can be used as a novel antithrombotic medication without the increase in risk of bleeding.
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Affiliation(s)
- Adam Belcher
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine of Marshall University, Huntington, WV, 25755, USA
| | - Abu Hasanat Md Zulfiker
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine of Marshall University, Huntington, WV, 25755, USA
| | - Oliver Qiyue Li
- Marshall Institute for Interdisciplinary Research; Huntington, WV, 25701, USA
| | - Hong Yue
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine of Marshall University, Huntington, WV, 25755, USA
| | - Anirban Sen Gupta
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland OH 44106, USA
| | - Wei Li
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine of Marshall University, Huntington, WV, 25755, USA
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27
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Joshi H, Vastrad B, Joshi N, Vastrad C, Tengli A, Kotturshetti I. Identification of Key Pathways and Genes in Obesity Using Bioinformatics Analysis and Molecular Docking Studies. Front Endocrinol (Lausanne) 2021; 12:628907. [PMID: 34248836 PMCID: PMC8264660 DOI: 10.3389/fendo.2021.628907] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 05/19/2021] [Indexed: 01/01/2023] Open
Abstract
Obesity is an excess accumulation of body fat. Its progression rate has remained high in recent years. Therefore, the aim of this study was to diagnose important differentially expressed genes (DEGs) associated in its development, which may be used as novel biomarkers or potential therapeutic targets for obesity. The gene expression profile of E-MTAB-6728 was downloaded from the database. After screening DEGs in each ArrayExpress dataset, we further used the robust rank aggregation method to diagnose 876 significant DEGs including 438 up regulated and 438 down regulated genes. Functional enrichment analysis was performed. These DEGs were shown to be significantly enriched in different obesity related pathways and GO functions. Then protein-protein interaction network, target genes - miRNA regulatory network and target genes - TF regulatory network were constructed and analyzed. The module analysis was performed based on the whole PPI network. We finally filtered out STAT3, CORO1C, SERPINH1, MVP, ITGB5, PCM1, SIRT1, EEF1G, PTEN and RPS2 hub genes. Hub genes were validated by ICH analysis, receiver operating curve (ROC) analysis and RT-PCR. Finally a molecular docking study was performed to find small drug molecules. The robust DEGs linked with the development of obesity were screened through the expression profile, and integrated bioinformatics analysis was conducted. Our study provides reliable molecular biomarkers for screening and diagnosis, prognosis as well as novel therapeutic targets for obesity.
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Affiliation(s)
- Harish Joshi
- Department of Endocrinology, Endocrine and Diabetes Care Center, Hubbali, India
| | - Basavaraj Vastrad
- Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, India
| | - Nidhi Joshi
- Department of Medicine, Dr. D. Y. Patil Medical College, Kolhapur, India
| | - Chanabasayya Vastrad
- Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad, India
- *Correspondence: Chanabasayya Vastrad,
| | - Anandkumar Tengli
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, Mysuru and JSS Academy of Higher Education & Research, Mysuru, India
| | - Iranna Kotturshetti
- Department of Ayurveda, Rajiv Gandhi Education Society`s Ayurvedic Medical College, Ron, India
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Song H, Liu D, Dong S, Zeng L, Wu Z, Zhao P, Zhang L, Chen ZS, Zou C. Epitranscriptomics and epiproteomics in cancer drug resistance: therapeutic implications. Signal Transduct Target Ther 2020; 5:193. [PMID: 32900991 PMCID: PMC7479143 DOI: 10.1038/s41392-020-00300-w] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/18/2020] [Accepted: 07/28/2020] [Indexed: 12/24/2022] Open
Abstract
Drug resistance is a major hurdle in cancer treatment and a key cause of poor prognosis. Epitranscriptomics and epiproteomics are crucial in cell proliferation, migration, invasion, and epithelial–mesenchymal transition. In recent years, epitranscriptomic and epiproteomic modification has been investigated on their roles in overcoming drug resistance. In this review article, we summarized the recent progress in overcoming cancer drug resistance in three novel aspects: (i) mRNA modification, which includes alternative splicing, A-to-I modification and mRNA methylation; (ii) noncoding RNAs modification, which involves miRNAs, lncRNAs, and circRNAs; and (iii) posttranslational modification on molecules encompasses drug inactivation/efflux, drug target modifications, DNA damage repair, cell death resistance, EMT, and metastasis. In addition, we discussed the therapeutic implications of targeting some classical chemotherapeutic drugs such as cisplatin, 5-fluorouridine, and gefitinib via these modifications. Taken together, this review highlights the importance of epitranscriptomic and epiproteomic modification in cancer drug resistance and provides new insights on potential therapeutic targets to reverse cancer drug resistance.
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Affiliation(s)
- Huibin Song
- Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518001, Guangdong, China
| | - Dongcheng Liu
- Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518001, Guangdong, China
| | - Shaowei Dong
- Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518001, Guangdong, China
| | - Leli Zeng
- College of Pharmacy and Health Sciences, St. John's University, Queens, 11439 New York, USA.,Tomas Lindahl Nobel Laureate Laboratory, Research Centre, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, Guangdong, China
| | - Zhuoxun Wu
- College of Pharmacy and Health Sciences, St. John's University, Queens, 11439 New York, USA
| | - Pan Zhao
- Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518001, Guangdong, China
| | - Litu Zhang
- Department of Research, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Zhe-Sheng Chen
- College of Pharmacy and Health Sciences, St. John's University, Queens, 11439 New York, USA.
| | - Chang Zou
- Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518001, Guangdong, China. .,Shenzhen Public Service Platform on Tumor Precision Medicine and Molecular Diagnosis, Shenzhen, 518001, Guangdong, China.
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Pagano E, Frank B, Jaggers J, Twite M, Urban TT, Klawitter J, Davidson J. Alterations in Metabolites Associated with Hypoxemia in Neonates and Infants with Congenital Heart Disease. CONGENIT HEART DIS 2020; 15:251-265. [PMID: 34413893 PMCID: PMC8372212 DOI: 10.32604/chd.2020.012219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Objectives: (1) To measure the global shift in the metabolome in hypoxemic versus non-hypoxemic infants with congenital heart disease; (2) To identify metabolites and metabolic pathways that are altered in hypoxemia. Study Design: Analysis of serum samples obtained prior to cardiopulmonary bypass from 82 infants ≤120 days old with congenital heart disease requiring surgery at Children’s Hospital Colorado. Infants were divided into groups based on pre-operative oxygen saturations: non-hypoxemic (>92%), mild hypoxemia (85–92%), and severe hypoxemia (<85%). Tandem mass spectrometry was used to analyze 165 targeted metabolites. Partial least squares discriminant analysis and t-tests were used to determine differences among metabolic profiles and individual metabolites respectively. Results: The broad metabolic fingerprint of neonates or older infants did not vary by degree of hypoxemia. There were 12 individual metabolites that differed between hypoxemic and non-hypoxemic neonates, including lower methylmalonic acid (p = 2.44 × 10−4), glutamate (p = 0.001), and hypoxanthine (p = 0.003), and higher thymine (p = 8.67 × 10−4) and myo-inositol (p = 0.014) seen in hypoxemic neonates. Individual metabolites did not vary significantly between older infants with or without hypoxemia. Conclusions: We did not find evidence supporting global metabolic changes associated with cyanotic congenital heart disease in neonates or older infants. However, specific metabolites did discriminate between hypoxemic and non-hypoxemic neonates. These include methylmalonic acid, as well as several metabolites known to change in hypoxia-reoxygenation states (hypoxanthine) and chronic hypoxemic states (glutamate, thymine, myo-inositol) and may represent specific metabolic changes triggered by hypoxemia among neonates with cyanotic congenital heart disease.
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Affiliation(s)
- Evan Pagano
- University of Colorado, Department of Pediatrics, Aurora, CO 80045, USA
| | - Benjamin Frank
- University of Colorado, Department of Pediatrics, Aurora, CO 80045, USA
| | - James Jaggers
- University of Colorado, Department of Surgery, Aurora, CO 80045, USA
| | - Mark Twite
- University of Colorado, Department of Anesthesiology, Aurora, CO 80045, USA
| | - Tracy T Urban
- Children's Hospital Colorado Research Institute, Aurora, CO 80045, USA
| | - Jelena Klawitter
- University of Colorado, Department of Surgery, Aurora, CO 80045, USA
| | - Jesse Davidson
- University of Colorado, Department of Pediatrics, Aurora, CO 80045, USA
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Li Y, Lin P, Wang S, Li S, Wang R, Yang L, Wang H. Quantitative analysis of differentially expressed proteins in psoriasis vulgaris using tandem mass tags and parallel reaction monitoring. Clin Proteomics 2020; 17:30. [PMID: 32817748 PMCID: PMC7425065 DOI: 10.1186/s12014-020-09293-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 08/06/2020] [Indexed: 12/29/2022] Open
Abstract
Background Psoriasis vulgaris (PV) is a chronic autoimmune inflammatory disease with epidermal hyperkeratosis and parakeratosis. Methods The study was to elucidate the pathogenesis of PV by quantitative proteomic analysis of skin lesion biopsies of PV and healthy tissues with tandem mass tags (TMTs) coupled with liquid chromatography–mass spectrometry (LC–MS)/MS. Results A total of 4562 differentially expressed proteins (DEPs) between PV lesional tissues (n = 11) and healthy tissues (n = 11) were identified, of which 299 were upregulated and 206 were downregulated using |fold change| > 1.3 as the cutoff threshold. The Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that the DEPs were mainly enriched in the activation of immune cells (drug metabolism pathway, NOD-like pathway, and IL-17 pathway), cell proliferation (ribosomal pathway, DNA replication pathway, and base replication pathway), metabolism-related pathways (fatty acid biosynthesis and metabolism, PPAR pathway, glycerophospholipid metabolism, and cortisol synthesis and breakdown), and glandular secretion (saliva secretion, gastric acid secretion, and pancreatic fluid secretion). Thirteen DEPs that were relatively highly expressed in the drug metabolism pathway were validated with parallel reaction monitoring (PRM), of which MPO, TYMP, IMPDH2, GSTM4, and ALDH3A1 were highly expressed in PV, whereas CES1, MAOB, MGST1, and GSTT1 were less expressed in PV. Conclusions These findings confirmed that these proteins participate in the drug metabolism-other enzyme pathways and play crucial roles in the activation and proliferation of immune cells in the pathogenesis of PV.
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Affiliation(s)
- Yu Li
- Tianjin University of Traditional Chinese Medicine, Tianjin, People's Republic of China
| | - Peng Lin
- Shenzhen Luohu District Hospital of Traditional Chinese Medicine, Shenzhen, Guangdong People's Republic of China
| | - Siyao Wang
- Tianjin University of Traditional Chinese Medicine, Tianjin, People's Republic of China
| | - Shuang Li
- Tianjin University of Traditional Chinese Medicine, Tianjin, People's Republic of China
| | - Rui Wang
- Tianjin University of Traditional Chinese Medicine, Tianjin, People's Republic of China
| | - Lin Yang
- Department of Dermatology, Tianjin Academy of Traditional Chinese Medicine Affiliated Hospital, Tianjin, People's Republic of China
| | - Hongmei Wang
- Department of Dermatology, Tianjin Academy of Traditional Chinese Medicine Affiliated Hospital, Tianjin, People's Republic of China
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31
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Liu M, Pan Q, Xiao R, Yu Y, Lu W, Wang L. A cluster of metabolism-related genes predict prognosis and progression of clear cell renal cell carcinoma. Sci Rep 2020; 10:12949. [PMID: 32737333 PMCID: PMC7395775 DOI: 10.1038/s41598-020-67760-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 06/03/2020] [Indexed: 02/07/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) has long been considered as a metabolic disease characterized by metabolic reprogramming due to the abnormal accumulation of lipid droplets in the cytoplasm. However, the prognostic value of metabolism-related genes in ccRCC remains unclear. In our study, we investigated the associations between metabolism-related gene profile and prognosis of ccRCC patients in the Cancer Genome Atlas (TCGA) database. Importantly, we first constructed a metabolism-related prognostic model based on ten genes (ALDH6A1, FBP1, HAO2, TYMP, PSAT1, IL4I1, P4HA3, HK3, CPT1B, and CYP26A1) using Lasso cox regression analysis. The Kaplan–Meier analysis revealed that our model efficiently predicts prognosis in TCGA_KIRC Cohort and the clinical proteomic tumor analysis consortium (CPTAC_ccRCC) Cohort. Using time-dependent ROC analysis, we showed the model has optimal performance in predicting long-term survival. Besides, the multivariate Cox regression analysis demonstrated our model is an independent prognostic factor. The risk score calculated for each patient was significantly associated with various clinicopathological parameters. Notably, the gene set enrichment analysis indicated that fatty acid metabolism was enriched considerably in low-risk patients. In contrast, the high-risk patients were more associated with non-metabolic pathways. In summary, our study provides novel insight into metabolism-related genes’ roles in ccRCC.
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Affiliation(s)
- Mei Liu
- Department of Anesthesiology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Qiufeng Pan
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Ruihai Xiao
- Department of Urology, Affiliated Hospital of Jiangxi Academy of Medical Sciences of Nanchang University, Nanchang, China
| | - Yi Yu
- Department of Urology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Wenbao Lu
- Department of Urology, Jiujiang University Affiliated Hospital, Jiujiang, China
| | - Longwang Wang
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, China.
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Watanabe S, Nishijima KI, Okamoto S, Magota K, Hirata K, Toyonaga T, Shiga T, Kuge Y, Tamaki N. Biodistribution and internal radiation dosimetry of a novel probe for thymidine phosphorylase imaging, [ 123I]IIMU, in healthy volunteers. Ann Nucl Med 2020; 34:595-599. [PMID: 32361818 DOI: 10.1007/s12149-020-01469-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/21/2020] [Indexed: 11/25/2022]
Abstract
OBJECTIVE We evaluated the radiation dosage, biodistribution, human safety, and tolerability of the injection of a single dose of [123I] 5-iodo-6-[(2-iminoimidazolidinyl)methyl]uracil (IIMU), a new radiotracer targeting thymidine phosphorylase (TP), in healthy volunteers. METHODS Potential participants were tested at our hospital to confirm their eligibility. Two healthy male adults passed the screening tests. They were injected with 56 and 111 MBq of [123I]IIMU, respectively. Safety assessments were performed before and at 1, 3, 6, 9, 24, 48 h, and 1-week post-injection. Whole-body emission scans were conducted at 1, 3, 6, 24, and 48 h post-injection. Regions of interest were manually drawn to enclose the entire body at each time point, identifying high-uptake organs to obtain the time-activity curves. Urine and blood samples were collected at 1, 2, 3, 4, 5, 6, 9, 24, and 48 h post-injection. The radiation dose for each organ and the effective doses were estimated using OLINDA/EXM 1.1 software. RESULTS No adverse events were observed as of the follow-up visit > 1-week post-injection. In both subjects, the highest uptake of [123I]IIMU occurred in the liver, with peak injected activity (%IA) values of 17.7% and 15.1%, respectively. The second highest uptake was in the thyroid (0.35% and 0.66% IA). The %IA decreased gradually toward the end of the study (48 h) in all organs except the liver and thyroid. By the end of the study, 52.5% and 51.5% of the injected activity of [123I]IIMU had been excreted via the subjects' renal systems. The estimated mean effective doses of [123I]IIMU were 9.19 μSv/MBq and 10.1 μSv/MBq, respectively. CONCLUSION In this preliminary study, [123I]IIMU was safely administered to healthy adults, and its potential clinical use in TP imaging was revealed.
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Affiliation(s)
- Shiro Watanabe
- Department of Nuclear Medicine, Hokkaido University Graduate School of Medicine, Kita-15, Nishi-7, Kita-ku, Sapporo, 060-8638, Japan. .,Department of Diagnostic Radiology, Hokkaido Cancer Center, 3-54, Kikusui4-2, Shiroishi-ku, Sapporo, 003-0804, Japan.
| | - Ken-Ichi Nishijima
- Central Institute of Isotope Science, Hokkaido University, Kita-15, Nishi-7, Kita-ku, Sapporo, 060-8638, Japan.,Advanced Clinical Research Center, Fukushima Global Medical Science Center, Fukushima Medical University, 1 Hikariga-oka, Fukushima, 960-1295, Japan
| | - Shozo Okamoto
- Department of Nuclear Medicine, Hokkaido University Graduate School of Medicine, Kita-15, Nishi-7, Kita-ku, Sapporo, 060-8638, Japan.,Department of Radiology, Obihiro Kosei Hospital, West 14, South 10-1, Obihiro, 080-0024, Japan
| | - Keiichi Magota
- Division of Medical Imaging and Technology, Hokkaido University Hospital, Kita-14, Nishi-5, Kita-ku, Sapporo, 060-8648, Japan
| | - Kenji Hirata
- Department of Nuclear Medicine, Hokkaido University Graduate School of Medicine, Kita-15, Nishi-7, Kita-ku, Sapporo, 060-8638, Japan.,Department of Diagnostic Imaging, Hokkaido University Graduate School of Medicine, Kita-15, Nishi-7, Kita-ku, Sapporo, 060-8638, Japan
| | - Takuya Toyonaga
- Department of Nuclear Medicine, Hokkaido University Graduate School of Medicine, Kita-15, Nishi-7, Kita-ku, Sapporo, 060-8638, Japan.,PET Center, Department of Radiology and Biomedical Imaging, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Tohru Shiga
- Department of Nuclear Medicine, Hokkaido University Graduate School of Medicine, Kita-15, Nishi-7, Kita-ku, Sapporo, 060-8638, Japan
| | - Yuji Kuge
- Central Institute of Isotope Science, Hokkaido University, Kita-15, Nishi-7, Kita-ku, Sapporo, 060-8638, Japan
| | - Nagara Tamaki
- Department of Nuclear Medicine, Hokkaido University Graduate School of Medicine, Kita-15, Nishi-7, Kita-ku, Sapporo, 060-8638, Japan.,Department of Radiology, Kyoto Prefectural University of Medicine, Kajii-cho, Kawaramachi-Hirokoji, Kamigyo-ku, Kyoto, 602-8566, Japan
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Tozer T, Heale K, Manto Chagas C, de Barros ALB, Alisaraie L. Interdomain twists of human thymidine phosphorylase and its active-inactive conformations: Binding of 5-FU and its analogues to human thymidine phosphorylase versus dihydropyrimidine dehydrogenase. Chem Biol Drug Des 2019; 94:1956-1972. [PMID: 31356728 DOI: 10.1111/cbdd.13596] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 07/02/2019] [Accepted: 07/15/2019] [Indexed: 12/19/2022]
Abstract
5-fluorouracil (5-FU) is an anticancer drug, which inhibits human thymidine phosphorylase (hTP) and plays a key role in maintaining the process of DNA replication and repair. It is involved in regulating pyrimidine nucleotide production, by which it inhibits the mechanism of cell proliferation and cancerous tumor growth. However, up to 80% of the administered drug is metabolized by dihydropyrimidine dehydrogenase (DPD). This work compares binding of 5-FU and its analogues to hTP and DPD, and suggests strategies to reduce drug binding to DPD to decrease the required dose of 5-FU. An important feature between the proteins studied here was the difference of charge distribution in their binding sites, which can be exploited for designing drugs to selectively bind to the hTP. The 5-FU presence was thought to be required for a closed conformation. Comparison of the calculation results pertaining to unliganded and liganded protein showed that hTP could still undergo open-closed conformations in the absence of the ligand; however, the presence of a positively charged ligand better stabilizes the closed conformation and rigidifies the core region of the protein more than unliganded or neutral liganded system. The study has also shown that one of the three hinge segments linking the two major α and α/β domains of the hTP is an important contributing factor to the enzyme's open-close conformational twist during its inactivation-activation process. In addition, the angle between the α/β-domain and the α-domain has shown to undergo wide rotations over the course of MD simulation in the absence of a phosphate, suggesting that it contributes to the stabilization of the closed conformation of the hTP.
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Affiliation(s)
- Tiffany Tozer
- School of Pharmacy, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Kali Heale
- School of Pharmacy, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Caroline Manto Chagas
- School of Pharmacy, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Andre Luis Branco de Barros
- Department of Clinical and Toxicological Analysis, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Laleh Alisaraie
- School of Pharmacy, Memorial University of Newfoundland, St. John's, Newfoundland, Canada.,Department of Chemistry, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
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Pacitti D, Levene M, Garone C, Nirmalananthan N, Bax BE. Mitochondrial Neurogastrointestinal Encephalomyopathy: Into the Fourth Decade, What We Have Learned So Far. Front Genet 2018; 9:669. [PMID: 30627136 PMCID: PMC6309918 DOI: 10.3389/fgene.2018.00669] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 12/04/2018] [Indexed: 02/05/2023] Open
Abstract
Mitochondrial neurogastrointestinal encephalomyopathy (MNGIE) is an ultra-rare metabolic autosomal recessive disease, caused by mutations in the nuclear gene TYMP which encodes the enzyme thymidine phosphorylase. The resulting enzyme deficiency leads to a systemic accumulation of the deoxyribonucleosides thymidine and deoxyuridine, and ultimately mitochondrial failure due to a progressive acquisition of secondary mitochondrial DNA (mtDNA) mutations and mtDNA depletion. Clinically, MNGIE is characterized by gastrointestinal and neurological manifestations, including cachexia, gastrointestinal dysmotility, peripheral neuropathy, leukoencephalopathy, ophthalmoplegia and ptosis. The disease is progressively degenerative and leads to death at an average age of 37.6 years. As with the vast majority of rare diseases, patients with MNGIE face a number of unmet needs related to diagnostic delays, a lack of approved therapies, and non-specific clinical management. We provide here a comprehensive collation of the available knowledge of MNGIE since the disease was first described 42 years ago. This review includes symptomatology, diagnostic procedures and hurdles, in vitro and in vivo disease models that have enhanced our understanding of the disease pathology, and finally experimental therapeutic approaches under development. The ultimate aim of this review is to increase clinical awareness of MNGIE, thereby reducing diagnostic delay and improving patient access to putative treatments under investigation.
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Affiliation(s)
- Dario Pacitti
- Molecular and Clinical Sciences Research Institute, St George's, University of London, London, United Kingdom
| | - Michelle Levene
- Molecular and Clinical Sciences Research Institute, St George's, University of London, London, United Kingdom
| | - Caterina Garone
- MRC Mitochondrial Biology Unit, Cambridge Biomedical, Cambridge, United Kingdom
| | | | - Bridget E. Bax
- Molecular and Clinical Sciences Research Institute, St George's, University of London, London, United Kingdom
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