1
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Lazar NH, Celik S, Chen L, Fay MM, Irish JC, Jensen J, Tillinghast CA, Urbanik J, Bone WP, Gibson CC, Haque IS. High-resolution genome-wide mapping of chromosome-arm-scale truncations induced by CRISPR-Cas9 editing. Nat Genet 2024; 56:1482-1493. [PMID: 38811841 PMCID: PMC11250378 DOI: 10.1038/s41588-024-01758-y] [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: 06/30/2023] [Accepted: 04/18/2024] [Indexed: 05/31/2024]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) is a powerful tool for introducing targeted mutations in DNA, but recent studies have shown that it can have unintended effects such as structural changes. However, these studies have not yet looked genome wide or across data types. Here we performed a phenotypic CRISPR-Cas9 scan targeting 17,065 genes in primary human cells, revealing a 'proximity bias' in which CRISPR knockouts show unexpected similarities to unrelated genes on the same chromosome arm. This bias was found to be consistent across cell types, laboratories, Cas9 delivery methods and assay modalities, and the data suggest that it is caused by telomeric truncations of chromosome arms, with cell cycle and apoptotic pathways playing a mediating role. Additionally, a simple correction is demonstrated to mitigate this pervasive bias while preserving biological relationships. This previously uncharacterized effect has implications for functional genomic studies using CRISPR-Cas9, with applications in discovery biology, drug-target identification, cell therapies and genetic therapeutics.
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Affiliation(s)
| | | | - Lu Chen
- Recursion, Salt Lake City, UT, USA
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2
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Hu Z, Guo X, Li Z, Meng Z, Huang S. The neoantigens derived from transposable elements - A hidden treasure for cancer immunotherapy. Biochim Biophys Acta Rev Cancer 2024; 1879:189126. [PMID: 38849060 DOI: 10.1016/j.bbcan.2024.189126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 05/26/2024] [Accepted: 06/02/2024] [Indexed: 06/09/2024]
Abstract
Neoantigen-based therapy is a promising approach that selectively activates the immune system of the host to recognize and eradicate cancer cells. Preliminary clinical trials have validated the feasibility, safety, and immunogenicity of personalized neoantigen-directed vaccines, enhancing their effectiveness and broad applicability in immunotherapy. While many ongoing oncological trials concentrate on neoantigens derived from mutations, these targets do not consistently provoke an immune response in all patients harboring the mutations. Additionally, tumors like ovarian cancer, which have a low tumor mutational burden (TMB), may be less amenable to mutation-based neoantigen therapies. Recent advancements in next-generation sequencing and bioinformatics have uncovered a rich source of neoantigens from non-canonical RNAs associated with transposable elements (TEs). Considering the substantial presence of TEs in the human genome and the proven immunogenicity of TE-derived neoantigens in various tumor types, this review investigates the latest findings on TE-derived neoantigens, examining their clinical implications, challenges, and unique advantages in enhancing tumor immunotherapy.
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Affiliation(s)
- Zhixiang Hu
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xinyi Guo
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ziteng Li
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhiqiang Meng
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Shenglin Huang
- Department of Integrative Oncology, Fudan University Shanghai Cancer Center, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
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3
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Wang J, Li H, Xue Y, Zhang Y, Ma X, Zhou C, Rong L, Zhang Y, Wang Y, Fang Y. Cell communication pathway prognostic model identified detrimental neurodevelopmental pathways in neuroblastoma. Neoplasia 2024; 52:100997. [PMID: 38669760 PMCID: PMC11061340 DOI: 10.1016/j.neo.2024.100997] [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: 03/10/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024]
Abstract
Neurodevelopmental cell communication plays a crucial role in neuroblastoma prognosis. However, determining the impact of these communication pathways on prognosis is challenging due to limited sample sizes and patchy clinical survival information of single cell RNA-seq data. To address this, we have developed the cell communication pathway prognostic model (CCPPM) in this study. CCPPM involves the identification of communication pathways through single-cell RNA-seq data, screening of prognosis-significant pathways using bulk RNA-seq data, conducting functional and attribute analysis of these pathways, and analyzing the post-effects of communication within these pathways. By employing the CCPPM, we have identified ten communication pathways significantly influencing neuroblastoma, all related to axongenesis and neural projection development, especially the BMP7-(BMPR1B-ACVR2B) communication pathway was found to promote tumor cell migration by activating the transcription factor SMAD1 and regulating UNK and MYCBP2. Notably, BMP7 expression was higher in neuroblastoma samples with distant metastases. In summary, CCPPM offers a novel approach to studying the influence of cell communication pathways on disease prognosis and identified detrimental communication pathways related to neurodevelopment.
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Affiliation(s)
- Jiali Wang
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Huimin Li
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Yao Xue
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Yidan Zhang
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaopeng Ma
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Chunlei Zhou
- Department of Pathology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Liucheng Rong
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Yixuan Zhang
- Medical Basic Research Innovation Center for Cardiovascular and Cerebrovascular Diseases, Ministry of Education, School of Pharmacy, Nanjing Medical University, Nanjing, China; International Joint Laboratory for Drug Target of Critical Illnesses, School of Pharmacy, Nanjing Medical University, Nanjing, China; Gusu School, Nanjing Medical University, Suzhou, China.
| | - Yaping Wang
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, Nanjing, China.
| | - Yongjun Fang
- Department of Hematology and Oncology, Children's Hospital of Nanjing Medical University, Nanjing, China.
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4
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Saldana-Guerrero IM, Montano-Gutierrez LF, Boswell K, Hafemeister C, Poon E, Shaw LE, Stavish D, Lea RA, Wernig-Zorc S, Bozsaky E, Fetahu IS, Zoescher P, Pötschger U, Bernkopf M, Wenninger-Weinzierl A, Sturtzel C, Souilhol C, Tarelli S, Shoeb MR, Bozatzi P, Rados M, Guarini M, Buri MC, Weninger W, Putz EM, Huang M, Ladenstein R, Andrews PW, Barbaric I, Cresswell GD, Bryant HE, Distel M, Chesler L, Taschner-Mandl S, Farlik M, Tsakiridis A, Halbritter F. A human neural crest model reveals the developmental impact of neuroblastoma-associated chromosomal aberrations. Nat Commun 2024; 15:3745. [PMID: 38702304 PMCID: PMC11068915 DOI: 10.1038/s41467-024-47945-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/15/2024] [Indexed: 05/06/2024] Open
Abstract
Early childhood tumours arise from transformed embryonic cells, which often carry large copy number alterations (CNA). However, it remains unclear how CNAs contribute to embryonic tumourigenesis due to a lack of suitable models. Here we employ female human embryonic stem cell (hESC) differentiation and single-cell transcriptome and epigenome analysis to assess the effects of chromosome 17q/1q gains, which are prevalent in the embryonal tumour neuroblastoma (NB). We show that CNAs impair the specification of trunk neural crest (NC) cells and their sympathoadrenal derivatives, the putative cells-of-origin of NB. This effect is exacerbated upon overexpression of MYCN, whose amplification co-occurs with CNAs in NB. Moreover, CNAs potentiate the pro-tumourigenic effects of MYCN and mutant NC cells resemble NB cells in tumours. These changes correlate with a stepwise aberration of developmental transcription factor networks. Together, our results sketch a mechanistic framework for the CNA-driven initiation of embryonal tumours.
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Affiliation(s)
- Ingrid M Saldana-Guerrero
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
- Sheffield Institute for Nucleic Acids (SInFoNiA), School of Medicine and Population Health, The University of Sheffield, Sheffield, UK
| | | | - Katy Boswell
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
| | | | - Evon Poon
- Division of Clinical Studies, The Institute of Cancer Research (ICR) & Royal Marsden NHS Trust, London, UK
| | - Lisa E Shaw
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Dylan Stavish
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
| | - Rebecca A Lea
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
| | - Sara Wernig-Zorc
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Eva Bozsaky
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Irfete S Fetahu
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- Medical University of Vienna, Department of Neurology, Division of Neuropathology and Neurochemistry, Vienna, Austria
| | - Peter Zoescher
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Ulrike Pötschger
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Marie Bernkopf
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- Labdia Labordiagnostik GmbH, Vienna, Austria
| | | | - Caterina Sturtzel
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Celine Souilhol
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
- Biomolecular Sciences Research Centre, Department of Biosciences and Chemistry, Sheffield Hallam University, Sheffield, UK
| | - Sophia Tarelli
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
| | - Mohamed R Shoeb
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Polyxeni Bozatzi
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Magdalena Rados
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Maria Guarini
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Michelle C Buri
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Wolfgang Weninger
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Eva M Putz
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Miller Huang
- Children's Hospital Los Angeles, Cancer and Blood Disease Institutes, and The Saban Research Institute, Los Angeles, CA, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ruth Ladenstein
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Peter W Andrews
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
| | - Ivana Barbaric
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
- Neuroscience Institute, The University of Sheffield, Sheffield, UK
| | | | - Helen E Bryant
- Sheffield Institute for Nucleic Acids (SInFoNiA), School of Medicine and Population Health, The University of Sheffield, Sheffield, UK
| | - Martin Distel
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Louis Chesler
- Division of Clinical Studies, The Institute of Cancer Research (ICR) & Royal Marsden NHS Trust, London, UK
| | | | - Matthias Farlik
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Anestis Tsakiridis
- Centre for Stem Cell Biology, School of Biosciences, The University of Sheffield, Sheffield, UK.
- Neuroscience Institute, The University of Sheffield, Sheffield, UK.
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5
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Huang JR, Li Y, Chen P, Wei JX, Yang X, Xu QQ, Chen JB. Effects of transcription factor SOX11 on the biological behavior of neuroblastoma cell and potential regulatory mechanism. Ann Surg Treat Res 2024; 106:284-295. [PMID: 38725807 PMCID: PMC11076950 DOI: 10.4174/astr.2024.106.5.284] [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: 01/22/2023] [Revised: 10/23/2023] [Accepted: 03/06/2024] [Indexed: 05/12/2024] Open
Abstract
Purpose This study aimed to analyze the expression and prognosis of SRY-box transcription factor 11 (SOX11) in neuroblastoma (NB), as well as the biological function and potential regulatory mechanism of SOX11 in NB. Methods Public RNA sequencing was used to detect the expression level of SOX11. The Kaplan-Meier curve and hazard ratios (HR) were used to determine the prognostic value of SOX11 in NB. Functional analyses were performed using CCK8, wound healing assay, and transwell invasion assay. Finally, the potential target genes of SOX11 were predicted by Harmonizonme (Ma'ayan Laboratory) and Cistrome Data Browser (Cistrome Project) database to explore the potential molecular mechanism of SOX11 in NB. Results Compared with normal adrenal tissue, the expression of SOX11 in NB tissue was significantly upregulated. The Kaplan-Meier curve showed that high expression of SOX11 was associated with poor prognosis in children with NB (HR, 1.719; P = 0.049). SOX11 knockdown suppressed the migration capacity of SK-N-SH cells but did not affect proliferation and invasion capacity. Enhancer of zeste homolog 2 (EZH2) may be a potential downstream target gene for the transcription factor SOX11 to play a role in NB. Conclusion The transcription factor SOX11 was significantly upregulated in NB. SOX11 knockdown suppressed the migration capacity of NB cell SK-N-SH. SOX11 may promote the progression of NB by targeting EZH2.
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Affiliation(s)
- Jing-Ru Huang
- Department of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yong Li
- Department of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Peng Chen
- Department of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Ji-Xiu Wei
- Department of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xia Yang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Qiong-Qian Xu
- Department of Pediatric Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - Jia-Bo Chen
- Department of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
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6
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Banerjee D, Bagchi S, Liu Z, Chou HC, Xu M, Sun M, Aloisi S, Vaksman Z, Diskin SJ, Zimmerman M, Khan J, Gryder B, Thiele CJ. Lineage specific transcription factor waves reprogram neuroblastoma from self-renewal to differentiation. Nat Commun 2024; 15:3432. [PMID: 38653778 DOI: 10.1038/s41467-024-47166-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 03/22/2024] [Indexed: 04/25/2024] Open
Abstract
Temporal regulation of super-enhancer (SE) driven transcription factors (TFs) underlies normal developmental programs. Neuroblastoma (NB) arises from an inability of sympathoadrenal progenitors to exit a self-renewal program and terminally differentiate. To identify SEs driving TF regulators, we use all-trans retinoic acid (ATRA) to induce NB growth arrest and differentiation. Time-course H3K27ac ChIP-seq and RNA-seq reveal ATRA coordinated SE waves. SEs that decrease with ATRA link to stem cell development (MYCN, GATA3, SOX11). CRISPR-Cas9 and siRNA verify SOX11 dependency, in vitro and in vivo. Silencing the SOX11 SE using dCAS9-KRAB decreases SOX11 mRNA and inhibits cell growth. Other TFs activate in sequential waves at 2, 4 and 8 days of ATRA treatment that regulate neural development (GATA2 and SOX4). Silencing the gained SOX4 SE using dCAS9-KRAB decreases SOX4 expression and attenuates ATRA-induced differentiation genes. Our study identifies oncogenic lineage drivers of NB self-renewal and TFs critical for implementing a differentiation program.
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Affiliation(s)
- Deblina Banerjee
- Cell & Molecular Biology Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
| | - Sukriti Bagchi
- Cell & Molecular Biology Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Zhihui Liu
- Cell & Molecular Biology Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Hsien-Chao Chou
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Man Xu
- Cell & Molecular Biology Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Ming Sun
- Cell & Molecular Biology Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Sara Aloisi
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, 40126, Italy
| | | | - Sharon J Diskin
- Department of Pediatrics, Division of Oncology, Perelman School of Medicine, Philadelphia, PA, USA
| | - Mark Zimmerman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Javed Khan
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Berkley Gryder
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA.
| | - Carol J Thiele
- Cell & Molecular Biology Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
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7
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Le D, Zhang C, Liu L, Zhao M, Liang Y, Liao P, Yang F. Neuropathic pain development following nerve injury is mediated by SOX11-ARID1A-SOCS3 transcriptional regulation in the spinal cord. Mol Biol Rep 2024; 51:281. [PMID: 38324208 DOI: 10.1007/s11033-023-09183-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/19/2023] [Indexed: 02/08/2024]
Abstract
BACKGROUND Neuropathic pain, a complex condition originating from nervous system damage, remains a significant clinical challenge due to limited understanding of its underlying mechanisms. Recent research highlights the SOX11 transcription factor, known for its role in nervous system development, as a crucial player in neuropathic pain development and maintenance. This study investigates the role of the SOX11-ARID1A-SOCS3 pathway in neuropathic pain modulation within the spinal cord. METHODS AND RESULTS Using a spinal nerve ligation (SNL) model in mice, we observed a significant upregulation of Sox11 in the spinal cord dorsal horn post-injury. Intrathecal administration of Sox11 shRNA mitigated SNL-induced neuropathic pain behaviors, including mechanical allodynia and heat hyperalgesia. Further, we demonstrated that Sox11 regulates neuropathic pain via transcriptional control of ARID1A, with subsequent modulation of SOCS3 expression. Knockdown of ARID1A and SOCS3 via shRNA resulted in alleviation of Sox11-induced pain sensitization. Additionally, Sox11 overexpression led to an increase in ARID1A binding to the SOCS3 promoter, enhancing chromatin accessibility and indicating a direct regulatory relationship. These findings were further supported by in vitro luciferase reporter assays and chromatin accessibility analysis. CONCLUSIONS The SOX11-ARID1A-SOCS3 pathway plays a pivotal role in the development and maintenance of neuropathic pain. Sox11 acts as a master regulator, modulating ARID1A, which in turn influences SOCS3 expression, thereby contributing to the modulation of neuropathic pain. These findings provide a deeper understanding of the molecular mechanisms underlying neuropathic pain and highlight potential therapeutic targets for its treatment. The differential regulation of this pathway in the spinal cord and dorsal root ganglia (DRG) underscores its complexity and the need for targeted therapeutic strategies.
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Affiliation(s)
- Dongsheng Le
- Department of Pain Management, Second Affiliated Hospital of Nanchang University, No. 1, Minde Road, Nanchang, 330006, Jiangxi Province, People's Republic of China
| | - Chao Zhang
- Department of Pain Management, Second Affiliated Hospital of Nanchang University, No. 1, Minde Road, Nanchang, 330006, Jiangxi Province, People's Republic of China
| | - Li Liu
- Department of Pain Management, Second Affiliated Hospital of Nanchang University, No. 1, Minde Road, Nanchang, 330006, Jiangxi Province, People's Republic of China
| | - Mailin Zhao
- Department of Pain Management, Second Affiliated Hospital of Nanchang University, No. 1, Minde Road, Nanchang, 330006, Jiangxi Province, People's Republic of China
| | - Yingping Liang
- Department of Pain Management, Second Affiliated Hospital of Nanchang University, No. 1, Minde Road, Nanchang, 330006, Jiangxi Province, People's Republic of China
| | - Pingsheng Liao
- Department of Pain Management, Second Affiliated Hospital of Nanchang University, No. 1, Minde Road, Nanchang, 330006, Jiangxi Province, People's Republic of China
| | - Fan Yang
- Department of Pain Management, Second Affiliated Hospital of Nanchang University, No. 1, Minde Road, Nanchang, 330006, Jiangxi Province, People's Republic of China.
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8
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Cherkaoui S, Yang L, McBride M, Turn CS, Lu W, Eigenmann C, Allen GE, Panasenko OO, Zhang L, Vu A, Liu K, Li Y, Gandhi OH, Surrey L, Wierer M, White E, Rabinowitz JD, Hogarty MD, Morscher RJ. Reprogramming neuroblastoma by diet-enhanced polyamine depletion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.07.573662. [PMID: 38260457 PMCID: PMC10802427 DOI: 10.1101/2024.01.07.573662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Neuroblastoma is a highly lethal childhood tumor derived from differentiation-arrested neural crest cells1,2. Like all cancers, its growth is fueled by metabolites obtained from either circulation or local biosynthesis3,4. Neuroblastomas depend on local polyamine biosynthesis, with the inhibitor difluoromethylornithine showing clinical activity5. Here we show that such inhibition can be augmented by dietary restriction of upstream amino acid substrates, leading to disruption of oncogenic protein translation, tumor differentiation, and profound survival gains in the TH-MYCN mouse model. Specifically, an arginine/proline-free diet decreases the polyamine precursor ornithine and augments tumor polyamine depletion by difluoromethylornithine. This polyamine depletion causes ribosome stalling, unexpectedly specifically at adenosine-ending codons. Such codons are selectively enriched in cell cycle genes and low in neuronal differentiation genes. Thus, impaired translation of these codons, induced by the diet-drug combination, favors a pro-differentiation proteome. These results suggest that the genes of specific cellular programs have evolved hallmark codon usage preferences that enable coherent translational rewiring in response to metabolic stresses, and that this process can be targeted to activate differentiation of pediatric cancers.
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Affiliation(s)
- Sarah Cherkaoui
- Pediatric Cancer Metabolism Laboratory, Children’s Research Center, University of Zurich, 8032 Zurich, Switzerland
- Division of Oncology, University Children’s Hospital Zurich and Children’s Research Center, University of Zurich, 8032 Zurich, Switzerland
| | - Lifeng Yang
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
- Ludwig Institute for Cancer Research, Princeton Branch, Princeton University, Princeton, NJ 08544, USA
| | - Matthew McBride
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
- Ludwig Institute for Cancer Research, Princeton Branch, Princeton University, Princeton, NJ 08544, USA
| | - Christina S. Turn
- Division of Oncology and Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wenyun Lu
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
- Ludwig Institute for Cancer Research, Princeton Branch, Princeton University, Princeton, NJ 08544, USA
| | - Caroline Eigenmann
- Pediatric Cancer Metabolism Laboratory, Children’s Research Center, University of Zurich, 8032 Zurich, Switzerland
- Division of Oncology, University Children’s Hospital Zurich and Children’s Research Center, University of Zurich, 8032 Zurich, Switzerland
| | - George E. Allen
- Bioinformatics Support Platform, Faculty of Medicine, University of Geneva 1211, Switzerland
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics Geneva, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Olesya O. Panasenko
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics Geneva, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
- BioCode: RNA to proteins (R2P) Platform, University of Geneva, 1211 Geneva, Switzerland
| | - Lu Zhang
- Ludwig Institute for Cancer Research, Princeton Branch, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08901, USA
- Department of Molecular Biology and Biochemistry, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
| | - Annette Vu
- Division of Oncology and Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kangning Liu
- Division of Oncology and Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yimei Li
- Division of Oncology and Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Om H. Gandhi
- Division of Oncology and Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Lea Surrey
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Michael Wierer
- Proteomics Research Infrastructure, Panum Institute, Blegdamsvej 3B, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Eileen White
- Ludwig Institute for Cancer Research, Princeton Branch, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08901, USA
- Department of Molecular Biology and Biochemistry, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
| | - Joshua D. Rabinowitz
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
- Ludwig Institute for Cancer Research, Princeton Branch, Princeton University, Princeton, NJ 08544, USA
| | - Michael D. Hogarty
- Division of Oncology and Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Raphael J. Morscher
- Pediatric Cancer Metabolism Laboratory, Children’s Research Center, University of Zurich, 8032 Zurich, Switzerland
- Division of Oncology, University Children’s Hospital Zurich and Children’s Research Center, University of Zurich, 8032 Zurich, Switzerland
- Division of Human Genetics, Medical University Innsbruck, Peter-Mayr-Str. 1, 6020 Innsbruck, Austria
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9
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Nunes C, Anckaert J, De Vloed F, De Wyn J, Durinck K, Vandesompele J, Speleman F, Vermeirssen V. HTSplotter: An end-to-end data processing, analysis and visualisation tool for chemical and genetic in vitro perturbation screening. PLoS One 2024; 19:e0296322. [PMID: 38181013 PMCID: PMC10769073 DOI: 10.1371/journal.pone.0296322] [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: 06/20/2022] [Accepted: 12/11/2023] [Indexed: 01/07/2024] Open
Abstract
In biomedical research, high-throughput screening is often applied as it comes with automatization, higher-efficiency, and more and faster results. High-throughput screening experiments encompass drug, drug combination, genetic perturbagen or a combination of genetic and chemical perturbagen screens. These experiments are conducted in real-time assays over time or in an endpoint assay. The data analysis consists of data cleaning and structuring, as well as further data processing and visualisation, which, due to the amount of data, can easily become laborious, time-consuming and error-prone. Therefore, several tools have been developed to aid researchers in this process, but these typically focus on specific experimental set-ups and are unable to process data of several time points and genetic-chemical perturbagen screens. To meet these needs, we developed HTSplotter, a web tool and Python module that performs automatic data analysis and visualization of visualization of eitherendpoint or real-time assays from different high-throughput screening experiments: drug, drug combination, genetic perturbagen and genetic-chemical perturbagen screens. HTSplotter implements an algorithm based on conditional statements to identify experiment types and controls. After appropriate data normalization, including growth rate normalization, HTSplotter executes downstream analyses such as dose-response relationship and drug synergism assessment by the Bliss independence (BI), Zero Interaction Potency (ZIP) and Highest Single Agent (HSA) methods. All results are exported as a text file and plots are saved in a PDF file. The main advantage of HTSplotter over other available tools is the automatic analysis of genetic-chemical perturbagen screens and real-time assays where growth rate and perturbagen effect results are plotted over time. In conclusion, HTSplotter allows for the automatic end-to-end data processing, analysis and visualisation of various high-throughput in vitro cell culture screens, offering major improvements in terms of versatility, efficiency and time over existing tools.
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Affiliation(s)
- Carolina Nunes
- Lab for Computational Biology, Integromics and Gene Regulation (CBIGR), Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Pediatric Precision Oncology Lab (PPOL), Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Jasper Anckaert
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Fanny De Vloed
- Pediatric Precision Oncology Lab (PPOL), Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Jolien De Wyn
- Pediatric Precision Oncology Lab (PPOL), Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Kaat Durinck
- Pediatric Precision Oncology Lab (PPOL), Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Jo Vandesompele
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Frank Speleman
- Pediatric Precision Oncology Lab (PPOL), Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Vanessa Vermeirssen
- Lab for Computational Biology, Integromics and Gene Regulation (CBIGR), Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Pediatric Precision Oncology Lab (PPOL), Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
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Fazilaty H, Basler K. Reactivation of embryonic genetic programs in tissue regeneration and disease. Nat Genet 2023; 55:1792-1806. [PMID: 37904052 DOI: 10.1038/s41588-023-01526-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 09/11/2023] [Indexed: 11/01/2023]
Abstract
Embryonic genetic programs are reactivated in response to various types of tissue damage, providing cell plasticity for tissue regeneration or disease progression. In acute conditions, these programs remedy the damage and then halt to allow a return to homeostasis. In chronic situations, including inflammatory diseases, fibrosis and cancer, prolonged activation of embryonic programs leads to disease progression and tissue deterioration. Induction of progenitor identity and cell plasticity, for example, epithelial-mesenchymal plasticity, are critical outcomes of reactivated embryonic programs. In this Review, we describe molecular players governing reactivated embryonic genetic programs, their role during disease progression, their similarities and differences and lineage reversion in pathology and discuss associated therapeutics and drug-resistance mechanisms across many organs. We also discuss the diversity of reactivated programs in different disease contexts. A comprehensive overview of commonalities between development and disease will provide better understanding of the biology and therapeutic strategies.
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Affiliation(s)
- Hassan Fazilaty
- Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland.
| | - Konrad Basler
- Department of Molecular Life Sciences, University of Zürich, Zürich, Switzerland
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11
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Changmeng Z, Hongfei W, Cheung MCH, Chan YS, Shea GKH. Revealing the developmental origin and lineage predilection of neural progenitors within human bone marrow via single-cell analysis: implications for regenerative medicine. Genome Med 2023; 15:66. [PMID: 37667405 PMCID: PMC10476295 DOI: 10.1186/s13073-023-01224-0] [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: 09/05/2022] [Accepted: 08/24/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND Human bone marrow stromal cells (BMSCs) are an easily accessible and expandable progenitor population with the capacity to generate neural cell types in addition to mesoderm. Lineage tracing studies in transgenic animals have indicated Nestin + BMSCs to be descended from the truncal neural crest. Single-cell analysis provides a means to identify the developmental origin and identity of human BMSC-derived neural progenitors when lineage tracing remains infeasible. This is a prerequisite towards translational application. METHODS We attained transcriptomic profiles of embryonic long bone, adult human bone marrow, cultured BMSCs and BMSC-derived neurospheres. Integrated scRNAseq analysis was supplemented by characterization of cells during culture expansion and following provision of growth factors and signalling agonists to bias lineage. RESULTS Reconstructed pseudotime upon the integrated dataset indicated distinct neural and osteogenic differentiation trajectories. The starting state towards the neural differentiation trajectory consisted of Nestin + /MKI67 + BMSCs, which could also be diverted towards the osteogenic trajectory via a branch point. Nestin + /PDGFRA + BMSCs responded to neurosphere culture conditions to generate a subpopulation of cells with a neuronal phenotype according to marker expression and gene ontogeny analysis that occupied the end state along the neural differentiation trajectory. Reconstructed pseudotime also revealed an upregulation of BMP4 expression during culture of BMSC-neurospheres. This provided the rationale for culture supplementation with the BMP signalling agonist SB4, which directed progenitors to upregulate Pax6 and downregulate Nestin. CONCLUSIONS This study suggested BMSCs originating from truncal neural crest to be the source of cells within long bone marrow possessing neural differentiation potential. Unravelling the transcriptomic dynamics of BMSC-derived neural progenitors promises to enhance differentiation efficiency and safety towards clinical application in cell therapy and disease modelling.
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Affiliation(s)
- Zhang Changmeng
- Department of Orthopaedics and Traumatology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Wang Hongfei
- Department of Orthopaedics and Traumatology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Martin Chi-Hang Cheung
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Ying-Shing Chan
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Graham Ka-Hon Shea
- Department of Orthopaedics and Traumatology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong.
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