1
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Wen X, Luo Z, Zhao W, Calandrelli R, Nguyen TC, Wan X, Charles Richard JL, Zhong S. Single-cell multiplex chromatin and RNA interactions in ageing human brain. Nature 2024; 628:648-656. [PMID: 38538789 PMCID: PMC11023937 DOI: 10.1038/s41586-024-07239-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 02/26/2024] [Indexed: 04/06/2024]
Abstract
Dynamically organized chromatin complexes often involve multiplex chromatin interactions and sometimes chromatin-associated RNA1-3. Chromatin complex compositions change during cellular differentiation and ageing, and are expected to be highly heterogeneous among terminally differentiated single cells4-7. Here we introduce the multinucleic acid interaction mapping in single cells (MUSIC) technique for concurrent profiling of multiplex chromatin interactions, gene expression and RNA-chromatin associations within individual nuclei. When applied to 14 human frontal cortex samples from older donors, MUSIC delineated diverse cortical cell types and states. We observed that nuclei exhibiting fewer short-range chromatin interactions were correlated with both an 'older' transcriptomic signature and Alzheimer's disease pathology. Furthermore, the cell type exhibiting chromatin contacts between cis expression quantitative trait loci and a promoter tends to be that in which these cis expression quantitative trait loci specifically affect the expression of their target gene. In addition, female cortical cells exhibit highly heterogeneous interactions between XIST non-coding RNA and chromosome X, along with diverse spatial organizations of the X chromosomes. MUSIC presents a potent tool for exploration of chromatin architecture and transcription at cellular resolution in complex tissues.
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Affiliation(s)
- Xingzhao Wen
- Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla, CA, USA
| | - Zhifei Luo
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Department of Genetics, School of Medicine, Stanford, CA, USA
| | - Wenxin Zhao
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Riccardo Calandrelli
- Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA, USA
| | - Tri C Nguyen
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Department of Genetics, School of Medicine, Stanford, CA, USA
| | - Xueyi Wan
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | | | - Sheng Zhong
- Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla, CA, USA.
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
- Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA, USA.
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2
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Wen X, Luo Z, Zhao W, Calandrelli R, Nguyen TC, Wan X, Richard JLC, Zhong S. Single-cell multiplex chromatin and RNA interactions in aging human brain. bioRxiv 2024:2023.06.28.546457. [PMID: 37425846 PMCID: PMC10326989 DOI: 10.1101/2023.06.28.546457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
The dynamically organized chromatin complexes often involve multiplex chromatin interactions and sometimes chromatin-associated RNA (caRNA) 1-3. Chromatin complex compositions change during cellular differentiation and aging, and are expected to be highly heterogeneous among terminally differentiated single cells 4-7. Here we introduce the Multi-Nucleic Acid Interaction Mapping in Single Cell (MUSIC) technique for concurrent profiling of multiplex chromatin interactions, gene expression, and RNA-chromatin associations within individual nuclei. Applied to 14 human frontal cortex samples from elderly donors, MUSIC delineates diverse cortical cell types and states. We observed the nuclei exhibiting fewer short-range chromatin interactions are correlated with an "older" transcriptomic signature and with Alzheimer's pathology. Furthermore, the cell type exhibiting chromatin contacts between cis expression quantitative trait loci (cis eQTLs) and a promoter tends to be the cell type where these cis eQTLs specifically affect their target gene's expression. Additionally, the female cortical cells exhibit highly heterogeneous interactions between the XIST non-coding RNA and Chromosome X, along with diverse spatial organizations of the X chromosomes. MUSIC presents a potent tool for exploring chromatin architecture and transcription at cellular resolution in complex tissues.
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Affiliation(s)
- Xingzhao Wen
- Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Zhifei Luo
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Wenxin Zhao
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Riccardo Calandrelli
- Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Tri C. Nguyen
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Xueyi Wan
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | | | - Sheng Zhong
- Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla, CA 92093, USA
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
- Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA 92093, USA
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3
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Sriram K, Qi Z, Yuan D, Malhi NK, Liu X, Calandrelli R, Luo Y, Tapia A, Jin S, Shi J, Salas M, Dang R, Armstrong B, Priceman SJ, Wang PH, Liao J, Natarajan R, Zhong S, Bouman Chen Z. Regulation of nuclear transcription by mitochondrial RNA in endothelial cells. eLife 2024; 13:e86204. [PMID: 38251974 PMCID: PMC10803041 DOI: 10.7554/elife.86204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 12/12/2023] [Indexed: 01/23/2024] Open
Abstract
Chromatin-associated RNAs (caRNAs) form a relatively poorly recognized layer of the epigenome. The caRNAs reported to date are transcribed from the nuclear genome. Here, leveraging a recently developed assay for detection of caRNAs and their genomic association, we report that mitochondrial RNAs (mtRNAs) are attached to the nuclear genome and constitute a subset of caRNA, thus termed mt-caRNA. In four human cell types analyzed, mt-caRNAs preferentially attach to promoter regions. In human endothelial cells (ECs), the level of mt-caRNA-promoter attachment changes in response to environmental stress that mimics diabetes. Suppression of a non-coding mt-caRNA in ECs attenuates stress-induced nascent RNA transcription from the nuclear genome, including that of critical genes regulating cell adhesion, and abolishes stress-induced monocyte adhesion, a hallmark of dysfunctional ECs. Finally, we report increased nuclear localization of multiple mtRNAs in the ECs of human diabetic donors, suggesting many mtRNA translocate to the nucleus in a cell stress and disease-dependent manner. These data nominate mt-caRNAs as messenger molecules responsible for mitochondrial-nuclear communication and connect the immediate product of mitochondrial transcription with the transcriptional regulation of the nuclear genome.
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Affiliation(s)
- Kiran Sriram
- Department of Diabetes Complications and Metabolism, City of HopeDuarteUnited States
- Irell and Manella Graduate School of Biological Sciences, City of HopeDuarteUnited States
| | - Zhijie Qi
- Department of Bioengineering, University of California San DiegoLa JollaUnited States
| | - Dongqiang Yuan
- Department of Diabetes Complications and Metabolism, City of HopeDuarteUnited States
| | - Naseeb Kaur Malhi
- Department of Diabetes Complications and Metabolism, City of HopeDuarteUnited States
| | - Xuejing Liu
- Department of Diabetes Complications and Metabolism, City of HopeDuarteUnited States
| | - Riccardo Calandrelli
- Department of Bioengineering, University of California San DiegoLa JollaUnited States
| | - Yingjun Luo
- Department of Diabetes Complications and Metabolism, City of HopeDuarteUnited States
| | - Alonso Tapia
- Department of Diabetes Complications and Metabolism, City of HopeDuarteUnited States
- Irell and Manella Graduate School of Biological Sciences, City of HopeDuarteUnited States
| | - Shengyan Jin
- Department of Genetics, Yale University School of MedicineNew HavenUnited States
| | - Ji Shi
- Translura, IncNew HavenUnited States
| | - Martha Salas
- Department of Stem Cell Biology and Regenerative Medicine, City of HopeDuarteUnited States
| | - Runrui Dang
- Department of Bioengineering, University of California RiversideRiversideUnited States
| | - Brian Armstrong
- Department of Stem Cell Biology and Regenerative Medicine, City of HopeDuarteUnited States
| | - Saul J Priceman
- Department of Hematology & Hematopoietic Cell Transplantation, Department of Immuno-oncology, City of HopeDuarteUnited States
| | - Ping H Wang
- Department of Diabetes, Endocrinology, and Metabolism, City of HopeDuarteUnited States
| | - Jiayu Liao
- Department of Bioengineering, University of California RiversideRiversideUnited States
| | - Rama Natarajan
- Department of Diabetes Complications and Metabolism, City of HopeDuarteUnited States
- Irell and Manella Graduate School of Biological Sciences, City of HopeDuarteUnited States
| | - Sheng Zhong
- Department of Bioengineering, University of California San DiegoLa JollaUnited States
| | - Zhen Bouman Chen
- Department of Diabetes Complications and Metabolism, City of HopeDuarteUnited States
- Irell and Manella Graduate School of Biological Sciences, City of HopeDuarteUnited States
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4
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Calandrelli R, Wen X, Charles Richard JL, Luo Z, Nguyen TC, Chen CJ, Qi Z, Xue S, Chen W, Yan Z, Wu W, Zaleta-Rivera K, Hu R, Yu M, Wang Y, Li W, Ma J, Ren B, Zhong S. Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells. Nat Commun 2023; 14:6519. [PMID: 37845234 PMCID: PMC10579264 DOI: 10.1038/s41467-023-42274-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 10/05/2023] [Indexed: 10/18/2023] Open
Abstract
The interphase genome is dynamically organized in the nucleus and decorated with chromatin-associated RNA (caRNA). It remains unclear whether the genome architecture modulates the spatial distribution of caRNA and vice versa. Here, we generate a resource of genome-wide RNA-DNA and DNA-DNA contact maps in human cells. These maps reveal the chromosomal domains demarcated by locally transcribed RNA, hereafter termed RNA-defined chromosomal domains. Further, the spreading of caRNA is constrained by the boundaries of topologically associating domains (TADs), demonstrating the role of the 3D genome structure in modulating the spatial distribution of RNA. Conversely, stopping transcription or acute depletion of RNA induces thousands of chromatin loops genome-wide. Activation or suppression of the transcription of specific genes suppresses or creates chromatin loops straddling these genes. Deletion of a specific caRNA-producing genomic sequence promotes chromatin loops that straddle the interchromosomal target sequences of this caRNA. These data suggest a feedback loop where the 3D genome modulates the spatial distribution of RNA, which in turn affects the dynamic 3D genome organization.
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Affiliation(s)
- Riccardo Calandrelli
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Xingzhao Wen
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | | | - Zhifei Luo
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Tri C Nguyen
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Chien-Ju Chen
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | - Zhijie Qi
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Shuanghong Xue
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Weizhong Chen
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Zhangming Yan
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Weixin Wu
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Kathia Zaleta-Rivera
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Rong Hu
- Department of Cellular and Molecular Medicine, Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Miao Yu
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Yuchuan Wang
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Wenbo Li
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
| | - Jian Ma
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Bing Ren
- Department of Cellular and Molecular Medicine, Center for Epigenomics, University of California San Diego, La Jolla, CA, USA
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Sheng Zhong
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
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5
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Dekker J, Alber F, Aufmkolk S, Beliveau BJ, Bruneau BG, Belmont AS, Bintu L, Boettiger A, Calandrelli R, Disteche CM, Gilbert DM, Gregor T, Hansen AS, Huang B, Huangfu D, Kalhor R, Leslie CS, Li W, Li Y, Ma J, Noble WS, Park PJ, Phillips-Cremins JE, Pollard KS, Rafelski SM, Ren B, Ruan Y, Shav-Tal Y, Shen Y, Shendure J, Shu X, Strambio-De-Castillia C, Vertii A, Zhang H, Zhong S. Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project. Mol Cell 2023; 83:2624-2640. [PMID: 37419111 PMCID: PMC10528254 DOI: 10.1016/j.molcel.2023.06.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 06/10/2023] [Accepted: 06/12/2023] [Indexed: 07/09/2023]
Abstract
The four-dimensional nucleome (4DN) consortium studies the architecture of the genome and the nucleus in space and time. We summarize progress by the consortium and highlight the development of technologies for (1) mapping genome folding and identifying roles of nuclear components and bodies, proteins, and RNA, (2) characterizing nuclear organization with time or single-cell resolution, and (3) imaging of nuclear organization. With these tools, the consortium has provided over 2,000 public datasets. Integrative computational models based on these data are starting to reveal connections between genome structure and function. We then present a forward-looking perspective and outline current aims to (1) delineate dynamics of nuclear architecture at different timescales, from minutes to weeks as cells differentiate, in populations and in single cells, (2) characterize cis-determinants and trans-modulators of genome organization, (3) test functional consequences of changes in cis- and trans-regulators, and (4) develop predictive models of genome structure and function.
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Affiliation(s)
- Job Dekker
- University of Massachusetts Chan Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Frank Alber
- University of California, Los Angeles, Los Angeles, CA, USA
| | | | | | - Benoit G Bruneau
- Gladstone Institutes, San Francisco, CA, USA; University of California, San Francisco, San Francisco, CA, USA
| | | | | | | | | | | | | | | | | | - Bo Huang
- University of California, San Francisco, San Francisco, CA, USA
| | - Danwei Huangfu
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Reza Kalhor
- Johns Hopkins University, Baltimore, MD, USA
| | | | - Wenbo Li
- University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Yun Li
- University of North Carolina, Gillings School of Global Public Health, Chapel Hill, NC, USA
| | - Jian Ma
- Carnegie Mellon University, Pittsburgh, PA, USA
| | | | | | | | - Katherine S Pollard
- Gladstone Institutes, San Francisco, CA, USA; University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA
| | | | - Bing Ren
- University of California, San Diego, La Jolla, CA, USA
| | - Yijun Ruan
- Zhejiang University, Hangzhou, Zhejiang, China
| | | | - Yin Shen
- University of California, San Francisco, San Francisco, CA, USA
| | | | - Xiaokun Shu
- University of California, San Francisco, San Francisco, CA, USA
| | | | | | | | - Sheng Zhong
- University of California, San Diego, La Jolla, CA, USA.
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6
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Xu T, Zhu E, Zhang C, Calandrelli R, Lin P, Zhong S. High-Resolution Characterization of Human Brain Cortex with High-Fidelity Spatial Transcriptomic Slides (HiFi-Slides). bioRxiv 2023:2023.06.12.544625. [PMID: 37398363 PMCID: PMC10312654 DOI: 10.1101/2023.06.12.544625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Spatial transcriptomic tools and platforms help researchers to inspect tissues and cells with fine details of how they differentiate in expressions and how they orient themselves. With the higher resolution we get and higher throughput of expression targets, spatial analysis can truly become the core player for cell clustering, migration study, and, eventually, the novel model for pathological study. We present the demonstration of HiFi-slide, a whole transcriptomic sequencing technique that recycles used sequenced-by-synthesis flow cell surfaces to a high-resolution spatial mapping tool that can be directly applied to tissue cell gradient analysis, gene expression analysis, cell proximity analysis, and other cellular-level spatial studies.
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7
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Tang X, Lai CH, Malhi NK, Chadha R, Luo Y, Liu X, Yuan D, Tapia A, Abdollahi M, Zhang G, Calandrelli R, Shiu YT, Wang ZV, Rhee JW, Zhong S, Natarajan R, Chen ZB. Genetic Deletion of the LINC00520 Homolog in Mouse Aggravates Angiotensin II-Induced Hypertension. Noncoding RNA 2023; 9:31. [PMID: 37218991 PMCID: PMC10204496 DOI: 10.3390/ncrna9030031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 05/24/2023] Open
Abstract
(1) Background: Hypertension is a complex, multifactorial disease that is caused by genetic and environmental factors. Apart from genetic predisposition, the mechanisms involved in this disease have yet to be fully understood. We previously reported that LEENE (lncRNA enhancing endothelial nitric oxide expression, transcribed from LINC00520 in the human genome) regulates endothelial cell (EC) function by promoting the expression of endothelial nitric oxide synthase (eNOS) and vascular growth factor receptor 2 (VEGFR2). Mice with genetic deletion of the LEENE/LINC00520 homologous region exhibited impaired angiogenesis and tissue regeneration in a diabetic hindlimb ischemia model. However, the role of LEENE in blood pressure regulation is unknown. (2) Methods: We subjected mice with genetic ablation of leene and wild-type littermates to Angiotensin II (AngII) and monitored their blood pressure and examined their hearts and kidneys. We used RNA-sequencing to identify potential leene-regulated molecular pathways in ECs that contributed to the observed phenotype. We further performed in vitro experiments with murine and human ECs and ex vivo experiments with murine aortic rings to validate the select mechanism. (3) Results: We identified an exacerbated hypertensive phenotype of leene-KO mice in the AngII model, evidenced by higher systolic and diastolic blood pressure. At the organ level, we observed aggravated hypertrophy and fibrosis in the heart and kidney. Moreover, the overexpression of human LEENE RNA, in part, restored the signaling pathways impaired by leene deletion in murine ECs. Additionally, Axitinib, a tyrosine kinase inhibitor that selectively inhibits VEGFR suppresses LEENE in human ECs. (4) Conclusions: Our study suggests LEENE as a potential regulator in blood pressure control, possibly through its function in ECs.
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Affiliation(s)
- Xiaofang Tang
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes Metabolism Research Institute and Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Chih-Hung Lai
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes Metabolism Research Institute and Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
- Cardiovascular Center, Taichung Veterans General Hospital, Taichung 40705, Taiwan
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 40705, Taiwan
| | - Naseeb K. Malhi
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes Metabolism Research Institute and Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Rahuljeet Chadha
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes Metabolism Research Institute and Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91010, USA
| | - Yingjun Luo
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes Metabolism Research Institute and Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Xuejing Liu
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes Metabolism Research Institute and Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Dongqiang Yuan
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes Metabolism Research Institute and Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Alonso Tapia
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes Metabolism Research Institute and Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Maryam Abdollahi
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes Metabolism Research Institute and Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Guangyu Zhang
- Department of Diabetes and Cancer Metabolism, Arthur Riggs Diabetes Metabolism Research Institute and Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Riccardo Calandrelli
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Yan-Ting Shiu
- Division of Nephrology & Hypertension, University of Utah, Salt Lake City, UT 84132, USA
- Veterans Affairs Salt Lake City Healthcare System, Salt Lake City, UT 84132, USA
| | - Zhao V. Wang
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
- Department of Diabetes and Cancer Metabolism, Arthur Riggs Diabetes Metabolism Research Institute and Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - June-Wha Rhee
- Department of Medicine, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Sheng Zhong
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Rama Natarajan
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes Metabolism Research Institute and Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Zhen Bouman Chen
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes Metabolism Research Institute and Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
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8
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Tang X, Luo Y, Yuan D, Calandrelli R, Malhi NK, Sriram K, Miao Y, Lou CH, Tsark W, Tapia A, Chen AT, Zhang G, Roeth D, Kalkum M, Wang ZV, Chien S, Natarajan R, Cooke JP, Zhong S, Chen ZB. Long noncoding RNA LEENE promotes angiogenesis and ischemic recovery in diabetes models. J Clin Invest 2023; 133:e161759. [PMID: 36512424 PMCID: PMC9888385 DOI: 10.1172/jci161759] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 12/08/2022] [Indexed: 12/15/2022] Open
Abstract
Impaired angiogenesis in diabetes is a key process contributing to ischemic diseases such as peripheral arterial disease. Epigenetic mechanisms, including those mediated by long noncoding RNAs (lncRNAs), are crucial links connecting diabetes and the related chronic tissue ischemia. Here we identify the lncRNA that enhances endothelial nitric oxide synthase (eNOS) expression (LEENE) as a regulator of angiogenesis and ischemic response. LEENE expression was decreased in diabetic conditions in cultured endothelial cells (ECs), mouse hind limb muscles, and human arteries. Inhibition of LEENE in human microvascular ECs reduced their angiogenic capacity with a dysregulated angiogenic gene program. Diabetic mice deficient in Leene demonstrated impaired angiogenesis and perfusion following hind limb ischemia. Importantly, overexpression of human LEENE rescued the impaired ischemic response in Leene-knockout mice at tissue functional and single-cell transcriptomic levels. Mechanistically, LEENE RNA promoted transcription of proangiogenic genes in ECs, such as KDR (encoding VEGFR2) and NOS3 (encoding eNOS), potentially by interacting with LEO1, a key component of the RNA polymerase II-associated factor complex and MYC, a crucial transcription factor for angiogenesis. Taken together, our findings demonstrate an essential role for LEENE in the regulation of angiogenesis and tissue perfusion. Functional enhancement of LEENE to restore angiogenesis for tissue repair and regeneration may represent a potential strategy to tackle ischemic vascular diseases.
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Affiliation(s)
- Xiaofang Tang
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, California, USA
| | - Yingjun Luo
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, California, USA
| | - Dongqiang Yuan
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, California, USA
| | | | - Naseeb Kaur Malhi
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, California, USA
| | - Kiran Sriram
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, California, USA
- Irell and Manella Graduate School of Biological Sciences
| | - Yifei Miao
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, California, USA
| | | | - Walter Tsark
- Transgenic Mouse Facility, Center for Comparative Medicine, City of Hope, Duarte, California, USA
| | - Alonso Tapia
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, California, USA
- Irell and Manella Graduate School of Biological Sciences
| | - Aleysha T. Chen
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, California, USA
| | | | - Daniel Roeth
- Department of Immunology & Theranostics, Arthur Riggs Diabetes and Metabolism Research Institute, Center for Comparative Medicine, City of Hope, Duarte, California, USA
| | - Markus Kalkum
- Department of Immunology & Theranostics, Arthur Riggs Diabetes and Metabolism Research Institute, Center for Comparative Medicine, City of Hope, Duarte, California, USA
| | - Zhao V. Wang
- Irell and Manella Graduate School of Biological Sciences
- Department of Diabetes and Cancer Metabolism and
| | - Shu Chien
- Department of Bioengineering, UCSD, La Jolla, California, USA
- Department of Medicine, UCSD, La Jolla, California, USA
| | - Rama Natarajan
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, California, USA
- Irell and Manella Graduate School of Biological Sciences
| | - John P. Cooke
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, Texas, USA
| | - Sheng Zhong
- Department of Bioengineering, UCSD, La Jolla, California, USA
| | - Zhen Bouman Chen
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, California, USA
- Irell and Manella Graduate School of Biological Sciences
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9
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Chen X, Calandrelli R, Girardini J, Yan Z, Tan Z, Xu X, Hiniker A, Zhong S. PHGDH expression increases with progression of Alzheimer's disease pathology and symptoms. Cell Metab 2022; 34:651-653. [PMID: 35508105 PMCID: PMC9531314 DOI: 10.1016/j.cmet.2022.02.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 09/26/2021] [Accepted: 02/10/2022] [Indexed: 11/03/2022]
Abstract
Chen et al. reveal an increase of phosphoglycerate dehydrogenase (PHGDH) mRNA and protein levels in two mouse models and four human cohorts in Alzheimer's disease brains compared to age- and sex-matched control brains. The increase of PHGDH expression in human brain correlates with symptomatic development and disease pathology.
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Affiliation(s)
- Xu Chen
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA.
| | - Riccardo Calandrelli
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - John Girardini
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Zhangming Yan
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Zhiqun Tan
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine School of Medicine, Irvine, CA, USA; Department of Anatomy and Neurobiology, University of California, Irvine School of Medicine, Irvine, CA, USA
| | - Xiangmin Xu
- Department of Anatomy and Neurobiology, University of California, Irvine School of Medicine, Irvine, CA, USA
| | - Annie Hiniker
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Sheng Zhong
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA; Genemo, Inc., San Diego, CA, USA.
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10
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Massaccesi M, Fuga V, Dinapoli N, Rupe C, Olivieri M, Beghella Bartoli F, Mazzarella C, Panfili M, Calandrelli R, Settimi S, Lajolo C, Gambacorta M, Miccichè F. PD-0827 Dose volume correlates of mouth opening reduction after radiotherapy for HNC: comprehensive analysis. Radiother Oncol 2022. [DOI: 10.1016/s0167-8140(22)02968-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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11
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Malhi NK, Luo Y, Tang X, Sriram K, Calandrelli R, Zhong S, Chen ZB. Isolation and Profiling of Human Primary Mesenteric Arterial Endothelial Cells at the Transcriptome Level. J Vis Exp 2022:10.3791/63307. [PMID: 35343966 PMCID: PMC9180814 DOI: 10.3791/63307] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023] Open
Abstract
Endothelial cells (ECs) are crucial for vascular and whole-body function through their dynamic response to environmental cues. Elucidating the transcriptome and epigenome of ECs is paramount to understanding their roles in development, health, and disease, but is limited in the availability of isolated primary cells. Recent technologies have enabled the high-throughput profiling of EC transcriptome and epigenome, leading to the identification of previously unknown EC cell subpopulations and developmental trajectories. While EC cultures are a useful tool in the exploration of EC function and dysfunction, the culture conditions and multiple passages can introduce external variables that alter the properties of native EC, including morphology, epigenetic state, and gene expression program. To overcome this limitation, the present paper demonstrates a method of isolating human primary ECs from donor mesenteric arteries aiming to capture their native state. ECs in the intimal layer are dissociated mechanically and biochemically with the use of particular enzymes. The resultant cells can be directly used for bulk RNA or single-cell RNA-sequencing or plated for culture. In addition, a workflow is described for the preparation of human arterial tissue for spatial transcriptomics, specifically for a commercially available platform, although this method is also suitable for other spatial transcriptome profiling techniques. This methodology can be applied to different vessels collected from a variety of donors in health or disease states to gain insights into EC transcriptional and epigenetic regulation, a pivotal aspect of endothelial cell biology.
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Affiliation(s)
| | - Yingjun Luo
- Department of Diabetes Complications and Metabolism, City of Hope
| | - Xiaofang Tang
- Department of Diabetes Complications and Metabolism, City of Hope
| | - Kiran Sriram
- Department of Diabetes Complications and Metabolism, City of Hope; Irell and Manella Graduate School of Biological Sciences, City of Hope
| | | | - Sheng Zhong
- Department of Bioengineering, University of California San Diego
| | - Zhen Bouman Chen
- Department of Diabetes Complications and Metabolism, City of Hope; Irell and Manella Graduate School of Biological Sciences, City of Hope;
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12
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Massimi L, Bianchi F, Frassanito P, Calandrelli R, Tamburrini G, Caldarelli M. Imaging in craniosynostosis: when and what? Childs Nerv Syst 2019; 35:2055-2069. [PMID: 31289853 DOI: 10.1007/s00381-019-04278-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 06/25/2019] [Indexed: 12/14/2022]
Abstract
PURPOSE Currently, the interest on craniosynostosis in the clinical practice is raised by their increased frequency and their genetic implications other than by the still existing search of less invasive surgical techniques. These reasons, together with the problem of legal issues, make the need of a definite diagnosis for a crucial problem, even in single-suture craniosynostosis (SSC). Although the diagnosis of craniosynostosis is primarily the result of physical examination, craniometrics measuring, and observation of the skull deformity, the radiological assessment currently plays an important role in the confirmation of the diagnosis, the surgical planning, and even the postoperative follow-up. On the other hand, in infants, the use of radiation or the need of sedation/anesthesia raises the problem to reduce them to minimum to preserve such a delicate category of patient from their adverse effects. METHODS, RESULTS AND CONCLUSIONS This review aims at summarizing the state of the art of the role of radiology in craniosynostosis, mainly focusing on indications and techniques, to provide an update not only to pediatric neurosurgeons or maxillofacial surgeons but also to all the other specialists involved in their management, like neonatologists, pediatricians, clinical geneticists, and pediatric neurologists.
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Affiliation(s)
- L Massimi
- Fondazione Policlinico Gemelli IRCCS, Neurochirurgia Infantile, Rome, Italy.
- Università Cattolica del Sacro Cuore, Istituto Neurochirurgia, Rome, Italy.
| | - F Bianchi
- Fondazione Policlinico Gemelli IRCCS, Neurochirurgia Infantile, Rome, Italy
| | - P Frassanito
- Fondazione Policlinico Gemelli IRCCS, Neurochirurgia Infantile, Rome, Italy
| | - R Calandrelli
- Polo scienze delle immagini, di laboratorio ed infettivologiche, Area diagnostica per immagini, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - G Tamburrini
- Fondazione Policlinico Gemelli IRCCS, Neurochirurgia Infantile, Rome, Italy
- Università Cattolica del Sacro Cuore, Istituto Neurochirurgia, Rome, Italy
| | - M Caldarelli
- Fondazione Policlinico Gemelli IRCCS, Neurochirurgia Infantile, Rome, Italy
- Università Cattolica del Sacro Cuore, Istituto Neurochirurgia, Rome, Italy
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Calandrelli R, Wu Q, Guan J, Zhong S. GITAR: An Open Source Tool for Analysis and Visualization of Hi-C Data. Genomics Proteomics Bioinformatics 2018; 16:365-372. [PMID: 30553884 PMCID: PMC6364044 DOI: 10.1016/j.gpb.2018.06.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 05/20/2018] [Accepted: 06/19/2018] [Indexed: 01/01/2023]
Abstract
Interactions between chromatin segments play a large role in functional genomic assays and developments in genomic interaction detection methods have shown interacting topological domains within the genome. Among these methods, Hi-C plays a key role. Here, we present the Genome Interaction Tools and Resources (GITAR), a software to perform a comprehensive Hi-C data analysis, including data preprocessing, normalization, and visualization, as well as analysis of topologically-associated domains (TADs). GITAR is composed of two main modules: (1) HiCtool, a Python library to process and visualize Hi-C data, including TAD analysis; and (2) processed data library, a large collection of human and mouse datasets processed using HiCtool. HiCtool leads the user step-by-step through a pipeline, which goes from the raw Hi-C data to the computation, visualization, and optimized storage of intra-chromosomal contact matrices and TAD coordinates. A large collection of standardized processed data allows the users to compare different datasets in a consistent way, while saving time to obtain data for visualization or additional analyses. More importantly, GITAR enables users without any programming or bioinformatic expertise to work with Hi-C data. GITAR is publicly available at http://genomegitar.org as an open-source software.
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Affiliation(s)
- Riccardo Calandrelli
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA.
| | - Qiuyang Wu
- Department of Computer Science and Technology, Tongji University, Shanghai 200092, China
| | - Jihong Guan
- Department of Computer Science and Technology, Tongji University, Shanghai 200092, China
| | - Sheng Zhong
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
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14
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Biase FH, Wu Q, Calandrelli R, Rivas-Astroza M, Zhou S, Chen Z, Zhong S. Rainbow-Seq: Combining Cell Lineage Tracing with Single-Cell RNA Sequencing in Preimplantation Embryos. iScience 2018; 7:16-29. [PMID: 30267678 PMCID: PMC6135740 DOI: 10.1016/j.isci.2018.08.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 08/01/2018] [Accepted: 08/10/2018] [Indexed: 02/06/2023] Open
Abstract
We developed the Rainbow-seq technology to trace cell division history and reveal single-cell transcriptomes. With distinct fluorescent protein genes as lineage markers, Rainbow-seq enables each single-cell RNA sequencing (RNA-seq) experiment to simultaneously decode the lineage marker genes and read single-cell transcriptomes. We triggered lineage tracking in each blastomere at the 2-cell stage, observed microscopically inequivalent contributions of the progeny to the two embryonic poles at the blastocyst stage, and analyzed every single cell at either 4- or 8-cell stage with deep paired-end sequencing of full-length transcripts. Although lineage difference was not marked unequivocally at a single-gene level, it became clear when the transcriptome was analyzed as a whole. Moreover, several groups of novel transcript isoforms with embedded repeat sequences exhibited lineage difference, suggesting a possible link between DNA demethylation and cell fate decision. Rainbow-seq bridged a critical gap between division history and single-cell RNA-seq assays.
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Affiliation(s)
- Fernando H Biase
- Department of Bioengineering, University of California San Diego, San Diego, CA 92130, USA
| | - Qiuyang Wu
- Department of Bioengineering, University of California San Diego, San Diego, CA 92130, USA; Department of Computer Science and Technology, Tongji University, Shanghai 201804, China
| | - Riccardo Calandrelli
- Department of Bioengineering, University of California San Diego, San Diego, CA 92130, USA
| | - Marcelo Rivas-Astroza
- Department of Bioengineering, University of California San Diego, San Diego, CA 92130, USA
| | - Shuigeng Zhou
- School of Computer Science, Fudan University, Shanghai 200433, China
| | - Zhen Chen
- Department of Diabetes Complications and Metabolism, City of Hope, Duarte, CA 91010, USA
| | - Sheng Zhong
- Department of Bioengineering, University of California San Diego, San Diego, CA 92130, USA.
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15
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Sgrigna G, Baldacchini C, Esposito R, Calandrelli R, Tiwary A, Calfapietra C. Characterization of leaf-level particulate matter for an industrial city using electron microscopy and X-ray microanalysis. Sci Total Environ 2016; 548-549:91-99. [PMID: 26802337 DOI: 10.1016/j.scitotenv.2016.01.057] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 01/11/2016] [Accepted: 01/11/2016] [Indexed: 05/22/2023]
Abstract
This study reports application of monitoring and characterization protocol for particulate matter (PM) deposited on tree leaves, using Quercus ilex as a case study species. The study area is located in the industrial city of Terni in central Italy, with high PM concentrations. Four trees were selected as representative of distinct pollution environments based on their proximity to a steel factory and a street. Wash off from leaves onto cellulose filters were characterized using scanning electron microscopy and energy dispersive X-ray spectroscopy, inferring the associations between particle sizes, chemical composition, and sampling location. Modeling of particle size distributions showed a tri-modal fingerprint, with the three modes centered at 0.6 (factory related), 1.2 (urban background), and 2.6μm (traffic related). Chemical detection identified 23 elements abundant in the PM samples. Principal component analysis recognized iron and copper as source-specific PM markers, attributed mainly to industrial and heavy traffic pollution respectively. Upscaling these results on leaf area basis provided a useful indicator for strategic evaluation of harmful PM pollutants using tree leaves.
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Affiliation(s)
- G Sgrigna
- University of Molise (UniMol), Department of Biosciences and Territory, Contrada Fonte Lappone Pesche (IS), Italy; Institute of Agro Environmental and Forest Biology, National Research Council (IBAF-CNR), Via Marconi, 2 Porano (TR) & Via Castellino 111, Napoli, Italy.
| | - C Baldacchini
- Institute of Agro Environmental and Forest Biology, National Research Council (IBAF-CNR), Via Marconi, 2 Porano (TR) & Via Castellino 111, Napoli, Italy.
| | - R Esposito
- Institute of Agro Environmental and Forest Biology, National Research Council (IBAF-CNR), Via Marconi, 2 Porano (TR) & Via Castellino 111, Napoli, Italy.
| | - R Calandrelli
- Institute of Agro Environmental and Forest Biology, National Research Council (IBAF-CNR), Via Marconi, 2 Porano (TR) & Via Castellino 111, Napoli, Italy.
| | - A Tiwary
- Faculty of Engineering and the Environment, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK.
| | - C Calfapietra
- Institute of Agro Environmental and Forest Biology, National Research Council (IBAF-CNR), Via Marconi, 2 Porano (TR) & Via Castellino 111, Napoli, Italy; Global Change Research Centre, Academy of Sciences of the Czech Republic, v. v. i., Bělidla 986/4a, 603 00 Brno, Czech Republic.
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16
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Gaudino S, Colantonio R, Schiarelli C, Martucci M, Calandrelli R, Botto A, Pileggi M, Gangemi E, Maira G, Colosimo C. Postoperative MR Imaging of Spontaneous Transdural Spinal Cord Herniation: Expected Findings and Complications. AJNR Am J Neuroradiol 2015; 37:558-64. [PMID: 26471753 DOI: 10.3174/ajnr.a4537] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 07/22/2015] [Indexed: 11/07/2022]
Abstract
BACKGROUND AND PURPOSE Spontaneous transdural spinal cord herniation is no longer a rare cause of myelopathy. The high frequency of diagnoses has led to an increase in the number of surgical procedures. The purpose of this study was to describe the spectrum of postoperative MR imaging findings concerning spontaneous transdural spinal cord herniation and to provide a practical imaging approach for differentiating expected changes and complications after an operation. MATERIALS AND METHODS We retrospectively reviewed MR images from 12 patients surgically treated for spontaneous transdural spinal cord herniation. Surgery comprised either dural defect enlargement or duraplasty procedures. Postoperative follow-ups included at least 3 (early, intermediate, late) MR imaging studies. MR images were analyzed with respect to 3 spinal compartments: intradural intramedullary, intradural extramedullary, and extradural. The meaning and reliability of changes detected on MR images were related to their radiologic and clinical evolution with time. RESULTS Spinal cord realignment has been stable since the early study, whereas spinal cord signal and thickness evolved during the following scans. Most extramedullary and extradural changes gradually reduced in later MR images. Three patients treated with dural defect enlargements experienced the onset of new neurologic symptoms. In those patients, late MR images showed extradural fluid collection and the development of pial siderosis. CONCLUSIONS Our findings demonstrate the spectrum of postoperative imaging findings in spontaneous transdural spinal cord herniation. Spinal cord thickness and signal intensity continued to evolve with time; most extramedullary postsurgical changes became stable. Changes observed in later images may be suggestive of complications.
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Affiliation(s)
- S Gaudino
- From the Institute of Radiology (S.G., R. Colantonio, C.S., M.M., R. Calandrelli, A.B., M.P., E.G., C.C.)
| | - R Colantonio
- From the Institute of Radiology (S.G., R. Colantonio, C.S., M.M., R. Calandrelli, A.B., M.P., E.G., C.C.)
| | - C Schiarelli
- From the Institute of Radiology (S.G., R. Colantonio, C.S., M.M., R. Calandrelli, A.B., M.P., E.G., C.C.)
| | - M Martucci
- From the Institute of Radiology (S.G., R. Colantonio, C.S., M.M., R. Calandrelli, A.B., M.P., E.G., C.C.)
| | - R Calandrelli
- From the Institute of Radiology (S.G., R. Colantonio, C.S., M.M., R. Calandrelli, A.B., M.P., E.G., C.C.)
| | - A Botto
- From the Institute of Radiology (S.G., R. Colantonio, C.S., M.M., R. Calandrelli, A.B., M.P., E.G., C.C.)
| | - M Pileggi
- From the Institute of Radiology (S.G., R. Colantonio, C.S., M.M., R. Calandrelli, A.B., M.P., E.G., C.C.)
| | - E Gangemi
- From the Institute of Radiology (S.G., R. Colantonio, C.S., M.M., R. Calandrelli, A.B., M.P., E.G., C.C.)
| | - G Maira
- Institute of Neurosurgery (G.M.), Catholic University of Rome, Rome, Italy
| | - C Colosimo
- From the Institute of Radiology (S.G., R. Colantonio, C.S., M.M., R. Calandrelli, A.B., M.P., E.G., C.C.)
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17
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Fundarò C, Filoni S, Giorgio V, Calabrese V, Monaco S, Onesimo R, Fantacci C, Molle F, Calandrelli R. An unusual case of neonatal cholestasis. Minerva Pediatr 2013; 65:97-101. [PMID: 23422579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Septo-optic dysplasia (SOD), otherwise called De Morsier syndrome, is a developmental anomaly of mid-line brain structures and includes optic nerve hypoplasia, absence of the septum pellucidum and hypothalamo-pituitary abnormalities). In literature an association between optic nerve hypoplasia and neonatal cholestasis is described. We report the case of a female infant with persistent cholestasis, low weight gain and onset of nystagmus that appeared at one month and a half of life. Ophthalmology evaluation showed left optic nerve hypoplasia. MRI scan of the brain demonstrated a thin left optic nerve, an ectoptic posterior pituitary gland, no visible infundibulum and lack of septum pellucidum. Endocrinological investigation showed GH and ACTH deficiency. We discuss about diagnosis and pathogenesis of De Morsier syndrome with a brief review of the literature.
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Affiliation(s)
- C Fundarò
- Pediatric Department, Sacro Cuore Catholic University, Gemelli Hospital, Rome, Italy.
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18
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Cianfoni A, Calandrelli R, De Simone M, Meduri A, Wintermark M, Colosimo C. Reduced time of arrival on brain perfusion CT in a patient with recurrent cryptogenic stroke: an indirect sign of a patent foramen ovale. Neuroradiology 2008; 50:613-5. [DOI: 10.1007/s00234-008-0414-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2008] [Accepted: 05/06/2008] [Indexed: 11/29/2022]
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