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Kulkarni A, Zhou J, Biyani N, Kathad U, Banerjee PP, Srivastava S, Prucsi Z, Solarczyk K, Bhatia K, Ewesuedo RB, Sharma P. LP-184, a Novel Acylfulvene Molecule, Exhibits Anticancer Activity against Diverse Solid Tumors with Homologous Recombination Deficiency. CANCER RESEARCH COMMUNICATIONS 2024; 4:1199-1210. [PMID: 38630886 PMCID: PMC11072798 DOI: 10.1158/2767-9764.crc-23-0554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/11/2024] [Accepted: 04/15/2024] [Indexed: 04/19/2024]
Abstract
Homologous recombination (HR)-related gene alterations are present in a significant subset of prostate, breast, ovarian, pancreatic, lung, and colon cancers rendering these tumors as potential responders to specific DNA damaging agents. A small molecule acylfulvene prodrug, LP-184, metabolizes to an active compound by the oxidoreductase activity of enzyme prostaglandin reductase 1 (PTGR1), which is frequently elevated in multiple solid tumor types. Prior work demonstrated that cancer cell lines deficient in a spectrum of DNA damage repair (DDR) pathway genes show increased susceptibility to LP-184. Here, we investigated the potential of LP-184 in targeting multiple tumors with impaired HR function and its mechanism of action as a DNA damaging agent. LP-184 induced elevated DNA double-strand breaks in HR deficient (HRD) cancer cells. Depletion of key HR components BRCA2 or ataxia telangiectasia mutated (ATM) in cancer cells conferred up to 12-fold increased sensitivity to the LP-184. LP-184 showed nanomolar potency in a diverse range of HRD cancer models, including prostate cancer organoids, leiomyosarcoma cell lines, and patient-derived tumor graft models of lung, pancreatic, and prostate cancers. LP-184 demonstrated complete, durable tumor regression in 10 patient-derived xenograft (PDX) models of HRD triple-negative breast cancer (TNBC) including those resistant to PARP inhibitors (PARPi). LP-184 further displayed strong synergy with PARPi in ovarian and prostate cancer cell lines as well as in TNBC PDX models. These preclinical findings illustrate the potential of LP-184 as a pan-HRD cancer therapeutic. Taken together, our results support continued clinical evaluation of LP-184 in a large subset of HRD solid tumors. SIGNIFICANCE New agents with activity against DDR-deficient solid tumors refractory to standard-of-care therapies are needed. We report multiple findings supporting the potential for LP-184, a novel alkylating agent with three FDA orphan drug designations, to fill this void clinically: strong nanomolar potency; sustained, durable regression of solid tumor xenografts; synthetic lethality with HR defects. LP-184 adult phase IA trial to assess safety in advanced solid tumors is ongoing.
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Affiliation(s)
| | | | | | | | - Partha P. Banerjee
- Department of Biochemistry, Molecular and Cellular Biology, Georgetown University Medical Center, Washington, District of Columbia
| | - Shiv Srivastava
- Department of Biochemistry, Molecular and Cellular Biology, Georgetown University Medical Center, Washington, District of Columbia
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Lee DH, Bae WH, Ha H, Kim WR, Park EG, Lee YJ, Kim JM, Shin HJ, Kim HS. The human PTGR1 gene expression is controlled by TE-derived Z-DNA forming sequence cooperating with miR-6867-5p. Sci Rep 2024; 14:4723. [PMID: 38413664 PMCID: PMC10899170 DOI: 10.1038/s41598-024-55332-x] [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: 12/04/2023] [Accepted: 02/22/2024] [Indexed: 02/29/2024] Open
Abstract
Z-DNA, a well-known non-canonical form of DNA involved in gene regulation, is often found in gene promoters. Transposable elements (TEs), which make up 45% of the human genome, can move from one location to another within the genome. TEs play various biological roles in host organisms, and like Z-DNA, can influence transcriptional regulation near promoter regions. MicroRNAs (miRNAs) are a class of small non-coding RNA molecules that play a critical role in the regulation of gene expression. Although TEs can generate Z-DNA and miRNAs can bind to Z-DNA, how these factors affect gene transcription has yet to be elucidated. Here, we identified potential Z-DNA forming sequence (ZFS), including TE-derived ZFS, in the promoter of prostaglandin reductase 1 (PTGR1) by data analysis. The transcriptional activity of these ZFS in PTGR1 was confirmed using dual-luciferase reporter assays. In addition, we discovered a novel ZFS-binding miRNA (miR-6867-5p) that suppressed PTGR1 expression by targeting to ZFS. In conclusion, these findings suggest that ZFS, including TE-derived ZFS, can regulate PTGR1 gene expression and that miR-6867-5p can suppress PTGR1 by interacting with ZFS.
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Affiliation(s)
- Du Hyeong Lee
- Department of Integrated Biological Sciences, Pusan National University, Busan, 46241, Republic of Korea
- Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Woo Hyeon Bae
- Department of Integrated Biological Sciences, Pusan National University, Busan, 46241, Republic of Korea
- Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Hongseok Ha
- Institute of Endemic Diseases, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
| | - Woo Ryung Kim
- Department of Integrated Biological Sciences, Pusan National University, Busan, 46241, Republic of Korea
- Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Eun Gyung Park
- Department of Integrated Biological Sciences, Pusan National University, Busan, 46241, Republic of Korea
- Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Yun Ju Lee
- Department of Integrated Biological Sciences, Pusan National University, Busan, 46241, Republic of Korea
- Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Jung-Min Kim
- Department of Integrated Biological Sciences, Pusan National University, Busan, 46241, Republic of Korea
- Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Hae Jin Shin
- Department of Integrated Biological Sciences, Pusan National University, Busan, 46241, Republic of Korea
- Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea
| | - Heui-Soo Kim
- Institute of Systems Biology, Pusan National University, Busan, 46241, Republic of Korea.
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan, 46241, Republic of Korea.
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3
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Shi M, Huang K, Wei J, Wang S, Yang W, Wang H, Li Y. Identification and Validation of a Prognostic Signature Derived from the Cancer Stem Cells for Oral Squamous Cell Carcinoma. Int J Mol Sci 2024; 25:1031. [PMID: 38256104 PMCID: PMC10816075 DOI: 10.3390/ijms25021031] [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: 12/26/2023] [Revised: 01/08/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
The progression and metastasis of oral squamous cell carcinoma (OSCC) are highly influenced by cancer stem cells (CSCs) due to their unique self-renewal and plasticity. In this study, data were obtained from a single-cell RNA-sequencing dataset (GSE172577) in the GEO database, and LASSO-Cox regression analysis was performed on 1344 CSCs-related genes to establish a six-gene prognostic signature (6-GPS) consisting of ADM, POLR1D, PTGR1, RPL35A, PGK1, and P4HA1. High-risk scores were significantly associated with unfavorable survival outcomes, and these features were thoroughly validated in the ICGC. The results of nomograms, calibration plots, and ROC curves confirmed the good prognostic accuracy of 6-GPS for OSCC. Additionally, the knockdown of ADM or POLR1D genes may significantly inhibit the proliferation, migration, and invasion of OSCC cells through the JAK/HIF-1 pathway. Furthermore, cell-cycle arrest occurred in the G1 phase by suppressing Cyclin D1. In summary, 6-GPS may play a crucial role in the occurrence and development of OSCC and has the potential to be developed further as a diagnostic, therapeutic, and prognostic tool for OSCC.
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Affiliation(s)
- Mingxuan Shi
- Key Laboratory of Dental Maxillofacial Reconstruction and Biological Intelligence Manufacturing, School of Stomatology, Lanzhou University, Lanzhou 730030, China; (M.S.); (K.H.); (J.W.); (S.W.); (W.Y.)
| | - Ke Huang
- Key Laboratory of Dental Maxillofacial Reconstruction and Biological Intelligence Manufacturing, School of Stomatology, Lanzhou University, Lanzhou 730030, China; (M.S.); (K.H.); (J.W.); (S.W.); (W.Y.)
- Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730030, China
| | - Jiaqi Wei
- Key Laboratory of Dental Maxillofacial Reconstruction and Biological Intelligence Manufacturing, School of Stomatology, Lanzhou University, Lanzhou 730030, China; (M.S.); (K.H.); (J.W.); (S.W.); (W.Y.)
| | - Shiqi Wang
- Key Laboratory of Dental Maxillofacial Reconstruction and Biological Intelligence Manufacturing, School of Stomatology, Lanzhou University, Lanzhou 730030, China; (M.S.); (K.H.); (J.W.); (S.W.); (W.Y.)
| | - Weijia Yang
- Key Laboratory of Dental Maxillofacial Reconstruction and Biological Intelligence Manufacturing, School of Stomatology, Lanzhou University, Lanzhou 730030, China; (M.S.); (K.H.); (J.W.); (S.W.); (W.Y.)
| | - Huihui Wang
- Key Laboratory of Dental Maxillofacial Reconstruction and Biological Intelligence Manufacturing, School of Stomatology, Lanzhou University, Lanzhou 730030, China; (M.S.); (K.H.); (J.W.); (S.W.); (W.Y.)
| | - Yi Li
- Key Laboratory of Dental Maxillofacial Reconstruction and Biological Intelligence Manufacturing, School of Stomatology, Lanzhou University, Lanzhou 730030, China; (M.S.); (K.H.); (J.W.); (S.W.); (W.Y.)
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Storås AM, Fineide F, Magnø M, Thiede B, Chen X, Strümke I, Halvorsen P, Galtung H, Jensen JL, Utheim TP, Riegler MA. Using machine learning model explanations to identify proteins related to severity of meibomian gland dysfunction. Sci Rep 2023; 13:22946. [PMID: 38135766 PMCID: PMC10746717 DOI: 10.1038/s41598-023-50342-7] [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: 07/14/2023] [Accepted: 12/19/2023] [Indexed: 12/24/2023] Open
Abstract
Meibomian gland dysfunction is the most common cause of dry eye disease and leads to significantly reduced quality of life and social burdens. Because meibomian gland dysfunction results in impaired function of the tear film lipid layer, studying the expression of tear proteins might increase the understanding of the etiology of the condition. Machine learning is able to detect patterns in complex data. This study applied machine learning to classify levels of meibomian gland dysfunction from tear proteins. The aim was to investigate proteomic changes between groups with different severity levels of meibomian gland dysfunction, as opposed to only separating patients with and without this condition. An established feature importance method was used to identify the most important proteins for the resulting models. Moreover, a new method that can take the uncertainty of the models into account when creating explanations was proposed. By examining the identified proteins, potential biomarkers for meibomian gland dysfunction were discovered. The overall findings are largely confirmatory, indicating that the presented machine learning approaches are promising for detecting clinically relevant proteins. While this study provides valuable insights into proteomic changes associated with varying severity levels of meibomian gland dysfunction, it should be noted that it was conducted without a healthy control group. Future research could benefit from including such a comparison to further validate and extend the findings presented here.
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Affiliation(s)
- Andrea M Storås
- Department of Holistic Systems, Simula Metropolitan Center for Digital Engineering, Oslo, Norway.
- Department of Computer Science, OsloMet - Oslo Metropolitan University, Oslo, Norway.
| | - Fredrik Fineide
- Department of Computer Science, OsloMet - Oslo Metropolitan University, Oslo, Norway
- The Norwegian Dry Eye Clinic, Oslo, Bergen, Norway
| | - Morten Magnø
- Department of Ophthalmology, Sørlandet Hospital Arendal, Arendal, Norway
- Department of Plastic and Reconstructive Surgery, Oslo University Hospital, Oslo, Norway
| | - Bernd Thiede
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Xiangjun Chen
- Department of Ophthalmology, Sørlandet Hospital Arendal, Arendal, Norway
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
- Department of Ophthalmology, Vestre Viken Hospital Trust, Drammen, Norway
| | - Inga Strümke
- Department of Computer Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Pål Halvorsen
- Department of Holistic Systems, Simula Metropolitan Center for Digital Engineering, Oslo, Norway
- Department of Computer Science, OsloMet - Oslo Metropolitan University, Oslo, Norway
| | - Hilde Galtung
- Institute of Oral Biology, University of Oslo, Oslo, Norway
| | - Janicke L Jensen
- Department of Oral Surgery and Oral Medicine, University of Oslo, Oslo, Norway
| | - Tor P Utheim
- Department of Computer Science, OsloMet - Oslo Metropolitan University, Oslo, Norway
- The Norwegian Dry Eye Clinic, Oslo, Bergen, Norway
- Department of Ophthalmology, Sørlandet Hospital Arendal, Arendal, Norway
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
- Department of Ophthalmology, Oslo University Hospital, Oslo, Norway
| | - Michael A Riegler
- Department of Holistic Systems, Simula Metropolitan Center for Digital Engineering, Oslo, Norway
- Department of Computer Science, OsloMet - Oslo Metropolitan University, Oslo, Norway
- Department of Computer Science, UiT The Arctic University of Norway, Tromsø, Norway
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5
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Aranciaga N, Ross AB, Morton JD, McDonald R, Gathercole JL, Berg DK. Metabolomic evolution of the postpartum dairy cow uterus. Mol Reprod Dev 2023; 90:835-848. [PMID: 37632839 DOI: 10.1002/mrd.23702] [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: 03/29/2023] [Revised: 07/24/2023] [Accepted: 07/30/2023] [Indexed: 08/28/2023]
Abstract
High rates of early pregnancy loss are a critical issue in dairy herds, particularly in seasonal, grazing systems. Components of the uterine luminal fluid (ULF), on which the early embryo depends for sustenance and growth, partly determine early pregnancy losses. Here, changes in ULF from early to mid-postpartum in crossbred dairy cows were explored, linking them with divergent embryo development. For this, the uteri of 87 cows at Day 7 of pregnancy at first and third estrus postpartum were flushed to collect ULF. Eighteen metabolites (chiefly organic acids and sugars) significantly varied in abundance across postpartum, indicating a molecular signature of physiological recovery consistent of the upregulation of pyrimidine metabolism and glycerophospholipid metabolism, and downregulation of pentose phosphate and taurine metabolism pathways. Joint pathway analysis of metabolomics data and a previously generated proteomics data set on the same ULF samples suggests key links between postpartum recovery and subsequent successful embryo development. These include upregulation of VEGFA and downregulation of metabolism, NRF2, T-cell receptor, which appear to improve the ULF's capacity of sustaining normal embryo development, and a putative osmo-protectant role of beta-alanine. These relationships should be further investigated to develop tools to detect and reduce early pregnancy loss in dairy cows.
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Affiliation(s)
- Nicolas Aranciaga
- Proteins and Metabolites Team, AgResearch, Christchurch, New Zealand
- Faculty of Agriculture and Life Sciences, Lincoln University, Christchurch, New Zealand
- Animal Biotechnology Team, AgResearch, Hamilton, New Zealand
| | - Alastair B Ross
- Proteins and Metabolites Team, AgResearch, Christchurch, New Zealand
| | - James D Morton
- Faculty of Agriculture and Life Sciences, Lincoln University, Christchurch, New Zealand
| | - Robin McDonald
- Animal Biotechnology Team, AgResearch, Hamilton, New Zealand
| | | | - Debra K Berg
- Animal Biotechnology Team, AgResearch, Hamilton, New Zealand
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6
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Liu K, Shu L, Huang AY, Chang Y, Chen Z, Zhang C. PTGR1 is involved in cell proliferation in thoracic ossification of the ligamentum flavum. PLoS One 2023; 18:e0292821. [PMID: 37910537 PMCID: PMC10619815 DOI: 10.1371/journal.pone.0292821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 09/28/2023] [Indexed: 11/03/2023] Open
Abstract
Thoracic ossification of the ligamentum flavum (TOLF) is a heterotopic ossification of spinal ligaments, leading to serious myelopathy. TOLF underlying mechanisms are not well understood. Our iTRAQ analysis have identified ten inflammatory factors related to TOLF, including l. We found that PTGR1 expressions increased in TOLF by RT-PCR and western blot in this study. Both cell proliferation and differentiation are important for the process of bone formation. In our previous study, we demonstrated that TOLF primary cells grew faster than control cells. It was reported that knockdown of PTGR1 inhibited cell proliferation. We hypothesize that PTGR1 may participate in cell proliferation in TOLF. To test this hypothesis, TOLF primary cells were treated for 24h with PTGR1. We observed that PTGR1 increased cell proliferation. The effect of PTGR1 on cell proliferation related genes was examined in TOLF primary cells. Our results showed that PTGR1 was able to activate expressions of c-Myc and CyclinD1. Moreover, blocking JNK pathway by selective JNK inhibitor SP600125 eliminated the positive effect of PTGR1 on c-Myc expression, indicating that PTGR1 activated the expression of c-Myc via JNK pathway. Our new findings suggest that PTGR1 is involved in cell proliferation of TOLF.
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Affiliation(s)
- Kuankuan Liu
- Central Laboratory, Peking University International Hospital, Beijing, China
| | - Li Shu
- Central Laboratory, Peking University International Hospital, Beijing, China
| | - Ann Yehong Huang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Yanan Chang
- Central Laboratory, Peking University International Hospital, Beijing, China
| | - Zhongqiang Chen
- Department of Orthopedics, Peking University International Hospital, Beijing, China
| | - Chi Zhang
- Central Laboratory, Peking University International Hospital, Beijing, China
- Department of Orthopedics, Peking University International Hospital, Beijing, China
- Biomedical Engineering Department, Peking University, Beijing, China
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7
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Ye J, Cai S, Feng Y, Li J, Cai Z, Deng Y, Liu R, Zhu X, Lu J, Zhuo Y, Liang Y, Xie J, Zhang Y, He H, Han Z, Jia Z, Zhong W. Metformin escape in prostate cancer by activating the PTGR1 transcriptional program through a novel super-enhancer. Signal Transduct Target Ther 2023; 8:303. [PMID: 37582751 PMCID: PMC10427640 DOI: 10.1038/s41392-023-01516-2] [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: 09/02/2022] [Revised: 05/25/2023] [Accepted: 05/30/2023] [Indexed: 08/17/2023] Open
Abstract
The therapeutic efficacy of metformin in prostate cancer (PCa) appears uncertain based on various clinical trials. Metformin treatment failure may be attributed to the high frequency of transcriptional dysregulation, which leads to drug resistance. However, the underlying mechanism is still unclear. In this study, we found evidences that metformin resistance in PCa cells may be linked to cell cycle reactivation. Super-enhancers (SEs), crucial regulatory elements, have been shown to be associated with drug resistance in various cancers. Our analysis of SEs in metformin-resistant (MetR) PCa cells revealed a correlation with Prostaglandin Reductase 1 (PTGR1) expression, which was identified as significantly increased in a cluster of cells with metformin resistance through single-cell transcriptome sequencing. Our functional experiments showed that PTGR1 overexpression accelerated cell cycle progression by promoting progression from the G0/G1 to the S and G2/M phases, resulting in reduced sensitivity to metformin. Additionally, we identified key transcription factors that significantly increase PTGR1 expression, such as SRF and RUNX3, providing potential new targets to address metformin resistance in PCa. In conclusion, our study sheds new light on the cellular mechanism underlying metformin resistance and the regulation of the SE-TFs-PTGR1 axis, offering potential avenues to enhance metformin's therapeutic efficacy in PCa.
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Affiliation(s)
- Jianheng Ye
- Department of Urology, Guangzhou First People's Hospital, South China University of Technology, 510180, Guangzhou, Guangdong, China
| | - Shanghua Cai
- Department of Urology, Guangzhou First People's Hospital, South China University of Technology, 510180, Guangzhou, Guangdong, China
- Urology Key Laboratory of Guangdong Province, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, 510230, Guangzhou, Guangdong, China
- Guangzhou National Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, 510005, Guangzhou, Guangdong, China
| | - Yuanfa Feng
- Department of Urology, Guangzhou First People's Hospital, South China University of Technology, 510180, Guangzhou, Guangdong, China
- Urology Key Laboratory of Guangdong Province, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, 510230, Guangzhou, Guangdong, China
| | - Jinchuang Li
- Department of Urology, Guangzhou First People's Hospital, South China University of Technology, 510180, Guangzhou, Guangdong, China
| | - Zhiduan Cai
- Department of Urology, Guangzhou First People's Hospital, South China University of Technology, 510180, Guangzhou, Guangdong, China
| | - Yulin Deng
- Urology Key Laboratory of Guangdong Province, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, 510230, Guangzhou, Guangdong, China
| | - Ren Liu
- Department of Urology, Guangzhou First People's Hospital, South China University of Technology, 510180, Guangzhou, Guangdong, China
| | - Xuejin Zhu
- Department of Urology, Guangzhou First People's Hospital, South China University of Technology, 510180, Guangzhou, Guangdong, China
| | - Jianming Lu
- Department of Urology, Guangzhou First People's Hospital, South China University of Technology, 510180, Guangzhou, Guangdong, China
| | - Yangjia Zhuo
- Department of Urology, Guangzhou First People's Hospital, South China University of Technology, 510180, Guangzhou, Guangdong, China
| | - Yingke Liang
- Department of Urology, Guangzhou First People's Hospital, South China University of Technology, 510180, Guangzhou, Guangdong, China
| | - Jianjiang Xie
- Department of Urology, Guangzhou First People's Hospital, South China University of Technology, 510180, Guangzhou, Guangdong, China
| | - Yanqiong Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Huichan He
- Urology Key Laboratory of Guangdong Province, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, 510230, Guangzhou, Guangdong, China
| | - Zhaodong Han
- Department of Urology, Guangzhou First People's Hospital, South China University of Technology, 510180, Guangzhou, Guangdong, China.
| | - Zhenyu Jia
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92507, USA.
- Graduate Program in Genetics, Genomics & Bioinformatics, University of California, Riverside, CA, 92507, USA.
| | - Weide Zhong
- Department of Urology, Guangzhou First People's Hospital, South China University of Technology, 510180, Guangzhou, Guangdong, China.
- Urology Key Laboratory of Guangdong Province, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, 510230, Guangzhou, Guangdong, China.
- Guangzhou National Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, 510005, Guangzhou, Guangdong, China.
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, 999078, Macau, China.
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8
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Yagishita Y, Chartoumpekis DV, Kensler TW, Wakabayashi N. NRF2 and the Moirai: Life and Death Decisions on Cell Fates. Antioxid Redox Signal 2023; 38:684-708. [PMID: 36509429 PMCID: PMC10025849 DOI: 10.1089/ars.2022.0200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Significance: The transcription factor NRF2 (NF-E2-related factor 2) plays an important role as a master regulator of the cellular defense system by activating transcriptional programs of NRF2 target genes encoding multiple enzymes related to cellular redox balance and xenobiotic detoxication. Comprehensive transcriptional analyses continue to reveal an ever-broadening range of NRF2 target genes, demonstrating the sophistication and diversification of NRF2 biological signatures beyond its canonical cytoprotective roles. Recent Advances: Accumulating evidence indicates that NRF2 has a strong association with the regulation of cell fates by influencing key processes of cellular transitions in the three major phases of the life cycle of the cell (i.e., cell birth, cell differentiation, and cell death). The molecular integration of NRF2 signaling into this regulatory program occurs through a wide range of NRF2 target genes encompassing canonical functions and those manipulating cell fate pathways. Critical Issues: A singular focus on NRF2 signaling for dissecting its actions limits in-depth understanding of its intersection with the molecular machinery of cell fate determinations. Compensatory responses of downstream pathways governed by NRF2 executed by a variety of transcription factors and multifactorial signaling crosstalk require further exploration. Future Directions: Further investigations using optimized in vivo models and active engagement of overarching approaches to probe the interplay of widespread pathways are needed to study the properties and capabilities of NRF2 signaling as a part of a large network within the cell fate regulatory domain. Antioxid. Redox Signal. 38, 684-708.
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Affiliation(s)
- Yoko Yagishita
- Translational Research Program, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Dionysios V Chartoumpekis
- Service of Endocrinology, Diabetology and Metabolism, Lausanne University Hospital, Lausanne, Switzerland
| | - Thomas W Kensler
- Translational Research Program, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Nobunao Wakabayashi
- Translational Research Program, Fred Hutchinson Cancer Center, Seattle, Washington, USA
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9
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Chen H, Liu X, Yao F, Yin M, Cheng B, Yang S. Identification of metabolic signatures related to metastasis and immunotherapy resistance in oral squamous cell carcinoma. Am J Transl Res 2023; 15:373-391. [PMID: 36777871 PMCID: PMC9908494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 12/19/2022] [Indexed: 02/14/2023]
Abstract
OBJECTIVES In this study, we aimed to identify the metabolic genes associated with the metastasis and immunotherapy resistance of oral squamous cell carcinoma (OSCC) and to construct a metabolic gene-related predictive model for the prognosis of OSCC. METHODS RNA-seq data were download from The Cancer Genome Atlas (TCGA). Weighted gene co-expression network analysis (WGCNA) was applied to identify the modules related to EMT, stemness, and checkpoint signatures in OSCC. Univariate Cox and the least absolute shrinkage and selection operator (LASSO) methods were used to construct the metabolic gene signature. Furthermore, the scRNA-seq data were obtained from Gene Expression Omnibus (GEO) database and analyzed using "Seurat" and "CopyKAT" packages. RESULTS The risk prediction model was constructed using the 12 metabolic-related gene signature. Based on this model, risk score of each sample was calculated and used to divide the samples into low- and high-risk groups. Our model was effective as the risk score was significantly associated with clinical features and genetic mutations. Meanwhile, we found that lipid metabolism, glycolysis, amino acid metabolism, and drug metabolism differed between high- and low-risk groups. Pathways associated with malignant tumor and immunosuppression were enriched in high-risk group. Furthermore, low-risk group showed a more activated immune status and was predicted to have better response to immunotherapy. Finally, through single-cell transcriptome analysis, we assessed the expression of these 12 genes in tumor and non-tumor cells and verified the existence of two clusters of tumor cells with different degrees of malignancy at the cellular level. CONCLUSIONS Our study demonstrates the clinical significance of metabolic related gene signature for the treatment of OSCC and suggests potential therapeutic targets and pathways for OSCC.
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Affiliation(s)
- Haoran Chen
- Department of Stomatology, Zhongnan Hospital of Wuhan UniversityWuhan, Hubei, China,Department of Immunology and National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical CollegeBeijing, China
| | - Xin Liu
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research InstituteBeijing, China
| | - Feng Yao
- Department of Stomatology, Zhongnan Hospital of Wuhan UniversityWuhan, Hubei, China
| | - Miao Yin
- Department of Stomatology, Zhongnan Hospital of Wuhan UniversityWuhan, Hubei, China
| | - Bo Cheng
- Department of Stomatology, Zhongnan Hospital of Wuhan UniversityWuhan, Hubei, China
| | - Sisi Yang
- Department of Stomatology, Zhongnan Hospital of Wuhan UniversityWuhan, Hubei, China
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Liu X, Fang X, Lu L, Liu G. Prognostic significance and immune landscape of a fatty acid metabolism-related gene signature in colon adenocarcinoma. Front Genet 2022; 13:996625. [PMID: 36568396 PMCID: PMC9780302 DOI: 10.3389/fgene.2022.996625] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022] Open
Abstract
Background: Fatty acid metabolism (FAM), as a hallmark of caner, plays important roles in tumor initiation and carcinogenesis. However, the significance of fatty acid metabolism-related genes in colon adenocarcinoma (COAD) are largely unknown. Methods: RNA sequencing data and clinical information were downloaded from the Cancer Genome Atlas (TCGA) cohort. Univariate and multivariate Cox regression analyses were utilized to construct a fatty acid metabolism-related gene signature. Kaplan-Meier survival and receiver operating characteristic (ROC) analyses were used to verify the performance of this signature. GEO datasets were applied to validate the signature. Maftools package was utilized to analyze the mutation profiles of this signature. Correlation between the risk signature and stemness scores was compared by RNA stemness score (RNAss). Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene set variation analysis (GSVA) were performed to explore the potential functions and signaling pathways. Immune landscape of the signature was explored by analyzing different immune cells infiltration, immune functions and microsatellite instability. A nomogram was constructed by combining the risk signature and multiple clinical factors. Expression levels and prognostic values of the risk genes were revealed in the cancer genome atlas and GEO databases. Moreover, the expression the risk genes were measured in cell lines using real time quantitative PCR (qRT-PCR). Results: Eight fatty acid metabolism-related genes (CD36, ENO3, MORC2, PTGR1, SUCLG2, ELOVL3, ELOVL6 and CPT2) were used to construct a risk signature. This signature demonstrated better prognostic value than other clinicopathological parameters, with AUC value was 0.734 according to the cancer genome atlas database. There was negative correlation between the riskscore and RNA stemness score. The patients in the high-risk group demonstrated higher infiltration of M0 macrophages, and less infiltration of activated CD4 memory T cells and Eosinophils. There were more MSI patients in the high-risk group than those in the low-risk group (38% vs. 30%). The risk scores of patients in the MSI group were slightly higher than those in the microsatellite stability group. Gene ontology, kyoto encyclopedia of genes and genomes and gene set variation analysis enrichment analyses showed that several metabolism-related functions and signaling pathways were enriched. A nomogram showed good predictive capability of the signature. Moreover, qRT-PCR revealed upregulated expression of ENO3, MORC2, SUCLG2 and ELOVL6, and downregulated expression of CPT2 in all examined colon adenocarcinoma cell lines. Conclusion: This study provided novel insights into a fatty acid metabolism-related signature in the prognosis an immune landscape of colon adenocarcinoma patients.
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Affiliation(s)
| | | | - Lin Lu
- *Correspondence: Guolong Liu, ; Lin Lu,
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Bittencourt LO, Damasceno-Silva RD, Aragão WAB, Eiró-Quirino L, Oliveira ACA, Fernandes RM, Freire MAM, Cartágenes SC, Dionizio A, Buzalaf MAR, Cassoli JS, Cirovic A, Cirovic A, Maia CDSF, Lima RR. Global Proteomic Profile of Aluminum-Induced Hippocampal Impairments in Rats: Are Low Doses of Aluminum Really Safe? Int J Mol Sci 2022; 23:ijms232012523. [PMID: 36293377 PMCID: PMC9603961 DOI: 10.3390/ijms232012523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/12/2022] [Accepted: 09/29/2022] [Indexed: 11/21/2022] Open
Abstract
Hippocampus is the brain area where aluminum (Al) accumulates in abundance and is widely associated with learning and memory. In the present study, we evaluate behavioral, tissue, and proteomic changes in the hippocampus of Wistar rats caused by exposure to doses that mimic human consumption of aluminum chloride (AlCl3) in urban areas. For this, male Wistar rats were divided into two groups: Control (distilled water) and AlCl3 (8.3 mg/kg/day), both groups were exposed orally for 60 days. After the Al exposure protocol, cognitive functions were assessed by the Water maze test, followed by a collection for analysis of the global proteomic profile of the hippocampus by mass spectrometry. Aside from proteomic analysis, we performed a histological analysis of the hippocampus, to the determination of cell body density by cresyl violet staining in Cornu Ammonis fields (CA) 1 and 3, and hilus regions. Our results indicated that exposure to low doses of aluminum chloride triggered a decreased cognitive performance in learning and memory, being associated with the deregulation of proteins expression, mainly those related to the regulation of the cytoskeleton, cellular metabolism, mitochondrial activity, redox regulation, nervous system regulation, and synaptic signaling, reduced cell body density in CA1, CA3, and hilus.
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Affiliation(s)
- Leonardo Oliveira Bittencourt
- Laboratory of Functional and Structural Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075110, Brazil
| | - Rakhel Dayanne Damasceno-Silva
- Laboratory of Functional and Structural Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075110, Brazil
| | - Walessa Alana Bragança Aragão
- Laboratory of Functional and Structural Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075110, Brazil
| | - Luciana Eiró-Quirino
- Laboratory of Functional and Structural Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075110, Brazil
| | - Ana Carolina Alves Oliveira
- Laboratory of Functional and Structural Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075110, Brazil
| | - Rafael Monteiro Fernandes
- Laboratory of Functional and Structural Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075110, Brazil
| | - Marco Aurelio M. Freire
- Graduate Program in Health and Society, Faculty of Health Sciences, State University of Rio Grande do Norte (UERN), Mossoro 59610210, Brazil
| | - Sabrina Carvalho Cartágenes
- Laboratory of Pharmacology of Inflammation and Behavior, Institute of Health Sciences, Federal University of Pará, Belém 66075110, Brazil
| | - Aline Dionizio
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru 05508060, Brazil
| | | | - Juliana Silva Cassoli
- Institute of Biological Sciences, Federal University of Pará, Belém 66075110, Brazil
| | - Ana Cirovic
- Faculty of Medicine, Institute of Anatomy, University of Belgrade, 11000 Belgrade, Serbia
| | - Aleksandar Cirovic
- Faculty of Medicine, Institute of Anatomy, University of Belgrade, 11000 Belgrade, Serbia
| | - Cristiane do Socorro Ferraz Maia
- Laboratory of Pharmacology of Inflammation and Behavior, Institute of Health Sciences, Federal University of Pará, Belém 66075110, Brazil
| | - Rafael Rodrigues Lima
- Laboratory of Functional and Structural Biology, Institute of Biological Sciences, Federal University of Pará, Belém 66075110, Brazil
- Correspondence:
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Ishikawa A, Yamanouchi S, Iwasaki W, Kitano J. Convergent copy number increase of genes associated with freshwater colonization in fishes. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200509. [PMID: 35634928 PMCID: PMC9149799 DOI: 10.1098/rstb.2020.0509] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 03/14/2022] [Indexed: 07/20/2023] Open
Abstract
Copy number variation (CNV) can cause phenotypic changes. However, in contrast to amino acid substitutions and cis-regulatory changes, little is known about the functional categories of genes in which CNV is important for adaptation to novel environments. It is also unclear whether the same genes repeatedly change the copy numbers for adapting to similar environments. Here, we investigate CNV associated with freshwater colonization in fishes, which was observed multiple times across different lineages. Using 48 ray-finned fishes across diverse orders, we identified 23 genes whose copy number increases were associated with freshwater colonization. These genes showed enrichment for peptide receptor activity, hexosyltransferase activity and unsaturated fatty acid metabolism. We further revealed that three of the genes showed copy number increases in freshwater populations compared to marine ancestral populations of the stickleback genus Gasterosteus. These results indicate that copy number increases of genes involved in fatty acid metabolism (FADS2), immune function (PSMB8a) and thyroid hormone metabolism (UGT2) may be important for freshwater colonization at both the inter-order macroevolutionary scale and at the intra-genus microevolutionary scale. Further analysis across diverse taxa will help to understand the role of CNV in the adaptation to novel environments. This article is part of the theme issue 'Genetic basis of adaptation and speciation: from loci to causative mutations'.
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Affiliation(s)
- Asano Ishikawa
- Ecological Genetics Laboratory, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Shun Yamanouchi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Wataru Iwasaki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
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Impact of Epithelial-Mesenchymal Immunophenotype on Local Aggressiveness in Papillary Thyroid Carcinoma Invading the Airway. J Clin Med 2021; 10:jcm10194351. [PMID: 34640369 PMCID: PMC8509765 DOI: 10.3390/jcm10194351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/14/2021] [Accepted: 09/21/2021] [Indexed: 11/17/2022] Open
Abstract
Primary thyroid tumours show different levels of aggressiveness, from indolent to rapidly growing infiltrating malignancies. The most effective therapeutic option is surgery when radical resection is feasible. Biomarkers of aggressiveness may help in scheduling extended resections such as airway infiltration, avoiding a non-radical approach. The aim of the study is to evaluate the prognostic role of E-cadherin, N-cadherin, Aryl hydrocarbon receptor (AhR), and CD147 in different biological behaviours. Fifty-five samples from three groups of thyroid carcinomas were stained: papillary thyroid carcinomas (PTCs) infiltrating the airway (PTC-A), papillary intra-thyroid carcinomas (PTC-B) and poorly differentiated or anaplastic thyroid carcinomas (PDTC/ATC). High expressions of N-cadherin and AhR were associated with higher locoregional tumour aggressiveness (p = 0.005 and p < 0.001 respectively); PDTC/ATC more frequently showed a high expression of CD147 (p = 0.011), and a trend of lower expression of E-cadherin was registered in more aggressive neoplasms. Moreover, high levels of AhR were found with recurrent/persistent diseases (p = 0.031), particularly when tumours showed a concomitant high N-cadherin expression (p = 0.043). The study suggests that knowing in advance onco-biological factors with a potential role to discriminate between different subsets of patients could help the decision-making process, providing a more solid therapeutic indication and an increased expectation for radical surgery.
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