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1.
Nature ; 625(7996): 788-796, 2024 Jan.
Article in English | MEDLINE | ID: mdl-38029793

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.


Subject(s)
Cerebellum , Evolution, Molecular , Mammals , Neurogenesis , Animals , Humans , Mice , Cell Lineage/genetics , Cerebellum/cytology , Cerebellum/embryology , Cerebellum/growth & development , Fetus/cytology , Fetus/embryology , Gene Expression Regulation, Developmental , Neurogenesis/genetics , Neurons/cytology , Neurons/metabolism , Opossums/embryology , Opossums/growth & development , Purkinje Cells/cytology , Purkinje Cells/metabolism , Single-Cell Gene Expression Analysis , Species Specificity , Transcriptome , Mammals/embryology , Mammals/growth & development
2.
Neurobiol Dis ; 199: 106600, 2024 Jul 10.
Article in English | MEDLINE | ID: mdl-38996985

ABSTRACT

Familial Dysautonomia (FD) is an autosomal recessive disorder caused by a splice site mutation in the gene ELP1, which disproportionally affects neurons. While classically characterized by deficits in sensory and autonomic neurons, neuronal defects in the central nervous system have also been described. Although ELP1 expression remains high in the normal developing and adult cerebellum, its role in cerebellar development is unknown. To explore the role of Elp1 in the cerebellum, we knocked out Elp1 in cerebellar granule cell progenitors (GCPs) and examined the outcome on animal behavior and cellular composition. We found that GCP-specific conditional knockout of Elp1 (Elp1cKO) resulted in ataxia by 8 weeks of age. Cellular characterization showed that the animals had smaller cerebella with fewer granule cells. This defect was already apparent as early as 7 days after birth, when Elp1cKO animals also had fewer mitotic GCPs and shorter Purkinje dendrites. Through molecular characterization, we found that loss of Elp1 was associated with an increase in apoptotic cell death and cell stress pathways in GCPs. Our study demonstrates the importance of ELP1 in the developing cerebellum, and suggests that loss of Elp1 in the GC lineage may also play a role in the progressive ataxia phenotypes of FD patients.

3.
Acta Neuropathol ; 145(1): 49-69, 2023 01.
Article in English | MEDLINE | ID: mdl-36437415

ABSTRACT

Pediatric central nervous system (CNS) tumors represent the most common cause of cancer-related death in children aged 0-14 years. They differ from their adult counterparts, showing extensive clinical and molecular heterogeneity as well as a challenging histopathological spectrum that often impairs accurate diagnosis. Here, we use DNA methylation-based CNS tumor classification in combination with copy number, RNA-seq, and ChIP-seq analysis to characterize a newly identified CNS tumor type. In addition, we report histology, patient characteristics, and survival data in this tumor type. We describe a biologically distinct pediatric CNS tumor type (n = 31 cases) that is characterized by focal high-level amplification and resultant overexpression of either PLAGL1 or PLAGL2, and an absence of recurrent genetic alterations characteristic of other pediatric CNS tumor types. Both genes act as transcription factors for a regulatory subset of imprinted genes (IGs), components of the Wnt/ß-Catenin pathway, and the potential drug targets RET and CYP2W1, which are also specifically overexpressed in this tumor type. A derived PLAGL-specific gene expression signature indicates dysregulation of imprinting control and differentiation/development. These tumors occurred throughout the neuroaxis including the cerebral hemispheres, cerebellum, and brainstem, and were predominantly composed of primitive embryonal-like cells lacking robust expression of markers of glial or neuronal differentiation (e.g., GFAP, OLIG2, and synaptophysin). Tumors with PLAGL1 amplification were typically diagnosed during adolescence (median age 10.5 years), whereas those with PLAGL2 amplification were diagnosed during early childhood (median age 2 years). The 10-year overall survival was 66% for PLAGL1-amplified tumors, 25% for PLAGL2-amplified tumors, 18% for male patients, and 82% for female patients. In summary, we describe a new type of biologically distinct CNS tumor characterized by PLAGL1/2 amplification that occurs predominantly in infants and toddlers (PLAGL2) or adolescents (PLAGL1) which we consider best classified as a CNS embryonal tumor and which is associated with intermediate survival. The cell of origin and optimal treatment strategies remain to be defined.


Subject(s)
Central Nervous System Neoplasms , Neuroectodermal Tumors, Primitive , Child , Child, Preschool , Female , Humans , Infant , Male , Cell Cycle Proteins/genetics , Central Nervous System Neoplasms/genetics , DNA Methylation , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Neuroectodermal Tumors, Primitive/genetics , RNA-Binding Proteins/genetics , Transcription Factors/genetics , Transcription Factors/metabolism , Tumor Suppressor Proteins/genetics , Wnt Signaling Pathway/genetics
4.
J Assoc Physicians India ; 70(1): 11-12, 2022 Jan.
Article in English | MEDLINE | ID: mdl-35062804

ABSTRACT

During COVID-19 pandemic, one of the most common arrythmia reported with this illness is sinus bradycardia. Treatment for COVID-19 and associated cardiac dysfunction is still evolving. Temporary pacemaker insertion is difficult due to pandemic and risk of spread of infection to the additional staff involved. Orciprenaline stimulates the sino-atrial and atrioventricular nodes and accelerates atrioventricular conduction. Theophylline improves sinus node function in subjects with sinus bradycardia and enhances atrioventricular nodal conduction We report a case series of 10 patients admitted in dedicated COVID-19 ICUs and developed sinus node dysfunction. All of these patients were started on etophylline and theophylline prolonged release tablet (150mg) once a day. On subsequent follow up after 72 hours, all patients reported heart rate well within normal range. COVID-19 virus directly involves the myocardium by entering the cardiac myocytes resulting in inflammation and injury. As the sinus bradycardia due to COVID-19 is usually transient and respond well this drug, short course of this drug could be added to treat this arrythmia in future.


Subject(s)
COVID-19 , Theophylline , Bradycardia , Humans , Pandemics , SARS-CoV-2 , Sick Sinus Syndrome , Tablets , Theophylline/analogs & derivatives
5.
J Biol Chem ; 295(12): 3875-3890, 2020 03 20.
Article in English | MEDLINE | ID: mdl-32047113

ABSTRACT

Available assays for measuring cellular manganese (Mn) levels require cell lysis, restricting longitudinal experiments and multiplexed outcome measures. Conducting a screen of small molecules known to alter cellular Mn levels, we report here that one of these chemicals induces rapid Mn efflux. We describe this activity and the development and implementation of an assay centered on this small molecule, named manganese-extracting small molecule (MESM). Using inductively-coupled plasma-MS, we validated that this assay, termed here "manganese-extracting small molecule estimation route" (MESMER), can accurately assess Mn in mammalian cells. Furthermore, we found evidence that MESM acts as a Mn-selective ionophore, and we observed that it has increased rates of Mn membrane transport, reduced cytotoxicity, and increased selectivity for Mn over calcium compared with two established Mn ionophores, calcimycin (A23187) and ionomycin. Finally, we applied MESMER to test whether prior Mn exposures subsequently affect cellular Mn levels. We found that cells receiving continuous, elevated extracellular Mn accumulate less Mn than cells receiving equally-elevated Mn for the first time for 24 h, indicating a compensatory cellular homeostatic response. Use of the MESMER assay versus a comparable detergent lysis-based assay, cellular Fura-2 Mn extraction assay, reduced the number of cells and materials required for performing a similar but cell lethality-based experiment to 25% of the normally required sample size. We conclude that MESMER can accurately quantify cellular Mn levels in two independent cells lines through an ionophore-based mechanism, maintaining cell viability and enabling longitudinal assessment within the same cultures.


Subject(s)
Ionophores/chemistry , Manganese/analysis , Animals , Calcimycin/chemistry , Calcimycin/pharmacology , Calcium/metabolism , Cell Line , Cell Survival/drug effects , Fura-2/chemistry , HEK293 Cells , Humans , Induced Pluripotent Stem Cells/cytology , Induced Pluripotent Stem Cells/drug effects , Induced Pluripotent Stem Cells/metabolism , Ionomycin/chemistry , Ionomycin/pharmacology , Ionophores/pharmacology , Male , Manganese/chemistry , Manganese/metabolism , Manganese/toxicity , Mass Spectrometry/methods , Mice
6.
Hum Mol Genet ; 28(22): 3825-3841, 2019 11 15.
Article in English | MEDLINE | ID: mdl-31600787

ABSTRACT

The molecular etiology linking the pathogenic mutations in the Huntingtin (Htt) gene with Huntington's disease (HD) is unknown. Prior work suggests a role for Htt in neuronal autophagic function and mutant HTT protein disrupts autophagic cargo loading. Reductions in the bioavailability of the essential metal manganese (Mn) are seen in models of HD. Excess cellular Mn impacts autophagic function, but the target and molecular basis of these changes are unknown. Thus, we sought to determine if changes in cellular Mn status impact autophagic processes in a wild-type or mutant Htt-dependent manner. We report that the HD genotype is associated with reduced Mn-induced autophagy and that acute Mn exposure increases autophagosome induction/formation. To determine if a deficit in bioavailable Mn is mechanistically linked to the autophagy-related HD cellular phenotypes, we examined autophagosomes by electron microscopy. We observed that a 24 h 100 uM Mn restoration treatment protocol attenuated an established HD 'cargo-recognition failure' in the STHdh HD model cells by increasing the percentage of filled autophagosomes. Mn restoration had no effect on HTT aggregate number, but a 72 h co-treatment with chloroquine (CQ) in GFP-72Q-expressing HEK293 cells increased the number of visible aggregates in a dose-dependent manner. As CQ prevents autophagic degradation this indicates that Mn restoration in HD cell models facilitates incorporation of aggregates into autophagosomes. Together, these findings suggest that defective Mn homeostasis in HD models is upstream of the impaired autophagic flux and provide proof-of-principle support for increasing bioavailable Mn in HD to restore autophagic function and promote aggregate clearance.


Subject(s)
Autophagy/drug effects , Huntington Disease/metabolism , Manganese/pharmacology , Animals , Autophagosomes/drug effects , Autophagosomes/metabolism , Cell Line , Disease Models, Animal , HEK293 Cells , Humans , Huntingtin Protein/metabolism , Huntingtin Protein/physiology , Huntington Disease/genetics , Huntington Disease/therapy , Induced Pluripotent Stem Cells , Manganese/metabolism , Mice , Microscopy, Electron/methods , Mutation , Neurons/metabolism
7.
Acta Neuropathol ; 141(2): 291-301, 2021 02.
Article in English | MEDLINE | ID: mdl-33331994

ABSTRACT

Atypical teratoid/rhabdoid tumors (ATRTs) are very aggressive childhood malignancies of the central nervous system. The underlying genetic cause are inactivating bi-allelic mutations in SMARCB1 or (rarely) in SMARCA4. ATRT-SMARCA4 have been associated with a higher frequency of germline mutations, younger age, and an inferior prognosis in comparison to SMARCB1 mutated cases. Based on their DNA methylation profiles and transcriptomics, SMARCB1 mutated ATRTs have been divided into three distinct molecular subgroups: ATRT-TYR, ATRT-SHH, and ATRT-MYC. These subgroups differ in terms of age at diagnosis, tumor location, type of SMARCB1 alterations, and overall survival. ATRT-SMARCA4 are, however, less well understood, and it remains unknown, whether they belong to one of the described ATRT subgroups. Here, we examined 14 ATRT-SMARCA4 by global DNA methylation analyses. We show that they form a separate group segregating from SMARCB1 mutated ATRTs and from other SMARCA4-deficient tumors like small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) or SMARCA4 mutated extra-cranial malignant rhabdoid tumors. In contrast, medulloblastoma (MB) samples with heterozygous SMARCA4 mutations do not group separately, but with established MB subgroups. RNA sequencing of ATRT-SMARCA4 confirmed the clustering results based on DNA methylation profiling and displayed an absence of typical signature genes upregulated in SMARCB1 deleted ATRT. In summary, our results suggest that, in line with previous clinical observations, ATRT-SMARCA4 should be regarded as a distinct molecular subgroup.


Subject(s)
Central Nervous System Neoplasms/genetics , DNA Helicases/genetics , Nuclear Proteins/genetics , Rhabdoid Tumor/genetics , SMARCB1 Protein/genetics , Teratoma/genetics , Transcription Factors/genetics , Adolescent , Adult , Age of Onset , Central Nervous System Neoplasms/pathology , Child , Child, Preschool , Computational Biology , DNA Methylation , Gene Expression Profiling , Humans , Middle Aged , Mutation/genetics , Rhabdoid Tumor/pathology , Survival Analysis , Teratoma/pathology , Young Adult
8.
Dev Biol ; 449(2): 132-142, 2019 05 15.
Article in English | MEDLINE | ID: mdl-30825428

ABSTRACT

The progression of cells down different lineage pathways is a collaborative effort between networks of extracellular signals and intracellular transcription factors. In the vertebrate spinal cord, FGF, Wnt and Retinoic Acid signaling pathways regulate the progressive caudal-to-rostral maturation of neural progenitors by regulating a poorly understood gene regulatory network of transcription factors. We have mapped out this gene regulatory network in the chicken pre-neural tube, identifying CDX4 as a dual-function core component that simultaneously regulates gradual loss of cell potency and acquisition of differentiation states: in a caudal-to-rostral direction, CDX4 represses the early neural differentiation marker Nkx1.2 and promotes the late neural differentiation marker Pax6. Significantly, CDX4 prevents premature PAX6-dependent neural differentiation by blocking Ngn2 activation. This regulation of CDX4 over Pax6 is restricted to the rostral pre-neural tube by Retinoic Acid signaling. Together, our results show that in the spinal cord, CDX4 is part of the gene regulatory network controlling the sequential and progressive transition of states from high to low potency during neural progenitor maturation. Given CDX well-known involvement in Hox gene regulation, we propose that CDX factors coordinate the maturation and axial specification of neural progenitor cells during spinal cord development.


Subject(s)
Avian Proteins/genetics , Gene Expression Regulation, Developmental , Homeodomain Proteins/genetics , Neural Tube/metabolism , Spinal Cord/metabolism , Transcription Factors/genetics , Animals , Avian Proteins/metabolism , Body Patterning/genetics , Cell Differentiation/genetics , Chick Embryo , Gene Regulatory Networks/genetics , Homeodomain Proteins/metabolism , Neural Tube/cytology , Neural Tube/embryology , Neurogenesis/genetics , Spinal Cord/embryology , Transcription Factors/metabolism
9.
Neurobiol Dis ; 141: 104873, 2020 07.
Article in English | MEDLINE | ID: mdl-32320737

ABSTRACT

Medulloblastoma is the most common malignant pediatric brain tumor with high fatality rate. Recent large-scale studies utilizing genome-wide technologies have sub-grouped medulloblastomas into four major subgroups: wingless (WNT), sonic hedgehog (SHH), group 3, and group 4. However, there has yet to be a global analysis of long non-coding RNAs, a crucial part of the regulatory transcriptome, in medulloblastoma. Here, we performed bioinformatic analysis of RNA-seq data from 175 medulloblastoma patients. Differential lncRNA expression sub-grouped medulloblastomas into the four main molecular subgroups. Some of these lncRNAs were subgroup-specific, with a random forest-based machine-learning algorithm identifying an 11-lncRNA diagnostic signature. We also validated the diagnostic signature in patient derived xenograft (PDX) models. We further identified a 17-lncRNA prognostic model using LASSO based penalized Cox' PH model (Score HR = 13.6301, 95% CI = 8.857-20.98, logrank p-value ≤ 2e-16). Our analysis represents the first global lncRNA analysis in medulloblastoma. Our results identify putative candidate lncRNAs that could be evaluated for their functional role in medulloblastoma genesis and progression or as diagnostic and prognostic biomarkers.


Subject(s)
Cerebellar Neoplasms/metabolism , Medulloblastoma/metabolism , RNA, Long Noncoding/metabolism , Biomarkers, Tumor/metabolism , Cerebellar Neoplasms/diagnosis , Computational Biology , Computer Simulation , Gene Expression Profiling , Humans , Medulloblastoma/diagnosis
10.
Indian J Med Res ; 151(1): 87-92, 2020 01.
Article in English | MEDLINE | ID: mdl-32134019

ABSTRACT

Background & objectives: Chikungunya (CHIK) is a neglected, re-emerging arboviral disease. Limited information on CHIK-confirmed cases during interepidemic period is available from India. This surveillance study was conducted in Madhya Pradesh (MP), India, during the years 2016-2017, to provide information about CHIK cases. Methods: Blood samples collected from patients suspected having CHIK were tested by immunoglobulin (Ig) IgM ELISA or real time reverse transcription-polymerase chain reaction (rRT-PCR) for the detection of CHIK virus (CHIKV)-specific IgM antibodies or viral RNA, respectively. Partial envelope-1 gene sequencing was done. Clinical and demographic data were collected and analyzed. Results: Of the 4019 samples tested, 494 (12.2%) were found positive for CHIKV infection. The positivity was detected in both rural and urban areas. The mean age of CHIK-positive cases was 33.12±18.25 yr. Headache and joint pain were the most prominent symptoms, 34.6 per cent (171/494) of the CHIK cases required hospitalization and six patients with CHIKV infection died. The East/Central/South African genotype of CHIKV was found to be circulating in the study area. Interpretation & conclusions: Our study recorded a higher CHIK positivity during 2016-2017 in comparison to earlier reports from MP, India. A high proportion of CHIK cases required hospitalization and deaths were also reported, which indicated the severity of the disease in the study area. In-depth molecular analysis of the virus and other risk factors is essential to understand the trends in disease severity.


Subject(s)
Chikungunya Fever/blood , Chikungunya virus/isolation & purification , Enzyme-Linked Immunosorbent Assay , Adolescent , Adult , Antibodies, Viral/blood , Chikungunya Fever/epidemiology , Chikungunya Fever/virology , Chikungunya virus/pathogenicity , Disease Outbreaks , Female , Genotype , Humans , Immunoglobulin M/blood , India/epidemiology , Male , Middle Aged , Real-Time Polymerase Chain Reaction , Young Adult
11.
RNA Biol ; 16(10): 1355-1363, 2019 10.
Article in English | MEDLINE | ID: mdl-31179855

ABSTRACT

RNA half-life is closely related to its cellular physiological function, so stability determinants may have regulatory functions. Micro(mi)RNAs have primarily been studied with respect to post-transcriptional mRNA regulation and target degradation. Here we study the impact of the tumour suppressive melanoma miRNA miR-211 on transcriptome stability and phenotype in the non-pigmented melanoma cell line, A375. Using 5'-bromouridine IP chase (BRIC)-seq, transcriptome-wide RNA stability profiles revealed highly regulated genes and pathways important in this melanoma cell line. By combining BRIC-seq, RNA-seq and in silico predictions, we identified both existing and novel direct miR-211 targets. We validated DUSP3 as one such novel miR-211 target, which itself sustains colony formation and invasion in A375 cells via MAPK/PI3K signalling. miRNAs have the capacity to control RNA turnover as a gene expression mechanism, and RNA stability profiling is an excellent tool for interrogating functionally relevant gene regulatory pathways and miRNA targets when combined with other high-throughput and in silico approaches.


Subject(s)
Gene Expression Regulation, Neoplastic , High-Throughput Nucleotide Sequencing , Melanoma/genetics , MicroRNAs/genetics , RNA Interference , Transcriptome , Cell Line, Tumor , Computational Biology/methods , Disease Progression , Gene Expression Profiling , Gene Ontology , Humans , Melanoma/diagnosis , Mitogen-Activated Protein Kinases/metabolism , Neoplasm Staging , Phosphatidylinositol 3-Kinases/metabolism , RNA Stability , RNA, Messenger/genetics , Signal Transduction
12.
Indian J Med Res ; 150(5): 492-497, 2019 11.
Article in English | MEDLINE | ID: mdl-31939393

ABSTRACT

Background & objectives: Dengue virus (DENV) causes outbreaks and sporadic cases in tropical and subtropical countries. Documenting intricacies of DEN outbreaks is important for future interventions. The objective of this study was to report clinical, laboratory and epidemiological features of DEN outbreaks reported in different districts of Central India in 2016. Methods: In 2016, outbreaks (n=4) suspected of DEN were investigated by rapid response team. Door-to-door fever and entomological surveys were conducted. Blood samples were collected and tested using NS1 or IgM ELISA; real-time reverse transcription-polymerase chain reaction was done to identify serotypes of DEN virus (DENV). NS1-positive samples were tested for the presence of IgG by ELISA. Clinical and demographic data were collected and analyzed. Results: Outbreaks occurred in both urban and rural areas in monsoon season and Aedes aegypti was identified as the vector. Fever, chills, headache and myalgia were the major symptoms; no fatality was recorded. Of the 268 DEN suspects, 135 (50.4%) were found serologically positive. DEN positivity was higher (n=75; 55.56%) among males and in the age group of 16-45 yr (n=78; 57.8%). DENV 3 followed by DENV 2 were detected as the major responsible serotypes. High attack rates (up to 38/1000) and low cumulative IgG prevalence (14.9%) were recorded in rural areas. Interpretation & conclusions: Our study showed that DENV 3 was the major serotype responsible for outbreaks that occurred in monsoon. High attack rates and lower number of secondary infections in rural areas indicated that DENV is emerging in rural parts of Central India. Early diagnosis at local level and timely intervention by mosquito control activities are needed to avoid such outbreaks in future.


Subject(s)
Dengue Virus/isolation & purification , Dengue/blood , Immunoglobulin G/blood , Immunoglobulin M/blood , Viral Nonstructural Proteins/blood , Adolescent , Adult , Aedes/virology , Animals , Child , Child, Preschool , Dengue/epidemiology , Dengue/virology , Dengue Virus/pathogenicity , Disease Outbreaks , Enzyme-Linked Immunosorbent Assay , Female , Humans , Infant , Infant, Newborn , Male , Middle Aged , Mosquito Vectors/virology , Serogroup , Young Adult
13.
Indian J Med Res ; 149(4): 548-553, 2019 04.
Article in English | MEDLINE | ID: mdl-31411180

ABSTRACT

Background & objectives: Dengue virus infection is endemic in India with all the four serotypes of dengue virus in circulation. This study was aimed to determine the geographic distribution of the primary and secondary dengue cases in India. Methods: A multicentre cross-sectional study was conducted at Department of Health Research / Indian Council of Medical Research (DHR)/(ICMR) viral research and diagnostic laboratories (VRDLs) and selected ICMR institutes located in India. Only laboratory-confirmed dengue cases with date of onset of illness less than or equal to seven days were included between September and October 2017. Dengue NS1 antigen ELISA and anti-dengue IgM capture ELISA were used to diagnose dengue cases while anti-dengue IgG capture ELISA was used for identifying the secondary dengue cases. Results: Of the 1372 dengue cases, 897 (65%) were classified as primary dengue and 475 (35%) as secondary dengue cases. However, the proportion varied widely geographically, with Theni, Tamil Nadu; Tirupati, Andhra Pradesh and Udupi-Manipal, Karnataka reporting more than 65 per cent secondary dengue cases while Srinagar, Jammu and Kashmir reporting as low as 10 per cent of the same. The median age of primary dengue cases was 25 yr [interquartile range (IQR 17-35] while that of secondary dengue cases was 23 yr (IQR 13.5-34). Secondary dengue was around 50 per cent among the children belonging to the age group 6-10 yr while it ranged between 20-43 per cent among other age groups. Interpretation & conclusions: Our findings showed a wide geographical variation in the distribution of primary and secondary dengue cases in India. It would prove beneficial to include primary and secondary dengue differentiation protocol in the national dengue surveillance programme.


Subject(s)
Antibodies, Viral/blood , Dengue Virus/pathogenicity , Dengue/blood , Viral Nonstructural Proteins/blood , Adolescent , Adult , Aged , Aged, 80 and over , Child , Child, Preschool , Dengue/classification , Dengue/epidemiology , Dengue/virology , Disease Outbreaks , Enzyme-Linked Immunosorbent Assay , Female , Humans , Immunoglobulin M/blood , India/epidemiology , Infant , Male , Middle Aged , Serogroup , Young Adult
15.
Dev Dyn ; 244(12): 1564-73, 2015 Dec.
Article in English | MEDLINE | ID: mdl-26335559

ABSTRACT

BACKGROUND: Cdx factors expressed in caudal regions of vertebrate embryos regulate hox patterning gene transcription. While loss of Cdx function is known to shift hox spatial expression domains posteriorly, the mechanism underlying the shift is not understood. We addressed this problem by analyzing the spatiotemporal expression profile of all 49 zebrafish hox genes in wild-type and Cdx4-deficient embryos. RESULTS: Loss of Cdx4 had distinct effects on hox spatial expression in a paralogous group-dependent manner: in the head, group 4 expression was expanded posteriorly; in the trunk, group 5-10 expression was shifted posteriorly; and in the tail, group 11-13 genes were expressed in the tail bud but not in more differentiated tissues. In the trunk neural tissue, loss of Cdx4 severely delayed both transcriptional activation of hox genes during the initiation phase, and the anterior-ward expansion of hox expression domains during the establishment phase. In contrast, in the trunk mesoderm, loss of Cdx4 only delayed the hox initiation phase. CONCLUSIONS: These results indicate that Cdx4 differentially regulates the transcription of head, trunk and tail hox genes. In the trunk, Cdx4 conveys spatial positional information to axial tissues primarily by regulating the time of hox gene transcriptional activation during the initiation phase.


Subject(s)
Body Patterning/genetics , Gene Expression Regulation, Developmental , Genes, Homeobox/genetics , Homeodomain Proteins/genetics , Zebrafish Proteins/genetics , Zebrafish/embryology , Animals , Homeodomain Proteins/metabolism , Transcription Factors , Transcriptional Activation , Zebrafish/genetics , Zebrafish Proteins/metabolism
17.
Nat Commun ; 15(1): 269, 2024 Jan 08.
Article in English | MEDLINE | ID: mdl-38191550

ABSTRACT

Medulloblastomas with extensive nodularity are cerebellar tumors characterized by two distinct compartments and variable disease progression. The mechanisms governing the balance between proliferation and differentiation in MBEN remain poorly understood. Here, we employ a multi-modal single cell transcriptome analysis to dissect this process. In the internodular compartment, we identify proliferating cerebellar granular neuronal precursor-like malignant cells, along with stromal, vascular, and immune cells. In contrast, the nodular compartment comprises postmitotic, neuronally differentiated malignant cells. Both compartments are connected through an intermediate cell stage resembling actively migrating CGNPs. Notably, we also discover astrocytic-like malignant cells, found in proximity to migrating and differentiated cells at the transition zone between the two compartments. Our study sheds light on the spatial tissue organization and its link to the developmental trajectory, resulting in a more benign tumor phenotype. This integrative approach holds promise to explore intercompartmental interactions in other cancers with varying histology.


Subject(s)
Cerebellar Neoplasms , Medulloblastoma , Humans , Medulloblastoma/genetics , Cell Differentiation , Cerebellar Neoplasms/genetics , Disease Progression , Histological Techniques
18.
Acta Neuropathol Commun ; 11(1): 25, 2023 02 09.
Article in English | MEDLINE | ID: mdl-36759899

ABSTRACT

Globally decreased histone 3, lysine 27 tri-methylation (H3K27me3) is a hallmark of H3K27-altered diffuse midline gliomas (DMGs) and group-A posterior fossa ependymomas (PFAs). H3K27-altered DMGs are largely characterized by lysine-to-methionine mutations in histone 3 at position 27 (H3K27M). Most PFAs overexpress EZH inhibitory protein (EZHIP), which possesses a region of similarity to the mutant H3K27M. Both H3K27M and EZHIP inhibit the function of the polycomb repressive complex 2 (PRC2) responsible for H3K27me3 deposition. These tumors often arise in neighboring regions of the brainstem and posterior fossa. In rare cases PFAs harbor H3K27M mutations, and DMGs overexpress EZHIP. These findings together raise the possibility that certain cell populations in the developing hindbrain/posterior fossa are especially sensitive to modulation of H3K27me3 states. We identified shared molecular features by comparing genomic, bulk transcriptomic, chromatin-based profiles, and single-cell RNA-sequencing (scRNA-seq) data from the two tumor classes. Our approach demonstrated that 1q gain, a key biomarker in PFAs, is prognostic in H3.1K27M, but not H3.3K27M gliomas. Conversely, Activin A Receptor Type 1 (ACVR1), which is associated with mutations in H3.1K27M gliomas, is overexpressed in a subset of PFAs with poor outcome. Despite diffuse H3K27me3 reduction, previous work shows that both tumors maintain genomic H3K27me3 deposition at select sites. We demonstrate heterogeneity in shared patterns of residual H3K27me3 for both tumors that largely segregated with inferred anatomic tumor origins and progenitor populations of tumor cells. In contrast, analysis of genes linked to H3K27 acetylation (H3K27ac)-marked enhancers showed higher expression in astrocytic-like tumor cells. Finally, common H3K27me3-marked genes mapped closely to expression patterns in the human developing hindbrain. Overall, our data demonstrate developmentally relevant molecular similarities between PFAs and H3K27M DMGs and support the overall hypothesis that deregulated mechanisms of hindbrain development are central to the biology of both tumors.


Subject(s)
Brain Neoplasms , Ependymoma , Fluorocarbons , Glioma , Humans , Histones/genetics , Histones/metabolism , Lysine/genetics , Ependymoma/pathology , Glioma/genetics , Glioma/pathology , Rhombencephalon/pathology , Mutation/genetics , Brain Neoplasms/genetics , Brain Neoplasms/pathology
19.
Neuro Oncol ; 25(10): 1895-1909, 2023 10 03.
Article in English | MEDLINE | ID: mdl-37534924

ABSTRACT

BACKGROUND: Distinguishing the cellular origins of childhood brain tumors is key for understanding tumor initiation and identifying lineage-restricted, tumor-specific therapeutic targets. Previous strategies to map the cell-of-origin typically involved comparing human tumors to murine embryonal tissues, which is potentially limited due to species-specific differences. The aim of this study was to unravel the cellular origins of the 3 most common pediatric brain tumors, ependymoma, pilocytic astrocytoma, and medulloblastoma, using a developing human cerebellar atlas. METHODS: We used a single-nucleus atlas of the normal developing human cerebellum consisting of 176 645 cells as a reference for an in-depth comparison to 4416 bulk and single-cell transcriptome tumor datasets, using gene set variation analysis, correlation, and single-cell matching techniques. RESULTS: We find that the astroglial cerebellar lineage is potentially the origin for posterior fossa ependymomas. We propose that infratentorial pilocytic astrocytomas originate from the oligodendrocyte lineage and MHC II genes are specifically enriched in these tumors. We confirm that SHH and Group 3/4 medulloblastomas originate from the granule cell and unipolar brush cell lineages. Radiation-induced gliomas stem from cerebellar glial lineages and demonstrate distinct origins from the primary medulloblastoma. We identify tumor genes that are expressed in the cerebellar lineage of origin, and genes that are tumor specific; both gene sets represent promising therapeutic targets for future study. CONCLUSION: Based on our results, individual cells within a tumor may resemble different cell types along a restricted developmental lineage. Therefore, we suggest that tumors can arise from multiple cellular states along the cerebellar "lineage of origin."


Subject(s)
Astrocytoma , Brain Neoplasms , Cerebellar Neoplasms , Ependymoma , Glioma , Medulloblastoma , Child , Humans , Animals , Mice , Medulloblastoma/genetics , Medulloblastoma/pathology , Brain Neoplasms/genetics , Brain Neoplasms/pathology , Glioma/pathology , Astrocytoma/genetics , Ependymoma/genetics , Ependymoma/pathology , Cerebellum/pathology , Cerebellar Neoplasms/genetics , Cerebellar Neoplasms/pathology
20.
Indian J Urol ; 28(4): 456-60, 2012 Oct.
Article in English | MEDLINE | ID: mdl-23450645

ABSTRACT

BACKGROUND: Image quality in an Intravenous Urogram (IVU) can occasionally be compromised by variables like bowel preparation, renal function and radiographic factors, posing a challenge to all Uroradiologists. The Computerised Tomography Urogram (CTU) yields better diagnostic information than an IVU, due to its inherent superior anatomic delineation and contrast sensitivity, against a trade-off involving radiation dose and cost. Our study was conducted to assess the utility and timing of performing a single-phase CTU, as a problem-solving tool, to clear the diagnostic dilemma in a selected subset of patients, in whom an ongoing IVU could potentially be inconclusive. MATERIAL AND METHODS: Five hundred and twelve patients who underwent IVU studies for urologic referrals at a tertiary care hospital, during the period of January to December 2009, formed the subject of the study, of whom 33 patients with inconclusive IVU findings after the first three radiographs underwent a single-phase CTU, to reach definitive imaging diagnoses. RESULTS: The percentage of inconclusive IVU studies amounted to only 33 / 512 (6.4%), in whom a CTU study revealed definitive diagnoses in 30 patients and no abnormality in three patients, thus conclusively clearing the ambiguities raised on the IVU in all the selected patients. CONCLUSIONS: The concept of a CTU limited to a single-phase study to supplement an inconclusive IVU optimizes the contrast and radiation dose to the affected patients. It is a cost-effective, timely, and definitive 'imaging intervention' and should be considered a viable hybrid technique to be utilized selectively and judiciously.

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