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Yan M, Luo X, Han H, Qiu J, Ye Q, Zhang L, Wang Y. ROCK2 increases drug resistance in acute myeloid leukemia via metabolic reprogramming and MAPK/PI3K/AKT signaling. Int Immunopharmacol 2024; 140:112897. [PMID: 39126734 DOI: 10.1016/j.intimp.2024.112897] [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: 03/05/2024] [Revised: 07/17/2024] [Accepted: 08/05/2024] [Indexed: 08/12/2024]
Abstract
Rho-associated coiled-coil kinase 2 (ROCK2) is classified as a member of the serine/threonine protein kinase family and has been identified as a key driver of the development of various forms of cancer. The cause of ROCK2's impact on acute myeloid leukemia (AML) is still unknown. We found that ROCK2 expression was higher in AML patients, leading to lower complete response rates and worse overall survival. Additionally, ROCK2 expression was elevated in the doxorubicin-resistant leukemia cell line HL-60/ADM when compared to their individual parent cells. Moreover, the suppression or inhibition of ROCK2 leads to enhanced drug sensitivity in both AML cell lines and primary AML specimens, along with a notable decrease in downstream signaling pathways. Furthermore, the suppression of ROCK2 caused disruption of cellular energy production pathways by directly affecting the functionality of proteins within the mitochondrial electron transport chain. Finally, we discovered that TRIM26, a specific E3 ligase, is capable of ubiquitylating ROCK2, and the upregulation of TRIM26 within HL-60/ADM cells resulted in heightened sensitivity to the drug and reduced resistance. Thus, our study presents a new strategy for overcoming drug resistance in AML through targeting ROCK2/AKT/MAPK signaling pathway.
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Affiliation(s)
- Muxia Yan
- Department of Hematology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Xin Luo
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou, China
| | - Hong Han
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou, China
| | - Jiachun Qiu
- Department of Hematology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Qian Ye
- Department of Hematology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Li Zhang
- Department of Hematology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China.
| | - Yiqian Wang
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou, China.
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2
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Qi Q, Zhu M, Li P, Mi Q, Xie Y, Li J, Wang C. Systematic analysis of PANoptosis-related genes identifies XIAP as a functional oncogene in breast cancer. Gene 2024; 912:148355. [PMID: 38467314 DOI: 10.1016/j.gene.2024.148355] [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: 11/13/2023] [Revised: 03/02/2024] [Accepted: 03/07/2024] [Indexed: 03/13/2024]
Abstract
BACKGROUND Breast cancer (BC) is the most prevalent malignant disease affecting women globally. PANoptosis, a novel form of cell death combining features of pyroptosis, apoptosis, and necroptosis, has recently gained attention. However, its precise function in BC and the predictive values of PANoptosis-related genes remain unclear. METHODS We used the expression data and clinical information of BC tissues or normal breast tissues from public databases, and then successfully developed and verified a BC PANoptosis-related risk model through a combination of univariate Cox regression, least absolute shrinkage and selection operator (LASSO) regression, and Kaplan-Meier (KM) analysis. A nomogram was constructed to estimate survival probability, and its accuracy was assessed using calibration curves. RESULTS Among 37 PANoptosis-related genes, we identified 4 differentially expressed genes related to overall survival (OS). Next, a risk model incorporating these four PANoptosis-related genes was established. Patients were stratified into low/high-risk groups based on the median risk score, with the low-risk group showing better prognoses and higher levels of immune infiltration. Utilizing the risk score and clinical features, we developed a nomogram to predict 1-, 3- and 5-year survival probability. X-linked inhibitor of apoptosis protein (XIAP) emerged as a potentially risky factor with the highest hazard ratio. In vitro experiments demonstrated that XIAP inhibition enhances the antitumor effect of doxorubicin through the PANoptosis pathway. CONCLUSION PANoptosis holds an important role in BC prognosis and treatment.
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Affiliation(s)
- Qiuchen Qi
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan 250033, PR China; Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan 250033, PR China
| | - Mengqian Zhu
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan 250033, PR China
| | - Peilong Li
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan 250033, PR China; Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan 250033, PR China
| | - Qi Mi
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan 250033, PR China
| | - Yan Xie
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan 250033, PR China
| | - Juan Li
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan 250033, PR China; Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan 250033, PR China.
| | - Chuanxin Wang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan 250033, PR China; Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan 250033, PR China; Shandong Provincial Key Laboratory of Innovation Technology in Laboratory Medicine, Jinan 250033, PR China.
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3
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Liu Y, Wang B, Cheng Y, Fang Y, Hou Y, Mao Y, Wu X, Jiang D, He Y, Jin C. ASIC1 promotes migration and invasion of hepatocellular carcinoma via the PRKACA/AP-1 signaling pathway. Carcinogenesis 2024; 45:399-408. [PMID: 38306794 DOI: 10.1093/carcin/bgae008] [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: 09/12/2023] [Revised: 01/21/2024] [Accepted: 01/30/2024] [Indexed: 02/04/2024] Open
Abstract
Hepatocellular carcinoma (HCC) exhibits a high mortality rate due to its high invasion and metastatic nature, and the acidic microenvironment plays a pivotal role. Acid-sensing ion channel 1 (ASIC1) is upregulated in HCC tissues and facilitates tumor progression in a pH-dependent manner, while the specific mechanisms therein remain currently unclear. Herein, we aimed to investigate the underlying mechanisms by which ASIC1 contributes to the development of HCC. Using bioinformatics analysis, we found a significant association between ASIC1 expression and malignant transformation of HCC, such as poor prognosis, metastasis and recurrence. Specifically, ASIC1 enhanced the migration and invasion capabilities of Li-7 cells in the in vivo experiment using an HCC lung metastasis mouse model, as well as in the in vitro experiments such as wound healing assay and Transwell assay. Furthermore, our comprehensive gene chip and molecular biology experiments revealed that ASIC1 promoted HCC migration and invasion by activating the PRKACA/AP-1 signaling pathway. Our findings indicate that targeting ASIC1 could have therapeutic potential for inhibiting HCC progression.
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Affiliation(s)
- Youyi Liu
- Department of Hepatobiliary Surgery, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214041, China
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
- Institute of Hepatobiliary Surgery, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214041, China
| | - Boshi Wang
- Department of Hepatobiliary Surgery, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214041, China
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
- Institute of Hepatobiliary Surgery, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214041, China
| | - Yang Cheng
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yipeng Fang
- Department of Hepatobiliary Surgery, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214041, China
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
- Institute of Hepatobiliary Surgery, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214041, China
| | - Yingjian Hou
- Department of Hepatobiliary Surgery, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214041, China
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
- Institute of Hepatobiliary Surgery, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214041, China
| | - Yong Mao
- Department of Oncology, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214041, China
| | - Xiaomin Wu
- Department of Oncology, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214041, China
| | - Donglin Jiang
- Department of Hepatobiliary Surgery, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214041, China
- Institute of Hepatobiliary Surgery, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214041, China
| | - Youzhao He
- Department of Hepatobiliary Surgery, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214041, China
- Institute of Hepatobiliary Surgery, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214041, China
| | - Cheng Jin
- Department of Hepatobiliary Surgery, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214041, China
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, China
- Institute of Hepatobiliary Surgery, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu 214041, China
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4
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Zhang Y, Li F, Han Z, Teng Z, Jin C, Yuan H, Zhang S, Sun K, Wang Y. Downregulated RBM5 Enhances CARM1 Expression and Activates the PRKACA/GSK3β Signaling Pathway through Alternative Splicing-Coupled Nonsense-Mediated Decay. Cancers (Basel) 2023; 16:139. [PMID: 38201567 PMCID: PMC10778212 DOI: 10.3390/cancers16010139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/13/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
Downregulated RNA-binding motif protein 5 (RBM5) promotes the development and progression of various tumors, including bladder cancer (BC). Alternative splicing (AS) plays a crucial role in the progression of cancer by producing protein isomers with different functions or by promoting nonsense-mediated mRNA decay (NMD). However, whether RBM5 modulates the progression of BC through AS-NMD remains unexplored. In this study, we revealed that the downregulation of RBM5 expression promoted the expression of coactivator-associated arginine methyltransferase 1 (CARM1) in BC cells and tissues. Increased expression of CARM1 facilitated the activation of the Wnt/β-catenin axis and cell proliferation, which then contributed to the poor prognosis of patients with BC. Interestingly, RBM5 bound directly to CARM1 mRNA and participated in AS-NMD, downregulating the expression of CARM1. In addition, we revealed that protein kinase catalytic subunit alpha (PRKACA) functioned as a phosphorylated kinase of GSK3β, was regulated by CARM1 at the transcription level, and promoted the growth and progression of BC cells. Furthermore, in this study, we demonstrated a regulatory mechanism of Wnt/β-catenin activation through the RBM5/CARM1/PRKACA axis and identified a novel potential target for treating BC.
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Affiliation(s)
- Yanping Zhang
- Department of Urology, The Second Hospital of Hebei Medical University, Shijiazhuang 050011, China; (Y.Z.); (Z.H.); (Z.T.); (C.J.); (H.Y.); (K.S.)
| | - Fang Li
- Department of Cardiology, The Second Hospital of Hebei Medical University, Shijiazhuang 050011, China
| | - Zhenwei Han
- Department of Urology, The Second Hospital of Hebei Medical University, Shijiazhuang 050011, China; (Y.Z.); (Z.H.); (Z.T.); (C.J.); (H.Y.); (K.S.)
| | - Zhihai Teng
- Department of Urology, The Second Hospital of Hebei Medical University, Shijiazhuang 050011, China; (Y.Z.); (Z.H.); (Z.T.); (C.J.); (H.Y.); (K.S.)
| | - Chenggen Jin
- Department of Urology, The Second Hospital of Hebei Medical University, Shijiazhuang 050011, China; (Y.Z.); (Z.H.); (Z.T.); (C.J.); (H.Y.); (K.S.)
| | - Hao Yuan
- Department of Urology, The Second Hospital of Hebei Medical University, Shijiazhuang 050011, China; (Y.Z.); (Z.H.); (Z.T.); (C.J.); (H.Y.); (K.S.)
| | - Sihao Zhang
- Department of Urology, The Second Hospital of Hebei Medical University, Shijiazhuang 050011, China; (Y.Z.); (Z.H.); (Z.T.); (C.J.); (H.Y.); (K.S.)
| | - Kexin Sun
- Department of Urology, The Second Hospital of Hebei Medical University, Shijiazhuang 050011, China; (Y.Z.); (Z.H.); (Z.T.); (C.J.); (H.Y.); (K.S.)
| | - Yaxuan Wang
- Department of Urology, The Second Hospital of Hebei Medical University, Shijiazhuang 050011, China; (Y.Z.); (Z.H.); (Z.T.); (C.J.); (H.Y.); (K.S.)
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5
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Basanta CDLAC, Bazzi M, Hijazi M, Bessant C, Cutillas PR. Community detection in empirical kinase networks identifies new potential members of signalling pathways. PLoS Comput Biol 2023; 19:e1010459. [PMID: 37352361 PMCID: PMC10325051 DOI: 10.1371/journal.pcbi.1010459] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 07/06/2023] [Accepted: 06/05/2023] [Indexed: 06/25/2023] Open
Abstract
Phosphoproteomics allows one to measure the activity of kinases that drive the fluxes of signal transduction pathways involved in biological processes such as immune function, senescence and cell growth. However, deriving knowledge of signalling network circuitry from these data is challenging due to a scarcity of phosphorylation sites that define kinase-kinase relationships. To address this issue, we previously identified around 6,000 phosphorylation sites as markers of kinase-kinase relationships (that may be conceptualised as network edges), from which empirical cell-model-specific weighted kinase networks may be reconstructed. Here, we assess whether the application of community detection algorithms to such networks can identify new components linked to canonical signalling pathways. Phosphoproteomics data from acute myeloid leukaemia (AML) cells treated separately with PI3K, AKT, MEK and ERK inhibitors were used to reconstruct individual kinase networks. We used modularity maximisation to detect communities in each network, and selected the community containing the main target of the inhibitor used to treat cells. These analyses returned communities that contained known canonical signalling components. Interestingly, in addition to canonical PI3K/AKT/mTOR members, the community assignments returned TTK (also known as MPS1) as a likely component of PI3K/AKT/mTOR signalling. We drew similar insights from an external phosphoproteomics dataset from breast cancer cells treated with rapamycin and oestrogen. We confirmed this observation with wet-lab laboratory experiments showing that TTK phosphorylation was decreased in AML cells treated with AKT and MTOR inhibitors. This study illustrates the application of community detection algorithms to the analysis of empirical kinase networks to uncover new members linked to canonical signalling pathways.
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Affiliation(s)
- Celia De Los Angeles Colomina Basanta
- Cell signaling and Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Marya Bazzi
- Warwick Mathematics Institute, University of Warwick, Coventry, United Kingdom
- The Alan Turing Institute, London, United Kingdom
| | - Maruan Hijazi
- Cell signaling and Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Conrad Bessant
- The Alan Turing Institute, London, United Kingdom
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Pedro R. Cutillas
- Cell signaling and Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
- The Alan Turing Institute, London, United Kingdom
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6
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Wilson BAP, Li N, Martinez Fiesco JA, Dalilian M, Wang D, Smith EA, Wamiru A, Shah R, Goncharova EI, Beutler JA, Grkovic T, Zhang P, O’Keefe BR. Biochemical Discovery, Intracellular Evaluation, and Crystallographic Characterization of Synthetic and Natural Product Adenosine 3',5'-Cyclic Monophosphate-Dependent Protein Kinase A (PKA) Inhibitors. ACS Pharmacol Transl Sci 2023; 6:633-650. [PMID: 37082750 PMCID: PMC10111623 DOI: 10.1021/acsptsci.3c00010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Indexed: 04/22/2023]
Abstract
The recent demonstration that adenosine 3',5'-cyclic monophosphate (cAMP)-dependent protein kinase A (PKA) plays an oncogenic role in a number of important cancers has led to a renaissance in drug development interest targeting this kinase. We therefore have established a suite of biochemical, cell-based, and structural biology assays for identifying and evaluating new pharmacophores for PKA inhibition. This discovery process started with a 384-well high-throughput screen of more than 200,000 substances, including fractionated natural product extracts. Identified active compounds were further prioritized in biochemical, biophysical, and cell-based assays. Priority lead compounds were assessed in detail to fully characterize several previously unrecognized PKA pharmacophores including the generation of new X-ray crystallography structures demonstrating unique interactions between PKA and bound inhibitor molecules.
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Affiliation(s)
- Brice A. P. Wilson
- Molecular
Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Ning Li
- Center
for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Juliana A. Martinez Fiesco
- Center
for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Masoumeh Dalilian
- Molecular
Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
- Basic
Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Dongdong Wang
- Molecular
Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Emily A. Smith
- Molecular
Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
- Basic
Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Antony Wamiru
- Molecular
Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
- Basic
Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Rohan Shah
- Molecular
Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Ekaterina I. Goncharova
- Molecular
Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
- Advanced
Biomedical Computational Science, Frederick
National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - John A. Beutler
- Molecular
Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Tanja Grkovic
- Molecular
Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
- Natural
Products Branch, Developmental Therapeutics Program, Division of Cancer
Treatment and Diagnosis, National Cancer
Institute, Frederick, Maryland 21702, United States
| | - Ping Zhang
- Center
for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Barry R. O’Keefe
- Molecular
Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
- Natural
Products Branch, Developmental Therapeutics Program, Division of Cancer
Treatment and Diagnosis, National Cancer
Institute, Frederick, Maryland 21702, United States
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7
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Rational combinations of targeted cancer therapies: background, advances and challenges. Nat Rev Drug Discov 2023; 22:213-234. [PMID: 36509911 DOI: 10.1038/s41573-022-00615-z] [Citation(s) in RCA: 72] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2022] [Indexed: 12/15/2022]
Abstract
Over the past two decades, elucidation of the genetic defects that underlie cancer has resulted in a plethora of novel targeted cancer drugs. Although these agents can initially be highly effective, resistance to single-agent therapies remains a major challenge. Combining drugs can help avoid resistance, but the number of possible drug combinations vastly exceeds what can be tested clinically, both financially and in terms of patient availability. Rational drug combinations based on a deep understanding of the underlying molecular mechanisms associated with therapy resistance are potentially powerful in the treatment of cancer. Here, we discuss the mechanisms of resistance to targeted therapies and how effective drug combinations can be identified to combat resistance. The challenges in clinically developing these combinations and future perspectives are considered.
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8
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Tomkova M, Tomek J, Chow J, McPherson JD, Segal DJ, Hormozdiari F. Dr.Nod: computational framework for discovery of regulatory non-coding drivers in tissue-matched distal regulatory elements. Nucleic Acids Res 2023; 51:e23. [PMID: 36625266 PMCID: PMC9976879 DOI: 10.1093/nar/gkac1251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 12/07/2022] [Accepted: 12/19/2022] [Indexed: 01/11/2023] Open
Abstract
The discovery of cancer driver mutations is a fundamental goal in cancer research. While many cancer driver mutations have been discovered in the protein-coding genome, research into potential cancer drivers in the non-coding regions showed limited success so far. Here, we present a novel comprehensive framework Dr.Nod for detection of non-coding cis-regulatory candidate driver mutations that are associated with dysregulated gene expression using tissue-matched enhancer-gene annotations. Applying the framework to data from over 1500 tumours across eight tissues revealed a 4.4-fold enrichment of candidate driver mutations in regulatory regions of known cancer driver genes. An overarching conclusion that emerges is that the non-coding driver mutations contribute to cancer by significantly altering transcription factor binding sites, leading to upregulation of tissue-matched oncogenes and down-regulation of tumour-suppressor genes. Interestingly, more than half of the detected cancer-promoting non-coding regulatory driver mutations are over 20 kb distant from the cancer-associated genes they regulate. Our results show the importance of tissue-matched enhancer-gene maps, functional impact of mutations, and complex background mutagenesis model for the prediction of non-coding regulatory drivers. In conclusion, our study demonstrates that non-coding mutations in enhancers play a previously underappreciated role in cancer and dysregulation of clinically relevant target genes.
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Affiliation(s)
- Marketa Tomkova
- Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA.,Ludwig Cancer Research, University of Oxford, Oxford, OX3 7DQ, UK.,UC Davis Genome Center, University of California, Davis, CA 95616, USA
| | - Jakub Tomek
- Department of Pharmacology, University of California, Davis, CA 95616, USA
| | - Julie Chow
- Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA
| | - John D McPherson
- Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA
| | - David J Segal
- Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA.,UC Davis Genome Center, University of California, Davis, CA 95616, USA.,UC Davis MIND Institute, University of California, Davis, CA 95616, USA
| | - Fereydoun Hormozdiari
- Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA.,UC Davis Genome Center, University of California, Davis, CA 95616, USA.,UC Davis MIND Institute, University of California, Davis, CA 95616, USA
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9
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Zhang C, Wu S, Chen B. A novel prognostic model based on pyroptosis-related genes for multiple myeloma. BMC Med Genomics 2023; 16:32. [PMID: 36823654 PMCID: PMC9948482 DOI: 10.1186/s12920-023-01455-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 02/11/2023] [Indexed: 02/25/2023] Open
Abstract
BACKGROUND Multiple myeloma (MM) is an incurable and relapse-prone disease with apparently prognostic heterogeneity. At present, the risk stratification of myeloma is still incomplete. Pyroptosis, a type of programmed cell death, has been shown to regulate tumor growth and may have potential prognostic value. However, the role of pyroptosis-related genes (PRGs) in MM remains undetermined. The aims of this study were to identify potential prognostic biomarkers and to construct a predictive model related to PRGs. METHODS Sequencing and clinical data were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Non-negative matrix factorization (NMF) was performed to identify molecular subtype screening. LASSO regression was used to screen for prognostic markers, and then a risk score model was constructed. The Maxstat package was utilized to calculate the optimal cutoff value, according to which patients were divided into a high-risk group and a low-risk group, and the survival curves were plotted using the Kaplan-Meier (K-M) method. Nomograms and calibration curves were established using the rms package. RESULTS A total of 33 PRGs were extracted from the TCGA database underlying which 4 MM molecular subtypes were defined. Patients in cluster 1 had poorer survival than those in cluster 2 (p = 0.035). A total of 9 PRGs were screened out as prognostic markers, and the predictive ability of the 9-gene risk score for 3-year survival was best (AUC = 0.658). Patients in the high-risk group had worse survival than those in the low-risk group (p < 0.001), which was consistent with the results verified by the GSE2658 dataset. The nomogram constructed by gender, age, International Staging System (ISS) stage, and risk score had the best prognostic predictive performance with a c-index of 0.721. CONCLUSION Our model could enhance the predictive ability of ISS staging and give a reference for clinical decision-making. The new, prognostic, and pyroptosis-related markers screened out by us may facilitate the development of novel risk stratification for MM. CLINICAL TRIAL REGISTRATION Not applicable.
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Affiliation(s)
- Cuiling Zhang
- grid.41156.370000 0001 2314 964XDepartment of Hematology, Affiliated Drum Tower Hospital, Medical School of Nanjing University, 210008 Nanjing, People’s Republic of China
| | - Sungui Wu
- grid.410745.30000 0004 1765 1045Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, 210023 Nanjing, People’s Republic of China
| | - Bing Chen
- Department of Hematology, Affiliated Drum Tower Hospital, Medical School of Nanjing University, 210008, Nanjing, People's Republic of China. .,Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, 210023, Nanjing, People's Republic of China.
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10
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Correlation analysis of lipid metabolism genes with the immune microenvironment in gastric cancer and the construction of a novel gene signature. Clin Transl Oncol 2022; 25:1315-1331. [PMID: 36520384 DOI: 10.1007/s12094-022-03038-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/25/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND Lipid metabolism reprogramming plays an important role in cell growth, proliferation, angiogenesis and invasion of cancer. However, the prognostic value of lipid metabolism during gastric cancer (GC) progression and the relationship with the immune microenvironment are still unclear. The aim of this study was to clarify the correlation between lipid metabolism genes and GC immunity. METHOD We obtained 350 patients from The Cancer Genome Atlas (TCGA) and 355 patients from Gene Expression Omnibus (GEO) databases. Lipid metabolism-related gene datasets were obtained from the Reactome and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Molecular subtypes were obtained by Consensus clustering, and subtype immune status was analyzed using ESTIMATE, TIMER and microenvironmental cell population counter (MCP Counter) algorithm for immune analysis. Functional analyses included the application of Gene Set Enrichment Analysis (GSEA), KEGG, gene ontology (GO), and Protein-Protein Interaction Networks (PPI) to evaluate the molecular mechanisms of different subtypes. Weighted gene co-expression network analysis (WGCNA) was used to identify genes associated with immunity. The LASSO algorithm and multivariate Cox regression analysis were used to construct prognostic risk models. RESULT Based on the lipid metabolism genes found in GC, patients with GC can be divided into two subgroups with significantly different survival. The subgroup with a better prognosis presented higher immune scores and immune infiltrating cell abundance. 1170 immune-related genes were screened by WGCNA, and further screening by PPI network analysis revealed that PTPRC, CD4, ITGB2 and LCP2 were closely associated with immune cells. Combined with the TIDE score results, it was found that the population with high expression of the above genes might be more sensitive to immunotherapy. In addition, a survival prediction model for GC was developed based on five survival-related lipid metabolism genes, PIAS4, PLA2R1, PRKACA, SLCO1A2 and STARD4. The ROC analysis over time showed that the risk prediction score model had good stability. CONCLUSION Lipid metabolism gene expression is correlated with the immune microenvironment in GC patients and can accurately predict their prognosis. Studies on lipid metabolism and GC immunity can help to screen the population for immunotherapy benefits.
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11
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Masood M, Masood MBE, Us Subah N, Shabbir M, Paracha RZ, Rafiq M. Investigating isoform switching in RHBDF2 and its role in neoplastic growth in breast cancer. PeerJ 2022; 10:e14124. [PMID: 36452073 PMCID: PMC9703992 DOI: 10.7717/peerj.14124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 09/06/2022] [Indexed: 11/27/2022] Open
Abstract
Background Breast cancer is the second leading cause of cancer-related deaths globally, and its prevalence rates are increasing daily. In the past, studies predicting therapeutic drug targets for cancer therapy focused on the assumption that one gene is responsible for producing one protein. Therefore, there is always an immense need to find promising and novel anti-cancer drug targets. Furthermore, proteases have an integral role in cell proliferation and growth because the proteolysis mechanism is an irreversible process that aids in regulating cellular growth during tumorigenesis. Therefore, an inactive rhomboid protease known as iRhom2 encoded by the gene RHBDF2 can be considered an important target for cancer treatment. Speculatively, previous studies on gene expression analysis of RHBDF2 showed heterogenous behaviour during tumorigenesis. Consistent with this, several studies have reported the antagonistic role of iRhom2 in tumorigenesis, i.e., either they are involved in negative regulation of EGFR ligands via the ERAD pathway or positively regulate EGFR ligands via the EGFR signalling pathway. Additionally, different opinions suggest iRhom2 mediated cleavage of EGFR ligands takes place TACE dependently or TACE independently. However, reconciling these seemingly opposing roles is still unclear and might be attributed to more than one transcript isoform of iRhom2. Methods To observe the differences at isoform resolution, the current strategy identified isoform switching in RHBDF2 via differential transcript usage using RNA-seq data during breast cancer initiation and progression. Furthermore, interacting partners were found via correlation and enriched to explain their antagonistic role. Results Isoform switching was observed at DCIS, grade 2 and grade 3, from canonical to the cub isoform. Neither EGFR nor ERAD was found enriched. However, pathways leading to TACE-dependent EGFR signalling pathways were more observant, specifically MAPK signalling pathways, GPCR signalling pathways, and toll-like receptor pathways. Nevertheless, it was noteworthy that during CTCs, the cub isoform switches back to the canonical isoform, and the proteasomal degradation pathway and cytoplasmic ribosomal protein pathways were significantly enriched. Therefore, it could be inferred that cub isoform functions during cancer initiation in EGFR signalling. In contrast, during metastasis, where invasion is the primary task, the isoform switches back to the canonical isoform.
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Affiliation(s)
- Mehar Masood
- School of Interdisciplinary Engineering and Sciences, National University of Sciences and Technology, Islamabad, Pakistan,Faculty of Rehabilitation & Allied Health Sciences, Riphah International University, Islamabad, Pakistan
| | - Madahiah Bint E Masood
- School of Interdisciplinary Engineering and Sciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Noor Us Subah
- School of Interdisciplinary Engineering and Sciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Maria Shabbir
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Rehan Zafar Paracha
- School of Interdisciplinary Engineering and Sciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Mehak Rafiq
- School of Interdisciplinary Engineering and Sciences, National University of Sciences and Technology, Islamabad, Pakistan
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12
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Schalm SS, O’Hearn E, Wilson K, LaBranche TP, Silva G, Zhang Z, DiPietro L, Bifulco N, Woessner R, Stransky N, Sappal D, Campbell R, Lobbardi R, Palmer M, Kim J, Ye C, Dorsch M, Lengauer C, Guzi T, Kadambi V, Garner A, Hoeflich KP. Evaluation of Protein Kinase cAMP-Activated Catalytic Subunit Alpha as a Therapeutic Target for Fibrolamellar Carcinoma. GASTRO HEP ADVANCES 2022; 2:307-321. [PMID: 39132655 PMCID: PMC11307690 DOI: 10.1016/j.gastha.2022.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 11/02/2022] [Indexed: 08/13/2024]
Abstract
Background and Aims Fibrolamellar carcinoma (FLC) is a rare, difficult-to-treat liver cancer primarily affecting pediatric and adolescent patients, and for which precision medicine approaches have historically not been possible. The DNAJB1-PRKACA gene fusion was identified as a driver of FLC pathogenesis. We aimed to assess whether FLC tumors maintain dependency on this gene fusion and determine if PRKACA is a viable therapeutic target. Methods FLC patient-derived xenograft (PDX) shRNA cell lines were implanted subcutaneously into female NOD-SCID mice and tumors were allowed to develop prior to randomization to doxycycline (to induce knockdown) or control groups. Tumor development was assessed every 2 days. To assess the effect of treatment with novel selective PRKACA small molecule kinase inhibitors, BLU0588 and BLU2864, FLC PDX tumor cells were implanted subcutaneously into NOD-SCID mice and tumors allowed to develop. Mice were randomized to treatment (BLU0588 and BLU2864, orally, once daily) or control groups and tumor size determined as previously. Results Knockdown of DNAJB1-PRKACA reversed a FLC-specific gene signature and reduced PDX tumor growth in mice compared to the control group. Furthermore, FLC PDX tumor growth was significantly reduced with BLU0588 and BLU2864 treatment vs control (P = .003 and P = .0005, respectively). Conclusion We demonstrated, using an inducible knockdown and small molecule approaches, that FLC PDX tumors were dependent upon DNAJB1-PRKACA fusion activity. In addition, this study serves as a proof-of-concept that PRKACA is a viable therapeutic target for FLC and warrants further investigation.
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Affiliation(s)
| | - Erin O’Hearn
- Blueprint Medicines Corporation, Cambridge, Massachusetts
| | - Kevin Wilson
- Blueprint Medicines Corporation, Cambridge, Massachusetts
| | | | - Grace Silva
- Blueprint Medicines Corporation, Cambridge, Massachusetts
| | - Zhuo Zhang
- Blueprint Medicines Corporation, Cambridge, Massachusetts
| | | | - Neil Bifulco
- Blueprint Medicines Corporation, Cambridge, Massachusetts
| | | | | | - Darshan Sappal
- Blueprint Medicines Corporation, Cambridge, Massachusetts
| | | | - Riadh Lobbardi
- Blueprint Medicines Corporation, Cambridge, Massachusetts
| | - Michael Palmer
- Blueprint Medicines Corporation, Cambridge, Massachusetts
| | - Joseph Kim
- Blueprint Medicines Corporation, Cambridge, Massachusetts
| | - Chaoyang Ye
- Blueprint Medicines Corporation, Cambridge, Massachusetts
| | - Marion Dorsch
- Blueprint Medicines Corporation, Cambridge, Massachusetts
| | | | - Timothy Guzi
- Blueprint Medicines Corporation, Cambridge, Massachusetts
| | - Vivek Kadambi
- Blueprint Medicines Corporation, Cambridge, Massachusetts
| | - Andrew Garner
- Blueprint Medicines Corporation, Cambridge, Massachusetts
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13
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Furrer D, Dragic D, Chang SL, Fournier F, Droit A, Jacob S, Diorio C. Association between genome-wide epigenetic and genetic alterations in breast cancer tissue and response to HER2-targeted therapies in HER2-positive breast cancer patients: new findings and a systematic review. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2022; 5:995-1015. [PMID: 36627894 PMCID: PMC9771759 DOI: 10.20517/cdr.2022.63] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 08/25/2022] [Accepted: 10/08/2022] [Indexed: 01/12/2023]
Abstract
Recent evidence suggests that genetic and epigenetic mechanisms might be associated with acquired resistance to cancer therapies. The aim of this study was to assess the association of genome-wide genetic and epigenetic alterations with the response to anti-HER2 agents in HER2-positive breast cancer patients. PubMed was screened for articles published until March 2021 on observational studies investigating the association of genome-wide genetic and epigenetic alterations, measured in breast cancer tissues or blood, with the response to targeted treatment in HER2-positive breast cancer patients. Sixteen studies were included in the review along with ours, in which we compared the genome-wide DNA methylation pattern in breast tumor tissues of patients who acquired resistance to treatment (case group, n = 6) to that of patients who did not develop resistance (control group, n = 6). Among genes identified as differentially methylated between the breast cancer tissue of cases and controls, one of them, PRKACA, was also reported as differentially expressed in two studies included in the review. Although included studies were heterogeneous in terms of methodology and study population, our review suggests that genes of the PI3K pathway may play an important role in developing resistance to anti-HER2 agents in breast cancer patients. Genome-wide genetic and epigenetic alterations measured in breast cancer tissue or blood might be promising markers of resistance to anti-HER2 agents in HER2-positive breast cancer patients. Further studies are needed to confirm these data.
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Affiliation(s)
- Daniela Furrer
- Centre de Recherche sur le cancer de l’Université Laval, 1050 Avenue de la Médecine, Québec, QC G1V 0A6, Canada.,Axe Oncologie, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1S 4L8, Canada. ,Département de médecine sociale et préventive, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada
| | - Dzevka Dragic
- Centre de Recherche sur le cancer de l’Université Laval, 1050 Avenue de la Médecine, Québec, QC G1V 0A6, Canada.,Axe Oncologie, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1S 4L8, Canada. ,Département de médecine sociale et préventive, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada.,Université Paris-Saclay, UVSQ, Inserm, CESP U1018, Exposome and Heredity Team, Gustave Roussy, Villejuif 94807, France
| | - Sue-Ling Chang
- Centre de Recherche sur le cancer de l’Université Laval, 1050 Avenue de la Médecine, Québec, QC G1V 0A6, Canada.,Axe Oncologie, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1S 4L8, Canada
| | - Frédéric Fournier
- Centre de Recherche sur le cancer de l’Université Laval, 1050 Avenue de la Médecine, Québec, QC G1V 0A6, Canada.,Axe Oncologie, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1S 4L8, Canada. ,Département de médecine moléculaire, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada
| | - Arnaud Droit
- Centre de Recherche sur le cancer de l’Université Laval, 1050 Avenue de la Médecine, Québec, QC G1V 0A6, Canada.,Axe Oncologie, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1S 4L8, Canada. ,Département de médecine moléculaire, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada
| | - Simon Jacob
- Centre de Recherche sur le cancer de l’Université Laval, 1050 Avenue de la Médecine, Québec, QC G1V 0A6, Canada.,Axe Oncologie, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1S 4L8, Canada. ,Département de biologie moléculaire, de biochimie médicale et de pathologie, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada.,Centre des Maladies du Sein, Hôpital du Saint-Sacrement, Québec, QC G1S 4L8, Canada
| | - Caroline Diorio
- Centre de Recherche sur le cancer de l’Université Laval, 1050 Avenue de la Médecine, Québec, QC G1V 0A6, Canada.,Axe Oncologie, Centre de Recherche du CHU de Québec-Université Laval, Québec, QC G1S 4L8, Canada. ,Département de médecine sociale et préventive, Faculté de Médecine, Université Laval, Québec, QC G1V 0A6, Canada.,Centre des Maladies du Sein, Hôpital du Saint-Sacrement, Québec, QC G1S 4L8, Canada.,Correspondence to: Prof. Caroline Diorio, Axe Oncologie, Centre de Recherche du CHU de Québec-Université Laval, 1050 chemin Ste-Foy, Québec, QC G1S 4L8, Canada. E-mail:
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Ramamoorthi G, Kodumudi K, Snyder C, Grover P, Zhang H, Greene MI, Basu A, Gallen C, Wiener D, Costa RLB, Han HS, Koski G, Czerniecki BJ. Intratumoral delivery of dendritic cells plus anti-HER2 therapy triggers both robust systemic antitumor immunity and complete regression in HER2 mammary carcinoma. J Immunother Cancer 2022; 10:jitc-2022-004841. [PMID: 35710296 PMCID: PMC9204433 DOI: 10.1136/jitc-2022-004841] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/31/2022] [Indexed: 11/23/2022] Open
Abstract
Background Human epidermal growth factor receptor 2 (HER2) targeted antibodies in combination with chemotherapy has improved outcomes of HER2 positive (pos) breast cancer (BC) but toxicity of therapy remains a problem. High levels of tumor-infiltrating lymphocytes are associated with increased pathologic complete responses for patients treated with neoadjuvant therapy. Here we sought to investigate whether delivery of intratumoral (i.t.) multiepitope major histocompatibility complex (MHC) class II HER2 peptides-pulsed type I polarized dendritic cells (HER2-DC1) in combination with anti-HER2 antibodies without chemotherapy could enhance tumor regression by increasing anti-HER2 lymphocyte infiltration into the tumor. Methods BALB/c mice bearing orthotopic TUBO tumors, BALB/c mice bearing subcutaneous (s.c.) CT26 hHER2 tumors, or BALB-HER2/neu transgenic mice were all treated with i.t. or s.c. HER2-DC1, anti-HER2 antibodies, paclitaxel, T-DM1 or in combination. Immune response, host immune cells and effector function were analyzed using flow cytometry, interferon-γ ELISA and cytokine/chemokine arrays. The contributions of CD4+ and CD8+ T cells and antibody dependent cellular cytotoxicity (ADCC) were assessed using depleting antibodies and FcγR KO mice. Molecular changes were evaluated by immunohistochemistry and western blot. Results HER2-DC1 combined with anti-HER2 antibodies delivered i.t. compared to s.c. induced complete tumor regression in 75–80% of treated mice, with increased tumor infiltrating CD4+ and CD8+ T, B, natural killer T cells (NKT) and natural killer cells, and strong anti-HER2 responses in all HER2pos BC models tested. The therapy caused regression of untreated distant tumors. Labeled HER2-DC1 migrated prominently into the distant tumor and induced infiltration of various DC subsets into tumors. HER2-DC1 i.t. combined with anti-HER2 antibodies displayed superior antitumor response compared to standard chemotherapy with anti-HER2 antibodies. Lasting immunity was attained which prevented secondary tumor formation. The presence of CD4+ and CD8+ T cells and ADCC were required for complete tumor regression. In the HER2pos BC models, HER2-DC1 i.t. combined with anti-HER2 antibodies effectively diminished activation of HER2-mediated oncogenic signaling pathways. Conclusions HER2-DC1 i.t. with anti-HER2 antibodies mediates tumor regression through combined activation of T and B cell compartments and provides evidence that HER2-DC1 i.t. in combination with anti-HER2 antibodies can be tested as an effective alternative therapeutic strategy to current chemotherapy and anti-HER2 antibodies in HER2pos BC.
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Affiliation(s)
- Ganesan Ramamoorthi
- Clinical Science & Immunology Program, Moffitt Cancer Center, Tampa, Florida, USA
| | - Krithika Kodumudi
- Clinical Science & Immunology Program, Moffitt Cancer Center, Tampa, Florida, USA
| | - Colin Snyder
- Clinical Science & Immunology Program, Moffitt Cancer Center, Tampa, Florida, USA
| | - Payal Grover
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Hongtao Zhang
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Mark I Greene
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Amrita Basu
- Clinical Science & Immunology Program, Moffitt Cancer Center, Tampa, Florida, USA
| | - Corey Gallen
- Clinical Science & Immunology Program, Moffitt Cancer Center, Tampa, Florida, USA
| | - Doris Wiener
- Clinical Science & Immunology Program, Moffitt Cancer Center, Tampa, Florida, USA
| | - Ricardo L B Costa
- Department of Breast Oncology, Moffitt Cancer Center, Tampa, Florida, USA
| | - Hyo S Han
- Department of Breast Oncology, Moffitt Cancer Center, Tampa, Florida, USA
| | - Gary Koski
- Biological Sciences, Kent State University, Kent, Ohio, USA
| | - Brian J Czerniecki
- Clinical Science & Immunology Program, Moffitt Cancer Center, Tampa, Florida, USA .,Department of Breast Oncology, Moffitt Cancer Center, Tampa, Florida, USA
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15
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A Novel Classification Model for Lower-Grade Glioma Patients Based on Pyroptosis-Related Genes. Brain Sci 2022; 12:brainsci12060700. [PMID: 35741587 PMCID: PMC9221219 DOI: 10.3390/brainsci12060700] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/13/2022] [Accepted: 05/23/2022] [Indexed: 02/06/2023] Open
Abstract
Recent studies demonstrated that pyroptosis plays a crucial role in shaping the tumor-immune microenvironment. However, the influence of pyroptosis on lower-grade glioma regarding immunotherapy and targeted therapy is still unknown. This study analyzed the variations of 33 pyroptosis-related genes in lower-grade glioma and normal tissues. Our study found considerable genetic and expression alterations in heterogeneity among lower-grade gliomas and normal brain tissues. There are two pyroptosis phenotypes in lower-grade glioma, and they exhibited differences in cell infiltration characteristics and clinical characters. Then, a PyroScore model using the lasso-cox method was constructed to measure the level of pyroptosis in each patient. PyroScore can refine the lower-grade glioma patients with a stratified prognosis and a distinct tumor immune microenvironment. Pyscore may also be an effective factor in predicting potential therapeutic benefits. In silico analysis showed that patients with a lower PyroScore are expected to be more sensitive to targeted therapy and immunotherapy. These findings may enhance our understanding of pyroptosis in lower-grade glioma and might help optimize risk stratification for the survival and personalized management of lower-grade glioma patients.
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16
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Gong Z, Li Q, Yang J, Zhang P, Sun W, Ren Q, Tang J, Wang W, Gong H, Li J. Identification of a Pyroptosis-Related Gene Signature for Predicting the Immune Status and Prognosis in Lung Adenocarcinoma. Front Bioeng Biotechnol 2022; 10:852734. [PMID: 35646872 PMCID: PMC9133407 DOI: 10.3389/fbioe.2022.852734] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/14/2022] [Indexed: 12/14/2022] Open
Abstract
Background: Pyroptosis is a form of programmed cell death triggered by the rupture of cell membranes and the release of inflammatory substances; it is essential in the occurrence and development of cancer. A considerable number of studies have revealed that pyroptosis is closely associated to the biological process of several cancers. However, the role of pyroptosis in lung adenocarcinoma (LUAD) remains elusive. The purpose of this study was to explore the prognostic role of pyroptosis-related genes (PRGs) and their relationship with the tumor immune microenvironment (TIME) in LUAD.Methods: Gene expression profiles and clinical information were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. A prognostic PRG signature was established in the training set and verified in the validation sets. Functional enrichment and immune microenvironment analyses related to PRGs were performed and a nomogram based on the risk score and clinical characteristics was established. What is more, quantitative real-time PCR (qRT-PCR) analysis was applied in order to verify the potential biomarkers for LUAD.Results: A prognostic signature based on five PRGs was constructed to separate LUAD patients into two risk groups. Patients in the high-risk group had worse prognoses than those in the low-risk group. The signature was identified as independent via Cox regression analyses and obtained the largest area under the curve (AUC = 0.677) in the receiver operating characteristic (ROC). Functional enrichment and immune microenvironment analyses demonstrated that the immune status was significantly different in the two subgroups and that immunotherapy may be effective for the high-risk group. Furthermore, qRT-PCR analysis verified that serum PRKACA and GPX4 could serve as diagnostic biomarkers for LUAD.Conclusion: Overall, a risk signature based on five PRGs was generated, providing a novel perspective on the determinants of prognosis and survival in LUAD, as well as a basis for the development of individualized regimes.
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Affiliation(s)
- Zetian Gong
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qifan Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jian Yang
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Pengpeng Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wei Sun
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qianhe Ren
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Junjie Tang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wei Wang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- *Correspondence: Wei Wang, ; Hui Gong, ; Jun Li,
| | - Hui Gong
- Department of Trauma Center, Affiliated Hospital of Nantong University, Nantong, China
- *Correspondence: Wei Wang, ; Hui Gong, ; Jun Li,
| | - Jun Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- *Correspondence: Wei Wang, ; Hui Gong, ; Jun Li,
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17
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Chang CA, Jen J, Jiang S, Sayad A, Mer AS, Brown KR, Nixon AM, Dhabaria A, Tang KH, Venet D, Sotiriou C, Deng J, Wong KK, Adams S, Meyn P, Heguy A, Skok JA, Tsirigos A, Ueberheide B, Moffat J, Singh A, Haibe-Kains B, Khodadadi-Jamayran A, Neel BG. Ontogeny and Vulnerabilities of Drug-Tolerant Persisters in HER2+ Breast Cancer. Cancer Discov 2022; 12:1022-1045. [PMID: 34911733 PMCID: PMC8983469 DOI: 10.1158/2159-8290.cd-20-1265] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/14/2021] [Accepted: 12/10/2021] [Indexed: 11/16/2022]
Abstract
Resistance to targeted therapies is an important clinical problem in HER2-positive (HER2+) breast cancer. "Drug-tolerant persisters" (DTP), a subpopulation of cancer cells that survive via reversible, nongenetic mechanisms, are implicated in resistance to tyrosine kinase inhibitors (TKI) in other malignancies, but DTPs following HER2 TKI exposure have not been well characterized. We found that HER2 TKIs evoke DTPs with a luminal-like or a mesenchymal-like transcriptome. Lentiviral barcoding/single-cell RNA sequencing reveals that HER2+ breast cancer cells cycle stochastically through a "pre-DTP" state, characterized by a G0-like expression signature and enriched for diapause and/or senescence genes. Trajectory analysis/cell sorting shows that pre-DTPs preferentially yield DTPs upon HER2 TKI exposure. Cells with similar transcriptomes are present in HER2+ breast tumors and are associated with poor TKI response. Finally, biochemical experiments indicate that luminal-like DTPs survive via estrogen receptor-dependent induction of SGK3, leading to rewiring of the PI3K/AKT/mTORC1 pathway to enable AKT-independent mTORC1 activation. SIGNIFICANCE DTPs are implicated in resistance to anticancer therapies, but their ontogeny and vulnerabilities remain unclear. We find that HER2 TKI-DTPs emerge from stochastically arising primed cells ("pre-DTPs") that engage either of two distinct transcriptional programs upon TKI exposure. Our results provide new insights into DTP ontogeny and potential therapeutic vulnerabilities. This article is highlighted in the In This Issue feature, p. 873.
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Affiliation(s)
- Chewei Anderson Chang
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jayu Jen
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA
| | - Shaowen Jiang
- Applied Bioinformatics Laboratories, Office of Science and Research, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA
| | - Azin Sayad
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Arvind Singh Mer
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Kevin R. Brown
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | | | - Avantika Dhabaria
- Proteomics Laboratory, Division of Advanced Research and Technology, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA
| | - Kwan Ho Tang
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA
| | - David Venet
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet Brussels and Université Libre de Bruxelles (ULB), Belgium
| | - Christos Sotiriou
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet Brussels and Université Libre de Bruxelles (ULB), Belgium.,Medical Oncology Department, Institut Jules Bordet Brussels and Université Libre de Bruxelles (ULB), Belgium
| | - Jiehue Deng
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA.,Division of Hematology and Medical Oncology, Department of Medicine, Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA
| | - Kwok-kin Wong
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA.,Division of Hematology and Medical Oncology, Department of Medicine, Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA
| | - Sylvia Adams
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA.,Division of Hematology and Medical Oncology, Department of Medicine, Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA
| | - Peter Meyn
- Genome Technology Center, Division of Advanced Research Technologies, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA
| | - Adriana Heguy
- Genome Technology Center, Division of Advanced Research Technologies, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA
| | - Jane A. Skok
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA.,Department of Pathology, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA
| | - Aristotelis Tsirigos
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA.,Applied Bioinformatics Laboratories, Office of Science and Research, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA.,Department of Pathology, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA
| | - Beatrix Ueberheide
- Proteomics Laboratory, Division of Advanced Research and Technology, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA
| | - Jason Moffat
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, Delaware, USA.,Department of Biomedical Engineering, University of Delaware, Newark, Delaware, USA
| | - Benjamin Haibe-Kains
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.,Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Vector Institute for Artificial Intelligence, Toronto, Ontario, Canada
| | - Alireza Khodadadi-Jamayran
- Applied Bioinformatics Laboratories, Office of Science and Research, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA
| | - Benjamin G. Neel
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA.,Division of Hematology and Medical Oncology, Department of Medicine, Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA
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18
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Feng L, Tian R, Mu X, Chen C, Zhang Y, Cui J, Song Y, Liu Y, Zhang M, Shi L, Sun Y, Li L, Yi W. Identification of Genes Linking Natural Killer Cells to Apoptosis in Acute Myocardial Infarction and Ischemic Stroke. Front Immunol 2022; 13:817377. [PMID: 35432334 PMCID: PMC9012496 DOI: 10.3389/fimmu.2022.817377] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 03/11/2022] [Indexed: 12/27/2022] Open
Abstract
Natural killer (NK) cells are a type of innate lymphoid cell that are involved in the progression of acute myocardial infarction and ischemic stroke. Although multiple forms of programmed cell death are known to play important roles in these diseases, the correlation between NK cells and apoptosis-related genes during acute myocardial infarction and ischemic stroke remains unclear. In this study, we explored the distinct patterns of NK cell infiltration and apoptosis during the pathological progression of acute myocardial infarction and ischemic stroke using mRNA expression microarrays from the Gene Expression Omnibus database. Since the abundance of NK cells correlated positively with apoptosis in both diseases, we further examined the correlation between NK cell abundance and the expression of apoptosis-related genes. Interestingly, APAF1 and IRAK3 expression correlated negatively with NK cell abundance in both acute myocardial infarction and ischemic stroke, whereas ATM, CAPN1, IL1B, IL1R1, PRKACA, PRKACB, and TNFRSF1A correlated negatively with NK cell abundance in acute myocardial infarction. Together, these findings suggest that these apoptosis-related genes may play important roles in the mechanisms underlying the patterns of NK cell abundance and apoptosis in acute myocardial infarction and ischemic stroke. Our study, therefore, provides novel insights for the further elucidation of the pathogenic mechanism of ischemic injury in both the heart and the brain, as well as potential useful therapeutic targets.
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Affiliation(s)
- Lele Feng
- Department of Cardiovascular Surgery, Xijing Hospital, The Fourth Military Medical University, Xi’an, China
| | - Ruofei Tian
- National Translational Science Center for Molecular Medicine and Department of Cell Biology, Fourth Military Medical University, Xi’an, China
| | - Xingdou Mu
- Department of Breast and Thyroid Surgery, Xijing Hospital, Fourth Military Medical University, Xi’an, China
| | - Cheng Chen
- Department of Geriatrics, Xijing Hospital, The Fourth Military Medical University, Xi’an, China
- Department of Internal Medicine, Central Health Center of Huilong Town, Shangluo, China
| | - Yuxi Zhang
- Department of Cardiovascular Surgery, Xijing Hospital, The Fourth Military Medical University, Xi’an, China
| | - Jun Cui
- Department of Cardiovascular Surgery, Xijing Hospital, The Fourth Military Medical University, Xi’an, China
| | - Yujie Song
- Department of Cardiovascular Surgery, Xijing Hospital, The Fourth Military Medical University, Xi’an, China
| | - Yingying Liu
- Department of Cardiovascular Surgery, Xijing Hospital, The Fourth Military Medical University, Xi’an, China
- College of Life Science, Northwest University, Xi’an, China
| | - Miao Zhang
- Department of Geriatrics, Xijing Hospital, The Fourth Military Medical University, Xi’an, China
- The Second Clinical Medicine College, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Lei Shi
- Department of Cardiovascular Surgery, Xijing Hospital, The Fourth Military Medical University, Xi’an, China
| | - Yang Sun
- Department of Geriatrics, Xijing Hospital, The Fourth Military Medical University, Xi’an, China
- *Correspondence: Yang Sun, ; Ling Li, ; Wei Yi,
| | - Ling Li
- National Translational Science Center for Molecular Medicine and Department of Cell Biology, Fourth Military Medical University, Xi’an, China
- *Correspondence: Yang Sun, ; Ling Li, ; Wei Yi,
| | - Wei Yi
- Department of Cardiovascular Surgery, Xijing Hospital, The Fourth Military Medical University, Xi’an, China
- *Correspondence: Yang Sun, ; Ling Li, ; Wei Yi,
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19
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Yao J, Hua X, Shi J, Hu X, Lui K, He K, Mai J, Lan T, Lu M. LncRNA THEMIS2-211, a tumor-originated circulating exosomal biomarker, promotes the growth and metastasis of hepatocellular carcinoma by functioning as a competing endogenous RNA. FASEB J 2022; 36:e22238. [PMID: 35224785 DOI: 10.1096/fj.202101564r] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 02/03/2022] [Accepted: 02/16/2022] [Indexed: 12/11/2022]
Abstract
Hepatocellular carcinoma (HCC) is a major challenge for human health. Finding reliable diagnostic biomarkers and therapeutic targets for HCC is highly desired in the clinic. Currently, circulating exosomal lncRNA is a promising biomarker for the diagnosis of cancer and lncRNA is also a potential target in cancer therapy. Here, the diagnostic value of a panel based on exosomal lncRNA THEMIS2-211 and PRKACA-202, superior to that of AFP, was identified for diagnosing human HCC. Besides, the performance of exosomal lncRNA THEMIS2-211 alone exceeds that of AFP in diagnosing early-stage HCC patients (stage I). Furthermore, lncRNA THEMIS2-211 is highly expressed in HCC tissues and correlated with the poor prognosis of HCC patients. LncRNA THEMIS2-211 is upregulated and localized in the cytoplasm of HCC cells. LncRNA THEMIS2-211 exerts its biological function as an oncogene that promotes the proliferation, migration, invasion, EMT of HCC cells by physically interacting with miR-940 and therefore promoting SPOCK1 expressions. Rescue assays show the regulation of SPOCK1 by lncRNA THEMIS2-211 dependents on miR-940. The discovery of lncRNA THEMIS2-211 further illuminates the molecular pathogenesis of HCC and the THEMIS2-211/miR-940/SPOCK1 axis may act as a potential therapeutic target for HCC.
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Affiliation(s)
- Jiyou Yao
- Department of HBP SURGERY II, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, People's Republic of China
| | - Xuefeng Hua
- Department of HBP SURGERY II, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, People's Republic of China
| | - Jiewei Shi
- Department of HBP SURGERY II, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, People's Republic of China
| | - Xiaoyuan Hu
- Department of HBP SURGERY II, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, People's Republic of China
| | - Kayin Lui
- The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Kaitao He
- Department of HBP SURGERY II, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, People's Republic of China
| | - Jialuo Mai
- Department of HBP SURGERY II, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, People's Republic of China
| | - Tian Lan
- Guangdong Metabolic Disease Research Center of Integrated Chinese and Western Medicine, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Minqiang Lu
- Department of HBP SURGERY II, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, People's Republic of China
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20
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Wang Q, Ai Y, Wang C, Liu Y, Zhong H, Yan W, He Y, Deng Z, Zou J, Feng H. PKACα negatively regulates TAK1/IRF7 signaling in black carp Mylopharyngodon piceus. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2022; 127:104306. [PMID: 34736993 DOI: 10.1016/j.dci.2021.104306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/16/2021] [Accepted: 10/29/2021] [Indexed: 06/13/2023]
Abstract
Protein Kinase A catalytic subunit α (PKACα), plays an important role in the PKA and NF-κB signaling pathway in mammals. However, the function of PKACα in teleost fish remains largely unknown. In this study, PKACα from black carp (bcPKACα) has been cloned and its role in the innate immune antiviral signaling pathway was investigated. The open reading frame of bcPKACα gene contains 1056 nucleotides and the immunofluorescence assay verified that PKACα was mainly distributed in the cytoplasm. The reporter assay showed that bcPKACα expression and co-expression of bcPKACα and black carp TAK1 (bcTAK1) could activate the transcription of NF-κB. However, bcTAK1/bcIRF7-mediated IFN transcription was inhibited by bcPKACα. Knockdown of bcPKACα showed slightly enhanced antiviral activity against spring viremia of carp virus (SVCV) compared with control group. Accordingly, the antiviral activity against SVCV and grass carp reovirus (GCRV) of EPC cells co-expressing bcPKACα, bcTAK1 and bcIRF7 was obviously lower than that of EPC cells co-expressing bcTAK1 and bcIRF7. The similar subcellular distribution and interaction between bcPKACα and bcTAK1 were detected by immunofluorescent staining and co-immunoprecipitation assay separately. The data generated in this study demonstrates that bcPKACα associates with bcTAK1 and positively regulates NF-κB signaling, however, negatively regulates TAK1/IRF7 signaling pathway.
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Affiliation(s)
- Qun Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Yue Ai
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Chanyuan Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Yankai Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Huijuan Zhong
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Weiyi Yan
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Yunfan He
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Zhuoyi Deng
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Jun Zou
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Hao Feng
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China.
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21
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Uddin MN, Wang X. Identification of key tumor stroma-associated transcriptional signatures correlated with survival prognosis and tumor progression in breast cancer. Breast Cancer 2022; 29:541-561. [PMID: 35020130 DOI: 10.1007/s12282-022-01332-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 01/05/2022] [Indexed: 12/21/2022]
Abstract
BACKGROUND The aberrant expression of stromal gene signatures in breast cancer has been widely studied. However, the association of stromal gene signatures with tumor immunity, progression, and clinical outcomes remains lacking. METHODS Based on eight breast tumor stroma (BTS) transcriptomics datasets, we identified differentially expressed genes (DEGs) between BTS and normal breast stroma. Based on the DEGs, we identified dysregulated pathways and prognostic hub genes, hub oncogenes, hub protein kinases, and other key marker genes associated with breast cancer. Moreover, we compared the enrichment levels of stromal and immune signatures between breast cancer patients with bad and good clinical outcomes. We also investigated the association between tumor stroma-related genes and breast cancer progression. RESULTS The DEGs included 782 upregulated and 276 downregulated genes in BTS versus normal breast stroma. The pathways significantly associated with the DEGs included cytokine-cytokine receptor interaction, chemokine signaling, T cell receptor signaling, cell adhesion molecules, focal adhesion, and extracellular matrix-receptor interaction. Protein-protein interaction network analysis identified the stromal hub genes with prognostic value in breast cancer, including two oncogenes (COL1A1 and IL21R), two protein kinases encoding genes (PRKACA and CSK), and a growth factor encoding gene (PLAU). Moreover, we observed that the patients with bad clinical outcomes were less enriched in stromal and antitumor immune signatures (CD8 + T cells and tumor-infiltrating lymphocytes) but more enriched in tumor cells and immunosuppressive signatures (MDSCs and CD4 + regulatory T cells) compared with the patients with good clinical outcomes. The ratios of CD8 + /CD4 + regulatory T cells were lower in the patients with bad clinical outcomes. Furthermore, we identified the tumor stroma-related genes, including MCM4, SPECC1, IMPA2, and AGO2, which were gradually upregulated through grade I, II, and III breast cancers. In contrast, COL14A1, ESR1, SLIT2, IGF1, CH25H, PRR5L, ABCA6, CEP126, IGDCC4, LHFP, MFAP3, PCSK5, RAB37, RBMS3, SETBP1, and TSPAN11 were gradually downregulated through grade I, II, and III breast cancers. It suggests that the expression of these stromal genes has an association with the progression of breast cancers. These progression-associated genes also displayed an expression association with recurrence-free survival in breast cancer patients. CONCLUSIONS This study identified tumor stroma-associated biomarkers correlated with deregulated pathways, tumor immunity, tumor progression, and clinical outcomes in breast cancer. Our findings provide new insights into the pathogenesis of breast cancer.
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Affiliation(s)
- Md Nazim Uddin
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
- Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
- Big Data Research Institute, China Pharmaceutical University, Nanjing, 211198, China
- Institute of Food Science and Technology, Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, 1205, Bangladesh
| | - Xiaosheng Wang
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
- Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
- Big Data Research Institute, China Pharmaceutical University, Nanjing, 211198, China.
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22
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Tsirvouli E, Ashcroft F, Johansen B, Kuiper M. Logical and experimental modeling of cytokine and eicosanoid signaling in psoriatic keratinocytes. iScience 2021; 24:103451. [PMID: 34877506 PMCID: PMC8633970 DOI: 10.1016/j.isci.2021.103451] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 10/28/2021] [Accepted: 11/11/2021] [Indexed: 12/11/2022] Open
Abstract
Psoriasis is a chronic skin disease, in which immune cells and keratinocytes keep each other in a state of inflammation. It is believed that phospholipase A2 (PLA2)-dependent eicosanoid release plays a key role in this. T-helper (Th) 1-derived cytokines are established activators of phospholipases in keratinocytes, whereas Th17-derived cytokines have largely unknown effects. Logical model simulations describing the function of cytokine and eicosanoid signaling networks combined with experimental data suggest that Th17 cytokines stimulate proinflammatory cytokine expression in psoriatic keratinocytes via activation of cPLA2α-Prostaglandin E2-EP4 signaling, which could be suppressed using the anti-psoriatic calcipotriol. cPLA2α inhibition and calcipotriol distinctly regulate expression of key psoriatic genes, possibly offering therapeutic advantage when applied together. Model simulations additionally suggest EP4 and protein kinase cAMP-activated catalytic subunit alpha as drug targets that may restore a normal phenotype. Our work illustrates how the study of complex diseases can benefit from an integrated systems approach.
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Affiliation(s)
- Eirini Tsirvouli
- Department of Biology, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Felicity Ashcroft
- Department of Biology, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Berit Johansen
- Department of Biology, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Martin Kuiper
- Department of Biology, Norwegian University of Science and Technology, 7491 Trondheim, Norway
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23
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Chao B, Jiang F, Bai H, Meng P, Wang L, Wang F. Predicting the prognosis of glioma by pyroptosis-related signature. J Cell Mol Med 2021; 26:133-143. [PMID: 34816605 PMCID: PMC8742236 DOI: 10.1111/jcmm.17061] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 10/21/2021] [Accepted: 10/26/2021] [Indexed: 02/04/2023] Open
Abstract
Glioma is the most common malignant primary brain tumour. It is of great significance for the prognosis and personalized treatment of glioma patients to accurate identification of glioma based on biomarkers. Pyroptosis, a kind of programmed cell death, is closely related to tumour progression and tumour immune microenvironment. However, the role of pyroptosis in glioma remained unclear. Herein, we used glioma clinical and expression data from TCGA and CGGA to explore the relationship between pyroptosis and glioma. We first summarized the incidence of copy number variations and somatic mutations of 33 pyroptosis‐related genes and explored prognostic correlation of these genes. Based on pyroptosis‐related genes, three molecular subgroups of glioma related to prognosis were identified. We also found that each subgroup has unique immune and biological behaviours characteristics. Finally, based on 7 pyroptosis‐related genes (CASP3, CASP4, CASP6, CASP8, CASP9, PRKACA and ELANE), we constructed a prognosis model by Lasso and Cox regression, which had a strong predictive power for the overall survival in CGGA test cohort (p < 0.05). In summary, we explored the role of pyroptosis‐related genes in gliomas and the association of these genes with tumour immunity. We found the biomarkers valuable to diagnosis and prognosis, hence, provide reference to the development and treatment of tumorigenesis in glioma.
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Affiliation(s)
- Bo Chao
- Department of Neurosurgery, Affiliated Hospital, Inner Mongolia Medical University, Inner Mongolia, China
| | - Fenjun Jiang
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Huiru Bai
- Basic Medicine college of Inner, Mongolia Medical University, Inner Mongolia, China
| | - Peipei Meng
- Academy of Chinese Medical Sciences, Guang'anmen Hospital, Beijing, China
| | - Lu Wang
- School of International Medical Technology, Shanghai Sanda University, Guang'anmen Hospital, Shanghai, China
| | - Fei Wang
- Department of Neurosurgery, Affiliated Hospital, Inner Mongolia Medical University, Inner Mongolia, China
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24
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Zhou D, Wu Y, Jiang K, Xu F, Hong R, Wang S. Identification of a risk prediction model for clinical prognosis in HER2 positive breast cancer patients. Genomics 2021; 113:4088-4097. [PMID: 34666190 DOI: 10.1016/j.ygeno.2021.10.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 10/03/2021] [Accepted: 10/12/2021] [Indexed: 12/24/2022]
Abstract
Background New biomarkers are needed to identify different clinical outcomes for HER2+ breast cancer (BC). Methods Differential genes of HER2+ BC were screened based on TCGA database. We used WGCNA to identify the genes related to the survival. Genetic Algorithm was used to structure risk prediction model. The prognostic model was validated in GSE data. Results We constructed a risk prediction model of 6 genes to identify prognosis of HER2+ BC, including CLEC9A, PLD4, PIM1, PTK2B, AKNAD1 and C15orf27. Kaplan-Meier curve showed that the model effectively distinguished the survival of HER2+ BC patients. The multivariate Cox regression suggested that the risk model was an independent predictor for HER2+ BC. Analysis related to immune showed that significant differences in immune infiltration between high- and low-risk groups classified by the prognostic model. Conclusions Our study identified a risk prediction model of 6 genes that could distinguish the prognosis of HER2+ BC.
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Affiliation(s)
- Danyang Zhou
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China.
| | - Ying Wu
- Department of Minimally Invasive Interventional Therapy, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China.
| | - Kuikui Jiang
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China.
| | - Fei Xu
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China.
| | - Ruoxi Hong
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China.
| | - Shusen Wang
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China.
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25
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Girimanchanaika SS, Dukanya D, Swamynayaka A, Govindachar DM, Madegowda M, Periyasamy G, Rangappa KS, Pandey V, Lobie PE, Basappa B. Investigation of NPB Analogs That Target Phosphorylation of BAD-Ser99 in Human Mammary Carcinoma Cells. Int J Mol Sci 2021; 22:ijms222011002. [PMID: 34681659 PMCID: PMC8540132 DOI: 10.3390/ijms222011002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 09/26/2021] [Accepted: 09/28/2021] [Indexed: 11/27/2022] Open
Abstract
The design and development of a small molecule named NPB [3-{(4(2,3-dichlorophenyl)piperazin-1-yl}{2-hydroxyphenyl)methyl}-N-cyclopentylbenzamide], which specifically inhibited the phosphorylation of BAD at Ser99 in human carcinoma cells has been previously reported. Herein, the synthesis, characterization, and effect on cancer cell viability of NPB analogs, and the single-crystal X-ray crystallographic studies of an example compound (4r), which was grown via slow-solvent evaporation technique is reported. Screening for loss of viability in mammary carcinoma cells revealed that compounds such as 2[(4(2,3-dichlorophenyl)piperazin-1-yl][naphthalen-1-yl]methyl)phenol (4e), 5[(4(2,3-dichlorophenyl)piperazin-1-yl][2-hydroxyphenyl)methyl)uran-2-carbaldehyde (4f), 3[(2-hydroxyphenyl][4(p-tolyl)piperazin-1-yl)methyl)benzaldehyde (4i), and NPB inhibited the viability of MCF-7 cells with IC50 values of 5.90, 3.11, 7.68, and 6.5 µM, respectively. The loss of cell viability was enhanced by the NPB analogs synthesized by adding newer rings such as naphthalene and furan-2-carbaldehyde in place of N-cyclopentyl-benzamide of NPB. Furthermore, these compounds decreased Ser99 phosphorylation of hBAD. Additional in silico density functional theory calculations suggested possibilities for other analogs of NPB that may be more suitable for further development.
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Affiliation(s)
- Swamy Savvemala Girimanchanaika
- Laboratory Chemical Biology, Department of Studies in Organic Chemistry, University of Mysore, Manasagangotri, Mysore 570006, India; (S.S.G.); (D.D.)
| | - Dukanya Dukanya
- Laboratory Chemical Biology, Department of Studies in Organic Chemistry, University of Mysore, Manasagangotri, Mysore 570006, India; (S.S.G.); (D.D.)
| | - Ananda Swamynayaka
- Department of Studies in Physics, University of Mysore, Manasagangotri, Mysore 570006, India; (A.S.); (M.M.)
| | | | - Mahendra Madegowda
- Department of Studies in Physics, University of Mysore, Manasagangotri, Mysore 570006, India; (A.S.); (M.M.)
| | - Ganga Periyasamy
- Department of Chemistry, Bangalore University, Bangalore 560056, India; (D.M.G.); (G.P.)
| | | | - Vijay Pandey
- Tsinghua Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China;
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Peter E. Lobie
- Tsinghua Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China;
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
- Shenzen Bay Laboratory, Shenzhen 518055, China
- Correspondence: (P.E.L.); (B.B.)
| | - Basappa Basappa
- Laboratory Chemical Biology, Department of Studies in Organic Chemistry, University of Mysore, Manasagangotri, Mysore 570006, India; (S.S.G.); (D.D.)
- Correspondence: (P.E.L.); (B.B.)
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26
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Ramms DJ, Raimondi F, Arang N, Herberg FW, Taylor SS, Gutkind JS. G αs-Protein Kinase A (PKA) Pathway Signalopathies: The Emerging Genetic Landscape and Therapeutic Potential of Human Diseases Driven by Aberrant G αs-PKA Signaling. Pharmacol Rev 2021; 73:155-197. [PMID: 34663687 PMCID: PMC11060502 DOI: 10.1124/pharmrev.120.000269] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Many of the fundamental concepts of signal transduction and kinase activity are attributed to the discovery and crystallization of cAMP-dependent protein kinase, or protein kinase A. PKA is one of the best-studied kinases in human biology, with emphasis in biochemistry and biophysics, all the way to metabolism, hormone action, and gene expression regulation. It is surprising, however, that our understanding of PKA's role in disease is largely underappreciated. Although genetic mutations in the PKA holoenzyme are known to cause diseases such as Carney complex, Cushing syndrome, and acrodysostosis, the story largely stops there. With the recent explosion of genomic medicine, we can finally appreciate the broader role of the Gαs-PKA pathway in disease, with contributions from aberrant functioning G proteins and G protein-coupled receptors, as well as multiple alterations in other pathway components and negative regulators. Together, these represent a broad family of diseases we term the Gαs-PKA pathway signalopathies. The Gαs-PKA pathway signalopathies encompass diseases caused by germline, postzygotic, and somatic mutations in the Gαs-PKA pathway, with largely endocrine and neoplastic phenotypes. Here, we present a signaling-centric review of Gαs-PKA-driven pathophysiology and integrate computational and structural analysis to identify mutational themes commonly exploited by the Gαs-PKA pathway signalopathies. Major mutational themes include hotspot activating mutations in Gαs, encoded by GNAS, and mutations that destabilize the PKA holoenzyme. With this review, we hope to incite further study and ultimately the development of new therapeutic strategies in the treatment of a wide range of human diseases. SIGNIFICANCE STATEMENT: Little recognition is given to the causative role of Gαs-PKA pathway dysregulation in disease, with effects ranging from infectious disease, endocrine syndromes, and many cancers, yet these disparate diseases can all be understood by common genetic themes and biochemical signaling connections. By highlighting these common pathogenic mechanisms and bridging multiple disciplines, important progress can be made toward therapeutic advances in treating Gαs-PKA pathway-driven disease.
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Affiliation(s)
- Dana J Ramms
- Department of Pharmacology (D.J.R., N.A., J.S.G.), Department of Chemistry and Biochemistry (S.S.T.), and Moores Cancer Center (D.J.R., N.A., J.S.G.), University of California, San Diego, La Jolla, California; Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Pisa, Italy (F.R.); and Department of Biochemistry, University of Kassel, Kassel, Germany (F.W.H.)
| | - Francesco Raimondi
- Department of Pharmacology (D.J.R., N.A., J.S.G.), Department of Chemistry and Biochemistry (S.S.T.), and Moores Cancer Center (D.J.R., N.A., J.S.G.), University of California, San Diego, La Jolla, California; Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Pisa, Italy (F.R.); and Department of Biochemistry, University of Kassel, Kassel, Germany (F.W.H.)
| | - Nadia Arang
- Department of Pharmacology (D.J.R., N.A., J.S.G.), Department of Chemistry and Biochemistry (S.S.T.), and Moores Cancer Center (D.J.R., N.A., J.S.G.), University of California, San Diego, La Jolla, California; Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Pisa, Italy (F.R.); and Department of Biochemistry, University of Kassel, Kassel, Germany (F.W.H.)
| | - Friedrich W Herberg
- Department of Pharmacology (D.J.R., N.A., J.S.G.), Department of Chemistry and Biochemistry (S.S.T.), and Moores Cancer Center (D.J.R., N.A., J.S.G.), University of California, San Diego, La Jolla, California; Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Pisa, Italy (F.R.); and Department of Biochemistry, University of Kassel, Kassel, Germany (F.W.H.)
| | - Susan S Taylor
- Department of Pharmacology (D.J.R., N.A., J.S.G.), Department of Chemistry and Biochemistry (S.S.T.), and Moores Cancer Center (D.J.R., N.A., J.S.G.), University of California, San Diego, La Jolla, California; Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Pisa, Italy (F.R.); and Department of Biochemistry, University of Kassel, Kassel, Germany (F.W.H.)
| | - J Silvio Gutkind
- Department of Pharmacology (D.J.R., N.A., J.S.G.), Department of Chemistry and Biochemistry (S.S.T.), and Moores Cancer Center (D.J.R., N.A., J.S.G.), University of California, San Diego, La Jolla, California; Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore, Pisa, Italy (F.R.); and Department of Biochemistry, University of Kassel, Kassel, Germany (F.W.H.)
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Casillas AL, Chauhan SS, Toth RK, Sainz AG, Clements AN, Jensen CC, Langlais PR, Miranti CK, Cress AE, Warfel NA. Direct phosphorylation and stabilization of HIF-1α by PIM1 kinase drives angiogenesis in solid tumors. Oncogene 2021; 40:5142-5152. [PMID: 34211090 PMCID: PMC8364516 DOI: 10.1038/s41388-021-01915-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 06/09/2021] [Accepted: 06/17/2021] [Indexed: 12/12/2022]
Abstract
Angiogenesis is essential for the sustained growth of solid tumors. Hypoxia-inducible factor 1 (HIF-1) is a master regulator of angiogenesis and constitutive activation of HIF-1 is frequently observed in human cancers. Therefore, understanding the mechanisms governing the activation of HIF-1 is critical for successful therapeutic targeting of tumor angiogenesis. Herein, we establish a new regulatory mechanism responsible for the constitutive activation of HIF-1α in cancer, irrespective of oxygen tension. PIM1 kinase directly phosphorylates HIF-1α at threonine 455, a previously uncharacterized site within its oxygen-dependent degradation domain. This phosphorylation event disrupts the ability of prolyl hydroxylases to bind and hydroxylate HIF-1α, interrupting its canonical degradation pathway and promoting constitutive transcription of HIF-1 target genes. Moreover, phosphorylation of the analogous site in HIF-2α (S435) stabilizes the protein through the same mechanism, indicating post-translational modification within the oxygen-dependent degradation domain as a mechanism of regulating the HIF-α subunits. In vitro and in vivo models demonstrate that expression of PIM1 is sufficient to stabilize HIF-1α and HIF-2α in normoxia and stimulate angiogenesis in a HIF-1-dependent manner. CRISPR mutants of HIF-1α (Thr455D) promoted increased tumor growth, proliferation, and angiogenesis. Moreover, HIF-1α-T455D xenograft tumors were refractory to the anti-angiogenic and cytotoxic effects of PIM inhibitors. These data identify a new signaling axis responsible for hypoxia-independent activation of HIF-1 and expand our understanding of the tumorigenic role of PIM1 in solid tumors.
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Affiliation(s)
- Andrea L Casillas
- Cancer Biology Graduate Interdisciplinary Program, The University of Arizona, Tucson, AZ, USA
| | | | - Rachel K Toth
- The University of Arizona Cancer Center, Tucson, AZ, USA
| | - Alva G Sainz
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Amber N Clements
- Cancer Biology Graduate Interdisciplinary Program, The University of Arizona, Tucson, AZ, USA
| | - Corbin C Jensen
- Cancer Biology Graduate Interdisciplinary Program, The University of Arizona, Tucson, AZ, USA
| | - Paul R Langlais
- Department of Medicine, The University of Arizona, Tucson, AZ, USA
| | - Cindy K Miranti
- The University of Arizona Cancer Center, Tucson, AZ, USA
- Department of Cellular and Molecular Medicine, The University of Arizona, Tucson, AZ, USA
| | - Anne E Cress
- The University of Arizona Cancer Center, Tucson, AZ, USA
- Department of Cellular and Molecular Medicine, The University of Arizona, Tucson, AZ, USA
| | - Noel A Warfel
- The University of Arizona Cancer Center, Tucson, AZ, USA.
- Department of Cellular and Molecular Medicine, The University of Arizona, Tucson, AZ, USA.
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28
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Cabanos HF, Hata AN. Emerging Insights into Targeted Therapy-Tolerant Persister Cells in Cancer. Cancers (Basel) 2021; 13:cancers13112666. [PMID: 34071428 PMCID: PMC8198243 DOI: 10.3390/cancers13112666] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/19/2021] [Accepted: 05/19/2021] [Indexed: 12/25/2022] Open
Abstract
Drug resistance is perhaps the greatest challenge in improving outcomes for cancer patients undergoing treatment with targeted therapies. It is becoming clear that "persisters," a subpopulation of drug-tolerant cells found in cancer populations, play a critical role in the development of drug resistance. Persisters are able to maintain viability under therapy but are typically slow cycling or dormant. These cells do not harbor classic drug resistance driver alterations, and their partial resistance phenotype is transient and reversible upon removal of the drug. In the clinic, the persister state most closely corresponds to minimal residual disease from which relapse can occur if treatment is discontinued or if acquired drug resistance develops in response to continuous therapy. Thus, eliminating persister cells will be crucial to improve outcomes for cancer patients. Using lung cancer targeted therapies as a primary paradigm, this review will give an overview of the characteristics of drug-tolerant persister cells, mechanisms associated with drug tolerance, and potential therapeutic opportunities to target this persister cell population in tumors.
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Affiliation(s)
- Heidie Frisco Cabanos
- Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA;
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Aaron N. Hata
- Massachusetts General Hospital Cancer Center, Charlestown, MA 02129, USA;
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Correspondence: ; Tel.: +1-617-724-3442
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29
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Gaudelet T, Malod-Dognin N, Pržulj N. Integrative Data Analytic Framework to Enhance Cancer Precision Medicine. NETWORK AND SYSTEMS MEDICINE 2021; 4:60-73. [PMID: 33796878 PMCID: PMC8006589 DOI: 10.1089/nsm.2020.0015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/15/2021] [Indexed: 12/20/2022] Open
Abstract
With the advancement of high-throughput biotechnologies, we increasingly accumulate biomedical data about diseases, especially cancer. There is a need for computational models and methods to sift through, integrate, and extract new knowledge from the diverse available data, to improve the mechanistic understanding of diseases and patient care. To uncover molecular mechanisms and drug indications for specific cancer types, we develop an integrative framework able to harness a wide range of diverse molecular and pan-cancer data. We show that our approach outperforms the competing methods and can identify new associations. Furthermore, it captures the underlying biology predictive of drug response. Through the joint integration of data sources, our framework can also uncover links between cancer types and molecular entities for which no prior knowledge is available. Our new framework is flexible and can be easily reformulated to study any biomedical problem.
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Affiliation(s)
- Thomas Gaudelet
- Department of Computer Science, University College London, London, United Kingdom
| | - Noël Malod-Dognin
- Department of Computer Science, University College London, London, United Kingdom
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Nataša Pržulj
- Department of Computer Science, University College London, London, United Kingdom
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
- ICREA, Barcelona, Spain
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30
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Grey W, Chauhan R, Piganeau M, Huerga Encabo H, Garcia-Albornoz M, McDonald NQ, Bonnet D. Activation of the receptor tyrosine kinase RET improves long-term hematopoietic stem cell outgrowth and potency. Blood 2020; 136:2535-2547. [PMID: 32589703 PMCID: PMC7714096 DOI: 10.1182/blood.2020006302] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 06/08/2020] [Indexed: 12/21/2022] Open
Abstract
Expansion of human hematopoietic stem cells (HSCs) is a rapidly advancing field showing great promise for clinical applications. Recent evidence has implicated the nervous system and glial family ligands (GFLs) as potential drivers of hematopoietic survival and self-renewal in the bone marrow niche; how to apply this process to HSC maintenance and expansion has yet to be explored. We show a role for the GFL receptor, RET, at the cell surface of HSCs in mediating sustained cellular growth, resistance to stress, and improved cell survival throughout in vitro expansion. HSCs treated with the key RET ligand/coreceptor complex, glial-derived neurotrophic factor and its coreceptor, exhibit improved progenitor function at primary transplantation and improved long-term HSC function at secondary transplantation. Finally, we show that RET drives a multifaceted intracellular signaling pathway, including key signaling intermediates protein kinase B, extracellular signal-regulated kinase 1/2, NF-κB, and p53, responsible for a wide range of cellular and genetic responses that improve cell growth and survival under culture conditions.
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Affiliation(s)
- W Grey
- Hematopoietic Stem Cell Laboratory and
| | - R Chauhan
- Signalling and Structural Biology Laboratory, Francis Crick Institute, London, United Kingdom; and
| | | | | | | | - N Q McDonald
- Signalling and Structural Biology Laboratory, Francis Crick Institute, London, United Kingdom; and
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, London, United Kingdom
| | - D Bonnet
- Hematopoietic Stem Cell Laboratory and
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31
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Zhang H, Kong Q, Wang J, Jiang Y, Hua H. Complex roles of cAMP-PKA-CREB signaling in cancer. Exp Hematol Oncol 2020; 9:32. [PMID: 33292604 PMCID: PMC7684908 DOI: 10.1186/s40164-020-00191-1] [Citation(s) in RCA: 201] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 11/19/2020] [Indexed: 02/08/2023] Open
Abstract
Cyclic adenosine monophosphate (cAMP) is the first discovered second messenger, which plays pivotal roles in cell signaling, and regulates many physiological and pathological processes. cAMP can regulate the transcription of various target genes, mainly through protein kinase A (PKA) and its downstream effectors such as cAMP-responsive element binding protein (CREB). In addition, PKA can phosphorylate many kinases such as Raf, GSK3 and FAK. Aberrant cAMP-PKA signaling is involved in various types of human tumors. Especially, cAMP signaling may have both tumor-suppressive and tumor-promoting roles depending on the tumor types and context. cAMP-PKA signaling can regulate cancer cell growth, migration, invasion and metabolism. This review highlights the important roles of cAMP-PKA-CREB signaling in tumorigenesis. The potential strategies to target this pathway for cancer therapy are also discussed.
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Affiliation(s)
- Hongying Zhang
- Laboratory of Oncogene, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Qingbin Kong
- Laboratory of Oncogene, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Jiao Wang
- School of Basic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yangfu Jiang
- Laboratory of Oncogene, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Hui Hua
- Laboratory of Stem Cell Biology, West China Hospital, Sichuan University, Chengdu, 610041, China.
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32
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Seçilmiş D, Hillerton T, Morgan D, Tjärnberg A, Nelander S, Nordling TEM, Sonnhammer ELL. Uncovering cancer gene regulation by accurate regulatory network inference from uninformative data. NPJ Syst Biol Appl 2020; 6:37. [PMID: 33168813 PMCID: PMC7652823 DOI: 10.1038/s41540-020-00154-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 10/15/2020] [Indexed: 01/11/2023] Open
Abstract
The interactions among the components of a living cell that constitute the gene regulatory network (GRN) can be inferred from perturbation-based gene expression data. Such networks are useful for providing mechanistic insights of a biological system. In order to explore the feasibility and quality of GRN inference at a large scale, we used the L1000 data where ~1000 genes have been perturbed and their expression levels have been quantified in 9 cancer cell lines. We found that these datasets have a very low signal-to-noise ratio (SNR) level causing them to be too uninformative to infer accurate GRNs. We developed a gene reduction pipeline in which we eliminate uninformative genes from the system using a selection criterion based on SNR, until reaching an informative subset. The results show that our pipeline can identify an informative subset in an overall uninformative dataset, allowing inference of accurate subset GRNs. The accurate GRNs were functionally characterized and potential novel cancer-related regulatory interactions were identified.
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Affiliation(s)
- Deniz Seçilmiş
- Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, 17121, Solna, Sweden
| | - Thomas Hillerton
- Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, 17121, Solna, Sweden
| | - Daniel Morgan
- Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, 17121, Solna, Sweden
| | - Andreas Tjärnberg
- Center for Developmental Genetics, New York University, New York, NY, USA
| | - Sven Nelander
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Torbjörn E M Nordling
- Department of Mechanical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Erik L L Sonnhammer
- Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Box 1031, 17121, Solna, Sweden.
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33
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Sun Z, Jiang Q, Li J, Guo J. The potent roles of salt-inducible kinases (SIKs) in metabolic homeostasis and tumorigenesis. Signal Transduct Target Ther 2020; 5:150. [PMID: 32788639 PMCID: PMC7423983 DOI: 10.1038/s41392-020-00265-w] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/22/2020] [Indexed: 01/26/2023] Open
Abstract
Salt-inducible kinases (SIKs) belong to AMP-activated protein kinase (AMPK) family, and functions mainly involve in regulating energy response-related physiological processes, such as gluconeogenesis and lipid metabolism. However, compared with another well-established energy-response kinase AMPK, SIK roles in human diseases, especially in diabetes and tumorigenesis, are rarely investigated. Recently, the pilot roles of SIKs in tumorigenesis have begun to attract more attention due to the finding that the tumor suppressor role of LKB1 in non-small-cell lung cancers (NSCLCs) is unexpectedly mediated by the SIK but not AMPK kinases. Thus, here we tend to comprehensively summarize the emerging upstream regulators, downstream substrates, mouse models, clinical relevance, and candidate inhibitors for SIKs, and shed light on SIKs as the potential therapeutic targets for cancer therapies.
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Affiliation(s)
- Zicheng Sun
- Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, 510275, China.,Department of Breast and Thyroid Surgery, the First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, 510275, China
| | - Qiwei Jiang
- Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, 510275, China
| | - Jie Li
- Department of Breast and Thyroid Surgery, the First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, 510275, China.
| | - Jianping Guo
- Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, 510275, China.
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34
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Demircioğlu D, Cukuroglu E, Kindermans M, Nandi T, Calabrese C, Fonseca NA, Kahles A, Lehmann KV, Stegle O, Brazma A, Brooks AN, Rätsch G, Tan P, Göke J. A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters. Cell 2020; 178:1465-1477.e17. [PMID: 31491388 DOI: 10.1016/j.cell.2019.08.018] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 12/13/2018] [Accepted: 08/07/2019] [Indexed: 02/08/2023]
Abstract
Most human protein-coding genes are regulated by multiple, distinct promoters, suggesting that the choice of promoter is as important as its level of transcriptional activity. However, while a global change in transcription is recognized as a defining feature of cancer, the contribution of alternative promoters still remains largely unexplored. Here, we infer active promoters using RNA-seq data from 18,468 cancer and normal samples, demonstrating that alternative promoters are a major contributor to context-specific regulation of transcription. We find that promoters are deregulated across tissues, cancer types, and patients, affecting known cancer genes and novel candidates. For genes with independently regulated promoters, we demonstrate that promoter activity provides a more accurate predictor of patient survival than gene expression. Our study suggests that a dynamic landscape of active promoters shapes the cancer transcriptome, opening new diagnostic avenues and opportunities to further explore the interplay of regulatory mechanisms with transcriptional aberrations in cancer.
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Affiliation(s)
- Deniz Demircioğlu
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore; School of Computing, National University of Singapore, Singapore 117417, Singapore
| | - Engin Cukuroglu
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Martin Kindermans
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Tannistha Nandi
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Claudia Calabrese
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK; Genome Biology Unit, EMBL, Heidelberg, 69117, Germany
| | - Nuno A Fonseca
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK; CIBIO/InBIO - Research Center in Biodiversity and Genetic Resources, Universidade do Porto, Vairão 4485-601, Portugal
| | - André Kahles
- Department of Computer Science, ETH Zurich, Zurich 8092, Switzerland; Department of Biology, ETH Zurich, Zurich 8093, Switzerland; Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; SIB Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland; Biomedical Informatics Research, University Hospital Zurich, Zurich 8091, Switzerland
| | - Kjong-Van Lehmann
- Department of Computer Science, ETH Zurich, Zurich 8092, Switzerland; Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; SIB Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland; Biomedical Informatics Research, University Hospital Zurich, Zurich 8091, Switzerland
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK; Genome Biology Unit, EMBL, Heidelberg, 69117, Germany; Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Angela N Brooks
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Gunnar Rätsch
- Department of Computer Science, ETH Zurich, Zurich 8092, Switzerland; Department of Biology, ETH Zurich, Zurich 8093, Switzerland; Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; SIB Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland; Biomedical Informatics Research, University Hospital Zurich, Zurich 8091, Switzerland; Weill Cornell Medical College, New York, NY 10065, USA
| | - Patrick Tan
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore; Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore 138672, Singapore; SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre Singapore, Singapore 169856, Singapore; Cellular and Molecular Research, National Cancer Centre, Singapore 169610, Singapore; Singapore Gastric Cancer Consortium, Singapore 119074, Singapore
| | - Jonathan Göke
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore; Cellular and Molecular Research, National Cancer Centre, Singapore 169610, Singapore.
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35
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Ferraro MG, Piccolo M, Misso G, Maione F, Montesarchio D, Caraglia M, Paduano L, Santamaria R, Irace C. Breast Cancer Chemotherapeutic Options: A General Overview on the Preclinical Validation of a Multi-Target Ruthenium(III) Complex Lodged in Nucleolipid Nanosystems. Cells 2020; 9:E1412. [PMID: 32517101 PMCID: PMC7349411 DOI: 10.3390/cells9061412] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/29/2020] [Accepted: 06/03/2020] [Indexed: 12/11/2022] Open
Abstract
In this review we have showcased the preclinical development of original amphiphilic nanomaterials designed for ruthenium-based anticancer treatments, to be placed within the current metallodrugs approach leading over the past decade to advanced multitarget agents endowed with limited toxicity and resistance. This strategy could allow for new options for breast cancer (BC) interventions, including the triple-negative subtype (TNBC) with poor therapeutic alternatives. BC is currently the second most widespread cancer and the primary cause of cancer death in women. Hence, the availability of novel chemotherapeutic weapons is a basic requirement to fight BC subtypes. Anticancer drugs based on ruthenium are among the most explored and advanced next-generation metallotherapeutics, with NAMI-A and KP1019 as two iconic ruthenium complexes having undergone clinical trials. In addition, many nanomaterial Ru complexes have been recently conceived and developed into anticancer drugs demonstrating attractive properties. In this field, we focused on the evaluation of a Ru(III) complex-named AziRu-incorporated into a suite of both zwitterionic and cationic nucleolipid nanosystems, which proved to be very effective for the in vivo targeting of breast cancer cells (BBC). Mechanisms of action have been widely explored in the context of preclinical evaluations in vitro, highlighting a multitarget action on cell death pathways which are typically deregulated in neoplasms onset and progression. Moreover, being AziRu inspired by the well-known NAMI-A complex, information on non-nanostructured Ru-based anticancer agents have been included in a precise manner.
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Affiliation(s)
- Maria Grazia Ferraro
- Department of Pharmacy, School of Medicine and Surgery, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy; (M.G.F.); (M.P.); (F.M.)
| | - Marialuisa Piccolo
- Department of Pharmacy, School of Medicine and Surgery, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy; (M.G.F.); (M.P.); (F.M.)
| | - Gabriella Misso
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio 7, 80138 Naples, Italy; (G.M.); (M.C.)
| | - Francesco Maione
- Department of Pharmacy, School of Medicine and Surgery, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy; (M.G.F.); (M.P.); (F.M.)
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia 421, 80126 Naples, Italy; (D.M.); (L.P.)
| | - Michele Caraglia
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio 7, 80138 Naples, Italy; (G.M.); (M.C.)
| | - Luigi Paduano
- Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia 421, 80126 Naples, Italy; (D.M.); (L.P.)
| | - Rita Santamaria
- Department of Pharmacy, School of Medicine and Surgery, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy; (M.G.F.); (M.P.); (F.M.)
| | - Carlo Irace
- Department of Pharmacy, School of Medicine and Surgery, University of Naples “Federico II”, Via D. Montesano 49, 80131 Naples, Italy; (M.G.F.); (M.P.); (F.M.)
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36
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Wu Y, Li Y, Liu J, Chen M, Li W, Chen Y, Xu M. The diagnostic value of extracellular protein kinase A (ECPKA) in serum for gastric and colorectal cancer. Transl Cancer Res 2020; 9:3870-3878. [PMID: 35117754 PMCID: PMC8797401 DOI: 10.21037/tcr-20-764] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/24/2020] [Indexed: 01/26/2023]
Abstract
Background For the biomarkers of cancer, many chromosomal and genetic alterations have been examined as possible. However, some tumors do not display a clear molecular and genetic signature. While there are some cellular processes regulated by second messenger intracellular pathways indeed involved in carcinogenesis. The first intracellular second messenger was described as cyclic adenosine 3',5'-monophosphate (cAMP), and cAMP-dependent protein kinase (PKA) play a crucial role in several biological processes; The dysregulation of PKA-mediated signaling in several types of cancer should be investigated. More interesting, the alpha catalytic subunit of PKA (PKACα) could be secreted into the conditioned medium by different types of cancer cells, and it also existed in the serum of some cancer patients, defined as extracellular protein kinase A (ECPKA). Methods The levels of serum PKACα from healthy people, gastric cancer and colon cancer patients were detected by ELISA kits. Western blotting was used to detect the expression of PKACα in cancer tissue and the adjacent mucosa. Mann-Whitney test was applied to analyze the patients’ characteristics and serum PKACα. ROC analyses were performed to further evaluate the utility of PKACα in cancer diagnosis. The correlation of serum PKACα and T stage, age, and tumor markers were analyzed by Spearman rank and Pearson correlation analysis, respectively. Results There were significant differences of PKACα in serum between the volunteers and the gastric cancers (P<0.01), but not the colorectal cancers (P>0.05). ROC analyses evaluated the utility of PKACα for gastric cancer with 61.90% sensitivities and 87.50% specificities. The serum PKACα was correlated with tumor marker CA50, while there was no significant difference of PKACα expression between the gastric/colorectal cancer tissue and the adjacent mucosa. Conclusions The above results implied that PKACα levels might be a potential biomarker for the early screening of gastric cancers. Moreover, further research is still needed to investigate the role of secreted PKACα and the regulatory mechanism in tumor progression.
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Affiliation(s)
- Yan Wu
- Department of Physiology, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Yafang Li
- Department of Physiology, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Junqiang Liu
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Mengjiao Chen
- Department of Physiology, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Wei Li
- The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Yongchang Chen
- Department of Physiology, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Min Xu
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
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37
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Combined inhibition of PIM and CDK4/6 suppresses both mTOR signaling and Rb phosphorylation and potentiates PI3K inhibition in cancer cells. Oncotarget 2020; 11:1478-1492. [PMID: 32391118 PMCID: PMC7197449 DOI: 10.18632/oncotarget.27539] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 03/14/2020] [Indexed: 12/31/2022] Open
Abstract
Aberrant activation of mitogenic signaling pathways in cancer promotes growth and proliferation of cells by activating mTOR and S6 phosphorylation, and D-cyclin kinases and Rb phosphorylation, respectively. Correspondingly, inhibition of phosphorylation of both Rb and S6 is required for robust anti-tumor efficacy of drugs that inhibit cell signaling. The best-established mechanism of mTOR activation in cancer is via PI3K/Akt signaling, but mTOR activity can also be stimulated by CDK4 and PIM kinases. In this study, we show that the CDK4/6 inhibitor abemaciclib inhibits PIM kinase and S6 phosphorylation in cancer cells and concurrent inhibition of PIM, CDK4, and CDK6 suppresses both S6 and Rb phosphorylation. TSC2 or PIK3CA mutations obviate the requirement for PIM kinase and circumvent the inhibition of S6 phosphorylation by abemaciclib. Combination with a PI3K inhibitor restored suppression of S6 phosphorylation and synergized to curtail cell growth. By combining abemaciclib with a PI3K inhibitor, three pathways (Akt, PIM, and CDK4) to mTOR activation are neutralized, suggesting a potential combination strategy for the treatment of PIK3CA-mutant ER+ breast cancer.
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38
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Kennedy SP, O'Neill M, Cunningham D, Morris PG, Toomey S, Blanco-Aparicio C, Martinez S, Pastor J, Eustace AJ, Hennessy BT. Preclinical evaluation of a novel triple-acting PIM/PI3K/mTOR inhibitor, IBL-302, in breast cancer. Oncogene 2020; 39:3028-3040. [PMID: 32042115 PMCID: PMC7118022 DOI: 10.1038/s41388-020-1202-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 01/20/2020] [Accepted: 01/30/2020] [Indexed: 11/09/2022]
Abstract
The proviral integration of Moloney virus (PIM) family of protein kinases are overexpressed in many haematological and solid tumours. PIM kinase expression is elevated in PI3K inhibitor-treated breast cancer samples, suggesting a major resistance pathway for PI3K inhibitors in breast cancer, potentially limiting their clinical utility. IBL-302 is a novel molecule that inhibits both PIM and PI3K/AKT/mTOR signalling. We thus evaluated the preclinical activity of IBL-302, in a range of breast cancer models. Our results demonstrate in vitro efficacy of IBL-302 in a range of breast cancer cell lines, including lines with acquired resistance to trastuzumab and lapatinib. IBL-302 demonstrated single-agent, anti-tumour efficacy in suppression of pAKT, pmTOR and pBAD in the SKBR-3, BT-474 and HCC-1954 HER2+/PIK3CA-mutated cell lines. We have also shown the in vivo single-agent efficacy of IBL-302 in the subcutaneous BT-474 and HCC-1954 xenograft model in BALB/c nude mice. The combination of trastuzumab and IBL-302 significantly increased the anti-proliferative effect in HER2+ breast cancer cell line, and matched trastuzumab-resistant line, relative to testing either drug alone. We thus believe that the novel PIM and PI3K/mTOR inhibitor, IBL-302, represents an exciting new potential treatment option for breast cancer, and that it should be considered for clinical investigation.
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Affiliation(s)
- Sean P Kennedy
- Medical Oncology Group, Department of Molecular Medicine, Royal College of Surgeons Ireland, Smurfit Building Beaumont Hospital, Beaumont, Dublin, Ireland.
| | - Michael O'Neill
- Inflection Biosciences, Anglesea House, Blackrock, Dublin, Ireland
| | | | - Patrick G Morris
- Medical Oncology Group, Department of Molecular Medicine, Royal College of Surgeons Ireland, Smurfit Building Beaumont Hospital, Beaumont, Dublin, Ireland.,Cancer Clinical Trials and Research Unit, Beaumont Hospital, Dublin, Ireland
| | - Sinead Toomey
- Medical Oncology Group, Department of Molecular Medicine, Royal College of Surgeons Ireland, Smurfit Building Beaumont Hospital, Beaumont, Dublin, Ireland
| | - Carmen Blanco-Aparicio
- Experimental Therapeutics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Sonia Martinez
- Experimental Therapeutics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Joaquin Pastor
- Experimental Therapeutics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Alex J Eustace
- Molecular Therapeutics for Cancer in Ireland, National Institute for Cellular Biotechnology, Dublin City University, Dublin, Ireland
| | - Bryan T Hennessy
- Medical Oncology Group, Department of Molecular Medicine, Royal College of Surgeons Ireland, Smurfit Building Beaumont Hospital, Beaumont, Dublin, Ireland.,Cancer Clinical Trials and Research Unit, Beaumont Hospital, Dublin, Ireland.,Cancer Trials Ireland, Innovation House, Old Finglas Road, Botanic, Dublin, Ireland
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39
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Luszczak S, Kumar C, Sathyadevan VK, Simpson BS, Gately KA, Whitaker HC, Heavey S. PIM kinase inhibition: co-targeted therapeutic approaches in prostate cancer. Signal Transduct Target Ther 2020; 5:7. [PMID: 32296034 PMCID: PMC6992635 DOI: 10.1038/s41392-020-0109-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 12/05/2019] [Accepted: 12/13/2019] [Indexed: 01/09/2023] Open
Abstract
PIM kinases have been shown to play a role in prostate cancer development and progression, as well as in some of the hallmarks of cancer, especially proliferation and apoptosis. Their upregulation in prostate cancer has been correlated with decreased patient overall survival and therapy resistance. Initial efforts to inhibit PIM with monotherapies have been hampered by compensatory upregulation of other pathways and drug toxicity, and as such, it has been suggested that co-targeting PIM with other treatment approaches may permit lower doses and be a more viable option in the clinic. Here, we present the rationale and basis for co-targeting PIM with inhibitors of PI3K/mTOR/AKT, JAK/STAT, MYC, stemness, and RNA Polymerase I transcription, along with other therapies, including androgen deprivation, radiotherapy, chemotherapy, and immunotherapy. Such combined approaches could potentially be used as neoadjuvant therapies, limiting the development of resistance to treatments or sensitizing cells to other therapeutics. To determine which drugs should be combined with PIM inhibitors for each patient, it will be key to develop companion diagnostics that predict response to each co-targeted option, hopefully providing a personalized medicine pathway for subsets of prostate cancer patients in the future.
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Affiliation(s)
- Sabina Luszczak
- Molecular Diagnostics and Therapeutics Group, University College London, London, UK
| | - Christopher Kumar
- Molecular Diagnostics and Therapeutics Group, University College London, London, UK
| | | | - Benjamin S Simpson
- Molecular Diagnostics and Therapeutics Group, University College London, London, UK
| | - Kathy A Gately
- Trinity Translational Medicine Institute, St. James's Hospital Dublin, Dublin 8, Dublin, Ireland
| | - Hayley C Whitaker
- Molecular Diagnostics and Therapeutics Group, University College London, London, UK
| | - Susan Heavey
- Molecular Diagnostics and Therapeutics Group, University College London, London, UK.
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40
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Malone T, Schäfer L, Simon N, Heavey S, Cuffe S, Finn S, Moore G, Gately K. Current perspectives on targeting PIM kinases to overcome mechanisms of drug resistance and immune evasion in cancer. Pharmacol Ther 2019; 207:107454. [PMID: 31836451 DOI: 10.1016/j.pharmthera.2019.107454] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 12/03/2019] [Indexed: 12/22/2022]
Abstract
PIM kinases are a class of serine/threonine kinases that play a role in several of the hallmarks of cancer including cell cycle progression, metabolism, inflammation and immune evasion. Their constitutively active nature and unique catalytic structure has led them to be an attractive anticancer target through the use of small molecule inhibitors. This review highlights the enhanced activity of PIM kinases in cancer that can be driven by hypoxia in the tumour microenvironment and the important role that aberrant PIM kinase activity plays in resistance mechanisms to chemotherapy, radiotherapy, anti-angiogenic therapies and targeted therapies. We highlight an interaction of PIM kinases with numerous major oncogenic players, including but not limited to, stabilisation of p53, synergism with c-Myc, and notable parallel signalling with PI3K/Akt. We provide a comprehensive overview of PIM kinase's role as an escape mechanism to targeted therapies including PI3K/mTOR inhibitors, MET inhibitors, anti-HER2/EGFR treatments and the immunosuppressant rapamycin, providing a rationale for co-targeting treatment strategies for a more durable patient response. The current status of PIM kinase inhibitors and their use as a combination therapy with other targeted agents, in addition to the development of novel multi-molecularly targeted single therapeutic agents containing a PIM kinase targeting moiety are discussed.
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Affiliation(s)
- Tom Malone
- Dept. of Clinical Medicine, Trinity Translational Medicine Institute, St. James's Hospital, Dublin, Ireland
| | - Lea Schäfer
- Dept. of Clinical Medicine, Trinity Translational Medicine Institute, St. James's Hospital, Dublin, Ireland
| | - Nathalie Simon
- Dept. of Clinical Medicine, Trinity Translational Medicine Institute, St. James's Hospital, Dublin, Ireland
| | - Susan Heavey
- Molecular Diagnostics and Therapeutics Group, University College London, London, UK
| | - Sinead Cuffe
- Dept. of Clinical Medicine, Trinity Translational Medicine Institute, St. James's Hospital, Dublin, Ireland
| | - Stephen Finn
- Dept. of Clinical Medicine, Trinity Translational Medicine Institute, St. James's Hospital, Dublin, Ireland
| | - Gillian Moore
- School of Pharmacy and Biomolecular Sciences, RCSI, Dublin, Ireland
| | - Kathy Gately
- Dept. of Clinical Medicine, Trinity Translational Medicine Institute, St. James's Hospital, Dublin, Ireland.
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41
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Yang F, Xie HY, Yang LF, Zhang L, Zhang FL, Liu HY, Li DQ, Shao ZM. Stabilization of MORC2 by estrogen and antiestrogens through GPER1- PRKACA-CMA pathway contributes to estrogen-induced proliferation and endocrine resistance of breast cancer cells. Autophagy 2019; 16:1061-1076. [PMID: 32401166 DOI: 10.1080/15548627.2019.1659609] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Aberrant activation of estrogen signaling through three ESR (estrogen receptor) subtypes, termed ESR1/ERα, ESR2/ERβ, and GPER1 (G protein-coupled estrogen receptor 1), is implicated in breast cancer pathogenesis and progression. Antiestrogens tamoxifen (TAM) and fulvestrant (FUL) are effective for treatment of ESR1-positive breast tumors, but development of resistance represents a major clinical challenge. However, the molecular mechanisms behind these events remain largely unknown. Here, we report that 17β-estradiol (E2), TAM, and FUL stabilize MORC2 (MORC family CW-type zinc finger 2), an emerging oncoprotein in human cancer, in a GPER1-dependent manner. Mechanistically, GPER1 activates PRKACA (protein kinase cAMP-activated catalytic subunit alpha), which in turn phosphorylates MORC2 at threonine 582 (T582). Phosphorylated MORC2 decreases its interaction with HSPA8 (heat shock protein family A [Hsp70] member 8) and LAMP2A (lysosomal associated membrane protein 2A), two core components of the chaperone-mediated autophagy (CMA) machinery, thus protecting MORC2 from lysosomal degradation by CMA. Functionally, knockdown of MORC2 attenuates E2-induced cell proliferation and enhances cellular sensitivity to TAM and FUL. Moreover, introduction of wild-type MORC2, but not its phosphorylation-lacking mutant (T582A), in MORC2-depleted cells restores resistance to antiestrogens. Clinically, the phosphorylation levels of MORC2 at T582 are elevated in breast tumors from patients undergoing recurrence after TAM treatment. Together, these findings delineate a phosphorylation-dependent mechanism for MORC2 stabilization in response to estrogen and antiestrogens via blocking CMA-mediated lysosomal degradation and uncover a dual role for MORC2 in both estrogen-induced proliferation and resistance to antiestrogen therapies of breast cancer cells. ABBREVIATIONS 4-OHT: 4-hydroxytamoxifen; Baf A1: bafilomycin A1; CMA: chaperone-mediated autophagy; E2: 17β-estradiol; ESR: estrogen receptor; FUL: fulvestrant; GPER1: G protein-coupled estrogen receptor 1; HSPA8: heat shock protein family A (Hsp70) member 8; LAMP2A: lysosomal associated membrane protein 2A; MORC2: MORC family CW-type zinc finger 2; PRKACA: protein kinase cAMP-activated catalytic subunit alpha; TAM: tamoxifen; VCL: vinculin.
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Affiliation(s)
- Fan Yang
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University , Shanghai, China.,Department of Breast Surgery, Shanghai Cancer Center, Shanghai Medical College, Fudan University , Shanghai, China
| | - Hong-Yan Xie
- Cancer Institute, Shanghai Cancer Center, Shanghai Medical College, Fudan University , Shanghai, China.,Department of Oncology, Shanghai Cancer Center, Shanghai Medical College, Fudan University , Shanghai, China
| | - Li-Feng Yang
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University , Shanghai, China
| | - Lin Zhang
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University , Shanghai, China.,Cancer Institute, Shanghai Cancer Center, Shanghai Medical College, Fudan University , Shanghai, China.,Department of Oncology, Shanghai Cancer Center, Shanghai Medical College, Fudan University , Shanghai, China
| | - Fang-Lin Zhang
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University , Shanghai, China.,Cancer Institute, Shanghai Cancer Center, Shanghai Medical College, Fudan University , Shanghai, China.,Department of Oncology, Shanghai Cancer Center, Shanghai Medical College, Fudan University , Shanghai, China
| | - Hong-Yi Liu
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University , Shanghai, China
| | - Da-Qiang Li
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University , Shanghai, China.,Department of Breast Surgery, Shanghai Cancer Center, Shanghai Medical College, Fudan University , Shanghai, China.,Cancer Institute, Shanghai Cancer Center, Shanghai Medical College, Fudan University , Shanghai, China.,Department of Oncology, Shanghai Cancer Center, Shanghai Medical College, Fudan University , Shanghai, China.,Key Laboratory of Medical Epigenetics and Metabolism, Shanghai Medical College, Fudan University , Shanghai, China.,Key Laboratory of Breast Cancer in Shanghai, Shanghai Medical College, Fudan University , Shanghai, China
| | - Zhi-Ming Shao
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University , Shanghai, China.,Department of Breast Surgery, Shanghai Cancer Center, Shanghai Medical College, Fudan University , Shanghai, China.,Cancer Institute, Shanghai Cancer Center, Shanghai Medical College, Fudan University , Shanghai, China.,Department of Oncology, Shanghai Cancer Center, Shanghai Medical College, Fudan University , Shanghai, China.,Key Laboratory of Medical Epigenetics and Metabolism, Shanghai Medical College, Fudan University , Shanghai, China
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42
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Kastenhuber ER, Craig J, Ramsey J, Sullivan KM, Sage J, de Oliveira S, Riehle KJ, Scott JD, Gordan JD, Bardeesy N, Abou-Alfa GK. Road map for fibrolamellar carcinoma: progress and goals of a diversified approach. J Hepatocell Carcinoma 2019; 6:41-48. [PMID: 30951568 PMCID: PMC6362920 DOI: 10.2147/jhc.s194764] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Fibrolamellar carcinoma is a rare liver cancer, which primarily afflicts adolescents and young adults worldwide and is frequently lethal. Given the rarity of this disease, patient recruitment for clinical trials remains a challenge. In November 2017, the Second Fibrolamellar Cancer Foundation Scientific Summit (Stamford, CT, USA) provided an opportunity for investigators to discuss recent advances in the characterization of the disease and its surrounding liver and immune context. The Fibrolamellar Cancer Foundation has thus set out a road map to identify and test therapeutic targets in the most efficient possible manner.
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Affiliation(s)
- Edward R Kastenhuber
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA, .,Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - John Craig
- Fibrolamellar Cancer Foundation, Greenwich, CT, USA
| | - Jon Ramsey
- Department of Biochemistry, University of Vermont Cancer Center, Burlington, VT, USA
| | - Kevin M Sullivan
- Northwest Liver Research Program, University of Washington, Seattle, WA, USA
| | - Julien Sage
- Department of Pediatrics, Stanford University, Stanford, CA, USA.,Department of Genetics, Stanford University, Stanford, CA, USA
| | - Sofia de Oliveira
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI, USA
| | - Kimberly J Riehle
- Northwest Liver Research Program, University of Washington, Seattle, WA, USA
| | - John D Scott
- Northwest Liver Research Program, University of Washington, Seattle, WA, USA
| | - John D Gordan
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Nabeel Bardeesy
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Ghassan K Abou-Alfa
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA, .,Department of Medicine, Weill Cornell School of Medicine, New York, NY, USA,
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43
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Xi Y, Niu J, Li D, He J, Qin L, Peng X. Mixed lineage kinase-4 promotes gastric carcinoma tumorigenesis through suppression of the c-Jun N-terminal kinase signaling pathway. Exp Ther Med 2018; 16:3317-3324. [PMID: 30233678 PMCID: PMC6143876 DOI: 10.3892/etm.2018.6618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 04/21/2017] [Indexed: 01/08/2023] Open
Abstract
Mixed lineage kinase-4 (MLK-4) is an important member of the mixed-lineage family of kinases that regulates the extracellular signal-regulated kinases and c-Jun N-terminal kinase (JNK) signaling pathways. The functions and mechanisms of MLK-4 in cancer initiation and progression have not been well understood. The present study investigated the expression, function and regulatory mechanism of MLK-4 in gastric carcinoma cells. Biochemical data indicated that normal MLK-4 was downregulated, which exerted dominant negative effects on gastric carcinoma cell viability, migration and invasion. The experimental data demonstrated that MLK-4 supplement abrogated activity of these mutants and induced inhibitory effects on gastric carcinoma cell viabilty, migration and invasion in vitro and in vivo. In addition, to determine the regulatory mechanism of MLK-4, its signaling pathway was assessed in gastric carcinoma cancer cells by regulating MLK-4. The present observations indicated that restoring MLK-4 activity by supplemental MLK-4 reduced gastric carcinoma cell colony formation in vitro and suppressed tumor viability, migration and invasion in vivo. The results of the present study indicated that MLK-4 may be a potential protein for targeting gastric carcinoma by suppressing kinases, which may lead to reduction of JNK signaling and enhance therapeutic efficacy in gastric carcinoma.
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Affiliation(s)
- Yu Xi
- Department of General Surgery, Tongji Hospital, Tongji Medical School, Huazhong University of Science and Technology, Wuhan, Hubei 430030, P.R. China
- Department of General Surgery, First Affiliated Hospital, School of Medicine, Shihezi University, Shihezi, Xinjiang 832008, P.R. China
| | - Jianhua Niu
- Department of General Surgery, First Affiliated Hospital, School of Medicine, Shihezi University, Shihezi, Xinjiang 832008, P.R. China
| | - Dongmei Li
- Department of General Surgery, First Affiliated Hospital, School of Medicine, Shihezi University, Shihezi, Xinjiang 832008, P.R. China
| | - Jiagen He
- Department of General Surgery, First Affiliated Hospital, School of Medicine, Shihezi University, Shihezi, Xinjiang 832008, P.R. China
| | - Le Qin
- Department of General Surgery, First Affiliated Hospital, School of Medicine, Shihezi University, Shihezi, Xinjiang 832008, P.R. China
| | - Xinyu Peng
- Department of General Surgery, First Affiliated Hospital, School of Medicine, Shihezi University, Shihezi, Xinjiang 832008, P.R. China
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44
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Ghasabi M, Mansoori B, Mohammadi A, Duijf PH, Shomali N, Shirafkan N, Mokhtarzadeh A, Baradaran B. MicroRNAs in cancer drug resistance: Basic evidence and clinical applications. J Cell Physiol 2018; 234:2152-2168. [PMID: 30146724 DOI: 10.1002/jcp.26810] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 04/30/2018] [Indexed: 12/19/2022]
Abstract
Development of drug resistance has considerably limited the efficacy of cancer treatments, including chemotherapy and targeted therapies. Hence, understanding the molecular mechanisms underpinning the innate or the acquired resistance to these therapies is critical to improve drug efficiency and clinical outcomes. Several studies have implicated microRNAs (miRNA) in this process. MiRNAs repress gene expression by specific binding to complementary sequences in the 3' region of target messenger RNAs (mRNAs), followed by target mRNA degradation or blocked translation. By targeting molecules specific to a particular pathway within tumor cells, the new generation of cancer treatment strategies has shown significant advantages over conventional chemotherapy. However, the long-term efficacy of targeted therapies often remains poor, because tumor cells develop resistance to such therapeutics. Targeted therapies often involve monoclonal antibodies (mAbs), such as those blocking the ErB/HER tyrosine kinases, epidermal growth factor receptor (cetuximab) and HER2 (trastuzumab), and those inhibiting vascular endothelial growth factor receptor signaling (e.g., bevacizumab). Even though these are among the most used agents in tumor medicine, clinical response to these drugs is reduced due to the emergence of drug resistance as a result of toxic effects in the tumor microenvironment. Research on different types of human cancers has revealed that aberrant expression of miRNAs promotes resistance to the aforementioned drugs. In this study, we review the mechanisms of tumor cell resistance to mAb therapies and the role of miRNAs therein. Emerging treatment strategies combine therapies using innovative miRNA mimics or antagonizers with conventional approaches to maximize outcomes of patients with cancer.
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Affiliation(s)
- Mehri Ghasabi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behzad Mansoori
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ali Mohammadi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Pascal Hg Duijf
- University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, Australia
| | - Navid Shomali
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Naghmeh Shirafkan
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ahad Mokhtarzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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45
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Kochanowski K, Morinishi L, Altschuler S, Wu L. Drug persistence - from antibiotics to cancer therapies. CURRENT OPINION IN SYSTEMS BIOLOGY 2018; 10:1-8. [PMID: 30740553 PMCID: PMC6366840 DOI: 10.1016/j.coisb.2018.03.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Drug-insensitive tumor subpopulations remain a significant barrier to effective cancer treatment. Recent works suggest that within isogenic drug-sensitive cancer populations, subsets of cells can enter a 'persister' state allowing them to survive prolonged drug treatment. Such persisters are well-described in antibiotic-treated bacterial populations. In this review, we compare mechanisms of drug persistence in bacteria and cancer. Both bacterial and cancer persisters are associated with slow-growing phenotypes, are metabolically distinct from non-persisters, and depend on the activation of specific regulatory programs. Moreover, evidence suggests that bacterial and cancer persisters are an important reservoir for the emergence of drug-resistant mutants. The emerging parallels between persistence in bacteria and cancer can guide efforts to untangle mechanistic links between growth, metabolism, and cellular regulation, and reveal exploitable therapeutic vulnerabilities.
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Affiliation(s)
| | - Leanna Morinishi
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Steven Altschuler
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Lani Wu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
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46
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Guo Y, Gao W, Wang D, Liu W, Liu Z. Gene alterations in monocytes are pathogenic factors for immunoglobulin a nephropathy by bioinformatics analysis of microarray data. BMC Nephrol 2018; 19:184. [PMID: 30029622 PMCID: PMC6053766 DOI: 10.1186/s12882-018-0944-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 06/07/2018] [Indexed: 11/27/2022] Open
Abstract
Background Immunoglobulin A nephropathy (IgAN) is the most frequent primary glomerulopathy worldwide. The study aimed to provide potential molecular biomarkers for IgAN management. Methods The public gene expression profiling GSE58539 was utilized, which contained 17 monocytes samples (8 monocytes samples isolated from IgAN patients and 9 monocytes samples isolated from healthy blood donors). Firstly, differentially expressed genes (DEGs) between the two kinds of samples were identified by limma package. Afterwards, pathway enrichment analysis was implemented. Thereafter, protein-protein interaction (PPI) network was constructed and key nodes in PPI network were predicted using four network centrality analyses. Ultimately, gene functional interaction (FI) was constructed according to expressions in each sample, and then module network was extracted from FI network. Results A total of 678 DEGs were screened out, of these, 72 DEGs were identified as crucial nodes in PPI network that could well distinguish IgAN and healthy samples. In particular, IL6, TNF, IL1B, PRKACA and CCL20 were closely related to pathways such as hematopoietic cell lineage, apoptosis and Toll-like receptor (TLR) signaling pathway. Moreover, 12 genes in the FI network belonged to the 72 identified key nodes, such as CCL20, HDAC10, FPR2 and PRKACA, which were also key genes in 4 module networks. Conclusions Several crucial genes were identified in monocytes of IgAN patients, such as IL6, TNF, IL1B, CCL20, PRKACA, FPR2 and HDAC10. These genes might co-involve in pathways such as TLR and apoptosis signaling during IgAN progression.
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Affiliation(s)
- Yingbo Guo
- Department of Nephropathy, Dongfang Hospital Affiliated to Beijing University of Chinese Medicine, Beijng, 100078, China
| | - Wenfeng Gao
- Department of Urology, Dongzhimen Hospital Affiliated to Beijing University of Chinese Medicine, Beijng, 100700, China
| | - Danyang Wang
- Department of Nephropathy and Endocrinology, Dongzhimen Hospital Affiliated to Beijing University of Chinese Medicine, No. 5 Haiyuncang, Dongcheng District, Beijng City, 100700, China
| | - Weijing Liu
- Department of Nephropathy and Endocrinology, Dongzhimen Hospital Affiliated to Beijing University of Chinese Medicine, No. 5 Haiyuncang, Dongcheng District, Beijng City, 100700, China
| | - Zhongjie Liu
- Department of Nephropathy and Endocrinology, Dongzhimen Hospital Affiliated to Beijing University of Chinese Medicine, No. 5 Haiyuncang, Dongcheng District, Beijng City, 100700, China.
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Bidkhori G, Benfeitas R, Elmas E, Kararoudi MN, Arif M, Uhlen M, Nielsen J, Mardinoglu A. Metabolic Network-Based Identification and Prioritization of Anticancer Targets Based on Expression Data in Hepatocellular Carcinoma. Front Physiol 2018; 9:916. [PMID: 30065658 PMCID: PMC6056771 DOI: 10.3389/fphys.2018.00916] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 06/22/2018] [Indexed: 12/23/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a deadly form of liver cancer with high mortality worldwide. Unfortunately, the large heterogeneity of this disease makes it difficult to develop effective treatment strategies. Cellular network analyses have been employed to study heterogeneity in cancer, and to identify potential therapeutic targets. However, the existing approaches do not consider metabolic growth requirements, i.e., biological network functionality, to rank candidate targets while preventing toxicity to non-cancerous tissues. Here, we developed an algorithm to overcome these issues based on integration of gene expression data, genome-scale metabolic models, network controllability, and dispensability, as well as toxicity analysis. This method thus predicts and ranks potential anticancer non-toxic controlling metabolite and gene targets. Our algorithm encompasses both objective-driven and-independent tasks, and uses network topology to finally rank the predicted therapeutic targets. We employed this algorithm to the analysis of transcriptomic data for 50 HCC patients with both cancerous and non-cancerous samples. We identified several potential targets that would prevent cell growth, including 74 anticancer metabolites, and 3 gene targets (PRKACA, PGS1, and CRLS1). The predicted anticancer metabolites showed good agreement with existing FDA-approved cancer drugs, and the 3 genes were experimentally validated by performing experiments in HepG2 and Hep3B liver cancer cell lines. Our observations indicate that our novel approach successfully identifies therapeutic targets for effective treatment of cancer. This approach may also be applied to any cancer type that has tumor and non-tumor gene or protein expression data.
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Affiliation(s)
- Gholamreza Bidkhori
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Rui Benfeitas
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Ezgi Elmas
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | | | - Muhammad Arif
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Mathias Uhlen
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Adil Mardinoglu
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden.,Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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48
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Characterizing Cancer Drug Response and Biological Correlates: A Geometric Network Approach. Sci Rep 2018; 8:6402. [PMID: 29686393 PMCID: PMC5913269 DOI: 10.1038/s41598-018-24679-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 04/09/2018] [Indexed: 12/13/2022] Open
Abstract
In the present work, we apply a geometric network approach to study common biological features of anticancer drug response. We use for this purpose the panel of 60 human cell lines (NCI-60) provided by the National Cancer Institute. Our study suggests that mathematical tools for network-based analysis can provide novel insights into drug response and cancer biology. We adopted a discrete notion of Ricci curvature to measure, via a link between Ricci curvature and network robustness established by the theory of optimal mass transport, the robustness of biological networks constructed with a pre-treatment gene expression dataset and coupled the results with the GI50 response of the cell lines to the drugs. Based on the resulting drug response ranking, we assessed the impact of genes that are likely associated with individual drug response. For genes identified as important, we performed a gene ontology enrichment analysis using a curated bioinformatics database which resulted in biological processes associated with drug response across cell lines and tissue types which are plausible from the point of view of the biological literature. These results demonstrate the potential of using the mathematical network analysis in assessing drug response and in identifying relevant genomic biomarkers and biological processes for precision medicine.
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49
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Wu J, Gao F, Xu T, Deng X, Wang C, Yang X, Hu Z, Long Y, He X, Liang G, Ren D, Dai T. miR-503 suppresses the proliferation and metastasis of esophageal squamous cell carcinoma by triggering autophagy via PKA/mTOR signaling. Int J Oncol 2018; 52:1427-1442. [PMID: 29568867 PMCID: PMC5873897 DOI: 10.3892/ijo.2018.4320] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 02/14/2018] [Indexed: 12/24/2022] Open
Abstract
MicroRNA (miR)-503 is involved in the regulation of the malignant phenotype in multiple tumor types, and has been proven to be a novel diagnostic and therapeutic target; however, its function and mechanisms of action have not yet been fully elucidated in esophageal squamous cell carcinoma (ESCC). In the current study, we detected miR‑503 expression by RT‑qPCR and found that miR‑503 expression was increased in ESCC, but negatively correlated with lymph node metastasis, TNM stage and tumor differentiation. Functionally, we confirmed that miR‑503 inhibited the proliferation and metastasis of ESCC cells by triggering cellular autophagy. Mechanistically, we confirmed that miR‑503 exerted its biological effects by targeting protein kinase CAMP‑activated catalytic subunit alpha (PRKACA) in ESCC by dual luciferase reporter assay. Moreover, miR‑503 was found to trigger autophagy in ESCC cells through the protein kinase A (PKA)/mammalian target of rapamycin (mTOR) pathway. Taken together, our results demonstrate that miR‑503 suppresses the proliferation and metastasis of ESCC via the activation of autophagy, mediated by the PKA/mTOR signaling pathway.
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Affiliation(s)
- Jian Wu
- Department of Thoracic Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Fengxia Gao
- Department of Immunology, College of Basic Medicine, Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Tao Xu
- Department of Thoracic Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Xin Deng
- Drug Discovery Research Center, Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Chao Wang
- Department of Thoracic Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Xiaoyan Yang
- Department of Thoracic Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Zhi Hu
- Department of Thoracic Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Yang Long
- Experiment Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Xuemei He
- Experiment Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Guannan Liang
- Experiment Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Delian Ren
- Department of Immunology, College of Basic Medicine, Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Tianyang Dai
- Department of Thoracic Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
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Jiang P, Lee W, Li X, Johnson C, Liu JS, Brown M, Aster JC, Liu XS. Genome-Scale Signatures of Gene Interaction from Compound Screens Predict Clinical Efficacy of Targeted Cancer Therapies. Cell Syst 2018; 6:343-354.e5. [PMID: 29428415 DOI: 10.1016/j.cels.2018.01.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 10/21/2017] [Accepted: 01/05/2018] [Indexed: 12/11/2022]
Abstract
Identifying reliable drug response biomarkers is a significant challenge in cancer research. We present computational analysis of resistance (CARE), a computational method focused on targeted therapies, to infer genome-wide transcriptomic signatures of drug efficacy from cell line compound screens. CARE outputs genome-scale scores to measure how the drug target gene interacts with other genes to affect the inhibitor efficacy in the compound screens. Such statistical interactions between drug targets and other genes were not considered in previous studies but are critical in identifying predictive biomarkers. When evaluated using transcriptome data from clinical studies, CARE can predict the therapy outcome better than signatures from other computational methods and genomics experiments. Moreover, the CARE signatures for the PLX4720 BRAF inhibitor are associated with an anti-programmed death 1 clinical response, suggesting a common efficacy signature between a targeted therapy and immunotherapy. When searching for genes related to lapatinib resistance, CARE identified PRKD3 as the top candidate. PRKD3 inhibition, by both small interfering RNA and compounds, significantly sensitized breast cancer cells to lapatinib. Thus, CARE should enable large-scale inference of response biomarkers and drug combinations for targeted therapies using compound screen data.
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Affiliation(s)
- Peng Jiang
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA
| | - Winston Lee
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Xujuan Li
- School of Life Science and Technology, Tongji University, Shanghai 200092, China
| | - Carl Johnson
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Jun S Liu
- Department of Statistics, Harvard University, Cambridge, MA 02138, USA
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02115, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | | | - X Shirley Liu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA; School of Life Science and Technology, Tongji University, Shanghai 200092, China; Department of Statistics, Harvard University, Cambridge, MA 02138, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02115, USA.
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