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Norris AC, Mansueto AJ, Jimenez M, Yazlovitskaya EM, Jain BK, Graham TR. Flipping the script: Advances in understanding how and why P4-ATPases flip lipid across membranes. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119700. [PMID: 38382846 DOI: 10.1016/j.bbamcr.2024.119700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 11/15/2023] [Accepted: 02/16/2024] [Indexed: 02/23/2024]
Abstract
Type IV P-type ATPases (P4-ATPases) are a family of transmembrane enzymes that translocate lipid substrates from the outer to the inner leaflet of biological membranes and thus create an asymmetrical distribution of lipids within membranes. On the cellular level, this asymmetry is essential for maintaining the integrity and functionality of biological membranes, creating platforms for signaling events and facilitating vesicular trafficking. On the organismal level, this asymmetry has been shown to be important in maintaining blood homeostasis, liver metabolism, neural development, and the immune response. Indeed, dysregulation of P4-ATPases has been linked to several diseases; including anemia, cholestasis, neurological disease, and several cancers. This review will discuss the evolutionary transition of P4-ATPases from cation pumps to lipid flippases, the new lipid substrates that have been discovered, the significant advances that have been achieved in recent years regarding the structural mechanisms underlying the recognition and flipping of specific lipids across biological membranes, and the consequences of P4-ATPase dysfunction on cellular and physiological functions. Additionally, we emphasize the requirement for additional research to comprehensively understand the involvement of flippases in cellular physiology and disease and to explore their potential as targets for therapeutics in treating a variety of illnesses. The discussion in this review will primarily focus on the budding yeast, C. elegans, and mammalian P4-ATPases.
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Affiliation(s)
- Adriana C Norris
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | | | - Mariana Jimenez
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | | | - Bhawik K Jain
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Todd R Graham
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.
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La Marca JE, Aubrey BJ, Yang B, Chang C, Wang Z, Kueh A, Tai L, Wilcox S, Milla L, Heinzel S, Vremec D, Whelan L, König C, Kaloni D, Voss AK, Strasser A, Diepstraten ST, Herold MJ, Kelly GL. Genome-wide CRISPR screening identifies a role for ARRDC3 in TRP53-mediated responses. Cell Death Differ 2024; 31:150-158. [PMID: 38097622 PMCID: PMC10850147 DOI: 10.1038/s41418-023-01249-3] [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: 08/31/2023] [Revised: 11/09/2023] [Accepted: 11/23/2023] [Indexed: 02/09/2024] Open
Abstract
Whole-genome screens using CRISPR technologies are powerful tools to identify novel tumour suppressors as well as factors that impact responses of malignant cells to anti-cancer agents. Applying this methodology to lymphoma cells, we conducted a genome-wide screen to identify novel inhibitors of tumour expansion that are induced by the tumour suppressor TRP53. We discovered that the absence of Arrestin domain containing 3 (ARRDC3) increases the survival and long-term competitiveness of MYC-driven lymphoma cells when treated with anti-cancer agents that activate TRP53. Deleting Arrdc3 in mice caused perinatal lethality due to various developmental abnormalities, including cardiac defects. Notably, the absence of ARRDC3 markedly accelerated MYC-driven lymphoma development. Thus, ARRDC3 is a new mediator of TRP53-mediated suppression of tumour expansion, and this discovery may open new avenues to harness this process for cancer therapy.
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Affiliation(s)
- John E La Marca
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
- Genome Engineering and Cancer Modelling Program, Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
| | - Brandon J Aubrey
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
- Department of Medicine, Massachusetts General Hospital, Boston, USA
| | - Bruce Yang
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Catherine Chang
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
| | - Zilu Wang
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Andrew Kueh
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
- Genome Engineering and Cancer Modelling Program, Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
| | - Lin Tai
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Genome Engineering and Cancer Modelling Program, Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
| | - Stephen Wilcox
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Liz Milla
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
- Environomics Future Science Platform, Centre for Australian National Biodiversity Research, CSIRO, Canberra, Australia
| | - Susanne Heinzel
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - David Vremec
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
| | - Lauren Whelan
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
| | - Christina König
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Genome Engineering and Cancer Modelling Program, Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
| | - Deeksha Kaloni
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Anne K Voss
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Andreas Strasser
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Sarah T Diepstraten
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Marco J Herold
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia.
- Genome Engineering and Cancer Modelling Program, Olivia Newton-John Cancer Research Institute, Melbourne, Victoria, Australia.
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia.
| | - Gemma L Kelly
- The Walter and Eliza Hall Institute, Parkville, Victoria, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia.
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Yang Z, Zhang S, Xiong J, Xia T, Zhu R, Miao M, Li K, Chen W, Zhang L, You Y, You B. The m 6A demethylases FTO and ALKBH5 aggravate the malignant progression of nasopharyngeal carcinoma by coregulating ARHGAP35. Cell Death Discov 2024; 10:43. [PMID: 38263362 PMCID: PMC10806234 DOI: 10.1038/s41420-024-01810-0] [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: 09/02/2023] [Revised: 12/23/2023] [Accepted: 01/08/2024] [Indexed: 01/25/2024] Open
Abstract
N6-methyladenosine (m6A) is an RNA modification that can be removed by demethylases [fat mass and obesity-associated protein (FTO) and AlkB homolog 5 (ALKBH5)], which regulate gene expression and cell function. We show that m6A levels and m6A demethylase levels are altered in nasopharyngeal carcinoma (NPC) tissues vs. normal tissues. High FTO and ALKBH5 predict a poor prognosis in NPC patients. Silencing FTO and ALKBH5 inhibited the malignant behavior of patient-derived NPC cells in a short time. However, as time progressed, the inhibitory effect of FTO or ALKBH5 was weakened, and the cosilencing of FTO and ALKBH5 maintained a better inhibitory effect. Combined transcriptome and m6A-seq analysis revealed a downstream target gene that was jointly regulated by FTO and ALKBH5 in NPC, and ARHGAP35 was chosen to do further study. The synergistic silencing of FTO and ALKBH5 increased the methylation level on the mRNA CDS of a new transcription factor (ARHGAP35) and positively regulate the protein coding capacity and mRNA stability of ARHGAP35, thus leading to increased expression of ARHGAP35 and inhibition of the malignant phenotype of tumor cells. Our study revealed that the growth and metastasis of NPC can be stably inhibited through synergistic silencing of the demethylases FTO and ALKBH5, which play a positive role in the treatment of NPC by regulating the downstream transcript ARHGAP35 and increasing its m6A level.
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Affiliation(s)
- Zhiyuan Yang
- Department of Otolaryngology Head and Neck Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
- Institute of Otolaryngology Head and Neck Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Siyu Zhang
- Department of Otolaryngology Head and Neck Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
- Institute of Otolaryngology Head and Neck Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Jiayan Xiong
- Institute of Otolaryngology Head and Neck Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
- Medical School of Nantong University, Nantong, China
| | - Tian Xia
- Department of Otolaryngology Head and Neck Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
- Institute of Otolaryngology Head and Neck Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Rui Zhu
- Institute of Otolaryngology Head and Neck Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
- Medical School of Nantong University, Nantong, China
| | - Mengyu Miao
- Institute of Otolaryngology Head and Neck Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
- Medical School of Nantong University, Nantong, China
| | - Keying Li
- Institute of Otolaryngology Head and Neck Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
- Medical School of Nantong University, Nantong, China
| | - Wenyue Chen
- Institute of Otolaryngology Head and Neck Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
- Medical School of Nantong University, Nantong, China
| | - Lin Zhang
- Haimen People's Hospital, Nantong, China
| | - Yiwen You
- Department of Otolaryngology Head and Neck Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China.
- Institute of Otolaryngology Head and Neck Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China.
| | - Bo You
- Department of Otolaryngology Head and Neck Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China.
- Institute of Otolaryngology Head and Neck Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China.
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Yazlovitskaya EM, Graham TR. Type IV P-Type ATPases: Recent Updates in Cancer Development, Progression, and Treatment. Cancers (Basel) 2023; 15:4327. [PMID: 37686603 PMCID: PMC10486736 DOI: 10.3390/cancers15174327] [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: 07/11/2023] [Revised: 08/15/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
Adaptations of cancer cells for survival are remarkable. One of the most significant properties of cancer cells to prevent the immune system response and resist chemotherapy is the altered lipid metabolism and resulting irregular cell membrane composition. The phospholipid distribution in the plasma membrane of normal animal cells is distinctly asymmetric. Lipid flippases are a family of enzymes regulating membrane asymmetry, and the main class of flippases are type IV P-type ATPases (P4-ATPases). Alteration in the function of flippases results in changes to membrane organization. For some lipids, such as phosphatidylserine, the changes are so drastic that they are considered cancer biomarkers. This review will analyze and discuss recent publications highlighting the role that P4-ATPases play in the development and progression of various cancer types, as well as prospects of targeting P4-ATPases for anti-cancer treatment.
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Affiliation(s)
| | - Todd R. Graham
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
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Plianchaisuk A, Kusama K, Kato K, Sriswasdi S, Tamura K, Iwasaki W. Origination of LTR retroelement-derived NYNRIN coincides with therian placental emergence. Mol Biol Evol 2022; 39:6661932. [PMID: 35959649 PMCID: PMC9447858 DOI: 10.1093/molbev/msac176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The emergence of the placenta is a revolutionary event in the evolution of therian mammals, to which some LTR retroelement–derived genes, such as PEG10, RTL1, and syncytin, are known to contribute. However, therian genomes contain many more LTR retroelement–derived genes that may also have contributed to placental evolution. We conducted large-scale evolutionary genomic and transcriptomic analyses to comprehensively search for LTR retroelement–derived genes whose origination coincided with therian placental emergence and that became consistently expressed in therian placentae. We identified NYNRIN as another Ty3/Gypsy LTR retroelement–derived gene likely to contribute to placental emergence in the therian stem lineage. NYNRIN knockdown inhibited the invasion of HTR8/SVneo invasive-type trophoblasts, whereas the knockdown of its nonretroelement-derived homolog KHNYN did not. Functional enrichment analyses suggested that NYNRIN modulates trophoblast invasion by regulating epithelial-mesenchymal transition and extracellular matrix remodeling and that the ubiquitin-proteasome system is responsible for the functional differences between NYNRIN and KHNYN. These findings extend our knowledge of the roles of LTR retroelement–derived genes in the evolution of therian mammals.
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Affiliation(s)
- Arnon Plianchaisuk
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-0882, Japan
| | - Kazuya Kusama
- Department of Endocrine Pharmacology, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Kiyoko Kato
- Department of Obstetrics and Gynecology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka, Japan
| | - Sira Sriswasdi
- Center of Excellence in Computational Molecular Biology, Research Affairs, Faculty of Medicine, Chulalongkorn University, Pathum Wan, Bangkok, 10330, Thailand
| | - Kazuhiro Tamura
- Department of Endocrine Pharmacology, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Wataru Iwasaki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-0882, Japan.,Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-0882, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan.,Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, 277-0882, Japan.,Institute for Quantitative Biosciences, The University of Tokyo. Bunkyo-ku, Tokyo 113-0032, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
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Bacolod MD, Fisher PB, Barany F. Multi-CpG linear regression models to accurately predict paclitaxel and docetaxel activity in cancer cell lines. Adv Cancer Res 2022; 158:233-292. [PMID: 36990534 DOI: 10.1016/bs.acr.2022.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The microtubule-targeting paclitaxel (PTX) and docetaxel (DTX) are widely used chemotherapeutic agents. However, the dysregulation of apoptotic processes, microtubule-binding proteins, and multi-drug resistance efflux and influx proteins can alter the efficacy of taxane drugs. In this review, we have created multi-CpG linear regression models to predict the activities of PTX and DTX drugs through the integration of publicly available pharmacological and genome-wide molecular profiling datasets generated using hundreds of cancer cell lines of diverse tissue of origin. Our findings indicate that linear regression models based on CpG methylation levels can predict PTX and DTX activities (log-fold change in viability relative to DMSO) with high precision. For example, a 287-CpG model predicts PTX activity at R2 of 0.985 among 399 cell lines. Just as precise (R2=0.996) is a 342-CpG model for predicting DTX activity in 390 cell lines. However, our predictive models, which employ a combination of mRNA expression and mutation as input variables, are less accurate compared to the CpG-based models. While a 290 mRNA/mutation model was able to predict PTX activity with R2 of 0.830 (for 546 cell lines), a 236 mRNA/mutation model could calculate DTX activity at R2 of 0.751 (for 531 cell lines). The CpG-based models restricted to lung cancer cell lines were also highly predictive (R2≥0.980) for PTX (74 CpGs, 88 cell lines) and DTX (58 CpGs, 83 cell lines). The underlying molecular biology behind taxane activity/resistance is evident in these models. Indeed, many of the genes represented in PTX or DTX CpG-based models have functionalities related to apoptosis (e.g., ACIN1, TP73, TNFRSF10B, DNASE1, DFFB, CREB1, BNIP3), and mitosis/microtubules (e.g., MAD1L1, ANAPC2, EML4, PARP3, CCT6A, JAKMIP1). Also represented are genes involved in epigenetic regulation (HDAC4, DNMT3B, and histone demethylases KDM4B, KDM4C, KDM2B, and KDM7A), and those that have never been previously linked to taxane activity (DIP2C, PTPRN2, TTC23, SHANK2). In summary, it is possible to accurately predict taxane activity in cell lines based entirely on methylation at multiple CpG sites.
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