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Pathania AS, Chava H, Balusu R, Pasupulati AK, Coulter DW, Challagundla KB. The crosstalk between non-coding RNAs and cell-cycle events: A new frontier in cancer therapy. MOLECULAR THERAPY. ONCOLOGY 2024; 32:200785. [PMID: 38595981 PMCID: PMC10973673 DOI: 10.1016/j.omton.2024.200785] [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] [Indexed: 04/11/2024]
Abstract
The cell cycle comprises sequential events during which a cell duplicates its genome and divides it into two daughter cells. This process is tightly regulated to ensure that the daughter cell receives identical copied chromosomal DNA and that any errors in the DNA during replication are correctly repaired. Cyclins and their enzyme partners, cyclin-dependent kinases (CDKs), are critical regulators of G- to M-phase transitions during the cell cycle. Mitogenic signals induce the formation of the cyclin/CDK complexes, resulting in phosphorylation and activation of the CDKs. Once activated, cyclin/CDK complexes phosphorylate specific substrates that drive the cell cycle forward. The sequential activation and inactivation of cyclin-CDK complexes are tightly controlled by activating and inactivating phosphorylation events induced by cell-cycle proteins. The non-coding RNAs (ncRNAs), which do not code for proteins, regulate cell-cycle proteins at the transcriptional and translational levels, thereby controlling their expression at different cell-cycle phases. Deregulation of ncRNAs can cause abnormal expression patterns of cell-cycle-regulating proteins, resulting in abnormalities in cell-cycle regulation and cancer development. This review explores how ncRNA dysregulation can disrupt cell division balance and discusses potential therapeutic approaches targeting these ncRNAs to control cell-cycle events in cancer treatment.
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Affiliation(s)
- Anup S. Pathania
- Department of Biochemistry and Molecular Biology & The Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Haritha Chava
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Ramesh Balusu
- Department of Hematologic Malignancies and Cellular Therapeutics, Kansas University Medical Center, Kansas City, KS 66160, USA
| | - Anil K. Pasupulati
- Department of Biochemistry, University of Hyderabad, Hyderabad, Telangana 500046, India
| | - Don W. Coulter
- Department of Pediatrics, Division of Hematology/Oncology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Kishore B. Challagundla
- Department of Biochemistry and Molecular Biology & The Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
- The Child Health Research Institute, University of Nebraska Medical Center, Omaha, NE 68198, USA
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2
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Royet C, Diot S, Onofre M, Lecki L, Pastore M, Reynes C, Lorcy F, Lacheretzszablewski V, Serre I, Morris MC. Multiplexed Profiling of CDK Kinase Activities in Tumor Biopsies with Fluorescent Peptide Biosensors. ACS Sens 2024. [PMID: 38863434 DOI: 10.1021/acssensors.4c00139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
Detection of disease biomarkers constitutes a major challenge for the development of personalized and predictive diagnostics as well as companion assays. Protein kinases (PKs) involved in the coordination of cell cycle progression and proliferation that are hyperactivated in human cancers constitute attractive pharmacological targets and relevant biomarkers. Although it is relatively straightforward to assess the relative abundance of PKs in a biological sample, there is not always a direct correlation with enzymatic activity, which is regulated by several posttranslational mechanisms. Studies of relative abundance therefore convey limited information, and the lack of selective, sensitive, and standardized tools together with the inherent complexity of biological samples makes it difficult to quantify PK activities in physio-pathological tissues. To address this challenge, we have developed a toolbox of fluorescent biosensors that report on CDK activities in a sensitive, selective, dose-dependent, and quantitative fashion, which we have implemented to profile CDK activity signatures in cancer cell lines and biopsies from human tumors. In this study, we report on a standardized and calibrated biosensing approach to quantify CDK1,2,4, and 6 activities simultaneously through a combination of four different biosensors in a panel of 40 lung adenocarcinoma and 40 follicular lymphoma samples. CDK activity profiling highlighted two major patterns which were further correlated with age, sex of patients, tumor size, grade, and genetic and immunohistochemical features of the biopsies. Multiplex CDKACT biosensing technology provides new and complementary information relative to current genetic and immunohistochemical characterization of tumor biopsies, which will be useful for diagnostic purposes, potentially guiding therapeutic decision. These fluorescent peptide biosensors offer promise for personalized diagnostics based on kinase activity profiling.
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Affiliation(s)
- Chloé Royet
- Institut des Biomolécules Max Mousseron, CNRS, UMR 5247, Montpellier University, 1919 Route de Mende, 34293 Montpellier, France
| | - Sébastien Diot
- Institut des Biomolécules Max Mousseron, CNRS, UMR 5247, Montpellier University, 1919 Route de Mende, 34293 Montpellier, France
| | - Mélanie Onofre
- Institut des Biomolécules Max Mousseron, CNRS, UMR 5247, Montpellier University, 1919 Route de Mende, 34293 Montpellier, France
| | - Lennard Lecki
- Institut des Biomolécules Max Mousseron, CNRS, UMR 5247, Montpellier University, 1919 Route de Mende, 34293 Montpellier, France
| | - Manuela Pastore
- StatABio Facility─Biocampus, UAR 3426 CNRS─US 09 INSERM, Montpellier University, 141 rue de la Cardonille, 34094 Montpellier Cedex 05, France
| | - Christelle Reynes
- StatABio Facility─Biocampus, UAR 3426 CNRS─US 09 INSERM, Montpellier University, 141 rue de la Cardonille, 34094 Montpellier Cedex 05, France
| | - Frederique Lorcy
- University Hospital Centre Montpellier, 80 Av. Augustin Fliche, 34295 Montpellier, France
| | | | - Isabelle Serre
- University Hospital Centre Montpellier, 80 Av. Augustin Fliche, 34295 Montpellier, France
| | - May C Morris
- Institut des Biomolécules Max Mousseron, CNRS, UMR 5247, Montpellier University, 1919 Route de Mende, 34293 Montpellier, France
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Siddique R, Thangavelu L, S R, Almalki WH, Kazmi I, Kumar A, Mahajan S, Kalra H, Alzarea SI, Pant K. lncRNAs and cyclin-dependent kinases: Unveiling their critical roles in cancer progression. Pathol Res Pract 2024; 258:155333. [PMID: 38723325 DOI: 10.1016/j.prp.2024.155333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/24/2024] [Accepted: 04/24/2024] [Indexed: 05/29/2024]
Abstract
Long non-coding RNAs (lncRNAs) are a diverse class of RNA molecules that do not code for proteins but play critical roles in gene regulation. One such role involves the modulation of cell cycle progression and proliferation through interactions with cyclin-dependent kinases (CDKs), key regulators of cell division. Dysregulation of CDK activity is a hallmark of cancer, contributing to uncontrolled cell growth and tumor formation. These lncRNA-CDK interactions are part of a complex network of molecular mechanisms underlying cancer pathogenesis, involving various signaling pathways and regulatory circuits. Understanding the interplay between lncRNAs, CDKs, and cancer biology holds promise for developing novel therapeutic strategies targeting these molecular targets for more effective cancer treatment. Furthermore, targeting CDKs, key cell cycle progression and proliferation regulators, offers another avenue for disrupting cancer pathways and overcoming drug resistance. This can open new possibilities for individualized treatment plans and focused therapeutic interventions.
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Affiliation(s)
- Raihan Siddique
- School of Pharmacy, Suresh Gyan Vihar University, Mahal Road, Jagatpura, Jaipur, India
| | - Lakshmi Thangavelu
- Center for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, India.
| | - RenukaJyothi S
- Department of Biotechnology and Genetics, School of Sciences, JAIN (Deemed to be University), Bangalore, Karnataka, India
| | - Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
| | - Ashwani Kumar
- Department of Pharmacy, Vivekananda Global University, Jaipur, Rajasthan 303012, India
| | - Shriya Mahajan
- Centre of Research Impact and Outcome, Chitkara University, Rajpura, Punjab 140417, India
| | - Hitesh Kalra
- Chitkara Centre for Research and Development, Chitkara University, Himachal Pradesh 174103, India
| | - Sami I Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, 72341, Sakaka, Al-Jouf, Saudi Arabia
| | - Kumud Pant
- Graphic Era (Deemed to be University), Clement Town, Dehradun 248002, India; Graphic Era Hill University, Clement Town, Dehradun 248002, India
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4
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Ramakanth S, Kennedy T, Yalcinkaya B, Neupane S, Tadic N, Buchler NE, Argüello-Miranda O. Deep learning-driven imaging of cell division and cell growth across an entire eukaryotic life cycle. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.591211. [PMID: 38712227 PMCID: PMC11071524 DOI: 10.1101/2024.04.25.591211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The life cycle of biomedical and agriculturally relevant eukaryotic microorganisms involves complex transitions between proliferative and non-proliferative states such as dormancy, mating, meiosis, and cell division. New drugs, pesticides, and vaccines can be created by targeting specific life cycle stages of parasites and pathogens. However, defining the structure of a microbial life cycle often relies on partial observations that are theoretically assembled in an ideal life cycle path. To create a more quantitative approach to studying complete eukaryotic life cycles, we generated a deep learning-driven imaging framework to track microorganisms across sexually reproducing generations. Our approach combines microfluidic culturing, life cycle stage-specific segmentation of microscopy images using convolutional neural networks, and a novel cell tracking algorithm, FIEST, based on enhancing the overlap of single cell masks in consecutive images through deep learning video frame interpolation. As proof of principle, we used this approach to quantitatively image and compare cell growth and cell cycle regulation across the sexual life cycle of Saccharomyces cerevisiae . We developed a fluorescent reporter system based on a fluorescently labeled Whi5 protein, the yeast analog of mammalian Rb, and a new High-Cdk1 activity sensor, LiCHI, designed to report during DNA replication, mitosis, meiotic homologous recombination, meiosis I, and meiosis II. We found that cell growth preceded the exit from non-proliferative states such as mitotic G1, pre-meiotic G1, and the G0 spore state during germination. A decrease in the total cell concentration of Whi5 characterized the exit from non-proliferative states, which is consistent with a Whi5 dilution model. The nuclear accumulation of Whi5 was developmentally regulated, being at its highest during meiotic exit and spore formation. The temporal coordination of cell division and growth was not significantly different across three sexually reproducing generations. Our framework could be used to quantitatively characterize other single-cell eukaryotic life cycles that remain incompletely described. An off-the-shelf user interface Yeastvision provides free access to our image processing and single-cell tracking algorithms.
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Athwal H, Kochiyanil A, Bhat V, Allan AL, Parsyan A. Centrosomes and associated proteins in pathogenesis and treatment of breast cancer. Front Oncol 2024; 14:1370565. [PMID: 38606093 PMCID: PMC11007099 DOI: 10.3389/fonc.2024.1370565] [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: 01/14/2024] [Accepted: 03/04/2024] [Indexed: 04/13/2024] Open
Abstract
Breast cancer is the most prevalent malignancy among women worldwide. Despite significant advances in treatment, it remains one of the leading causes of female mortality. The inability to effectively treat advanced and/or treatment-resistant breast cancer demonstrates the need to develop novel treatment strategies and targeted therapies. Centrosomes and their associated proteins have been shown to play key roles in the pathogenesis of breast cancer and thus represent promising targets for drug and biomarker development. Centrosomes are fundamental cellular structures in the mammalian cell that are responsible for error-free execution of cell division. Centrosome amplification and aberrant expression of its associated proteins such as Polo-like kinases (PLKs), Aurora kinases (AURKs) and Cyclin-dependent kinases (CDKs) have been observed in various cancers, including breast cancer. These aberrations in breast cancer are thought to cause improper chromosomal segregation during mitosis, leading to chromosomal instability and uncontrolled cell division, allowing cancer cells to acquire new genetic changes that result in evasion of cell death and the promotion of tumor formation. Various chemical compounds developed against PLKs and AURKs have shown meaningful antitumorigenic effects in breast cancer cells in vitro and in vivo. The mechanism of action of these inhibitors is likely related to exacerbation of numerical genomic instability, such as aneuploidy or polyploidy. Furthermore, growing evidence demonstrates enhanced antitumorigenic effects when inhibitors specific to centrosome-associated proteins are used in combination with either radiation or chemotherapy drugs in breast cancer. This review focuses on the current knowledge regarding the roles of centrosome and centrosome-associated proteins in breast cancer pathogenesis and their utility as novel targets for breast cancer treatment.
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Affiliation(s)
- Harjot Athwal
- Department of Anatomy and Cell Biology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Arpitha Kochiyanil
- Faculty of Science, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Vasudeva Bhat
- Department of Anatomy and Cell Biology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- London Regional Cancer Program, London Health Sciences Centre, Lawson Health Research Institute, London, ON, Canada
| | - Alison L. Allan
- Department of Anatomy and Cell Biology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- London Regional Cancer Program, London Health Sciences Centre, Lawson Health Research Institute, London, ON, Canada
- Department of Oncology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Armen Parsyan
- Department of Anatomy and Cell Biology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- London Regional Cancer Program, London Health Sciences Centre, Lawson Health Research Institute, London, ON, Canada
- Department of Oncology, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Division of General Surgery, Department of Surgery, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Department of Surgery, St. Joseph’s Health Care London and London Health Sciences Centre, London, ON, Canada
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6
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Kang X, Chen H, Zhou Z, Tu S, Cui B, Li Y, Dong S, Zhang Q, Xu Y. Targeting Cyclin-Dependent Kinase 1 Induces Apoptosis and Cell Cycle Arrest of Activated Hepatic Stellate Cells. Adv Biol (Weinh) 2024; 8:e2300403. [PMID: 38103005 DOI: 10.1002/adbi.202300403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/08/2023] [Indexed: 12/17/2023]
Abstract
Liver fibrosis is the integral process of chronic liver diseases caused by multiple etiologies and characterized by excessive deposition of extracellular matrix (ECM). During liver fibrosis, hepatic stellate cells (HSCs) transform into a highly proliferative, activated state, producing various cytokines, chemokines, and ECM. However, the precise mechanisms that license HSCs into the highly proliferative state remain unclear. Cyclin-dependent kinase 1 (CDK1) is a requisite event for the transition of the G1/S and G2/M phases in eukaryotic cells. In this study, it is demonstrated that CDK1 and its activating partners, Cyclin A2 and Cyclin B1, are upregulated in both liver fibrosis/cirrhosis patient specimens and the murine hepatic fibrosis models, especially in activated HSCs. In vitro, CDK1 is upregulated in spontaneously activated HSCs, and inhibiting CDK1 with specific small-molecule inhibitors (CGP74514A, RO-3306, or Purvalanol A) orshort hairpin RNAs (shRNAs) resulted in HSC apoptosis and cell cycle arrest by regulating Survivin expression. Above all, it is illustrated that increased CDK1 expression licenses the HSCs into a highly proliferative state and can serve as a potential therapeutic target in liver fibrosis.
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Affiliation(s)
- Xinmei Kang
- Biotherapy Centre, the Third Affiliated Hospital, Sun Yat-sen University, 600# Tianhe Road, Guangzhou, 510630, China
| | - Huaxin Chen
- Biotherapy Centre, the Third Affiliated Hospital, Sun Yat-sen University, 600# Tianhe Road, Guangzhou, 510630, China
| | - Zhuowei Zhou
- Biotherapy Centre, the Third Affiliated Hospital, Sun Yat-sen University, 600# Tianhe Road, Guangzhou, 510630, China
| | - Silin Tu
- Biotherapy Centre, the Third Affiliated Hospital, Sun Yat-sen University, 600# Tianhe Road, Guangzhou, 510630, China
| | - Bo Cui
- Biotherapy Centre, the Third Affiliated Hospital, Sun Yat-sen University, 600# Tianhe Road, Guangzhou, 510630, China
| | - Yanli Li
- Biotherapy Centre, the Third Affiliated Hospital, Sun Yat-sen University, 600# Tianhe Road, Guangzhou, 510630, China
| | - Shuai Dong
- Biotherapy Centre, the Third Affiliated Hospital, Sun Yat-sen University, 600# Tianhe Road, Guangzhou, 510630, China
| | - Qi Zhang
- Biotherapy Centre, the Third Affiliated Hospital, Sun Yat-sen University, 600# Tianhe Road, Guangzhou, 510630, China
- Cell-gene Therapy Translational Medicine Research Centre, the Third Affiliated Hospital, Sun Yat-sen University, 600# Tianhe Road, Guangzhou, 510630, China
- Guangdong Provincial Key Laboratory of Liver Disease Research, the Third Affiliated Hospital, Sun Yat-sen University, 600# Tianhe Road, Guangzhou, 510630, China
| | - Yan Xu
- Biotherapy Centre, the Third Affiliated Hospital, Sun Yat-sen University, 600# Tianhe Road, Guangzhou, 510630, China
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7
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Hyodo T, Asano-Inami E, Ito S, Sugiyama M, Nawa A, Rahman ML, Hasan MN, Mihara Y, Lam VQ, Karnan S, Ota A, Tsuzuki S, Hamaguchi M, Hosokawa Y, Konishi H. Leucine zipper protein 1 (LUZP1) regulates the constriction velocity of the contractile ring during cytokinesis. FEBS J 2024; 291:927-944. [PMID: 38009294 DOI: 10.1111/febs.17017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 09/11/2023] [Accepted: 11/22/2023] [Indexed: 11/28/2023]
Abstract
There has been a great deal of research on cell division and its mechanisms; however, its processes still have many unknowns. To find novel proteins that regulate cell division, we performed the screening using siRNAs and/or the expression plasmid of the target genes and identified leucine zipper protein 1 (LUZP1). Recent studies have shown that LUZP1 interacts with various proteins and stabilizes the actin cytoskeleton; however, the function of LUZP1 in mitosis is not known. In this study, we found that LUZP1 colocalized with the chromosomal passenger complex (CPC) at the centromere in metaphase and at the central spindle in anaphase and that these LUZP1 localizations were regulated by CPC activity and kinesin family member 20A (KIF20A). Mass spectrometry analysis identified that LUZP1 interacted with death-associated protein kinase 3 (DAPK3), one regulator of the cleavage furrow ingression in cytokinesis. In addition, we found that LUZP1 also interacted with myosin light chain 9 (MYL9), a substrate of DAPK3, and comprehensively inhibited MYL9 phosphorylation by DAPK3. In line with a known role for MYL9 in the actin-myosin contraction, LUZP1 suppression accelerated the constriction velocity at the division plane in our time-lapse analysis. Our study indicates that LUZP1 is a novel regulator for cytokinesis that regulates the constriction velocity of the contractile ring.
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Affiliation(s)
- Toshinori Hyodo
- Department of Biochemistry, Aichi Medical University School of Medicine, Nagakute, Japan
| | - Eri Asano-Inami
- Department of Obstetrics and Gynecology Collaborative Research, Bell Research Center, Nagoya University Graduate School of Medicine, Japan
| | | | - Mai Sugiyama
- Department of Obstetrics and Gynecology Collaborative Research, Bell Research Center, Nagoya University Graduate School of Medicine, Japan
| | - Akihiro Nawa
- Department of Obstetrics and Gynecology Collaborative Research, Bell Research Center, Nagoya University Graduate School of Medicine, Japan
| | - Md Lutfur Rahman
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Muhammad Nazmul Hasan
- Department of Biochemistry, Aichi Medical University School of Medicine, Nagakute, Japan
| | - Yuko Mihara
- Department of Biochemistry, Aichi Medical University School of Medicine, Nagakute, Japan
| | - Vu Quang Lam
- Division of Hematology, Department of Internal Medicine, Aichi Medical University School of Medicine, Nagakute, Japan
| | - Sivasundaram Karnan
- Department of Biochemistry, Aichi Medical University School of Medicine, Nagakute, Japan
| | - Akinobu Ota
- Department of Biochemistry, Aichi Medical University School of Medicine, Nagakute, Japan
| | - Shinobu Tsuzuki
- Department of Biochemistry, Aichi Medical University School of Medicine, Nagakute, Japan
| | | | - Yoshitaka Hosokawa
- Department of Biochemistry, Aichi Medical University School of Medicine, Nagakute, Japan
| | - Hiroyuki Konishi
- Department of Biochemistry, Aichi Medical University School of Medicine, Nagakute, Japan
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Joshi JN, Lerner AD, Scallo F, Grumet AN, Matteson P, Millonig JH, Valvezan AJ. mTORC1 activity oscillates throughout the cell cycle promoting mitotic entry and differentially influencing autophagy induction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579216. [PMID: 38370755 PMCID: PMC10871213 DOI: 10.1101/2024.02.06.579216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Mechanistic Target of Rapamycin Complex 1 (mTORC1) is a master metabolic regulator that stimulates anabolic cell growth while suppressing catabolic processes such as autophagy. mTORC1 is active in most, if not all, proliferating eukaryotic cells. However, it remains unclear whether and how mTORC1 activity changes from one cell cycle phase to another. Here we tracked mTORC1 activity through the complete cell cycle and uncover oscillations in its activity. We find that mTORC1 activity peaks in S and G2, and is lowest in mitosis and G1. We further demonstrate that multiple mechanisms are involved in controlling this oscillation. The interphase oscillation is mediated through the TSC complex, an upstream negative regulator of mTORC1, but is independent of major known regulatory inputs to the TSC complex, including Akt, Mek/Erk, and CDK4/6 signaling. By contrast, suppression of mTORC1 activity in mitosis does not require the TSC complex, and instead involves CDK1-dependent control of the subcellular localization of mTORC1 itself. Functionally, we find that in addition to its well-established role in promoting progression through G1, mTORC1 also promotes progression through S and G2, and is important for satisfying the Wee1- and Chk1- dependent G2/M checkpoint to allow entry into mitosis. We also find that low mTORC1 activity in G1 sensitizes cells to autophagy induction in response to partial mTORC1 inhibition or reduced nutrient levels. Together these findings demonstrate that mTORC1 is differentially regulated throughout the cell cycle, with important phase-specific functional consequences in proliferating cells.
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Affiliation(s)
- Jay N. Joshi
- Molecular Biosciences Program, Rutgers University, Piscataway, NJ, USA
- Center for Advanced Biotechnology and Medicine, Piscataway, NJ, USA
| | - Ariel D. Lerner
- Center for Advanced Biotechnology and Medicine, Piscataway, NJ, USA
| | - Frank Scallo
- Center for Advanced Biotechnology and Medicine, Piscataway, NJ, USA
- Present affiliation: Yale School of Medicine, New Haven, CT, USA
| | | | - Paul Matteson
- Center for Advanced Biotechnology and Medicine, Piscataway, NJ, USA
| | - James H. Millonig
- Center for Advanced Biotechnology and Medicine, Piscataway, NJ, USA
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | - Alexander J. Valvezan
- Center for Advanced Biotechnology and Medicine, Piscataway, NJ, USA
- Department of Pharmacology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
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9
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Paul S, Sarraf SA, Nam KH, Zavar L, DeFoor N, Biswas SR, Fritsch LE, Yaron TM, Johnson JL, Huntsman EM, Cantley LC, Ordureau A, Pickrell AM. NAK-associated protein 1/NAP1 activates TBK1 to ensure accurate mitosis and cytokinesis. J Cell Biol 2024; 223:e202303082. [PMID: 38059900 PMCID: PMC10702366 DOI: 10.1083/jcb.202303082] [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: 03/20/2023] [Revised: 10/03/2023] [Accepted: 11/10/2023] [Indexed: 12/08/2023] Open
Abstract
Subcellular location and activation of Tank Binding Kinase 1 (TBK1) govern precise progression through mitosis. Either loss of activated TBK1 or its sequestration from the centrosomes causes errors in mitosis and growth defects. Yet, what regulates its recruitment and activation on the centrosomes is unknown. We identified that NAK-associated protein 1 (NAP1) is essential for mitosis, binding to and activating TBK1, which both localize to centrosomes. Loss of NAP1 causes several mitotic and cytokinetic defects due to inactivation of TBK1. Our quantitative phosphoproteomics identified numerous TBK1 substrates that are not only confined to the centrosomes but are also associated with microtubules. Substrate motifs analysis indicates that TBK1 acts upstream of other essential cell cycle kinases like Aurora and PAK kinases. We also identified NAP1 as a TBK1 substrate phosphorylating NAP1 at S318 to promote its degradation by the ubiquitin proteasomal system. These data uncover an important distinct function for the NAP1-TBK1 complex during cell division.
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Affiliation(s)
- Swagatika Paul
- Graduate Program in Biomedical and Veterinary Sciences, Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA, USA
| | - Shireen A. Sarraf
- Biochemistry Section, National Institutes of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Ki Hong Nam
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Leila Zavar
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Nicole DeFoor
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Sahitya Ranjan Biswas
- Translational Biology, Medicine, and Health Graduate Program, Virginia Polytechnic Institute and State University, Roanoke, VA, USA
| | - Lauren E. Fritsch
- Translational Biology, Medicine, and Health Graduate Program, Virginia Polytechnic Institute and State University, Roanoke, VA, USA
| | - Tomer M. Yaron
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | | | - Emily M. Huntsman
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Lewis C. Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Alban Ordureau
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alicia M. Pickrell
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
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10
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Wang S, Wang J, Xia Y, Zhang L, Jiang Y, Liu M, Gao Q, Zhang C. Harnessing the potential of HLA-G in cancer therapy: advances, challenges, and prospects. J Transl Med 2024; 22:130. [PMID: 38310272 PMCID: PMC10838004 DOI: 10.1186/s12967-024-04938-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/27/2024] [Indexed: 02/05/2024] Open
Abstract
Immune checkpoint blockades have been prized in circumventing and ablating the impediments posed by immunosuppressive receptors, reaching an exciting juncture to be an innovator in anticancer therapy beyond traditional therapeutics. Thus far, approved immune checkpoint blockades have principally targeted PD-1/PD-L1 and CTLA-4 with exciting success in a plethora of tumors and yet are still trapped in dilemmas of limited response rates and adverse effects. Hence, unveiling new immunotherapeutic targets has aroused immense scientific interest in the hope of expanding the clinical application of immune checkpoint blockades to scale new heights. Human leukocyte antigen-G (HLA-G), a non-classical major histocompatibility complex (MHC) class I molecule, is enriched on various malignant cells and is involved in the hindrance of immune effector cells and the facilitation of immunosuppressive cells. HLA-G stands out as a crucial next-generation immune checkpoint showing great promise for the benefit of cancer patients. Here, we provide an overview of the current understanding of the expression pattern and immunological functions of HLA-G, as well as its interaction with well-characterized immune checkpoints. Since HLA-G can be shed from the cell surface or released by various cells as free soluble HLA-G (sHLA-G) or as part of extracellular vesicles (EVs), namely HLA-G-bearing EVs (HLA-GEV), we discuss the potential of sHLA-G and HLA-GEV as predictive biomarkers. This review also addresses the advancement of HLA-G-based therapies in preclinical and clinical settings, with a focus on their clinical application in cancer.
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Affiliation(s)
- Siyuan Wang
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China
- Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China
| | - Jiaxin Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China
| | - Yu Xia
- Cancer Biology Research Center (Key Laboratory of Chinese Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Ave, Wuhan, 430030, China
- Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China
| | - Le Zhang
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China
- Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China
| | - Yueqiang Jiang
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China
- Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China
| | - Man Liu
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China
- Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China
| | - Qinglei Gao
- Cancer Biology Research Center (Key Laboratory of Chinese Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Ave, Wuhan, 430030, China.
- Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China.
| | - Cuntai Zhang
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China.
- Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, China.
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11
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Ros-Carrero C, Spiridon-Bodi M, Igual JC, Gomar-Alba M. The CDK Pho85 inhibits Whi7 Start repressor to promote cell cycle entry in budding yeast. EMBO Rep 2024; 25:745-769. [PMID: 38233717 PMCID: PMC10897450 DOI: 10.1038/s44319-023-00049-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 12/15/2023] [Accepted: 12/19/2023] [Indexed: 01/19/2024] Open
Abstract
Pho85 is a multifunctional CDK that signals to the cell when environmental conditions are favorable. It has been connected to cell cycle control, mainly in Start where it promotes the G1/S transition. Here we describe that the Start repressor Whi7 is a key target of Pho85 in the regulation of cell cycle entry. The phosphorylation of Whi7 by Pho85 inhibits the repressor and explains most of the contribution of the CDK in the activation of Start. Mechanistically, Pho85 downregulates Whi7 protein levels through the control of Whi7 protein stability and WHI7 gene transcription. Whi7 phosphorylation by Pho85 also restrains the intrinsic ability of Whi7 to associate with promoters. Furthermore, although Whi5 is the main Start repressor in normal cycling cells, in the absence of Pho85, Whi7 becomes the major repressor leading to G1 arrest. Overall, our results reveal a novel mechanism by which Pho85 promotes Start through the regulation of the Whi7 repressor at multiple levels, which may confer to Whi7 a functional specialization to connect the response to adverse conditions with the cell cycle control.
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Affiliation(s)
- Cristina Ros-Carrero
- Institut de Biotecnologia i Biomedicina (BIOTECMED) and Departament de Bioquímica i Biologia Molecular, Universitat de València, 46100, Burjassot, Spain
| | - Mihai Spiridon-Bodi
- Institut de Biotecnologia i Biomedicina (BIOTECMED) and Departament de Bioquímica i Biologia Molecular, Universitat de València, 46100, Burjassot, Spain
| | - J Carlos Igual
- Institut de Biotecnologia i Biomedicina (BIOTECMED) and Departament de Bioquímica i Biologia Molecular, Universitat de València, 46100, Burjassot, Spain.
| | - Mercè Gomar-Alba
- Institut de Biotecnologia i Biomedicina (BIOTECMED) and Departament de Bioquímica i Biologia Molecular, Universitat de València, 46100, Burjassot, Spain.
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12
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Zhang B, Zhou B, Huang G, Huang J, Lin X, Li Z, Lian Y, Huang Q, Ye Y. Nitidine chloride inhibits G2/M phase by regulating the p53/14-3-3 Sigma/CDK1 axis for hepatocellular carcinoma treatment. Heliyon 2024; 10:e24012. [PMID: 38283241 PMCID: PMC10818205 DOI: 10.1016/j.heliyon.2024.e24012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 01/30/2024] Open
Abstract
Background Liver cancer had become the sixth most common cancer. Nitidine chloride (NC) has demonstrated promising anti-HCC properties; however, further elucidation of its mechanism of action is necessary. Methods The anti-HCC targets of NC were identified through the utilization of multiple databases and ChIPs data analysis. The GO and KEGG analyses to determine the specific pathway affected by NC. The Huh 7 and Hep G2 cells were subjected to a 24-h treatment with NC, followed by evaluating the impact of NC on cell proliferation and cell cycle. The involvement of the p53/14-3-3 Sigma/CDK1 axis in HCC cells was confirmed by qPCR and WB analysis of the corresponding genes and proteins. Results The GO and KEGG analysis showed the targets were related to cell cycle and p53 signaling pathways. In vitro experiments showed that NC significantly inhibited the proliferation of HCC cells and induced G2/M phase arrest. In addition, qPCR and WB experiments showed that the expression of p53 in HCC cells increased after NC intervention, while the expression of 14-3-3 Sigma and CDK1 decreased. Conclusion NC can inhibit the proliferation of HCC cells and induce G2/M cell cycle arrest, potentially by regulating the p53/14-3-3 Sigma/CDK1 axis.
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Affiliation(s)
- Bo Zhang
- Scientific Research Center, Guilin Medical University, Guilin, China
| | - Bo Zhou
- Scientific Research Center, Guilin Medical University, Guilin, China
| | - Guihong Huang
- Department of Pharmacy, The Second Affiliated Hospital of Guilin Medical University, Guilin, China
- Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, Key Laboratory of Diabetic Systems Medicine, The Second Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, 541199, China
- Guangxi Key Laboratory of Drug Discovery and Optimization, Guangxi Engineering Research Center for Pharmaceutical Molecular Screening and Druggability Evaluation, School of Pharmacy, Guilin Medical University, Guilin, Guangxi, 541199, China
| | - Jing'an Huang
- Scientific Research Center, Guilin Medical University, Guilin, China
| | - Xiaoxin Lin
- Scientific Research Center, Guilin Medical University, Guilin, China
| | - Zonghuai Li
- Scientific Research Center, Guilin Medical University, Guilin, China
| | - Yuanchu Lian
- Scientific Research Center, Guilin Medical University, Guilin, China
| | - Qiujie Huang
- Guangxi University of Chinese Medicine, Teaching Experiment and Training Center, Nanning, China
| | - Yong Ye
- School of Pharmacy, Guangxi Medical University, Guangxi, China
- Guangxi Key Laboratory of Bioactive Molecules Research and Evaluation, China
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13
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Chen YJ, Ferdousi F, Bejaoui M, Sasaki K, Isoda H. Microarray meta-analysis reveals comprehensive effects of 3,4,5-tricaffeolyquinic acid in cell differentiation and signaling. Eur J Pharmacol 2023; 960:176143. [PMID: 37866748 DOI: 10.1016/j.ejphar.2023.176143] [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: 08/30/2023] [Revised: 10/14/2023] [Accepted: 10/19/2023] [Indexed: 10/24/2023]
Abstract
Caffeoylquinic acids (CQA) are polyphenolic compounds found in fruits, vegetables, coffee, and spices that have exhibited several beneficial activities, including antioxidant, antibacterial, neuroprotective, anti-inflammatory, anticancer, antiviral, antidiabetic, and cardiovascular effects. A derivative, TCQA (3,4,5-Tri-O-caffeoylquinic acid), has also shown both neurogenic and pigment differentiation potential. A transcriptomic-based meta-analysis was conducted to explore potential biochemical processes and molecular targets of TCQA. This approach involved integrating data from various cell and tissue types, including human amniotic stem cells, human neural stem cells, human dermal papilla cells, and the brain cortex of aging model mice. It offered a comprehensive perspective on the significant gene regulations in response to TCQA treatment. The objective was to uncover the mechanism and novel targets of TCQA, facilitating a further understanding of its functions. New areas of interest found were TCQA's effect on adipogenesis, heart, and muscle tissue development. In addition, significantly enhanced biological activities found through meta-analysis included cell cycle, VEGFA-VEGFR2 pathway, and BMP signaling. Overall, a comprehensive functional and visual analysis using available biological databases uncovered the multi-target potential of this natural compound.
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Affiliation(s)
- Yu Jia Chen
- Tsukuba Life Science Innovation Program (T-LSI), Graduate School of Science and Technology, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan; Open Innovation Laboratory for Food and Medicinal Resource Engineering (FoodMed-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8577, Japan
| | - Farhana Ferdousi
- Tsukuba Life Science Innovation Program (T-LSI), Graduate School of Science and Technology, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan; Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan; Alliance for Research on the Mediterranean and North Africa (ARENA), University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Meriem Bejaoui
- Open Innovation Laboratory for Food and Medicinal Resource Engineering (FoodMed-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8577, Japan; Alliance for Research on the Mediterranean and North Africa (ARENA), University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Kazunori Sasaki
- Open Innovation Laboratory for Food and Medicinal Resource Engineering (FoodMed-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8577, Japan; Alliance for Research on the Mediterranean and North Africa (ARENA), University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Hiroko Isoda
- Tsukuba Life Science Innovation Program (T-LSI), Graduate School of Science and Technology, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan; Open Innovation Laboratory for Food and Medicinal Resource Engineering (FoodMed-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8577, Japan; Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan; Alliance for Research on the Mediterranean and North Africa (ARENA), University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan.
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14
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Liu Y, Xiong Y. HADHA promotes ovarian cancer outgrowth via up-regulating CDK1. Cancer Cell Int 2023; 23:283. [PMID: 37986001 PMCID: PMC10658966 DOI: 10.1186/s12935-023-03120-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 10/30/2023] [Indexed: 11/22/2023] Open
Abstract
BACKGROUND Ovarian cancer, a prevalent cause of cancer-related mortality among gynecological cancers, still lacks a clear understanding of its pathogenesis. In this study, our objective was to investigate the functional roles and pathogenic mechanisms of HADHA in ovarian cancer. METHODS We utilized an ovarian cancer tissue microarray and three ovarian cancer cell lines (HO-8910, A2780, and SK-OV-3) for our analysis. Lentiviral-mediated short hairpin RNA (shRNA) was employed to interfere with HADHA expression in ovarian cancer cells. Various cellular events associated with tumor development were assessed using techniques such as Celigo cell counting assay, wound healing assay, Transwell assay, and flow cytometry analysis. Additionally, xenograft tumor models were developed to visualize the impacts of HADHA/CDK1 on ovarian cancer progression. RESULTS Our data revealed significant HADHA overexpression in both ovarian cancer tissues and cell lines. Patients with elevated HADHA levels tended to experience poor survival outcomes. Moreover, HADHA upregulation correlated with several pathological parameters, including pathological stage, tumor size, tumor infiltrate, metastasis, and recurrence. Loss-of-function experiments targeting HADHA demonstrated that its suppression in ovarian cancer cells hindered cell growth and migration, while promoting apoptosis. To elucidate the underlying mechanism by which HADHA regulates ovarian cancer, we identified CDK1 as a target of HADHA. HADHA upregulated CDK1 expression by inhibiting its ubiquitination-dependent proteasomal degradation. Significantly, the overexpression of CDK1 reversed the impaired cell development caused by HADHA depletion, both in vitro and in vivo. CONCLUSION Our study highlights the involvement of HADHA in ovarian cancer tumorigenesis and suggests its potential as a promising prognostic marker in ovarian cancer. Through its regulation of CDK1, HADHA influences critical cellular processes in ovarian cancer, providing insights into its pathogenic mechanism.
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Affiliation(s)
- Yinglan Liu
- Department of Obsdetrics and Gynecology, First Affiliated Hospital of Harbin Medical University, No.23, Youzheng Road, Harbin city, 150001, Heilongjiang Province, China
| | - Ying Xiong
- Department of Gynecology, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-Sen University Cancer Center, No.651, Dongfengdong Road, Guangzhou, 5100160, Guangdong Province, China.
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15
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Moens U, Passerini S, Falquet M, Sveinbjørnsson B, Pietropaolo V. Phosphorylation of Human Polyomavirus Large and Small T Antigens: An Ignored Research Field. Viruses 2023; 15:2235. [PMID: 38005912 PMCID: PMC10674619 DOI: 10.3390/v15112235] [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: 10/17/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Protein phosphorylation and dephosphorylation are the most common post-translational modifications mediated by protein kinases and protein phosphatases, respectively. These reversible processes can modulate the function of the target protein, such as its activity, subcellular localization, stability, and interaction with other proteins. Phosphorylation of viral proteins plays an important role in the life cycle of a virus. In this review, we highlight biological implications of the phosphorylation of the monkey polyomavirus SV40 large T and small t antigens, summarize our current knowledge of the phosphorylation of these proteins of human polyomaviruses, and conclude with gaps in the knowledge and a proposal for future research directions.
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Affiliation(s)
- Ugo Moens
- Department of Medical Biology, Faculty of Health Sciences, University of Tromsø—The Arctic University of Norway, 9037 Tromsø, Norway; (M.F.); (B.S.)
| | - Sara Passerini
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00185 Rome, Italy;
| | - Mar Falquet
- Department of Medical Biology, Faculty of Health Sciences, University of Tromsø—The Arctic University of Norway, 9037 Tromsø, Norway; (M.F.); (B.S.)
| | - Baldur Sveinbjørnsson
- Department of Medical Biology, Faculty of Health Sciences, University of Tromsø—The Arctic University of Norway, 9037 Tromsø, Norway; (M.F.); (B.S.)
| | - Valeria Pietropaolo
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00185 Rome, Italy;
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16
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Valk E, Örd M, Faustova I, Loog M. CDK signaling via nonconventional CDK phosphorylation sites. Mol Biol Cell 2023; 34:pe5. [PMID: 37906435 PMCID: PMC10846619 DOI: 10.1091/mbc.e22-06-0196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/09/2023] [Accepted: 08/14/2023] [Indexed: 11/02/2023] Open
Abstract
Since the discovery of cyclin-dependent kinases (CDKs), it has been perceived as a dogma that CDK signaling in the cell cycle is mediated via targeting the CDK consensus sites: the optimal and the minimal motifs S/T-P-x-K/R and S/T-P, respectively. However, more recent evidence suggests that often the CDK phosphorylation events of regulatory importance are mediated via nonconventional CDK sites that lack the required +1Pro of the consensus site motif. In these cases, the loss of specificity seems to be compensated via distant docking interactions facilitated by 1) phosphorylated priming sites binding to phospho-adaptor Cks1 and/or 2) cyclin-specific docking interactions via Short Linear Motifs (SLiMs) in substrates. This Perspective discusses the possible reasons why nonconventional CDK sites are used for CDK signaling. First, the nonconventional CDK sites can act as specificity filters to recognize and distinguish the CDK signal from many other proline-directed kinases in cells. Second, the nonconventional CDK sites in combination with the docking mechanisms provide a much wider range of phosphorylation rates, and thus, also a wider range of CDK thresholds during the accumulation and decline of CDK activity during the cell cycle. As a large number of Cks1-dependent nonconventional CDK sites have been discovered recently, past studies focusing on mutating only the consensus sites should likely be critically reexamined. It is also very likely that phosphorylation of nonconventional sites is crucial in many other kinase-signaling networks.
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Affiliation(s)
- Ervin Valk
- Institute of Technology, University of Tartu, Tartu, 50411, Estonia
| | - Mihkel Örd
- Institute of Technology, University of Tartu, Tartu, 50411, Estonia
| | - Ilona Faustova
- Institute of Technology, University of Tartu, Tartu, 50411, Estonia
| | - Mart Loog
- Institute of Technology, University of Tartu, Tartu, 50411, Estonia
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17
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Priyamvada P, Ramaiah S. Potential Signature Therapeutic Biomarkers TOP2A, MAD2L1, and CDK1 in Colorectal Cancer: A Systems Biomedicine-Based Approach. Biochem Genet 2023:10.1007/s10528-023-10544-0. [PMID: 37884851 DOI: 10.1007/s10528-023-10544-0] [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: 03/17/2023] [Accepted: 10/02/2023] [Indexed: 10/28/2023]
Abstract
Colorectal cancer is the third deadliest and fourth most diagnosed cancer. It is heterogeneously driven by varied mutations and mutagens, and thus, it is challenging for targeted therapy. The rapid advancement of high-throughput technology presents considerable opportunities for discovering new colon cancer biomarkers. In the present study, we have explored and identified the biomarkers based on molecular interactions. We curated cancer datasets that were not micro-dissected and performed gene expression analysis. The protein-protein interactions were curated, and a network was constructed for the up-regulated genes. The hub genes were analyzed using 12 different topological parameters. The correlation analysis selected TOP2A, CDK1, CCNB1, AURKA, and MAD2L1 as hub genes. Further, survival analysis was performed to determine the effectiveness of the hub gene on the patient's survival rate. Our findings explore various transcription factors such as E2F4, FOXM1, E2F6, MAX, and SIN3A, along with kinases CSNK2A1, MAPK14, CDK1, CDK4, and CDK2, as potential molecular signatures and aid researchers in understanding the pathophysiological mechanisms underlying CRC development and thus providing novel therapeutic and diagnostic recourse. Furthermore, investigating miRNAs, we focused on hsa-miR-215-5p, hsa-miR-192-5p, and hsa-miR-193b-3p due to their observed impact on a diverse set of colorectal cancer genes. Thereby, the current approach brings into light CRC- related genes at the RNA and protein levels that can potentially act as novel biomarkers opening doors to diagnostic and treatment purposes.
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Affiliation(s)
- P Priyamvada
- Medical and Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India
- Department of Bio Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India
| | - Sudha Ramaiah
- Medical and Biological Computing Laboratory, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India.
- Department of Bio Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, 632014, India.
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18
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Martell DJ, Merens HE, Caulier A, Fiorini C, Ulirsch JC, Ietswaart R, Choquet K, Graziadei G, Brancaleoni V, Cappellini MD, Scott C, Roberts N, Proven M, Roy NBA, Babbs C, Higgs DR, Sankaran VG, Churchman LS. RNA polymerase II pausing temporally coordinates cell cycle progression and erythroid differentiation. Dev Cell 2023; 58:2112-2127.e4. [PMID: 37586368 PMCID: PMC10615711 DOI: 10.1016/j.devcel.2023.07.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/23/2023] [Accepted: 07/25/2023] [Indexed: 08/18/2023]
Abstract
Controlled release of promoter-proximal paused RNA polymerase II (RNA Pol II) is crucial for gene regulation. However, studying RNA Pol II pausing is challenging, as pause-release factors are almost all essential. In this study, we identified heterozygous loss-of-function mutations in SUPT5H, which encodes SPT5, in individuals with β-thalassemia. During erythropoiesis in healthy human cells, cell cycle genes were highly paused as cells transition from progenitors to precursors. When the pathogenic mutations were recapitulated by SUPT5H editing, RNA Pol II pause release was globally disrupted, and as cells began transitioning from progenitors to precursors, differentiation was delayed, accompanied by a transient lag in erythroid-specific gene expression and cell cycle kinetics. Despite this delay, cells terminally differentiate, and cell cycle phase distributions normalize. Therefore, hindering pause release perturbs proliferation and differentiation dynamics at a key transition during erythropoiesis, identifying a role for RNA Pol II pausing in temporally coordinating the cell cycle and erythroid differentiation.
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Affiliation(s)
- Danya J Martell
- Department of Genetics, Harvard University, Boston, MA, USA; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hope E Merens
- Department of Genetics, Harvard University, Boston, MA, USA
| | - Alexis Caulier
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Claudia Fiorini
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jacob C Ulirsch
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Karine Choquet
- Department of Genetics, Harvard University, Boston, MA, USA
| | - Giovanna Graziadei
- Department of Clinical Sciences and Community, University of Milan, IRCCS Ca'Granda Foundation Maggiore Policlinico Hospital, Milan, Italy
| | - Valentina Brancaleoni
- Department of Clinical Sciences and Community, University of Milan, IRCCS Ca'Granda Foundation Maggiore Policlinico Hospital, Milan, Italy
| | - Maria Domenica Cappellini
- Department of Clinical Sciences and Community, University of Milan, IRCCS Ca'Granda Foundation Maggiore Policlinico Hospital, Milan, Italy
| | - Caroline Scott
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Nigel Roberts
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Melanie Proven
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Noémi B A Roy
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre and BRC/NHS Translational Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford, UK; Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Christian Babbs
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Douglas R Higgs
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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19
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Park K, Lim JY, Kim JH, Lee J, Shin S, Park HM. LAMMER Kinase Modulates Cell Cycle by Phosphorylating the MBF Repressor, Yox1, in Schizosaccharomyces pombe. MYCOBIOLOGY 2023; 51:372-378. [PMID: 37929004 PMCID: PMC10621261 DOI: 10.1080/12298093.2023.2262806] [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: 07/23/2023] [Accepted: 09/11/2023] [Indexed: 11/07/2023]
Abstract
Lkh1, a LAMMER kinase homolog in the fission yeast Schizosaccharomyces pombe, acts as a negative regulator of filamentous growth and flocculation. It is also involved in the response to oxidative stress. The lkh1-deletion mutant displays slower cell growth, shorter cell size, and abnormal DNA content compared to the wild type. These phenotypes suggest that Lkh1 controls cell size and cell cycle progression. When we performed microarray analysis using the lkh1-deletion mutant, we found that only four of the up-regulated genes in the lkh1-deletion were associated with the cell cycle. Interestingly, all of these genes are regulated by the Mlu1 cell cycle box binding factor (MBF), which is a transcription complex responsible for regulating the expression of cell cycle genes during the G1/S phase. Transcription analyses of the MBF-dependent cell-cycle genes, including negative feedback regulators, confirmed the up-regulation of these genes by the deletion of lkh1. Pull-down assay confirmed the interaction between Lkh1 and Yox1, which is a negative feedback regulator of MBF. This result supports the involvement of LAMMER kinase in cell cycle regulation by modulating MBF activity. In vitro kinase assay and NetPhosK 2.0 analysis with the Yox1T40,41A mutant allele revealed that T40 and T41 residues are the phosphorylation sites mediated by Lkh1. These sites affect the G1/S cell cycle progression of fission yeast by modulating the activity of the MBF complex.
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Affiliation(s)
- Kibum Park
- Laboratory of Cellular Differentiation, Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Joo-Yeon Lim
- Department of Microbiology and Immunology, Indiana University School of Medicine-Terre Haute, Terre Haute, IN, USA
| | - Je-Hoon Kim
- Laboratory of Cellular Differentiation, Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Jieun Lee
- Laboratory of Cellular Differentiation, Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Songju Shin
- Laboratory of Cellular Differentiation, Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Hee-Moon Park
- Laboratory of Cellular Differentiation, Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
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20
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Wiyono T, Dwiningsih SR, Widjiati W. The Impact of Endometriosis on Intracellular Calcium Levels, Cyclic Dependent Kinase 1 (Cdk1) Expression, and Cyclin B Expression in Post-Ovulation Oocytes of Mice Model. J Reprod Infertil 2023; 24:232-239. [PMID: 38164432 PMCID: PMC10757684 DOI: 10.18502/jri.v24i4.14150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 10/07/2023] [Indexed: 01/03/2024] Open
Abstract
Background Since endometriosis causes a decrease in oocyte quality, the success rate of in vitro fertilization cycles decreases. The purpose of the current study was to analyze the effect of endometriosis on intracellular calcium levels, Cdk1 expression, and cyclin B expression in oocytes. Methods Thirty-two mice (Mus musculus) were divided into control and endometriosis groups. The cumulus oocyte complex (COC) were obtained in all groups. Denudated cells were assessed for calcium levels by calorimetric examinations. Complex oocytes were examined for Cdk1 and cyclin B expression by immune-cytochemistry and were read under a microscope. Results Intercellular calcium levels, Cdk1, and cyclin B expression were significantly lower in the endometriosis group than in the control group. There was a significant relationship between calcium levels and Cdk1 expression (p<0.05, r=0.659), a significant relationship between calcium levels and cyclin B expression (p<0.05, r=0.885), and also a significant correlation between Cdk1 and cyclin B expression (p<0.05, r=0.537). Conclusion The data presented in this study suggested that the intracellular oocyte calcium level, Cdk1 expression, and cyclin B expression were lower in mice with endometriosis. A positive correlation was observed between calcium levels and the expression of Cdk1 and cyclin B. Furthermore, a positive correlation was also found between Cdk1 and cyclin B expression.
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Affiliation(s)
- Teguh Wiyono
- Department of Obstetrics and Gynecology, Faculty of Medicine, Airlangga University, Surabaya, Indonesia
| | - Sri Ratna Dwiningsih
- Department of Obstetrics and Gynecology, Faculty of Medicine, Airlangga University, Surabaya, Indonesia
| | - Widjiati Widjiati
- Department of Veterinary Embryology, Faculty of Veterinary Medicine, Airlangga University, Surabaya, Indonesia
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21
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Pluta AJ, Studniarek C, Murphy S, Norbury CJ. Cyclin-dependent kinases: Masters of the eukaryotic universe. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 15:e1816. [PMID: 37718413 PMCID: PMC10909489 DOI: 10.1002/wrna.1816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/21/2023] [Accepted: 08/03/2023] [Indexed: 09/19/2023]
Abstract
A family of structurally related cyclin-dependent protein kinases (CDKs) drives many aspects of eukaryotic cell function. Much of the literature in this area has considered individual members of this family to act primarily either as regulators of the cell cycle, the context in which CDKs were first discovered, or as regulators of transcription. Until recently, CDK7 was the only clear example of a CDK that functions in both processes. However, new data points to several "cell-cycle" CDKs having important roles in transcription and some "transcriptional" CDKs having cell cycle-related targets. For example, novel functions in transcription have been demonstrated for the archetypal cell cycle regulator CDK1. The increasing evidence of the overlap between these two CDK types suggests that they might play a critical role in coordinating the two processes. Here we review the canonical functions of cell-cycle and transcriptional CDKs, and provide an update on how these kinases collaborate to perform important cellular functions. We also provide a brief overview of how dysregulation of CDKs contributes to carcinogenesis, and possible treatment avenues. This article is categorized under: RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Processing > 3' End Processing RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
| | | | - Shona Murphy
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUK
| | - Chris J. Norbury
- Sir William Dunn School of PathologyUniversity of OxfordOxfordUK
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22
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Zhong S, Borlak J. Sex disparities in non-small cell lung cancer: mechanistic insights from a cRaf transgenic disease model. EBioMedicine 2023; 95:104763. [PMID: 37625265 PMCID: PMC10470261 DOI: 10.1016/j.ebiom.2023.104763] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 07/10/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND Women are at greater risk of developing non-small cell lung cancer (NSCLC), yet the underlying causes remain unclear. METHODS We performed whole genome scans in lung tumours of cRaf transgenic mice and identified miRNA, transcription factor and hormone receptor dependent gene regulations. We confirmed hormone receptors by immunohistochemistry and constructed regulatory gene networks by considering experimentally validated miRNA-gene and transcription factor-miRNA/gene targets. Bioinformatics, genomic foot-printing and gene enrichment analysis established sex-specific circuits of lung tumour growth. Translational research involved a large cohort of NSCLC patients. We evaluated commonalities in sex-specific NSCLC gene regulations between mice and humans and determined their prognostic value in Kaplan-Meier survival statistics and COX proportional hazard regression analysis. FINDINGS Overexpression of the cRaf kinase elicited an extraordinary 8-fold increase in tumour growth among females, and nearly 70% of the 112 differentially expressed genes (DEGs) were female specific. We identified oncogenes, oncomirs, tumour suppressors, cell cycle regulators and MAPK/EGFR signalling molecules, which prompted sex-based differences in NSCLC, and we deciphered a regulatory gene-network, which protected males from accelerated tumour growth. Strikingly, 41% of DEGs are targets of hormone receptors, and the majority (85%) are oestrogen receptor (ER) dependent. We confirmed the role of ER in a large cohort of NSCLC patients and validated 40% of DEGs induced by cRaf in clinical tumour samples. INTERPRETATION We report the molecular wiring that prompted sex disparities in tumour growth. This allowed us to propose the development of molecular targeted therapies by jointly blocking ER, CDK1 and arginase 2 in NSCLC. FUNDING We gratefully acknowledge the financial support of the Lower Saxony Ministry of Culture and Sciences and Volkswagen Foundation, Germany to JB (25A.5-7251-99-3/00) and of the Chinese Scholarship Council to SZ (202008080022). This publication is funded by the Deutsche Forschungsgemeinschaft (DFG) as part of the "Open Access Publikationskosten" program.
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Affiliation(s)
- Shen Zhong
- Centre for Pharmacology and Toxicology, Hannover Medical School, Carl-Neuberg-Str. 1, Hannover 30625, Germany
| | - Jürgen Borlak
- Centre for Pharmacology and Toxicology, Hannover Medical School, Carl-Neuberg-Str. 1, Hannover 30625, Germany.
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23
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Schneider P, Wander P, Arentsen-Peters STCJM, Vrenken KS, Rockx-Brouwer D, Adriaanse FRS, Hoeve V, Paassen I, Drost J, Pieters R, Stam RW. CRISPR-Cas9 Library Screening Identifies Novel Molecular Vulnerabilities in KMT2A-Rearranged Acute Lymphoblastic Leukemia. Int J Mol Sci 2023; 24:13207. [PMID: 37686014 PMCID: PMC10487613 DOI: 10.3390/ijms241713207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 08/11/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
In acute lymphoblastic leukemia (ALL), chromosomal translocations involving the KMT2A gene represent highly unfavorable prognostic factors and most commonly occur in patients less than 1 year of age. Rearrangements of the KMT2A gene drive epigenetic changes that lead to aberrant gene expression profiles that strongly favor leukemia development. Apart from this genetic lesion, the mutational landscape of KMT2A-rearranged ALL is remarkably silent, providing limited insights for the development of targeted therapy. Consequently, identifying potential therapeutic targets often relies on differential gene expression, yet the inhibition of these genes has rarely translated into successful therapeutic strategies. Therefore, we performed CRISPR-Cas9 knock-out screens to search for genetic dependencies in KMT2A-rearranged ALL. We utilized small-guide RNA libraries directed against the entire human epigenome and kinome in various KMT2A-rearranged ALL, as well as wild-type KMT2A ALL cell line models. This screening approach led to the discovery of the epigenetic regulators ARID4B and MBD3, as well as the receptor kinase BMPR2 as novel molecular vulnerabilities and attractive therapeutic targets in KMT2A-rearranged ALL.
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Affiliation(s)
- Pauline Schneider
- Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands
| | - Priscilla Wander
- Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands
| | | | - Kirsten S. Vrenken
- Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands
| | | | | | - Veerle Hoeve
- Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands
| | - Irene Paassen
- Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands
- Oncode Institute, 3521 AL Utrecht, The Netherlands
| | - Jarno Drost
- Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands
- Oncode Institute, 3521 AL Utrecht, The Netherlands
| | - Rob Pieters
- Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands
| | - Ronald W. Stam
- Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands
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24
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Liang P, Lister K, Yates L, Argunhan B, Zhang X. Phosphoregulation of DNA repair via the Rad51 auxiliary factor Swi5-Sfr1. J Biol Chem 2023; 299:104929. [PMID: 37330173 PMCID: PMC10366545 DOI: 10.1016/j.jbc.2023.104929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/19/2023] Open
Abstract
Homologous recombination (HR) is a major pathway for the repair of DNA double-strand breaks, the most severe form of DNA damage. The Rad51 protein is central to HR, but multiple auxiliary factors regulate its activity. The heterodimeric Swi5-Sfr1 complex is one such factor. It was previously shown that two sites within the intrinsically disordered domain of Sfr1 are critical for the interaction with Rad51. Here, we show that phosphorylation of five residues within this domain regulates the interaction of Swi5-Sfr1 with Rad51. Biochemical reconstitutions demonstrated that a phosphomimetic mutant version of Swi5-Sfr1 is defective in both the physical and functional interaction with Rad51. This translated to a defect in DNA repair, with the phosphomimetic mutant yeast strain phenocopying a previously established interaction mutant. Interestingly, a strain in which Sfr1 phosphorylation was blocked also displayed sensitivity to DNA damage. Taken together, we propose that controlled phosphorylation of Sfr1 is important for the role of Swi5-Sfr1 in promoting Rad51-dependent DNA repair.
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Affiliation(s)
- Pengtao Liang
- Section of Structural and Synthetic Biology, Faculty of Medicine, Imperial College London, London, UK
| | - Katie Lister
- Section of Structural and Synthetic Biology, Faculty of Medicine, Imperial College London, London, UK
| | - Luke Yates
- Section of Structural and Synthetic Biology, Faculty of Medicine, Imperial College London, London, UK
| | - Bilge Argunhan
- Section of Structural and Synthetic Biology, Faculty of Medicine, Imperial College London, London, UK.
| | - Xiaodong Zhang
- Section of Structural and Synthetic Biology, Faculty of Medicine, Imperial College London, London, UK.
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25
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Jiang L, Yu Y, Li Z, Gao Y, Zhang H, Zhang M, Cao W, Peng Q, Chen X. BMS-265246, a Cyclin-Dependent Kinase Inhibitor, Inhibits the Infection of Herpes Simplex Virus Type 1. Viruses 2023; 15:1642. [PMID: 37631985 PMCID: PMC10459710 DOI: 10.3390/v15081642] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023] Open
Abstract
Herpes simplex virus type 1 (HSV-1) infections are prevalent illnesses that can cause mucocutaneous ulcerative disease, keratitis, and genital herpes. In patients with compromised immune systems, the infection can lead to serious problems, such as encephalitis. Additionally, neonatal infections can cause brain problems and even death. Current first-line antiviral drugs are nucleoside analog inhibitors that target viral polymerase, and resistant strains have emerged. As a result, new drugs with distinct action modes are needed. Recent research indicates that cyclin-dependent kinases (CDKs) are prospective antiviral targets. Thus, CDK inhibitors may be effective antiviral agents against HSV-1 infection. In this study, we examined a panel of CDK inhibitors that target CDKs in the present study. BMS-265246 (BMS), a CDK 1/2 inhibitor, was found to effectively limit HSV-1 multiplication in Vero, HepG2, and Hela cells. A mechanism of action study suggested that BMS inhibits the early stages of viral replication when added early in the viral infection. The suppression of multiple steps in viral replication by BMS was revealed when HSV-1 infected cells were treated at different time periods in the viral life cycle. Our results suggest that BMS is a potent anti-HSV-1 agent and unique in that it may interfere with multiple steps in HSV-1 replication.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Xulin Chen
- Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou 510632, China; (L.J.); (Y.Y.)
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26
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Song Y, Huang T, Pan H, Du A, Wu T, Lan J, Zhou X, Lv Y, Xue S, Yuan K. The influence of COVID-19 on colorectal cancer was investigated using bioinformatics and systems biology techniques. Front Med (Lausanne) 2023; 10:1169562. [PMID: 37457582 PMCID: PMC10348756 DOI: 10.3389/fmed.2023.1169562] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 06/15/2023] [Indexed: 07/18/2023] Open
Abstract
Introduction Coronavirus disease 2019 (COVID-19) is a global pandemic and highly contagious, posing a serious threat to human health. Colorectal cancer (CRC) is a risk factor for COVID-19 infection. Therefore, it is vital to investigate the intrinsic link between these two diseases. Methods In this work, bioinformatics and systems biology techniques were used to detect the mutual pathways, molecular biomarkers, and potential drugs between COVID-19 and CRC. Results A total of 161 common differentially expressed genes (DEGs) were identified based on the RNA sequencing datasets of the two diseases. Functional analysis was performed using ontology keywords, and pathway analysis was also performed. The common DEGs were further utilized to create a protein-protein interaction (PPI) network and to identify hub genes and key modules. The datasets revealed transcription factors-gene interactions, co-regulatory networks with DEGs-miRNAs of common DEGs, and predicted possible drugs as well. The ten predicted drugs include troglitazone, estradiol, progesterone, calcitriol, genistein, dexamethasone, lucanthone, resveratrol, retinoic acid, phorbol 12-myristate 13-acetate, some of which have been investigated as potential CRC and COVID-19 therapies. Discussion By clarifying the relationship between COVID-19 and CRC, we hope to provide novel clues and promising therapeutic drugs to treat these two illnesses.
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Affiliation(s)
- Yujia Song
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Tengda Huang
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Hongyuan Pan
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Ao Du
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Tian Wu
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Jiang Lan
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Xinyi Zhou
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Yue Lv
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Shuai Xue
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Kefei Yuan
- Division of Liver Surgery, Department of General Surgery and Laboratory of Liver Surgery, and State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
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27
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Wang Q, Bode AM, Zhang T. Targeting CDK1 in cancer: mechanisms and implications. NPJ Precis Oncol 2023; 7:58. [PMID: 37311884 DOI: 10.1038/s41698-023-00407-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/25/2023] [Indexed: 06/15/2023] Open
Abstract
Cyclin dependent kinases (CDKs) are serine/threonine kinases that are proposed as promising candidate targets for cancer treatment. These proteins complexed with cyclins play a critical role in cell cycle progression. Most CDKs demonstrate substantially higher expression in cancer tissues compared with normal tissues and, according to the TCGA database, correlate with survival rate in multiple cancer types. Deregulation of CDK1 has been shown to be closely associated with tumorigenesis. CDK1 activation plays a critical role in a wide range of cancer types; and CDK1 phosphorylation of its many substrates greatly influences their function in tumorigenesis. Enrichment of CDK1 interacting proteins with Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was conducted to demonstrate that the associated proteins participate in multiple oncogenic pathways. This abundance of evidence clearly supports CDK1 as a promising target for cancer therapy. A number of small molecules targeting CDK1 or multiple CDKs have been developed and evaluated in preclinical studies. Notably, some of these small molecules have also been subjected to human clinical trials. This review evaluates the mechanisms and implications of targeting CDK1 in tumorigenesis and cancer therapy.
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Affiliation(s)
- Qiushi Wang
- The Hormel Institute, University of Minnesota, 801 16th Ave NE, Austin, MN, 55912, USA
| | - Ann M Bode
- The Hormel Institute, University of Minnesota, 801 16th Ave NE, Austin, MN, 55912, USA.
| | - Tianshun Zhang
- The Hormel Institute, University of Minnesota, 801 16th Ave NE, Austin, MN, 55912, USA.
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28
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Roshan P, Kuppa S, Mattice JR, Kaushik V, Chadda R, Pokhrel N, Tumala BR, Biswas A, Bothner B, Antony E, Origanti S. An Aurora B-RPA signaling axis secures chromosome segregation fidelity. Nat Commun 2023; 14:3008. [PMID: 37230964 PMCID: PMC10212944 DOI: 10.1038/s41467-023-38711-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 05/09/2023] [Indexed: 05/27/2023] Open
Abstract
Errors in chromosome segregation underlie genomic instability associated with cancers. Resolution of replication and recombination intermediates and protection of vulnerable single-stranded DNA (ssDNA) intermediates during mitotic progression requires the ssDNA binding protein Replication Protein A (RPA). However, the mechanisms that regulate RPA specifically during unperturbed mitotic progression are poorly resolved. RPA is a heterotrimer composed of RPA70, RPA32 and RPA14 subunits and is predominantly regulated through hyperphosphorylation of RPA32 in response to DNA damage. Here, we have uncovered a mitosis-specific regulation of RPA by Aurora B kinase. Aurora B phosphorylates Ser-384 in the DNA binding domain B of the large RPA70 subunit and highlights a mode of regulation distinct from RPA32. Disruption of Ser-384 phosphorylation in RPA70 leads to defects in chromosome segregation with loss of viability and a feedback modulation of Aurora B activity. Phosphorylation at Ser-384 remodels the protein interaction domains of RPA. Furthermore, phosphorylation impairs RPA binding to DSS1 that likely suppresses homologous recombination during mitosis by preventing recruitment of DSS1-BRCA2 to exposed ssDNA. We showcase a critical Aurora B-RPA signaling axis in mitosis that is essential for maintaining genomic integrity.
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Affiliation(s)
- Poonam Roshan
- Department of Biology, St. Louis University, St. Louis, MO, 63103, USA
| | - Sahiti Kuppa
- Department of Biochemistry and Molecular Biology, St. Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Jenna R Mattice
- Department of Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Vikas Kaushik
- Department of Biochemistry and Molecular Biology, St. Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Rahul Chadda
- Department of Biochemistry and Molecular Biology, St. Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Nilisha Pokhrel
- Department of Biological Sciences, Marquette University, Milwaukee, WI, 53217, USA
| | - Brunda R Tumala
- Department of Biochemistry and Molecular Biology, St. Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Aparna Biswas
- Department of Biology, St. Louis University, St. Louis, MO, 63103, USA
| | - Brian Bothner
- Department of Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Edwin Antony
- Department of Biochemistry and Molecular Biology, St. Louis University School of Medicine, St. Louis, MO, 63104, USA.
| | - Sofia Origanti
- Department of Biology, St. Louis University, St. Louis, MO, 63103, USA.
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29
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Sun W, Xie G, Jiang X, Khaitovich P, Han D, Liu X. Epigenetic regulation of human-specific gene expression in the prefrontal cortex. BMC Biol 2023; 21:123. [PMID: 37226244 DOI: 10.1186/s12915-023-01612-3] [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: 11/04/2022] [Accepted: 05/03/2023] [Indexed: 05/26/2023] Open
Abstract
BACKGROUND Changes in gene expression levels during brain development are thought to have played an important role in the evolution of human cognition. With the advent of high-throughput sequencing technologies, changes in brain developmental expression patterns, as well as human-specific brain gene expression, have been characterized. However, interpreting the origin of evolutionarily advanced cognition in human brains requires a deeper understanding of the regulation of gene expression, including the epigenomic context, along the primate genome. Here, we used chromatin immunoprecipitation sequencing (ChIP-seq) to measure the genome-wide profiles of histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 lysine 27 acetylation (H3K27ac), both of which are associated with transcriptional activation in the prefrontal cortex of humans, chimpanzees, and rhesus macaques. RESULTS We found a discrete functional association, in which H3K4me3HP gain was significantly associated with myelination assembly and signaling transmission, while H3K4me3HP loss played a vital role in synaptic activity. Moreover, H3K27acHP gain was enriched in interneuron and oligodendrocyte markers, and H3K27acHP loss was enriched in CA1 pyramidal neuron markers. Using strand-specific RNA sequencing (ssRNA-seq), we first demonstrated that approximately 7 and 2% of human-specific expressed genes were epigenetically marked by H3K4me3HP and H3K27acHP, respectively, providing robust support for causal involvement of histones in gene expression. We also revealed the co-activation role of epigenetic modification and transcription factors in human-specific transcriptome evolution. Mechanistically, histone-modifying enzymes at least partially contribute to an epigenetic disturbance among primates, especially for the H3K27ac epigenomic marker. In line with this, peaks enriched in the macaque lineage were found to be driven by upregulated acetyl enzymes. CONCLUSIONS Our results comprehensively elucidated a causal species-specific gene-histone-enzyme landscape in the prefrontal cortex and highlighted the regulatory interaction that drove transcriptional activation.
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Affiliation(s)
- Weifen Sun
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, 200063, China
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, CAS, Shanghai, 200031, China
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Gangcai Xie
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, CAS, Shanghai, 200031, China
| | - Xi Jiang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, CAS, Shanghai, 200031, China
| | - Philipp Khaitovich
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, CAS, Shanghai, 200031, China.
- Skolkovo Institute of Science and Technology, Moscow, 121205, Russia.
| | - Dingding Han
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, CAS, Shanghai, 200031, China.
- Department of Clinical Laboratory, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200062, China.
| | - Xiling Liu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, 200063, China.
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, CAS, Shanghai, 200031, China.
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Ford K, Munson BP, Fong SH, Panwala R, Chu WK, Rainaldi J, Plongthongkum N, Arunachalam V, Kostrowicki J, Meluzzi D, Kreisberg JF, Jensen-Pergakes K, VanArsdale T, Paul T, Tamayo P, Zhang K, Bienkowska J, Mali P, Ideker T. Multimodal perturbation analyses of cyclin-dependent kinases reveal a network of synthetic lethalities associated with cell-cycle regulation and transcriptional regulation. Sci Rep 2023; 13:7678. [PMID: 37169829 PMCID: PMC10175263 DOI: 10.1038/s41598-023-33329-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 04/11/2023] [Indexed: 05/13/2023] Open
Abstract
Cell-cycle control is accomplished by cyclin-dependent kinases (CDKs), motivating extensive research into CDK targeting small-molecule drugs as cancer therapeutics. Here we use combinatorial CRISPR/Cas9 perturbations to uncover an extensive network of functional interdependencies among CDKs and related factors, identifying 43 synthetic-lethal and 12 synergistic interactions. We dissect CDK perturbations using single-cell RNAseq, for which we develop a novel computational framework to precisely quantify cell-cycle effects and diverse cell states orchestrated by specific CDKs. While pairwise disruption of CDK4/6 is synthetic-lethal, only CDK6 is required for normal cell-cycle progression and transcriptional activation. Multiple CDKs (CDK1/7/9/12) are synthetic-lethal in combination with PRMT5, independent of cell-cycle control. In-depth analysis of mRNA expression and splicing patterns provides multiple lines of evidence that the CDK-PRMT5 dependency is due to aberrant transcriptional regulation resulting in premature termination. These inter-dependencies translate to drug-drug synergies, with therapeutic implications in cancer and other diseases.
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Affiliation(s)
- Kyle Ford
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Brenton P Munson
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Samson H Fong
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Rebecca Panwala
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Wai Keung Chu
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Joseph Rainaldi
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
- Biomedical Sciences Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Nongluk Plongthongkum
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | | | | | - Dario Meluzzi
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jason F Kreisberg
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | | | - Todd VanArsdale
- Pfizer Inc, 10555 Science Center Drive, San Diego, CA, 92121, USA
| | - Thomas Paul
- Pfizer Inc, 10555 Science Center Drive, San Diego, CA, 92121, USA
| | - Pablo Tamayo
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA
| | - Kun Zhang
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | | | - Prashant Mali
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Trey Ideker
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA.
- Department of Medicine, University of California San Diego, La Jolla, CA, 92093, USA.
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31
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Robertson CM, Xue Y, Chowdhury S, Maringele L. A CDK-Dependent Phosphorylation of a Novel Domain of Rif1 Regulates its Function during Telomere Damage and Other Types of Stress. Mol Cell Biol 2023; 43:185-199. [PMID: 37140180 PMCID: PMC10184589 DOI: 10.1080/10985549.2023.2193768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023] Open
Abstract
Rif1 mediates telomere length, DNA replication, and DNA damage responses in budding yeast. Previous work identified several posttranslational modifications of Rif1, however none of these was shown to mediate the molecular or cellular responses to DNA damage, including telomere damage. We searched for such modifications using immunoblotting methods and the cdc13-1 and tlc1Δ models of telomere damage. We found that Rif1 is phosphorylated during telomere damage, and that serines 57 and 110 within a novel phospho-gate domain (PGD) of Rif1 are important for this modification, in cdc13-1 cells. The phosphorylation of Rif1 appeared to inhibit its accumulation on damaged chromosomes and the proliferation of cells with telomere damage. Moreover, we found that checkpoint kinases were upstream of this Rif1 phosphorylation and that the Cdk1 activity was essential for maintaining it. Apart from telomere damage, S57 and S110 were essential for Rif1 phosphorylation during the treatment of cells with genotoxic agents or during mitotic stress. We propose a speculative "Pliers" model to explain the role of the PGD phosphorylation during telomere and other types of damage.
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Affiliation(s)
- Cameron M Robertson
- Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Yuan Xue
- Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Shobir Chowdhury
- Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Laura Maringele
- Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
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Morimoto Y, Yamashita N, Hirose H, Fushimi A, Haratake N, Daimon T, Bhattacharya A, Ahmad R, Suzuki Y, Takahashi H, Kufe DW. MUC1-C is necessary for SHP2 activation and BRAF inhibitor resistance in BRAF(V600E) mutant colorectal cancer. Cancer Lett 2023; 559:216116. [PMID: 36878307 PMCID: PMC10408991 DOI: 10.1016/j.canlet.2023.216116] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/19/2023] [Accepted: 03/02/2023] [Indexed: 03/07/2023]
Abstract
Colorectal cancers (CRCs) harboring the BRAF(V600E) mutation are associated with aggressive disease and resistance to BRAF inhibitors by feedback activation of the receptor tyrosine kinase (RTK)→RAS→MAPK pathway. The oncogenic MUC1-C protein promotes progression of colitis to CRC; whereas there is no known involvement of MUC1-C in BRAF(V600E) CRCs. The present work demonstrates that MUC1 expression is significantly upregulated in BRAF(V600E) vs wild-type CRCs. We show that BRAF(V600E) CRC cells are dependent on MUC1-C for proliferation and BRAF inhibitor (BRAFi) resistance. Mechanistically, MUC1-C integrates induction of MYC in driving cell cycle progression with activation of the SHP2 phosphotyrosine phosphatase, which enhances RTK-mediated RAS→ERK signaling. We demonstrate that targeting MUC1-C genetically and pharmacologically suppresses (i) activation of MYC, (ii) induction of the NOTCH1 stemness factor, and (iii) the capacity for self-renewal. We also show that MUC1-C associates with SHP2 and is required for SHP2 activation in driving BRAFi-induced feedback of ERK signaling. In this way, targeting MUC1-C in BRAFi-resistant BRAF(V600E) CRC tumors inhibits growth and sensitizes to BRAF inhibition. These findings demonstrate that MUC1-C is a target for the treatment of BRAF(V600E) CRCs and for reversing their resistance to BRAF inhibitors by suppressing the feedback MAPK pathway.
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Affiliation(s)
| | - Nami Yamashita
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Haruka Hirose
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Atsushi Fushimi
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Naoki Haratake
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Tatsuaki Daimon
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | - Rehan Ahmad
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Yozo Suzuki
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Hidekazu Takahashi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Donald W Kufe
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
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Martell DJ, Merens HE, Fiorini C, Caulier A, Ulirsch JC, Ietswaart R, Choquet K, Graziadei G, Brancaleoni V, Cappellini MD, Scott C, Roberts N, Proven M, Roy NB, Babbs C, Higgs DR, Sankaran VG, Churchman LS. RNA Polymerase II pausing temporally coordinates cell cycle progression and erythroid differentiation. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.03.23286760. [PMID: 36945604 PMCID: PMC10029049 DOI: 10.1101/2023.03.03.23286760] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The controlled release of promoter-proximal paused RNA polymerase II (Pol II) into productive elongation is a major step in gene regulation. However, functional analysis of Pol II pausing is difficult because factors that regulate pause release are almost all essential. In this study, we identified heterozygous loss-of-function mutations in SUPT5H , which encodes SPT5, in individuals with β-thalassemia unlinked to HBB mutations. During erythropoiesis in healthy human cells, cell cycle genes were highly paused at the transition from progenitors to precursors. When the pathogenic mutations were recapitulated by SUPT5H editing, Pol II pause release was globally disrupted, and the transition from progenitors to precursors was delayed, marked by a transient lag in erythroid-specific gene expression and cell cycle kinetics. Despite this delay, cells terminally differentiate, and cell cycle phase distributions normalize. Therefore, hindering pause release perturbs proliferation and differentiation dynamics at a key transition during erythropoiesis, revealing a role for Pol II pausing in the temporal coordination between the cell cycle and differentiation.
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Affiliation(s)
- Danya J Martell
- Harvard University, Department of Genetics, Boston, MA
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Hope E Merens
- Harvard University, Department of Genetics, Boston, MA
| | - Claudia Fiorini
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Alexis Caulier
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Jacob C Ulirsch
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
| | | | | | - Giovanna Graziadei
- Department of Clinical Sciences and Community, University of Milan, IRCCS Ca'Granda Foundation Maggiore Policlinico Hospital, Milan, Italy
| | - Valentina Brancaleoni
- Department of Clinical Sciences and Community, University of Milan, IRCCS Ca'Granda Foundation Maggiore Policlinico Hospital, Milan, Italy
| | - Maria Domenica Cappellini
- Department of Clinical Sciences and Community, University of Milan, IRCCS Ca'Granda Foundation Maggiore Policlinico Hospital, Milan, Italy
| | - Caroline Scott
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Nigel Roberts
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Melanie Proven
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Noémi Ba Roy
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre and BRC/NHS Translational Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford, UK
- Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Christian Babbs
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Douglas R Higgs
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
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He F, Wang X, Wu Q, Liu S, Cao Y, Guo X, Yin S, Yin N, Li B, Fang M. Identification of potential ATP-competitive cyclin-dependent kinase 1 inhibitors: De novo drug generation, molecular docking, and molecular dynamics simulation. Comput Biol Med 2023; 155:106645. [PMID: 36774892 DOI: 10.1016/j.compbiomed.2023.106645] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/27/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023]
Abstract
Cyclin-dependent kinases 1 (CDK1) has been identified as a potential target for the search for new antitumor drugs. However, no clinically effective CDK1 inhibitors are now available for cancer treatment. Therefore, this study aimed to offer potential CDK1 inhibitors using de novo drug generation, molecular docking, and molecular dynamics (MD) simulation studies. We first utilized the BREED algorithm (a de novo drug generation approach) to produce a novel library of small molecules targeting CDK1. To initially obtain novel potential CDK1 inhibitors with favorable physicochemical properties and excellent druggability, we performed a virtual rule-based rational drug screening on our generated library and found ten initial hits. Then, the molecular interactions and dynamic stability of these ten initial hits and CDK1 complexes during their all-atom MD simulations (total 18 μs) and binding pose metadynamics simulations were investigated, resulting in five final hits. Furthermore, another MD simulation (total 2.1 μs) with different force fields demonstrated the binding ability of the five hits to CDK1. It was found that these five hits, CBMA001 (ΔG = -29.88 kcal/mol), CBMA002 (ΔG = -34.89 kcal/mol), CBMA004 (ΔG = -32.47 kcal/mol), CBMA007 (ΔG = -31.16 kcal/mol), and CBMA008 (ΔG = -34.78 kcal/mol) possessed much greater binding affinity to CDK1 than positive compound Flavopiridol (FLP, ΔG = -25.38 kcal/mol). Finally, CBMA002 and CBMA004 were identified as excellent selective CDK1 inhibitors in silico. Together, this study provides a workflow for rational drug design and two promising selective CDK1 inhibitors that deserve further investigation.
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Affiliation(s)
- Fengming He
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102, China
| | - Xiumei Wang
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102, China
| | - Qiaoqiong Wu
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102, China
| | - Shunzhi Liu
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102, China
| | - Yin Cao
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102, China
| | - Xiaodan Guo
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102, China
| | - Sihang Yin
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102, China
| | - Na Yin
- School of Pharmaceutical Sciences, Sun Yat-Sen University, University Town, Guangzhou, 510006, China
| | - Baicun Li
- National Center for Respiratory Medicine Laboratories, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, 100029, China; National Clinical Research Center for Respiratory Diseases, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, 100029, China.
| | - Meijuan Fang
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, 361102, China.
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Bernal L, Pinzi L, Rastelli G. Identification of Promising Drug Candidates against Prostate Cancer through Computationally-Driven Drug Repurposing. Int J Mol Sci 2023; 24:ijms24043135. [PMID: 36834548 PMCID: PMC9964599 DOI: 10.3390/ijms24043135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/02/2023] [Accepted: 02/03/2023] [Indexed: 02/08/2023] Open
Abstract
Prostate cancer (PC) is one of the most common types of cancer in males. Although early stages of PC are generally associated with favorable outcomes, advanced phases of the disease present a significantly poorer prognosis. Moreover, currently available therapeutic options for the treatment of PC are still limited, being mainly focused on androgen deprivation therapies and being characterized by low efficacy in patients. As a consequence, there is a pressing need to identify alternative and more effective therapeutics. In this study, we performed large-scale 2D and 3D similarity analyses between compounds reported in the DrugBank database and ChEMBL molecules with reported anti-proliferative activity on various PC cell lines. The analyses included also the identification of biological targets of ligands with potent activity on PC cells, as well as investigations on the activity annotations and clinical data associated with the more relevant compounds emerging from the ligand-based similarity results. The results led to the prioritization of a set of drugs and/or clinically tested candidates potentially useful in drug repurposing against PC.
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Affiliation(s)
- Leonardo Bernal
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125 Modena, Italy
- Clinical and Experimental Medicine PhD Program, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Luca Pinzi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125 Modena, Italy
| | - Giulio Rastelli
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125 Modena, Italy
- Correspondence: ; Tel.: +39-059-2058564
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36
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Miller KJ, Henry I, Maylin Z, Smith C, Arunachalam E, Pandha H, Asim M. A compendium of Androgen Receptor Variant 7 target genes and their role in Castration Resistant Prostate Cancer. Front Oncol 2023; 13:1129140. [PMID: 36937454 PMCID: PMC10014620 DOI: 10.3389/fonc.2023.1129140] [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: 12/21/2022] [Accepted: 02/13/2023] [Indexed: 03/05/2023] Open
Abstract
Persistent androgen receptor (AR) signalling is the main driver of prostate cancer (PCa). Truncated isoforms of the AR called androgen receptor variants (AR-Vs) lacking the ligand binding domain often emerge during treatment resistance against AR pathway inhibitors such as Enzalutamide. This review discusses how AR-Vs drive a more aggressive form of PCa through the regulation of some of their target genes involved in oncogenic pathways, enabling disease progression. There is a pressing need for the development of a new generation of AR inhibitors which can repress the activity of both the full-length AR and AR-Vs, for which the knowledge of differentially expressed target genes will allow evaluation of inhibition efficacy. This review provides a detailed account of the most common variant, AR-V7, the AR-V7 regulated genes which have been experimentally validated, endeavours to understand their relevance in aggressive AR-V driven PCa and discusses the utility of the downstream protein products as potential drug targets for PCa treatment.
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Affiliation(s)
| | | | - Zoe Maylin
- *Correspondence: Zoe Maylin, ; Mohammad Asim,
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37
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Hiramoto K, Kubo S, Tsuji K, Sugiyama D, Iizuka Y, Hamano H. Bacillus coagulans (species of lactic acid-forming Bacillus bacteria) ameliorates azoxymethane and dextran sodium sulfate-induced colon cancer in mice. J Funct Foods 2023. [DOI: 10.1016/j.jff.2023.105406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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38
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Sang D, Shu T, Pantoja CF, Ibáñez de Opakua A, Zweckstetter M, Holt LJ. Condensed-phase signaling can expand kinase specificity and respond to macromolecular crowding. Mol Cell 2022; 82:3693-3711.e10. [PMID: 36108633 PMCID: PMC10101210 DOI: 10.1016/j.molcel.2022.08.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 05/18/2022] [Accepted: 08/12/2022] [Indexed: 10/14/2022]
Abstract
Phase separation can concentrate biomolecules and accelerate reactions. However, the mechanisms and principles connecting this mesoscale organization to signaling dynamics are difficult to dissect because of the pleiotropic effects associated with disrupting endogenous condensates. To address this limitation, we engineered new phosphorylation reactions within synthetic condensates. We generally found increased activity and broadened kinase specificity. Phosphorylation dynamics within condensates were rapid and could drive cell-cycle-dependent localization changes. High client concentration within condensates was important but not the main factor for efficient phosphorylation. Rather, the availability of many excess client-binding sites together with a flexible scaffold was crucial. Phosphorylation within condensates was also modulated by changes in macromolecular crowding. Finally, the phosphorylation of the Alzheimer's-disease-associated protein Tau by cyclin-dependent kinase 2 was accelerated within condensates. Thus, condensates enable new signaling connections and can create sensors that respond to the biophysical properties of the cytoplasm.
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Affiliation(s)
- Dajun Sang
- Institute for Systems Genetics, New York University Langone Medical Center, 435 E 30th Street, New York, NY 10010, USA
| | - Tong Shu
- Institute for Systems Genetics, New York University Langone Medical Center, 435 E 30th Street, New York, NY 10010, USA
| | - Christian F Pantoja
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075 Göttingen, Germany
| | - Alain Ibáñez de Opakua
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075 Göttingen, Germany
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Str. 3a, 37075 Göttingen, Germany; Max Planck Institute for Multidisciplinary Sciences, Department of NMR-based Structural Biology, Am Fassberg 11, 37077 Göttingen, Germany.
| | - Liam J Holt
- Institute for Systems Genetics, New York University Langone Medical Center, 435 E 30th Street, New York, NY 10010, USA.
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39
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Yam CQX, Lim HH, Surana U. DNA damage checkpoint execution and the rules of its disengagement. Front Cell Dev Biol 2022; 10:1020643. [PMID: 36274841 PMCID: PMC9582513 DOI: 10.3389/fcell.2022.1020643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/21/2022] [Indexed: 11/13/2022] Open
Abstract
Chromosomes are susceptible to damage during their duplication and segregation or when exposed to genotoxic stresses. Left uncorrected, these lesions can result in genomic instability, leading to cells’ diminished fitness, unbridled proliferation or death. To prevent such fates, checkpoint controls transiently halt cell cycle progression to allow time for the implementation of corrective measures. Prominent among these is the DNA damage checkpoint which operates at G2/M transition to ensure that cells with damaged chromosomes do not enter the mitotic phase. The execution and maintenance of cell cycle arrest are essential aspects of G2/M checkpoint and have been studied in detail. Equally critical is cells’ ability to switch-off the checkpoint controls after a successful completion of corrective actions and to recommence cell cycle progression. Interestingly, when corrective measures fail, cells can mount an unusual cellular response, termed adaptation, where they escape checkpoint arrest and resume cell cycle progression with damaged chromosomes at the cost of genome instability or even death. Here, we discuss the DNA damage checkpoint, the mitotic networks it inhibits to prevent segregation of damaged chromosomes and the strategies cells employ to quench the checkpoint controls to override the G2/M arrest.
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Affiliation(s)
| | - Hong Hwa Lim
- A*STAR Singapore Immunology Network, Singapore, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Uttam Surana
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Department of Pharmacology, National University of Singapore, Singapore, Singapore
- *Correspondence: Uttam Surana,
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40
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miR-3059-3p Regulates Glioblastoma Multiforme Radiosensitivity Enhancement through the Homologous Recombination Pathway of DNA Repair. JOURNAL OF ONCOLOGY 2022; 2022:7250278. [PMID: 36185623 PMCID: PMC9519319 DOI: 10.1155/2022/7250278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 09/07/2022] [Indexed: 11/18/2022]
Abstract
Background Glioblastoma multiforme (GBM) is one of the most deadly and recalcitrant illnesses of the neurocentral nervous system in humans. MicroRNAs (miRNAs) are a class of noncoding RNAs that play important roles in the regulation of gene expression and biological processes, including radiosensitivity. In this study, we demonstrated the relationship between miR-3059-3p and radiation in GBM. Materials and Methods Radioresistant (RR) cells were obtained by exposing GBM8401 cells to 80 Gy radiation in 20 weekly 4 Gy fractions. miR-3059-3p mRNA and DNA replication helicase/nuclease 2 (DNA2) protein expressions were detected using real-time polymerase chain reaction and immunoblotting. Using flow cytometry, colony formation and apoptosis were identified using miR-3059-3p mimic, miR-3059-3p inhibitor, DNA2 siRNA, and DNA2 plasmid. Immunoblotting was used to detect DNA repair proteins. Results Low levels of miR-3059-3p and high levels of DNA2 were observed in RR cells. Colony formation and apoptosis assays revealed that miR-3059-3p targeted DNA2 to regulate radioresistance. Immunoblotting revealed that miR-3059-3p regulated the homologous recombination (HR) pathway (Rad51 and Rad52) but not the nonhomologous end joining pathway (ku70 and ku80). Conclusion Downregulation of DNA2 via miR-3059-3p enhanced the radiosensitivity of GBM cells through the inhibition of the HR pathway.
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Saleh AB, Hassan NH, Ismail MA, El-Sayed WM. New fluorobenzamidine exerts antitumor activity against breast cancer in mice via pro-apoptotic activity. Discov Oncol 2022; 13:88. [PMID: 36107265 PMCID: PMC9478011 DOI: 10.1007/s12672-022-00554-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 08/30/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Breast cancer is one of the leading causes of cancer-related morbidities. The present study aimed to evaluate the efficacy of bithiophene-fluorobenzamidine (BFB) against breast cancer induced by 7,12-dimethylbenz(a)anthracene (DMBA) in female Swiss mice and reveal the underlining mechanisms. METHODS The mice were randomly divided into five groups; control, BFB-treated group, DMBA-treated group, and the last two groups received DMBA then tamoxifen or BFB. RESULTS BFB reduced the tumor incidence by ~ 88% versus 30% after TAM. DMBA significantly increased the expression of CDK1 and HER2 and reduced the expression of p53, p21 (CDKN1A), ESR-α, and CAS3. BFB caused significant down-regulation of CDK1 and HER2 and upregulation of p53, p21, ESR-α, and CAS3. In the DMBA-treated mice, cancerous cells metastasized to several organs. This was prevented by the administration of BFB. The antimetastatic and proapoptotic activities were confirmed in MCF7 cells in vitro by the wound healing and annexin V assays, respectively. Kaplan-Meier analysis showed that the BFB increased survival. In the DMBA group, tumors showed invasive carcinoma of grade III with central necrosis, polymorphism, mitotic activity, and numerous newly formed ductules, and colloidal mucinous secretions within adenoid cysts. BFB administration restored the normal structure of the mammary glands. CONCLUSION Taken together, BFB has antitumor, pro-apoptotic, and anti-metastatic activities against breast cancer in mice and therefore, it merits further investigations.
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Affiliation(s)
- AbdelRahman B Saleh
- Department of Zoology, Faculty of Science, Ain Shams University, Cairo, 11566, Egypt
| | - Nagwa H Hassan
- Department of Zoology, Faculty of Science, Ain Shams University, Cairo, 11566, Egypt
| | - Mohamed A Ismail
- Department of Chemistry, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt
| | - Wael M El-Sayed
- Department of Zoology, Faculty of Science, Ain Shams University, Cairo, 11566, Egypt.
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Choudhary K, Itzkovich Z, Alonso-Perez E, Bishara H, Dunn B, Sherlock G, Kupiec M. S. cerevisiae Cells Can Grow without the Pds5 Cohesin Subunit. mBio 2022; 13:e0142022. [PMID: 35708277 PMCID: PMC9426526 DOI: 10.1128/mbio.01420-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 05/31/2022] [Indexed: 12/11/2022] Open
Abstract
During DNA replication, the newly created sister chromatids are held together until their separation at anaphase. The cohesin complex is in charge of creating and maintaining sister chromatid cohesion (SCC) in all eukaryotes. In Saccharomyces cerevisiae cells, cohesin is composed of two elongated proteins, Smc1 and Smc3, bridged by the kleisin Mcd1/Scc1. The latter also acts as a scaffold for three additional proteins, Scc3/Irr1, Wpl1/Rad61, and Pds5. Although the HEAT-repeat protein Pds5 is essential for cohesion, its precise function is still debated. Deletion of the ELG1 gene, encoding a PCNA unloader, can partially suppress the temperature-sensitive pds5-1 allele, but not a complete deletion of PDS5. We carried out a genetic screen for high-copy-number suppressors and another for spontaneously arising mutants, allowing the survival of a pds5Δ elg1Δ strain. Our results show that cells remain viable in the absence of Pds5 provided that there is both an elevation in the level of Mcd1 (which can be due to mutations in the CLN2 gene, encoding a G1 cyclin), and an increase in the level of SUMO-modified PCNA on chromatin (caused by lack of PCNA unloading in elg1Δ mutants). The elevated SUMO-PCNA levels increase the recruitment of the Srs2 helicase, which evicts Rad51 molecules from the moving fork, creating single-stranded DNA (ssDNA) regions that serve as sites for increased cohesin loading and SCC establishment. Thus, our results delineate a double role for Pds5 in protecting the cohesin ring and interacting with the DNA replication machinery. IMPORTANCE Sister chromatid cohesion is vital for faithful chromosome segregation, chromosome folding into loops, and gene expression. A multisubunit protein complex known as cohesin holds the sister chromatids from S phase until the anaphase stage. In this study, we explore the function of the essential cohesin subunit Pds5 in the regulation of sister chromatid cohesion. We performed two independent genetic screens to bypass the function of the Pds5 protein. We observe that Pds5 protein is a cohesin stabilizer, and elevating the levels of Mcd1 protein along with SUMO-PCNA accumulation on chromatin can compensate for the loss of the PDS5 gene. In addition, Pds5 plays a role in coordinating the DNA replication and sister chromatid cohesion establishment. This work elucidates the function of cohesin subunit Pds5, the G1 cyclin Cln2, and replication factors PCNA, Elg1, and Srs2 in the proper regulation of sister chromatid cohesion.
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Affiliation(s)
- Karan Choudhary
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, Israel
| | - Ziv Itzkovich
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, Israel
| | - Elisa Alonso-Perez
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, Israel
| | - Hend Bishara
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, Israel
| | - Barbara Dunn
- Departments of Genetics, Stanford University, Stanford, California, USA
| | - Gavin Sherlock
- Departments of Genetics, Stanford University, Stanford, California, USA
| | - Martin Kupiec
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv, Israel
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Faustova I, Örd M, Kiselev V, Fedorenko D, Borovko I, Macs D, Pääbo K, Lõoke M, Loog M. A synthetic biology approach reveals diverse and dynamic CDK response profiles via multisite phosphorylation of NLS-NES modules. SCIENCE ADVANCES 2022; 8:eabp8992. [PMID: 35977012 PMCID: PMC9385143 DOI: 10.1126/sciadv.abp8992] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
The complexity of multisite phosphorylation mechanisms in regulating nuclear localization signals (NLSs) and nuclear export signals (NESs) is not understood, and its potential has not been used in synthetic biology. The nucleocytoplasmic shuttling of many proteins is regulated by cyclin-dependent kinases (CDKs) that rely on multisite phosphorylation patterns and short linear motifs (SLiMs) to dynamically control proteins in the cell cycle. We studied the role of motif patterns in nucleocytoplasmic shuttling using sensors based on the CDK targets Dna2, Psy4, and Mcm2/3 of Saccharomyces cerevisiae. We designed multisite phosphorylation modules by rearranging phosphorylation sites, cyclin-specific SLiMs, phospho-priming, phosphatase specificity, and NLS/NES phospho-regulation and obtained very different substrate localization dynamics. These included ultrasensitive responses with and without a delay, graded responses, and different homeostatic plateaus. Thus, CDK can do much more than trigger sequential switches during the cell cycle as it can drive complex patterns of protein localization and activity by using multisite phosphorylation networks.
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Nakatsukasa K, Fujisawa M, Yang X, Kawarasaki T, Okumura F, Kamura T. Triacylglycerol lipase Tgl4 is a stable protein and its dephosphorylation is regulated in a cell cycle-dependent manner in Saccharomyces cerevisiae. Biochem Biophys Res Commun 2022; 626:85-91. [PMID: 35981421 DOI: 10.1016/j.bbrc.2022.08.022] [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: 07/28/2022] [Revised: 08/03/2022] [Accepted: 08/09/2022] [Indexed: 11/30/2022]
Abstract
Triacylglycerols (TGs) serve as reservoirs for diacylglycerols and fatty acids, which play important roles in synthesizing energy and membrane lipids that are required for cell cycle progression. In the yeast, Saccharomyces cerevisiae, Tgl4, the functional ortholog of murine adipose triacylglycerol lipase (ATGL), is activated by Cdk1/Cdc28-mediated phosphorylation and facilitates the G1/S transition. However, little is known about how Tgl4 is inactivated during the cell cycle. To monitor the phosphorylation status and the stability of endogenous Tgl4, we raised a specific antibody against Tgl4. We found that in contrast to the previous suggestion, Tgl4 was a stable protein throughout the cell cycle. We also showed that Tgl4 was dephosphorylated upon entry into G1 phase. These results suggest that Tgl4 is a stable protein and is inactivated during G1 phase by dephosphorylation.
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Affiliation(s)
- Kunio Nakatsukasa
- Graduate School of Science, Nagoya City University, Yamanohata 1, Mizuho-cho, Mizuho-ku, Nagoya, Aichi, 467-8501, Japan.
| | - Munetaka Fujisawa
- Division of Biological Sciences, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Xiaotan Yang
- Graduate School of Science, Nagoya City University, Yamanohata 1, Mizuho-cho, Mizuho-ku, Nagoya, Aichi, 467-8501, Japan
| | - Tomoyuki Kawarasaki
- Graduate School of Science, Nagoya City University, Yamanohata 1, Mizuho-cho, Mizuho-ku, Nagoya, Aichi, 467-8501, Japan
| | - Fumihiko Okumura
- Department of Food and Health Sciences, International College of Arts and Sciences, Fukuoka Women's University, Fukuoka, 813-8582, Japan
| | - Takumi Kamura
- Division of Biological Sciences, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan.
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Interactive bioinformatics analysis for the screening of hub genes and molecular docking of phytochemicals present in kitchen spices to inhibit CDK1 in cervical cancer. Comput Biol Med 2022; 149:105994. [DOI: 10.1016/j.compbiomed.2022.105994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 07/07/2022] [Accepted: 08/14/2022] [Indexed: 11/17/2022]
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46
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Ekuban A, Shichino S, Zong C, Ekuban FA, Kinoshita K, Ichihara S, Matsushima K, Ichihara G. Transcriptome analysis of human cholangiocytes exposed to carcinogenic 1,2-dichloropropane in the presence of macrophages in vitro. Sci Rep 2022; 12:11222. [PMID: 35780190 PMCID: PMC9250500 DOI: 10.1038/s41598-022-15295-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 06/22/2022] [Indexed: 11/09/2022] Open
Abstract
1,2-Dichloropropane (1,2-DCP), a synthetic organic solvent, has been implicated in causality of cholangiocarcinoma (bile duct cancer). 1,2-DCP-induced occupational cholangiocarcinoma show a different carcinogenic process compared to common cholangiocarcinoma, but its mechanism remains elusive. We reported previously that exposure of MMNK-1 cholangiocytes co-cultured with THP-1 macrophages, but not monocultured MMNK-1 cholangiocytes, to 1,2-DCP induced activation-induced cytidine deaminase (AID) expression, DNA damage and ROS production. The aim of this study was to identify relevant biological processes or target genes expressed in response to 1,2-DCP, using an in vitro system where cholangiocytes are co-cultured with macrophages. The co-cultured cells were exposed to 1,2-DCP at 0, 0.1 or 0.4 mM for 24 h, and then the cell lysates were assessed by transcriptome analysis. 1,2-DCP upregulated the expression of base excision repair genes in MMNK-1 cholangiocytes in the co-cultures, whereas it upregulated the expression of cell cycle-related genes in THP-1 macrophages. Activation of the base excision repair pathway might result from the previously observed DNA damage in MMNK-1 cholangiocytes co-cultured with THP-1 macrophages, although involvement of other mechanisms such as DNA replication, cell death or other types of DNA repair was not disproved. Cross talk interactions between cholangiocytes and macrophages leading to DNA damage in the cholangiocytes should be explored.
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Affiliation(s)
- Abigail Ekuban
- Department of Occupational and Environmental Health, Faculty of Pharmaceutical Sciences, Building No. 15, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Shigeyuki Shichino
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute of Biomedical Sciences, Tokyo University of Science, Noda, 278-0022, Japan
| | - Cai Zong
- Department of Occupational and Environmental Health, Faculty of Pharmaceutical Sciences, Building No. 15, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Frederick Adams Ekuban
- Department of Occupational and Environmental Health, Faculty of Pharmaceutical Sciences, Building No. 15, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Kazuo Kinoshita
- Evolutionary Medicine, Shizuoka Graduate University of Public Health, Shizuoka, 420-0881, Japan
| | - Sahoko Ichihara
- Department of Environmental and Preventive Medicine, Jichi Medical University School of Medicine, Shimotsuke, 329-0498, Japan
| | - Kouji Matsushima
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute of Biomedical Sciences, Tokyo University of Science, Noda, 278-0022, Japan
| | - Gaku Ichihara
- Department of Occupational and Environmental Health, Faculty of Pharmaceutical Sciences, Building No. 15, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan.
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Wang BJ, Huang SH, Kao CL, Muller CJF, Wang YP, Chang KH, Wen HC, Yeh CC, Shih LJ, Kao YH, Huang SP, Li CY, Chuu CP. Aspalathus linearis suppresses cell survival and proliferation of enzalutamide-resistant prostate cancer cells via inhibition of c-Myc and stability of androgen receptor. PLoS One 2022; 17:e0270803. [PMID: 35776912 PMCID: PMC9249401 DOI: 10.1371/journal.pone.0270803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 06/06/2022] [Indexed: 11/18/2022] Open
Abstract
Enzalutamide, a nonsteroidal antiandrogen, significantly prolonged the survival of patients with metastatic castration-resistant prostate cancer (CRPC). However, patients receiving enzalutamide frequently develop drug resistance. Rooibos (Aspalathus linearis) is a shrub-like leguminous fynbos plant endemic to the Cedarberg Mountains area in South Africa. We evaluated the possibility of using a pharmaceutical-grade green rooibos extract (GRT, containing 12.78% aspalathin) to suppress the proliferation and survival of enzalutamide-resistant prostate cancer (PCa) cells. Treatment with GRT dose-dependently suppressed the proliferation, survival, and colony formation of enzalutamide-resistant C4-2 MDV3100r cells and PC-3 cells. Non-cancerous human cells were more resistant to GRT treatment. GRT suppressed the expression of proteins involved in phosphoinositide 3-kinase (PI3K)-Akt signaling, androgen receptor (AR), phospho-AR (Ser81), cyclin-dependent kinase 1 (Cdk1), c-Myc and Bcl-2 but increased the expression of apoptotic proteins. Overexpression of c-Myc antagonized the suppressive effects of GRT, while knockdown of c-Myc increased the sensitivity of PCa cells to GRT treatment. Expression level of c-Myc correlated to resistance of PCa cells to GRT treatment. Additionally, immunofluorescence microscopy demonstrated that GRT reduced the abundance of AR proteins both in nucleus and cytoplasm. Treatment with cycloheximide revealed that GRT reduced the stability of AR. GRT suppressed protein expression of AR and AR’s downstream target prostate specific antigen (PSA) in C4-2 MDV3100r cells. Interestingly, we observed that AR proteins accumulate in nucleus and PSA expression is activated in the AR-positive enzalutamide-resistant PCa cells even in the absence of androgen. Our results suggested that GRT treatment suppressed the cell proliferation and survival of enzalutamide-resistant PCa cells via inhibition of c-Myc, induction of apoptosis, as well as the suppression of expression, signaling and stability of AR. GRT is a potential adjuvant therapeutic agent for enzalutamide-resistant PCa.
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Affiliation(s)
- Bi-Juan Wang
- Institute of Cellular and System Medicine, National Health Research Institutes, Miaoli County, Taiwan
| | - Shih-Han Huang
- Institute of Cellular and System Medicine, National Health Research Institutes, Miaoli County, Taiwan
- Department of Life Sciences, National Central University, Taoyuan City, Taiwan
| | - Cheng-Li Kao
- Division of Urology, Departments of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
- Division of Urology, Department of Surgery, Taoyuan Armed Forces General Hospital, Taoyuan, Taiwan
| | - Christo J. F. Muller
- Biomedical Research and Innovation Platform (BRIP), South African Medical Research Council, Tygerberg, South Africa
- Division of Medical Physiology, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa
- Department of Biochemistry and Microbiology, University of Zululand, KwaDlangezwa, South Africa
| | - Ya-Pei Wang
- Institute of Cellular and System Medicine, National Health Research Institutes, Miaoli County, Taiwan
| | - Kai-Hsiung Chang
- Institute of Cellular and System Medicine, National Health Research Institutes, Miaoli County, Taiwan
| | - Hui-Chin Wen
- Institute of Cellular and System Medicine, National Health Research Institutes, Miaoli County, Taiwan
| | - Chien-Chih Yeh
- Department of Education and Medical Research, Taoyuan Armed Forces General Hospital, Taoyuan, Taiwan
- Division of Colon and Rectal Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Li-Jane Shih
- Department of Education and Medical Research, Taoyuan Armed Forces General Hospital, Taoyuan, Taiwan
- Graduate Institute of Medical Science, National Defense Medical Center, Taipei, Taiwan
| | - Yung-Hsi Kao
- Department of Life Sciences, National Central University, Taoyuan City, Taiwan
| | - Shu-Pin Huang
- Department of Urology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung Taiwan
- Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Institute of Biomedical Science, National Sun Yat-sen University, Kaohsiung City, Taiwan
| | - Chia-Yang Li
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chih-Pin Chuu
- Institute of Cellular and System Medicine, National Health Research Institutes, Miaoli County, Taiwan
- Department of Life Sciences, National Central University, Taoyuan City, Taiwan
- PhD Program for Aging and Graduate Institute of Basic Medical Science, China Medical University, Taichung City, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung City, Taiwan
- * E-mail:
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48
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Liu X, Wu H, Liu Z. An Integrative Human Pan-Cancer Analysis of Cyclin-Dependent Kinase 1 (CDK1). Cancers (Basel) 2022; 14:cancers14112658. [PMID: 35681641 PMCID: PMC9179585 DOI: 10.3390/cancers14112658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/13/2022] [Accepted: 05/25/2022] [Indexed: 12/11/2022] Open
Abstract
Simple Summary Cyclin-dependent kinase 1 (CDK1), one of the key regulators of the G2/M checkpoint, is expressed in many cells and plays an important role in cell cycle control. However, CDK1 expression is substantially increased in many tumors of diverse origins and is associated with tumorigenesis. Targeting CDK1 shows promising results for several tumors. However, a systematic and integrative analysis of CDK1 in cancer has not been conducted. The present study aims to use pan-cancer analysis to investigate the relationship, similarities, and differences in genetic and cellular changes associated with CDK1 in various tumors and tumor microenvironments. Our findings elucidate that CDK1 expression increases in more than 20 human tumors and is highly correlated with oncogenic signature gene sets, biological pathways, immune cell infiltration, tumor mutational burden, microsatellite instability, and lower survival rate across multiple tumors. Targeting CDK1 may provide a novel and effective strategy for cancer immunotherapy. Abstract Cyclin-dependent kinase 1 (CDK1) is essential for cell division by regulating the G2/M phase and mitosis. CDK1 overexpression can also promote the development and progression of a variety of cancers. However, the significance of CDK1 in the formation, progression, and prognosis of human pan-cancer remains unclear. In the present study, we used The Cancer Genome Atlas database, Clinical Proteomic Tumor Analysis Consortium, Human Protein Atlas, Genotype-Tissue Expression, and other well-established databases to comprehensively examine CDK1 genetic alterations and gene/protein expression in various cancers and their relationships with the prognosis, immune reactivities, and clinical outcomes for 33 tumor types. Gene set enrichment analysis was also conducted to examine the potential mechanisms of CDK1 in tumorigenesis. The data showed that CDK1 mutation was frequently present in multiple tumors. CDK1 expression was significantly increased in various types of tumors as compared with normal tissues and was associated with poor overall and disease-free survival. In addition, CDK1 expression was significantly correlated with oncogenic genes, proteins, cellular components, myeloid-derived suppressor cell infiltration, ESTMATEScore, and signaling pathways associated with tumor development and progression and tumor microenvironments. These data indicate that CDK1 could serve as a promising biomarker for predicting tumor prognosis and a potential target for cancer treatment.
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Affiliation(s)
- Xuanyou Liu
- Department of Medical Pharmacology and Physiology, University of Missouri School of Medicine, Columbia, MO 65212, USA;
- Center for Precision Medicine and Division of Cardiovascular Medicine, Department of Medicine, University of Missouri School of Medicine, Columbia, MO 65212, USA;
| | - Hao Wu
- Center for Precision Medicine and Division of Cardiovascular Medicine, Department of Medicine, University of Missouri School of Medicine, Columbia, MO 65212, USA;
| | - Zhenguo Liu
- Center for Precision Medicine and Division of Cardiovascular Medicine, Department of Medicine, University of Missouri School of Medicine, Columbia, MO 65212, USA;
- Correspondence: ; Tel.: +573-884-3278
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49
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Adler SO, Spiesser TW, Uschner F, Münzner U, Hahn J, Krantz M, Klipp E. A yeast cell cycle model integrating stress, signaling, and physiology. FEMS Yeast Res 2022; 22:6592118. [PMID: 35617157 PMCID: PMC9246278 DOI: 10.1093/femsyr/foac026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 04/22/2022] [Accepted: 05/23/2022] [Indexed: 11/25/2022] Open
Abstract
The cell division cycle in eukaryotic cells is a series of highly coordinated molecular interactions that ensure that cell growth, duplication of genetic material, and actual cell division are precisely orchestrated to give rise to two viable progeny cells. Moreover, the cell cycle machinery is responsible for incorporating information about external cues or internal processes that the cell must keep track of to ensure a coordinated, timely progression of all related processes. This is most pronounced in multicellular organisms, but also a cardinal feature in model organisms such as baker's yeast. The complex and integrative behavior is difficult to grasp and requires mathematical modeling to fully understand the quantitative interplay of the single components within the entire system. Here, we present a self-oscillating mathematical model of the yeast cell cycle that comprises all major cyclins and their main regulators. Furthermore, it accounts for the regulation of the cell cycle machinery by a series of external stimuli such as mating pheromones and changes in osmotic pressure or nutrient quality. We demonstrate how the external perturbations modify the dynamics of cell cycle components and how the cell cycle resumes after adaptation to or relief from stress.
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Affiliation(s)
- Stephan O Adler
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, Germany
| | - Thomas W Spiesser
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, Germany
| | - Friedemann Uschner
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, Germany.,Institute for Medical Informatics and Biometry, Technische Universität Dresden, Fetscherstr. 74, 01307 Dresden, Sachsen, Germany
| | - Ulrike Münzner
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, Germany.,Laboratory of Cell Systems, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, 565-0871, Suita, Osaka, Japan
| | - Jens Hahn
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, Germany
| | - Marcus Krantz
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, Germany
| | - Edda Klipp
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Invalidenstr. 42, 10115 Berlin, Germany
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50
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Khondker S, Han GS, Carman GM. Phosphorylation-mediated regulation of the Nem1-Spo7/Pah1 phosphatase cascade in yeast lipid synthesis. Adv Biol Regul 2022; 84:100889. [PMID: 35231723 PMCID: PMC9149063 DOI: 10.1016/j.jbior.2022.100889] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/08/2022] [Accepted: 02/15/2022] [Indexed: 05/03/2023]
Abstract
The PAH1-encoded phosphatidate phosphatase, which catalyzes the dephosphorylation of phosphatidate to produce diacylglycerol, controls the divergence of phosphatidate into triacylglycerol synthesis and phospholipid synthesis. Pah1 is inactive in the cytosol as a phosphorylated form and becomes active on the nuclear/endoplasmic reticulum membrane as a dephosphorylated form by the Nem1-Spo7 protein phosphatase complex. The phosphorylation of Pah1 by protein kinases, which include casein kinases I and II, Pho85-Pho80, Cdc28-cyclin B, and protein kinases A and C, controls its cellular location, catalytic activity, and susceptibility to proteasomal degradation. Nem1 (catalytic subunit) and Spo7 (regulatory subunit), which form a protein phosphatase complex catalyzing the dephosphorylation of Pah1 for its activation, are phosphorylated by protein kinases A and C. In this review, we discuss the functions and interrelationships of the protein kinases in the control of the Nem1-Spo7/Pah1 phosphatase cascade and lipid synthesis.
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Affiliation(s)
- Shoily Khondker
- Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Gil-Soo Han
- Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, NJ, 08901, USA
| | - George M Carman
- Department of Food Science and the Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, NJ, 08901, USA.
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