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Bayat M, Nahand JS. Let's make it personal: CRISPR tools in manipulating cell death pathways for cancer treatment. Cell Biol Toxicol 2024; 40:61. [PMID: 39075259 PMCID: PMC11286699 DOI: 10.1007/s10565-024-09907-z] [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: 04/27/2024] [Accepted: 07/18/2024] [Indexed: 07/31/2024]
Abstract
Advancements in the CRISPR technology, a game-changer in experimental research, have revolutionized various fields of life sciences and more profoundly, cancer research. Cell death pathways are among the most deregulated in cancer cells and are considered as critical aspects in cancer development. Through decades, our knowledge of the mechanisms orchestrating programmed cellular death has increased substantially, attributed to the revolution of cutting-edge technologies. The heroic appearance of CRISPR systems have expanded the available screening platform and genome engineering toolbox to detect mutations and create precise genome edits. In that context, the precise ability of this system for identification and targeting of mutations in cell death signaling pathways that result in cancer development and therapy resistance is an auspicious choice to transform and accelerate the individualized cancer therapy. The concept of personalized cancer therapy stands on the identification of molecular characterization of the individual tumor and its microenvironment in order to provide a precise treatment with the highest possible outcome and minimum toxicity. This study explored the potential of CRISPR technology in precision cancer treatment by identifying and targeting specific cell death pathways. It showed the promise of CRISPR in finding key components and mutations involved in programmed cell death, making it a potential tool for targeted cancer therapy. However, this study also highlighted the challenges and limitations that need to be addressed in future research to fully realize the potential of CRISPR in cancer treatment.
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Affiliation(s)
- Mobina Bayat
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, 15731, Iran
| | - Javid Sadri Nahand
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, 15731, Iran.
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Villagra UMM, da Cunha BR, Polachini GM, Henrique T, Stefanini ACB, de Castro TB, da Silva CHTP, Feitosa OA, Fukuyama EE, López RVM, Dias-Neto E, Nunes FD, Severino P, Tajara EH. Expression of Truncated Products at the 5'-Terminal Region of RIPK2 and Evolutive Aspects that Support Their Biological Importance. Genome Biol Evol 2024; 16:evae106. [PMID: 38752399 PMCID: PMC11221433 DOI: 10.1093/gbe/evae106] [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] [Accepted: 05/10/2024] [Indexed: 07/04/2024] Open
Abstract
Alternative splicing is the process of generating different mRNAs from the same primary transcript, which contributes to increase the transcriptome and proteome diversity. Abnormal splicing has been associated with the development of several diseases including cancer. Given that mutations and abnormal levels of the RIPK2 transcript and RIP-2 protein are frequent in tumors, and that RIP-2 modulates immune and inflammatory responses, we investigated alternative splicing events that result in partial deletions of the kinase domain at the N-terminus of RIP-2. We also investigated the structure and expression of the RIPK2 truncated variants and isoforms in different environments. In addition, we searched data throughout Supraprimates evolution that could support the biological importance of RIPK2 alternatively spliced products. We observed that human variants and isoforms were differentially regulated following temperature stress, and that the truncated transcript was more expressed than the long transcript in tumor samples. The inverse was found for the longer protein isoform. The truncated variant was also detected in chimpanzee, gorilla, hare, pika, mouse, rat, and tree shrew. The fact that the same variant has been preserved in mammals with divergence times up to 70 million years raises the hypothesis that it may have a functional significance.
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Affiliation(s)
- Ulises M M Villagra
- Faculty of Exact Sciences, Biotechnology and Molecular Biology Institute (IBBM), National University of La Plata-CCT, CONICET, La Plata, Argentina
| | - Bianca R da Cunha
- Department of Molecular Biology, School of Medicine of São José do Rio Preto/FAMERP, São José do Rio Preto, SP, Brazil
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo/USP, São Paulo, SP, Brazil
| | - Giovana M Polachini
- Department of Molecular Biology, School of Medicine of São José do Rio Preto/FAMERP, São José do Rio Preto, SP, Brazil
| | - Tiago Henrique
- Department of Molecular Biology, School of Medicine of São José do Rio Preto/FAMERP, São José do Rio Preto, SP, Brazil
| | - Ana Carolina Buzzo Stefanini
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo/USP, São Paulo, SP, Brazil
| | - Tialfi Bergamin de Castro
- Department of Molecular Biology, School of Medicine of São José do Rio Preto/FAMERP, São José do Rio Preto, SP, Brazil
- Microbial Pathogenesis Department, University of Maryland Baltimore, School of Dentistry, Baltimore, MD, USA
| | - Carlos H T P da Silva
- Computational Laboratory of Pharmaceutical Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo/USP, Ribeirão Preto, SP, Brazil
| | - Olavo A Feitosa
- Computational Laboratory of Pharmaceutical Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo/USP, Ribeirão Preto, SP, Brazil
| | - Erica E Fukuyama
- Head and Neck Surgery Department, Arnaldo Vieira de Carvalho Cancer Institute, São Paulo, SP, Brazil
| | - Rossana V M López
- Comprehensive Center for Precision Oncology, Center for Translational Research in Oncology, State of São Paulo Cancer Institute—ICESP, Clinics Hospital, Sao Paulo University Medical School, São Paulo, SP, Brazil
| | - Emmanuel Dias-Neto
- Laboratory of Medical Genomics, A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | - Fabio D Nunes
- Department of Stomatology, School of Dentistry, University of São Paulo/USP, São Paulo, SP, Brazil
| | - Patricia Severino
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo/USP, São Paulo, SP, Brazil
- Albert Einstein Research and Education Institute, Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Eloiza H Tajara
- Department of Molecular Biology, School of Medicine of São José do Rio Preto/FAMERP, São José do Rio Preto, SP, Brazil
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo/USP, São Paulo, SP, Brazil
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3
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Bhat KP, Vijay J, Vilas CK, Asundi J, Zou J, Lau T, Cai X, Ahmed M, Kabza M, Weng J, Fortin JP, Lun A, Durinck S, Hafner M, Costa MR, Ye X. CRISPR activation screens identify the SWI/SNF ATPases as suppressors of ferroptosis. Cell Rep 2024; 43:114345. [PMID: 38870012 DOI: 10.1016/j.celrep.2024.114345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 04/22/2024] [Accepted: 05/24/2024] [Indexed: 06/15/2024] Open
Abstract
Ferroptosis is an iron-dependent cell death mechanism characterized by the accumulation of toxic lipid peroxides and cell membrane rupture. GPX4 (glutathione peroxidase 4) prevents ferroptosis by reducing these lipid peroxides into lipid alcohols. Ferroptosis induction by GPX4 inhibition has emerged as a vulnerability of cancer cells, highlighting the need to identify ferroptosis regulators that may be exploited therapeutically. Through genome-wide CRISPR activation screens, we identify the SWI/SNF (switch/sucrose non-fermentable) ATPases BRM (SMARCA2) and BRG1 (SMARCA4) as ferroptosis suppressors. Mechanistically, they bind to and increase chromatin accessibility at NRF2 target loci, thus boosting NRF2 transcriptional output to counter lipid peroxidation and confer resistance to GPX4 inhibition. We further demonstrate that the BRM/BRG1 ferroptosis connection can be leveraged to enhance the paralog dependency of BRG1 mutant cancer cells on BRM. Our data reveal ferroptosis induction as a potential avenue for broadening the efficacy of BRM degraders/inhibitors and define a specific genetic context for exploiting GPX4 dependency.
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Affiliation(s)
- Kamakoti P Bhat
- Department of Discovery Oncology, Genentech, South San Francisco, CA 94080, USA
| | - Jinchu Vijay
- Roche Canada, Mississauga, Ontario L5N 5M8, Canada
| | - Caroline K Vilas
- Oncology Bioinformatics, Genentech, South San Francisco, CA 94080, USA
| | - Jyoti Asundi
- Department of Discovery Oncology, Genentech, South San Francisco, CA 94080, USA
| | - Jun Zou
- Department of Discovery Oncology, Genentech, South San Francisco, CA 94080, USA
| | - Ted Lau
- Department of Discovery Oncology, Genentech, South San Francisco, CA 94080, USA
| | - Xiaoyu Cai
- Regenerative Medicine, Genentech, South San Francisco, CA 94080, USA
| | | | - Michal Kabza
- 7N Sp. Z O. O. by order of Roche Polska, 02-670 Warsaw, Poland
| | - Julie Weng
- Department of Discovery Oncology, Genentech, South San Francisco, CA 94080, USA
| | - Jean-Philippe Fortin
- Data Science and Statistical Computing, Genentech, South San Francisco, CA 94080, USA
| | - Aaron Lun
- Data Science and Statistical Computing, Genentech, South San Francisco, CA 94080, USA
| | - Steffen Durinck
- Oncology Bioinformatics, Genentech, South San Francisco, CA 94080, USA
| | - Marc Hafner
- Department of Discovery Oncology, Genentech, South San Francisco, CA 94080, USA; Oncology Bioinformatics, Genentech, South San Francisco, CA 94080, USA
| | - Michael R Costa
- Department of Discovery Oncology, Genentech, South San Francisco, CA 94080, USA
| | - Xin Ye
- Department of Discovery Oncology, Genentech, South San Francisco, CA 94080, USA.
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Zhuravskaya A, Yap K, Hamid F, Makeyev EV. Alternative splicing coupled to nonsense-mediated decay coordinates downregulation of non-neuronal genes in developing mouse neurons. Genome Biol 2024; 25:162. [PMID: 38902825 PMCID: PMC11188260 DOI: 10.1186/s13059-024-03305-8] [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: 07/08/2023] [Accepted: 06/07/2024] [Indexed: 06/22/2024] Open
Abstract
BACKGROUND The functional coupling between alternative pre-mRNA splicing (AS) and the mRNA quality control mechanism called nonsense-mediated decay (NMD) can modulate transcript abundance. Previous studies have identified several examples of such a regulation in developing neurons. However, the systems-level effects of AS-NMD in this context are poorly understood. RESULTS We developed an R package, factR2, which offers a comprehensive suite of AS-NMD analysis functions. Using this tool, we conducted a longitudinal analysis of gene expression in pluripotent stem cells undergoing induced neuronal differentiation. Our analysis uncovers hundreds of AS-NMD events with significant potential to regulate gene expression. Notably, this regulation is significantly overrepresented in specific functional groups of developmentally downregulated genes. Particularly strong association with gene downregulation is detected for alternative cassette exons stimulating NMD upon their inclusion into mature mRNA. By combining bioinformatic analyses with CRISPR/Cas9 genome editing and other experimental approaches we show that NMD-stimulating cassette exons regulated by the RNA-binding protein PTBP1 dampen the expression of their genes in developing neurons. We also provided evidence that the inclusion of NMD-stimulating cassette exons into mature mRNAs is temporally coordinated with NMD-independent gene repression mechanisms. CONCLUSIONS Our study provides an accessible workflow for the discovery and prioritization of AS-NMD targets. It further argues that the AS-NMD pathway plays a widespread role in developing neurons by facilitating the downregulation of functionally related non-neuronal genes.
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Affiliation(s)
- Anna Zhuravskaya
- Centre for Developmental Neurobiology, King's College London, London, SE1 1UL, UK
| | - Karen Yap
- Centre for Developmental Neurobiology, King's College London, London, SE1 1UL, UK
| | - Fursham Hamid
- Centre for Developmental Neurobiology, King's College London, London, SE1 1UL, UK.
| | - Eugene V Makeyev
- Centre for Developmental Neurobiology, King's College London, London, SE1 1UL, UK.
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Ward GA, Zhang Z, Jueliger S, Potapov IS, Davis MP, Boxall AR, Taylor J, Keer H, Biondo A, Lyons JF, Sims M, Smyth T. Epigenetic Priming by Hypomethylation Enhances the Immunogenic Potential of Tolinapant in T-cell Lymphoma. CANCER RESEARCH COMMUNICATIONS 2024; 4:1441-1453. [PMID: 38727208 PMCID: PMC11155518 DOI: 10.1158/2767-9764.crc-23-0415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 03/02/2024] [Accepted: 05/08/2024] [Indexed: 06/07/2024]
Abstract
Programmed cell death mechanisms are important for the regulation of tumor development and progression. Evasion of and resistance to apoptosis are significant factors in tumorigenesis and drug resistance. Bypassing apoptotic pathways and eliciting another form of regulated cell death, namely necroptosis, an immunogenic cell death (ICD), may override apoptotic resistance. Here, we present the mechanistic rationale for combining tolinapant, an antagonist of the inhibitor of apoptosis proteins (IAP), with decitabine, a hypomethylating agent (HMA), in T-cell lymphoma (TCL). Tolinapant treatment alone of TCL cells in vitro and in syngeneic in vivo models demonstrated that ICD markers can be upregulated, and we have shown that epigenetic priming with decitabine further enhances this effect. The clinical relevance of ICD markers was confirmed by the direct measurement of plasma proteins from patients with peripheral TCL treated with tolinapant. We showed increased levels of necroptosis in TCL lines, along with the expression of cancer-specific antigens (such as cancer testis antigens) and increases in genes involved in IFN signaling induced by HMA treatment, together deliver a strong adaptive immune response to the tumor. These results highlight the potential of a decitabine and tolinapant combination for TCL and could lead to clinical evaluation. SIGNIFICANCE The IAP antagonist tolinapant can induce necroptosis, a key immune-activating event, in TCL. Combination with DNA hypomethylation enhances tolinapant sensitivity and primes resistant cells by re-expressing necrosome proteins. In addition, this combination leads to increases in genes involved in IFN signaling and neoantigen expression, providing further molecular rationale for this novel therapeutic option.
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Affiliation(s)
| | | | | | | | | | | | - Jason Taylor
- Astex Pharmaceuticals, Inc., Pleasanton, California
| | - Harold Keer
- Astex Pharmaceuticals, Inc., Pleasanton, California
| | | | | | - Martin Sims
- Astex Pharmaceuticals, Cambridge, United Kingdom
| | - Tomoko Smyth
- Astex Pharmaceuticals, Cambridge, United Kingdom
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Adamiec-Organisciok M, Wegrzyn M, Cienciala L, Magate N, Skonieczna M, Nackiewicz J. Resistance to death pathway induction as a potential targeted therapy in CRISPR/Cas-9 knock-out colorectal cancer cell lines. PRZEGLAD GASTROENTEROLOGICZNY 2024; 19:112-120. [PMID: 38939059 PMCID: PMC11200076 DOI: 10.5114/pg.2024.134872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 12/05/2023] [Indexed: 06/29/2024]
Abstract
Regulated cell death is a fundamental biological process that plays a crucial role in maintaining tissue homeostasis and eliminating damaged or unnecessary cells. Ferroptosis is an iron-dependent process, characterized by the accumulation of oxidized and damaged lipids, which leads to programmed cell death. Among the ferroptotic pathway genes regulating this process, GPX4, TFRC, ACSL4, FSP1, SLC7A11, and PROM2 could be considered. There are many well-known ferroptotic pathway regulators, which are discussed in this compact review. Cells with tissues of different origin display sensitive or resistant phenotypes to such regulators. In some cases, unexpected changes during cell treatment occurred, suggesting the possibility of regulating the death pathway. We assumed that possible changing of ferro-sensitivity to ferro-resistance in cells, especially in colorectal cancer cell lines, is responded for induced chemoresistance. Using novel techniques, such as CRISPR/Cas-9 genome editing, an induced phenotype "switching" is possible.
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Affiliation(s)
- Malgorzata Adamiec-Organisciok
- Department of Systems Engineering and Biology, Silesian University of Technology, Faculty of Automatic Control, Electronics and Computer Science, Gliwice, Poland
| | - Magdalena Wegrzyn
- Department of Systems Engineering and Biology, Silesian University of Technology, Faculty of Automatic Control, Electronics and Computer Science, Gliwice, Poland
| | - Lukasz Cienciala
- Department of Systems Engineering and Biology, Silesian University of Technology, Faculty of Automatic Control, Electronics and Computer Science, Gliwice, Poland
| | - Ngoni Magate
- Department of Systems Engineering and Biology, Silesian University of Technology, Faculty of Automatic Control, Electronics and Computer Science, Gliwice, Poland
| | - Magdalena Skonieczna
- Department of Systems Engineering and Biology, Silesian University of Technology, Faculty of Automatic Control, Electronics and Computer Science, Gliwice, Poland
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7
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Pilarte KA, Reichert EC, Green YS, Halberg LMT, McFarland SA, Mimche PN, Golkowski M, Kamdem SD, Maguire KM, Summers SA, Maschek JA, Reelitz JW, Cox JE, Evason KJ, Koh MY. HAF Prevents Hepatocyte Apoptosis and Hepatocellular Carcinoma through Transcriptional Regulation of the NF-κB pathway. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574894. [PMID: 38260413 PMCID: PMC10802431 DOI: 10.1101/2024.01.09.574894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Background Hepatocellular carcinoma (HCC) incidence is increasing worldwide due to the obesity epidemic, which drives metabolic dysfunction-associated steatohepatitis (MASH) that can lead to HCC. However, the molecular pathways that lead to MASH-HCC are poorly understood. We have previously reported that male mice with global haploinsufficiency of hypoxia-associated factor, HAF ( SART1 +/ - ) spontaneously develop MASH/HCC. However, the cell type(s) responsible for HCC associated with HAF loss are unclear. Results SART1 -floxed mice were crossed with mice expressing Cre-recombinase within hepatocytes (Alb-Cre; hepS -/- ) or macrophages (LysM-Cre, macS -/- ). Only hepS -/- mice (both male and female) developed HCC suggesting that HAF protects against HCC primarily within hepatocytes. HAF-deficient macrophages showed decreased P-p65 and P-p50 and in many major components of the NF-κB pathway, which was recapitulated using HAF siRNA in vitro . HAF depletion increased apoptosis both in vitro and in vivo , suggesting that HAF mediates a tumor suppressor role by suppressing hepatocyte apoptosis. We show that HAF regulates NF-κB activity by controlling transcription of TRADD and RIPK1 . Mice fed a high-fat diet (HFD) showed marked suppression of HAF, P-p65 and TRADD within their livers after 26 weeks, but manifest profound upregulation of HAF, P-65 and TRADD within their livers after 40 weeks of HFD, implicating deregulation of the HAF-NF-κB axis in the progression to MASH. In humans, HAF was significantly decreased in livers with simple steatosis but significantly increased in HCC compared to normal liver. Conclusions HAF is novel transcriptional regulator of the NF-κB pathway that protects against hepatocyte apoptosis and is a key determinant of cell fate during progression to MASH and MASH-HCC.
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Liu HL, Lu XM, Wang HY, Hu KB, Wu QY, Liao P, Li S, Long ZY, Wang YT. The role of RNA splicing factor PTBP1 in neuronal development. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119506. [PMID: 37263298 DOI: 10.1016/j.bbamcr.2023.119506] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 05/23/2023] [Accepted: 05/26/2023] [Indexed: 06/03/2023]
Abstract
Alternative pre-mRNA splicing, which produces various mRNA isoforms with distinct structures and functions from a single gene, is regulated by specific RNA-binding proteins and is an essential method for regulating gene expression in mammals. Recent studies have shown that abnormal change during neuronal development triggered by splicing mis-regulation is an important feature of various neurological diseases. Polypyrimidine tract binding protein 1 (PTBP1) is a kind of RNA-binding proteins with extensive biological functions. As a well-known splicing regulator, it affects the neuronal development process through its involvement in axon formation, synaptogenesis, and neuronal apoptosis, according to the most recent studies. Here, we summarized the mechanism of alternative splicing, structure and function of PTBP1, and the latest research progress on the role of alternative splicing events regulated by PTBP1 in axon formation, synaptogenesis and neuronal apoptosis, to reveal the mechanism of PTBP1-regulated changes in neuronal development process.
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Affiliation(s)
- Hui-Lin Liu
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, PR China; State Key Laboratory of Trauma, Burns and Combined Injury, Daping Hospital, Army Medical University, Chongqing 400042, PR China
| | - Xiu-Min Lu
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, PR China
| | - Hai-Yan Wang
- State Key Laboratory of Trauma, Burns and Combined Injury, Daping Hospital, Army Medical University, Chongqing 400042, PR China
| | - Kai-Bin Hu
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, PR China
| | - Qing-Yun Wu
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, PR China
| | - Ping Liao
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing 400054, PR China
| | - Sen Li
- State Key Laboratory of Trauma, Burns and Combined Injury, Daping Hospital, Army Medical University, Chongqing 400042, PR China
| | - Zai-Yun Long
- State Key Laboratory of Trauma, Burns and Combined Injury, Daping Hospital, Army Medical University, Chongqing 400042, PR China
| | - Yong-Tang Wang
- State Key Laboratory of Trauma, Burns and Combined Injury, Daping Hospital, Army Medical University, Chongqing 400042, PR China.
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Malireddi RS, Bynigeri RR, Mall R, Nadendla EK, Connelly JP, Pruett-Miller SM, Kanneganti TD. Whole-genome CRISPR screen identifies RAVER1 as a key regulator of RIPK1-mediated inflammatory cell death, PANoptosis. iScience 2023; 26:106938. [PMID: 37324531 PMCID: PMC10265528 DOI: 10.1016/j.isci.2023.106938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/24/2023] [Accepted: 05/18/2023] [Indexed: 06/17/2023] Open
Abstract
Transforming growth factor-β-activated kinase 1 (TAK1) is a central regulator of innate immunity, cell death, inflammation, and cellular homeostasis. Therefore, many pathogens carry TAK1 inhibitors (TAK1i). As a host strategy to counteract this, inhibition or deletion of TAK1 induces spontaneous inflammatory cell death, PANoptosis, through the RIPK1-PANoptosome complex, containing the NLRP3 inflammasome and caspase-8/FADD/RIPK3 as integral components; however, PANoptosis also promotes pathological inflammation. Therefore, understanding molecular mechanisms that regulate TAK1i-induced cell death is essential. Here, we report a genome-wide CRISPR screen in macrophages that identified TAK1i-induced cell death regulators, including polypyrimidine tract-binding (PTB) protein 1 (PTBP1), a known regulator of RIPK1, and a previously unknown regulator RAVER1. RAVER1 blocked alternative splicing of Ripk1, and its genetic depletion inhibited TAK1i-induced, RIPK1-mediated inflammasome activation and PANoptosis. Overall, our CRISPR screen identified several positive regulators of PANoptosis. Moreover, our study highlights the utility of genome-wide CRISPR-Cas9 screens in myeloid cells for comprehensive characterization of complex cell death pathways to discover therapeutic targets.
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Affiliation(s)
| | - Ratnakar R. Bynigeri
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Raghvendra Mall
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Eswar Kumar Nadendla
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jon P. Connelly
- Center for Advanced Genome Engineering (CAGE), St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Shondra M. Pruett-Miller
- Center for Advanced Genome Engineering (CAGE), St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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Horne CR, Samson AL, Murphy JM. The web of death: the expanding complexity of necroptotic signaling. Trends Cell Biol 2023; 33:162-174. [PMID: 35750616 DOI: 10.1016/j.tcb.2022.05.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/28/2022] [Accepted: 05/30/2022] [Indexed: 01/25/2023]
Abstract
The past decade has seen the emergence of the necroptosis programmed cell death pathway as an important contributor to the pathophysiology of myriad diseases. The receptor interacting protein kinase (RIPK)1 and RIPK3, and the pseudokinase executioner protein, mixed lineage kinase domain-like (MLKL), have grown to prominence as the core pathway components. Depending on cellular context, these proteins also serve as integrators of signals, such as post-translational modifications and protein or metabolite interactions, adding layers of complexity to pathway regulation. Here, we describe the emerging picture of the web of proteins that tune necroptotic signal transduction and how these events have diverged across species, presumably owing to selective pressures of pathogens upon the RIPK3-MLKL protein pair.
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Affiliation(s)
- Christopher R Horne
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - André L Samson
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia.
| | - James M Murphy
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia.
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11
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Splice factor polypyrimidine tract-binding protein 1 (Ptbp1) primes endothelial inflammation in atherogenic disturbed flow conditions. Proc Natl Acad Sci U S A 2022; 119:e2122227119. [PMID: 35858420 PMCID: PMC9335344 DOI: 10.1073/pnas.2122227119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Plaque forms in low and disturbed flow regions of the vasculature, where platelets adhere and endothelial cells are “primed” to respond to cytokines (e.g., tumor necrosis factor-α) with elevated levels of cell adhesion molecules via the NF-κB signaling pathway. We show that the splice factor polypyrimidine tract binding protein (Ptbp1; purple) mediates priming. Ptbp1 is induced in endothelial cells by platelet recruitment, promoting priming and subsequent myeloid cell infiltration into plaque. Mechanistically, Ptbp1 regulates splicing of genes (e.g., Ripk1) involved in the NF-κB signaling pathway and is required for efficient nuclear translocation of NF-κB in endothelial cells. This provides new insight into the molecular mechanisms underlying an endothelial priming process that reinforces vascular inflammation. NF-κB–mediated endothelial activation drives leukocyte recruitment and atherosclerosis, in part through adhesion molecules Icam1 and Vcam1. The endothelium is primed for cytokine activation of NF-κB by exposure to low and disturbed blood flow (LDF)but the molecular underpinnings are not fully understood. In an experimental in vivo model of LDF, platelets were required for the increased expression of several RNA-binding splice factors, including polypyrimidine tract binding protein (Ptbp1). This was coordinated with changes in RNA splicing in the NF-κB pathway in primed cells, leading us to examine splice factors as mediators of priming. Using Icam1 and Vcam1 induction by tumor necrosis factor (TNF)-α stimulation as a readout, we performed a CRISPR Cas9 knockout screen and identified a requirement for Ptbp1 in priming. Deletion of Ptbp1 had no effect on cell growth or response to apoptotic stimuli, but reversed LDF splicing patterns and inhibited NF-κB nuclear translocation and transcriptional activation of downstream targets, including Icam1 and Vcam1. In human coronary arteries, elevated PTBP1 correlates with expression of TNF pathway genes and plaque. In vivo, endothelial-specific deletion of Ptbp1 reduced Icam1 expression and myeloid cell infiltration at regions of LDF in atherosclerotic mice, limiting atherosclerosis. This may be mediated, in part, by allowing inclusion of a conserved alternative exon in Ripk1 leading to a reduction in Ripk1 protein. Our data show that Ptbp1, which is induced in a subset of the endothelium by platelet recruitment at regions of LDF, is required for priming of the endothelium for subsequent NF-κB activation, myeloid cell recruitment and atherosclerosis.
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12
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Deficiency of PPP6C protects TNF-induced necroptosis through activation of TAK1. Cell Death Dis 2022; 13:618. [PMID: 35842423 PMCID: PMC9288536 DOI: 10.1038/s41419-022-05076-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 01/21/2023]
Abstract
Necroptotic cell death is mediated by a super-molecular complex called necrosome which consists of receptor-interacting protein kinase 1 and 3 (RIPK1, RIPK3) and mixed-lineage kinase domain-like protein (MLKL). The role of these kinases has been extensively investigated in the regulation of necroptosis. However, whether the protein phosphatase is involved in necroptosis is still largely unknown. Here, we identified protein phosphatase 6 catalytic subunit (PPP6C) promotes TNF-induced necroptosis by genome-wide CRISPR/Cas9 library screening. We found that PPP6C deficiency protects cells from TNF-induced necroptosis in a phosphatase-activity-dependent manner. Mechanistically, PPP6C acts as a TGF-β activated kinase 1 (TAK1) phosphatase to inactivate its kinase activity. Deletion of PPP6C leads to hyperactivation of TAK1 and reduced RIPK1 kinase activity upon TNF stimulation. We further showed that heterozygous deletion of Ppp6c in mouse gastrointestinal tract alleviates necroptosis-related tissue injury and inflammation. Thus, our study identifies PPP6C as an important regulator of necroptosis and highlights a central role of phosphatase in the regulation of necroptosis-related diseases.
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13
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Libner CD, Salapa HE, Hutchinson C, Stang TE, Thibault PA, Hammond SA, Levin MC. Autoimmunity to a ribonucleoprotein drives neuron loss in multiple sclerosis models. Neurobiol Dis 2022; 170:105775. [PMID: 35618205 DOI: 10.1016/j.nbd.2022.105775] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 11/15/2022] Open
Abstract
Neurodegeneration, the progressive loss or damage to neurons and axons, underlies permanent disability in multiple sclerosis (MS); yet its mechanisms are incompletely understood. Recent data indicates autoimmunity to several intraneuronal antigens, including the RNA binding protein (RBP) heterogenous nuclear ribonucleoprotein A1 (hnRNP A1), as contributors to neurodegeneration. We previously showed that addition of anti-hnRNP A1 antibodies, which target the same immunodominant domain of MS IgG, to mice with experimental autoimmune encephalomyelitis (EAE) worsened disease and resulted in an exacerbation of hnRNP A1 dysfunction including cytoplasmic mislocalization of hnRNP A1, stress granule (SG) formation and neurodegeneration in the chronic stages of disease. Because this previous study focused on a singular timepoint during EAE, it is unclear whether anti-hnRNP A1 antibody induced hnRNP A1 dysfunction caused neurodegeneration or was result of it. In the present study, we analyzed in vivo and in vitro models of anti-hnRNP A1 antibody-mediated autoimmunity for markers of hnRNP A1 dysfunction and neurodegeneration over a time course to gain a better understanding of the connection between hnRNP A1 dysfunction and neurodegeneration. Anti-hnRNP A1 antibody treatment resulted in increased neuronal hnRNP A1 mislocalization and nuclear depletion temporally followed by altered RNA expression and SG formation, and lastly an increase in necroptotic signalling and neuronal cell death. Treatment with necrostatin-1s inhibited necroptosis and partially rescued anti-hnRNP A1 antibody-mediated neurodegeneration while clathrin knockdown specifically inhibited anti-hnRNP A1 antibody uptake into neurons. This data identifies a novel antibody-mediated mechanism of neurodegeneration, which may be targeted to inhibit neurodegeneration and prevent permanent neurological decline in persons living with MS.
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Affiliation(s)
- Cole D Libner
- Department of Health Sciences, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada; Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK S7K 0M7, Canada; Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK S7K 0M7, Canada
| | - Hannah E Salapa
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK S7K 0M7, Canada; Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK S7K 0M7, Canada; Neurology Division, Department of Medicine, University of Saskatchewan, Saskatoon, SK S7N 0X8, Canada
| | - Catherine Hutchinson
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK S7K 0M7, Canada; Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK S7K 0M7, Canada; Neurology Division, Department of Medicine, University of Saskatchewan, Saskatoon, SK S7N 0X8, Canada
| | - Todd E Stang
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK S7K 0M7, Canada; Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK S7K 0M7, Canada; Department of Anatomy, Physiology and Pharmacology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Patricia A Thibault
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK S7K 0M7, Canada; Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK S7K 0M7, Canada; Neurology Division, Department of Medicine, University of Saskatchewan, Saskatoon, SK S7N 0X8, Canada
| | - S Austin Hammond
- Next-Generation Sequencing Facility, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Michael C Levin
- Office of the Saskatchewan Multiple Sclerosis Clinical Research Chair, University of Saskatchewan, Saskatoon, SK S7K 0M7, Canada; Cameco MS Neuroscience Research Centre, College of Medicine, University of Saskatchewan, Saskatoon, SK S7K 0M7, Canada; Neurology Division, Department of Medicine, University of Saskatchewan, Saskatoon, SK S7N 0X8, Canada; Department of Anatomy, Physiology and Pharmacology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada.
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14
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RIP1 post-translational modifications. Biochem J 2022; 479:929-951. [PMID: 35522161 DOI: 10.1042/bcj20210725] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 04/13/2022] [Accepted: 04/19/2022] [Indexed: 11/17/2022]
Abstract
Receptor interacting protein 1 (RIP1) kinase is a critical regulator of inflammation and cell death signaling, and plays a crucial role in maintaining immune responses and proper tissue homeostasis. Mounting evidence argues for the importance of RIP1 post-translational modifications in control of its function. Ubiquitination by E3 ligases, such as inhibitors of apoptosis (IAP) proteins and LUBAC, as well as the reversal of these modifications by deubiquitinating enzymes, such as A20 and CYLD, can greatly influence RIP1 mediated signaling. In addition, cleavage by caspase-8, RIP1 autophosphorylation, and phosphorylation by a number of signaling kinases can greatly impact cellular fate. Disruption of the tightly regulated RIP1 modifications can lead to signaling disbalance in TNF and/or TLR controlled and other inflammatory pathways, and result in severe human pathologies. This review will focus on RIP1 and its many modifications with an emphasis on ubiquitination, phosphorylation, and cleavage, and their functional impact on the RIP1's role in signaling pathways.
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15
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Liao KC, Garcia-Blanco MA. Role of Alternative Splicing in Regulating Host Response to Viral Infection. Cells 2021; 10:1720. [PMID: 34359890 PMCID: PMC8306335 DOI: 10.3390/cells10071720] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 06/28/2021] [Accepted: 06/30/2021] [Indexed: 01/26/2023] Open
Abstract
The importance of transcriptional regulation of host genes in innate immunity against viral infection has been widely recognized. More recently, post-transcriptional regulatory mechanisms have gained appreciation as an additional and important layer of regulation to fine-tune host immune responses. Here, we review the functional significance of alternative splicing in innate immune responses to viral infection. We describe how several central components of the Type I and III interferon pathways encode spliced isoforms to regulate IFN activation and function. Additionally, the functional roles of splicing factors and modulators in antiviral immunity are discussed. Lastly, we discuss how cell death pathways are regulated by alternative splicing as well as the potential role of this regulation on host immunity and viral infection. Altogether, these studies highlight the importance of RNA splicing in regulating host-virus interactions and suggest a role in downregulating antiviral innate immunity; this may be critical to prevent pathological inflammation.
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Affiliation(s)
- Kuo-Chieh Liao
- Genome Institute of Singapore, A*STAR, Singapore 138672, Singapore
| | - Mariano A. Garcia-Blanco
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77550, USA
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77550, USA
- Institute of Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77550, USA
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore
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16
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Mabe NW, Garcia NMG, Wolery SE, Newcomb R, Meingasner RC, Vilona BA, Lupo R, Lin CC, Chi JT, Alvarez JV. G9a Promotes Breast Cancer Recurrence through Repression of a Pro-inflammatory Program. Cell Rep 2021; 33:108341. [PMID: 33147463 PMCID: PMC7656293 DOI: 10.1016/j.celrep.2020.108341] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 03/30/2020] [Accepted: 10/09/2020] [Indexed: 02/07/2023] Open
Abstract
Dysregulated gene expression is a common feature of cancer and may underlie some aspects of tumor progression, including tumor relapse. Here, we show that recurrent mammary tumors exhibit global changes in gene expression and histone modifications and acquire dependence on the G9a histone methyltransferase. Genetic ablation of G9a delays tumor recurrence, and pharmacologic inhibition of G9a slows the growth of recurrent tumors. Mechanistically, G9a activity is required to silence pro-inflammatory cytokines, including tumor necrosis factor (TNF), through H3K9 methylation at gene promoters. G9a inhibition induces re-expression of these cytokines, leading to p53 activation and necroptosis. Recurrent tumors upregulate receptor interacting protein kinase-3 (RIPK3) expression and are dependent upon RIPK3 activity. High RIPK3 expression renders recurrent tumors sensitive to necroptosis following G9a inhibition. These findings demonstrate that G9a-mediated silencing of pro-necroptotic proteins is a critical step in tumor recurrence and suggest that G9a is a targetable dependency in recurrent breast cancer.
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Affiliation(s)
- Nathaniel W Mabe
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA
| | - Nina Marie G Garcia
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA
| | - Shayna E Wolery
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA
| | - Rachel Newcomb
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA
| | - Ryan C Meingasner
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA
| | - Brittany A Vilona
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA
| | - Ryan Lupo
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA
| | - Chao-Chieh Lin
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710, USA; Center for Genomic and Computational Biology, Duke University, Durham, NC 27710, USA
| | - Jen-Tsan Chi
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710, USA; Center for Genomic and Computational Biology, Duke University, Durham, NC 27710, USA
| | - James V Alvarez
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC 27710, USA.
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17
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Samson AL, Garnish SE, Hildebrand JM, Murphy JM. Location, location, location: A compartmentalized view of TNF-induced necroptotic signaling. Sci Signal 2021; 14:14/668/eabc6178. [PMID: 33531383 DOI: 10.1126/scisignal.abc6178] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Necroptosis is a lytic, proinflammatory cell death pathway, which has been implicated in host defense and, when dysregulated, the pathology of many human diseases. The central mediators of this pathway are the receptor-interacting serine/threonine protein kinases RIPK1 and RIPK3 and the terminal executioner, the pseudokinase mixed lineage kinase domain-like (MLKL). Here, we review the chronology of signaling along the RIPK1-RIPK3-MLKL axis and highlight how the subcellular compartmentalization of signaling events controls the initiation and execution of necroptosis. We propose that a network of modulators surrounds the necroptotic signaling core and that this network, rather than acting universally, tunes necroptosis in a context-, cell type-, and species-dependent manner. Such a high degree of mechanistic flexibility is likely an important property that helps necroptosis operate as a robust, emergency form of cell death.
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Affiliation(s)
- André L Samson
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia. .,Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Sarah E Garnish
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Joanne M Hildebrand
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
| | - James M Murphy
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia. .,Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia
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18
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Capietto AH, Jhunjhunwala S, Pollock SB, Lupardus P, Wong J, Hänsch L, Cevallos J, Chestnut Y, Fernandez A, Lounsbury N, Nozawa T, Singh M, Fan Z, de la Cruz CC, Phung QT, Taraborrelli L, Haley B, Lill JR, Mellman I, Bourgon R, Delamarre L. Mutation position is an important determinant for predicting cancer neoantigens. J Exp Med 2020; 217:133605. [PMID: 31940002 PMCID: PMC7144530 DOI: 10.1084/jem.20190179] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 09/28/2019] [Accepted: 12/02/2019] [Indexed: 12/21/2022] Open
Abstract
Tumor-specific mutations can generate neoantigens that drive CD8 T cell responses against cancer. Next-generation sequencing and computational methods have been successfully applied to identify mutations and predict neoantigens. However, only a small fraction of predicted neoantigens are immunogenic. Currently, predicted peptide binding affinity for MHC-I is often the major criterion for prioritizing neoantigens, although little progress has been made toward understanding the precise functional relationship between affinity and immunogenicity. We therefore systematically assessed the immunogenicity of peptides containing single amino acid mutations in mouse tumor models and divided them into two classes of immunogenic mutations. The first comprises mutations at a nonanchor residue, for which we find that the predicted absolute binding affinity is predictive of immunogenicity. The second involves mutations at an anchor residue; here, predicted relative affinity (compared with the WT counterpart) is a better predictor. Incorporating these features into an immunogenicity model significantly improves neoantigen ranking. Importantly, these properties of neoantigens are also predictive in human datasets, suggesting that they can be used to prioritize neoantigens for individualized neoantigen-specific immunotherapies.
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Affiliation(s)
| | | | | | | | - Jim Wong
- Genentech, South San Francisco, CA
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19
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Raisner R, Bainer R, Haverty PM, Benedetti KL, Gascoigne KE. Super-enhancer acquisition drives oncogene expression in triple negative breast cancer. PLoS One 2020; 15:e0235343. [PMID: 32584896 PMCID: PMC7316302 DOI: 10.1371/journal.pone.0235343] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/14/2020] [Indexed: 01/12/2023] Open
Abstract
Triple Negative Breast Cancer (TNBC) is a heterogeneous disease lacking known molecular drivers and effective targeted therapies. Cytotoxic chemotherapy remains the mainstay of treatment for TNBCs, which have significantly poorer survival rates compared to other breast cancer subtypes. In addition to changes within the coding genome, aberrant enhancer activity is a well-established contributor to tumorigenesis. Here we use H3K27Ac chromatin immunoprecipitation followed by sequencing (ChIP-Seq) to map the active cis-regulatory landscape in TNBC. We identify distinct disease subtypes associated with specific enhancer activity, and over 2,500 unique superenhancers acquired by tumor cells but absent from normal breast tissue. To identify potential actionable disease drivers, we probed the dependency on genes that associate with tumor-specific enhancers by CRISPR screening. In this way we identify a number of tumor-specific dependencies, including a previously uncharacterized dependency on the TGFβ pseudo-receptor BAMBI.
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Affiliation(s)
- Ryan Raisner
- Department of Discovery Oncology, Genentech, Inc., South San Francisco, California, United States of America
| | - Russell Bainer
- Maze Therapeutics, South San Francisco, California, United States of America
| | - Peter M. Haverty
- Department of Bioinformatics, Genentech, Inc., South San Francisco, California, United States of America
| | - Kelli L. Benedetti
- Department of Cell and Tissue Biology, University of California, San Francisco, California, United States of America
| | - Karen E. Gascoigne
- Department of Discovery Oncology, Genentech, Inc., South San Francisco, California, United States of America
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20
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Newton K. Multitasking Kinase RIPK1 Regulates Cell Death and Inflammation. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a036368. [PMID: 31427374 DOI: 10.1101/cshperspect.a036368] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Receptor-interacting serine threonine kinase 1 (RIPK1) is a widely expressed kinase that is essential for limiting inflammation in both mice and humans. Mice lacking RIPK1 die at birth from multiorgan inflammation and aberrant cell death, whereas humans lacking RIPK1 are immunodeficient and develop very early-onset inflammatory bowel disease. In contrast to complete loss of RIPK1, inhibiting the kinase activity of RIPK1 genetically or pharmacologically prevents cell death and inflammation in several mouse disease models. Indeed, small molecule inhibitors of RIPK1 are in phase I clinical trials for amyotrophic lateral sclerosis, and phase II clinical trials for psoriasis, rheumatoid arthritis, and ulcerative colitis. This review focuses on which signaling pathways use RIPK1, how activation of RIPK1 is regulated, and when activation of RIPK1 appears to be an important driver of inflammation.
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Affiliation(s)
- Kim Newton
- Department of Physiological Chemistry, Genentech, South San Francisco, California 94080, USA
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21
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Yuan W, Goldstein LD, Durinck S, Chen YJ, Nguyen TT, Kljavin NM, Sokol ES, Stawiski EW, Haley B, Ziai J, Modrusan Z, Seshagiri S. S100a4 upregulation in Pik3caH1047R;Trp53R270H;MMTV-Cre-driven mammary tumors promotes metastasis. Breast Cancer Res 2019; 21:152. [PMID: 31881983 PMCID: PMC6935129 DOI: 10.1186/s13058-019-1238-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 12/06/2019] [Indexed: 11/10/2022] Open
Abstract
Background PIK3CA mutations are frequent in human breast cancer. Pik3caH1047R mutant expression in mouse mammary gland promotes tumorigenesis. TP53 mutations co-occur with PIK3CA mutations in human breast cancers. We previously generated a conditionally activatable Pik3caH1047R;MMTV-Cre mouse model and found a few malignant sarcomatoid (spindle cell) carcinomas that had acquired spontaneous dominant-negative Trp53 mutations. Methods A Pik3caH1047R;Trp53R270H;MMTV-Cre double mutant mouse breast cancer model was generated. Tumors were characterized by histology, marker analysis, transcriptional profiling, single-cell RNA-seq, and bioinformatics. Cell lines were developed from mutant tumors and used to identify and confirm genes involved in metastasis. Results We found Pik3caH1047R and Trp53R270H cooperate in driving oncogenesis in mammary glands leading to a shorter latency than either alone. Double mutant mice develop multiple histologically distinct mammary tumors, including adenocarcinoma and sarcomatoid (spindle cell) carcinoma. We found some tumors to be invasive and a few metastasized to the lung and/or the lymph node. Single-cell RNA-seq analysis of the tumors identified epithelial, stromal, myeloid, and T cell groups. Expression analysis of the metastatic tumors identified S100a4 as a top candidate gene associated with metastasis. Metastatic tumors contained a much higher percentage of epithelial–mesenchymal transition (EMT)-signature positive and S100a4-expressing cells. CRISPR/CAS9-mediated knockout of S100a4 in a metastatic tumor-derived cell line disrupted its metastatic potential indicating a role for S100a4 in metastasis. Conclusions Pik3caH1047R;Trp53R270H;MMTV-Cre mouse provides a preclinical model to mimic a subtype of human breast cancers that carry both PIK3CA and TP53 mutations. It also allows for understanding the cooperation between the two mutant genes in tumorigenesis. Our model also provides a system to study metastasis and develop therapeutic strategies for PIK3CA/TP53 double-positive cancers. S100a4 found involved in metastasis in this model can be a potential diagnostic and therapeutic target.
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Affiliation(s)
- Wenlin Yuan
- Department of Molecular Biology, Genentech Inc, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Leonard D Goldstein
- Department of Molecular Biology, Genentech Inc, 1 DNA Way, South San Francisco, CA, 94080, USA.,Department of Bioinformatics and Computational Biology, Genentech Inc, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Steffen Durinck
- Department of Molecular Biology, Genentech Inc, 1 DNA Way, South San Francisco, CA, 94080, USA.,Department of Bioinformatics and Computational Biology, Genentech Inc, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Ying-Jiun Chen
- Department of Molecular Biology, Genentech Inc, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Thong T Nguyen
- Department of Molecular Biology, Genentech Inc, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Noelyn M Kljavin
- Department of Cancer Signaling, Genentech Inc, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Ethan S Sokol
- Foundation Medicine Inc., 150 Second Street, Cambridge, MA, 02141, USA
| | - Eric W Stawiski
- Research and Development Department, MedGenome Inc., Foster City, CA, 94404, USA
| | - Benjamin Haley
- Department of Molecular Biology, Genentech Inc, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - James Ziai
- Department of Pathology, Genentech Inc, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Zora Modrusan
- Department of Molecular Biology, Genentech Inc, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Somasekar Seshagiri
- Department of Molecular Biology, Genentech Inc, 1 DNA Way, South San Francisco, CA, 94080, USA. .,SciGenom Research Foundation, Bangalore, 560099, India.
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22
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Zhang Y, Hyle J, Wright S, Shao Y, Zhao X, Zhang H, Li C. A cis-element within the ARF locus mediates repression of p16INK4A expression via long-range chromatin interactions. Proc Natl Acad Sci U S A 2019; 116:26644-26652. [PMID: 31818950 PMCID: PMC6936709 DOI: 10.1073/pnas.1909720116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Loss of function of CDKN2A/B, also known as INK4/ARF [encoding p16INK4A, p15INK4B, and p14ARF (mouse p19Arf)], confers susceptibility to cancers, whereas its up-regulation during organismal aging provokes cellular senescence and tissue degenerative disorders. To better understand the transcriptional regulation of p16INK4A, a CRISPR screen targeting open, noncoding chromatin regions adjacent to p16INK4A was performed in a human p16INK4A-P2A-mCherry reporter cell line. We identified a repressive element located in the 3' region adjacent to the ARF promoter that controls p16INK4A expression via long-distance chromatin interactions. Coinfection of lentiviral dCas9-KRAB with selected single-guide RNAs against the repressive element abrogated the ARF/p16INK4A chromatin contacts, thus reactivating p16INK4A expression. Genetic CRISPR screening identified candidate transcription factors inhibiting p16INK4A regulation, including ZNF217, which was confirmed to bind the ARF/p16INK4A interaction loop. In summary, direct physical interactions between p16INK4A and ARF genes provide mechanistic insights into their cross-regulation.
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Affiliation(s)
- Yang Zhang
- Department of Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Judith Hyle
- Department of Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Shaela Wright
- Department of Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Ying Shao
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Xujie Zhao
- Department of Pharmaceutical Sciences, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Hui Zhang
- Department of Hematology and Oncology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, 510623 Guangdong, People’s Republic of China
| | - Chunliang Li
- Department of Tumor Cell Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105
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Uncovering human mixed lineage kinase domain-like activation in necroptosis. Future Med Chem 2019; 11:2831-2844. [DOI: 10.4155/fmc-2019-0229] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
MLKL and its obligate upstream receptor interacting protein kinase 3 are essential components of necroptosis. It is well established that MLKL is the executioner of plasma membrane rupture in necroptosis. In healthy cells MLKL is dormant. Several dormant configurations have emerged from high-resolution structural studies revealing distinct mechanisms of MLKL autoinhibition in mammals. MLKL is activated through the concerted actions of receptor interacting protein kinase 3, which phosphorylates MLKL, and, in the case of the human pathway, inositol phosphate (IP) metabolites synthesized by the IP kinases of the IP metabolic pathway. Here, we highlight recent progress toward understanding the mechanisms of regulation of human MLKL, and survey the latest opportunities for targeting MLKL in pathophysiology.
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24
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Gulei D, Berindan-Neagoe I. Activation of Necroptosis by Engineered Self Tumor-Derived Exosomes Loaded with CRISPR/Cas9. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 17:448-451. [PMID: 31323464 PMCID: PMC6639591 DOI: 10.1016/j.omtn.2019.05.032] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 05/27/2019] [Accepted: 05/28/2019] [Indexed: 12/16/2022]
Abstract
CRISPR/Cas9 has proved its efficiency in vitro, where we now know that this tool can efficiently target specific parts of the genome. These modifications can be used to generate advanced models of human diseases, address specific functions of genes, and develop new therapeutic strategies. Even if these advancements are promising, there are still two great issues associated with CRISPR/Cas9: how we can specifically and safely deliver the editing tool in vivo and how we can address the impossibility of CRISPR/Cas9 to attack all the cells within the targeted pool? This work presents an alternative method for engagement of cell death in cancer cells with immediate application in the preclinical sector and significant translational relevance toward clinics.
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Affiliation(s)
- Diana Gulei
- MEDFUTURE - Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Marinescu 23 Street, 400337 Cluj-Napoca, Romania
| | - Ioana Berindan-Neagoe
- MEDFUTURE - Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Marinescu 23 Street, 400337 Cluj-Napoca, Romania; Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Marinescu 23 Street, 400337 Cluj-Napoca, Romania; Department of Functional Genomics and Experimental Pathology, The Oncology Institute Prof. Dr. Ion Chiricuta, Republicii 34-36 Street, Cluj-Napoca, Romania.
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25
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Fauster A, Rebsamen M, Willmann KL, César-Razquin A, Girardi E, Bigenzahn JW, Schischlik F, Scorzoni S, Bruckner M, Konecka J, Hörmann K, Heinz LX, Boztug K, Superti-Furga G. Systematic genetic mapping of necroptosis identifies SLC39A7 as modulator of death receptor trafficking. Cell Death Differ 2019; 26:1138-1155. [PMID: 30237509 PMCID: PMC6748104 DOI: 10.1038/s41418-018-0192-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 07/04/2018] [Accepted: 07/22/2018] [Indexed: 12/13/2022] Open
Abstract
Regulation of cell and tissue homeostasis by programmed cell death is a fundamental process with wide physiological and pathological implications. The advent of scalable somatic cell genetic technologies creates the opportunity to functionally map such essential pathways, thereby identifying potential disease-relevant components. We investigated the genetic basis underlying necroptotic cell death by performing a complementary set of loss-of-function and gain-of-function genetic screens. To this end, we established FADD-deficient haploid human KBM7 cells, which specifically and efficiently undergo necroptosis after a single treatment with either TNFα or the SMAC mimetic compound birinapant. A series of unbiased gene-trap screens identified key signaling mediators, such as TNFR1, RIPK1, RIPK3, and MLKL. Among the novel components, we focused on the zinc transporter SLC39A7, whose knock-out led to necroptosis resistance by affecting TNF receptor surface levels. Orthogonal, solute carrier (SLC)-focused CRISPR/Cas9-based genetic screens revealed the exquisite specificity of SLC39A7, among ~400 SLC genes, for TNFR1-mediated and FAS-mediated but not TRAIL-R1-mediated responses. Mechanistically, we demonstrate that loss of SLC39A7 resulted in augmented ER stress and impaired receptor trafficking, thereby globally affecting downstream signaling. The newly established cellular model also allowed genome-wide gain-of-function screening for genes conferring resistance to necroptosis via the CRISPR/Cas9-based synergistic activation mediator approach. Among these, we found cIAP1 and cIAP2, and characterized the role of TNIP1, which prevented pathway activation in a ubiquitin-binding dependent manner. Altogether, the gain-of-function and loss-of-function screens described here provide a global genetic chart of the molecular factors involved in necroptosis and death receptor signaling, prompting further investigation of their individual contribution and potential role in pathological conditions.
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Affiliation(s)
- Astrid Fauster
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Manuele Rebsamen
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria.
| | - Katharina L Willmann
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, 1090, Vienna, Austria
| | - Adrian César-Razquin
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Enrico Girardi
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Johannes W Bigenzahn
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Fiorella Schischlik
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Stefania Scorzoni
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Manuela Bruckner
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Justyna Konecka
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Katrin Hörmann
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Leonhard X Heinz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Kaan Boztug
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, 1090, Vienna, Austria
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, 1090, Vienna, Austria
- Department of Pediatrics, St. Anna Kinderspital and Children's Cancer Research Institute, Medical University of Vienna, 1090, Vienna, Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria.
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria.
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26
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He M, Chaurushiya MS, Webster JD, Kummerfeld S, Reja R, Chaudhuri S, Chen YJ, Modrusan Z, Haley B, Dugger DL, Eastham-Anderson J, Lau S, Dey A, Caothien R, Roose-Girma M, Newton K, Dixit VM. Intrinsic apoptosis shapes the tumor spectrum linked to inactivation of the deubiquitinase BAP1. SCIENCE (NEW YORK, N.Y.) 2019; 364:283-285. [PMID: 31000662 DOI: 10.1126/science.aav4902] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 03/15/2019] [Indexed: 11/02/2022]
Abstract
Malignancies arising from mutation of tumor suppressors have unexplained tissue proclivity. For example, BAP1 encodes a widely expressed deubiquitinase for histone H2A, but germline mutations are predominantly associated with uveal melanomas and mesotheliomas. We show that BAP1 inactivation causes apoptosis in mouse embryonic stem cells, fibroblasts, liver, and pancreatic tissue but not in melanocytes and mesothelial cells. Ubiquitin ligase RNF2, which silences genes by monoubiquitinating H2A, promoted apoptosis in BAP1-deficient cells by suppressing expression of the prosurvival genes Bcl2 and Mcl1. In contrast, BAP1 loss in melanocytes had little impact on expression of prosurvival genes, instead inducing Mitf Thus, BAP1 appears to modulate gene expression by countering H2A ubiquitination, but its loss only promotes tumorigenesis in cells that do not engage an RNF2-dependent apoptotic program.
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Affiliation(s)
- Meng He
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Mira S Chaurushiya
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Joshua D Webster
- Department of Pathology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Sarah Kummerfeld
- Department of Bioinformatics, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Rohit Reja
- Department of Bioinformatics, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Subhra Chaudhuri
- Department of Molecular Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Ying-Jiun Chen
- Department of Molecular Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Zora Modrusan
- Department of Molecular Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Benjamin Haley
- Department of Molecular Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Debra L Dugger
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | | | - Shari Lau
- Department of Pathology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Anwesha Dey
- Department of Discovery Oncology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Roger Caothien
- Department of Molecular Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Merone Roose-Girma
- Department of Molecular Biology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Kim Newton
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.
| | - Vishva M Dixit
- Department of Physiological Chemistry, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.
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27
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Wang Z, Guo LM, Wang SC, Chen D, Yan J, Liu FX, Huang JF, Xiong K. Progress in studies of necroptosis and its relationship to disease processes. Pathol Res Pract 2018; 214:1749-1757. [PMID: 30244947 DOI: 10.1016/j.prp.2018.09.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 08/21/2018] [Accepted: 09/11/2018] [Indexed: 12/15/2022]
Abstract
This review briefly introduces the mechanism and detection methods of necroptosis in recent years. The most significant points of this review focus on the involvement of necroptotic proteins in disease progression. The following aspects are summarized: 1) RIPs, MLKL, and the upstream and downstream molecules that mediate necroptosis; 2) The development of detection methods for necroptosis; 3) The involvement of related necroptotic proteins in diverse diseases etiology; and 4) The application of necroptotic proteins in disease diagnosis.
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Affiliation(s)
- Zhen Wang
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Li-Min Guo
- Department of Neurobiology and Human Anatomy, School of Basic Medical Science, Central South University, Changsha, Hunan, 410013, China
| | - Shu-Chao Wang
- Department of Neurobiology and Human Anatomy, School of Basic Medical Science, Central South University, Changsha, Hunan, 410013, China
| | - Dan Chen
- Department of Neurobiology and Human Anatomy, School of Basic Medical Science, Central South University, Changsha, Hunan, 410013, China
| | - Jie Yan
- Department of Forensic Science, School of Basic Medical Science, Central South University, Changsha, Hunan, 410013, China
| | - Feng-Xia Liu
- Department of Human Anatomy, School of Basic Medical Science, Xinjiang Medical University, Urumqi, Xinjiang, 830011, China
| | - Ju-Fang Huang
- Department of Neurobiology and Human Anatomy, School of Basic Medical Science, Central South University, Changsha, Hunan, 410013, China.
| | - Kun Xiong
- Department of Neurobiology and Human Anatomy, School of Basic Medical Science, Central South University, Changsha, Hunan, 410013, China.
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