title: Differential gene expression in dentate granule cells in mesial temporal lobe epilepsy with and without hippocampal sclerosis.
abstract: OBJECTIVE
  Hippocampal sclerosis is the most common neuropathologic finding in cases of medically intractable mesial temporal lobe epilepsy. In this study, we analyzed the gene expression profiles of dentate granule cells of patients with mesial temporal lobe epilepsy with and without hippocampal sclerosis to show that next-generation sequencing methods can produce interpretable genomic data from RNA collected from small homogenous cell populations, and to shed light on the transcriptional changes associated with hippocampal sclerosis.
  
  
  METHODS
  RNA was extracted, and complementary DNA (cDNA) was prepared and amplified from dentate granule cells that had been harvested by laser capture microdissection from surgically resected hippocampi from patients with mesial temporal lobe epilepsy with and without hippocampal sclerosis. Sequencing libraries were sequenced, and the resulting sequencing reads were aligned to the reference genome. Differential expression analysis was used to ascertain expression differences between patients with and without hippocampal sclerosis.
  
  
  RESULTS
  Greater than 90% of the RNA-Seq reads aligned to the reference. There was high concordance between transcriptional profiles obtained for duplicate samples. Principal component analysis revealed that the presence or absence of hippocampal sclerosis was the main determinant of the variance within the data. Among the genes up-regulated in the hippocampal sclerosis samples, there was significant enrichment for genes involved in oxidative phosphorylation.
  
  
  CONCLUSIONS
  By analyzing the gene expression profiles of dentate granule cells from surgically resected hippocampal specimens from patients with mesial temporal lobe epilepsy with and without hippocampal sclerosis, we have demonstrated the utility of next-generation sequencing methods for producing biologically relevant results from small populations of homogeneous cells, and have provided insight on the transcriptional changes associated with this pathology.
authors.affiliation: Institute for Genomic Medicine, Columbia University, New York, New York, U.S.A.
authors.forename: Nicole G
authors.initials: NG
authors.lastname: Griffin
authors.affiliation: Department of Neurobiology, Duke University School of Medicine, Durham, North Carolina, U.S.A.
authors.forename: Yu
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Department of Pathology, Duke University School of Medicine, Durham, North Carolina, U.S.A.
authors.forename: Christine M
authors.initials: CM
authors.lastname: Hulette
authors.affiliation: Institute for Genomic Medicine, Columbia University, New York, New York, U.S.A.
authors.forename: Matt
authors.initials: M
authors.lastname: Halvorsen
authors.affiliation: Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, U.S.A.
authors.forename: Kenneth D
authors.initials: KD
authors.lastname: Cronin
authors.affiliation: Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, U.S.A.
authors.forename: Nicole M
authors.initials: NM
authors.lastname: Walley
authors.affiliation: Department of Neurosurgery, Duke University School of Medicine, Durham, North Carolina, U.S.A.
authors.forename: Michael M
authors.initials: MM
authors.lastname: Haglund
authors.affiliation: Department of Neurology, Duke University School of Medicine, Durham, North Carolina, U.S.A.
authors.forename: Rodney A
authors.initials: RA
authors.lastname: Radtke
authors.affiliation: Department of Neurobiology, Duke University School of Medicine, Durham, North Carolina, U.S.A.
authors.forename: J H Pate
authors.initials: JH
authors.lastname: Skene
authors.affiliation: Department of Neurology, Duke University School of Medicine, Durham, North Carolina, U.S.A.
authors.forename: Saurabh R
authors.initials: SR
authors.lastname: Sinha
authors.affiliation: Institute for Genomic Medicine, Columbia University, New York, New York, U.S.A.|Department of Pathology and Cell Biology, Columbia University, New York, New York, U.S.A.
authors.forename: Erin L
authors.initials: EL
authors.lastname: Heinzen
mesh_terms: D000328:Adult; D018891:Dentate Gyrus / Q000378:metabolism* / Q000473:pathology* / Q000601:surgery; D004569:Electroencephalography / Q000379:methods; D004833:Epilepsy, Temporal Lobe / Q000175:diagnosis* / Q000378:metabolism* / Q000601:surgery; D005260:Female; D005786:Gene Expression Regulation; D006624:Hippocampus / Q000378:metabolism / Q000473:pathology / Q000601:surgery; D006801:Humans; D008297:Male; D008875:Middle Aged; D025341:Principal Component Analysis / Q000379:methods*; D012598:Sclerosis; D055815:Young Adult
keywords: Hippocampus; Mesial temporal sclerosis; RNA-Seq; Temporal lobe epilepsy