1
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Lin L, Zhao J, Kubota N, Li Z, Lam YL, Nguyen LP, Yang L, Pokharel SP, Blue SM, Yee BA, Chen R, Yeo GW, Chen CW, Chen L, Zheng S. Epistatic interactions between NMD and TRP53 control progenitor cell maintenance and brain size. Neuron 2024; 112:2157-2176.e12. [PMID: 38697111 DOI: 10.1016/j.neuron.2024.04.006] [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: 01/04/2023] [Revised: 02/14/2024] [Accepted: 04/05/2024] [Indexed: 05/04/2024]
Abstract
Mutations in human nonsense-mediated mRNA decay (NMD) factors are enriched in neurodevelopmental disorders. We show that deletion of key NMD factor Upf2 in mouse embryonic neural progenitor cells causes perinatal microcephaly but deletion in immature neurons does not, indicating NMD's critical roles in progenitors. Upf2 knockout (KO) prolongs the cell cycle of radial glia progenitor cells, promotes their transition into intermediate progenitors, and leads to reduced upper-layer neurons. CRISPRi screening identified Trp53 knockdown rescuing Upf2KO progenitors without globally reversing NMD inhibition, implying marginal contributions of most NMD targets to the cell cycle defect. Integrated functional genomics shows that NMD degrades selective TRP53 downstream targets, including Cdkn1a, which, without NMD suppression, slow the cell cycle. Trp53KO restores the progenitor cell pool and rescues the microcephaly of Upf2KO mice. Therefore, one physiological role of NMD in the developing brain is to degrade selective TRP53 targets to control progenitor cell cycle and brain size.
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Affiliation(s)
- Lin Lin
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA 92521, USA; Center for RNA Biology and Medicine, University of California, Riverside, Riverside, CA 92521, USA
| | - Jingrong Zhao
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA 92521, USA; Center for RNA Biology and Medicine, University of California, Riverside, Riverside, CA 92521, USA
| | - Naoto Kubota
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA 92521, USA; Center for RNA Biology and Medicine, University of California, Riverside, Riverside, CA 92521, USA
| | - Zhelin Li
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA 92521, USA
| | - Yi-Li Lam
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA 92521, USA; Center for RNA Biology and Medicine, University of California, Riverside, Riverside, CA 92521, USA
| | - Lauren P Nguyen
- Interdepartmental Neuroscience Program, University of California, Riverside, Riverside, CA 92521, USA
| | - Lu Yang
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Sheela P Pokharel
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Steven M Blue
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Brian A Yee
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Renee Chen
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Chun-Wei Chen
- Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA; City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Liang Chen
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Sika Zheng
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA 92521, USA; Center for RNA Biology and Medicine, University of California, Riverside, Riverside, CA 92521, USA; Interdepartmental Neuroscience Program, University of California, Riverside, Riverside, CA 92521, USA.
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2
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Ishikawa C, Mori N. Inhibitory effect of a neddylation blockade on HTLV-1-infected T cells via modulation of NF-κB, AP-1, and Akt signaling. Leuk Lymphoma 2024; 65:978-988. [PMID: 38489672 DOI: 10.1080/10428194.2024.2328219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 03/03/2024] [Indexed: 03/17/2024]
Abstract
Adult T-cell leukemia (ATL), caused by HTLV-1, is the most lethal hematological malignancy. NEDD8-activating enzyme (NAE) is a component of the NEDD8 conjunction pathway that regulates cullin-RING ubiquitin ligase (CRL) activity. HTLV-1-infected T cells expressed higher levels of NAE catalytic subunit UBA3 than normal peripheral blood mononuclear cells. NAE1 knockdown inhibited proliferation of HTLV-1-infected T cells. The NAE1 inhibitor MLN4924 suppressed neddylation of cullin and inhibited the CRL-mediated turnover of tumor suppressor proteins. MLN4924 inhibited proliferation of HTLV-1-infected T cells by inducing DNA damage, leading to S phase arrest and caspase-dependent apoptosis. S phase arrest was associated with CDK2 and cyclin A downregulation. MLN4924-induced apoptosis was mediated by the upregulation of pro-apoptotic and downregulation of anti-apoptotic proteins. Furthermore, MLN4924 inhibited NF-κB, AP-1, and Akt signaling pathways and activated JNK. Therefore, neddylation inhibition is an attractive strategy for ATL therapy. Our findings support the use of MLN4924 in ATL clinical trials.
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Affiliation(s)
- Chie Ishikawa
- Department of Microbiology and Oncology, Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan
- Division of Health Sciences, Transdisciplinary Research Organization for Subtropics and Island Studies, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Naoki Mori
- Department of Microbiology and Oncology, Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan
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3
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Chen J, Chen X, Tang A, Wang Z, Cheong KL, Liu X, Zhong S. Chondroitin sulfate-functionalized selenium nanoparticle-induced S-phase cell cycle arrest and apoptosis in HeLa Cells. J Food Sci 2024; 89:4469-4479. [PMID: 38837700 DOI: 10.1111/1750-3841.17137] [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: 01/31/2024] [Revised: 04/09/2024] [Accepted: 05/03/2024] [Indexed: 06/07/2024]
Abstract
This study aimed to evaluate the anti-cervical cancer activity of chondroitin sulfate-functionalized selenium nanoparticles (SeCS) and to elucidate their action mechanism. Cytotoxic effect of SeCS on HeLa cells was assessed by MTT assay. Further molecular mechanism of SeCS was analyzed by flow cytometric assay and western blotting. The results showed that treatment with SeCS resulted in a dose- and time-dependent inhibition in the proliferation of HeLa cells. The data obtained from flow cytometry demonstrated that SeCS inhibited HeLa cell growth via the induction of S-phase arrest and cell apoptosis. Further mechanism analysis found that SeCS down-regulated expression levels of cyclin A and CDK2 and up-regulated p21 expression, which contributed to S arrest. Moreover, SeCS increased the level of Bax and decreased the expression of Bcl-2, resulting in the release of cytochrome C from mitochondria and activating caspase-3/8/9 for caspase-dependent apoptosis. Meanwhile, intracellular reactive oxygen species (ROS) levels were elevated after SeCS treatment, suggesting that ROS might be upstream of SeCS-induced S-phase arrest and cell apoptosis. These data show that SeCS has anti-tumor effects and possesses the potential to become a new therapeutic agent or adjuvant therapy for cancer patients. PRACTICAL APPLICATION: In our previous study, we used chondroitin sulfate to stabilize nano-selenium to obtain SeCS to improve the bioactivity and stability of nano-selenium. We found that it possessed an inhibitory effect on HeLa cells. However, the molecular mechanism remains unclear. This study elucidated the mechanism of SeCS damage to HeLa cells. SeCS has the potential to become a new therapeutic agent or adjuvant therapy for cancer patients.
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Affiliation(s)
- Jianping Chen
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Province Engineering Laboratory for Marine Biological Products, Key Laboratory of Advanced Processing of Aquatic Product of Guangdong Higher Education Institution, Zhanjiang, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Xuehua Chen
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Province Engineering Laboratory for Marine Biological Products, Key Laboratory of Advanced Processing of Aquatic Product of Guangdong Higher Education Institution, Zhanjiang, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Anqi Tang
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Province Engineering Laboratory for Marine Biological Products, Key Laboratory of Advanced Processing of Aquatic Product of Guangdong Higher Education Institution, Zhanjiang, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Zhuo Wang
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Province Engineering Laboratory for Marine Biological Products, Key Laboratory of Advanced Processing of Aquatic Product of Guangdong Higher Education Institution, Zhanjiang, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Kit-Leong Cheong
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Province Engineering Laboratory for Marine Biological Products, Key Laboratory of Advanced Processing of Aquatic Product of Guangdong Higher Education Institution, Zhanjiang, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Xiaofei Liu
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Province Engineering Laboratory for Marine Biological Products, Key Laboratory of Advanced Processing of Aquatic Product of Guangdong Higher Education Institution, Zhanjiang, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
| | - Saiyi Zhong
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Province Engineering Laboratory for Marine Biological Products, Key Laboratory of Advanced Processing of Aquatic Product of Guangdong Higher Education Institution, Zhanjiang, China
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian, China
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Di Giorgio E, Dalla E, Tolotto V, D'Este F, Paluvai H, Ranzino L, Brancolini C. HDAC4 influences the DNA damage response and counteracts senescence by assembling with HDAC1/HDAC2 to control H2BK120 acetylation and homology-directed repair. Nucleic Acids Res 2024:gkae501. [PMID: 38874468 DOI: 10.1093/nar/gkae501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 05/27/2024] [Accepted: 05/30/2024] [Indexed: 06/15/2024] Open
Abstract
Access to DNA is the first level of control in regulating gene transcription, a control that is also critical for maintaining DNA integrity. Cellular senescence is characterized by profound transcriptional rearrangements and accumulation of DNA lesions. Here, we discovered an epigenetic complex between HDAC4 and HDAC1/HDAC2 that is involved in the erase of H2BK120 acetylation. The HDAC4/HDAC1/HDAC2 complex modulates the efficiency of DNA repair by homologous recombination, through dynamic deacetylation of H2BK120. Deficiency of HDAC4 leads to accumulation of H2BK120ac, impaired recruitment of BRCA1 and CtIP to the site of lesions, accumulation of damaged DNA and senescence. In senescent cells this complex is disassembled because of increased proteasomal degradation of HDAC4. Forced expression of HDAC4 during RAS-induced senescence reduces the genomic spread of γH2AX. It also affects H2BK120ac levels, which are increased in DNA-damaged regions that accumulate during RAS-induced senescence. In summary, degradation of HDAC4 during senescence causes the accumulation of damaged DNA and contributes to the activation of the transcriptional program controlled by super-enhancers that maintains senescence.
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Affiliation(s)
- Eros Di Giorgio
- Laboratory of Biochemistry, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100 Udine, Italy
| | - Emiliano Dalla
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100 Udine, Italy
| | - Vanessa Tolotto
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100 Udine, Italy
| | - Francesca D'Este
- Laboratory of Biochemistry, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100 Udine, Italy
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100 Udine, Italy
| | - Harikrishnareddy Paluvai
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100 Udine, Italy
| | - Liliana Ranzino
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100 Udine, Italy
| | - Claudio Brancolini
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100 Udine, Italy
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5
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Huber HF, Li C, Xie D, Gerow KG, Register TC, Shively CA, Cox LA, Nathanielsz PW. Female baboon adrenal zona fasciculata and zona reticularis regulatory and functional proteins decrease across the life course. GeroScience 2024; 46:3405-3417. [PMID: 38311700 PMCID: PMC11009170 DOI: 10.1007/s11357-024-01080-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/09/2024] [Indexed: 02/06/2024] Open
Abstract
Debate exists on life-course adrenocortical zonal function trajectories. Rapid, phasic blood steroid concentration changes, such as circadian rhythms and acute stress responses, complicate quantification. To avoid pitfalls and account for life-stage changes in adrenocortical activity indices, we quantified zonae fasciculata (ZF) and reticularis (ZR) across the life-course, by immunohistochemistry of key regulatory and functional proteins. In 28 female baboon adrenals (7.5-22.1 years), we quantified 12 key proteins involved in cell metabolism, division, proliferation, steroidogenesis (including steroid acute regulatory protein, StAR), oxidative stress, and glucocorticoid and mitochondrial function. Life-course abundance of ten ZF proteins decreased with age. Cell cycle inhibitor and oxidative stress markers increased. Seven of the 12 proteins changed in the same direction for ZR and ZF. Importantly, ZF StAR decreased, while ZR StAR was unchanged. Findings indicate ZF function decreased, and less markedly ZR function, with age. Causes and aging consequences of these changes remain to be determined.
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Affiliation(s)
- Hillary Fries Huber
- Southwest National Primate Research Center, Texas Biomedical Research Institute, 8715 W. Military, San Antonio, TX, 78227, USA.
| | - Cun Li
- Texas Pregnancy & Life-Course Health Research Center, Animal Science, University of Wyoming, Laramie, WY, USA
| | - Dongbin Xie
- Texas Pregnancy & Life-Course Health Research Center, Animal Science, University of Wyoming, Laramie, WY, USA
| | | | - Thomas C Register
- Pathology-Comparative Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Carol A Shively
- Pathology-Comparative Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Laura A Cox
- Southwest National Primate Research Center, Texas Biomedical Research Institute, 8715 W. Military, San Antonio, TX, 78227, USA
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Peter W Nathanielsz
- Southwest National Primate Research Center, Texas Biomedical Research Institute, 8715 W. Military, San Antonio, TX, 78227, USA
- Texas Pregnancy & Life-Course Health Research Center, Animal Science, University of Wyoming, Laramie, WY, USA
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6
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Kida M, Abe J, Hori H, Hirai Y. PRSS3/mesotrypsin as a putative regulator of the biophysical characteristics of epidermal keratinocytes in superficial layers. Sci Rep 2024; 14:12383. [PMID: 38811772 PMCID: PMC11137022 DOI: 10.1038/s41598-024-63271-w] [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: 03/08/2024] [Accepted: 05/27/2024] [Indexed: 05/31/2024] Open
Abstract
Mesotrypsin, encoded by the PRSS3 gene, is a distinctive trypsin isoform renowned for its exceptional resistance to traditional trypsin inhibitors and unique substrate specificity. Within the skin epidermis, this protein primarily expresses in the upper layers of the stratified epidermis and plays a crucial role in processing pro-filaggrin (Pro-FLG). Although prior studies have partially elucidated its functions using primary cultured keratinocytes, challenges persist due to these cells' differentiation-activated cell death program. In the present study, HaCaT keratinocytes, characterized by minimal endogenous mesotrypsin expression and sustained proliferation in differentiated states, were utilized to further scrutinize the function of mesotrypsin. Despite the ready degradation of the intact form of active mesotrypsin in these cells, fusion with Venus, flanked by a peptide linker, enables evasion from the protein elimination machinery, thus facilitating activation of the Pro-FLG processing system. Inducing Venus-mesotrypsin expression in the cells resulted in a flattened phenotype and reduced proliferative capacity. Moreover, these cells displayed altered F-actin assembly, enhanced E-cadherin adhesive activity, and facilitated tight junction formation without overtly influencing epidermal differentiation. These findings underscore mesotrypsin's potentially pivotal role in shaping the characteristic cellular morphology of upper epidermal layers.
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Affiliation(s)
- Moeko Kida
- Department of Biomedical Sciences, Graduate School of Science and Technology, Kwansei Gakuin University, 1 Gakuen-Uegahara, Sanda, 669-1330, Japan
| | - Junya Abe
- Department of Biomedical Sciences, Graduate School of Science and Technology, Kwansei Gakuin University, 1 Gakuen-Uegahara, Sanda, 669-1330, Japan
| | - Haruna Hori
- Department of Biomedical Sciences, Graduate School of Science and Technology, Kwansei Gakuin University, 1 Gakuen-Uegahara, Sanda, 669-1330, Japan
| | - Yohei Hirai
- Department of Biomedical Sciences, Graduate School of Science and Technology, Kwansei Gakuin University, 1 Gakuen-Uegahara, Sanda, 669-1330, Japan.
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Piho P, Thomas P. Feedback between stochastic gene networks and population dynamics enables cellular decision-making. SCIENCE ADVANCES 2024; 10:eadl4895. [PMID: 38787956 PMCID: PMC11122677 DOI: 10.1126/sciadv.adl4895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 04/24/2024] [Indexed: 05/26/2024]
Abstract
Phenotypic selection occurs when genetically identical cells are subject to different reproductive abilities due to cellular noise. Such noise arises from fluctuations in reactions synthesizing proteins and plays a crucial role in how cells make decisions and respond to stress or drugs. We propose a general stochastic agent-based model for growing populations capturing the feedback between gene expression and cell division dynamics. We devise a finite state projection approach to analyze gene expression and division distributions and infer selection from single-cell data in mother machines and lineage trees. We use the theory to quantify selection in multi-stable gene expression networks and elucidate that the trade-off between phenotypic switching and selection enables robust decision-making essential for synthetic circuits and developmental lineage decisions. Using live-cell data, we demonstrate that combining theory and inference provides quantitative insights into bet-hedging-like response to DNA damage and adaptation during antibiotic exposure in Escherichia coli.
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Affiliation(s)
- Paul Piho
- Department of Mathematics, Imperial College London, London, UK
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8
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Holtzen SE, Navid E, Kainov JD, Palmer AE. Transient Zn 2+ deficiency induces replication stress and compromises daughter cell proliferation. Proc Natl Acad Sci U S A 2024; 121:e2321216121. [PMID: 38687796 PMCID: PMC11087780 DOI: 10.1073/pnas.2321216121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 03/13/2024] [Indexed: 05/02/2024] Open
Abstract
Cells must replicate their genome quickly and accurately, and they require metabolites and cofactors to do so. Ionic zinc (Zn2+) is an essential micronutrient that is required for hundreds of cellular processes, including DNA synthesis and adequate proliferation. Deficiency in this micronutrient impairs DNA synthesis and inhibits proliferation, but the mechanism is unknown. Using fluorescent reporters to track single cells via long-term live-cell imaging, we find that Zn2+ is required at the G1/S transition and during S phase for timely completion of S phase. A short pulse of Zn2+ deficiency impairs DNA synthesis and increases markers of replication stress. These markers of replication stress are reversed upon resupply of Zn2+. Finally, we find that if Zn2+ is chelated during the mother cell's S phase, daughter cells enter a transient quiescent state, maintained by sustained expression of p21, which disappears upon reentry into the cell cycle. In summary, short pulses of mild Zn2+ deficiency in S phase specifically induce replication stress, which causes downstream proliferation impairments in daughter cells.
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Affiliation(s)
- Samuel E. Holtzen
- Department of Molecular Cellular and Developmental Biology, University of Colorado, Boulder, CO80309
| | - Elnaz Navid
- Department of Biochemistry, University of Colorado, Boulder, CO80309
| | - Joseph D. Kainov
- Department of Biochemistry, University of Colorado, Boulder, CO80309
| | - Amy E. Palmer
- Department of Biochemistry, University of Colorado, Boulder, CO80309
- BioFrontiers Institute, University of Colorado, Boulder, CO80309
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Joshi AS, Bapat MV, Singh P, Mijakovic I. Viridibacillus culture derived silver nanoparticles exert potent anticancer action in 2D and 3D models of lung cancer via mitochondrial depolarization-mediated apoptosis. Mater Today Bio 2024; 25:100997. [PMID: 38379934 PMCID: PMC10876681 DOI: 10.1016/j.mtbio.2024.100997] [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: 11/27/2023] [Revised: 02/03/2024] [Accepted: 02/09/2024] [Indexed: 02/22/2024] Open
Abstract
Lung cancer is one of the most commonly occurring cancer types that accounts for almost 2 million cases per year. Its resistance to anticancer drugs, failure of new molecules in clinical trials, severe side-effects of current treatments, and its recurrence limit the success of anticancer therapies. Nanotherapeutic agents offer several advantages over conventional anticancer therapies, including improved retention in tumors, specificity, and anticancer effects at lower concentrations, hence reducing the side-effects. Here, we have explored the anticancer activity of silver nanoparticles synthesized in Viridibacillus sp. enriched culture medium for the first time. Such green nanoparticles, synthesized by biological systems, are superior to chemically synthesized ones in terms of their environmental footprint and production cost, and have one crucial advantage of excellent stability owing to their biological corona. To assess anticancer activity of these nanoparticles, we used conventional 2D cultured A549 cells as well as 3D spheroids of A549 cells. In both models of lung cancer, our silver nanoparticles diminished cell proliferation, arrested DNA synthesis, and showed a dose dependent cytotoxic effect. The nanoparticles damaged the DNA and mitochondrial structures in both A549 cells and A549 spheroids, leading to mitochondrial depolarization and increased cell permeability. Low lethal median doses (LD50) for 2D cultured A549 cells (1 μg/ml) and for A549 spheroids (13 μg/ml) suggest that our nanoparticles are potent anticancer agents. We also developed in vitro tumor progression model and in vitro tumor size model using 3D spheroids to test anticancer potential of our nanoparticles which otherwise would require longer experimental duration along with large number of animals and trained personnel. In these models, our nanoparticles showed strong dose dependent anticancer activity. In case of in vitro tumor progression model, the A549 cells failed to form tight spheroidal mass and showed increased dead cell fraction since day 1 as compared to control. On the other hand, in case of in vitro tumor size model, the 4 and 8 μg/ml nanoparticle treatment led to reduction in spheroid size from 615 ± 53 μm to 440 ± 45 μm and 612 ± 44 μm to 368 ± 62 μm respectively, within the time span of 3 days post treatment. We believe that use of such novel experimental models offers excellent and fast alternative to in vivo studies, and to the best of our knowledge, this is the first report that gives proof-of-concept for use of such novel in vitro cancer models to test anticancer agents such as Viridibacilli culture derived silver nanoparticles. Based on our results, we propose that these nanoparticles offer an interesting alternative for anticancer therapies, especially if they can be combined with classical anticancer drugs.
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Affiliation(s)
- Abhayraj S. Joshi
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Mugdha V. Bapat
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Priyanka Singh
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ivan Mijakovic
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
- Department of Biology and Biological Engineering, Division of Systems and Synthetic Biology, Chalmers University of Technology, Sweden
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10
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Meitinger F, Belal H, Davis RL, Martinez MB, Shiau AK, Oegema K, Desai A. Control of cell proliferation by memories of mitosis. Science 2024; 383:1441-1448. [PMID: 38547292 DOI: 10.1126/science.add9528] [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: 07/14/2022] [Accepted: 02/04/2024] [Indexed: 04/02/2024]
Abstract
Mitotic duration is tightly constrained, and extended mitosis is characteristic of problematic cells prone to chromosome missegregation and genomic instability. We show here that mitotic extension leads to the formation of p53-binding protein 1 (53BP1)-ubiquitin-specific protease 28 (USP28)-p53 protein complexes that are transmitted to, and stably retained by, daughter cells. Complexes assembled through a Polo-like kinase 1-dependent mechanism during extended mitosis and elicited a p53 response in G1 that prevented the proliferation of the progeny of cells that experienced an approximately threefold extended mitosis or successive less extended mitoses. The ability to monitor mitotic extension was lost in p53-mutant cancers and some p53-wild-type (p53-WT) cancers, consistent with classification of TP53BP1 and USP28 as tumor suppressors. Cancers retaining the ability to monitor mitotic extension exhibited sensitivity to antimitotic agents.
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Affiliation(s)
- Franz Meitinger
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA
- Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Hazrat Belal
- Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Robert L Davis
- Small Molecule Discovery Program, Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA
| | - Mallory B Martinez
- Small Molecule Discovery Program, Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA
| | - Andrew K Shiau
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Small Molecule Discovery Program, Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA
| | - Karen Oegema
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA
| | - Arshad Desai
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA
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11
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Li C, Xie SS, Wang J, Sharvia S, Chan KY. SC-Track: a robust cell-tracking algorithm for generating accurate single-cell lineages from diverse cell segmentations. Brief Bioinform 2024; 25:bbae192. [PMID: 38704671 PMCID: PMC11070058 DOI: 10.1093/bib/bbae192] [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: 01/12/2024] [Revised: 03/18/2024] [Accepted: 04/10/2024] [Indexed: 05/06/2024] Open
Abstract
Computational analysis of fluorescent timelapse microscopy images at the single-cell level is a powerful approach to study cellular changes that dictate important cell fate decisions. Core to this approach is the need to generate reliable cell segmentations and classifications necessary for accurate quantitative analysis. Deep learning-based convolutional neural networks (CNNs) have emerged as a promising solution to these challenges. However, current CNNs are prone to produce noisy cell segmentations and classifications, which is a significant barrier to constructing accurate single-cell lineages. To address this, we developed a novel algorithm called Single Cell Track (SC-Track), which employs a hierarchical probabilistic cache cascade model based on biological observations of cell division and movement dynamics. Our results show that SC-Track performs better than a panel of publicly available cell trackers on a diverse set of cell segmentation types. This cell-tracking performance was achieved without any parameter adjustments, making SC-Track an excellent generalized algorithm that can maintain robust cell-tracking performance in varying cell segmentation qualities, cell morphological appearances and imaging conditions. Furthermore, SC-Track is equipped with a cell class correction function to improve the accuracy of cell classifications in multiclass cell segmentation time series. These features together make SC-Track a robust cell-tracking algorithm that works well with noisy cell instance segmentation and classification predictions from CNNs to generate accurate single-cell lineages and classifications.
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Affiliation(s)
- Chengxin Li
- Department of Cardiovascular Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, P. R. China
- Centre for Cellular Biology and Signalling, Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, 314400, P. R. China
| | - Shuang Shuang Xie
- Centre for Cellular Biology and Signalling, Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, 314400, P. R. China
| | - Jiaqi Wang
- Centre for Cellular Biology and Signalling, Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, 314400, P. R. China
| | - Septavera Sharvia
- Department of Computer Science, University of Hull, Hull, HU6 7RX, UK
| | - Kuan Yoow Chan
- Department of Cardiovascular Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, P. R. China
- Centre for Cellular Biology and Signalling, Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, 314400, P. R. China
- College of Medicine and Veterinary Medicine, The University of Edinburgh, Edinburgh, EH4 2XR, UK
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12
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Köberlin MS, Fan Y, Liu C, Chung M, Pinto AFM, Jackson PK, Saghatelian A, Meyer T. A fast-acting lipid checkpoint in G1 prevents mitotic defects. Nat Commun 2024; 15:2441. [PMID: 38499565 PMCID: PMC10948896 DOI: 10.1038/s41467-024-46696-9] [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: 07/24/2023] [Accepted: 03/06/2024] [Indexed: 03/20/2024] Open
Abstract
Lipid synthesis increases during the cell cycle to ensure sufficient membrane mass, but how insufficient synthesis restricts cell-cycle entry is not understood. Here, we identify a lipid checkpoint in G1 phase of the mammalian cell cycle by using live single-cell imaging, lipidome, and transcriptome analysis of a non-transformed cell. We show that synthesis of fatty acids in G1 not only increases lipid mass but extensively shifts the lipid composition to unsaturated phospholipids and neutral lipids. Strikingly, acute lowering of lipid synthesis rapidly activates the PERK/ATF4 endoplasmic reticulum (ER) stress pathway that blocks cell-cycle entry by increasing p21 levels, decreasing Cyclin D levels, and suppressing Retinoblastoma protein phosphorylation. Together, our study identifies a rapid anticipatory ER lipid checkpoint in G1 that prevents cells from starting the cell cycle as long as lipid synthesis is low, thereby preventing mitotic defects, which are triggered by low lipid synthesis much later in mitosis.
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Affiliation(s)
- Marielle S Köberlin
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Yilin Fan
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Chad Liu
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94111, USA
| | - Mingyu Chung
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Antonio F M Pinto
- Clayton Foundation Laboratories for Peptide Biology and Mass Spectrometry Core, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology and Mass Spectrometry Core, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Tobias Meyer
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, 10065, USA.
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13
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Thoma OM, Naschberger E, Kubánková M, Larafa I, Kramer V, Menchicchi B, Merkel S, Britzen-Laurent N, Jefremow A, Grützmann R, Koop K, Neufert C, Atreya R, Guck J, Stürzl M, Neurath MF, Waldner MJ. p21 Prevents the Exhaustion of CD4 + T Cells Within the Antitumor Immune Response Against Colorectal Cancer. Gastroenterology 2024; 166:284-297.e11. [PMID: 37734420 DOI: 10.1053/j.gastro.2023.09.017] [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: 12/13/2022] [Revised: 08/30/2023] [Accepted: 09/05/2023] [Indexed: 09/23/2023]
Abstract
BACKGROUND & AIMS T cells are crucial for the antitumor response against colorectal cancer (CRC). T-cell reactivity to CRC is nevertheless limited by T-cell exhaustion. However, molecular mechanisms regulating T-cell exhaustion are only poorly understood. METHODS We investigated the functional role of cyclin-dependent kinase 1a (Cdkn1a or p21) in cluster of differentiation (CD) 4+ T cells using murine CRC models. Furthermore, we evaluated the expression of p21 in patients with stage I to IV CRC. In vitro coculture models were used to understand the effector function of p21-deficient CD4+ T cells. RESULTS We observed that the activation of cell cycle regulator p21 is crucial for CD4+ T-cell cytotoxic function and that p21 deficiency in type 1 helper T cells (Th1) leads to increased tumor growth in murine CRC. Similarly, low p21 expression in CD4+ T cells infiltrated into tumors of CRC patients is associated with reduced cancer-related survival. In mouse models of CRC, p21-deficient Th1 cells show signs of exhaustion, where an accumulation of effector/effector memory T cells and CD27/CD28 loss are predominant. Immune reconstitution of tumor-bearing Rag1-/- mice using ex vivo-treated p21-deficient T cells with palbociclib, an inhibitor of cyclin-dependent kinase 4/6, restored cytotoxic function and prevented exhaustion of p21-deficient CD4+ T cells as a possible concept for future immunotherapy of human disease. CONCLUSIONS Our data reveal the importance of p21 in controlling the cell cycle and preventing exhaustion of Th1 cells. Furthermore, we unveil the therapeutic potential of cyclin-dependent kinase inhibitors such as palbociclib to reduce T-cell exhaustion for future treatment of patients with colorectal cancer.
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Affiliation(s)
- Oana-Maria Thoma
- Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; German Center for Immunotherapy, Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany.
| | - Elisabeth Naschberger
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany; Division of Molecular and Experimental Surgery, Department of Surgery, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Markéta Kubánková
- Max Planck Institute for the Science of Light & Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
| | - Imen Larafa
- Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; German Center for Immunotherapy, Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany
| | - Viktoria Kramer
- Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; German Center for Immunotherapy, Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany
| | - Bianca Menchicchi
- Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; German Center for Immunotherapy, Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany
| | - Susanne Merkel
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany; Department of Surgery, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Nathalie Britzen-Laurent
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany; Department of Surgery, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - André Jefremow
- Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; German Center for Immunotherapy, Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany
| | - Robert Grützmann
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany; Department of Surgery, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Kristina Koop
- Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; German Center for Immunotherapy, Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany
| | - Clemens Neufert
- Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; German Center for Immunotherapy, Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany
| | - Raja Atreya
- Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; German Center for Immunotherapy, Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany
| | - Jochen Guck
- Max Planck Institute for the Science of Light & Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
| | - Michael Stürzl
- Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany; Division of Molecular and Experimental Surgery, Department of Surgery, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Markus F Neurath
- Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; German Center for Immunotherapy, Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany
| | - Maximilian J Waldner
- Department of Medicine 1, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; German Center for Immunotherapy, Deutsches Zentrum Immuntherapie (DZI), University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN), Erlangen, Germany; Erlangen Graduate School in Advanced Optical Technologies (SAOT), Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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14
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Jing X, Jia S, Teng M, Day BW, Afolayan AJ, Jarzembowski JA, Lin CW, Hessner MJ, Pritchard KA, Naylor S, Konduri GG, Teng RJ. Cellular Senescence Contributes to the Progression of Hyperoxic Bronchopulmonary Dysplasia. Am J Respir Cell Mol Biol 2024; 70:94-109. [PMID: 37874230 DOI: 10.1165/rcmb.2023-0038oc] [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: 01/31/2023] [Accepted: 10/23/2023] [Indexed: 10/25/2023] Open
Abstract
Oxidative stress, inflammation, and endoplasmic reticulum (ER) stress sequentially occur in bronchopulmonary dysplasia (BPD), and all result in DNA damage. When DNA damage becomes irreparable, tumor suppressors increase, followed by apoptosis or senescence. Although cellular senescence contributes to wound healing, its persistence inhibits growth. Therefore, we hypothesized that cellular senescence contributes to BPD progression. Human autopsy lungs were obtained. Sprague-Dawley rat pups exposed to 95% oxygen between Postnatal Day 1 (P1) and P10 were used as the BPD phenotype. N-acetyl-lysyltyrosylcysteine-amide (KYC), tauroursodeoxycholic acid (TUDCA), and Foxo4 dri were administered intraperitoneally to mitigate myeloperoxidase oxidant generation, ER stress, and cellular senescence, respectively. Lungs were examined by histology, transcriptomics, and immunoblotting. Cellular senescence increased in rat and human BPD lungs, as evidenced by increased oxidative DNA damage, tumor suppressors, GL-13 stain, and inflammatory cytokines with decreased cell proliferation and lamin B expression. Cellular senescence-related transcripts in BPD rat lungs were enriched at P10 and P21. Single-cell RNA sequencing showed increased cellular senescence in several cell types, including type 2 alveolar cells. In addition, Foxo4-p53 binding increased in BPD rat lungs. Daily TUDCA or KYC, administered intraperitoneally, effectively decreased cellular senescence, improved alveolar complexity, and partially maintained the numbers of type 2 alveolar cells. Foxo4 dri administered at P4, P6, P8, and P10 led to outcomes similar to TUDCA and KYC. Our data suggest that cellular senescence plays an essential role in BPD after initial inducement by hyperoxia. Reducing myeloperoxidase toxic oxidant production, ER stress, and attenuating cellular senescence are potential therapeutic strategies for halting BPD progression.
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Affiliation(s)
- Xigang Jing
- Department of Pediatrics
- Children's Research Institute
| | - Shuang Jia
- Department of Pediatrics
- Children's Research Institute
| | - Maggie Teng
- Department of Anthropology, Washington University in St. Louis, St. Louis, Missouri; and
| | | | | | | | - Chien-Wei Lin
- Division of Biostatistics, Institute for Health and Equity, and
| | | | - Kirkwood A Pritchard
- Children's Research Institute
- Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin
- ReNeuroGen LLC, Milwaukee, Wisconsin
| | | | | | - Ru-Jeng Teng
- Department of Pediatrics
- Children's Research Institute
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15
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Ćurčić V, Olszewski M, Maciejewska N, Višnjevac A, Srdić-Rajić T, Dobričić V, García-Sosa AT, Kokanov SB, Araškov JB, Silvestri R, Schüle R, Jung M, Nikolić M, Filipović NR. Quinoline-based thiazolyl-hydrazones target cancer cells through autophagy inhibition. Arch Pharm (Weinheim) 2024; 357:e2300426. [PMID: 37991233 DOI: 10.1002/ardp.202300426] [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: 08/01/2023] [Revised: 10/23/2023] [Accepted: 10/26/2023] [Indexed: 11/23/2023]
Abstract
Heterocyclic pharmacophores such as thiazole and quinoline rings have a significant role in medicinal chemistry. They are considered privileged structures since they constitute several Food and Drug Administration (FDA)-approved drugs for cancer treatment. Herein, we report the synthesis, in silico evaluation of the ADMET profiles, and in vitro investigation of the anticancer activity of a series of novel thiazolyl-hydrazones based on the 8-quinoline (1a-c), 2-quinoline (2a-c), and 8-hydroxy-2-quinolyl moiety (3a-c). The panel of several human cancer cell lines and the nontumorigenic human embryonic kidney cell line HEK-293 were used to evaluate the compound-mediated in vitro anticancer activities, leading to [2-(2-(quinolyl-8-ol-2-ylmethylene)hydrazinyl)]-4-(4-methoxyphenyl)-1,3-thiazole (3c) as the most promising compound. The study revealed that 3c blocks the cell-cycle progression of a human colon cancer cell line (HCT-116) in the S phase and induces DNA double-strand breaks. Also, our findings demonstrate that 3c accumulates in lysosomes, ultimately leading to the cell death of the hepatocellular carcinoma cell line (Hep-G2) and HCT-116 cells, by the mechanism of autophagy inhibition.
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Affiliation(s)
- Vladimir Ćurčić
- Faculty of Chemistry, University of Belgrade, Belgrade, Serbia
| | - Mateusz Olszewski
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Gdansk, Poland
| | - Natalia Maciejewska
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Gdansk, Poland
| | | | - Tatjana Srdić-Rajić
- Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Belgrade, Serbia
| | - Vladimir Dobričić
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | | | - Sanja B Kokanov
- Faculty of Chemistry, University of Belgrade, Belgrade, Serbia
| | | | - Romano Silvestri
- Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
| | - Roland Schüle
- Klinik für Urologie und Zentrale Klinische Forschung, Klinikum der Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
- Deutsches Konsortium für Translationale Krebsforschung, Standort Freiburg, Freiburg, Germany
- CIBSS Centre of Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Manfred Jung
- Deutsches Konsortium für Translationale Krebsforschung, Standort Freiburg, Freiburg, Germany
- CIBSS Centre of Biological Signalling Studies, University of Freiburg, Freiburg, Germany
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Milan Nikolić
- Faculty of Chemistry, University of Belgrade, Belgrade, Serbia
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16
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Diehl FF, Sapp KM, Vander Heiden MG. The bidirectional relationship between metabolism and cell cycle control. Trends Cell Biol 2024; 34:136-149. [PMID: 37385879 DOI: 10.1016/j.tcb.2023.05.012] [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: 02/03/2023] [Revised: 05/30/2023] [Accepted: 05/31/2023] [Indexed: 07/01/2023]
Abstract
The relationship between metabolism and cell cycle progression is complex and bidirectional. Cells must rewire metabolism to meet changing biosynthetic demands across cell cycle phases. In turn, metabolism can influence cell cycle progression through direct regulation of cell cycle proteins, through nutrient-sensing signaling pathways, and through its impact on cell growth, which is linked to cell division. Furthermore, metabolism is a key player in mediating quiescence-proliferation transitions in physiologically important cell types, such as stem cells. How metabolism impacts cell cycle progression, exit, and re-entry, as well as how these processes impact metabolism, is not fully understood. Recent advances uncovering mechanistic links between cell cycle regulators and metabolic processes demonstrate a complex relationship between metabolism and cell cycle control, with many questions remaining.
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Affiliation(s)
- Frances F Diehl
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Koch Institute for Integrative Cancer Research and the Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kiera M Sapp
- Koch Institute for Integrative Cancer Research and the Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research and the Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Dana-Farber Cancer Institute, Boston, MA, USA.
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17
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Yang HW. Investigating Heterogeneous Cell-Cycle Progression Using Single-Cell Imaging Approaches. Methods Mol Biol 2024; 2740:263-273. [PMID: 38393481 DOI: 10.1007/978-1-0716-3557-5_16] [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] [Indexed: 02/25/2024]
Abstract
Investigating cell-cycle progression has been challenging due to the complex interconnectivity of regulatory processes and inherent cell-to-cell heterogeneity, which often require synchronization procedures. However, recent advancements in cell-cycle sensors and single-cell imaging techniques have turned this heterogeneity into an advantage for investigating the molecular mechanisms underlying diverse responses. This has led to significant progress in our understanding of cell-cycle regulation. In this paper, we present a comprehensive live single-cell imaging workflow that leverages cutting-edge live-cell sensors. These advanced single-cell imaging procedures provide promising opportunities for elucidating the molecular mechanisms underpinnings of heterogeneous responses in cell-cycle progression.
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Affiliation(s)
- Hee Won Yang
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.
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18
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Sieler M, Dittmar T. Cell Fusion and Syncytia Formation in Cancer. Results Probl Cell Differ 2024; 71:433-465. [PMID: 37996689 DOI: 10.1007/978-3-031-37936-9_20] [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] [Indexed: 11/25/2023]
Abstract
The natural phenomenon of cell-cell fusion does not only take place in physiological processes, such as placentation, myogenesis, or osteoclastogenesis, but also in pathophysiological processes, such as cancer. More than a century ago postulated, today the hypothesis that the fusion of cancer cells with normal cells leads to the formation of cancer hybrid cells with altered properties is in scientific consensus. Some studies that have investigated the mechanisms and conditions for the fusion of cancer cells with other cells, as well as studies that have characterized the resulting cancer hybrid cells, are presented in this review. Hypoxia and the cytokine TNFα, for example, have been found to promote cell fusion. In addition, it has been found that both the protein Syncytin-1, which normally plays a role in placentation, and phosphatidylserine signaling on the cell membrane are involved in the fusion of cancer cells with other cells. In human cancer, cancer hybrid cells were detected not only in the primary tumor, but also in the circulation of patients as so-called circulating hybrid cells, where they often correlated with a worse outcome. Although some data are available, the questions of how and especially why cancer cells fuse with other cells are still not fully answered.
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Affiliation(s)
- Mareike Sieler
- Institute of Immunology, Center for Biomedical Education and Research (ZBAF), University of Witten/Herdecke, Witten, Germany.
| | - Thomas Dittmar
- Institute of Immunology, Center for Biomedical Education and Research (ZBAF), University of Witten/Herdecke, Witten, Germany
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19
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Lang PF, Penas DR, Banga JR, Weindl D, Novak B. Reusable rule-based cell cycle model explains compartment-resolved dynamics of 16 observables in RPE-1 cells. PLoS Comput Biol 2024; 20:e1011151. [PMID: 38190398 PMCID: PMC10773963 DOI: 10.1371/journal.pcbi.1011151] [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: 05/03/2023] [Accepted: 11/24/2023] [Indexed: 01/10/2024] Open
Abstract
The mammalian cell cycle is regulated by a well-studied but complex biochemical reaction system. Computational models provide a particularly systematic and systemic description of the mechanisms governing mammalian cell cycle control. By combining both state-of-the-art multiplexed experimental methods and powerful computational tools, this work aims at improving on these models along four dimensions: model structure, validation data, validation methodology and model reusability. We developed a comprehensive model structure of the full cell cycle that qualitatively explains the behaviour of human retinal pigment epithelial-1 cells. To estimate the model parameters, time courses of eight cell cycle regulators in two compartments were reconstructed from single cell snapshot measurements. After optimisation with a parallel global optimisation metaheuristic we obtained excellent agreements between simulations and measurements. The PEtab specification of the optimisation problem facilitates reuse of model, data and/or optimisation results. Future perturbation experiments will improve parameter identifiability and allow for testing model predictive power. Such a predictive model may aid in drug discovery for cell cycle-related disorders.
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Affiliation(s)
- Paul F. Lang
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - David R. Penas
- Computational Biology Lab, MBG-CSIC (Spanish National Research Council), Pontevedra, Spain
| | - Julio R. Banga
- Computational Biology Lab, MBG-CSIC (Spanish National Research Council), Pontevedra, Spain
| | - Daniel Weindl
- Computational Health Center, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
| | - Bela Novak
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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20
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Rong Y, Darnell AM, Sapp KM, Vander Heiden MG, Spencer SL. Cells use multiple mechanisms for cell-cycle arrest upon withdrawal of individual amino acids. Cell Rep 2023; 42:113539. [PMID: 38070134 DOI: 10.1016/j.celrep.2023.113539] [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: 04/17/2023] [Revised: 09/29/2023] [Accepted: 11/17/2023] [Indexed: 12/30/2023] Open
Abstract
Amino acids are required for cell growth and proliferation, but it remains unclear when and how amino acid availability impinges on the proliferation-quiescence decision. Here, we used time-lapse microscopy and single-cell tracking of cyclin-dependent kinase 2 (CDK2) activity to assess the response of individual cells to withdrawal of single amino acids and found strikingly different cell-cycle effects depending on the amino acid. For example, upon leucine withdrawal, MCF10A cells complete two cell cycles and then enter a CDK2-low quiescence, whereas lysine withdrawal causes immediate cell-cycle stalling. Methionine withdrawal triggers a restriction point phenotype similar to serum starvation or Mek inhibition: upon methionine withdrawal, cells complete their current cell cycle and enter a CDK2-low quiescence after mitosis. Modulation of restriction point regulators p21/p27 or cyclin D1 enables short-term rescue of proliferation under methionine and leucine withdrawal, and to a lesser extent lysine withdrawal, revealing a checkpoint connecting nutrient signaling to cell-cycle entry.
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Affiliation(s)
- Yao Rong
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA
| | - Alicia M Darnell
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kiera M Sapp
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Dana-Farber Cancer Institute, Boston, MA 02215, USA; Broad Institute, Cambridge, MA 02139, USA
| | - Sabrina L Spencer
- Department of Biochemistry and BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA.
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21
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Manousakis E, Miralles CM, Esquerda MG, Wright RHG. CDKN1A/p21 in Breast Cancer: Part of the Problem, or Part of the Solution? Int J Mol Sci 2023; 24:17488. [PMID: 38139316 PMCID: PMC10743848 DOI: 10.3390/ijms242417488] [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: 10/18/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Cyclin-dependent kinase inhibitor 1A (Cip1/Waf1/CDKN1A/p21) is a well-established protein, primarily recognised for its pivotal role in the cell cycle, where it induces cell cycle arrest by inhibiting the activity of cyclin-dependent kinases (CDKs). Over the years, extensive research has shed light on various additional mechanisms involving CDKN1A/p21, implicating it in processes such as apoptosis, DNA damage response (DDR), and the regulation of stem cell fate. Interestingly, p21 can function either as an oncogene or as a tumour suppressor in these contexts. Complicating matters further, the expression of CDKN1A/p21 is elevated in certain tumour types while downregulated in others. In this comprehensive review, we provide an overview of the multifaceted functions of CDKN1A/p21, present clinical data pertaining to cancer patients, and delve into potential strategies for targeting CDKN1A/p21 as a therapeutic approach to cancer. Manipulating CDKN1A/p21 shows great promise for therapy given its involvement in multiple cancer hallmarks, such as sustained cell proliferation, the renewal of cancer stem cells (CSCs), epithelial-mesenchymal transition (EMT), cell migration, and resistance to chemotherapy. Given the dual role of CDKN1A/p21 in these processes, a more in-depth understanding of its specific mechanisms of action and its regulatory network is imperative to establishing successful therapeutic interventions.
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Affiliation(s)
| | | | | | - Roni H. G. Wright
- Basic Sciences Department, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, 08195 Barcelona, Spain
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22
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Holtzen SE, Navid E, Kainov JD, Palmer AE. Transient Zn 2+ deficiency induces replication stress and compromises daughter cell proliferation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.08.570860. [PMID: 38106081 PMCID: PMC10723434 DOI: 10.1101/2023.12.08.570860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Cells must replicate their genome quickly and accurately, and they require metabolites and cofactors to do so. Ionic zinc (Zn2+) is an essential micronutrient that is required for hundreds of cellular processes, including DNA synthesis and adequate proliferation. Deficiency in this micronutrient impairs DNA synthesis and inhibits proliferation, but the mechanism is unknown. Using fluorescent reporters to track single cells via long-term live-cell imaging, we find that Zn2+ is required at the G1/S transition and during S-phase for timely completion of S-phase. A short pulse of Zn2+ deficiency impairs DNA synthesis and increases markers of replication stress. These markers of replication stress are reversed upon resupply of Zn2+. Finally, we find that if Zn2+ is removed during the mother cell's S-phase, daughter cells enter a transient quiescent state, maintained by sustained expression of p21, which disappears upon reentry into the cell cycle. In summary, short pulses of mild Zn2+ deficiency in S-phase specifically induce replication stress, which causes downstream proliferation impairments in daughter cells.
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Affiliation(s)
- Samuel E. Holtzen
- Department of Molecular Cellular and Developmental Biology and BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, 80309
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309
| | - Elnaz Navid
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309
| | - Joseph D. Kainov
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309
| | - Amy E. Palmer
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309
- Department of Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, CO, 80309
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23
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Crozier L, Foy R, Adib R, Kar A, Holt JA, Pareri AU, Valverde JM, Rivera R, Weston WA, Wilson R, Regnault C, Whitfield P, Badonyi M, Bennett LG, Vernon EG, Gamble A, Marsh JA, Staples CJ, Saurin AT, Barr AR, Ly T. CDK4/6 inhibitor-mediated cell overgrowth triggers osmotic and replication stress to promote senescence. Mol Cell 2023; 83:4062-4077.e5. [PMID: 37977118 DOI: 10.1016/j.molcel.2023.10.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 07/10/2023] [Accepted: 10/16/2023] [Indexed: 11/19/2023]
Abstract
Abnormal increases in cell size are associated with senescence and cell cycle exit. The mechanisms by which overgrowth primes cells to withdraw from the cell cycle remain unknown. We address this question using CDK4/6 inhibitors, which arrest cells in G0/G1 and are licensed to treat advanced HR+/HER2- breast cancer. We demonstrate that CDK4/6-inhibited cells overgrow during G0/G1, causing p38/p53/p21-dependent cell cycle withdrawal. Cell cycle withdrawal is triggered by biphasic p21 induction. The first p21 wave is caused by osmotic stress, leading to p38- and size-dependent accumulation of p21. CDK4/6 inhibitor washout results in some cells entering S-phase. Overgrown cells experience replication stress, resulting in a second p21 wave that promotes cell cycle withdrawal from G2 or the subsequent G1. We propose that the levels of p21 integrate signals from overgrowth-triggered stresses to determine cell fate. This model explains how hypertrophy can drive senescence and why CDK4/6 inhibitors have long-lasting effects in patients.
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Affiliation(s)
- Lisa Crozier
- Cellular and Systems Medicine, Jacqui Wood Cancer Centre, School of Medicine, University of Dundee, Dundee, UK
| | - Reece Foy
- Cellular and Systems Medicine, Jacqui Wood Cancer Centre, School of Medicine, University of Dundee, Dundee, UK
| | - Rozita Adib
- MRC Laboratory of Medical Sciences, London, UK
| | - Ananya Kar
- Molecular Cell and Developmental Biology, School of Life Sciences, Dundee, UK
| | | | - Aanchal U Pareri
- Cellular and Systems Medicine, Jacqui Wood Cancer Centre, School of Medicine, University of Dundee, Dundee, UK
| | - Juan M Valverde
- Cellular and Systems Medicine, Jacqui Wood Cancer Centre, School of Medicine, University of Dundee, Dundee, UK
| | - Rene Rivera
- Molecular Cell and Developmental Biology, School of Life Sciences, Dundee, UK
| | | | - Rona Wilson
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Clement Regnault
- Glasgow Polyomics College of Medical, Veterinary, and Life Sciences, University of Glasgow, UK
| | - Phil Whitfield
- Glasgow Polyomics College of Medical, Veterinary, and Life Sciences, University of Glasgow, UK
| | - Mihaly Badonyi
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, UK
| | - Laura G Bennett
- North West Cancer Research Institute, School of Medical and Health Sciences, Brambell Building, Deiniol Rd, Bangor LL57 2UW, UK
| | - Ellen G Vernon
- North West Cancer Research Institute, School of Medical and Health Sciences, Brambell Building, Deiniol Rd, Bangor LL57 2UW, UK
| | - Amelia Gamble
- North West Cancer Research Institute, School of Medical and Health Sciences, Brambell Building, Deiniol Rd, Bangor LL57 2UW, UK
| | - Joseph A Marsh
- MRC Human Genetics Unit, University of Edinburgh, Edinburgh, UK
| | - Christopher J Staples
- North West Cancer Research Institute, School of Medical and Health Sciences, Brambell Building, Deiniol Rd, Bangor LL57 2UW, UK
| | - Adrian T Saurin
- Cellular and Systems Medicine, Jacqui Wood Cancer Centre, School of Medicine, University of Dundee, Dundee, UK.
| | - Alexis R Barr
- MRC Laboratory of Medical Sciences, London, UK; Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK.
| | - Tony Ly
- Molecular Cell and Developmental Biology, School of Life Sciences, Dundee, UK; Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK; Glasgow Polyomics College of Medical, Veterinary, and Life Sciences, University of Glasgow, UK.
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24
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Wang N, Xu S, Egli D. Replication stress in mammalian embryo development, differentiation, and reprogramming. Trends Cell Biol 2023; 33:872-886. [PMID: 37202286 PMCID: PMC11214770 DOI: 10.1016/j.tcb.2023.03.015] [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: 01/04/2023] [Revised: 03/24/2023] [Accepted: 03/29/2023] [Indexed: 05/20/2023]
Abstract
Duplicating a genome of 3 billion nucleotides is challenged by a variety of obstacles that can cause replication stress and affect the integrity of the genome. Recent studies show that replication fork slowing and stalling is prevalent in early mammalian development, resulting in genome instability and aneuploidy, and constituting a barrier to development in human reproduction. Genome instability resulting from DNA replication stress is a barrier to the cloning of animals and to the reprogramming of differentiated cells to induced pluripotent stem cells, as well as a barrier to cell transformation. Remarkably, the regions most impacted by replication stress are shared in these different cellular contexts, affecting long genes and flanking intergenic areas. In this review we integrate our knowledge of DNA replication stress in mammalian embryos, in programming, and in reprogramming, and we discuss a potential role for fragile sites in sensing replication stress and restricting cell cycle progression in health and disease.
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Affiliation(s)
- Ning Wang
- Division of Molecular Genetics, Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Shuangyi Xu
- Division of Molecular Genetics, Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Dieter Egli
- Division of Molecular Genetics, Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA.
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25
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Singh G, Sharma SK, Dorata A, Singh SK. miR-17 ~ 92 suppresses proliferation and invasion of cervical cancer cells by inhibiting cell cycle regulator Cdt2. Discov Oncol 2023; 14:172. [PMID: 37707654 PMCID: PMC10501107 DOI: 10.1007/s12672-023-00775-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/21/2023] [Indexed: 09/15/2023] Open
Abstract
Cervical cancer (CC) is the 4th most leading cause of death among women worldwide, and if diagnosed in late stages the treatment options are almost negligible. 99% of CC is caused by high-risk human papilloma viruses (HR-HPV). Upon integration into human genome, the encoded viral proteins mis-regulate various onco-suppressors and checkpoint factors including cell cycle regulators. One such protein is cell cycle S phase licensing factor, CDC-10 dependent transcript-2 (Cdt2) which has been reported to be highly upregulated in various cancers including CC. Also, in CC cells, several tumor suppressor miRNAs are suppressed, including miR-17 ~ 92 cluster. In this study, we report that miR-17 ~ 92 directly recruits to 3'UTR of Cdt2 and downregulates this oncogene which suppresses the proliferation, migration and invasion capabilities of the CC cell lines without affecting non-cancerous cells. We further show that suppression of Cdt2 by miR-17 ~ 92, blocks the cancerous cells in S phase and induces apoptosis, eventually leading to their death. Hence, our work for the first time, mechanistically shows how miR-17 ~ 92 could work as tumor suppressor in cervical cancer cells, opening up the potential of miR-17 ~ 92 to be used in developing therapy for cervical cancer treatment.
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Affiliation(s)
- Garima Singh
- Cell Cycle and Cancer Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, UP, 221005, India
| | - Sonika Kumari Sharma
- Cell Cycle and Cancer Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, UP, 221005, India
| | - Aastha Dorata
- Cell Cycle and Cancer Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, UP, 221005, India
| | - Samarendra Kumar Singh
- Cell Cycle and Cancer Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, UP, 221005, India.
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26
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Milletti G, Colicchia V, Cecconi F. Cyclers' kinases in cell division: from molecules to cancer therapy. Cell Death Differ 2023; 30:2035-2052. [PMID: 37516809 PMCID: PMC10482880 DOI: 10.1038/s41418-023-01196-z] [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: 04/27/2023] [Revised: 07/08/2023] [Accepted: 07/18/2023] [Indexed: 07/31/2023] Open
Abstract
Faithful eucaryotic cell division requires spatio-temporal orchestration of multiple sequential events. To ensure the dynamic nature of these molecular and morphological transitions, a swift modulation of key regulatory pathways is necessary. The molecular process that most certainly fits this description is phosphorylation, the post-translational modification provided by kinases, that is crucial to allowing the progression of the cell cycle and that culminates with the separation of two identical daughter cells. In detail, from the early stages of the interphase to the cytokinesis, each critical step of this process is tightly regulated by multiple families of kinases including the Cyclin-dependent kinases (CDKs), kinases of the Aurora, Polo, Wee1 families, and many others. While cell-cycle-related CDKs control the timing of the different phases, preventing replication machinery errors, the latter modulate the centrosome cycle and the spindle function, avoiding karyotypic abnormalities typical of chromosome instability. Such chromosomal abnormalities may result from replication stress (RS) and chromosome mis-segregation and are considered a hallmark of poor prognosis, therapeutic resistance, and metastasis in cancer patients. Here, we discuss recent advances in the understanding of how different families of kinases concur to govern cell cycle, preventing RS and mitotic infidelity. Additionally, considering the growing number of clinical trials targeting these molecules, we review to what extent and in which tumor context cell-cycle-related kinases inhibitors are worth exploiting as an effective therapeutic strategy.
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Affiliation(s)
- Giacomo Milletti
- DNA Replication and Cancer Group, Danish Cancer Institute, 2100, Copenhagen, Denmark.
- Department of Pediatric Hematology and Oncology and of Cell and Gene Therapy, IRCCS Ospedale Pediatrico Bambino Gesù, Rome, Italy.
| | - Valeria Colicchia
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
- IRBM S.p.A., Via Pontina Km 30.60, 00070, Pomezia, Italy
| | - Francesco Cecconi
- Cell Stress and Survival Group, Center for Autophagy, Recycling and Disease (CARD), Danish Cancer Institute, Copenhagen, Denmark.
- Università Cattolica del Sacro Cuore and Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy.
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27
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Huang Y, Zhang J, Li X, Wu Z, Xie G, Wang Y, Liu Z, Jiao M, Zhang H, Shi B, Wang Y, Zhang Y. Chromatin accessibility memory of donor cells disrupts bovine somatic cell nuclear transfer blastocysts development. FASEB J 2023; 37:e23111. [PMID: 37531300 DOI: 10.1096/fj.202300131rrr] [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: 01/25/2023] [Revised: 06/30/2023] [Accepted: 07/11/2023] [Indexed: 08/04/2023]
Abstract
The post-transfer developmental capacity of bovine somatic cell nuclear transfer (SCNT) blastocysts is reduced, implying that abnormalities in gene expression regulation are present at blastocyst stage. Chromatin accessibility, as an indicator for transcriptional regulatory elements mediating gene transcription activity, has heretofore been largely unexplored in SCNT embryos, especially at blastocyst stage. In the present study, single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq) of in vivo and SCNT blastocysts were conducted to segregate lineages and demonstrate the aberrant chromatin accessibility of transcription factors (TFs) related to inner cell mass (ICM) development in SCNT blastocysts. Pseudotime analysis of lineage segregation further reflected dysregulated chromatin accessibility dynamics of TFs in the ICM of SCNT blastocysts compared to their in vivo counterparts. ATAC- and ChIP-seq results of SCNT donor cells revealed that the aberrant chromatin accessibility in the ICM of SCNT blastocysts was due to the persistence of chromatin accessibility memory at corresponding loci in the donor cells, with strong enrichment of trimethylation of histone H3 at lysine 4 (H3K4me3) at these loci. Correction of the aberrant chromatin accessibility through demethylation of H3K4me3 by KDM5B diminished the expression of related genes (e.g., BCL11B) and significantly improved the ICM proliferation in SCNT blastocysts. This effect was confirmed by knocking down BCL11B in SCNT embryos to down-regulate p21 and alleviate the inhibition of ICM proliferation. These findings expand our understanding of the chromatin accessibility abnormalities in SCNT blastocysts and BCL11B may be a potential target to improve SCNT efficiency.
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Affiliation(s)
- Yuemeng Huang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Jingcheng Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Xinmei Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zhipei Wu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Guoxiang Xie
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yong Wang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Zhengqing Liu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Mei Jiao
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Hexu Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Binqiang Shi
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
| | - Yu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yong Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Engineering Center for Animal Embryo Technology, Yangling, China
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28
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Osia B, Merkell A, Lopezcolorado FW, Ping X, Stark JM. RAD52 and ERCC6L/PICH have a compensatory relationship for genome stability in mitosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.23.554522. [PMID: 37662271 PMCID: PMC10473716 DOI: 10.1101/2023.08.23.554522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The mammalian RAD52 protein is a DNA repair factor that has both strand annealing and recombination mediator activities, yet is dispensable for cell viability. To characterize genetic contexts that reveal dependence on RAD52 to sustain cell viability (i.e., synthetic lethal relationships), we performed genome-wide CRISPR knock-out screens. Subsequent secondary screening found that depletion of ERCC6L in RAD52-deficient cells causes reduced viability and elevated genome instability, measured as accumulation of 53BP1 into nuclear foci. Furthermore, loss of RAD52 causes elevated levels of anaphase ultrafine bridges marked by ERCC6L, and conversely depletion of ERCC6L causes elevated RAD52 foci both in prometaphase and interphase cells. These effects were enhanced with combination treatments using hydroxyurea and the topoisomerase IIα inhibitor ICRF-193, and the timing of these treatments are consistent with defects in addressing such stress in mitosis. Thus, loss of RAD52 appears to cause an increased reliance on ERCC6L in mitosis, and vice versa. Consistent with this notion, combined depletion of ERCC6L and disrupting G2/M progression via CDK1 inhibition causes a marked loss of viability in RAD52-deficient cells. We suggest that RAD52 and ERCC6L play compensatory roles in protecting genome stability in mitosis.
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29
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Zheng D, Mao Y, Gao Y, He F, Ma J. Daughter cell fate choice instructed preemptively by mother cells facing nutrient limitation. iScience 2023; 26:107198. [PMID: 37485365 PMCID: PMC10359942 DOI: 10.1016/j.isci.2023.107198] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/03/2023] [Accepted: 06/20/2023] [Indexed: 07/25/2023] Open
Abstract
Nutrients are vital to cellular activities, yet it is largely unknown how individual cells respond to nutrient deprivation. Live imaging results show that unlike the removal of amino acids or glutamine that immediately halts cell cycle progression, glucose withdrawal does not prevent cells from completing their current cycle. Although cells that begin to experience glucose withdrawal in S phase give rise to daughter cells with an equal choice of proliferation or quiescence, those enduring such experience in G1 phase give rise to daughter cells that predominantly enter quiescence. This fate choice difference stems from p21 protein accumulated during G2/M of the latter cells. Induced degradation of p21 permits daughter cells to enter S phase but with a consequent accumulation of DNA damage. These results suggest that mother cells that begin to experience glucose limitation in G1 phase take preemptive steps toward preventing daughter cells from making a harmful choice.
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Affiliation(s)
- Dianpeng Zheng
- Women’s Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Genetic and Developmental Disorder, Hangzhou, Zhejiang 310058, China
| | - Yaowen Mao
- Women’s Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Genetic and Developmental Disorder, Hangzhou, Zhejiang 310058, China
| | - Yinglong Gao
- Zhejiang Provincial Key Laboratory of Genetic and Developmental Disorder, Hangzhou, Zhejiang 310058, China
- National Clinical Research Center for Child Health, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310052, China
| | - Feng He
- Women’s Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Genetic and Developmental Disorder, Hangzhou, Zhejiang 310058, China
- National Clinical Research Center for Child Health, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310052, China
| | - Jun Ma
- Women’s Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Genetic and Developmental Disorder, Hangzhou, Zhejiang 310058, China
- National Clinical Research Center for Child Health, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310052, China
- Women’s Reproductive Health Research Laboratory of Zhejiang Province, Hangzhou, Zhejiang 310006, China
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30
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Venkatachalapathy H, Brzakala C, Batchelor E, Azarin SM, Sarkar CA. Inertial effect of cell state velocity on the quiescence-proliferation fate decision in breast cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.22.541793. [PMID: 37292599 PMCID: PMC10245870 DOI: 10.1101/2023.05.22.541793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Energy landscapes can provide intuitive depictions of population heterogeneity and dynamics. However, it is unclear whether individual cell behavior, hypothesized to be determined by initial position and noise, is faithfully recapitulated. Using the p21-/Cdk2-dependent quiescence-proliferation decision in breast cancer dormancy as a testbed, we examined single-cell dynamics on the landscape when perturbed by hypoxia, a dormancy-inducing stress. Combining trajectory-based energy landscape generation with single-cell time-lapse microscopy, we found that initial position on a p21/Cdk2 landscape did not fully explain the observed cell-fate heterogeneity under hypoxia. Instead, cells with higher cell state velocities prior to hypoxia, influenced by epigenetic parameters, tended to remain proliferative under hypoxia. Thus, the fate decision on this landscape is significantly influenced by "inertia", a velocity-dependent ability to resist directional changes despite reshaping of the underlying landscape, superseding positional effects. Such inertial effects may markedly influence cell-fate trajectories in tumors and other dynamically changing microenvironments.
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Affiliation(s)
- Harish Venkatachalapathy
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA
| | - Cole Brzakala
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA
| | - Eric Batchelor
- Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Samira M. Azarin
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA
| | - Casim A. Sarkar
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
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31
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Hatshan MR, Saquib Q, Siddiqui MA, Faisal M, Ahmad J, Al-Khedhairy AA, Shaik MR, Khan M, Wahab R, Matteis VD, Adil SF. Effectiveness of Nonfunctionalized Graphene Oxide Nanolayers as Nanomedicine against Colon, Cervical, and Breast Cancer Cells. Int J Mol Sci 2023; 24:ijms24119141. [PMID: 37298090 DOI: 10.3390/ijms24119141] [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: 03/05/2023] [Revised: 04/26/2023] [Accepted: 05/17/2023] [Indexed: 06/12/2023] Open
Abstract
Recent studies in nanomedicine have intensively explored the prospective applications of surface-tailored graphene oxide (GO) as anticancer entity. However, the efficacy of nonfunctionalized graphene oxide nanolayers (GRO-NLs) as an anticancer agent is less explored. In this study, we report the synthesis of GRO-NLs and their in vitro anticancer potential in breast (MCF-7), colon (HT-29), and cervical (HeLa) cancer cells. GRO-NLs-treated HT-29, HeLa, and MCF-7 cells showed cytotoxicity in the MTT and NRU assays via defects in mitochondrial functions and lysosomal activity. HT-29, HeLa, and MCF-7 cells treated with GRO-NLs exhibited substantial elevations in ROS, disturbances of the mitochondrial membrane potential, an influx of Ca2+, and apoptosis. The qPCR quantification showed the upregulation of caspase 3, caspase 9, bax, and SOD1 genes in GRO-NLs-treated cells. Western blotting showed the depletion of P21, P53, and CDC25C proteins in the above cancer cell lines after GRO-NLs treatment, indicating its function as a mutagen to induce mutation in the P53 gene, thereby affecting P53 protein and downstream effectors P21 and CDC25C. In addition, there may be a mechanism other than P53 mutation that controls P53 dysfunction. We conclude that nonfunctionalized GRO-NLs exhibit prospective biomedical application as a putative anticancer entity against colon, cervical, and breast cancers.
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Affiliation(s)
- Mohammad Rafe Hatshan
- Department of Chemistry, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Quaiser Saquib
- Chair for DNA Research, Zoology Department, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Maqsood A Siddiqui
- Chair for DNA Research, Zoology Department, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Mohammad Faisal
- Botany and Microbiology Department, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Javed Ahmad
- Chair for DNA Research, Zoology Department, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Abdulaziz A Al-Khedhairy
- Chair for DNA Research, Zoology Department, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Mohammed Rafi Shaik
- Department of Chemistry, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Mujeeb Khan
- Department of Chemistry, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Rizwan Wahab
- Chair for DNA Research, Zoology Department, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Valeria De Matteis
- Department of Mathematics and Physics "Ennio De Giorgi", University of Salento, Via Arnesano, 73100 Lecce, Italy
| | - Syed Farooq Adil
- Department of Chemistry, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
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Wiecek AJ, Cutty SJ, Kornai D, Parreno-Centeno M, Gourmet LE, Tagliazucchi GM, Jacobson DH, Zhang P, Xiong L, Bond GL, Barr AR, Secrier M. Genomic hallmarks and therapeutic implications of G0 cell cycle arrest in cancer. Genome Biol 2023; 24:128. [PMID: 37221612 PMCID: PMC10204193 DOI: 10.1186/s13059-023-02963-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 05/07/2023] [Indexed: 05/25/2023] Open
Abstract
BACKGROUND Therapy resistance in cancer is often driven by a subpopulation of cells that are temporarily arrested in a non-proliferative G0 state, which is difficult to capture and whose mutational drivers remain largely unknown. RESULTS We develop methodology to robustly identify this state from transcriptomic signals and characterise its prevalence and genomic constraints in solid primary tumours. We show that G0 arrest preferentially emerges in the context of more stable, less mutated genomes which maintain TP53 integrity and lack the hallmarks of DNA damage repair deficiency, while presenting increased APOBEC mutagenesis. We employ machine learning to uncover novel genomic dependencies of this process and validate the role of the centrosomal gene CEP89 as a modulator of proliferation and G0 arrest capacity. Lastly, we demonstrate that G0 arrest underlies unfavourable responses to various therapies exploiting cell cycle, kinase signalling and epigenetic mechanisms in single-cell data. CONCLUSIONS We propose a G0 arrest transcriptional signature that is linked with therapeutic resistance and can be used to further study and clinically track this state.
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Affiliation(s)
- Anna J. Wiecek
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Stephen J. Cutty
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
| | - Daniel Kornai
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Mario Parreno-Centeno
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Lucie E. Gourmet
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, UK
| | | | - Daniel H. Jacobson
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, UK
- UCL Cancer Institute, Paul O’Gorman Building, University College London, London, UK
| | - Ping Zhang
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Lingyun Xiong
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Gareth L. Bond
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Alexis R. Barr
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, UK
- Cell Cycle Control Team, MRC London Institute of Medical Sciences (LMS), London, UK
| | - Maria Secrier
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, UK
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Johnson J, Yang Y, Bian Z, Schena G, Li Y, Zhang X, Eaton DM, Gross P, Angheloiu A, Shaik A, Foster M, Berretta R, Kubo H, Mohsin S, Tian Y, Houser SR. Systemic Hypoxemia Induces Cardiomyocyte Hypertrophy and Right Ventricular Specific Induction of Proliferation. Circ Res 2023; 132:723-740. [PMID: 36799218 PMCID: PMC10023496 DOI: 10.1161/circresaha.122.321604] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 02/06/2023] [Indexed: 02/18/2023]
Abstract
BACKGROUND A recent study suggests that systemic hypoxemia in adult male mice can induce cardiac myocytes to proliferate. The goal of the present experiments was to confirm these results, provide new insights on the mechanisms that induce adult cardiomyocyte cell cycle reentry, and to determine if hypoxemia also induces cardiomyocyte proliferation in female mice. METHODS EdU-containing mini pumps were implanted in 3-month-old, male and female C57BL/6 mice. Mice were placed in a hypoxia chamber, and the oxygen was lowered by 1% every day for 14 days to reach 7% oxygen. The animals remained in 7% oxygen for 2 weeks before terminal studies. Myocyte proliferation was also studied with a mosaic analysis with double markers mouse model. RESULTS Hypoxia induced cardiac hypertrophy in both left ventricular (LV) and right ventricular (RV) myocytes, with LV myocytes lengthening and RV myocytes widening and lengthening. Hypoxia induced an increase (0.01±0.01% in normoxia to 0.11±0.09% in hypoxia) in the number of EdU+ RV cardiomyocytes, with no effect on LV myocytes in male C57BL/6 mice. Similar results were observed in female mice. Furthermore, in mosaic analysis with double markers mice, hypoxia induced a significant increase in RV myocyte proliferation (0.03±0.03% in normoxia to 0.32±0.15% in hypoxia of RFP+ myocytes), with no significant change in LV myocyte proliferation. RNA sequencing showed upregulation of mitotic cell cycle genes and a downregulation of Cullin genes, which promote the G1 to S phase transition in hypoxic mice. There was significant proliferation of nonmyocytes and mild cardiac fibrosis in hypoxic mice that did not disrupt cardiac function. Male and female mice exhibited similar gene expression following hypoxia. CONCLUSIONS Systemic hypoxia induces a global hypertrophic stress response that was associated with increased RV proliferation, and while LV myocytes did not show increased proliferation, our results minimally confirm previous reports that hypoxia can induce cardiomyocyte cell cycle activity in vivo.
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Affiliation(s)
- Jaslyn Johnson
- Independence Blue Cross Cardiovascular Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Yijun Yang
- Independence Blue Cross Cardiovascular Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Zilin Bian
- Tandon School of Engineering, New York University, Brooklyn, NY, USA
| | | | - Yijia Li
- Independence Blue Cross Cardiovascular Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Xiaoying Zhang
- Department of Cardiovascular Sciences, Center for Translational Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Deborah M. Eaton
- Penn Cardiovascular Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Polina Gross
- Independence Blue Cross Cardiovascular Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | | | | | | | - Remus Berretta
- Independence Blue Cross Cardiovascular Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Hajime Kubo
- Independence Blue Cross Cardiovascular Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Sadia Mohsin
- Independence Blue Cross Cardiovascular Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Ying Tian
- Department of Cardiovascular Sciences, Center for Translational Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Steven R. Houser
- Independence Blue Cross Cardiovascular Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
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Natural and synthetic compounds for glioma treatment based on ROS-mediated strategy. Eur J Pharmacol 2023:175537. [PMID: 36871663 DOI: 10.1016/j.ejphar.2023.175537] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 01/08/2023] [Accepted: 01/23/2023] [Indexed: 03/06/2023]
Abstract
Glioma is the most frequent and most malignant tumor of the central nervous system (CNS),accounting for about 50% of all CNS tumor and approximately 80% of the malignant primary tumors in the CNS. Patients with glioma benefit from surgical resection, chemo- and radio-therapy. However these therapeutical strategies do not significantly improve the prognosis, nor increase survival rates owing to restricted drug contribution in the CNS and to the malignant characteristics of glioma. Reactive oxygen species (ROS) are important oxygen-containing molecules that regulate tumorigenesis and tumor progression. When ROS accumulates to cytotoxic levels, this can lead to anti-tumor effects. Multiple chemicals used as therapeutic strategies are based on this mechanism. They regulate intracellular ROS levels directly or indirectly, resulting in the inability of glioma cells to adapt to the damage induced by these substances. In the current review, we summarize the natural products, synthetic compounds and interdisciplinary techniques used for the treatment of glioma. Their possible molecular mechanisms are also presented. Some of them are also used as sensitizers: they modulate ROS levels to improve the outcomes of chemo- and radio-therapy. In addition, we summarize some new targets upstream or downstream of ROS to provide ideas for developing new anti-glioma therapies.
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Tran AP, Tralie CJ, Reyes J, Moosmüller C, Belkhatir Z, Kevrekidis IG, Levine AJ, Deasy JO, Tannenbaum AR. Long-term p21 and p53 dynamics regulate the frequency of mitosis events and cell cycle arrest following radiation damage. Cell Death Differ 2023; 30:660-672. [PMID: 36182991 PMCID: PMC9984379 DOI: 10.1038/s41418-022-01069-x] [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: 04/19/2022] [Revised: 09/12/2022] [Accepted: 09/14/2022] [Indexed: 11/07/2022] Open
Abstract
Radiation exposure of healthy cells can halt cell cycle temporarily or permanently. In this work, we analyze the time evolution of p21 and p53 from two single cell datasets of retinal pigment epithelial cells exposed to several levels of radiation, and in particular, the effect of radiation on cell cycle arrest. Employing various quantification methods from signal processing, we show how p21 levels, and to a lesser extent p53 levels, dictate whether the cells are arrested in their cell cycle and how frequently these mitosis events are likely to occur. We observed that single cells exposed to the same dose of DNA damage exhibit heterogeneity in cellular outcomes and that the frequency of cell division is a more accurate monitor of cell damage rather than just radiation level. Finally, we show how heterogeneity in DNA damage signaling is manifested early in the response to radiation exposure level and has potential to predict long-term fate.
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Affiliation(s)
- Anh Phong Tran
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christopher J Tralie
- Department of Mathematics and Computer Science, Ursinus College, Collegeville, PA, USA
| | - José Reyes
- Cancer Biology and Genetics Program and Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Caroline Moosmüller
- Department of Mathematics, University of California, San Diego, La Jolla, CA, USA
| | - Zehor Belkhatir
- School of Engineering and Sustainable Development, De Montfort University, Leicester, UK
| | - Ioannis G Kevrekidis
- Department of Chemical and Biological Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Arnold J Levine
- Simons Center for Systems Biology, Institute for Advanced Study, Princeton, NJ, USA
| | - Joseph O Deasy
- Department of Medical Physics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Allen R Tannenbaum
- Departments of Computer Science and Applied Mathematics & Statistics, Stony Brook University, Stony Brook, NY, USA.
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Lebrec V, Gavet O. Monitoring Chk1 kinase activity dynamics in live single cell imaging assays. Methods Cell Biol 2023; 182:221-236. [PMID: 38359979 DOI: 10.1016/bs.mcb.2022.12.018] [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] [Indexed: 02/16/2023]
Abstract
The ATR/Chk1 pathway is an important regulator of cell cycle progression, notably upon genotoxic stress where it can detect a large variety of DNA alterations and induce a transient cell cycle arrest that promotes DNA repair. In addition to its role in DNA damage response (DDR), Chk1 is also active during a non-perturbed S phase and contributes to prevent a premature entry into mitosis with an incompletely replicated genome, meaning the ATR/Chk1 pathway is an integral part of the cell cycle machinery that preserves genome integrity during cell growth. We recently developed a FRET-based Chk1 kinase activity reporter to directly monitor and quantify the kinetics of Chk1 activation in live single cell imaging assays with unprecedented sensitivity and time resolution. This tool allowed us to monitor Chk1 activity dynamics over time during a normal S phase and following genotoxic stress, and to elucidate the underlying mechanisms leading to its activation. Here, we review available fluorescent tools to study the interplay of cell cycle progression, DNA damage and DDR in individual live cells, and present the full protocol and image analysis pipeline to monitor Chk1 activity in two imaging assays.
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Affiliation(s)
- Vivianne Lebrec
- Division of Cancer Biology, The Institute of Cancer Research, London, United Kingdom
| | - Olivier Gavet
- Sorbonne Université, Faculté des Sciences et Ingénierie, UFR927, Paris, France; UMR9019 CNRS, Université Paris-Saclay, Villejuif, Cedex, France.
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37
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Jones I, Dent L, Higo T, Roumeliotis T, Arias Garcia M, Shree H, Choudhary J, Pedersen M, Bakal C. Characterization of proteome-size scaling by integrative omics reveals mechanisms of proliferation control in cancer. SCIENCE ADVANCES 2023; 9:eadd0636. [PMID: 36696495 PMCID: PMC9876555 DOI: 10.1126/sciadv.add0636] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Almost all living cells maintain size uniformity through successive divisions. Proteins that over and underscale with size can act as rheostats, which regulate cell cycle progression. Using a multiomic strategy, we leveraged the heterogeneity of melanoma cell lines to identify peptides, transcripts, and phosphorylation events that differentially scale with cell size. Subscaling proteins are enriched in regulators of the DNA damage response and cell cycle progression, whereas super-scaling proteins included regulators of the cytoskeleton, extracellular matrix, and inflammatory response. Mathematical modeling suggested that decoupling growth and proliferative signaling may facilitate cell cycle entry over senescence in large cells when mitogenic signaling is decreased. Regression analysis reveals that up-regulation of TP53 or CDKN1A/p21CIP1 is characteristic of proliferative cancer cells with senescent-like sizes/proteomes. This study provides one of the first demonstrations of size-scaling phenomena in cancer and how morphology influences the chemistry of the cell.
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Affiliation(s)
- Ian Jones
- Chester Beatty Laboratories, Institute of Cancer Research, London SW3 6JB, UK
| | - Lucas Dent
- Chester Beatty Laboratories, Institute of Cancer Research, London SW3 6JB, UK
| | - Tomoaki Higo
- Chester Beatty Laboratories, Institute of Cancer Research, London SW3 6JB, UK
| | | | - Maria Arias Garcia
- Chester Beatty Laboratories, Institute of Cancer Research, London SW3 6JB, UK
| | - Hansa Shree
- Chester Beatty Laboratories, Institute of Cancer Research, London SW3 6JB, UK
| | - Jyoti Choudhary
- Chester Beatty Laboratories, Institute of Cancer Research, London SW3 6JB, UK
| | - Malin Pedersen
- Chester Beatty Laboratories, Institute of Cancer Research, London SW3 6JB, UK
| | - Chris Bakal
- Chester Beatty Laboratories, Institute of Cancer Research, London SW3 6JB, UK
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38
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Johnson MS, Cook JG. Cell cycle exits and U-turns: Quiescence as multiple reversible forms of arrest. Fac Rev 2023; 12:5. [PMID: 36923701 PMCID: PMC10009890 DOI: 10.12703/r/12-5] [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: 03/10/2023] Open
Abstract
Cell proliferation control is essential during development and for maintaining adult tissues. Loss of that control promotes not only oncogenesis when cells proliferate inappropriately but also developmental abnormalities or degeneration when cells fail to proliferate when and where needed. To ensure that cells are produced at the right place and time, an intricate balance of pro-proliferative and anti-proliferative signals impacts the probability that cells undergo cell cycle exit to quiescence, or G0 phase. This brief review describes recent advances in our understanding of how and when quiescence is initiated and maintained in mammalian cells. We highlight the growing appreciation for quiescence as a collection of context-dependent distinct states.
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Affiliation(s)
- Martha Sharisha Johnson
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, NC, USA
| | - Jeanette Gowen Cook
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, NC, USA
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39
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Wang Z, Wang H, Guo C, Yu F, Zhang Y, Qiao L, Zhang H, Zhang C. Role of hsa_circ_0000280 in regulating vascular smooth muscle cell function and attenuating neointimal hyperplasia via ELAVL1. Cell Mol Life Sci 2023; 80:3. [PMID: 36477660 PMCID: PMC9729135 DOI: 10.1007/s00018-022-04602-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 09/25/2022] [Accepted: 10/07/2022] [Indexed: 12/12/2022]
Abstract
The pathological proliferation of cells in vascular smooth muscle underlies neointimal hyperplasia (NIH) development during atherosclerosis. Circular RNAs (circRNAs), which represent novel functional biomarkers and RNA-binding proteins, contribute to multiple cardiovascular diseases; however, their roles in regulating the vascular smooth muscle cell cycle remain unknown. Thus, we aimed to identify the roles of circRNAs in vascular smooth muscle during coronary heart disease (CHD). Through circRNA sequencing of CHD samples and human antigen R (ELAVL1) immunoprecipitation, we identified circRNAs that are associated with CHD and interact with ELAVL1. Our results suggested that the hsa_circ_0000280 associated with CHD inhibits cell proliferation and induces ELAVL1-dependent cell cycle arrest. Gain/loss-of-function experiments and assays in vivo indicated that hsa_circ_0000280 facilitates interactions between ELAVL1 and cyclin-dependent kinase suppressor 1 (CDKN1A) mRNA and stabilization of this complex and leads to cell cycle arrest at the G1/S checkpoint, inhibiting cell proliferation of vascular smooth muscle cells in vitro and NIH in vivo. Importantly, hsa_circ_0000280 reduced neointimal thickness and smooth muscle cell proliferation in vivo. Taken together, these findings reveal a novel pathway in which hsa_circ_0000280 facilitates the regulation of ELAVL1 on CDKN1A mRNA to inhibit NIH. Therefore, measuring and modulating their expression might represent a potential diagnostic or therapeutic strategy for CHD.
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Affiliation(s)
- Zunzhe Wang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhuaxi Road, Jinan City, 250012, Shandong, China
- Department of Geriatric Cardiology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China
| | - Huating Wang
- Department of Cardiology, Jinan Central Hospital Affiliated to Shandong First Medical University, Jinan, 250013, Shandong, China
| | - Chenghu Guo
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhuaxi Road, Jinan City, 250012, Shandong, China
| | - Fangpu Yu
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhuaxi Road, Jinan City, 250012, Shandong, China
| | - Ya Zhang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhuaxi Road, Jinan City, 250012, Shandong, China
| | - Lei Qiao
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhuaxi Road, Jinan City, 250012, Shandong, China
| | - Haijun Zhang
- Institute of Vascular Intervention, Medical College of Tongji University, Shanghai, 200072, China
| | - Cheng Zhang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhuaxi Road, Jinan City, 250012, Shandong, China.
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40
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Fischer M, Schade AE, Branigan TB, Müller GA, DeCaprio JA. Coordinating gene expression during the cell cycle. Trends Biochem Sci 2022; 47:1009-1022. [PMID: 35835684 DOI: 10.1016/j.tibs.2022.06.007] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 06/08/2022] [Accepted: 06/14/2022] [Indexed: 02/08/2023]
Abstract
Cell cycle-dependent gene transcription is tightly controlled by the retinoblastoma (RB):E2F and DREAM complexes, which repress all cell cycle genes during quiescence. Cyclin-dependent kinase (CDK) phosphorylation of RB and DREAM allows for the expression of two gene sets. The first set of genes, with peak expression in G1/S, is activated by E2F transcription factors (TFs) and is required for DNA synthesis. The second set, with maximum expression during G2/M, is required for mitosis and is coordinated by the MuvB complex, together with B-MYB and Forkhead box M1 (FOXM1). In this review, we summarize the key findings that established the distinct control mechanisms regulating G1/S and G2/M gene expression in mammals and discuss recent advances in the understanding of the temporal control of these genes.
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Affiliation(s)
- Martin Fischer
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745, Jena, Germany.
| | - Amy E Schade
- Genetics Division, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Timothy B Branigan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Gerd A Müller
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
| | - James A DeCaprio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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41
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Ginsenoside Rh2 sensitizes the anti-cancer effects of sunitinib by inducing cell cycle arrest in renal cell carcinoma. Sci Rep 2022; 12:19752. [PMID: 36396667 PMCID: PMC9672391 DOI: 10.1038/s41598-022-20075-0] [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: 03/23/2022] [Accepted: 09/08/2022] [Indexed: 11/18/2022] Open
Abstract
Sunitinib, a VEGF blockade, is used to treat clear cell renal cell carcinoma (ccRCC). However, the anti-cancer treatment effects of sunitinib do not last long in ccRCC patients. Ginsenoside, a natural medicine extracted from ginseng, has been studied in cancer treatment and shown to have anti-tumor effects and low toxicity. We assessed cell viability and cell cycle analysis in ccRCC cell lines after treatment with ginsenoside and sunitinib. DNA damage was evaluated by measuring 8-OHdG levels and comet assay. ROS levels, reflecting the cause of oxidative stress, were also measured. Ginsenoside significantly enhanced the inhibition of cell viability by sunitinib, a result that was also confirmed in the xenograft model. In cell cycle analysis, combination treatment of ginsenoside and sunitinib enhanced G2M arrest in comparison with single-treatment groups. In addition, DNA damage was increased by ginsenoside and sunitinib according to the comet assay, and the level of 8-OHdG, which reflects oxidative DNA damage, also increased. We verified that ginsenoside enhances the efficacy of sunitinib to inhibit the proliferation of ccRCC cells via induction of oxidative DNA damage. The combination therapy of sunitinib and ginsenoside suggested the possibility of effectively treating ccRCC patients.
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42
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Hughes FA, Barr AR, Thomas P. Patterns of interdivision time correlations reveal hidden cell cycle factors. eLife 2022; 11:e80927. [PMID: 36377847 PMCID: PMC9822260 DOI: 10.7554/elife.80927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 11/14/2022] [Indexed: 11/16/2022] Open
Abstract
The time taken for cells to complete a round of cell division is a stochastic process controlled, in part, by intracellular factors. These factors can be inherited across cellular generations which gives rise to, often non-intuitive, correlation patterns in cell cycle timing between cells of different family relationships on lineage trees. Here, we formulate a framework of hidden inherited factors affecting the cell cycle that unifies known cell cycle control models and reveals three distinct interdivision time correlation patterns: aperiodic, alternator, and oscillator. We use Bayesian inference with single-cell datasets of cell division in bacteria, mammalian and cancer cells, to identify the inheritance motifs that underlie these datasets. From our inference, we find that interdivision time correlation patterns do not identify a single cell cycle model but generally admit a broad posterior distribution of possible mechanisms. Despite this unidentifiability, we observe that the inferred patterns reveal interpretable inheritance dynamics and hidden rhythmicity of cell cycle factors. This reveals that cell cycle factors are commonly driven by circadian rhythms, but their period may differ in cancer. Our quantitative analysis thus reveals that correlation patterns are an emergent phenomenon that impact cell proliferation and these patterns may be altered in disease.
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Affiliation(s)
- Fern A Hughes
- Department of Mathematics, Imperial College LondonLondonUnited Kingdom
- MRC London Institute of Medical SciencesLondonUnited Kingdom
| | - Alexis R Barr
- MRC London Institute of Medical SciencesLondonUnited Kingdom
- Institute of Clinical Sciences, Imperial College LondonLondonUnited Kingdom
| | - Philipp Thomas
- Department of Mathematics, Imperial College LondonLondonUnited Kingdom
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Slade L, Biswas D, Kienesberger PC, Pulinilkunnil T. Loss of transcription factor EB dysregulates the G1/S transition and DNA replication in mammary epithelial cells. J Biol Chem 2022; 298:102692. [PMID: 36372230 PMCID: PMC9764199 DOI: 10.1016/j.jbc.2022.102692] [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: 03/14/2022] [Revised: 10/25/2022] [Accepted: 10/27/2022] [Indexed: 11/13/2022] Open
Abstract
Triple-negative breast cancer (TNBC) poses significant challenges for treatment given the lack of targeted therapies and increased probability of relapse. It is pertinent to identify vulnerabilities in TNBC and develop newer treatments. Our prior research demonstrated that transcription factor EB (TFEB) is necessary for TNBC survival by regulating DNA repair, apoptosis signaling, and the cell cycle. However, specific mechanisms by which TFEB targets DNA repair and cell cycle pathways are unclear, and whether these effects dictate TNBC survival is yet to be determined. Here, we show that TFEB knockdown decreased the expression of genes and proteins involved in DNA replication and cell cycle progression in MDA-MB-231 TNBC cells. DNA replication was decreased in cells lacking TFEB, as measured by EdU incorporation. TFEB silencing in MDA-MB-231 and noncancerous MCF10A cells impaired progression through the S-phase following G1/S synchronization; however, this proliferation defect could not be rescued by co-knockdown of suppressor RB1. Instead, TFEB knockdown reduced origin licensing in G1 and early S-phase MDA-MB-231 cells. TFEB silencing was associated with replication stress in MCF10A but not in TNBC cells. Lastly, we identified that TFEB knockdown renders TNBC cells more sensitive to inhibitors of Aurora Kinase A, a protein facilitating mitosis. Thus, inhibition of TFEB impairs cell cycle progress by decreasing origin licensing, leading to delayed entry into the S-phase, while rendering TNBC cells sensitive to Aurora kinase A inhibitors and decreasing cell viability. In contrast, TFEB silencing in noncancerous cells is associated with replication stress and leads to G1/S arrest.
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Wang B, Xu S, Sun Q, Li X, Wang T, Xu K, Yin L, Sun R, Pu Y, Zhang J. Let-7e-5p, a promising novel biomarker for benzene toxicity, is involved in benzene-induced hematopoietic toxicity through targeting caspase-3 and p21. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 246:114142. [PMID: 36193590 DOI: 10.1016/j.ecoenv.2022.114142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/12/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
Benzene is a common industrial chemical and environmental pollutant. However, the mechanism of hematotoxicity caused by exposure to low doses of benzene is unknown. Let-7e-5p pathway regulatory networks were constructed by bioinformatics analysis using a benzene-induced aplastic anemia (BIAA) mouse model. The MTT assay, EdU staining, flow cytometric analysis, dual luciferase reporter gene assay, and RIP assay were utilized to evaluate the effects of benzoquinone (1,4-BQ) on let-7e-5p pathway. This study consisted of 159 workers with a history of low-level benzene exposure and 159 workers with no history of benzene exposure. After the confounding factors were identified, the associations between let-7e-5p expression and hematotoxicity were assessed by multiple linear regression. Furthermore, we used four machine learning algorithms (decision trees, neural network, Bayesian network, and support vector machines) to construct a predictive model for detecting benzene-causing hematotoxicity in workers. In this study, compared with respective controls, let-7e-5p expression was decreased in BIAA mice and benzene-exposed workers. After 1,4-BQ exposure, let-7e-5p overexpression negatively regulated caspase-3 and p21 expression, protected cells from apoptosis, and facilitated cell proliferation. RIP assays, and dual luciferase reporter gene assays confirmed that let-7e-5p could target p21 and caspase-3 and regulate the cell cycle and apoptosis. The support vector machines classifier achieved the best prediction of benzene-induced hematotoxicity (prediction accuracy = 88.27, AUC = 0.83) by statistically characterizing the internal dose of benzene exposure and the oxidative stress index, as well as the expression levels of let-7e-5p pathway-related genes in benzene-exposed workers. Let-7e-5p may be a potential therapeutic target of benzene-induced hematotoxicity, provide a basis for evaluating the health hazards of long-term and low-dose benzene exposure in workers, and supply a reference for revising occupational health standards.
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Affiliation(s)
- Boshen Wang
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, Jiangsu, China; Jiangsu Provincial Center for Disease Prevention and Control, Nanjing 210000, Jiangsu, China
| | - Shouxiang Xu
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, Jiangsu, China
| | - Qianyu Sun
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, Jiangsu, China
| | - Xiaoqin Li
- Yangzhou Center for Disease Control and Prevention, China
| | - Tong Wang
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, Jiangsu, China
| | - Kai Xu
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, Jiangsu, China
| | - Lihong Yin
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, Jiangsu, China
| | - Rongli Sun
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, Jiangsu, China
| | - Yuepu Pu
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, Jiangsu, China
| | - Juan Zhang
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, Jiangsu, China.
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Zhou X, Zhou M, Zheng M, Tian S, Yang X, Ning Y, Li Y, Zhang S. Polyploid giant cancer cells and cancer progression. Front Cell Dev Biol 2022; 10:1017588. [PMID: 36274852 PMCID: PMC9581214 DOI: 10.3389/fcell.2022.1017588] [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: 08/12/2022] [Accepted: 09/21/2022] [Indexed: 12/02/2022] Open
Abstract
Polyploid giant cancer cells (PGCCs) are an important feature of cellular atypia, the detailed mechanisms of their formation and function remain unclear. PGCCs were previously thought to be derived from repeated mitosis/cytokinesis failure, with no intrinsic ability to proliferate and divide. However, recently, PGCCs have been confirmed to have cancer stem cell (CSC)-like characteristics, and generate progeny cells through asymmetric division, which express epithelial-mesenchymal transition-related markers to promote invasion and migration. The formation of PGCCs can be attributed to multiple stimulating factors, including hypoxia, chemotherapeutic reagents, and radiation, can induce the formation of PGCCs, by regulating the cell cycle and cell fusion-related protein expression. The properties of CSCs suggest that PGCCs can be induced to differentiate into non-tumor cells, and produce erythrocytes composed of embryonic hemoglobin, which have a high affinity for oxygen, and thereby allow PGCCs survival from the severe hypoxia. The number of PGCCs is associated with metastasis, chemoradiotherapy resistance, and recurrence of malignant tumors. Targeting relevant proteins or signaling pathways related with the formation and transdifferentiation of adipose tissue and cartilage in PGCCs may provide new strategies for solid tumor therapy.
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Affiliation(s)
- Xinyue Zhou
- Graduate School, Tianjin Medical University, Tianjin, China
| | - Mingming Zhou
- Graduate School, Tianjin Medical University, Tianjin, China
| | - Minying Zheng
- Department of Pathology, Tianjin Union Medical Center, Tianjin, China
| | - Shifeng Tian
- Graduate School, Tianjin Medical University, Tianjin, China
| | - Xiaohui Yang
- Nankai University School of Medicine, Nankai University, Tianjin, China
| | - Yidi Ning
- Nankai University School of Medicine, Nankai University, Tianjin, China
| | - Yuwei Li
- Department of Colorectal Surgery, Tianjin Union Medical Center, Tianjin, China
| | - Shiwu Zhang
- Department of Pathology, Tianjin Union Medical Center, Tianjin, China
- *Correspondence: Shiwu Zhang,
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Ilouz N, Harazi A, Guttman M, Daya A, Ruppo S, Yakovlev L, Mitrani-Rosenbaum S. In vivo and in vitro genome editing to explore GNE functions. Front Genome Ed 2022; 4:930110. [PMID: 36237634 PMCID: PMC9552322 DOI: 10.3389/fgeed.2022.930110] [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: 04/27/2022] [Accepted: 08/23/2022] [Indexed: 11/28/2022] Open
Abstract
GNE myopathy is an adult onset neuromuscular disorder characterized by slowly progressive distal and proximal muscle weakness, caused by missense recessive mutations in the GNE gene. Although the encoded bifunctional enzyme is well known as the limiting factor in the biosynthesis of sialic acid, no clear mechanisms have been recognized to account for the muscle atrophic pathology, and novel functions for GNE have been hypothesized. Two major issues impair studies on this protein. First, the expression of the GNE protein is minimal in human and mice muscles and there is no reliable antibody to follow up endogenous expression. Second, no reliable animal model is available for the disease and cellular models from GNE myopathy patients’ muscle cells (expressing the mutated protein) are less informative than expected. In order to broaden our knowledge on GNE functions in muscle, we have taken advantage of the CRISPR/Cas9 method for genome editing to first, add a tag to the endogenous Gne gene in mouse, allowing the determination of the spatiotemporal expression of the protein in the organism, using well established and reliable antibodies against the specific tag. In addition we have generated a Gne knock out murine muscle cell lineage to identify the events resulting from the total lack of the protein. A thorough multi-omics analysis of both cellular systems including transcriptomics, proteomics, phosphoproteomics and ubiquitination, unraveled novel pathways for Gne, in particular its involvement in cell cycle control and in the DNA damage/repair pathways. The elucidation of fundamental mechanisms of Gne in normal muscle may contribute to the identification of the disrupted functions in GNE myopathy, thus, to the definition of novel biomarkers and possible therapeutic targets for this disease.
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Affiliation(s)
- Nili Ilouz
- Goldyne Savad Institute of Gene Therapy, Hadassah Medical Center, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Avi Harazi
- Goldyne Savad Institute of Gene Therapy, Hadassah Medical Center, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Miriam Guttman
- Goldyne Savad Institute of Gene Therapy, Hadassah Medical Center, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Alon Daya
- Faculty of Marine Sciences, Ruppin Academic Center, Michmoret, Israel
| | - Shmuel Ruppo
- Bioinformatics Unit of the I-CORE at the Hebrew University and Hadassah Medical Center, Jerusalem, Israel
| | - Lena Yakovlev
- Goldyne Savad Institute of Gene Therapy, Hadassah Medical Center, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Stella Mitrani-Rosenbaum
- Goldyne Savad Institute of Gene Therapy, Hadassah Medical Center, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
- *Correspondence: Stella Mitrani-Rosenbaum,
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Hybrids of 1,4-Quinone with Quinoline Derivatives: Synthesis, Biological Activity, and Molecular Docking with DT-Diaphorase (NQO1). Molecules 2022; 27:molecules27196206. [PMID: 36234741 PMCID: PMC9572083 DOI: 10.3390/molecules27196206] [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: 08/09/2022] [Revised: 09/14/2022] [Accepted: 09/17/2022] [Indexed: 11/16/2022] Open
Abstract
Hybrids 1,4-quinone with quinoline were obtained by connecting two active structures through an oxygen atom. This strategy allows to obtain new compounds with a high biological activity and suitable bioavailability. Newly synthesized compounds were characterized by various spectroscopic methods. The enzymatic assay used showed that these compounds were a suitable DT-diaphorase (NQO1) substrates as evidenced by increasing enzymatic conversion rates relative to that of streptonigrin. Hybrids were tested in vitro against a panel of human cell lines including melanoma, breast, and lung cancers. They showed also a high cytotoxic activity depending on the type of 1,4-quinone moiety and the applied tumor cell lines. It was found that cytotoxic activity of the studied hybrids was increasing against the cell lines with higher NQO1 protein level, such as breast (MCF-7 and T47D) and lung (A549) cancers. Selected hybrids were tested for the transcriptional activity of the gene encoding a proliferation marker (H3 histone), cell cycle regulators (p53 and p21) and the apoptosis pathway (BCL-2 and BAX). The molecular docking was used to examine the probable interaction between the hybrids and NQO1 protein.
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Hattori EY, Masuda T, Mineharu Y, Mikami M, Terada Y, Matsui Y, Kubota H, Matsuo H, Hirata M, Kataoka TR, Nakahata T, Ikeda S, Miyamoto S, Sugiyama H, Arakawa Y, Kamikubo Y. A RUNX-targeted gene switch-off approach modulates the BIRC5/PIF1-p21 pathway and reduces glioblastoma growth in mice. Commun Biol 2022; 5:939. [PMID: 36085167 PMCID: PMC9463152 DOI: 10.1038/s42003-022-03917-5] [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: 06/05/2021] [Accepted: 08/30/2022] [Indexed: 11/14/2022] Open
Abstract
Glioblastoma is the most common adult brain tumour, representing a high degree of malignancy. Transcription factors such as RUNX1 are believed to be involved in the malignancy of glioblastoma. RUNX1 functions as an oncogene or tumour suppressor gene with diverse target genes. Details of the effects of RUNX1 on the acquisition of malignancy in glioblastoma remain unclear. Here, we show that RUNX1 downregulates p21 by enhancing expressions of BIRC5 and PIF1, conferring anti-apoptotic properties on glioblastoma. A gene switch-off therapy using alkylating agent-conjugated pyrrole-imidazole polyamides, designed to fit the RUNX1 DNA groove, decreased expression levels of BIRC5 and PIF1 and induced apoptosis and cell cycle arrest via p21. The RUNX1-BIRC5/PIF1-p21 pathway appears to reflect refractory characteristics of glioblastoma and thus holds promise as a therapeutic target. RUNX gene switch-off therapy may represent a novel treatment for glioblastoma. Interfering with RUNX family proteins reduces glioblastoma growth in mice and reveals pathways involved in the maintenance of tumour growth.
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Stallaert W, Taylor SR, Kedziora KM, Taylor CD, Sobon HK, Young CL, Limas JC, Varblow Holloway J, Johnson MS, Cook JG, Purvis JE. The molecular architecture of cell cycle arrest. Mol Syst Biol 2022; 18:e11087. [PMID: 36161508 PMCID: PMC9511499 DOI: 10.15252/msb.202211087] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 09/07/2022] [Accepted: 09/09/2022] [Indexed: 11/09/2022] Open
Abstract
The cellular decision governing the transition between proliferative and arrested states is crucial to the development and function of every tissue. While the molecular mechanisms that regulate the proliferative cell cycle are well established, we know comparatively little about what happens to cells as they diverge into cell cycle arrest. We performed hyperplexed imaging of 47 cell cycle effectors to obtain a map of the molecular architecture that governs cell cycle exit and progression into reversible (“quiescent”) and irreversible (“senescent”) arrest states. Using this map, we found multiple points of divergence from the proliferative cell cycle; identified stress‐specific states of arrest; and resolved the molecular mechanisms governing these fate decisions, which we validated by single‐cell, time‐lapse imaging. Notably, we found that cells can exit into senescence from either G1 or G2; however, both subpopulations converge onto a single senescent state with a G1‐like molecular signature. Cells can escape from this “irreversible” arrest state through the upregulation of G1 cyclins. This map provides a more comprehensive understanding of the overall organization of cell proliferation and arrest.
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Affiliation(s)
- Wayne Stallaert
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sovanny R Taylor
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Katarzyna M Kedziora
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Bioinformatics and Analytics Research Collaborative (BARC), University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Colin D Taylor
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Holly K Sobon
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Catherine L Young
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Juanita C Limas
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jonah Varblow Holloway
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Martha S Johnson
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jeanette Gowen Cook
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jeremy E Purvis
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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50
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Gui Y, Xie S, Wang Y, Wang P, Yao R, Gao X, Dong Y, Wang G, Chan K. pcnaDeep: A Fast and Robust Single-Cell Tracking Method Using Deep-Learning Mediated Cell Cycle Profiling. Bioinformatics 2022; 38:4846-4847. [PMID: 36047834 DOI: 10.1093/bioinformatics/btac602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 07/16/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
Computational methods that track single-cells and quantify fluorescent biosensors in time-lapse microscopy images have revolutionised our approach in studying the molecular control of cellular decisions. One barrier that limits the adoption of single-cell analysis in biomedical research is the lack of efficient methods to robustly track single-cells over cell division events. Here, we developed an application that automatically tracks and assigns mother-daughter relationships of single-cells. By incorporating cell cycle information from a well-established fluorescent cell cycle reporter, we associate mitosis relationships enabling high fidelity long-term single-cell tracking. This was achieved by integrating a deep-learning based fluorescent PCNA signal instance segmentation module with a cell tracking and cell cycle resolving pipeline. The application offers a user-friendly interface and extensible APIs for customized cell cycle analysis and manual correction for various imaging configurations. AVAILABILITY pcnaDeep is an open-source Python application under the Apache 2.0 licence. The source code, documentation and tutorials are available at https://github.com/chan-labsite/PCNAdeep. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yifan Gui
- Department of Breast Surgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310029, P. R. China.,Zhejiang University-University of Edinburgh Institute (ZJE), Zhejiang University School of Medicine, Zhejiang University, Haining, 314400, P. R. China
| | - Shuangshuang Xie
- Department of Breast Surgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310029, P. R. China.,Zhejiang University-University of Edinburgh Institute (ZJE), Zhejiang University School of Medicine, Zhejiang University, Haining, 314400, P. R. China
| | - Yanan Wang
- Zhejiang University-University of Edinburgh Institute (ZJE), Zhejiang University School of Medicine, Zhejiang University, Haining, 314400, P. R. China
| | - Ping Wang
- Department of Breast Surgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310029, P. R. China.,Zhejiang University-University of Edinburgh Institute (ZJE), Zhejiang University School of Medicine, Zhejiang University, Haining, 314400, P. R. China
| | - Renzhi Yao
- Department of Breast Surgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310029, P. R. China.,Zhejiang University-University of Edinburgh Institute (ZJE), Zhejiang University School of Medicine, Zhejiang University, Haining, 314400, P. R. China
| | - Xukai Gao
- Zhejiang University-University of Edinburgh Institute (ZJE), Zhejiang University School of Medicine, Zhejiang University, Haining, 314400, P. R. China
| | - Yutian Dong
- Zhejiang University-University of Edinburgh Institute (ZJE), Zhejiang University School of Medicine, Zhejiang University, Haining, 314400, P. R. China
| | - Gaoang Wang
- Zhejiang University-University of Illinois at Urbana-Champaign Institute (ZJUI), Zhejiang University, Haining, 314400, P. R. China
| | - KuanYoow Chan
- Department of Breast Surgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310029, P. R. China.,Zhejiang University-University of Edinburgh Institute (ZJE), Zhejiang University School of Medicine, Zhejiang University, Haining, 314400, P. R. China
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