Ontology highlight
ABSTRACT:
PROVIDER: PRJNA657267 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12455222_1.fastq.gz | Fastqsanger.gz | |||
| SRR12455222_2.fastq.gz | Fastqsanger.gz |
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Project description:Esophageal squamous cell carcinoma (ESCC) is an aggressive cancer with one of the highest world incidences in the Eastern Cape region of South Africa. Several genome wide studies have been performed on ESCC cohorts from Asian countries, North America, Malawi and other parts of the world but none has been conducted on ESCC tumors from South Africa to date, where the molecular pathology and etiology of this disease remains unclear. We report here tumor associated copy number changes observed in 51 ESCC patients’ samples from the Eastern Cape province of South Africa. We extracted tumor DNA from 51 archived ESCC specimens and interrogated tumor associated DNA copy number changes using Affymetrix® 500K SNP array technology. The Genomic Identification of Significant Targets in Cancer (GISTIC) algorithm was applied to identify significant focal regions of gains and losses. Gains of the top recurrent cancer genes were validated by fluorescence in situ hybridization and their protein expression assessed by immunohistochemistry. Twenty-three significant focal gains were identified across samples. Gains involving the CCND1, MYC, EGFR and JAG1 loci recapitulated those described in studies on Asian and Malawian cohorts. The two most significant gains involved the chromosomal sub-bands 3q28, encompassing the TPRG1 gene and 11q13.3 including the CTTN, PPFIA1and SHANK2 genes. There was no significant homozygous loss and the most recurrent hemizygous deletion involved the B3GAT1 gene on chromosome11q25. Focal gains on 11q13.3 in 37% of cases (19/51), consistently involved CTTN and SHANK2 genes. Twelve of these cases (23,5%), had a broader region of gain that also included the CCND1, FGF19, FGF4 and FGF3 genes. SHANK2 and CTTN are co-amplified in several cancers, these proteins interact functionally together and are involved in cell motility. Immunohistochemistry confirmed both Shank2 (79%) and cortactin (69%) protein overexpression in samples with gains of these genes. In contrast, cyclin D1 (65%) was moderately expressed in samples with CCND1 DNA gain. This study reports copy number changes in a South African ESCC cohort and highlights similarities and differences with cohorts from Asia and Malawi. Our results strongly suggest a role for CTTN and SHANK2 in the pathogenesis of ESCC in South Africa.
2020-04-07 | GSE59105 | GEO
Project description:The emergence and fast global spread of COVID-19 has presented one of the greatest public health challenges in modern times with no proven cure or vaccine. Africa is still early in this epidemic, therefore the extent of disease severity is not yet clear. We used a mathematical model to fit to the observed cases of COVID-19 in South Africa to estimate the basic reproductive number and critical vaccination coverage to control the disease for different hypothetical vaccine efficacy scenarios. We also estimated the percentage reduction in effective contacts due to the social distancing measures implemented. Early model estimates show that COVID-19 outbreak in South Africa had a basic reproductive number of 2.95 (95% credible interval [CrI] 2.83–3.33). A vaccine with 70% efficacy had the capacity to contain COVID-19 outbreak but at very higher vaccination coverage 94.44% (95% Crl 92.44–99.92%) with a vaccine of 100% efficacy requiring 66.10% (95% Crl 64.72–69.95%) coverage. Social distancing measures put in place have so far reduced the number of social contacts by 80.31% (95% Crl 79.76–80.85%). These findings suggest that a highly efficacious vaccine would have been required to contain COVID-19 in South Africa. Therefore, the current social distancing measures to reduce contacts will remain key in controlling the infection in the absence of vaccines and other therapeutics.
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Project description:First occurrence of Sugarcane Streak Mosaic Virus (SCSMV) infecting Sugarcane in Côte d’Ivoire, West Africa
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Project description:First occurrence of Sugarcane Streak Mosaic Virus (SCSMV) infecting Sugarcane in Côte d’Ivoire, West Africa
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Project description:Cassava mosaic disease caused by cassava begomoviruses is the most serious disease of cassava in Africa. However, the molecular mechanisms leading to symptom development of infected cassava plants are poorly understood. Here a high throughput digital gene expression profiling (DGE) based on Illumina Solexa sequencing technology was used to investigate the global transcriptional response of cassava to the African cassava mosaic virus infection. Results showed that 3,210 genes were differentially expressed in virus-infected cassava leaves. Gene Ontology (GO) term and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that photosynthesis related genes were most affected, which was consistent with the chlorotic symptom on the infected leaves. The upregulation of chlorophyll degradation genes, e.g. the genes encoding chlorophyllase and pheophorbide a oxygenase, as well as the downregulation of the major apoproteins genes in light harvesting complex II (LHCII) identified by the DGE analysis were confirmed by qRT-PCR. Together with the reduction of chlorophyll b content and fewer grana stacks in the infected leaf cells, this study reveals that the degradation of chlorophyll plays an important role during ACMV symptom development for the first time. Meanwhile, we believe that the non-lethal effect on photosystem is a trick for virus to avoid fierce host immune response and a result of the long-term co-evolution. This study will provide a road map for future investigations into virus symptom development. ACMV-infected cassava leaves mixture from three independent replicates were collected for RNA extractions at 20 dpi. Control samples were harvested from empty agrobacteria treated leaves incubated under the same conditions.
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