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Rajan A, Fame RM. Brain development and bioenergetic changes. Neurobiol Dis 2024; 199:106550. [PMID: 38849103 DOI: 10.1016/j.nbd.2024.106550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/29/2024] [Accepted: 06/01/2024] [Indexed: 06/09/2024] Open
Abstract
Bioenergetics describe the biochemical processes responsible for energy supply in organisms. When these changes become dysregulated in brain development, multiple neurodevelopmental diseases can occur, implicating bioenergetics as key regulators of neural development. Historically, the discovery of disease processes affecting individual stages of brain development has revealed critical roles that bioenergetics play in generating the nervous system. Bioenergetic-dependent neurodevelopmental disorders include neural tube closure defects, microcephaly, intellectual disability, autism spectrum disorders, epilepsy, mTORopathies, and oncogenic processes. Developmental timing and cell-type specificity of these changes determine the long-term effects of bioenergetic disease mechanisms on brain form and function. Here, we discuss key metabolic regulators of neural progenitor specification, neuronal differentiation (neurogenesis), and gliogenesis. In general, transitions between glycolysis and oxidative phosphorylation are regulated in early brain development and in oncogenesis, and reactive oxygen species (ROS) and mitochondrial maturity play key roles later in differentiation. We also discuss how bioenergetics interface with the developmental regulation of other key neural elements, including the cerebrospinal fluid brain environment. While questions remain about the interplay between bioenergetics and brain development, this review integrates the current state of known key intersections between these processes in health and disease.
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Affiliation(s)
- Arjun Rajan
- Developmental Biology Graduate Program, Stanford University, Stanford, CA 94305, USA
| | - Ryann M Fame
- Department of Neurosurgery, Stanford University, Stanford, CA 94305, USA.
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2
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Buthmann JL, Miller JG, Aghaeepour N, King LS, Stevenson DK, Shaw GM, Wong RJ, Gotlib IH. Large-scale proteomics in the first trimester of pregnancy predict psychopathology and temperament in preschool children: an exploratory study. J Child Psychol Psychiatry 2024; 65:1098-1107. [PMID: 38287782 PMCID: PMC11265978 DOI: 10.1111/jcpp.13948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/23/2023] [Indexed: 01/31/2024]
Abstract
BACKGROUND Understanding the prenatal origins of children's psychopathology is a fundamental goal in developmental and clinical science. Recent research suggests that inflammation during pregnancy can trigger a cascade of fetal programming changes that contribute to vulnerability for the emergence of psychopathology. Most studies, however, have focused on a handful of proinflammatory cytokines and have not explored a range of prenatal biological pathways that may be involved in increasing postnatal risk for emotional and behavioral difficulties. METHODS Using extreme gradient boosted machine learning models, we explored large-scale proteomics, considering over 1,000 proteins from first trimester blood samples, to predict behavior in early childhood. Mothers reported on their 3- to 5-year-old children's (N = 89, 51% female) temperament (Child Behavior Questionnaire) and psychopathology (Child Behavior Checklist). RESULTS We found that machine learning models of prenatal proteomics predict 5%-10% of the variance in children's sadness, perceptual sensitivity, attention problems, and emotional reactivity. Enrichment analyses identified immune function, nervous system development, and cell signaling pathways as being particularly important in predicting children's outcomes. CONCLUSIONS Our findings, though exploratory, suggest processes in early pregnancy that are related to functioning in early childhood. Predictive features included far more proteins than have been considered in prior work. Specifically, proteins implicated in inflammation, in the development of the central nervous system, and in key cell-signaling pathways were enriched in relation to child temperament and psychopathology measures.
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Affiliation(s)
- Jessica L. Buthmann
- Department of Psychology, Stanford University, 450 Serra Mall, Stanford CA 94305
| | - Jonas G. Miller
- Department of Psychological Sciences, University of Connecticut, 406 Babbidge Road, Unit 1020, Storrs, CT 06269-1020
| | - Nima Aghaeepour
- Department of Pediatrics, Stanford University School of Medicine, 291 Campus Drive, Stanford, CA 94305
- Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University School of Medicine, 291 Campus Drive, Stanford, CA 94305
- Department of Biomedical Data Science, Stanford University School of Medicine, 291 Campus Drive, Stanford, CA 94305
| | - Lucy S. King
- Department of Psychology, Stanford University, 450 Serra Mall, Stanford CA 94305
| | - David K. Stevenson
- Department of Pediatrics, Stanford University School of Medicine, 291 Campus Drive, Stanford, CA 94305
| | - Gary M. Shaw
- Department of Pediatrics, Stanford University School of Medicine, 291 Campus Drive, Stanford, CA 94305
| | - Ronald J. Wong
- Department of Pediatrics, Stanford University School of Medicine, 291 Campus Drive, Stanford, CA 94305
| | - Ian H. Gotlib
- Department of Psychology, Stanford University, 450 Serra Mall, Stanford CA 94305
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3
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Godthi A, Min S, Das S, Cruz-Corchado J, Deonarine A, Misel-Wuchter K, Issuree PD, Prahlad V. Neuronal IL-17 controls Caenorhabditis elegans developmental diapause through CEP-1/p53. Proc Natl Acad Sci U S A 2024; 121:e2315248121. [PMID: 38483995 PMCID: PMC10963014 DOI: 10.1073/pnas.2315248121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 02/06/2024] [Indexed: 03/19/2024] Open
Abstract
During metazoan development, how cell division and metabolic programs are coordinated with nutrient availability remains unclear. Here, we show that nutrient availability signaled by the neuronal cytokine, ILC-17.1, switches Caenorhabditis elegans development between reproductive growth and dormancy by controlling the activity of the tumor suppressor p53 ortholog, CEP-1. Specifically, upon food availability, ILC-17.1 signaling by amphid neurons promotes glucose utilization and suppresses CEP-1/p53 to allow growth. In the absence of ILC-17.1, CEP-1/p53 is activated, up-regulates cell-cycle inhibitors, decreases phosphofructokinase and cytochrome C expression, and causes larvae to arrest as stress-resistant, quiescent dauers. We propose a model whereby ILC-17.1 signaling links nutrient availability and energy metabolism to cell cycle progression through CEP-1/p53. These studies describe ancestral functions of IL-17 s and the p53 family of proteins and are relevant to our understanding of neuroimmune mechanisms in cancer. They also reveal a DNA damage-independent function of CEP-1/p53 in invertebrate development and support the existence of a previously undescribed C. elegans dauer pathway.
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Affiliation(s)
- Abhishiktha Godthi
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY14263
- Department of Biology, The University of Iowa, Iowa City, IA52242-1324
| | - Sehee Min
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY14263
- Department of Biology, The University of Iowa, Iowa City, IA52242-1324
| | - Srijit Das
- Department of Biology, The University of Iowa, Iowa City, IA52242-1324
| | - Johnny Cruz-Corchado
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY14263
- Department of Biology, The University of Iowa, Iowa City, IA52242-1324
| | - Andrew Deonarine
- Department of Biology, The University of Iowa, Iowa City, IA52242-1324
| | - Kara Misel-Wuchter
- Department of Internal Medicine, The University of Iowa, Iowa City, IA52242
| | - Priya D. Issuree
- Department of Internal Medicine, The University of Iowa, Iowa City, IA52242
| | - Veena Prahlad
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY14263
- Department of Biology, The University of Iowa, Iowa City, IA52242-1324
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4
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Sojka C, Sloan SA. Gliomas: a reflection of temporal gliogenic principles. Commun Biol 2024; 7:156. [PMID: 38321118 PMCID: PMC10847444 DOI: 10.1038/s42003-024-05833-2] [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: 09/11/2023] [Accepted: 01/18/2024] [Indexed: 02/08/2024] Open
Abstract
The hijacking of early developmental programs is a canonical feature of gliomas where neoplastic cells resemble neurodevelopmental lineages and possess mechanisms of stem cell resilience. Given these parallels, uncovering how and when in developmental time gliomagenesis intersects with normal trajectories can greatly inform our understanding of tumor biology. Here, we review how elapsing time impacts the developmental principles of astrocyte (AS) and oligodendrocyte (OL) lineages, and how these same temporal programs are replicated, distorted, or circumvented in pathological settings such as gliomas. Additionally, we discuss how normal gliogenic processes can inform our understanding of the temporal progression of gliomagenesis, including when in developmental time gliomas originate, thrive, and can be pushed towards upon therapeutic coercion.
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Affiliation(s)
- Caitlin Sojka
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Steven A Sloan
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA.
- Emory Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA, USA.
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5
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Johns DA, Williams RJ, Smith CM, Nadaminti PP, Samarasinghe RM. Novel insights on genetics and epigenetics as clinical targets for paediatric astrocytoma. Clin Transl Med 2024; 14:e1560. [PMID: 38299304 PMCID: PMC10831580 DOI: 10.1002/ctm2.1560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 01/07/2024] [Accepted: 01/12/2024] [Indexed: 02/02/2024] Open
Abstract
Paediatric and adult astrocytomas are notably different, where clinical treatments used for adults are not as effective on children with the same form of cancer and these treatments lead to adverse long-term health concerns. Integrative omics-based studies have shown the pathology and fundamental molecular characteristics differ significantly and cannot be extrapolated from the more widely studied adult disease. Recent clinical advances in our understanding of paediatric astrocytomas, with the aid of next-generation sequencing and epigenome-wide profiling, have led to the identification of key canonical mutations that vary based on the tumour location and age of onset. These driver mutations, in particular the identification of the recurrent histone H3 mutations in high-grade tumours, have confirmed the important role epigenetic dysregulations play in cancer progression. This review summarises the current updates of the classification, epidemiology, pathogenesis and clinical management of paediatric astrocytoma based on their grades and the ongoing clinical trials. It also provides novel insights on genetic and epigenetic alterations as diagnostic biomarkers, highlighting the potential of targeting these pathways as therapeutics for this devastating childhood cancer.
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Affiliation(s)
- Dona A. Johns
- School of Medicine, Deakin UniversityGeelongVictoriaAustralia
| | - Richard J. Williams
- School of Medicine, Deakin UniversityGeelongVictoriaAustralia
- Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin UniversityGeelongVictoriaAustralia
- The Graeme Clark Institute, The University of MelbourneMelbourneVICAustralia
| | - Craig M. Smith
- School of Medicine, Deakin UniversityGeelongVictoriaAustralia
- Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin UniversityGeelongVictoriaAustralia
| | - Pavani P. Nadaminti
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, ParkvilleMelbourneVictoriaAustralia
| | - Rasika M. Samarasinghe
- School of Medicine, Deakin UniversityGeelongVictoriaAustralia
- Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin UniversityGeelongVictoriaAustralia
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6
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Golán-Cancela I, Caja L. The TGF-β Family in Glioblastoma. Int J Mol Sci 2024; 25:1067. [PMID: 38256140 PMCID: PMC10816220 DOI: 10.3390/ijms25021067] [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: 11/14/2023] [Revised: 01/03/2024] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
Members of the transforming growth factor β (TGF-β) family have been implicated in the biology of several cancers. In this review, we focus on the role of TGFβ and bone morphogenetic protein (BMP) signaling in glioblastoma. Glioblastoma (GBM) is the most common malignant brain tumor in adults; it presents at a median age of 64 years, but can occur at any age, including childhood. Unfortunately, there is no cure, and even patients undergoing current treatments (surgical resection, radiotherapy, and chemotherapy) have a median survival of 15 months. There is a great need to identify new therapeutic targets to improve the treatment of GBM patients. TGF-βs signaling promotes tumorigenesis in glioblastoma, while BMPs suppress tumorigenic potential by inducing tumor cell differentiation. In this review, we discuss the actions of TGF-βs and BMPs on cancer cells as well as in the tumor microenvironment, and their use in potential therapeutic intervention.
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Affiliation(s)
| | - Laia Caja
- Department of Medical Biochemistry and Microbiology, Biomedical Center, Uppsala University, SE-75123 Uppsala, Sweden;
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7
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Coulter DW, Chhonker YS, Kumar D, Kesherwani V, Aldhafiri WN, McIntyre EM, Alexander G, Ray S, Joshi SS, Li R, Murry DJ, Chaturvedi NK. Marinopyrrole derivative MP1 as a novel anti-cancer agent in group 3 MYC-amplified Medulloblastoma. J Exp Clin Cancer Res 2024; 43:18. [PMID: 38200580 PMCID: PMC10782703 DOI: 10.1186/s13046-024-02944-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 01/01/2024] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND Medulloblastoma (MB) patients with MYC oncogene amplification or overexpression exhibit extremely poor prognoses and therapy resistance. However, MYC itself has been one of the most challenging targets for cancer treatment. Here, we identify a novel marinopyrrole natural derivative, MP1, that shows desirable anti-MYC and anti-cancer activities in MB. METHODS In this study, using MYC-amplified (Group 3) and non-MYC amplified MB cell lines in vitro and in vivo, we evaluated anti-cancer efficacies and molecular mechanism(s) of MP1. RESULTS MP1 significantly suppressed MB cell growth and sphere counts and induced G2 cell cycle arrest and apoptosis in a MYC-dependent manner. Mechanistically, MP1 strongly downregulated the expression of MYC protein. Our results with RNA-seq revealed that MP1 significantly modulated global gene expression and inhibited MYC-associated transcriptional targets including translation/mTOR targets. In addition, MP1 inhibited MYC-target metabolism, leading to declined energy levels. The combination of MP1 with an FDA-approved mTOR inhibitor temsirolimus synergistically inhibited MB cell growth/survival by downregulating the expression of MYC and mTOR signaling components. Our results further showed that as single agents, both MP1 and temsirolimus, were able to significantly inhibit tumor growth and MYC expression in subcutaneously or orthotopically MYC-amplified MB bearing mice. In combination, there were further anti-MB effects on the tumor growth and MYC expression in mice. CONCLUSION These preclinical findings highlight the promise of marinopyrrole MP1 as a novel MYC inhibition approach for MYC-amplified MB.
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Affiliation(s)
- Don W Coulter
- Department of Pediatrics, Hematology/Oncology Division, University of Nebraska Medical Center, Omaha, NE, 68198, USA
- Child Health Research Institute, University of Nebraska Medical Center, Omaha, NE, 68198, USA
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Yashpal S Chhonker
- Department of Pharmacy Practice & Science, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Devendra Kumar
- Department of Pediatrics, Hematology/Oncology Division, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Varun Kesherwani
- Child Health Research Institute, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Wafaa N Aldhafiri
- Department of Pharmacy Practice & Science, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Erin M McIntyre
- Department of Pediatrics, Hematology/Oncology Division, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Gracey Alexander
- Department of Pediatrics, Hematology/Oncology Division, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Sutapa Ray
- Department of Pediatrics, Hematology/Oncology Division, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Shantaram S Joshi
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Rongshi Li
- Department of Pharmacy Practice & Science, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Daryl J Murry
- Department of Pharmacy Practice & Science, University of Nebraska Medical Center, Omaha, NE, 68198, USA
- Child Health Research Institute, University of Nebraska Medical Center, Omaha, NE, 68198, USA
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Nagendra K Chaturvedi
- Department of Pediatrics, Hematology/Oncology Division, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
- Child Health Research Institute, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
- Department of Pediatrics, Hematology and Oncology Division, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
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8
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Nakano H, Sakai T. Impact of Drosophila LIM homeodomain protein Apterous on the morphology of the adult mushroom body. Biochem Biophys Res Commun 2023; 682:77-84. [PMID: 37804590 DOI: 10.1016/j.bbrc.2023.09.071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 09/23/2023] [Indexed: 10/09/2023]
Abstract
A LIM homeodomain transcription factor Apterous (Ap) regulates embryonic and larval neurodevelopment in Drosophila. Although Ap is still expressed in the adult brain, it remains elusive whether Ap is involved in neurodevelopmental events in the adult brain because flies homozygous for ap mutations are usually lethal before they reach the adult stage. In this study, using adult escapers of ap knockout (KO) homozygotes, we examined whether the complete lack of ap expression affects the morphology of the mushroom body (MB) neurons and Pigment-dispersing factor (Pdf)-positive clock neurons in the adult brain. Although ap KO escapers showed severe structural defects of MB neurons, no clear morphological defects were found in Pdf-positive clock neurons. These results suggest that Ap in the adult brain is essential for the neurodevelopment of specific ap-positive neurons, but it is not necessarily involved in the development of all ap-positive neurons.
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Affiliation(s)
- Hikari Nakano
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, 192-0397, Japan
| | - Takaomi Sakai
- Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, 192-0397, Japan.
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9
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Hazra R, Utama R, Naik P, Dobin A, Spector DL. Identification of glioblastoma stem cell-associated lncRNAs using single-cell RNA sequencing datasets. Stem Cell Reports 2023; 18:2056-2070. [PMID: 37922916 PMCID: PMC10679778 DOI: 10.1016/j.stemcr.2023.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 11/07/2023] Open
Abstract
Glioblastoma multiforme (GBM) is an aggressive, heterogeneous brain tumor in which glioblastoma stem cells (GSCs) are known culprits of therapy resistance. Long non-coding RNAs (lncRNAs) have been shown to play a critical role in both cancer and normal biology. A few studies have suggested that aberrant expression of lncRNAs is associated with GSCs. However, a comprehensive single-cell analysis of the GSC-associated lncRNA transcriptome has not been carried out. Here, we analyzed recently published single-cell RNA sequencing datasets of adult GBM tumors, GBM organoids, GSC-enriched GBM tumors, and developing human brain samples to identify lncRNAs highly expressed in GSCs. We further revealed that the GSC-specific lncRNAs GIHCG and LINC01563 promote proliferation, migration, and stemness in the GSC population. Together, this study identified a panel of uncharacterized GSC-enriched lncRNAs and set the stage for future in-depth studies to examine their role in GBM pathology and their potential as biomarkers and/or therapeutic targets in GBM.
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Affiliation(s)
- Rasmani Hazra
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
| | - Raditya Utama
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Payal Naik
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Alexander Dobin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - David L Spector
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
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10
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Yavuz BR, Arici MK, Demirel HC, Tsai CJ, Jang H, Nussinov R, Tuncbag N. Neurodevelopmental disorders and cancer networks share pathways, but differ in mechanisms, signaling strength, and outcome. NPJ Genom Med 2023; 8:37. [PMID: 37925498 PMCID: PMC10625621 DOI: 10.1038/s41525-023-00377-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 10/02/2023] [Indexed: 11/06/2023] Open
Abstract
Epidemiological studies suggest that individuals with neurodevelopmental disorders (NDDs) are more prone to develop certain types of cancer. Notably, however, the case statistics can be impacted by late discovery of cancer in individuals afflicted with NDDs, such as intellectual disorders, autism, and schizophrenia, which may bias the numbers. As to NDD-associated mutations, in most cases, they are germline while cancer mutations are sporadic, emerging during life. However, somatic mosaicism can spur NDDs, and cancer-related mutations can be germline. NDDs and cancer share proteins, pathways, and mutations. Here we ask (i) exactly which features they share, and (ii) how, despite their commonalities, they differ in clinical outcomes. To tackle these questions, we employed a statistical framework followed by network analysis. Our thorough exploration of the mutations, reconstructed disease-specific networks, pathways, and transcriptome levels and profiles of autism spectrum disorder (ASD) and cancers, point to signaling strength as the key factor: strong signaling promotes cell proliferation in cancer, and weaker (moderate) signaling impacts differentiation in ASD. Thus, we suggest that signaling strength, not activating mutations, can decide clinical outcome.
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Affiliation(s)
- Bengi Ruken Yavuz
- Graduate School of Informatics, Middle East Technical University, Ankara, 06800, Turkey
- Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - M Kaan Arici
- Graduate School of Informatics, Middle East Technical University, Ankara, 06800, Turkey
| | - Habibe Cansu Demirel
- Graduate School of Sciences and Engineering, Koc University, Istanbul, 34450, Turkey
| | - Chung-Jung Tsai
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD, 21702, USA.
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel.
| | - Nurcan Tuncbag
- Chemical and Biological Engineering, College of Engineering, Koc University, Istanbul, Turkey.
- School of Medicine, Koc University, Istanbul, 34450, Turkey.
- Koc University Research Center for Translational Medicine (KUTTAM), Istanbul, Turkey.
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11
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Fabro F, Kers TV, Feller KJ, Beerens C, Ntafoulis I, Idbaih A, Verreault M, Connor K, Biswas A, Salvucci M, Prehn JHM, Byrne AT, O’Farrell AC, Lambrechts D, Dilcan G, Lodi F, Arijs I, Kremer A, Tching Chi Yen R, Chien MP, Lamfers MLM, Leenstra S. Genomic Exploration of Distinct Molecular Phenotypes Steering Temozolomide Resistance Development in Patient-Derived Glioblastoma Cells. Int J Mol Sci 2023; 24:15678. [PMID: 37958662 PMCID: PMC10647455 DOI: 10.3390/ijms242115678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Chemotherapy using temozolomide is the standard treatment for patients with glioblastoma. Despite treatment, prognosis is still poor largely due to the emergence of temozolomide resistance. This resistance is closely linked to the widely recognized inter- and intra-tumoral heterogeneity in glioblastoma, although the underlying mechanisms are not yet fully understood. To induce temozolomide resistance, we subjected 21 patient-derived glioblastoma cell cultures to Temozolomide treatment for a period of up to 90 days. Prior to treatment, the cells' molecular characteristics were analyzed using bulk RNA sequencing. Additionally, we performed single-cell RNA sequencing on four of the cell cultures to track the evolution of temozolomide resistance. The induced temozolomide resistance was associated with two distinct phenotypic behaviors, classified as "adaptive" (ADA) or "non-adaptive" (N-ADA) to temozolomide. The ADA phenotype displayed neurodevelopmental and metabolic gene signatures, whereas the N-ADA phenotype expressed genes related to cell cycle regulation, DNA repair, and protein synthesis. Single-cell RNA sequencing revealed that in ADA cell cultures, one or more subpopulations emerged as dominant in the resistant samples, whereas N-ADA cell cultures remained relatively stable. The adaptability and heterogeneity of glioblastoma cells play pivotal roles in temozolomide treatment and contribute to the tumor's ability to survive. Depending on the tumor's adaptability potential, subpopulations with acquired resistance mechanisms may arise.
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Affiliation(s)
- Federica Fabro
- Department of Neurosurgery Rotterdam, Brain Tumor Center, Erasmus Medical Center Cancer Institute, Erasmus Medical Center, Wytemaweg 80, Ee2236, 3015 CN Rotterdam, The Netherlands; (F.F.); (M.L.M.L.)
| | - Trisha V. Kers
- Department of Neurosurgery Rotterdam, Brain Tumor Center, Erasmus Medical Center Cancer Institute, Erasmus Medical Center, Wytemaweg 80, Ee2236, 3015 CN Rotterdam, The Netherlands; (F.F.); (M.L.M.L.)
| | - Kate J. Feller
- Department of Molecular Genetics, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands
| | - Cecile Beerens
- Department of Molecular Genetics, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands
| | - Ioannis Ntafoulis
- Department of Neurosurgery Rotterdam, Brain Tumor Center, Erasmus Medical Center Cancer Institute, Erasmus Medical Center, Wytemaweg 80, Ee2236, 3015 CN Rotterdam, The Netherlands; (F.F.); (M.L.M.L.)
| | - Ahmed Idbaih
- DMU Neurosciences, Service de Neurologie 2-Mazarin, Sorbonne Université, AP-HP, Institut du Cerveau—Paris Brain Institute—ICM, CNRS, University Hospital La Pitié Salpêtrière—Charles Foix, Inserm, F-75013 Paris, France
| | - Maite Verreault
- DMU Neurosciences, Service de Neurologie 2-Mazarin, Sorbonne Université, AP-HP, Institut du Cerveau—Paris Brain Institute—ICM, CNRS, University Hospital La Pitié Salpêtrière—Charles Foix, Inserm, F-75013 Paris, France
| | - Kate Connor
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, D02 YN77 Dublin, Ireland
| | - Archita Biswas
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, D02 YN77 Dublin, Ireland
| | - Manuela Salvucci
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, D02 YN77 Dublin, Ireland
| | - Jochen H. M. Prehn
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, D02 YN77 Dublin, Ireland
| | - Annette T. Byrne
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, D02 YN77 Dublin, Ireland
| | - Alice C. O’Farrell
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, D02 YN77 Dublin, Ireland
| | - Diether Lambrechts
- Department of Human Genetics, Laboratory for Translational Genetics, VIB Center for Cancer Biology, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Gonca Dilcan
- Department of Human Genetics, Laboratory for Translational Genetics, VIB Center for Cancer Biology, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Francesca Lodi
- Department of Human Genetics, Laboratory for Translational Genetics, VIB Center for Cancer Biology, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Ingrid Arijs
- Department of Human Genetics, Laboratory for Translational Genetics, VIB Center for Cancer Biology, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Andreas Kremer
- Information Technologies for Translational Medicine, L-4354 Esch-Sur-Alzette, Luxembourg
| | - Romain Tching Chi Yen
- Information Technologies for Translational Medicine, L-4354 Esch-Sur-Alzette, Luxembourg
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-Belval Esch-Sur-Alzette, Luxembourg
| | - Miao-Ping Chien
- Department of Molecular Genetics, Erasmus University Medical Center, 3015 CN Rotterdam, The Netherlands
- Oncode Institute, 3521 AL Utrecht, The Netherlands
| | - Martine L. M. Lamfers
- Department of Neurosurgery Rotterdam, Brain Tumor Center, Erasmus Medical Center Cancer Institute, Erasmus Medical Center, Wytemaweg 80, Ee2236, 3015 CN Rotterdam, The Netherlands; (F.F.); (M.L.M.L.)
| | - Sieger Leenstra
- Department of Neurosurgery Rotterdam, Brain Tumor Center, Erasmus Medical Center Cancer Institute, Erasmus Medical Center, Wytemaweg 80, Ee2236, 3015 CN Rotterdam, The Netherlands; (F.F.); (M.L.M.L.)
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12
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Wen J, Liu F, Cheng Q, Weygant N, Liang X, Fan F, Li C, Zhang L, Liu Z. Applications of organoid technology to brain tumors. CNS Neurosci Ther 2023; 29:2725-2743. [PMID: 37248629 PMCID: PMC10493676 DOI: 10.1111/cns.14272] [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: 04/04/2023] [Revised: 05/07/2023] [Accepted: 05/09/2023] [Indexed: 05/31/2023] Open
Abstract
Lacking appropriate model impedes basic and preclinical researches of brain tumors. Organoids technology applying on brain tumors enables great recapitulation of the original tumors. Here, we compared brain tumor organoids (BTOs) with common models including cell lines, tumor spheroids, and patient-derived xenografts. Different BTOs can be customized to research objectives and particular brain tumor features. We systematically introduce the establishments and strengths of four different BTOs. BTOs derived from patient somatic cells are suitable for mimicking brain tumors caused by germline mutations and abnormal neurodevelopment, such as the tuberous sclerosis complex. BTOs derived from human pluripotent stem cells with genetic manipulations endow for identifying and understanding the roles of oncogenes and processes of oncogenesis. Brain tumoroids are the most clinically applicable BTOs, which could be generated within clinically relevant timescale and applied for drug screening, immunotherapy testing, biobanking, and investigating brain tumor mechanisms, such as cancer stem cells and therapy resistance. Brain organoids co-cultured with brain tumors (BO-BTs) own the greatest recapitulation of brain tumors. Tumor invasion and interactions between tumor cells and brain components could be greatly explored in this model. BO-BTs also offer a humanized platform for testing the therapeutic efficacy and side effects on neurons in preclinical trials. We also introduce the BTOs establishment fused with other advanced techniques, such as 3D bioprinting. So far, over 11 brain tumor types of BTOs have been established, especially for glioblastoma. We conclude BTOs could be a reliable model to understand brain tumors and develop targeted therapies.
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Affiliation(s)
- Jie Wen
- Department of NeurosurgeryXiangya Hospital, Central South UniversityChangshaHunanChina
- Hypothalamic‐pituitary Research CenterXiangya Hospital, Central South UniversityChangshaHunanChina
- National Clinical Research Center for Geriatric DisordersXiangya Hospital, Central South UniversityChangshaHunanChina
| | - Fangkun Liu
- Department of NeurosurgeryXiangya Hospital, Central South UniversityChangshaHunanChina
- Hypothalamic‐pituitary Research CenterXiangya Hospital, Central South UniversityChangshaHunanChina
- National Clinical Research Center for Geriatric DisordersXiangya Hospital, Central South UniversityChangshaHunanChina
| | - Quan Cheng
- Department of NeurosurgeryXiangya Hospital, Central South UniversityChangshaHunanChina
- Hypothalamic‐pituitary Research CenterXiangya Hospital, Central South UniversityChangshaHunanChina
- National Clinical Research Center for Geriatric DisordersXiangya Hospital, Central South UniversityChangshaHunanChina
| | - Nathaniel Weygant
- Academy of Integrative MedicineFujian University of Traditional Chinese MedicineFuzhouFujianChina
- Fujian Key Laboratory of Integrative Medicine in GeriatricsFujian University of Traditional Chinese MedicineFuzhouFujianChina
| | - Xisong Liang
- Department of NeurosurgeryXiangya Hospital, Central South UniversityChangshaHunanChina
- Hypothalamic‐pituitary Research CenterXiangya Hospital, Central South UniversityChangshaHunanChina
- National Clinical Research Center for Geriatric DisordersXiangya Hospital, Central South UniversityChangshaHunanChina
| | - Fan Fan
- Department of NeurosurgeryXiangya Hospital, Central South UniversityChangshaHunanChina
- Hypothalamic‐pituitary Research CenterXiangya Hospital, Central South UniversityChangshaHunanChina
- National Clinical Research Center for Geriatric DisordersXiangya Hospital, Central South UniversityChangshaHunanChina
| | - Chuntao Li
- Department of NeurosurgeryXiangya Hospital, Central South UniversityChangshaHunanChina
- Hypothalamic‐pituitary Research CenterXiangya Hospital, Central South UniversityChangshaHunanChina
- National Clinical Research Center for Geriatric DisordersXiangya Hospital, Central South UniversityChangshaHunanChina
| | - Liyang Zhang
- Department of NeurosurgeryXiangya Hospital, Central South UniversityChangshaHunanChina
- Hypothalamic‐pituitary Research CenterXiangya Hospital, Central South UniversityChangshaHunanChina
- National Clinical Research Center for Geriatric DisordersXiangya Hospital, Central South UniversityChangshaHunanChina
| | - Zhixiong Liu
- Department of NeurosurgeryXiangya Hospital, Central South UniversityChangshaHunanChina
- Hypothalamic‐pituitary Research CenterXiangya Hospital, Central South UniversityChangshaHunanChina
- National Clinical Research Center for Geriatric DisordersXiangya Hospital, Central South UniversityChangshaHunanChina
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13
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Gonçalves TM, Stewart CL, Baxley SD, Xu J, Li D, Gabel HW, Wang T, Avraham O, Zhao G. Towards a comprehensive regulatory map of Mammalian Genomes. RESEARCH SQUARE 2023:rs.3.rs-3294408. [PMID: 37841836 PMCID: PMC10571623 DOI: 10.21203/rs.3.rs-3294408/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Genome mapping studies have generated a nearly complete collection of genes for the human genome, but we still lack an equivalently vetted inventory of human regulatory sequences. Cis-regulatory modules (CRMs) play important roles in controlling when, where, and how much a gene is expressed. We developed a training data-free CRM-prediction algorithm, the Mammalian Regulatory MOdule Detector (MrMOD) for accurate CRM prediction in mammalian genomes. MrMOD provides genome position-fixed CRM models similar to the fixed gene models for the mouse and human genomes using only genomic sequences as the inputs with one adjustable parameter - the significance p-value. Importantly, MrMOD predicts a comprehensive set of high-resolution CRMs in the mouse and human genomes including all types of regulatory modules not limited to any tissue, cell type, developmental stage, or condition. We computationally validated MrMOD predictions used a compendium of 21 orthogonal experimental data sets including thousands of experimentally defined CRMs and millions of putative regulatory elements derived from hundreds of different tissues, cell types, and stimulus conditions obtained from multiple databases. In ovo transgenic reporter assay demonstrates the power of our prediction in guiding experimental design. We analyzed CRMs located in the chromosome 17 using unsupervised machine learning and identified groups of CRMs with multiple lines of evidence supporting their functionality, linking CRMs with upstream binding transcription factors and downstream target genes. Our work provides a comprehensive base pair resolution annotation of the functional regulatory elements and non-functional regions in the mammalian genomes.
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Affiliation(s)
| | | | | | - Jason Xu
- Missouri University of Science & Technology
| | - Daofeng Li
- Washington University School of Medicine
| | | | - Ting Wang
- Washington University School of Medicine
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14
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Schoof M, Epplen GD, Walter C, Ballast A, Holdhof D, Göbel C, Neyazi S, Varghese J, Albert TK, Kerl K, Schüller U. The tumor suppressor CREBBP and the oncogene MYCN cooperate to induce malignant brain tumors in mice. Oncogenesis 2023; 12:36. [PMID: 37407554 DOI: 10.1038/s41389-023-00481-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 05/26/2023] [Accepted: 06/20/2023] [Indexed: 07/07/2023] Open
Abstract
The tumor suppressor and chromatin modifier cAMP response element-binding protein binding protein (CREBBP) and v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog (MYCN), a member of the MYC oncogene family, are critically involved in brain development. Both genes are frequently mutated in the same tumor entities, including high-grade glioma and medulloblastoma. Therefore, we hypothesized that alterations in both genes cooperate to induce brain tumor formation. For further investigation, hGFAP-cre::CrebbpFl/Fl::lsl-MYCN mice were generated, which combine Crebbp deletion with overexpression of MYCN in neural stem cells (NSCs). Within eight months, these animals developed aggressive forebrain tumors. The first tumors were detectable in the olfactory bulbs of seven-day-old mice. This location raises the possibility that presumptive founder cells are derived from the ventricular-subventricular zone (V-SVZ). To examine the cellular biology of these tumors, single-cell RNA sequencing was performed, which revealed high intratumoral heterogeneity. Data comparison with reference CNS cell types indicated the highest similarity of tumor cells with transit-amplifying NSCs or activated NSCs of the V-SVZ. Consequently, we analyzed V-SVZ NSCs of our mouse model aiming to confirm that the tumors originate from this stem cell niche. Mutant V-SVZ NSCs showed significantly increased cell viability and proliferation as well as reduced glial and neural differentiation in vitro compared to control cells. In summary, we demonstrate the oncogenic potential of a combined loss of function of CREBBP and overexpression of MYCN in this cell population. hGFAP-cre::CrebbpFl/Fl::lsl-MYCN mice thus provide a valuable tool to study tumor-driving mechanisms in a key neural stem/ progenitor cell niche.
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Affiliation(s)
- Melanie Schoof
- Research Institute Children`s Cancer Center, Hamburg, Germany
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Carolin Walter
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Annika Ballast
- Department of Pediatric Hematology and Oncology, University Children's Hospital Münster, Münster, Germany
| | - Dörthe Holdhof
- Research Institute Children`s Cancer Center, Hamburg, Germany
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Carolin Göbel
- Research Institute Children`s Cancer Center, Hamburg, Germany
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sina Neyazi
- Research Institute Children`s Cancer Center, Hamburg, Germany
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julian Varghese
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Thomas Karl Albert
- Department of Pediatric Hematology and Oncology, University Children's Hospital Münster, Münster, Germany
| | - Kornelius Kerl
- Department of Pediatric Hematology and Oncology, University Children's Hospital Münster, Münster, Germany
| | - Ulrich Schüller
- Research Institute Children`s Cancer Center, Hamburg, Germany.
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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15
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Han YP, Lin HW, Li H. Cancer Stem Cells in Tumours of the Central Nervous System in Children: A Comprehensive Review. Cancers (Basel) 2023; 15:3154. [PMID: 37370764 DOI: 10.3390/cancers15123154] [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: 04/14/2023] [Revised: 05/30/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Cancer stem cells (CSCs) are a subgroup of cells found in various kinds of tumours with stem cell characteristics, such as self-renewal, induced differentiation, and tumourigenicity. The existence of CSCs is regarded as a major source of tumour recurrence, metastasis, and resistance to conventional chemotherapy and radiation treatment. Tumours of the central nervous system (CNS) are the most common solid tumours in children, which have many different types including highly malignant embryonal tumours and midline gliomas, and low-grade gliomas with favourable prognoses. Stem cells from the CNS tumours have been largely found and reported by researchers in the last decade and their roles in tumour biology have been deeply studied. However, the cross-talk of CSCs among different CNS tumour types and their clinical impacts have been rarely discussed. This article comprehensively reviews the achievements in research on CSCs in paediatric CNS tumours. Biological functions, diagnostic values, and therapeutic perspectives are reviewed in detail. Further investigations into CSCs are warranted to improve the clinical practice in treating children with CNS tumours.
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Affiliation(s)
- Yi-Peng Han
- Department of Neurosurgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Hou-Wei Lin
- Department of Paediatric Urology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
- Department of Paediatric Surgery, Jiaxing Women and Children Hospital Affiliated to Jiaxing University, Jiaxing 314001, China
| | - Hao Li
- Department of Neurosurgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
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16
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Perrault EN, Shireman JM, Ali ES, Lin P, Preddy I, Park C, Budhiraja S, Baisiwala S, Dixit K, James CD, Heiland DH, Ben-Sahra I, Pott S, Basu A, Miska J, Ahmed AU. Ribonucleotide reductase regulatory subunit M2 drives glioblastoma TMZ resistance through modulation of dNTP production. SCIENCE ADVANCES 2023; 9:eade7236. [PMID: 37196077 PMCID: PMC10191446 DOI: 10.1126/sciadv.ade7236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 04/13/2023] [Indexed: 05/19/2023]
Abstract
During therapy, adaptations driven by cellular plasticity are partly responsible for driving the inevitable recurrence of glioblastoma (GBM). To investigate plasticity-induced adaptation during standard-of-care chemotherapy temozolomide (TMZ), we performed in vivo single-cell RNA sequencing in patient-derived xenograft (PDX) tumors of GBM before, during, and after therapy. Comparing single-cell transcriptomic patterns identified distinct cellular populations present during TMZ therapy. Of interest was the increased expression of ribonucleotide reductase regulatory subunit M2 (RRM2), which we found to regulate dGTP and dCTP production vital for DNA damage response during TMZ therapy. Furthermore, multidimensional modeling of spatially resolved transcriptomic and metabolomic analysis in patients' tissues revealed strong correlations between RRM2 and dGTP. This supports our data that RRM2 regulates the demand for specific dNTPs during therapy. In addition, treatment with the RRM2 inhibitor 3-AP (Triapine) enhances the efficacy of TMZ therapy in PDX models. We present a previously unidentified understanding of chemoresistance through critical RRM2-mediated nucleotide production.
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Affiliation(s)
- Ella N. Perrault
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Jack M. Shireman
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Eunus S. Ali
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Peiyu Lin
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Isabelle Preddy
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Cheol Park
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Shreya Budhiraja
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Shivani Baisiwala
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Karan Dixit
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - C. David James
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Northwestern Medicine Malnati Brain Tumor Institute of the Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Dieter H Heiland
- Microenvironment and Immunology Research Laboratory, Medical-Center, University of Freiburg, Freiburg, Germany
- Department of Neurosurgery, Medical-Center, University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), partner site Freiburg, Freiburg, Germany
| | - Issam Ben-Sahra
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Sebastian Pott
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Anindita Basu
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Jason Miska
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Atique U. Ahmed
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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17
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Hazra R, Utama R, Naik P, Dobin A, Spector DL. Identification of glioblastoma stem cell-associated lncRNAs using single-cell RNA-sequencing datasets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.20.524887. [PMID: 36711961 PMCID: PMC9882256 DOI: 10.1101/2023.01.20.524887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Glioblastoma multiforme (GBM) is an aggressive, heterogeneous grade IV brain tumor. Glioblastoma stem cells (GSCs) initiate the tumor and are known culprits of therapy resistance. Mounting evidence has demonstrated a regulatory role of long non-coding RNAs (lncRNAs) in various biological processes, including pluripotency, differentiation, and tumorigenesis. A few studies have suggested that aberrant expression of lncRNAs is associated with GSCs. However, a comprehensive single-cell analysis of the GSC-associated lncRNA transcriptome has not been carried out. Here, we analyzed recently published single-cell RNA-sequencing datasets of adult human GBM tumors, GBM organoids, GSC-enriched GBM tumors, and developing human brains to identify lncRNAs highly expressed in GBM. To categorize GSC populations in the GBM tumors, we used the GSC marker genes SOX2, PROM1, FUT4, and L1CAM. We found three major GSC population clusters: radial glia, oligodendrocyte progenitor cells, and neurons. We found 10â€"100 lncRNAs significantly enriched in different GSC populations. We also validated the level of expression and localization of several GSC-enriched lncRNAs using qRT-PCR, single-molecule RNA FISH, and sub-cellular fractionation. We found that the radial glia GSC-enriched lncRNA PANTR1 is highly expressed in GSC lines and is localized to both the cytoplasmic and nuclear fractions. In contrast, the neuronal GSC-enriched lncRNAs LINC01563 and MALAT1 are highly enriched in the nuclear fraction of GSCs. Together, this study identified a panel of uncharacterized GSC-specific lncRNAs. These findings set the stage for future in-depth studies to examine their role in GBM pathology and their potential as biomarkers and/or therapeutic targets in GBM.
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18
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Singh A, Rajeevan A, Gopalan V, Agrawal P, Day CP, Hannenhalli S. Broad misappropriation of developmental splicing profile by cancer in multiple organs. Nat Commun 2022; 13:7664. [PMID: 36509773 PMCID: PMC9744839 DOI: 10.1038/s41467-022-35322-1] [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: 12/18/2021] [Accepted: 11/29/2022] [Indexed: 12/14/2022] Open
Abstract
Oncogenesis mimics key aspects of embryonic development. However, the underlying mechanisms are incompletely understood. Here, we demonstrate that the splicing events specifically active during human organogenesis, are broadly reactivated in the organ-specific tumor. Such events are associated with key oncogenic processes and predict proliferation rates in cancer cell lines as well as patient survival. Such events preferentially target nitrosylation and transmembrane-region domains, whose coordinated splicing in multiple genes respectively affect intracellular transport and N-linked glycosylation. We infer critical splicing factors potentially regulating embryonic splicing events and show that such factors are potential oncogenic drivers and are upregulated specifically in malignant cells. Multiple complementary analyses point to MYC and FOXM1 as potential transcriptional regulators of critical splicing factors in brain and liver. Our study provides a comprehensive demonstration of a splicing-mediated link between development and cancer, and suggest anti-cancer targets including splicing events, and their upstream splicing and transcriptional regulators.
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Affiliation(s)
- Arashdeep Singh
- grid.48336.3a0000 0004 1936 8075Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Arati Rajeevan
- grid.48336.3a0000 0004 1936 8075Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Vishaka Gopalan
- grid.48336.3a0000 0004 1936 8075Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Piyush Agrawal
- grid.48336.3a0000 0004 1936 8075Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Chi-Ping Day
- grid.94365.3d0000 0001 2297 5165Laboratory of Cancer Biology and Genetics National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Sridhar Hannenhalli
- grid.48336.3a0000 0004 1936 8075Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
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19
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D’Amico M, De Amicis F. Aberrant Notch signaling in gliomas: a potential landscape of actionable converging targets for combination approach in therapies resistance. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2022; 5:939-953. [PMID: 36627893 PMCID: PMC9771760 DOI: 10.20517/cdr.2022.46] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/06/2022] [Accepted: 09/02/2022] [Indexed: 11/06/2022]
Abstract
The current therapeutic protocols and prognosis of gliomas still depend on clinicopathologic and radiographic characteristics. For high-grade gliomas, the standard of care is resection followed by radiotherapy plus temozolomide chemotherapy. However, treatment resistance develops due to different mechanisms, among which is the dynamic interplay between the tumor and its microenvironment. Different signaling pathways cause the proliferation of so-called glioma stem cells, a minor cancer cell population with stem cell-like characteristics and aggressive phenotype. In the last decades, numerous studies have indicated that Notch is a crucial pathway that maintains the characteristics of resistant glioma stem cells. Data obtained from preclinical models indicate that downregulation of the Notch pathway could induce multifaceted drug sensitivity, acting on the expression of drug-transporter proteins, inducing epithelial-mesenchymal transition, and shaping the tumor microenvironment. This review provides a brief overview of the published data supporting the roles of Notch in drug resistance and demonstrates how potential novel strategies targeting Notch could become an efficacious action to improve the therapy of high-grade glioma to overcome drug resistance.
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Affiliation(s)
- Maria D’Amico
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Via P. Bucci, Rende 87036, Italy
| | - Francesca De Amicis
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Via P. Bucci, Rende 87036, Italy.,Health Center, University of Calabria, Via P. Bucci, Rende 87036, Italy.,Correspondence to: Prof. Francesca De Amicis, Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Via P. Bucci, Rende 87036, Italy. E-mail:
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20
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Current Opportunities for Targeting Dysregulated Neurodevelopmental Signaling Pathways in Glioblastoma. Cells 2022; 11:cells11162530. [PMID: 36010607 PMCID: PMC9406959 DOI: 10.3390/cells11162530] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/06/2022] [Accepted: 08/09/2022] [Indexed: 11/29/2022] Open
Abstract
Glioblastoma (GBM) is the most common and highly lethal type of brain tumor, with poor survival despite advances in understanding its complexity. After current standard therapeutic treatment, including tumor resection, radiotherapy and concomitant chemotherapy with temozolomide, the median overall survival of patients with this type of tumor is less than 15 months. Thus, there is an urgent need for new insights into GBM molecular characteristics and progress in targeted therapy in order to improve clinical outcomes. The literature data revealed that a number of different signaling pathways are dysregulated in GBM. In this review, we intended to summarize and discuss current literature data and therapeutic modalities focused on targeting dysregulated signaling pathways in GBM. A better understanding of opportunities for targeting signaling pathways that influences malignant behavior of GBM cells might open the way for the development of novel GBM-targeted therapies.
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21
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Abstract
Immunity could be viewed as the common factor in neurodevelopmental disorders and cancer. The immune and nervous systems coevolve as the embryo develops. Immunity can release cytokines that activate MAPK signaling in neural cells. In specific embryonic brain cell types, dysregulated signaling that results from germline or embryonic mutations can promote changes in chromatin organization and gene accessibility, and thus expression levels of essential genes in neurodevelopment. In cancer, dysregulated signaling can emerge from sporadic somatic mutations during human life. Neurodevelopmental disorders and cancer share similarities. In neurodevelopmental disorders, immunity, and cancer, there appears an almost invariable involvement of small GTPases (e.g., Ras, RhoA, and Rac) and their pathways. TLRs, IL-1, GIT1, and FGFR signaling pathways, all can be dysregulated in neurodevelopmental disorders and cancer. Although there are signaling similarities, decisive differentiating factors are timing windows, and cell type specific perturbation levels, pointing to chromatin reorganization. Finally, we discuss drug discovery.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702, USA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Corresponding author
| | - Chung-Jung Tsai
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702, USA
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22
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Single cell RNA sequencing reveals differentiation related genes with drawing implications in predicting prognosis and immunotherapy response in gliomas. Sci Rep 2022; 12:1872. [PMID: 35115572 PMCID: PMC8814011 DOI: 10.1038/s41598-022-05686-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 01/17/2022] [Indexed: 11/30/2022] Open
Abstract
Differentiation states of glioma cells correlated with prognosis and tumor-immune microenvironment (TIME) in patients with gliomas. We aimed to identify differentiation related genes (DRGs) for predicting the prognosis and immunotherapy response in patients with gliomas. We identified three differentiation states and the corresponding DRGs in glioma cells through single-cell transcriptomics analysis. Based on the DRGs, we separated glioma patients into three clusters with distinct clinicopathological features in combination with bulk RNA-seq data. Weighted correlation network analysis, univariate cox regression analysis and least absolute shrinkage and selection operator analysis were involved in the construction of the prognostic model based on DRGs. Distinct clinicopathological characteristics, TIME, immunogenomic patterns and immunotherapy responses were identified across three clusters. A DRG signature composing of 12 genes were identified for predicting the survival of glioma patients and nomogram model integrating the risk score and multi-clinicopathological factors were constructed for clinical practice. Patients in high-risk group tended to get shorter overall survival and better response to immune checkpoint blockage therapy. We obtained 9 candidate drugs through comprehensive analysis of the differentially expressed genes between the low and high-risk groups in the model. Our findings indicated that the risk score may not only contribute to the determination of prognosis but also facilitate in the prediction of immunotherapy response in glioma patients.
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Nussinov R, Tsai CJ, Jang H. How can same-gene mutations promote both cancer and developmental disorders? SCIENCE ADVANCES 2022; 8:eabm2059. [PMID: 35030014 PMCID: PMC8759737 DOI: 10.1126/sciadv.abm2059] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/22/2021] [Indexed: 05/05/2023]
Abstract
The question of how same-gene mutations can drive both cancer and neurodevelopmental disorders has been puzzling. It has also been puzzling why those with neurodevelopmental disorders have a high risk of cancer. Ras, MEK, PI3K, PTEN, and SHP2 are among the oncogenic proteins that can harbor mutations that encode diseases other than cancer. Understanding why some of their mutations can promote cancer, whereas others promote neurodevelopmental diseases, and why even the same mutations may promote both phenotypes, has important clinical ramifications. Here, we review the literature and address these tantalizing questions. We propose that cell type–specific expression of the mutant protein, and of other proteins in the respective pathway, timing of activation (during embryonic development or sporadic emergence), and the absolute number of molecules that the mutations activate, alone or in combination, are pivotal in determining the pathological phenotypes—cancer and (or) developmental disorders.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Chung-Jung Tsai
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
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