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Yu H, Liu Y, Xu F, Fu Y, Yang M, Ding L, Wu Y, Tang F, Qiao J, Wen L. A human fetal cerebellar map of the late second trimester reveals developmental molecular characteristics and abnormality in trisomy 21. Cell Rep 2024; 43:114586. [PMID: 39137113 DOI: 10.1016/j.celrep.2024.114586] [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: 02/06/2024] [Revised: 05/29/2024] [Accepted: 07/19/2024] [Indexed: 08/15/2024] Open
Abstract
Our understanding of human fetal cerebellum development during the late second trimester, a critical period for the generation of astrocytes, oligodendrocytes, and unipolar brush cells (UBCs), remains limited. Here, we performed single-cell RNA sequencing (scRNA-seq) in human fetal cerebellum samples from gestational weeks (GWs) 18-25. We find that proliferating UBC progenitors distribute in the subventricular zone of the rhombic lip (RLSVZ) near white matter (WM), forming a layer structure. We also delineate two trajectories from astrogenic radial glia (ARGs) to Bergmann glial progenitors (BGPs) and recognize oligodendrogenic radial glia (ORGs) as one source of primitive oligodendrocyte progenitor cells (PriOPCs). Additionally, our scRNA-seq analysis of the trisomy 21 fetal cerebellum at this stage reveals abnormal upregulated genes in pathways such as the cell adhesion pathway and focal adhesion pathway, which potentially promote neuronal differentiation. Overall, our research provides valuable insights into normal and abnormal development of the human fetal cerebellum.
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Affiliation(s)
- Hongmin Yu
- Biomedical Pioneering Innovation Center, Department of Obstetrics and Gynecology, Academy for Advanced Interdisciplinary Studies, Third Hospital, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing 100871, China
| | - Yun Liu
- Biomedical Pioneering Innovation Center, Department of Obstetrics and Gynecology, Academy for Advanced Interdisciplinary Studies, Third Hospital, Peking University, Beijing 100871, China; Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing 100871, China; Changping Laboratory, Changping Laboratory, Yard 28, Science Park Road, Changping District, Beijing 102206, China
| | - Fanqing Xu
- Biomedical Pioneering Innovation Center, Department of Obstetrics and Gynecology, Academy for Advanced Interdisciplinary Studies, Third Hospital, Peking University, Beijing 100871, China; Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Yuanyuan Fu
- Biomedical Pioneering Innovation Center, Department of Obstetrics and Gynecology, Academy for Advanced Interdisciplinary Studies, Third Hospital, Peking University, Beijing 100871, China; Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing 100871, China
| | - Ming Yang
- Biomedical Pioneering Innovation Center, Department of Obstetrics and Gynecology, Academy for Advanced Interdisciplinary Studies, Third Hospital, Peking University, Beijing 100871, China; Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Ling Ding
- Biomedical Pioneering Innovation Center, Department of Obstetrics and Gynecology, Academy for Advanced Interdisciplinary Studies, Third Hospital, Peking University, Beijing 100871, China; Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Yixuan Wu
- Biomedical Pioneering Innovation Center, Department of Obstetrics and Gynecology, Academy for Advanced Interdisciplinary Studies, Third Hospital, Peking University, Beijing 100871, China; Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Fuchou Tang
- Biomedical Pioneering Innovation Center, Department of Obstetrics and Gynecology, Academy for Advanced Interdisciplinary Studies, Third Hospital, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing 100871, China; Changping Laboratory, Changping Laboratory, Yard 28, Science Park Road, Changping District, Beijing 102206, China
| | - Jie Qiao
- Biomedical Pioneering Innovation Center, Department of Obstetrics and Gynecology, Academy for Advanced Interdisciplinary Studies, Third Hospital, Peking University, Beijing 100871, China; Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, China; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China.
| | - Lu Wen
- Biomedical Pioneering Innovation Center, Department of Obstetrics and Gynecology, Academy for Advanced Interdisciplinary Studies, Third Hospital, Peking University, Beijing 100871, China; Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing 100871, China; Changping Laboratory, Changping Laboratory, Yard 28, Science Park Road, Changping District, Beijing 102206, China.
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Munoz-Gualan AP, Güngör A, Cezayirli PC, Rahmanov S, Gurses ME, Puelles L, Türe U. Human Adapted Prosomeric Model: A Future for Brainstem Tumor Classification. Brain Res 2024; 1837:148961. [PMID: 38679312 DOI: 10.1016/j.brainres.2024.148961] [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: 12/12/2023] [Revised: 03/30/2024] [Accepted: 04/24/2024] [Indexed: 05/01/2024]
Abstract
This study reevaluates the conventional understanding of midbrain anatomy and neuroanatomical nomenclature in the context of recent genetic and anatomical discoveries. The authors assert that the midbrain should be viewed as an integral part of the forebrain due to shared genetic determinants and evolutionary lineage. The isthmo-mesencephalic boundary is recognized as a significant organizer for both the caudal midbrain and the isthmo-cerebellar area. The article adopts the prosomeric model, redefining the whole brain as neuromeres, offering a more precise depiction of brain development, including processes like proliferation, neurogenesis, cell migration, and differentiation. This shift in understanding challenges traditional definitions of the midbrain based on external brain morphology. The study also delves into the historical context of neuroanatomical models, including the columnar model proposed by Herrick in 1910, which has influenced our understanding of brain structure. Furthermore, the study has clinical implications, affecting neuroanatomy, neurodevelopmental studies, and the diagnosis and treatment of brain disorders. It emphasizes the need to integrate molecular research into human neuroanatomical studies and advocates for updating neuroanatomical terminology to reflect modern genetic and molecular insights. The authors propose two key revisions. First, we suggest reclassifying the isthmo-cerebellar prepontine region as part of the hindbrain, due to its role in cerebellar development and distinct location caudal to the genetically-defined midbrain. Second, we recommend redefining the anterior boundary of the genetically-defined midbrain to align with genetic markers. In conclusion, the authors highlight the importance of harmonizing neuroanatomical nomenclature with current scientific knowledge, promoting a more precise and informed understanding of brain structure, which is crucial for both research and clinical applications related to the human brain.
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Affiliation(s)
| | - Abuzer Güngör
- Department of Neurosurgery, Yeditepe University School of Medicine, Istanbul, Turkey; Department of Neurosurgery, Istinye University, Istanbul, Turkey
| | - Phillip Cem Cezayirli
- Department of Neurosurgery, Yeditepe University School of Medicine, Istanbul, Turkey; Haynes Neurosurgical Group, Birmingham, AL, United States
| | - Serdar Rahmanov
- Department of Neurosurgery, Yeditepe University School of Medicine, Istanbul, Turkey
| | - Muhammet Enes Gurses
- Department of Neurosurgery, Yeditepe University School of Medicine, Istanbul, Turkey; Department of Neurosurgery, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Luis Puelles
- Department of Human Anatomy and Psychobiology, School of Medicine, University of Murcia, Murcia, Spain; Institute of Biomedical Research of Murcia -IMIB, Virgen de la Arrixaca University Hospital, Murcia, Spain
| | - Uğur Türe
- Department of Neurosurgery, Yeditepe University School of Medicine, Istanbul, Turkey.
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3
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Camiolo G, Mullen CG, Ottersbach K. Mechanistic insights into the developmental origin of pediatric hematologic disorders. Exp Hematol 2024; 136:104583. [PMID: 39059457 DOI: 10.1016/j.exphem.2024.104583] [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: 05/27/2024] [Revised: 07/18/2024] [Accepted: 07/19/2024] [Indexed: 07/28/2024]
Abstract
Embryonic and fetal hematopoietic stem and progenitor cells differ in some key properties from cells that are part of the adult hematopoietic system. These include higher proliferation and self-renewal capacity, different globin gene usage, and differing lineage biases. Although these evolved to cover specific requirements of embryonic development, they can have serious consequences for the pathogenesis of hematologic malignancies that initiate prebirth in fetal blood cells and may result in a particularly aggressive disease that does not respond well to treatments that have been designed for adult leukemias. This indicates that these infant/pediatric leukemias should be considered developmental diseases, where a thorough understanding of their unique biology is essential for designing more effective therapies. In this review, we will highlight some of these unique fetal properties and detail the underlying molecular drivers of these phenotypes. We specifically focus on those that are pertinent to disease pathogenesis and that may therefore reveal disease vulnerabilities. We have also included an extensive description of the origins, phenotypes, and key molecular drivers of the main infant and pediatric leukemias that have a known prenatal origin. Importantly, successes in recent years in generating faithful models of these malignancies in which cellular origins, key drivers, and potential vulnerabilities can be investigated have resulted in uncovering potential, new therapeutic avenues.
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Affiliation(s)
- Giuseppina Camiolo
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, United Kingdom
| | - Christopher G Mullen
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, United Kingdom
| | - Katrin Ottersbach
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, United Kingdom.
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4
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Yimit Y, Yasin P, Tuersun A, Wang J, Wang X, Huang C, Abudoubari S, Chen X, Ibrahim I, Nijiati P, Wang Y, Zou X, Nijiati M. Multiparametric MRI-Based Interpretable Radiomics Machine Learning Model Differentiates Medulloblastoma and Ependymoma in Children: A Two-Center Study. Acad Radiol 2024; 31:3384-3396. [PMID: 38508934 DOI: 10.1016/j.acra.2024.02.040] [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: 02/08/2024] [Revised: 02/23/2024] [Accepted: 02/24/2024] [Indexed: 03/22/2024]
Abstract
RATIONALE AND OBJECTIVES Medulloblastoma (MB) and Ependymoma (EM) in children, share similarities in age group, tumor location, and clinical presentation. Distinguishing between them through clinical diagnosis is challenging. This study aims to explore the effectiveness of using radiomics and machine learning on multiparametric magnetic resonance imaging (MRI) to differentiate between MB and EM and validate its diagnostic ability with an external set. MATERIALS AND METHODS Axial T2 weighted image (T2WI) and contrast-enhanced T1weighted image (CE-T1WI) MRI sequences of 135 patients from two centers were collected as train/test sets. Volume of interest (VOI) was manually delineated by an experienced neuroradiologist, supervised by a senior. Feature selection analysis and the least absolute shrinkage and selection operator (LASSO) algorithm identified valuable features, and Shapley additive explanations (SHAP) evaluated their significance. Five machine-learning classifiers-extreme gradient boosting (XGBoost), Bernoulli naive Bayes (Bernoulli NB), Logistic Regression (LR), support vector machine (SVM), linear support vector machine (Linear SVC) classifiers were built based on T2WI (T2 model), CE-T1WI (T1 model), and T1 + T2WI (T1 + T2 model). A human expert diagnosis was developed and corrected by senior radiologists. External validation was performed at Sun Yat-Sen University Cancer Center. RESULTS 31 valuable features were extracted from T2WI and CE-T1WI. XGBoost demonstrated the highest performance with an area under the curve (AUC) of 0.92 on the test set and maintained an AUC of 0.80 during external validation. For the T1 model, XGBoost achieved the highest AUC of 0.85 on the test set and the highest accuracy of 0.71 on the external validation set. In the T2 model, XGBoost achieved the highest AUC of 0.86 on the test set and the highest accuracy of 0.82 on the external validation set. The human expert diagnosis had an AUC of 0.66 on the test set and 0.69 on the external validation set. The integrated T1 + T2 model achieved an AUC of 0.92 on the test set, 0.80 on the external validation set, achieved the best performance. Overall, XGBoost consistently outperformed in different classification models. CONCLUSION The combination of radiomics and machine learning on multiparametric MRI effectively distinguishes between MB and EM in childhood, surpassing human expert diagnosis in training and testing sets.
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Affiliation(s)
- Yasen Yimit
- Department of Radiology, The First People's Hospital of Kashi (Kashgar) Prefecture, Xinjiang, China, 844000; Xinjiang Key Laboratory of Artificial Intelligence assisted Imaging Diagnosis, Kashi (Kashgar), China, 844000
| | - Parhat Yasin
- Department of Spine Surgery, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China, 830054
| | - Abudouresuli Tuersun
- Department of Radiology, The First People's Hospital of Kashi (Kashgar) Prefecture, Xinjiang, China, 844000; Xinjiang Key Laboratory of Artificial Intelligence assisted Imaging Diagnosis, Kashi (Kashgar), China, 844000
| | - Jingru Wang
- Department of Research Collaboration, R&D center, Beijing Deepwise & League of PHD Technology Co., Ltd, Beijing, PR China, 100080
| | - Xiaohong Wang
- Department of Radiology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China, 510630
| | - Chencui Huang
- Department of Research Collaboration, R&D center, Beijing Deepwise & League of PHD Technology Co., Ltd, Beijing, PR China, 100080
| | - Saimaitikari Abudoubari
- Department of Radiology, The First People's Hospital of Kashi (Kashgar) Prefecture, Xinjiang, China, 844000; Xinjiang Key Laboratory of Artificial Intelligence assisted Imaging Diagnosis, Kashi (Kashgar), China, 844000
| | - Xingzhi Chen
- Department of Research Collaboration, R&D center, Beijing Deepwise & League of PHD Technology Co., Ltd, Beijing, PR China, 100080
| | - Irshat Ibrahim
- Department of General Surgery, The First People's Hospital of Kashi (Kashgar) Prefecture, Xinjiang, China, 844000
| | - Pahatijiang Nijiati
- Department of Radiology, The First People's Hospital of Kashi (Kashgar) Prefecture, Xinjiang, China, 844000; Xinjiang Key Laboratory of Artificial Intelligence assisted Imaging Diagnosis, Kashi (Kashgar), China, 844000
| | - Yunling Wang
- Department of Imaging Center, First Affiliated Hospital of Xinjiang Medical University, Urumqi, China, 830054
| | - Xiaoguang Zou
- Xinjiang Key Laboratory of Artificial Intelligence assisted Imaging Diagnosis, Kashi (Kashgar), China, 844000; Clinical Medical Research Center, The First People's Hospital of Kashi (Kashgar) Prefecture, Xinjiang, China, 844000
| | - Mayidili Nijiati
- Department of Radiology, The First People's Hospital of Kashi (Kashgar) Prefecture, Xinjiang, China, 844000; Xinjiang Key Laboratory of Artificial Intelligence assisted Imaging Diagnosis, Kashi (Kashgar), China, 844000.
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Okonechnikov K, Schrimpf D, Koster J, Sievers P, Milde T, Sahm F, Jones DTW, von Deimling A, Pfister SM, Kool M, Korshunov A. Clinically unfavorable transcriptome subtypes of non-WNT/non-SHH medulloblastomas are associated with a predominance in proliferating and progenitor-like cell subpopulations. Acta Neuropathol 2024; 147:95. [PMID: 38847845 DOI: 10.1007/s00401-024-02746-6] [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: 02/26/2024] [Revised: 05/10/2024] [Accepted: 05/24/2024] [Indexed: 06/23/2024]
Abstract
The non-WNT/non-SHH (Grp3/Grp4) medulloblastomas (MBs) include eight second-generation subgroups (SGS; I-VIII) each with distinct molecular and clinical characteristics. Recently, we also identified two prognostically relevant transcriptome subtypes within each SGS MB, which are associated with unique gene expression signatures and signaling pathways. These prognostic subsets may be in connection to the intra-tumoral cell landscape that underlies SGS MB clinical-molecular diversity. Here, we performed a deconvolution analysis of the Grp3/Grp4 MB bulk RNA profiles using the previously identified single-cell RNA-seq reference dataset and focusing on variability in the cellular composition of SGS MB. RNA deconvolution analysis of the Grp3/Grp4 MB disclosed the subgroup-specific neoplastic cell subpopulations. Neuronally differentiated axodendritic GP3-C1 and glutamatergic GP4-C1 subpopulations were distributed within Grp3- and Grp4-associated SGS MB, respectively. Progenitor GP3-B2 subpopulation was prominent in aggressive SGS II MB, whereas photoreceptor/visual perception GP3/4-C2 cell content was typical for SGS III/IV MB. The current study also revealed significant variability in the proportions of cell subpopulations between clinically relevant SGS MB transcriptome subtypes, where unfavorable cohorts were enriched with cell cycle and progenitor-like cell subpopulations and, vice versa, favorable subtypes were composed of neuronally differentiated cell fractions predominantly. A higher than median proportion of proliferating and progenitor cell subpopulations conferred the shortest survival of the Grp3 and Grp 4 MB, and similar survival associations were identified for all SGS MB except SGS IV MB. In summary, the recently identified clinically relevant Grp3/Grp4 MB transcriptome subtypes are composed of different cell populations. Future studies should aim to validate the prognostic and therapeutic role of the identified Grp3/Grp4 MB inter-tumoral cellular heterogeneity. The application of the single-cell techniques on each SGS MB separately could help to clarify the clinical significance of subgroup-specific variability in tumor cell content and its relation with prognostic transcriptome signatures identified before.
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Affiliation(s)
- Konstantin Okonechnikov
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-Oncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Daniel Schrimpf
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Jan Koster
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, University of Amsterdam and Cancer Center Amsterdam, Amsterdam, The Netherlands
| | - Philipp Sievers
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Till Milde
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Felix Sahm
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andreas von Deimling
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-Oncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-Oncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, The Netherlands
- University Medical Center Utrecht, Utrecht, the Netherlands
| | - Andrey Korshunov
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany.
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6
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Sheng H, Li H, Zeng H, Zhang B, Lu Y, Liu X, Xu Z, Zhang J, Zhang L. Heterogeneity and tumoral origin of medulloblastoma in the single-cell era. Oncogene 2024; 43:839-850. [PMID: 38355808 PMCID: PMC10942862 DOI: 10.1038/s41388-024-02967-9] [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: 09/25/2023] [Accepted: 02/05/2024] [Indexed: 02/16/2024]
Abstract
Medulloblastoma is one of the most common malignant pediatric brain tumors derived from posterior fossa. The current treatment includes maximal safe surgical resection, radiotherapy, whole cranio-spinal radiation and adjuvant with chemotherapy. However, it can only limitedly prolong the survival time with severe side effects and relapse. Defining the intratumoral heterogeneity, cellular origin and identifying the interaction network within tumor microenvironment are helpful for understanding the mechanisms of medulloblastoma tumorigenesis and relapse. Due to technological limitations, the mechanisms of cellular heterogeneity and tumor origin have not been fully understood. Recently, the emergence of single-cell technology has provided a powerful tool for achieving the goal of understanding the mechanisms of tumorigenesis. Several studies have demonstrated the intratumoral heterogeneity and tumor origin for each subtype of medulloblastoma utilizing the single-cell RNA-seq, which has not been uncovered before using conventional technologies. In this review, we present an overview of the current progress in understanding of cellular heterogeneity and tumor origin of medulloblastoma and discuss novel findings in the age of single-cell technologies.
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Affiliation(s)
- Hui Sheng
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Haotai Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Han Zeng
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Bin Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yu Lu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xixi Liu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Zhongwen Xu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jing Zhang
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Liguo Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
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7
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Observing mammalian cerebellum development through an evolutionary lens. Nature 2024:10.1038/d41586-023-03836-3. [PMID: 38200332 DOI: 10.1038/d41586-023-03836-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
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8
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Gold MP, Ong W, Masteller AM, Ghasemi DR, Galindo JA, Park NR, Huynh NC, Donde A, Pister V, Saurez RA, Vladoiu MC, Hwang GH, Eisemann T, Donovan LK, Walker AD, Benetatos J, Dufour C, Garzia L, Segal RA, Wechsler-Reya RJ, Mesirov JP, Korshunov A, Pajtler KW, Pomeroy SL, Ayrault O, Davidson SM, Cotter JA, Taylor MD, Fraenkel E. Developmental basis of SHH medulloblastoma heterogeneity. Nat Commun 2024; 15:270. [PMID: 38191555 PMCID: PMC10774283 DOI: 10.1038/s41467-023-44300-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 12/07/2023] [Indexed: 01/10/2024] Open
Abstract
Many genes that drive normal cellular development also contribute to oncogenesis. Medulloblastoma (MB) tumors likely arise from neuronal progenitors in the cerebellum, and we hypothesized that the heterogeneity observed in MBs with sonic hedgehog (SHH) activation could be due to differences in developmental pathways. To investigate this question, here we perform single-nucleus RNA sequencing on highly differentiated SHH MBs with extensively nodular histology and observed malignant cells resembling each stage of canonical granule neuron development. Through innovative computational approaches, we connect these results to published datasets and find that some established molecular subtypes of SHH MB appear arrested at different developmental stages. Additionally, using multiplexed proteomic imaging and MALDI imaging mass spectrometry, we identify distinct histological and metabolic profiles for highly differentiated tumors. Our approaches are applicable to understanding the interplay between heterogeneity and differentiation in other cancers and can provide important insights for the design of targeted therapies.
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Grants
- R35 NS122339 NINDS NIH HHS
- U01 CA253547 NCI NIH HHS
- U24 CA220341 NCI NIH HHS
- R01 NS089076 NINDS NIH HHS
- R01 CA255369 NCI NIH HHS
- P50 HD105351 NICHD NIH HHS
- R01 NS106155 NINDS NIH HHS
- R01 CA159859 NCI NIH HHS
- P30 CA014089 NCI NIH HHS
- U01 CA184898 NCI NIH HHS
- EIF | Stand Up To Cancer (SU2C)
- The Pediatric Brain Tumour Foundation, The Terry Fox Research Institute, The Canadian Institutes of Health Research, The Cure Search Foundation, Matthew Larson Foundation (IronMatt), b.r.a.i.n.child, Meagan’s Walk, SWIFTY Foundation, The Brain Tumour Charity, Genome Canada, Genome BC, Genome Quebec, the Ontario Research Fund, Worldwide Cancer Research, V-Foundation for Cancer Research, and the Ontario Institute for Cancer Research through funding provided by the Government of Ontario, Canadian Cancer Society Research Institute Impact grant, a Cancer Research UK Brain Tumour Award, and the Garron Family Chair in Childhood Cancer Research at the Hospital for Sick Children and the University of Toronto. We also thank Yoon-Jae Cho, John Michaels, Koei Chin, Joe Gray, Connie New, and Ali Abdullatif for their help with the manuscript. Additionally, we appreciate support from the USC Norris Comprehensive Cancer Center Translational Pathology Core (P30CA014089), the Pediatric Research Biorepository at CHLA, and the Histology Core at the Koch Institute at MIT.
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Affiliation(s)
- Maxwell P Gold
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Winnie Ong
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Andrew M Masteller
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - David R Ghasemi
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-oncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Julie Anne Galindo
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles (CHLA), Los Angeles, CA, USA
| | - Noel R Park
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Ludwig Institute for Cancer Research, Princeton University, Princeton, NJ, USA
| | - Nhan C Huynh
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Aneesh Donde
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Veronika Pister
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Raul A Saurez
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Maria C Vladoiu
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Grace H Hwang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Tanja Eisemann
- Cancer Genome and Epigenetics Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Laura K Donovan
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Adam D Walker
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles (CHLA), Los Angeles, CA, USA
| | - Joseph Benetatos
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Christelle Dufour
- Department of Child and Adolescent Oncology, Gustave Roussy, Villejuif, France
- INSERM U981, Molecular Predictors and New Targets in Oncology, University Paris-Saclay, Villejuif, France
| | - Livia Garzia
- Cancer Research Program, McGill University, Montreal, QC, Canada
- MUHC Research Institute, McGill University, Montreal, QC, Canada
| | - Rosalind A Segal
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Robert J Wechsler-Reya
- Cancer Genome and Epigenetics Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Jill P Mesirov
- Department of Medicine, Moores Cancer Center, UC San Diego, La Jolla, CA, USA
| | - Andrey Korshunov
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology (B300), German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Kristian W Pajtler
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro-oncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Scott L Pomeroy
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Olivier Ayrault
- Institut Curie, PSL Research University, CNRS UMR, INSERM, Orsay, France
- Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, Orsay, France
| | - Shawn M Davidson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, The Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Jennifer A Cotter
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles (CHLA), Los Angeles, CA, USA
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Michael D Taylor
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
- Division of Neurosurgery, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Surgery, University of Toronto, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Texas Children's Cancer Center, Hematology-Oncology Section, Houston, TX, USA
- Department of Pediatrics - Hematology/Oncology and Neurosurgery, Baylor College of Medicine, Houston, TX, USA
| | - Ernest Fraenkel
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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9
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Sepp M, Leiss K, Murat F, Okonechnikov K, Joshi P, Leushkin E, Spänig L, Mbengue N, Schneider C, Schmidt J, Trost N, Schauer M, Khaitovich P, Lisgo S, Palkovits M, Giere P, Kutscher LM, Anders S, Cardoso-Moreira M, Sarropoulos I, Pfister SM, Kaessmann H. Cellular development and evolution of the mammalian cerebellum. Nature 2024; 625:788-796. [PMID: 38029793 PMCID: PMC10808058 DOI: 10.1038/s41586-023-06884-x] [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: 11/28/2021] [Accepted: 11/21/2023] [Indexed: 12/01/2023]
Abstract
The expansion of the neocortex, a hallmark of mammalian evolution1,2, was accompanied by an increase in cerebellar neuron numbers3. However, little is known about the evolution of the cellular programmes underlying the development of the cerebellum in mammals. In this study we generated single-nucleus RNA-sequencing data for around 400,000 cells to trace the development of the cerebellum from early neurogenesis to adulthood in human, mouse and the marsupial opossum. We established a consensus classification of the cellular diversity in the developing mammalian cerebellum and validated it by spatial mapping in the fetal human cerebellum. Our cross-species analyses revealed largely conserved developmental dynamics of cell-type generation, except for Purkinje cells, for which we observed an expansion of early-born subtypes in the human lineage. Global transcriptome profiles, conserved cell-state markers and gene-expression trajectories across neuronal differentiation show that cerebellar cell-type-defining programmes have been overall preserved for at least 160 million years. However, we also identified many orthologous genes that gained or lost expression in cerebellar neural cell types in one of the species or evolved new expression trajectories during neuronal differentiation, indicating widespread gene repurposing at the cell-type level. In sum, our study unveils shared and lineage-specific gene-expression programmes governing the development of cerebellar cells and expands our understanding of mammalian brain evolution.
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Affiliation(s)
- Mari Sepp
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.
| | - Kevin Leiss
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.
| | - Florent Murat
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
- INRAE, LPGP, Rennes, France
| | - Konstantin Okonechnikov
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Piyush Joshi
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Developmental Origins of Pediatric Cancer Junior Group, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Evgeny Leushkin
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Lisa Spänig
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Developmental Origins of Pediatric Cancer Junior Group, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Noe Mbengue
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Céline Schneider
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Julia Schmidt
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Nils Trost
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Maria Schauer
- Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Philipp Khaitovich
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Steven Lisgo
- Biosciences Institute, Newcastle University, Newcastle, UK
| | - Miklós Palkovits
- Human Brain Tissue Bank, Semmelweis University, Budapest, Hungary
| | - Peter Giere
- Museum für Naturkunde Berlin, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Lena M Kutscher
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Developmental Origins of Pediatric Cancer Junior Group, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Simon Anders
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
- BioQuant, Heidelberg University, Heidelberg, Germany
| | | | - Ioannis Sarropoulos
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.
- Wellcome Sanger Institute, Cambridge, UK.
| | - Stefan M Pfister
- Hopp-Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany.
- National Center for Tumor Diseases (NCT), Heidelberg, Germany.
| | - Henrik Kaessmann
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.
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