Analysis of Expression Profiles to Elucidate Pathogenic Mechanisms of Temporal Lobe Epilepsy with Hippocampal Sclerosis by Sam Jose https://padlet.com/samjose1/lpsmm4b1f1hguug7 en-us 2022-12-02 20:45:11 UTC 2022-12-04 05:28:46 UTC hello@padlet.com Future Directions jys011006 https://padlet.com/samjose1/lpsmm4b1f1hguug7/wish/2407145539
  • The authors successfully identified 3 differentially expressed signatures in TLE+HS patients. However, expression profiling on larger samples should be performed later on to validate their findings. Further investigations should also focus on the underlying mechanism of the 3 signatures of the disease. 
  • Among the 3 signatures, FGFR3 might be a more critical focus for future studies. Multiple studies have revealed that there is a non-causal correlation between mutations in FGFR3 and diseases led by impaired temporal lobe function, including epilepsy. For example, Bernardo et al. reported three cases of temporal lobe malfunction with focal epilepsy patients having FGFR3 mutations.4
  • To investigate how FGFR3 is associated with TLE+HS, an experiment that traces the development of temporal lobe epilepsy in the hippocampus kindling model of TLE5 after regulating FGFR3 expression level by methylation might be a practicable approach. The hippocampus kindling model of TLE is a classic model and the most widely used model in current TLE studies.5 Another study focusing on epigenetics has successfully inhibited the development of TLE by inhibiting histone deacetylation with this model.6 If the upregulation of FGFR3 can inhibit or slow down the progression of temporal lobe epilepsy, it could become a potential target for future gene therapy. 
    • ]]>     2022-12-02 20:49:51 UTC https://padlet.com/samjose1/lpsmm4b1f1hguug7/wish/2407145539     Discussion: Major Findings jys011006 https://padlet.com/samjose1/lpsmm4b1f1hguug7/wish/2407146516 The development of TLE+HS might be associated with:
    • FGFR3, has-miR-486-5p, and lnc-KCNH5-1 
    • Pathways associated with Olfactory transduction, Cytokine-cytokine receptor interaction, Oxidative phosphorylation, and Parkinson’s disease
    ]]>     2022-12-02 20:51:10 UTC https://padlet.com/samjose1/lpsmm4b1f1hguug7/wish/2407146516     Strengths & Weaknesses jys011006 https://padlet.com/samjose1/lpsmm4b1f1hguug7/wish/2407150601 Strengths 
    • First to perform a comprehensive expression profile analysis on mRNA, miRNA, and lncRNA in TLE+HS patients
    • Supportive evidence from previous studies for the findings

    Limitations
    • Even with the high sensitivity of microarray, the researchers failed to rule out the false negative rate due to the small sample size
    • Methylation was the only epigenetic modifier studied
    • Does not determine if the differential expression of signatures is causative for TLE+HS development
    ]]>     2022-12-02 20:57:19 UTC https://padlet.com/samjose1/lpsmm4b1f1hguug7/wish/2407150601     Goal of the Study samjose1 https://padlet.com/samjose1/lpsmm4b1f1hguug7/wish/2407171788
  • To investigate the potential pathogenic mechanisms of TLE+HS by analyzing the expression profiles of microRNA/mRNA/lncRNA/DNA methylation in brain tissue2
  • Elucidation of a mechanism of action may suggest potential therapeutic targets that can lead to the development of a novel cure
    • ]]>     2022-12-02 21:31:51 UTC https://padlet.com/samjose1/lpsmm4b1f1hguug7/wish/2407171788     Differentially Expressed Signatures Between Patients With TLS+HS and Normal Temporal or Parietal Cortices samjose1 https://padlet.com/samjose1/lpsmm4b1f1hguug7/wish/2407173658
  • The first objective of the authors was to find epigenetic signatures that were differentially expressed between individuals with TLE+HS and NTPs 
  • A total of 30 miRNAs, 1,908 genes, and 4,010 lncRNAs were found to be differentially expressed with a p-value less than 0.05 indicating statistical significance (Fig. 1)
  • The BrainScan database was used for filtering and revealed 11 miRNAs, 592 genes, and 1,028 lncRNAs were differentially expressed between patients with TLE+HS and NTP in comparison to the signatures that were not differentially expressed in normal human hippocampus and cortex database (Fig. 1)
  • A total of 116 miRNA-gene co-expression pairs & 224 lncRNA-miRNA co-expression pairs were identified after further correlational and target analysis (Fig. 2)
    • ]]>     2022-12-02 21:35:07 UTC https://padlet.com/samjose1/lpsmm4b1f1hguug7/wish/2407173658     A Brief Introduction to the Methods: Expression Profiling & Functional Analysis jys011006 https://padlet.com/samjose1/lpsmm4b1f1hguug7/wish/2407174487 Sample Collection
    • Experimental group: the hippocampal tissue of 6 patients with TLE+HS
    • Control: NTPs of 9 patients undergoing internal decompression for traumatic brain injury
    DNA & RNA profiling
    • Human microRNA Microarray: miRNA profiling
    • lncRNA + mRNA Human Gene Expression Microarray: mRNA & lncRNA profiling
    • Illumina 450K Infinitum Methylation BeadChip: DNA methylation detection
    Functional Analysis
    • Gene Ontology Analysis: predicting the potential pathological mechanism of TLE+HS
    • Gene Set Enrichment Analysis (GSEA): revealing the association between the signatures and the disease phenotype
    ]]>     2022-12-02 21:36:21 UTC https://padlet.com/samjose1/lpsmm4b1f1hguug7/wish/2407174487     What is Epilepsy? samjose1 https://padlet.com/samjose1/lpsmm4b1f1hguug7/wish/2407179993
  • Epilepsies are a class of neurological disorders where abnormal brain activity can result in seizures or other unusual behavior such as loss of muscle control & consciousness1
  • Temporal Lobe Epilepsy (TLE) is a type of epilepsy that affects the Temporal Lobe in the patient's brain, which is relevant for auditory processing and memory encoding2. Hippocampal Sclerosis (HS) is the loss of neurons in the hippocampus resulting in changes in nearby brain structures2
  • TLE can be idiopathic or caused by traumatic brain injury, infection, genetic disorders, etc2
  • Consequences include cell death via excitotoxicity, physical injuries, and psychological disorders like depression and anxiety2
  • TLE + HS is the most common TLE (70-80%)2
  • TLE + HS is resistant to drug treatment so therapeutic interventions are limited2
    • ]]>     2022-12-02 21:46:27 UTC https://padlet.com/samjose1/lpsmm4b1f1hguug7/wish/2407179993     What are Epigenetics? samjose1 https://padlet.com/samjose1/lpsmm4b1f1hguug7/wish/2407180203
  • Epigenetic factors are the modifications in gene expression not directly caused by changes in the genetic code3
  • These modifications are tissue-specific, allowing for the same genetic code in all cells but the differential expression in different tissues allowing for unique biological functions in different cells3
  • Wang et al., compared differential expression of mRNAs, microRNAs (miRNAs), Long-Non-CodingRNAs (lncRNA), and DNA methylation in the brain tissues of individuals with TLE+HS compared to normal temporal patients (NTPs)2
    • ]]>     2022-12-02 21:46:47 UTC https://padlet.com/samjose1/lpsmm4b1f1hguug7/wish/2407180203     Gene Ontology and Pathway Analysis of Differential Expressed Signatures samjose1 https://padlet.com/samjose1/lpsmm4b1f1hguug7/wish/2407181666
  • Gene Ontology and Pathway analysis revealed a significant increase in the differential expression of signatures related to leukocyte migration, the external side of the plasma membrane, and receptor-ligand activity (Fig. 3a)
  • A significant increase in the differential expression of signatures related to Cytokine-cytokine receptor interaction was also observed (Fig. 3b)
  • These differential expressed signatures may be due to differences in cell populations between the tested groups
  • A GSEA was used to demonstrate increased microglia and astrocytes which indicated the differential expression of mRNA was due to differences in cell populations (Fig. 3c)
    • ]]>     2022-12-02 21:49:27 UTC https://padlet.com/samjose1/lpsmm4b1f1hguug7/wish/2407181666     Global DNA Methylation Analysis samjose1 https://padlet.com/samjose1/lpsmm4b1f1hguug7/wish/2407181985
  • The authors found that six genes were hypomethylated in TLE+HS
  • They also found that FGFR3 was the most severely hypomethylated and also highly expressed in TLE+HS
    • ]]>     2022-12-02 21:49:56 UTC https://padlet.com/samjose1/lpsmm4b1f1hguug7/wish/2407181985     Validation of the Expression of the Critical mRNAs samjose1 https://padlet.com/samjose1/lpsmm4b1f1hguug7/wish/2407182214
  • To validate studies, researchers used a validation cohort of 15 patients with TLE+HS and 5 NTPs
  • Both studies demonstrated that FGFR3 was highly expressed in patients with TLE+HS
  • Results suggested that there was no difference in the expression of FGFR3, has-miR-486-5p, and lnc-KCNH5-1 between the normal hippocampus and the temporal or parietal cortices from NTPs
  • This indicated that the differential expression of the FGFR3, has-miR-486-5p, and lnc-KCNH5-1 between hippocampal tissue from patients with TLE+HS and cortical tissue from NTP was not due to tissue site differences
    • ]]>     2022-12-02 21:50:28 UTC https://padlet.com/samjose1/lpsmm4b1f1hguug7/wish/2407182214     Function Prediction of FGFR3, Has-miR-486-5p, and lnc-KCNH5-1 samjose1 https://padlet.com/samjose1/lpsmm4b1f1hguug7/wish/2407182405
  • The Gene Set Enrichment Analysis (GSEA) was performed using gene correlation coefficients of  FGFR3, has-miR-486-5p,lnc-KCNH5-1 against all genes
  • It showed that Olfactory transduction, Cytokine-cytokine receptor interaction, Oxidative phosphorylation, and Parkinson’s disease were associated with expression levels of these signatures 
    • ]]>     2022-12-02 21:50:53 UTC https://padlet.com/samjose1/lpsmm4b1f1hguug7/wish/2407182405     Significance jys011006 https://padlet.com/samjose1/lpsmm4b1f1hguug7/wish/2407192161 How are the 3 signatures related to TLE+HS?
    FGFR3
    • Responsible for regulating neuronal growth in nervous system development and hippocampal formation
    • Mutation in FGFR3 is linked with medial temporal lobe dysgenesis and seizures
    miRNA-486-5p
    • Targets for GABRB3, which encodes for a subunit of the GABA receptor
    • A missense mutation in GABRB3 is observed in multiple neurological disorders including epilepsy
    lnc-KCNH5-1
    • Mutations in KCNH5 are correlated with epilepsy and impaired neuronal functions. Hypothetically, as a member of the KCNH5 family, lnc-KCNH5-1 might be involved in relevant neuronal activities. 

    How are the pathways related to the disease?
    • Olfactory transduction: deficiencies are widely found in temporal lobe epilepsy patients due to the spread of neuroinflammation throughout the brain
    • Cytokine-cytokine receptor interaction pathway and oxidative phosphorylation pathway are also linked with the occurrence of epilepsy
    • One of the pathological changes is found in both Parkinson's disease and hippocampal sclerosis
    ]]>     2022-12-02 22:08:16 UTC https://padlet.com/samjose1/lpsmm4b1f1hguug7/wish/2407192161     References samjose1 https://padlet.com/samjose1/lpsmm4b1f1hguug7/wish/2407197041
  • Stafstrom, C.E., et al. Seizures and epilepsy: an overview for neuroscientists. Cold Spring Harb Perspect Med, (2015).
  • Wang, Z.-B. et al. Integrated Analysis of expression profile and potential pathogenic mechanism of temporal lobe epilepsy with hippocampal sclerosis. Frontiers in Neuroscience 16, (2022). 
  • Dupont, C., et al. Epigenetics: definition, mechanisms and clinical perspective. Semin Reprod Med 27(5), 351-357 (2009).
  • Bernardo, P., et al. Temporal lobe malformations, focal epilepsy, and FGFR3 mutations: a non-causal association?. Neurol Sci 42, 2063–2067 (2021). 
  • Gorter, J. A., et al. Which insights have we gained from the kindling and post-status epilepticus models?. Journal of Neuroscience Methods 260, 96-108 (2016).
  • Reddy, S.D., et al. Epigenetic Histone Deacetylation Inhibition Prevents the Development and Persistence of Temporal Lobe Epilepsy. J Pharmacol Exp Ther. 364(1), 97-109 (2018).
  • Löscher, W. Fit for purpose application of currently existing animal models in the discovery of novel epilepsy therapies. Epilepsy Research 126, 157-184 (2016).
    • ]]>     2022-12-02 22:19:23 UTC https://padlet.com/samjose1/lpsmm4b1f1hguug7/wish/2407197041     Proposed Mechanism samjose1 https://padlet.com/samjose1/lpsmm4b1f1hguug7/wish/2407373888
  • Using this evidence, they hypothesized that the upregulation of lnc-KCNH5-1 reduced the expression of has-miR-486-5p by adsorbing it
  • Reduced has-miR-486-5p reduced its repressive effect on FGFR3
  • Resulting in the upregulation of FGFR3 expression
  • Decreased FGFR3 methylation also contributed to the upregulation of FGFR3 expression
    • ]]>     2022-12-03 07:13:30 UTC https://padlet.com/samjose1/lpsmm4b1f1hguug7/wish/2407373888     Acknowledgements jys011006 https://padlet.com/samjose1/lpsmm4b1f1hguug7/wish/2407698155 Sam Jose: Title, Background, Goal of Study, Results
    Xiaoting Yuan: Methods, Discussions, Future Directions
    All members contributed to References & Formatting]]>     2022-12-03 21:45:45 UTC https://padlet.com/samjose1/lpsmm4b1f1hguug7/wish/2407698155     samjose1 https://padlet.com/samjose1/lpsmm4b1f1hguug7/wish/2407760894 2022-12-04 02:05:57 UTC https://padlet.com/samjose1/lpsmm4b1f1hguug7/wish/2407760894 samjose1 https://padlet.com/samjose1/lpsmm4b1f1hguug7/wish/2407760979 2022-12-04 02:06:16 UTC https://padlet.com/samjose1/lpsmm4b1f1hguug7/wish/2407760979 samjose1 https://padlet.com/samjose1/lpsmm4b1f1hguug7/wish/2407761066 2022-12-04 02:06:34 UTC https://padlet.com/samjose1/lpsmm4b1f1hguug7/wish/2407761066 samjose1 https://padlet.com/samjose1/lpsmm4b1f1hguug7/wish/2407794309 2022-12-04 04:01:01 UTC https://padlet.com/samjose1/lpsmm4b1f1hguug7/wish/2407794309 samjose1 https://padlet.com/samjose1/lpsmm4b1f1hguug7/wish/2407796159 2022-12-04 04:07:27 UTC https://padlet.com/samjose1/lpsmm4b1f1hguug7/wish/2407796159