1
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Walter RM, Majumder K, Kalejta RF. ATRX restricts Human Cytomegalovirus (HCMV) viral DNA replication through heterochromatinization and minimizes unpackaged viral genomes. PLoS Pathog 2024; 20:e1012516. [PMID: 39236084 DOI: 10.1371/journal.ppat.1012516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 08/20/2024] [Indexed: 09/07/2024] Open
Abstract
ATRX limits the accumulation of human cytomegalovirus (HCMV) Immediate Early (IE) proteins at the start of productive, lytic infections, and thus is a part of the cell-intrinsic defenses against infecting viruses. ATRX is a chromatin remodeler and a component of a histone chaperone complex. Therefore, we hypothesized ATRX would inhibit the transcription of HCMV IE genes by increasing viral genome heterochromatinization and decreasing its accessibility. To test this hypothesis, we quantitated viral transcription and genome structure in cells replete with or depleted of ATRX. We found ATRX did indeed limit viral IE transcription, increase viral genome chromatinization, and decrease viral genome accessibility. The inhibitory effects of ATRX extended to Early (E) and Late (L) viral protein accumulation, viral DNA replication, and progeny virion output. However, we found the negative effects of ATRX on HCMV viral DNA replication were independent of its effects on viral IE and E protein accumulation but correlated with viral genome heterochromatinization. Interestingly, the increased number of viral genomes synthesized in ATRX-depleted cells were not efficiently packaged, indicating the ATRX-mediated restriction to HCMV viral DNA replication may benefit productive infection by increasing viral fitness. Our work mechanistically describes the antiviral function of ATRX and introduces a novel, pro-viral role for this protein, perhaps explaining why, unlike during infections with other herpesviruses, it is not directly targeted by a viral countermeasure in HCMV infected cells.
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Affiliation(s)
- Ryan M Walter
- Institute for Molecular Virology and McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Kinjal Majumder
- Institute for Molecular Virology and McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Robert F Kalejta
- Institute for Molecular Virology and McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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2
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Patty B, Jordan C, Lardo S, Troy K, Hainer S. H3.3K122A results in a neomorphic phenotype in mouse embryonic stem cells. RESEARCH SQUARE 2024:rs.3.rs-4824795. [PMID: 39257982 PMCID: PMC11384023 DOI: 10.21203/rs.3.rs-4824795/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Abstract
The histone variant H3.3 acts in coordination with histone posttranslational modifications and other chromatin features to facilitate appropriate transcription. Canonical histone H3 and histone variant H3.3 are post-translationally modified with the genomic distribution of these marks denoting different features and with more recent evidence suggesting that these modifications may influence transcription. While the majority of posttranslational modifications occur on histone tails, there are defined modifications within the globular domain, such as acetylation of H3K122/H3.3K122. To understand the function of the residue H3.3K122 in transcriptional regulation, we attempted to generate H3.3K122A mouse embryonic stem (mES) cells but were unsuccessful. Through multi-omic profiling of mutant cell lines harboring two or three of four H3.3 targeted alleles, we have uncovered that H3.3K122A is neomorphic and results in lethality. This is surprising as prior studies demonstrate H3.3-null mES cells are viable and pluripotent, albeit with reduced differentiation capacity. Together, these studies have uncovered a novel dependence of a globular domain residue of H3.3 for viability and broadened our understanding of how histone variants contribute to transcription regulation and pluripotency in mES cells.
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3
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Graham MK, Xu B, Davis C, Meeker AK, Heaphy CM, Yegnasubramanian S, Dyer MA, Zeineldin M. The TERT Promoter is Polycomb-Repressed in Neuroblastoma Cells with Long Telomeres. CANCER RESEARCH COMMUNICATIONS 2024; 4:1533-1547. [PMID: 38837897 PMCID: PMC11188873 DOI: 10.1158/2767-9764.crc-22-0287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 05/04/2023] [Accepted: 05/22/2024] [Indexed: 06/07/2024]
Abstract
Acquiring a telomere maintenance mechanism is a hallmark of high-risk neuroblastoma and commonly occurs by expressing telomerase (TERT). Telomerase-negative neuroblastoma has long telomeres and utilizes the telomerase-independent alternative lengthening of telomeres (ALT) mechanism. Conversely, no discernable telomere maintenance mechanism is detected in a fraction of neuroblastoma with long telomeres. Here, we show, unlike most cancers, DNA of the TERT promoter is broadly hypomethylated in neuroblastoma. In telomerase-positive neuroblastoma cells, the hypomethylated DNA promoter is approximately 1.5 kb. The TERT locus shows active chromatin marks with low enrichment for the repressive mark, H3K27me3. MYCN, a commonly amplified oncogene in neuroblstoma, binds to the promoter and induces TERT expression. Strikingly, in neuroblastoma with long telomeres, the hypomethylated region spans the entire TERT locus, including multiple nearby genes with enrichment for the repressive H3K27me3 chromatin mark. Furthermore, subtelomeric regions showed enrichment of repressive chromatin marks in neuroblastomas with long telomeres relative to those with short telomeres. These repressive marks were even more evident at the genic loci, suggesting a telomere position effect (TPE). Inhibiting H3K27 methylation by three different EZH2 inhibitors induced the expression of TERT in cell lines with long telomeres and H3K27me3 marks in the promoter region. EZH2 inhibition facilitated MYCN binding to the TERT promoter in neuroblastoma cells with long telomeres. Taken together, these data suggest that epigenetic regulation of TERT expression differs in neuroblastoma depending on the telomere maintenance status, and H3K27 methylation is important in repressing TERT expression in neuroblastoma with long telomeres. SIGNIFICANCE The epigenetic landscape of the TERT locus is unique in neuroblastoma. The DNA at the TERT locus, unlike other cancer cells and similar to normal cells, are hypomethylated in telomerase-positive neuroblastoma cells. The TERT locus is repressed by polycomb repressive complex-2 complex in neuroblastoma cells that have long telomeres and do not express TERT. Long telomeres in neuroblastoma cells are also associated with repressive chromatin states at the chromosomal termini, suggesting TPE.
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Affiliation(s)
- Mindy K. Graham
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Urology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Christine Davis
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Alan K. Meeker
- Department of Urology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Christopher M. Heaphy
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Srinivasan Yegnasubramanian
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Urology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Michael A. Dyer
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee
- Howard Hughes Medical Institute, Chevy Chase, Maryland
- Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, Tennessee
| | - Maged Zeineldin
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
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4
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Zhao Y, Chen Y, Liu R, Liu M, You N, Zhao K, Zhang J, Xu B. Knockdown of ATRX enhances radiosensitivity in glioblastoma. Chin Neurosurg J 2024; 10:19. [PMID: 38898533 PMCID: PMC11186225 DOI: 10.1186/s41016-024-00371-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 06/03/2024] [Indexed: 06/21/2024] Open
Abstract
BACKGROUND Glioblastoma are highly malignant type of primary brain tumors. Treatment for glioblastoma multiforme (GBM) generally involves surgery combined with chemotherapy and radiotherapy. However, the development of tumoral chemo- and radioresistance induces complexities in clinical practice. Multiple signaling pathways are known to be involved in radiation-induced cell survival. However, the role of alpha-thalassemia X-linked mutant retardation syndrome (ATRX), a chromatin remodeling protein, in GBM radioresistance remains unclear. METHODS In the present study, the ATRX mutation rate in patients with glioma was obtained from The Cancer Genome Atlas, while its expression analyzed using bioinformatics. Datasets were also obtained from the Gene Expression Omnibus, and ATRX expression levels following irradiation of GBM were determined. The effects of ATRX on radiosensitivity were investigated using a knockdown assays. RESULTS The present study demonstrated that the ATRX mutation rate in patients with GBM was significantly lower than that in patients with low-grade glioma, and that patients harboring an ATRX mutation exhibited a prolonged survival, compared with to those harboring the wild-type gene. Single-cell RNA sequencing demonstrated that ATRX counts increased 2 days after irradiation, with ATRX expression levels also increasing in U-251MG radioresistant cells. Moreover, the results of in vitro irradiation assays revealed that ATRX expression was increased in U-251MG cells, while ATRX knockdown was associated with increased levels of radiosensitivity. CONCLUSIONS High ATRX expression levels in primary GBM may contribute to high levels of radioresistance. Thus ATRX is a potential target for overcoming the radioresistance in GBM.
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Affiliation(s)
- Yue Zhao
- Medical School of Chinese PLA, Beijing, 100853, China
- Department of Emergency Medicine, Hainan Hospital of Chinese PLA General Hospital, Sanya, 572014, Hainan, China
- Department of Neurosurgery, The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Yifei Chen
- Center of Cognition and Brain Science, Beijing Institute of Basic Medical Sciences, Beijing, 100850, China
| | - Ruoyu Liu
- Department of Neurosurgery, The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Minghang Liu
- Medical School of Chinese PLA, Beijing, 100853, China
- Department of Neurosurgery, The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Na You
- Medical School of Chinese PLA, Beijing, 100853, China
- Department of Neurosurgery, The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Kai Zhao
- Department of Neurosurgery, The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Jiashu Zhang
- Department of Neurosurgery, The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China.
| | - Bainan Xu
- Department of Neurosurgery, The First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China.
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5
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Waitkus MS, Erman EN, Reitman ZJ, Ashley DM. Mechanisms of telomere maintenance and associated therapeutic vulnerabilities in malignant gliomas. Neuro Oncol 2024; 26:1012-1024. [PMID: 38285162 PMCID: PMC11145458 DOI: 10.1093/neuonc/noae016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Indexed: 01/30/2024] Open
Abstract
A majority of cancers (~85%) activate the enzyme telomerase to maintain telomere length over multiple rounds of cellular division. Telomerase-negative cancers activate a distinct, telomerase-independent mechanism of telomere maintenance termed alternative lengthening of telomeres (ALT). ALT uses homologous recombination to maintain telomere length and exhibits features of break-induced DNA replication. In malignant gliomas, the activation of either telomerase or ALT is nearly ubiquitous in pediatric and adult tumors, and the frequency with which these distinct telomere maintenance mechanisms (TMMs) is activated varies according to genetically defined glioma subtypes. In this review, we summarize the current state of the field of TMMs and their relevance to glioma biology and therapy. We review the genetic alterations and molecular mechanisms leading to telomerase activation or ALT induction in pediatric and adult gliomas. With this background, we review emerging evidence on strategies for targeting TMMs for glioma therapy. Finally, we comment on critical gaps and issues for moving the field forward to translate our improved understanding of glioma telomere maintenance into better therapeutic strategies for patients.
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Affiliation(s)
- Matthew S Waitkus
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Elise N Erman
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Zachary J Reitman
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina, USA
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina, USA
| | - David M Ashley
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, North Carolina, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, North Carolina, USA
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6
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Fang Y, Barrows D, Dabas Y, Carroll T, Singer S, Tap W, Nacev B. ATRX guards against aberrant differentiation in mesenchymal progenitor cells. Nucleic Acids Res 2024; 52:4950-4968. [PMID: 38477352 PMCID: PMC11109985 DOI: 10.1093/nar/gkae160] [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: 09/20/2023] [Revised: 01/19/2024] [Accepted: 03/05/2024] [Indexed: 03/14/2024] Open
Abstract
Alterations in the tumor suppressor ATRX are recurrently observed in mesenchymal neoplasms. ATRX has multiple epigenetic functions including heterochromatin formation and maintenance and regulation of transcription through modulation of chromatin accessibility. Here, we show in murine mesenchymal progenitor cells (MPCs) that Atrx deficiency aberrantly activated mesenchymal differentiation programs. This includes adipogenic pathways where ATRX loss induced expression of adipogenic transcription factors and enhanced adipogenic differentiation in response to differentiation stimuli. These changes are linked to loss of heterochromatin near mesenchymal lineage genes together with increased chromatin accessibility and gains of active chromatin marks. We additionally observed depletion of H3K9me3 at transposable elements, which are derepressed including near mesenchymal genes where they could serve as regulatory elements. Finally, we demonstrated that loss of ATRX in a mesenchymal malignancy, undifferentiated pleomorphic sarcoma, results in similar epigenetic disruption and de-repression of transposable elements. Together, our results reveal a role for ATRX in maintaining epigenetic states and transcriptional repression in mesenchymal progenitors and tumor cells and in preventing aberrant differentiation in the progenitor context.
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Affiliation(s)
- Yan Fang
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY10065, USA
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA
| | - Douglas Barrows
- Bioinformatics Resource Center, The Rockefeller University, New York, NY10065, USA
| | - Yakshi Dabas
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA
| | - Thomas S Carroll
- Bioinformatics Resource Center, The Rockefeller University, New York, NY10065, USA
| | - Sam Singer
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY10065, USA
| | - William D Tap
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY10065, USA
| | - Benjamin A Nacev
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15213, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA
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7
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León NY, Le TNU, Garvie A, Wong LH, Bagheri-Fam S, Harley VR. Y chromosome damage underlies testicular abnormalities in ATR-X syndrome. iScience 2024; 27:109629. [PMID: 38616920 PMCID: PMC11015497 DOI: 10.1016/j.isci.2024.109629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/27/2024] [Accepted: 03/26/2024] [Indexed: 04/16/2024] Open
Abstract
ATR-X (alpha thalassemia, mental retardation, X-linked) syndrome features genital and testicular abnormalities including atypical genitalia and small testes with few seminiferous tubules. Our mouse model recapitulated the testicular defects when Atrx was deleted in Sertoli cells (ScAtrxKO) which displayed G2/M arrest and apoptosis. Here, we investigated the mechanisms underlying these defects. In control mice, Sertoli cells contain a single novel "GATA4 PML nuclear body (NB)" that contained the transcription factor GATA4, ATRX, DAXX, HP1α, and PH3 and co-localized with the Y chromosome short arm (Yp). ScAtrxKO mice contain single giant GATA4 PML-NBs with frequent DNA double-strand breaks (DSBs) in G2/M-arrested apoptotic Sertoli cells. HP1α and PH3 were absent from giant GATA4 PML-NBs indicating a failure in heterochromatin formation and chromosome condensation. Our data suggest that ATRX protects a Yp region from DNA damage, thereby preventing Sertoli cell death. We discuss Y chromosome damage/decondensation as a mechanism for testicular failure.
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Affiliation(s)
- Nayla Y. León
- Hudson Institute of Medical Research, Melbourne, VIC 3168, Australia
- Department of Molecular & Translational Science, Monash University, Melbourne, VIC 3168, Australia
| | - Thanh Nha Uyen Le
- Hudson Institute of Medical Research, Melbourne, VIC 3168, Australia
- Department of Molecular & Translational Science, Monash University, Melbourne, VIC 3168, Australia
| | - Andrew Garvie
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - Lee H. Wong
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - Stefan Bagheri-Fam
- Hudson Institute of Medical Research, Melbourne, VIC 3168, Australia
- Department of Molecular & Translational Science, Monash University, Melbourne, VIC 3168, Australia
| | - Vincent R. Harley
- Hudson Institute of Medical Research, Melbourne, VIC 3168, Australia
- Department of Molecular & Translational Science, Monash University, Melbourne, VIC 3168, Australia
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8
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Tomoszková S, Škarda J, Lipina R. Potential Diagnostic and Clinical Significance of Selected Genetic Alterations in Glioblastoma. Int J Mol Sci 2024; 25:4438. [PMID: 38674026 PMCID: PMC11050250 DOI: 10.3390/ijms25084438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/08/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Glioblastoma is currently considered the most common and, unfortunately, also the most aggressive primary brain tumor, with the highest morbidity and mortality rates. The average survival of patients diagnosed with glioblastoma is 14 months, and only 2% of patients survive 3 years after surgery. Based on our clinical experience and knowledge from extensive clinical studies, survival is mainly related to the molecular biological properties of glioblastoma, which are of interest to the general medical community. Our study examined a total of 71 retrospective studies published from 2016 through 2022 and available on PubMed that deal with mutations of selected genes in the pathophysiology of GBM. In conclusion, we can find other mutations within a given gene group that have different effects on the prognosis and quality of survival of a patient with glioblastoma. These mutations, together with the associated mutations of other genes, as well as intratumoral heterogeneity itself, offer enormous potential for further clinical research and possible application in therapeutic practice.
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Affiliation(s)
- Silvia Tomoszková
- Neurosurgery Clinic, University Hospital Ostrava, 17. listopadu 1790/5, 708 00 Ostrava, Czech Republic;
- Medical Faculty, University of Ostrava, Syllabova 19, 703 00 Ostrava, Czech Republic;
| | - Jozef Škarda
- Medical Faculty, University of Ostrava, Syllabova 19, 703 00 Ostrava, Czech Republic;
- Institute of Molecular and Clinical Pathology and Medical Genetics, University Hospital Ostrava, 17. listopadu 1790/5, 708 00 Ostrava, Czech Republic
| | - Radim Lipina
- Neurosurgery Clinic, University Hospital Ostrava, 17. listopadu 1790/5, 708 00 Ostrava, Czech Republic;
- Medical Faculty, University of Ostrava, Syllabova 19, 703 00 Ostrava, Czech Republic;
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9
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Patty BJ, Hainer SJ. Widespread impact of nucleosome remodelers on transcription at cis-regulatory elements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.12.589208. [PMID: 38659863 PMCID: PMC11042195 DOI: 10.1101/2024.04.12.589208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Nucleosome remodeling complexes and other regulatory factors work in concert to build a chromatin environment that directs the expression of a distinct set of genes in each cell using cis-regulatory elements (CREs), such as promoters and enhancers, that drive transcription of both mRNAs and CRE-associated non-coding RNAs (ncRNAs). Two classes of CRE-associated ncRNAs include upstream antisense RNAs (uaRNAs), which are transcribed divergently from a shared mRNA promoter, and enhancer RNAs (eRNAs), which are transcribed bidirectionally from active enhancers. The complicated network of CRE regulation by nucleosome remodelers remains only partially explored, with a focus on a select, limited number of remodelers. We endeavored to elucidate a remodeler-based regulatory network governing CRE-associated transcription (mRNA, eRNA, and uaRNA) in murine embryonic stem (ES) cells to test the hypothesis that many SNF2-family nucleosome remodelers collaborate to regulate the coding and non-coding transcriptome via alteration of underlying nucleosome architecture. Using depletion followed by transient transcriptome sequencing (TT-seq), we identified thousands of misregulated mRNAs and CRE-associated ncRNAs across the remodelers examined, identifying novel contributions by understudied remodelers in the regulation of coding and noncoding transcription. Our findings suggest that mRNA and eRNA transcription are coordinately co-regulated, while mRNA and uaRNAs sharing a common promoter are independently regulated. Subsequent mechanistic studies suggest that while remodelers SRCAP and CHD8 modulate transcription through classical mechanisms such as transcription factors and histone variants, a broad set of remodelers including SMARCAL1 indirectly contribute to transcriptional regulation through maintenance of genomic stability and proper Integrator complex localization. This study systematically examines the contribution of SNF2-remodelers to the CRE-associated transcriptome, identifying at least two classes for remodeler action.
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Affiliation(s)
- Benjamin J. Patty
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA USA
| | - Sarah J. Hainer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA USA
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA USA
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10
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Chen P, Li G, Li W. Nucleosome Dynamics Derived at the Single-Molecule Level Bridges Its Structures and Functions. JACS AU 2024; 4:866-876. [PMID: 38559720 PMCID: PMC10976579 DOI: 10.1021/jacsau.3c00658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 04/04/2024]
Abstract
Nucleosome, the building block of chromatin, plays pivotal roles in all DNA-related processes. While cryogenic-electron microscopy (cryo-EM) has significantly advanced our understanding of nucleosome structures, the emerging field of single-molecule force spectroscopy is illuminating their dynamic properties. This technique is crucial for revealing how nucleosome behavior is influenced by chaperones, remodelers, histone variants, and post-translational modifications, particularly in their folding and unfolding mechanisms under tension. Such insights are vital for deciphering the complex interplay in nucleosome assembly and structural regulation, highlighting the nucleosome's versatility in response to DNA activities. In this Perspective, we aim to consolidate the latest advancements in nucleosome dynamics, with a special focus on the revelations brought forth by single-molecule manipulation. Our objective is to highlight the insights gained from studying nucleosome dynamics through this innovative approach, emphasizing the transformative impact of single-molecule manipulation techniques in the field of chromatin research.
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Affiliation(s)
- Ping Chen
- National
Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation
and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P. R. China
- Department
of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory
for Tumor Invasion and Metastasis, Capital
Medical University, Beijing 100069, P. R. China
| | - Guohong Li
- National
Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation
and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P. R. China
- University
of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Wei Li
- National
Laboratory of Biomacromolecules and Key Laboratory of Epigenetic Regulation
and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P. R. China
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11
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Lämmerhirt L, Kappelmann-Fenzl M, Fischer S, Meier P, Staebler S, Kuphal S, Bosserhoff AK. Loss of miR-101-3p in melanoma stabilizes genomic integrity, leading to cell death prevention. Cell Mol Biol Lett 2024; 29:29. [PMID: 38431560 PMCID: PMC10909299 DOI: 10.1186/s11658-024-00552-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 02/21/2024] [Indexed: 03/05/2024] Open
Abstract
Malignant melanoma remains the most lethal form of skin cancer, exhibiting poor prognosis after forming distant metastasis. Owing to their potential tumor-suppressive properties by regulating oncogenes and tumor suppressor genes, microRNAs are important player in melanoma development and progression. We defined the loss of miR-101-3p expression in melanoma cells compared with melanocytes and melanoblast-related cells as an early event in tumor development and aimed to understand the tumor suppressive role of miR-101-3p and its regulation of important cellular processes. Reexpression of miR-101-3p resulted in inhibition of proliferation, increase in DNA damage, and induction of apoptosis. We further determined the nuclear structure protein Lamin B1, which influences nuclear processes and heterochromatin structure, ATRX, CASP3, and PARP as an important direct target of miR-101-3p. RNA sequencing and differential gene expression analysis after miR-101-3p reexpression supported our findings and the importance of loss of mir-101-3p for melanoma progression. The validated functional effects are related to genomic instability, as recent studies suggest miRNAs plays a key role in mediating this cellular process. Therefore, we concluded that miR-101-3p reexpression increases the genomic instability, leading to irreversible DNA damage, which leads to apoptosis induction. Our findings suggest that the loss of miR-101-3p in melanoma serves as an early event in melanoma progression by influencing the genomic integrity to maintain the increased bioenergetic demand.
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Affiliation(s)
- Lisa Lämmerhirt
- Institute of Biochemistry, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Fahrstraße 17, 91054, Erlangen, Germany
| | - Melanie Kappelmann-Fenzl
- Faculty of Computer Science, Deggendorf Institute of Technology, Dieter-Görlitz-Platz 1, 94469, Deggendorf, Germany
| | - Stefan Fischer
- Faculty of Computer Science, Deggendorf Institute of Technology, Dieter-Görlitz-Platz 1, 94469, Deggendorf, Germany
| | - Paula Meier
- Institute of Biochemistry, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Fahrstraße 17, 91054, Erlangen, Germany
- Julius-Maximilians-University Würzburg (JMU), Sanderring 2, 97070, Würzburg, Germany
| | - Sebastian Staebler
- Institute of Biochemistry, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Fahrstraße 17, 91054, Erlangen, Germany
| | - Silke Kuphal
- Institute of Biochemistry, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Fahrstraße 17, 91054, Erlangen, Germany
| | - Anja-Katrin Bosserhoff
- Institute of Biochemistry, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Fahrstraße 17, 91054, Erlangen, Germany.
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12
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Paniri A, Hosseini MM, Akhavan-Niaki H. Alzheimer's Disease-Related Epigenetic Changes: Novel Therapeutic Targets. Mol Neurobiol 2024; 61:1282-1317. [PMID: 37700216 DOI: 10.1007/s12035-023-03626-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 08/30/2023] [Indexed: 09/14/2023]
Abstract
Aging is a significant risk factor for Alzheimer's disease (AD), although the precise mechanism and molecular basis of AD are not yet fully understood. Epigenetic mechanisms, such as DNA methylation and hydroxymethylation, mitochondrial DNA methylation, histone modifications, and non-coding RNAs (ncRNAs), play a role in regulating gene expression related to neuron plasticity and integrity, which are closely associated with learning and memory development. This review describes the impact of dynamic and reversible epigenetic modifications and factors on memory and plasticity throughout life, emphasizing their potential as target for therapeutic intervention in AD. Additionally, we present insight from postmortem and animal studies on abnormal epigenetics regulation in AD, as well as current strategies aiming at targeting these factors in the context of AD therapy.
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Affiliation(s)
- Alireza Paniri
- Genetics Department, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran
- Zoonoses Research Center, Pasteur Institute of Iran, Amol, Iran
| | | | - Haleh Akhavan-Niaki
- Genetics Department, Faculty of Medicine, Babol University of Medical Sciences, Babol, Iran.
- Zoonoses Research Center, Pasteur Institute of Iran, Amol, Iran.
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13
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Schmidt A, Zhang H, Schmitt S, Rausch C, Popp O, Chen J, Cmarko D, Butter F, Dittmar G, Lermyte F, Cardoso MC. The Proteomic Composition and Organization of Constitutive Heterochromatin in Mouse Tissues. Cells 2024; 13:139. [PMID: 38247831 PMCID: PMC10814525 DOI: 10.3390/cells13020139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/13/2023] [Accepted: 01/09/2024] [Indexed: 01/23/2024] Open
Abstract
Pericentric heterochromatin (PCH) forms spatio-temporarily distinct compartments and affects chromosome organization and stability. Albeit some of its components are known, an elucidation of its proteome and how it differs between tissues in vivo is lacking. Here, we find that PCH compartments are dynamically organized in a tissue-specific manner, possibly reflecting compositional differences. As the mouse brain and liver exhibit very different PCH architecture, we isolated native PCH fractions from these tissues, analyzed their protein compositions using quantitative mass spectrometry, and compared them to identify common and tissue-specific PCH proteins. In addition to heterochromatin-enriched proteins, the PCH proteome includes RNA/transcription and membrane-related proteins, which showed lower abundance than PCH-enriched proteins. Thus, we applied a cut-off of PCH-unspecific candidates based on their abundance and validated PCH-enriched proteins. Amongst the hits, MeCP2 was classified into brain PCH-enriched proteins, while linker histone H1 was not. We found that H1 and MeCP2 compete to bind to PCH and regulate PCH organization in opposite ways. Altogether, our workflow of unbiased PCH isolation, quantitative mass spectrometry, and validation-based analysis allowed the identification of proteins that are common and tissue-specifically enriched at PCH. Further investigation of selected hits revealed their opposing role in heterochromatin higher-order architecture in vivo.
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Affiliation(s)
- Annika Schmidt
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany (S.S.)
| | - Hui Zhang
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany (S.S.)
| | - Stephanie Schmitt
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany (S.S.)
| | - Cathia Rausch
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany (S.S.)
| | - Oliver Popp
- Proteomics Platform, Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Jiaxuan Chen
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Dusan Cmarko
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00 Prague, Czech Republic
| | - Falk Butter
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Gunnar Dittmar
- Proteomics Platform, Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Frederik Lermyte
- Clemens-Schöpf Institute of Organic Chemistry and Biochemistry, Department of Chemistry, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - M. Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany (S.S.)
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14
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Huang R, Feng Y, Gao Z, Ahmed A, Zhang W. The Epigenomic Features and Potential Functions of PEG- and PDS-Favorable DNA G-Quadruplexes in Rice. Int J Mol Sci 2024; 25:634. [PMID: 38203805 PMCID: PMC10779103 DOI: 10.3390/ijms25010634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/26/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
A G-quadruplex (G4) is a typical non-B DNA structure and involved in various DNA-templated events in eukaryotic genomes. PEG and PDS chemicals have been widely applied for promoting the folding of in vivo or in vitro G4s. However, how PEG and PDS preferentially affect a subset of G4 formation genome-wide is still largely unknown. We here conducted a BG4-based IP-seq in vitro under K++PEG or K++PDS conditions in the rice genome. We found that PEG-favored IP-G4s+ have distinct sequence features, distinct genomic distributions and distinct associations with TEGs, non-TEGs and subtypes of TEs compared to PDS-favored ones. Strikingly, PEG-specific IP-G4s+ are associated with euchromatin with less enrichment levels of DNA methylation but with more enriched active histone marks, while PDS-specific IP-G4s+ are associated with heterochromatin with higher enrichment levels of DNA methylation and repressive marks. Moreover, we found that genes with PEG-specific IP-G4s+ are more expressed than those with PDS-specific IP-G4s+, suggesting that PEG/PDS-specific IP-G4s+ alone or coordinating with epigenetic marks are involved in the regulation of the differential expression of related genes, therefore functioning in distinct biological processes. Thus, our study provides new insights into differential impacts of PEG and PDS on G4 formation, thereby advancing our understanding of G4 biology.
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Affiliation(s)
| | | | | | | | - Wenli Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China; (R.H.); (Y.F.); (Z.G.); (A.A.)
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15
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Modica R, Liccardi A, Minotta R, Cannavale G, Benevento E, Colao A. Current understanding of pathogenetic mechanisms in neuroendocrine neoplasms. Expert Rev Endocrinol Metab 2024; 19:49-61. [PMID: 37936421 DOI: 10.1080/17446651.2023.2279540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 11/01/2023] [Indexed: 11/09/2023]
Abstract
INTRODUCTION Despite the fact that important advances in research on neuroendocrine neoplasms (NENs) have been made, consistent data about their pathogenetic mechanism are still lacking. Furthermore, different primary sites may recognize different pathogenetic mechanisms. AREAS COVERED This review analyzes the possible biological and molecular mechanisms that may lead to NEN onset and progression in different organs. Through extensive research of the literature, risk factors including hypercholesterolemia, inflammatory bowel disease, chronic atrophic gastritis are evaluated as potential pathogenetic mechanisms. Consistent evidence is available regarding sporadic gastric NENs and MEN1 related duodenopancreatic NENs precursor lesions, and genetic-epigenetic mutations may play a pivotal role in tumor development and bone metastases onset. In lung neuroendocrine tumors (NETs), diffuse proliferation of neuroendocrine cells on the bronchial wall (DIPNECH) has been proposed as a premalignant lesion, while in lung neuroendocrine carcinoma nicotine and smoke could be responsible for carcinogenic processes. Also, rare primary NENs such as thymic (T-NENs) and Merkel cell carcinoma (MCC) have been analyzed, finding different possible pathogenetic mechanisms. EXPERT OPINION New technologies in genomics and epigenomics are bringing new light to the pathogenetic landscape of NENs, but further studies are needed to improve both prevention and treatment in these heterogeneous neoplasms.
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Affiliation(s)
- Roberta Modica
- Endocrinology Unit, Department of Clinical Medicine and Surgery, Federico II University, Naples, Napoli, Italy
| | - Alessia Liccardi
- Endocrinology Unit, Department of Clinical Medicine and Surgery, Federico II University, Naples, Napoli, Italy
| | - Roberto Minotta
- Endocrinology Unit, Department of Clinical Medicine and Surgery, Federico II University, Naples, Napoli, Italy
| | - Giuseppe Cannavale
- Endocrinology Unit, Department of Clinical Medicine and Surgery, Federico II University, Naples, Napoli, Italy
| | - Elio Benevento
- Endocrinology Unit, Department of Clinical Medicine and Surgery, Federico II University, Naples, Napoli, Italy
| | - Annamaria Colao
- Endocrinology Unit, Department of Clinical Medicine and Surgery, Federico II University, Naples, Napoli, Italy
- UNESCO Chair "Education for Health and Sustainable Development, " Federico II University, Naples, Italy
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16
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Kumar N, Sethi G. Telomerase and hallmarks of cancer: An intricate interplay governing cancer cell evolution. Cancer Lett 2023; 578:216459. [PMID: 37863351 DOI: 10.1016/j.canlet.2023.216459] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/02/2023] [Accepted: 10/17/2023] [Indexed: 10/22/2023]
Abstract
Transformed cells must acquire specific characteristics to be malignant. Weinberg and Hanahan characterize these characteristics as cancer hallmarks. Though these features are independently driven, substantial signaling crosstalk in transformed cells efficiently promotes these feature acquisitions. Telomerase is an enzyme complex that maintains telomere length. However, its main component, Telomere reverse transcriptase (TERT), has been found to interact with various signaling molecules like cMYC, NF-kB, BRG1 and cooperate in transcription and metabolic reprogramming, acting as a strong proponent of malignant features such as cell death resistance, sustained proliferation, angiogenesis activation, and metastasis, among others. It allows cells to avoid replicative senescence and achieve endless replicative potential. This review summarizes both the canonical and noncanonical functions of TERT and discusses how they promote cancer hallmarks. Understanding the role of Telomerase in promoting cancer hallmarks provides vital insight into the underlying mechanism of cancer genesis and progression and telomerase intervention as a possible therapeutic target for cancer treatment. More investigation into the precise molecular mechanisms of telomerase-mediated impacts on cancer hallmarks will contribute to developing more focused and customized cancer treatment methods.
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Affiliation(s)
- Naveen Kumar
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore, 138673, Singapore
| | - Gautam Sethi
- Department of Pharmacology and NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117600, Singapore.
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17
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Melnikova L, Golovnin A. Multiple Roles of dXNP and dADD1- Drosophila Orthologs of ATRX Chromatin Remodeler. Int J Mol Sci 2023; 24:16486. [PMID: 38003676 PMCID: PMC10671109 DOI: 10.3390/ijms242216486] [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: 10/09/2023] [Revised: 11/11/2023] [Accepted: 11/16/2023] [Indexed: 11/26/2023] Open
Abstract
The Drosophila melanogaster dADD1 and dXNP proteins are orthologues of the ADD and SNF2 domains of the vertebrate ATRX (Alpha-Thalassemia with mental Retardation X-related) protein. ATRX plays a role in general molecular processes, such as regulating chromatin status and gene expression, while dADD1 and dXNP have similar functions in the Drosophila genome. Both ATRX and dADD1/dXNP interact with various protein partners and participate in various regulatory complexes. Disruption of ATRX expression in humans leads to the development of α-thalassemia and cancer, especially glioma. However, the mechanisms that allow ATRX to regulate various cellular processes are poorly understood. Studying the functioning of dADD1/dXNP in the Drosophila model may contribute to understanding the mechanisms underlying the multifunctional action of ATRX and its connection with various cellular processes. This review provides a brief overview of the currently available information in mammals and Drosophila regarding the roles of ATRX, dXNP, and dADD1. It discusses possible mechanisms of action of complexes involving these proteins.
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Affiliation(s)
- Larisa Melnikova
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
| | - Anton Golovnin
- Department of Drosophila Molecular Genetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
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18
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Quesnel KM, Martin-Kenny N, Bérubé NG. A mouse model of ATRX deficiency with cognitive deficits and autistic traits. J Neurodev Disord 2023; 15:39. [PMID: 37957569 PMCID: PMC10644498 DOI: 10.1186/s11689-023-09508-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 11/01/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND ATRX is an ATP-dependent chromatin remodeling protein with essential roles in safeguarding genome integrity and modulating gene expression. Deficiencies in this protein cause ATR-X syndrome, a condition characterized by intellectual disability and an array of developmental abnormalities, including features of autism. Previous studies demonstrated that deleting ATRX in mouse forebrain excitatory neurons postnatally resulted in male-specific memory deficits, but no apparent autistic-like behaviours. METHODS We generated mice with an earlier embryonic deletion of ATRX in forebrain excitatory neurons and characterized their behaviour using a series of memory and autistic-related paradigms. RESULTS We found that mutant mice displayed a broader spectrum of impairments, including fear memory, decreased anxiety-like behaviour, hyperactivity, as well as self-injurious and repetitive grooming. Sex-specific alterations were also observed, including male-specific aggression, sensory gating impairments, and decreased social memory. CONCLUSIONS Collectively, the findings indicate that early developmental abnormalities arising from ATRX deficiency in forebrain excitatory neurons contribute to the presentation of fear memory deficits as well as autistic-like behaviours.
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Affiliation(s)
- Katherine M Quesnel
- Department of Anatomy & Cell Biology, Western University, London, Canada
- Department of Paediatrics, Western University, London, Canada
- Division of Genetics & Development, Children's Health Research Institute, London, ON, Canada
| | - Nicole Martin-Kenny
- Department of Anatomy & Cell Biology, Western University, London, Canada
- Department of Paediatrics, Western University, London, Canada
- Division of Genetics & Development, Children's Health Research Institute, London, ON, Canada
| | - Nathalie G Bérubé
- Department of Anatomy & Cell Biology, Western University, London, Canada.
- Department of Paediatrics, Western University, London, Canada.
- Division of Genetics & Development, Children's Health Research Institute, London, ON, Canada.
- Department of Oncology, Western University, London, Canada.
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19
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Park S, Lee J, Ahn KS, Shim HW, Yoon J, Hyun J, Lee JH, Jang S, Yoo KH, Jang Y, Kim T, Kim HK, Lee MR, Jang J, Shim H, Kim H. Cyclic Stretch Promotes Cellular Reprogramming Process through Cytoskeletal-Nuclear Mechano-Coupling and Epigenetic Modification. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303395. [PMID: 37727069 PMCID: PMC10646259 DOI: 10.1002/advs.202303395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/27/2023] [Indexed: 09/21/2023]
Abstract
Advancing the technologies for cellular reprogramming with high efficiency has significant impact on regenerative therapy, disease modeling, and drug discovery. Biophysical cues can tune the cell fate, yet the precise role of external physical forces during reprogramming remains elusive. Here the authors show that temporal cyclic-stretching of fibroblasts significantly enhances the efficiency of induced pluripotent stem cell (iPSC) production. Generated iPSCs are proven to express pluripotency markers and exhibit in vivo functionality. Bulk RNA-sequencing reveales that cyclic-stretching enhances biological characteristics required for pluripotency acquisition, including increased cell division and mesenchymal-epithelial transition. Of note, cyclic-stretching activates key mechanosensitive molecules (integrins, perinuclear actins, nesprin-2, and YAP), across the cytoskeletal-to-nuclear space. Furthermore, stretch-mediated cytoskeletal-nuclear mechano-coupling leads to altered epigenetic modifications, mainly downregulation in H3K9 methylation, and its global gene occupancy change, as revealed by genome-wide ChIP-sequencing and pharmacological inhibition tests. Single cell RNA-sequencing further identifies subcluster of mechano-responsive iPSCs and key epigenetic modifier in stretched cells. Collectively, cyclic-stretching activates iPSC reprogramming through mechanotransduction process and epigenetic changes accompanied by altered occupancy of mechanosensitive genes. This study highlights the strong link between external physical forces with subsequent mechanotransduction process and the epigenetic changes with expression of related genes in cellular reprogramming, holding substantial implications in the field of cell biology, tissue engineering, and regenerative medicine.
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20
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Loe TK, Lazzerini Denchi E, Tricola GM, Azeroglu B. ALTercations at telomeres: stress, recombination and extrachromosomal affairs. Biochem Soc Trans 2023; 51:1935-1946. [PMID: 37767563 DOI: 10.1042/bst20230265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 09/29/2023]
Abstract
Approximately 15% of human cancers depend on the alternative lengthening of telomeres (ALT) pathway to maintain telomeres and proliferate. Telomeres that are elongated using ALT display unique features raising the exciting prospect of tailored cancer therapies. ALT-mediated telomere elongation shares several features with recombination-based DNA repair. Strikingly, cells that use the ALT pathway display abnormal levels of replication stress at telomeres and accumulate abundant extrachromosomal telomeric DNA. In this review, we examine recent findings that shed light on the ALT mechanisms and the strategies currently available to suppress this telomere elongation mechanism.
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Affiliation(s)
- Taylor K Loe
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, U.S.A
| | - Eros Lazzerini Denchi
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892, U.S.A
| | - Gianna M Tricola
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892, U.S.A
| | - Benura Azeroglu
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892, U.S.A
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21
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Morozov VM, Riva A, Sarwar S, Kim WJ, Li J, Zhou L, Licht J, Daaka Y, Ishov A. HIRA-mediated loading of histone variant H3.3 controls androgen-induced transcription by regulation of AR/BRD4 complex assembly at enhancers. Nucleic Acids Res 2023; 51:10194-10217. [PMID: 37638746 PMCID: PMC10602887 DOI: 10.1093/nar/gkad700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 07/21/2023] [Accepted: 08/14/2023] [Indexed: 08/29/2023] Open
Abstract
Incorporation of histone variant H3.3 comprises active territories of chromatin. Exploring the function of H3.3 in prostate cancer (PC), we found that knockout (KO) of H3.3 chaperone HIRA suppresses PC growth in vitro and in xenograft settings, deregulates androgen-induced gene expression and alters androgen receptor (AR) binding within enhancers of target genes. H3.3 affects transcription in multiple ways, including activation of p300 by phosphorylated H3.3 at Ser-31 (H3.3S31Ph), which results in H3K27 acetylation (H3K27Ac) at enhancers. In turn, H3K27Ac recruits bromodomain protein BRD4 for enhancer-promoter interaction and transcription activation. We observed that HIRA KO reduces H3.3 incorporation, diminishes H3.3S31Ph and H3K27Ac, modifies recruitment of BRD4. These results suggest that H3.3-enriched enhancer chromatin serves as a platform for H3K27Ac-mediated BRD4 recruitment, which interacts with and retains AR at enhancers, resulting in transcription reprogramming. In addition, HIRA KO deregulates glucocorticoid- (GR) driven transcription of genes co-regulated by AR and GR, suggesting a common H3.3/HIRA-dependent mechanism of nuclear receptors function. Expression of HIRA complex proteins is increased in PC compared with normal prostate tissue, especially in high-risk PC groups, and is associated with a negative prognosis. Collectively, our results demonstrate function of HIRA-dependent H3.3 pathway in regulation of nuclear receptors activity.
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Affiliation(s)
- Viacheslav M Morozov
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL, USA
| | - Alberto Riva
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
| | - Sadia Sarwar
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL, USA
| | - Wan-Ju Kim
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL, USA
| | - Jianping Li
- Division of Hematology/Oncology, University of Florida College of Medicine, Gainesville, FL, USA
| | - Lei Zhou
- Department of Molecular Genetics & Microbiology, University of Florida College of Medicine, Gainesville, FL, USA
- University of Florida Health Cancer Center, Gainesville, FL, USA
| | - Jonathan D Licht
- Division of Hematology/Oncology, University of Florida College of Medicine, Gainesville, FL, USA
- University of Florida Health Cancer Center, Gainesville, FL, USA
| | - Yehia Daaka
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL, USA
- University of Florida Health Cancer Center, Gainesville, FL, USA
| | - Alexander M Ishov
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL, USA
- University of Florida Health Cancer Center, Gainesville, FL, USA
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22
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Grieco JP, Compton SLE, Davis GN, Guinan J, Schmelz EM. Genetic and Functional Modifications Associated with Ovarian Cancer Cell Aggregation and Limited Culture Conditions. Int J Mol Sci 2023; 24:14867. [PMID: 37834315 PMCID: PMC10573375 DOI: 10.3390/ijms241914867] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
The aggregation of cancer cells provides a survival signal for disseminating cancer cells; however, the underlying molecular mechanisms have yet to be elucidated. Using qPCR gene arrays, this study investigated the changes in cancer-specific genes as well as genes regulating mitochondrial quality control, metabolism, and oxidative stress in response to aggregation and hypoxia in our progressive ovarian cancer models representing slow- and fast-developing ovarian cancer. Aggregation increased the expression of anti-apoptotic, stemness, epithelial-mesenchymal transition (EMT), angiogenic, mitophagic, and reactive oxygen species (ROS) scavenging genes and functions, and decreased proliferation, apoptosis, metabolism, and mitochondrial content genes and functions. The incorporation of stromal vascular cells (SVF) from obese mice into the spheroids increased DNA repair and telomere regulatory genes that may represent a link between obesity and ovarian cancer risk. While glucose had no effect, glutamine was essential for aggregation and supported proliferation of the spheroid. In contrast, low glucose and hypoxic culture conditions delayed adhesion and outgrowth capacity of the spheroids independent of their phenotype, decreased mitochondrial mass and polarity, and induced a shift of mitochondrial dynamics towards mitophagy. However, these conditions did not reduce the appearance of polarized mitochondria at adhesion sites, suggesting that adhesion signals that either reversed mitochondrial fragmentation or induced mitobiogenesis can override the impact of low glucose and oxygen levels. Thus, the plasticity of the spheroids' phenotype supports viability during dissemination, allows for the adaptation to changing conditions such as oxygen and nutrient availability. This may be critical for the development of an aggressive cancer phenotype and, therefore, could represent druggable targets for clinical interventions.
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Affiliation(s)
- Joseph P. Grieco
- Graduate Program in Translational Biology, Medicine, and Health, Virginia Tech, Blacksburg, VA 24061, USA;
| | - Stephanie L. E. Compton
- Department of Human Nutrition, Foods and Exercise, Virginia Tech, Blacksburg, VA 24061, USA; (S.L.E.C.); (G.D.N.)
| | - Grace N. Davis
- Department of Human Nutrition, Foods and Exercise, Virginia Tech, Blacksburg, VA 24061, USA; (S.L.E.C.); (G.D.N.)
| | - Jack Guinan
- Department of Human Nutrition, Foods and Exercise, Virginia Tech, Blacksburg, VA 24061, USA; (S.L.E.C.); (G.D.N.)
| | - Eva M. Schmelz
- Department of Human Nutrition, Foods and Exercise, Virginia Tech, Blacksburg, VA 24061, USA; (S.L.E.C.); (G.D.N.)
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23
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Feng L, Barrows D, Zhong L, Mätlik K, Porter EG, Djomo AM, Yau I, Soshnev AA, Carroll TS, Wen D, Hatten ME, Garcia BA, Allis CD. Altered chromatin occupancy of patient-associated H4 mutants misregulate neuronal differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.29.560141. [PMID: 37808786 PMCID: PMC10557780 DOI: 10.1101/2023.09.29.560141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Chromatin is a crucial regulator of gene expression and tightly controls development across species. Mutations in only one copy of multiple histone genes were identified in children with developmental disorders characterized by microcephaly, but their mechanistic roles in development remain unclear. Here we focus on dominant mutations affecting histone H4 lysine 91. These H4K91 mutants form aberrant nuclear puncta at specific heterochromatin regions. Mechanistically, H4K91 mutants demonstrate enhanced binding to the histone variant H3.3, and ablation of H3.3 or the H3.3-specific chaperone DAXX diminishes the mutant localization to chromatin. Our functional studies demonstrate that H4K91 mutant expression increases chromatin accessibility, alters developmental gene expression through accelerating pro-neural differentiation, and causes reduced mouse brain size in vivo, reminiscent of the microcephaly phenotypes of patients. Together, our studies unveil a distinct molecular pathogenic mechanism from other known histone mutants, where H4K91 mutants misregulate cell fate during development through abnormal genomic localization.
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Affiliation(s)
- Lijuan Feng
- The Rockefeller University, Laboratory of Chromatin Biology and Epigenetics, New York, NY
| | - Douglas Barrows
- The Rockefeller University, Bioinformatics Resource Center, New York, NY
| | - Liangwen Zhong
- Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY
| | - Kärt Mätlik
- The Rockefeller University, Laboratory of Developmental Neurobiology, New York, NY
| | - Elizabeth G. Porter
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
| | - Annaelle M. Djomo
- The Rockefeller University, Laboratory of Chromatin Biology and Epigenetics, New York, NY
| | - Iris Yau
- The Rockefeller University, Laboratory of Chromatin Biology and Epigenetics, New York, NY
- Hunter College of the City University of New York, Yalow Honors Scholar Program, New York, NY
| | - Alexey A. Soshnev
- The Rockefeller University, Laboratory of Chromatin Biology and Epigenetics, New York, NY
- Department of Neuroscience, Developmental and Regenerative Biology, The University of Texas at San Antonio, San Antonio, TX
| | - Thomas S. Carroll
- The Rockefeller University, Bioinformatics Resource Center, New York, NY
| | - Duancheng Wen
- Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY
| | - Mary E. Hatten
- The Rockefeller University, Laboratory of Developmental Neurobiology, New York, NY
| | - Benjamin A. Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
| | - C. David Allis
- The Rockefeller University, Laboratory of Chromatin Biology and Epigenetics, New York, NY
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Fang Y, Barrows D, Dabas Y, Carroll TS, Tap WD, Nacev BA. ATRX guards against aberrant differentiation in mesenchymal progenitor cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.08.552433. [PMID: 37609273 PMCID: PMC10441338 DOI: 10.1101/2023.08.08.552433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Alterations in the tumor suppressor ATRX are recurrently observed in several cancer types including sarcomas, which are mesenchymal neoplasms. ATRX has multiple epigenetic functions including heterochromatin formation and maintenance and regulation of transcription through modulation of chromatin accessibility. Here, we show in murine mesenchymal progenitor cells (MPCs) that Atrx deficiency aberrantly activated mesenchymal differentiation programs. This includes adipogenic pathways where ATRX loss induced expression of adipogenic transcription factors (Pparγ and Cebpα) and enhanced adipogenic differentiation in response to differentiation stimuli. These changes are linked to loss of heterochromatin near mesenchymal lineage genes together with increased chromatin accessibility and gains of active chromatin marks at putative enhancer elements and promoters. Finally, we observed depletion of H3K9me3 at transposable elements, which are derepressed including near mesenchymal genes where they could serve as regulatory elements. Our results demonstrate that ATRX functions to buffer against differentiation in mesenchymal progenitor cells, which has implications for understanding ATRX loss of function in sarcomas.
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Affiliation(s)
- Yan Fang
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY10065
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY10065
| | - Douglas Barrows
- Bioinformatics Resource Center, The Rockefeller University, New York, NY10065
| | - Yakshi Dabas
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY10065
| | - Thomas S Carroll
- Bioinformatics Resource Center, The Rockefeller University, New York, NY10065
| | - William D. Tap
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Benjamin A. Nacev
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15213
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15213
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213
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25
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Rose AM, Goncalves T, Cunniffe S, Geiller HEB, Kent T, Shepherd S, Ratnaweera M, O’Sullivan R, Gibbons R, Clynes D. Induction of the alternative lengthening of telomeres pathway by trapping of proteins on DNA. Nucleic Acids Res 2023; 51:6509-6527. [PMID: 36940725 PMCID: PMC10359465 DOI: 10.1093/nar/gkad150] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 02/06/2023] [Accepted: 02/21/2023] [Indexed: 03/23/2023] Open
Abstract
Telomere maintenance is a hallmark of malignant cells and allows cancers to divide indefinitely. In some cancers, this is achieved through the alternative lengthening of telomeres (ALT) pathway. Whilst loss of ATRX is a near universal feature of ALT-cancers, it is insufficient in isolation. As such, other cellular events must be necessary - but the exact nature of the secondary events has remained elusive. Here, we report that trapping of proteins (such as TOP1, TOP2A and PARP1) on DNA leads to ALT induction in cells lacking ATRX. We demonstrate that protein-trapping chemotherapeutic agents, such as etoposide, camptothecin and talazoparib, induce ALT markers specifically in ATRX-null cells. Further, we show that treatment with G4-stabilising drugs cause an increase in trapped TOP2A levels which leads to ALT induction in ATRX-null cells. This process is MUS81-endonuclease and break-induced replication dependent, suggesting that protein trapping leads to replication fork stalling, with these forks being aberrantly processed in the absence of ATRX. Finally, we show ALT-positive cells harbour a higher load of genome-wide trapped proteins, such as TOP1, and knockdown of TOP1 reduced ALT activity. Taken together, these findings suggest that protein trapping is a fundamental driving force behind ALT-biology in ATRX-deficient malignancies.
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Affiliation(s)
- Anna M Rose
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
- Department of Paediatrics, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Tomas Goncalves
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Siobhan Cunniffe
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | | | - Thomas Kent
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Sam Shepherd
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | | | - Roderick J O’Sullivan
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Richard J Gibbons
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - David Clynes
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
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26
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Ruden X, Singh A, Marben T, Tang W, Awonuga A, Ruden DM, Puscheck E, Feng H, Rappolee D. A single cell transcriptomic fingerprint of stressed premature, imbalanced differentiation of embryonic stem cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.23.541952. [PMID: 37292812 PMCID: PMC10245821 DOI: 10.1101/2023.05.23.541952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cultured naïve pluripotent ESC differentiate into first lineage, XEN or second lineage, formative pluripotency. Hyperosmotic stress (sorbitol), like retinoic acid, decreases naive pluripotency and increases XEN in two ESC lines, as reported by bulk and scRNAseq, analyzed by UMAP. Sorbitol overrides pluripotency in two ESC lines as reported by bulk and scRNAseq, analyzed by UMAP. UMAP analyzed the effects of 5 stimuli - three stressed (200-300mM sorbitol with leukemia inhibitory factor +LIF) and two unstressed (+LIF, normal stemness-NS and -LIF, normal differentiation-ND). Sorbitol and RA decrease naive pluripotency and increase subpopulations of 2-cell embryo-like and XEN sub-lineages; primitive, parietal, and visceral endoderm (VE). Between the naïve pluripotency and primitive endoderm clusters is a stress-induced cluster with transient intermediate cells with higher LIF receptor signaling, with increased Stat3, Klf4, and Tbx3 expression. Sorbitol, like RA, also suppresses formative pluripotency, increasing lineage imbalance. Although bulk RNAseq and gene ontology group analyses suggest that stress induces head organizer and placental markers, scRNAseq reveals few cells. But VE and placental markers/cells were in adjacent clusters, like recent reports. UMAPs show that dose-dependent stress overrides stemness to force premature lineage imbalance. Hyperosmotic stress induces lineage imbalance, and other toxicological stresses, like drugs with RA, may cause lineage imbalance, resulting in miscarriages or birth defects.
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27
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Tal A, Aguilera JD, Bren I, Strauss C, Schlesinger S. Differential effect of histone H3.3 depletion on retroviral repression in embryonic stem cells. Clin Epigenetics 2023; 15:83. [PMID: 37170146 PMCID: PMC10176700 DOI: 10.1186/s13148-023-01499-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/03/2023] [Indexed: 05/13/2023] Open
Abstract
BACKGROUND Integration of retroviruses into the host genome can impair the genomic and epigenomic integrity of the cell. As a defense mechanism, epigenetic modifications on the proviral DNA repress retroviral sequences in mouse embryonic stem cells (ESC). Here, we focus on the histone 3 variant H3.3, which is abundant in active transcription zones, as well as centromeres and heterochromatinized repeat elements, e.g., endogenous retroviruses (ERV). RESULTS To understand the involvement of H3.3 in the epigenetic silencing of retroviral sequences in ESC, we depleted the H3.3 genes in ESC and transduced the cells with GFP-labeled MLV pseudovirus. This led to altered retroviral repression and reduced Trim28 recruitment, which consequently led to a loss of heterochromatinization in proviral sequences. Interestingly, we show that H3.3 depletion has a differential effect depending on which of the two genes coding for H3.3, H3f3a or H3f3b, are knocked out. Depletion of H3f3a resulted in a transient upregulation of incoming retroviral expression and ERVs, while the depletion of H3f3b did not have the same effect and repression was maintained. However, the depletion of both genes resulted in a stable activation of the retroviral promoter. These findings suggest that H3.3 is important for regulating retroviral gene expression in mouse ESC and provide evidence for a distinct function of the two H3.3 genes in this regulation. Furthermore, we show that Trim28 is needed for depositing H3.3 in retroviral sequences, suggesting a functional interaction between Trim28 recruitment and H3.3 loading. CONCLUSIONS Identifying the molecular mechanisms by which H3.3 and Trim28 interact and regulate retroviral gene expression could provide a deeper understanding of the fundamental processes involved in retroviral silencing and the general regulation of gene expression, thus providing new answers to a central question of stem cell biology.
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Affiliation(s)
- Ayellet Tal
- Department of Animal Science, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Jose David Aguilera
- Department of Animal Science, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Igor Bren
- Department of Animal Science, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Carmit Strauss
- Department of Animal Science, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Sharon Schlesinger
- Department of Animal Science, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.
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28
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Morozov VM, Riva A, Sarwar S, Kim W, Li J, Zhou L, Licht JD, Daaka Y, Ishov AM. HIRA-mediated loading of histone variant H3.3 controls androgen-induced transcription by regulation of AR/BRD4 complex assembly at enhancers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.08.536256. [PMID: 37214820 PMCID: PMC10197601 DOI: 10.1101/2023.05.08.536256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Incorporation of histone variant H3.3 comprises active territories of chromatin. Exploring the function of H3.3 in prostate cancer (PC), we found that knockout (KO) of H3.3 chaperone HIRA suppresses PC growth in vitro and in xenograft settings, deregulates androgen-induced gene expression and alters androgen receptor (AR) binding within enhancers of target genes. H3.3 affects transcription in multiple ways, including activation of p300 by phosphorylated H3.3 at Ser-31 (H3.3S31Ph), which results in H3K27 acetylation (H3K27Ac) at enhancers. In turn, H3K27Ac recruits bromodomain protein BRD4 for enhancer-promoter interaction and transcription activation. We observed that HIRA KO reduces H3.3 incorporation, diminishes H3.3S31Ph and H3K27Ac, modifies recruitment of BRD4. These results suggest that H3.3-enriched enhancer chromatin serves as a platform for H3K27Ac-mediated BRD4 recruitment, which interacts with and retains AR at enhancers, resulting in transcription reprogramming. AR KO reduced levels of H3.3 at enhancers, indicating feedback mechanism. In addition, HIRA KO deregulates glucocorticoid-driven transcription, suggesting a common H3.3/HIRA-dependent mechanism of nuclear receptors function. Expression of HIRA complex proteins is increased in PC compared with normal prostate tissue, especially in high-risk PC groups, and is associated with a negative prognosis. Collectively, our results demonstrate function of HIRA-dependent H3.3 pathway in regulation of nuclear receptors activity. Key points *H3.3 at enhancers promotes acetylation of H3K27Ac and retention of AR/BRD4 complex for transcription regulation*Knockout of H3.3 chaperone HIRA suppresses PC cells growth and deregulates androgen-induced transcription*H3.3/HIRA pathway regulates both AR and GR, suggesting a common HIRA/H3.3 mechanism of nuclear receptors function.
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29
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Hulett RE, Kimura JO, Bolaños DM, Luo YJ, Rivera-López C, Ricci L, Srivastava M. Acoel single-cell atlas reveals expression dynamics and heterogeneity of adult pluripotent stem cells. Nat Commun 2023; 14:2612. [PMID: 37147314 PMCID: PMC10163032 DOI: 10.1038/s41467-023-38016-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 04/11/2023] [Indexed: 05/07/2023] Open
Abstract
Adult pluripotent stem cell (aPSC) populations underlie whole-body regeneration in many distantly-related animal lineages, but how the underlying cellular and molecular mechanisms compare across species is unknown. Here, we apply single-cell RNA sequencing to profile transcriptional cell states of the acoel worm Hofstenia miamia during postembryonic development and regeneration. We identify cell types shared across stages and their associated gene expression dynamics during regeneration. Functional studies confirm that the aPSCs, also known as neoblasts, are the source of differentiated cells and reveal transcription factors needed for differentiation. Subclustering of neoblasts recovers transcriptionally distinct subpopulations, the majority of which are likely specialized to differentiated lineages. One neoblast subset, showing enriched expression of the histone variant H3.3, appears to lack specialization. Altogether, the cell states identified in this study facilitate comparisons to other species and enable future studies of stem cell fate potentials.
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Affiliation(s)
- Ryan E Hulett
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Julian O Kimura
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - D Marcela Bolaños
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Yi-Jyun Luo
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Carlos Rivera-López
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
- Department of Molecular and Cell Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Lorenzo Ricci
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Mansi Srivastava
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA.
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30
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Pang Y, Chen X, Ji T, Cheng M, Wang R, Zhang C, Liu M, Zhang J, Zhong C. The Chromatin Remodeler ATRX: Role and Mechanism in Biology and Cancer. Cancers (Basel) 2023; 15:cancers15082228. [PMID: 37190157 DOI: 10.3390/cancers15082228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 03/30/2023] [Accepted: 04/06/2023] [Indexed: 05/17/2023] Open
Abstract
The alpha-thalassemia mental retardation X-linked (ATRX) syndrome protein is a chromatin remodeling protein that primarily promotes the deposit of H3.3 histone variants in the telomere area. ATRX mutations not only cause ATRX syndrome but also influence development and promote cancer. The primary molecular characteristics of ATRX, including its molecular structures and normal and malignant biological roles, are reviewed in this article. We discuss the role of ATRX in its interactions with the histone variant H3.3, chromatin remodeling, DNA damage response, replication stress, and cancers, particularly gliomas, neuroblastomas, and pancreatic neuroendocrine tumors. ATRX is implicated in several important cellular processes and serves a crucial function in regulating gene expression and genomic integrity throughout embryogenesis. However, the nature of its involvement in the growth and development of cancer remains unknown. As mechanistic and molecular investigations on ATRX disclose its essential functions in cancer, customized therapies targeting ATRX will become accessible.
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Affiliation(s)
- Ying Pang
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, 150 Jimo Road, Shanghai 200120, China
| | - Xu Chen
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, 150 Jimo Road, Shanghai 200120, China
| | - Tongjie Ji
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, 150 Jimo Road, Shanghai 200120, China
| | - Meng Cheng
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, 150 Jimo Road, Shanghai 200120, China
| | - Rui Wang
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, 150 Jimo Road, Shanghai 200120, China
| | - Chunyu Zhang
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, 150 Jimo Road, Shanghai 200120, China
| | - Min Liu
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, 150 Jimo Road, Shanghai 200120, China
| | - Jing Zhang
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, 150 Jimo Road, Shanghai 200120, China
- Institute for Advanced Study, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Chunlong Zhong
- Department of Neurosurgery, Shanghai East Hospital, School of Medicine, Tongji University, 150 Jimo Road, Shanghai 200120, China
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31
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Clatterbuck Soper SF, Meltzer PS. ATRX/DAXX: Guarding the Genome against the Hazards of ALT. Genes (Basel) 2023; 14:genes14040790. [PMID: 37107548 PMCID: PMC10137841 DOI: 10.3390/genes14040790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
Proliferating cells must enact a telomere maintenance mechanism to ensure genomic stability. In a subset of tumors, telomeres are maintained not by telomerase, but through a homologous recombination-based mechanism termed Alternative Lengthening of Telomeres or ALT. The ALT process is linked to mutations in the ATRX/DAXX/H3.3 histone chaperone complex. This complex is responsible for depositing non-replicative histone variant H3.3 at pericentric and telomeric heterochromatin but has also been found to have roles in ameliorating replication in repeat sequences and in promoting DNA repair. In this review, we will discuss ways in which ATRX/DAXX helps to protect the genome, and how loss of this complex allows ALT to take hold.
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32
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Bush K, Cervantes V, Yee JQ, Klein RH, Knoepfler PS. A knockout-first model of H3f3a gene targeting leads to developmental lethality. Genesis 2023; 61:e23507. [PMID: 36656301 PMCID: PMC10038898 DOI: 10.1002/dvg.23507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 11/29/2022] [Accepted: 12/01/2022] [Indexed: 01/20/2023]
Abstract
Histone variant H3.3 is encoded by two genes, H3f3a and H3f3b, which can be expressed differentially depending on tissue type. Previous work in our lab has shown that knockout of H3f3b causes some neonatal lethality and infertility in mice, and chromosomal defects in mouse embryonic fibroblasts (MEFs). Studies of H3f3a and H3f3b null mice by others have produced generally similar phenotypes to what we found in our H3f3b nulls, but the relative impacts of the loss of either H3f3a or H3f3b have varied depending on the approach and genetic background. Here we used a knockout-first approach to target the H3f3a gene for inactivation in C57BL6 mice. Homozygous H3f3a targeting produced a lethal phenotype at or before birth. E13.5 null embryos had some potential morphological differences from WT littermates including smaller size and reduced head size. An E18.5 null embryo was smaller than its control littermates with several potential defects including small head and brain size as well as small lungs, which would be consistent with a late gestation lethal phenotype. Despite a reduction in H3.3 and total H3 protein levels, the only histone H3 post-translational modification in the small panel assessed that was significantly altered was the unique H3.3 mark phospho-Serine31, which was consistently increased in null neurospheres. H3f3a null neurospheres also exhibited consistent gene expression changes including in protocadherins. Overall, our findings are consistent with the model that there are differential, cell-type-specific contributions of H3f3a and H3f3b to H3.3 functions in epigenetic and developmental processes.
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Affiliation(s)
- Kelly Bush
- Department of Cell Biology and Human Anatomy, University of California Davis, Davis, California, USA
- Institute for Pediatric Regenerative Medicine, Shriners Hospital for Children Northern California, Sacramento, California, USA
- Genome Center, University of California Davis, Davis, California, USA
| | - Vanessa Cervantes
- Department of Cell Biology and Human Anatomy, University of California Davis, Davis, California, USA
- Institute for Pediatric Regenerative Medicine, Shriners Hospital for Children Northern California, Sacramento, California, USA
- Genome Center, University of California Davis, Davis, California, USA
| | - Jennifer Q Yee
- Department of Cell Biology and Human Anatomy, University of California Davis, Davis, California, USA
- Institute for Pediatric Regenerative Medicine, Shriners Hospital for Children Northern California, Sacramento, California, USA
- Genome Center, University of California Davis, Davis, California, USA
| | - Rachel H Klein
- Department of Cell Biology and Human Anatomy, University of California Davis, Davis, California, USA
- Institute for Pediatric Regenerative Medicine, Shriners Hospital for Children Northern California, Sacramento, California, USA
- Genome Center, University of California Davis, Davis, California, USA
| | - Paul S Knoepfler
- Department of Cell Biology and Human Anatomy, University of California Davis, Davis, California, USA
- Institute for Pediatric Regenerative Medicine, Shriners Hospital for Children Northern California, Sacramento, California, USA
- Genome Center, University of California Davis, Davis, California, USA
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33
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A non-genetic switch triggers alternative telomere lengthening and cellular immortalization in ATRX deficient cells. Nat Commun 2023; 14:939. [PMID: 36805596 PMCID: PMC9941109 DOI: 10.1038/s41467-023-36294-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 01/25/2023] [Indexed: 02/22/2023] Open
Abstract
Alternative Lengthening of Telomeres (ALT) is an aberrant DNA recombination pathway which grants replicative immortality to approximately 10% of all cancers. Despite this high prevalence of ALT in cancer, the mechanism and genetics by which cells activate this pathway remain incompletely understood. A major challenge in dissecting the events that initiate ALT is the extremely low frequency of ALT induction in human cell systems. Guided by the genetic lesions that have been associated with ALT from cancer sequencing studies, we genetically engineered primary human pluripotent stem cells to deterministically induce ALT upon differentiation. Using this genetically defined system, we demonstrate that disruption of the p53 and Rb pathways in combination with ATRX loss-of-function is sufficient to induce all hallmarks of ALT and results in functional immortalization in a cell type-specific manner. We further demonstrate that ALT can be induced in the presence of telomerase, is neither dependent on telomere shortening nor crisis, but is rather driven by continuous telomere instability triggered by the induction of differentiation in ATRX-deficient stem cells.
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34
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Voon HPJ, Wong LH. Chromatin mutations in pediatric high grade gliomas. Front Oncol 2023; 12:1104129. [PMID: 36686810 PMCID: PMC9853562 DOI: 10.3389/fonc.2022.1104129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 12/19/2022] [Indexed: 01/07/2023] Open
Abstract
Pediatric high grade gliomas (HGG) are lethal tumors which are currently untreatable. A number of recent studies have provided much needed insights into the mutations and mechanisms which drive oncogenesis in pediatric HGGs. It is now clear that mutations in chromatin proteins, particularly H3.3 and its associated chaperone complex (ATRX), are a hallmark feature of pediatric HGGs. We review the current literature on the normal roles of the ATRX/H3.3 complex and how these functions are disrupted by oncogenic mutations. We discuss the current clinical trials and pre-clinical models that target chromatin and DNA, and how these agents fit into the ATRX/H3.3 mutation model. As chromatin mutations are a relatively new discovery in pediatric HGGs, developing clear mechanistic insights are a key step to improving therapies for these tumors.
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35
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Abdallah AS, Cardona HJ, Gadd SL, Brat DJ, Powla PP, Alruwalli WS, Shen C, Picketts DJ, Li XN, Becher OJ. Novel genetically engineered H3.3G34R model reveals cooperation with ATRX loss in upregulation of Hoxa cluster genes and promotion of neuronal lineage. Neurooncol Adv 2023; 5:vdad003. [PMID: 36845293 PMCID: PMC9950856 DOI: 10.1093/noajnl/vdad003] [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] [Indexed: 01/09/2023] Open
Abstract
Background Pediatric high-grade gliomas (pHGGs) are aggressive pediatric CNS tumors and an important subset are characterized by mutations in H3F3A, the gene that encodes Histone H3.3 (H3.3). Substitution of Glycine at position 34 of H3.3 with either Arginine or Valine (H3.3G34R/V), was recently described and characterized in a large cohort of pHGG samples as occurring in 5-20% of pHGGs. Attempts to study the mechanism of H3.3G34R have proven difficult due to the lack of knowledge regarding the cell-of-origin and the requirement for co-occurring mutations for model development. We sought to develop a biologically relevant animal model of pHGG to probe the downstream effects of the H3.3G34R mutation in the context of vital co-occurring mutations. Methods We developed a genetically engineered mouse model (GEMM) that incorporates PDGF-A activation, TP53 loss and the H3.3G34R mutation both in the presence and loss of Alpha thalassemia/mental retardation syndrome X-linked (ATRX), which is commonly mutated in H3.3G34 mutant pHGGs. Results We demonstrated that ATRX loss significantly increases tumor latency in the absence of H3.3G34R and inhibits ependymal differentiation in the presence of H3.3G34R. Transcriptomic analysis revealed that ATRX loss in the context of H3.3G34R upregulates Hoxa cluster genes. We also found that the H3.3G34R overexpression leads to enrichment of neuronal markers but only in the context of ATRX loss. Conclusions This study proposes a mechanism in which ATRX loss is the major contributor to many key transcriptomic changes in H3.3G34R pHGGs. Accession number GSE197988.
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Affiliation(s)
- Aalaa S Abdallah
- Department of Pediatrics, Northwestern University, Chicago, Illinois, USA
- Stanley Manne Children’s Research Institute, Molecular and Translational Cancer Biology, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA
| | - Herminio J Cardona
- Stanley Manne Children’s Research Institute, Molecular and Translational Cancer Biology, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA
| | - Samantha L Gadd
- Department of Pathology, Northwestern University, Chicago, Illinois, USA
| | - Daniel J Brat
- Department of Pathology, Northwestern University, Chicago, Illinois, USA
| | - Plamena P Powla
- Department of Psychiatry and Behavioral Sciences, Northwestern University, Chicago, Illinois, USA
| | - Waleed S Alruwalli
- Department of Psychiatry and Behavioral Sciences, Northwestern University, Chicago, Illinois, USA
| | - Chen Shen
- Stanley Manne Children’s Research Institute, Molecular and Translational Cancer Biology, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA
| | - David J Picketts
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Xiao-Nan Li
- Department of Pediatrics, Northwestern University, Chicago, Illinois, USA
- Stanley Manne Children’s Research Institute, Molecular and Translational Cancer Biology, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA
- Developmental Therapeutic Core, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Program of Precision Medicine PDOX Modeling of Pediatric Tumors, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA
| | - Oren J Becher
- Department of Pediatrics, Northwestern University, Chicago, Illinois, USA
- Stanley Manne Children’s Research Institute, Molecular and Translational Cancer Biology, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA
- Department of Pediatrics, Kravis Children’s Hospital, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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36
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Geiller HEB, Harvey A, Jones RE, Grimstead JW, Cleal K, Hendrickson EA, Baird DM. ATRX modulates the escape from a telomere crisis. PLoS Genet 2022; 18:e1010485. [PMID: 36350851 PMCID: PMC9678338 DOI: 10.1371/journal.pgen.1010485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 11/21/2022] [Accepted: 10/20/2022] [Indexed: 11/11/2022] Open
Abstract
Telomerase activity is the principal telomere maintenance mechanism in human cancers, however 15% of cancers utilise a recombination-based mechanism referred to as alternative lengthening of telomeres (ALT) that leads to long and heterogenous telomere length distributions. Loss-of-function mutations in the Alpha Thalassemia/Mental Retardation Syndrome X-Linked (ATRX) gene are frequently found in ALT cancers. Here, we demonstrate that the loss of ATRX, coupled with telomere dysfunction during crisis, is sufficient to initiate activation of the ALT pathway and that it confers replicative immortality in human fibroblasts. Additionally, loss of ATRX combined with a telomere-driven crisis in HCT116 epithelial cancer cells led to the initiation of an ALT-like pathway. In these cells, a rapid and precise telomeric elongation and the induction of C-circles was observed; however, this process was transient and the telomeres ultimately continued to erode such that the cells either died or the escape from crisis was associated with telomerase activation. In both of these instances, telomere sequencing revealed that all alleles, irrespective of whether they were elongated, were enriched in variant repeat types, that appeared to be cell-line specific. Thus, our data show that the loss of ATRX combined with telomere dysfunction during crisis induces the ALT pathway in fibroblasts and enables a transient activation of ALT in epithelial cells.
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Affiliation(s)
- Helene E. B. Geiller
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, United Kingdom
| | - Adam Harvey
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
| | - Rhiannon E. Jones
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, United Kingdom
| | - Julia W. Grimstead
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, United Kingdom
| | - Kez Cleal
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, United Kingdom
| | - Eric A. Hendrickson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, Minnesota, United States of America
| | - Duncan M. Baird
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, United Kingdom
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37
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Zeineldin M, Patel AG, Dyer MA. Neuroblastoma: When differentiation goes awry. Neuron 2022; 110:2916-2928. [PMID: 35985323 PMCID: PMC9509448 DOI: 10.1016/j.neuron.2022.07.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 04/21/2022] [Accepted: 07/13/2022] [Indexed: 10/15/2022]
Abstract
Neuroblastoma is a leading cause of cancer-related death in children. Accumulated data suggest that differentiation arrest of the neural-crest-derived sympathoadrenal lineage contributes to neuroblastoma formation. The developmental arrest of these cell types explains many biological features of the disease, including its cellular heterogeneity, mutational spectrum, spontaneous regression, and response to drugs that induce tumor cell differentiation. In this review, we provide evidence that supports the notion that arrested neural-crest-derived progenitor cells give rise to neuroblastoma and discuss how this concept could be exploited for clinical management of the disease.
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Affiliation(s)
- Maged Zeineldin
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Anand G Patel
- Departments of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Michael A Dyer
- Department of Developmental Neurobiology, MS-323, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
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38
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Cui C, Tang X, Xing J, Sheng X, Chi H, Zhan W. Single-cell RNA-seq uncovered hemocyte functional subtypes and their differentiational characteristics and connectivity with morphological subpopulations in Litopenaeus vannamei. Front Immunol 2022; 13:980021. [PMID: 36177045 PMCID: PMC9513592 DOI: 10.3389/fimmu.2022.980021] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/22/2022] [Indexed: 12/01/2022] Open
Abstract
Hemocytes play central roles in shrimp immune system, whereas whose subclasses have not yet been completely defined. At present, the morphological classification of hemocytes is inadequate to classify the complete hemocyte repertoire and elucidate the functions and differentiation and maturation processes. Based on single-cell RNA sequencing (scRNA-seq) of hemocytes in healthy Litopenaeus vannamei, combined with RNA-FISH and flow cytometric sorting, we identified three hemocyte clusters including TGase+ cells, CTL+ cells and Crustin+ cells, and further determined their functional properties, potential differentiation trajectory and correspondence with morphological subpopulations. The TGase+ cells were mainly responsible for the coagulation, exhibiting distinguishable characteristics of hyalinocyte, and appeared to be developmentally arrested at an early stage of hemocyte differentiation. The CTL+ cells and Crustin+ cells arrested at terminal stages of differentiation mainly participated in recognizing foreign pathogens and initiating immune defense responses, owning distinctive features of granule-containing hemocytes. Furthermore, we have revealed the functional sub-clusters of three hemocyte clusters and their potential differentiation pathways according to the expression of genes involved in cell cycle, cell differentiation and immune response, and the successive differentiation and maturation of hyalinocytes to granule-containing hemocytes have also mapped. The results revealed the diversity of shrimp hemocytes and provide new theoretical rationale for hemocyte classification, which also facilitate systematic research on crustacean immunity.
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Affiliation(s)
- Chuang Cui
- Laboratory of Pathology and Immunology of Aquatic Animals, The Key Laboratory of Mariculture, Ministry of Education (KLMME), Ocean University of China, Qingdao, China
| | - Xiaoqian Tang
- Laboratory of Pathology and Immunology of Aquatic Animals, The Key Laboratory of Mariculture, Ministry of Education (KLMME), Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jing Xing
- Laboratory of Pathology and Immunology of Aquatic Animals, The Key Laboratory of Mariculture, Ministry of Education (KLMME), Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiuzhen Sheng
- Laboratory of Pathology and Immunology of Aquatic Animals, The Key Laboratory of Mariculture, Ministry of Education (KLMME), Ocean University of China, Qingdao, China
| | - Heng Chi
- Laboratory of Pathology and Immunology of Aquatic Animals, The Key Laboratory of Mariculture, Ministry of Education (KLMME), Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Wenbin Zhan
- Laboratory of Pathology and Immunology of Aquatic Animals, The Key Laboratory of Mariculture, Ministry of Education (KLMME), Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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39
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de Nonneville A, Salas S, Bertucci F, Sobinoff AP, Adélaïde J, Guille A, Finetti P, Noble JR, Churikov D, Chaffanet M, Lavit E, Pickett HA, Bouvier C, Birnbaum D, Reddel RR, Géli V. TOP3A amplification and ATRX inactivation are mutually exclusive events in pediatric osteosarcomas using ALT. EMBO Mol Med 2022; 14:e15859. [PMID: 35920001 PMCID: PMC9549729 DOI: 10.15252/emmm.202215859] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 07/13/2022] [Accepted: 07/14/2022] [Indexed: 02/05/2023] Open
Abstract
In some types of cancer, telomere length is maintained by the alternative lengthening of telomeres (ALT) mechanism. In many ALT cancers, the α-thalassemia/mental retardation syndrome X-linked (ATRX) gene is mutated leading to the conclusion that the ATRX complex represses ALT. Here, we report that most high-grade pediatric osteosarcomas maintain their telomeres by ALT, and that the majority of these ALT tumors are ATRX wild-type (wt) and instead carry an amplified 17p11.2 chromosomal region containing TOP3A. We found that TOP3A was overexpressed in the ALT-positive ATRX-wt tumors consistent with its amplification. We demonstrated the functional significance of these results by showing that TOP3A overexpression in ALT cancer cells countered ATRX-mediated ALT inhibition and that TOP3A knockdown disrupted the ALT phenotype in ATRX-wt cells. Moreover, we report that TOP3A is required for proper BLM localization and promotes ALT DNA synthesis in ALT cell lines. Collectively, our results identify TOP3A as a major ALT player and potential therapeutic target.
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Affiliation(s)
- Alexandre de Nonneville
- Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐Calmettes, Team « Telomere and Chromatin ». Equipe labellisée Ligue Nationale Contre Le CancerAix‐Marseille UnivMarseilleFrance,Cancer Research Unit, Faculty of Medicine and Health, Children's Medical Research InstituteUniversity of SydneyWestmeadNSWAustralia,Predictive Oncology Laboratory, Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐CalmettesAix‐Marseille UniversityMarseilleFrance,Department of Medical Oncology, CRCM, CNRS, INSERM, Institut Paoli‐CalmettesAix‐Marseille UnivMarseilleFrance
| | - Sébastien Salas
- Department of Medical OncologyAssistance Publique Hôpitaux de Marseille ‐ Timone HospitalMarseilleFrance
| | - François Bertucci
- Predictive Oncology Laboratory, Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐CalmettesAix‐Marseille UniversityMarseilleFrance,Department of Medical Oncology, CRCM, CNRS, INSERM, Institut Paoli‐CalmettesAix‐Marseille UnivMarseilleFrance
| | - Alexander P Sobinoff
- Telomere Length Regulation Unit, Faculty of Medicine and Health, Children's Medical Research InstituteUniversity of SydneyWestmeadNSWAustralia
| | - José Adélaïde
- Predictive Oncology Laboratory, Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐CalmettesAix‐Marseille UniversityMarseilleFrance
| | - Arnaud Guille
- Predictive Oncology Laboratory, Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐CalmettesAix‐Marseille UniversityMarseilleFrance
| | - Pascal Finetti
- Predictive Oncology Laboratory, Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐CalmettesAix‐Marseille UniversityMarseilleFrance
| | - Jane R Noble
- Cancer Research Unit, Faculty of Medicine and Health, Children's Medical Research InstituteUniversity of SydneyWestmeadNSWAustralia
| | - Dimitri Churikov
- Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐Calmettes, Team « Telomere and Chromatin ». Equipe labellisée Ligue Nationale Contre Le CancerAix‐Marseille UnivMarseilleFrance
| | - Max Chaffanet
- Predictive Oncology Laboratory, Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐CalmettesAix‐Marseille UniversityMarseilleFrance
| | - Elise Lavit
- Department of Medical OncologyAssistance Publique Hôpitaux de Marseille ‐ Timone HospitalMarseilleFrance
| | - Hilda A Pickett
- Telomere Length Regulation Unit, Faculty of Medicine and Health, Children's Medical Research InstituteUniversity of SydneyWestmeadNSWAustralia
| | - Corinne Bouvier
- Department of PathologyAssistance Publique Hôpitaux de Marseille ‐ Timone HospitalMarseilleFrance
| | - Daniel Birnbaum
- Predictive Oncology Laboratory, Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐CalmettesAix‐Marseille UniversityMarseilleFrance
| | - Roger R Reddel
- Cancer Research Unit, Faculty of Medicine and Health, Children's Medical Research InstituteUniversity of SydneyWestmeadNSWAustralia
| | - Vincent Géli
- Marseille Cancer Research Centre (CRCM), Inserm U1068, CNRS UMR7258, Institut Paoli‐Calmettes, Team « Telomere and Chromatin ». Equipe labellisée Ligue Nationale Contre Le CancerAix‐Marseille UnivMarseilleFrance
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40
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Fatima C, Tahir MHN, Ikram RM, Khan Z, Sajjad M, Qanmber G, Darwish E, Geng Z, Xiangkuo G, Ur Rehman S. Characterization of Histone H3 Gene Family Reveals That GmHH3-3 is Associated With Higher Seed Weight in Glycine max. Front Genet 2022; 13:949027. [PMID: 35937992 PMCID: PMC9353304 DOI: 10.3389/fgene.2022.949027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 06/15/2022] [Indexed: 11/23/2022] Open
Abstract
The main function of histone protein is to provide support to the structure of chromosomes. It helps in binding a long thread of DNA into a more condensed shape to fit into the nucleus. From histone variants, histone H3 (HH3) plays a crucial role in plant growth and development. Characterization of histones has not been reported in Glycine max till now. The objective of this study was to characterize the HH3 gene family for molecular breeding of G. max. In this study, 17 HH3 members in G. max were identified by performing local BLASTp using HH3 members from Arabidopsis as a query. Phylogenetic analysis classified HH3 genes in seven clades. Sequence logo analysis among Arabidopsis thaliana, Oryza sativa, and Glycine max showed a higher level of similarity in amino acids. Furthermore, conserveness of G. max HH3 genes was also confirmed by Gene Structure Display. Ten paralogous gene pairs were identified in GmHH3 genes in the Glycine max genome by conducting collinearity analysis. G. max HH3 genes have experienced strong purifying selection pressure, with limited functional divergence originating from the segmental and whole-genome duplication, as evidenced by the Ka/Ks ratio. The KASP marker was developed for GmHH3-3 gene. Genotyping was performed on 46 G. max genotypes. This differentiation was based upon the presence of either GmHH3-3-C or GmHH3-3-T allele in the CDS region. The results showed that G. max accessions containing the GmHH3-3-T allele at respective locus showed higher thousand seed weight than that of those accessions that contain the GmHH3-3-C allele. This research provides the basic information to further decipher the function of HH3 in soybean.
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Affiliation(s)
- Chahat Fatima
- Institute of Plant Breeding and Biotechnology, MNS University of Agriculture, Multan, Pakistan
| | | | | | - Zulqurnain Khan
- Institute of Plant Breeding and Biotechnology, MNS University of Agriculture, Multan, Pakistan
| | - Muhammad Sajjad
- Department of Biosciences, COMSATS University Islamabad (CUI), Islamabad, Pakistan
| | - Ghulam Qanmber
- State Key Laboratory of Cotton Biology, Cotton Research Institute of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Essam Darwish
- Plant Physiology Section, Agricultural Botany Department, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Zhide Geng
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Gao Xiangkuo
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, China
- *Correspondence: Gao Xiangkuo, ; Shoaib Ur Rehman,
| | - Shoaib Ur Rehman
- Institute of Plant Breeding and Biotechnology, MNS University of Agriculture, Multan, Pakistan
- *Correspondence: Gao Xiangkuo, ; Shoaib Ur Rehman,
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41
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The chromatin remodeller ATRX facilitates diverse nuclear processes, in a stochastic manner, in both heterochromatin and euchromatin. Nat Commun 2022; 13:3485. [PMID: 35710802 PMCID: PMC9203812 DOI: 10.1038/s41467-022-31194-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 06/07/2022] [Indexed: 12/20/2022] Open
Abstract
The chromatin remodeller ATRX interacts with the histone chaperone DAXX to deposit the histone variant H3.3 at sites of nucleosome turnover. ATRX is known to bind repetitive, heterochromatic regions of the genome including telomeres, ribosomal DNA and pericentric repeats, many of which are putative G-quadruplex forming sequences (PQS). At these sites ATRX plays an ancillary role in a wide range of nuclear processes facilitating replication, chromatin modification and transcription. Here, using an improved protocol for chromatin immunoprecipitation, we show that ATRX also binds active regulatory elements in euchromatin. Mutations in ATRX lead to perturbation of gene expression associated with a reduction in chromatin accessibility, histone modification, transcription factor binding and deposition of H3.3 at the sequences to which it normally binds. In erythroid cells where downregulation of α-globin expression is a hallmark of ATR-X syndrome, perturbation of chromatin accessibility and gene expression occurs in only a subset of cells. The stochastic nature of this process suggests that ATRX acts as a general facilitator of cell specific transcriptional and epigenetic programmes, both in heterochromatin and euchromatin.
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42
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Vaghari-Tabari M, Hassanpour P, Sadeghsoltani F, Malakoti F, Alemi F, Qujeq D, Asemi Z, Yousefi B. CRISPR/Cas9 gene editing: a new approach for overcoming drug resistance in cancer. Cell Mol Biol Lett 2022; 27:49. [PMID: 35715750 PMCID: PMC9204876 DOI: 10.1186/s11658-022-00348-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 05/24/2022] [Indexed: 12/18/2022] Open
Abstract
The CRISPR/Cas9 system is an RNA-based adaptive immune system in bacteria and archaea. Various studies have shown that it is possible to target a wide range of human genes and treat some human diseases, including cancers, by the CRISPR/Cas9 system. In fact, CRISPR/Cas9 gene editing is one of the most efficient genome manipulation techniques. Studies have shown that CRISPR/Cas9 technology, in addition to having the potential to be used as a new therapeutic approach in the treatment of cancers, can also be used to enhance the effectiveness of existing treatments. Undoubtedly, the issue of drug resistance is one of the main obstacles in the treatment of cancers. Cancer cells resist anticancer drugs by a variety of mechanisms, such as enhancing anticancer drugs efflux, enhancing DNA repair, enhancing stemness, and attenuating apoptosis. Mutations in some proteins of different cellular signaling pathways are associated with these events and drug resistance. Recent studies have shown that the CRISPR/Cas9 technique can be used to target important genes involved in these mechanisms, thereby increasing the effectiveness of anticancer drugs. In this review article, studies related to the applications of this technique in overcoming drug resistance in cancer cells will be reviewed. In addition, we will give a brief overview of the limitations of the CRISP/Cas9 gene-editing technique.
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Affiliation(s)
- Mostafa Vaghari-Tabari
- Department of Clinical Biochemistry and Laboratory Medicine, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Parisa Hassanpour
- Department of Clinical Biochemistry and Laboratory Medicine, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Fatemeh Sadeghsoltani
- Department of Clinical Biochemistry and Laboratory Medicine, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Faezeh Malakoti
- Department of Clinical Biochemistry and Laboratory Medicine, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Forough Alemi
- Department of Clinical Biochemistry and Laboratory Medicine, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Durdi Qujeq
- Cellular and Molecular Biology Research Center (CMBRC), Health Research Institute, Babol University of Medical Sciences, Babol, Iran.,Department of Clinical Biochemistry, Babol University of Medical Sciences, Babol, Iran
| | - Zatollah Asemi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, Iran.
| | - Bahman Yousefi
- Department of Clinical Biochemistry and Laboratory Medicine, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran. .,Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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43
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Furth N, Algranati D, Dassa B, Beresh O, Fedyuk V, Morris N, Kasper LH, Jones D, Monje M, Baker SJ, Shema E. H3-K27M-mutant nucleosomes interact with MLL1 to shape the glioma epigenetic landscape. Cell Rep 2022; 39:110836. [PMID: 35584667 DOI: 10.1016/j.celrep.2022.110836] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 03/01/2022] [Accepted: 04/27/2022] [Indexed: 01/08/2023] Open
Abstract
Cancer-associated mutations in genes encoding histones dramatically reshape chromatin and support tumorigenesis. Lysine to methionine substitution of residue 27 on histone H3 (K27M) is a driver mutation in high-grade pediatric gliomas, known to abrogate polycomb repressive complex 2 (PRC2) activity. We applied single-molecule systems to image individual nucleosomes and delineate the combinatorial epigenetic patterns associated with H3-K27M expression. We found that chromatin marks on H3-K27M-mutant nucleosomes are dictated both by their incorporation preferences and by intrinsic properties of the mutation. Mutant nucleosomes not only preferentially bind PRC2 but also directly interact with MLL1, leading to genome-wide redistribution of H3K4me3. H3-K27M-mediated deregulation of repressive and active chromatin marks leads to unbalanced "bivalent" chromatin, which may support a poorly differentiated cellular state. This study provides evidence for a direct effect of H3-K27M oncohistone on the MLL1-H3K4me3 pathway and highlights the capability of single-molecule tools to reveal mechanisms of chromatin deregulation in cancer.
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Affiliation(s)
- Noa Furth
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Danielle Algranati
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Bareket Dassa
- Bioinformatics Unit, Department of Life Sciences Core Facilities, Faculty of Biochemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Olga Beresh
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Vadim Fedyuk
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Natasha Morris
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Lawryn H Kasper
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | | | - Michelle Monje
- Department of Neurology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Suzanne J Baker
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Efrat Shema
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel.
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Xu X, Duan S, Hua X, Li Z, He R, Zhaang Z. Stable inheritance of H3.3-containing nucleosomes during mitotic cell divisions. Nat Commun 2022; 13:2514. [PMID: 35523900 PMCID: PMC9076889 DOI: 10.1038/s41467-022-30298-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 04/22/2022] [Indexed: 12/13/2022] Open
Abstract
Newly synthesized H3.1 and H3.3 histones are assembled into nucleosomes by different histone chaperones in replication-coupled and replication-independent pathways, respectively. However, it is not clear how parental H3.3 molecules are transferred following DNA replication, especially when compared to H3.1. Here, by monitoring parental H3.1- and H3.3-SNAP signals, we show that parental H3.3, like H3.1, are stably transferred into daughter cells. Moreover, Mcm2-Pola1 and Pole3-Pole4, two pathways involved in parental histone transfer based upon the analysis of modifications on parental histones, participate in the transfer of both H3.1 and H3.3 following DNA replication. Lastly, we found that Mcm2, Pole3 and Pole4 mutants defective in parental histone transfer show defects in chromosome segregation. These results indicate that in contrast to deposition of newly synthesized H3.1 and H3.3, transfer of parental H3.1 and H3.3 is mediated by these shared mechanisms, which contributes to epigenetic memory of gene expression and maintenance of genome stability. How nucleosome assembly of parental histones is regulated following DNA replication is still an open question. Here the authors show that unlike deposition of new histones H3.1 and H3.3 that utilizes different histone chaperones, parental H3.1 and H3.3 are both stably inherited during mitotic cell division in mouse embryonic stem cells, and this involves histone chaperones Mcm2, Pole3 and Pole4.
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Affiliation(s)
- Xiaowei Xu
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY, USA.,Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.,Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA.,Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Shoufu Duan
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY, USA.,Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.,Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA.,Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Xu Hua
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY, USA.,Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.,Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA.,Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Zhiming Li
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY, USA.,Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.,Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA.,Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Richard He
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY, USA.,Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.,Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA.,Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Zhiguo Zhaang
- Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY, USA. .,Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA. .,Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA. .,Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA.
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Hou K, Yu Y, Li D, Zhang Y, Zhang K, Tong J, Yang K, Jia S. Alternative Lengthening of Telomeres and Mediated Telomere Synthesis. Cancers (Basel) 2022; 14:cancers14092194. [PMID: 35565323 PMCID: PMC9105334 DOI: 10.3390/cancers14092194] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/24/2022] [Accepted: 04/25/2022] [Indexed: 12/01/2022] Open
Abstract
Simple Summary Alternative lengthing of telomere (ALT) is an important mechanism for maintaining telomere length and cell proliferation in telomerase-negative tumor cells. However, the molecular mechanism of ALT is still poorly understood. ALT occurs in a wide range of tumor types and usually associated with a worse clinical consequence. Here, we review the recent findings of ALT mechanisms, which promise ALT could be a valuable drug target for clinical telomerase-negative tumor treatment. Abstract Telomeres are DNA–protein complexes that protect eukaryotic chromosome ends from being erroneously repaired by the DNA damage repair system, and the length of telomeres indicates the replicative potential of the cell. Telomeres shorten during each division of the cell, resulting in telomeric damage and replicative senescence. Tumor cells tend to ensure cell proliferation potential and genomic stability by activating telomere maintenance mechanisms (TMMs) for telomere lengthening. The alternative lengthening of telomeres (ALT) pathway is the most frequently activated TMM in tumors of mesenchymal and neuroepithelial origin, and ALT also frequently occurs during experimental cellular immortalization of mesenchymal cells. ALT is a process that relies on homologous recombination (HR) to elongate telomeres. However, some processes in the ALT mechanism remain poorly understood. Here, we review the most recent understanding of ALT mechanisms and processes, which may help us to better understand how the ALT pathway is activated in cancer cells and determine the potential therapeutic targets in ALT pathway-stabilized tumors.
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Affiliation(s)
- Kailong Hou
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 Jing Ming Nan Road, Kunming 650500, China;
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, 727 Jing Ming Nan Road, Kunming 650500, China; (Y.Y.); (D.L.); (Y.Z.); (K.Z.); (J.T.)
- First People’s Hospital of Yunnan Province, 157 Jinbi Road, Kunming 650032, China
| | - Yuyang Yu
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, 727 Jing Ming Nan Road, Kunming 650500, China; (Y.Y.); (D.L.); (Y.Z.); (K.Z.); (J.T.)
| | - Duda Li
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, 727 Jing Ming Nan Road, Kunming 650500, China; (Y.Y.); (D.L.); (Y.Z.); (K.Z.); (J.T.)
| | - Yanduo Zhang
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, 727 Jing Ming Nan Road, Kunming 650500, China; (Y.Y.); (D.L.); (Y.Z.); (K.Z.); (J.T.)
| | - Ke Zhang
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, 727 Jing Ming Nan Road, Kunming 650500, China; (Y.Y.); (D.L.); (Y.Z.); (K.Z.); (J.T.)
| | - Jinkai Tong
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, 727 Jing Ming Nan Road, Kunming 650500, China; (Y.Y.); (D.L.); (Y.Z.); (K.Z.); (J.T.)
| | - Kunxian Yang
- First People’s Hospital of Yunnan Province, 157 Jinbi Road, Kunming 650032, China
- Correspondence: (K.Y.); (S.J.)
| | - Shuting Jia
- Laboratory of Molecular Genetics of Aging and Tumor, Medical School, Kunming University of Science and Technology, 727 Jing Ming Nan Road, Kunming 650500, China; (Y.Y.); (D.L.); (Y.Z.); (K.Z.); (J.T.)
- Correspondence: (K.Y.); (S.J.)
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Udugama M, Vinod B, Chan FL, Hii L, Garvie A, Collas P, Kalitsis P, Steer D, Das P, Tripathi P, Mann J, Voon HPJ, Wong L. Histone H3.3 phosphorylation promotes heterochromatin formation by inhibiting H3K9/K36 histone demethylase. Nucleic Acids Res 2022; 50:4500-4514. [PMID: 35451487 PMCID: PMC9071403 DOI: 10.1093/nar/gkac259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 03/25/2022] [Accepted: 04/03/2022] [Indexed: 12/24/2022] Open
Abstract
Histone H3.3 is an H3 variant which differs from the canonical H3.1/2 at four residues, including a serine residue at position 31 which is evolutionarily conserved. The H3.3 S31 residue is phosphorylated (H3.3 S31Ph) at heterochromatin regions including telomeres and pericentric repeats. However, the role of H3.3 S31Ph in these regions remains unknown. In this study, we find that H3.3 S31Ph regulates heterochromatin accessibility at telomeres during replication through regulation of H3K9/K36 histone demethylase KDM4B. In mouse embryonic stem (ES) cells, substitution of S31 with an alanine residue (H3.3 A31 -phosphorylation null mutant) results in increased KDM4B activity that removes H3K9me3 from telomeres. In contrast, substitution with a glutamic acid (H3.3 E31, mimics S31 phosphorylation) inhibits KDM4B, leading to increased H3K9me3 and DNA damage at telomeres. H3.3 E31 expression also increases damage at other heterochromatin regions including the pericentric heterochromatin and Y chromosome-specific satellite DNA repeats. We propose that H3.3 S31Ph regulation of KDM4B is required to control heterochromatin accessibility of repetitive DNA and preserve chromatin integrity.
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Affiliation(s)
| | | | - F Lyn Chan
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Linda Hii
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Andrew Garvie
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Philippe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0317 Oslo, Norway,Department of Immunology and Transfusion Medicine, Oslo University Hospital, 0424 Oslo, Norway
| | - Paul Kalitsis
- Victorian Clinical Genetics Service, Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria 3052, Australia
| | - David Steer
- Biomedical Proteomics Facility, Monash University, Wellington Road, Clayton, Victoria 3800, Australia
| | - Partha P Das
- Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Pratibha Tripathi
- Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Jeffrey R Mann
- Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Hsiao P J Voon
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Lee H Wong
- To whom correspondence should be addressed.
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Dall GV, Hamilton A, Ratnayake G, Scott C, Barker H. Interrogating the Genomic Landscape of Uterine Leiomyosarcoma: A Potential for Patient Benefit. Cancers (Basel) 2022; 14:cancers14061561. [PMID: 35326717 PMCID: PMC8946513 DOI: 10.3390/cancers14061561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/10/2022] [Accepted: 03/16/2022] [Indexed: 11/16/2022] Open
Abstract
Uterine leiomyosarcoma (uLMS) is a rare and aggressive gynaecological malignancy. Surgical removal and chemotherapy are commonly used to treat uLMS, but recurrence rates are high. Over the last few decades, clarification of the genomic landscape of uLMS has revealed a number of recurring mutations, including TP53, RB1, ATRX, PTEN, and MED12. Such genomic aberrations are difficult to target therapeutically or are actively targeted in other malignancies, and their potential as targets for the treatment of uLMS remains largely unexplored. Recent identification of deficiencies in homologous recombination in a minority of these tumours, however, has provided a rationale for investigation of PARP inhibitors in this sub-set. Here, we review these mutations and the evidence for therapeutic avenues that may be applied in uLMS. We also provide a comprehensive background on diagnosis and current therapeutic strategies as well as reviewing preclinical models of uLMS, which may be employed not only in testing emerging therapies but also in understanding this challenging and deadly disease.
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Affiliation(s)
- Genevieve V. Dall
- Walter and Eliza Hall, Institute of Medical Research, Parkville, VIC 3052, Australia; (C.S.); (H.B.)
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia;
- Correspondence:
| | - Anne Hamilton
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia;
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
- Royal Women’s Hospital, Parkville, VIC 3052, Australia;
| | | | - Clare Scott
- Walter and Eliza Hall, Institute of Medical Research, Parkville, VIC 3052, Australia; (C.S.); (H.B.)
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia;
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
- Royal Women’s Hospital, Parkville, VIC 3052, Australia;
| | - Holly Barker
- Walter and Eliza Hall, Institute of Medical Research, Parkville, VIC 3052, Australia; (C.S.); (H.B.)
- Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia;
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Shahbazi Z, Rostami G, Hamid M. New heritable ATRX mutation identified by whole exome sequencing and review. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2022. [DOI: 10.1186/s43042-022-00227-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
The mutations in the ATRX gene have been shown to cause two types of disorders: inherited mutations lead to alpha thalassemia X-linked mental retardation (ATR-X) syndrome and acquired somatic mutations cause alpha thalassemia myelodysplastic syndrome (ATMDS). Here we report a case of ATRX gene mutation without completely features of ATR-X or ATMDS syndromes. Moreover we review previous reports of ATRX gene mutations in both ATR-X syndrome and ATMDS.
Methods
After sample collection and DNA extraction, whole exome sequencing was performed using Illumina HiSeq PE150 apparatus. The results were confirmed using Sanger sequencing for the patients and his relatives. Literature review was performed based on the published data in Web of science, Science direct, Springer link and Pubmed databases.
Results
We identified a hemizygous missense ATRX gene mutation (ATRX, c.2388A > C, p. K796N) as a new disease-causing variant in the patient, heterozygous situation for his mother and his father was hemizygous for wild type allele. The literatures of patients were reviewed regarding the ATR-X syndrome.
Conclusions
According to previous findings, inherited ATRX mutations are associated with a broad spectrum of clinical presentations. Therefore a person with a mild α-thalassemia phenotype may also has mutation in ATRX gene. Accordingly, it is critical for geneticist and physicians to increase awareness in molecular diagnosis of α-thalassemia patients.
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Cheng L, Wang L, Yao Q, Ma L, Duan W, Guan J, Zhang C, Wang K, Liu Z, Wang X, Wang Z, Wu H, Chen Z, Jian F. Clinicoradiological characteristics of primary spinal cord H3 K27M-mutant diffuse midline glioma. J Neurosurg Spine 2022; 36:303-314. [PMID: 34560639 DOI: 10.3171/2021.4.spine2140] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 04/12/2021] [Indexed: 11/06/2022]
Abstract
OBJECTIVE Primary spinal cord H3 K27M-mutant diffuse midline glioma (DMG) is a rare and devastating pathological entity. However, little attention has been paid to this disease. As a result, its clinicoradiological characteristics have yet to be described. The aim of this study was to describe the clinicoradiological characteristics of primary intramedullary H3 K27M-mutant DMG and to compare this tumor with the H3 K27 wild-type to explore potential features that could differentiate the two. METHODS A total of 59 patients with pathologically confirmed intramedullary astrocytoma were included in this study. The cohort was divided into an H3 K27M-mutant group and H3 K27 wild-type group based on the status of H3 K27M according to an immunohistochemistry method. Demographic data, MRI features, and molecular information were collected. Multivariate logistic regression was conducted to investigate variables that might have a role in differentiating an H3 K27M DMG from an H3 K27 wild-type tumor. RESULTS Only symptom duration showed an independent association with the H3 K27M mutation (OR 0.82, 95% CI 0.68-0.94, p = 0.016). Patients with spinal cord H3 K27M-mutant DMG had a shorter symptom duration than patients with H3 K27 wild-type glioma. No significant difference was found in terms of MRI features between the H3 K27M-mutant and H3 K27 wild-type groups. Additionally, H3 K27M-mutant DMG frequently demonstrated overexpression of p53. Survival outcome did not show a statistical difference between the H3 K27-mutant subgroup and H3 K27 wild-type subgroup in histologically high-grade astrocytoma. CONCLUSIONS Symptom duration was associated with an H3 K27M mutation in intramedullary astrocytoma. MRI features were heterogeneous, and no imaging feature was able to predict the H3 K27M mutation. The H3 K27M mutation did not impact survival outcome in spinal histologically high-grade astrocytoma.
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Affiliation(s)
- Lei Cheng
- 1Department of Neurosurgery, Xuanwu Hospital, China International Neuroscience Institute, Capital Medical University, Beijing; and
| | - Leiming Wang
- 2Department of Pathology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Qingyu Yao
- 1Department of Neurosurgery, Xuanwu Hospital, China International Neuroscience Institute, Capital Medical University, Beijing; and
| | - Longbing Ma
- 1Department of Neurosurgery, Xuanwu Hospital, China International Neuroscience Institute, Capital Medical University, Beijing; and
| | - Wanru Duan
- 1Department of Neurosurgery, Xuanwu Hospital, China International Neuroscience Institute, Capital Medical University, Beijing; and
| | - Jian Guan
- 1Department of Neurosurgery, Xuanwu Hospital, China International Neuroscience Institute, Capital Medical University, Beijing; and
| | - Can Zhang
- 1Department of Neurosurgery, Xuanwu Hospital, China International Neuroscience Institute, Capital Medical University, Beijing; and
| | - Kai Wang
- 1Department of Neurosurgery, Xuanwu Hospital, China International Neuroscience Institute, Capital Medical University, Beijing; and
| | - Zhenlei Liu
- 1Department of Neurosurgery, Xuanwu Hospital, China International Neuroscience Institute, Capital Medical University, Beijing; and
| | - Xingwen Wang
- 1Department of Neurosurgery, Xuanwu Hospital, China International Neuroscience Institute, Capital Medical University, Beijing; and
| | - Zuowei Wang
- 1Department of Neurosurgery, Xuanwu Hospital, China International Neuroscience Institute, Capital Medical University, Beijing; and
| | - Hao Wu
- 1Department of Neurosurgery, Xuanwu Hospital, China International Neuroscience Institute, Capital Medical University, Beijing; and
| | - Zan Chen
- 1Department of Neurosurgery, Xuanwu Hospital, China International Neuroscience Institute, Capital Medical University, Beijing; and
| | - Fengzeng Jian
- 1Department of Neurosurgery, Xuanwu Hospital, China International Neuroscience Institute, Capital Medical University, Beijing; and
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50
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Guo P, Liu Y, Geng F, Daman AW, Liu X, Zhong L, Ravishankar A, Lis R, Durán JGB, Itkin T, Tang F, Zhang T, Xiang J, Shido K, Ding BS, Wen D, Josefowicz SZ, Rafii S. Histone variant H3.3 maintains adult haematopoietic stem cell homeostasis by enforcing chromatin adaptability. Nat Cell Biol 2022; 24:99-111. [PMID: 34961794 PMCID: PMC9166935 DOI: 10.1038/s41556-021-00795-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 10/14/2021] [Indexed: 01/25/2023]
Abstract
Histone variants and the associated post-translational modifications that govern the stemness of haematopoietic stem cells (HSCs) and differentiation thereof into progenitors (HSPCs) have not been well defined. H3.3 is a replication-independent H3 histone variant in mammalian systems that is enriched at both H3K4me3- and H3K27me3-marked bivalent genes as well as H3K9me3-marked endogenous retroviral repeats. Here we show that H3.3, but not its chaperone Hira, prevents premature HSC exhaustion and differentiation into granulocyte-macrophage progenitors. H3.3-null HSPCs display reduced expression of stemness and lineage-specific genes with a predominant gain of H3K27me3 marks at their promoter regions. Concomitantly, loss of H3.3 leads to a reduction of H3K9me3 marks at endogenous retroviral repeats, opening up binding sites for the interferon regulatory factor family of transcription factors, allowing the survival of rare, persisting H3.3-null HSCs. We propose a model whereby H3.3 maintains adult HSC stemness by safeguarding the delicate interplay between H3K27me3 and H3K9me3 marks, enforcing chromatin adaptability.
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Affiliation(s)
- Peipei Guo
- Department of Medicine, Division of Regenerative Medicine, Ansary Stem Cell Institute, Weill Cornell Medicine, New York, NY, USA. .,Fibrosis Research Center, Mount Sinai-National Jewish Respiratory Institute, Division of Pulmonary, Critical Care and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Ying Liu
- Department of Medicine, Division of Regenerative Medicine, Ansary Stem Cell Institute, Weill Cornell Medicine, New York, NY, USA.,These authors contributed equally: Peipei Guo, Ying Liu
| | - Fuqiang Geng
- Department of Medicine, Division of Regenerative Medicine, Ansary Stem Cell Institute, Weill Cornell Medicine, New York, NY, USA
| | - Andrew W. Daman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Xiaoyu Liu
- Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY, USA.,Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Liangwen Zhong
- Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Arjun Ravishankar
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Raphael Lis
- Department of Medicine, Division of Regenerative Medicine, Ansary Stem Cell Institute, Weill Cornell Medicine, New York, NY, USA.,Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY, USA
| | - José Gabriel Barcia Durán
- Department of Medicine, Division of Regenerative Medicine, Ansary Stem Cell Institute, Weill Cornell Medicine, New York, NY, USA
| | - Tomer Itkin
- Department of Medicine, Division of Regenerative Medicine, Ansary Stem Cell Institute, Weill Cornell Medicine, New York, NY, USA
| | - Fanying Tang
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.,Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA.,Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Tuo Zhang
- Weill Cornell Genomics Core Facility, New York, NY, USA
| | - Jenny Xiang
- Weill Cornell Genomics Core Facility, New York, NY, USA
| | - Koji Shido
- Department of Medicine, Division of Regenerative Medicine, Ansary Stem Cell Institute, Weill Cornell Medicine, New York, NY, USA
| | - Bi-sen Ding
- Department of Medicine, Division of Regenerative Medicine, Ansary Stem Cell Institute, Weill Cornell Medicine, New York, NY, USA.,Fibrosis Research Center, Mount Sinai–National Jewish Respiratory Institute, Division of Pulmonary, Critical Care and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Duancheng Wen
- Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY, USA.
| | - Steven Z. Josefowicz
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Shahin Rafii
- Department of Medicine, Division of Regenerative Medicine, Ansary Stem Cell Institute, Weill Cornell Medicine, New York, NY, USA.
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