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Omidsalar AA, McCullough CG, Xu L, Boedijono S, Gerke D, Webb MG, Manojlovic Z, Sequeira A, Lew MF, Santorelli M, Serrano GE, Beach TG, Limon A, Vawter MP, Hjelm BE. Common mitochondrial deletions in RNA-Seq: evaluation of bulk, single-cell, and spatial transcriptomic datasets. Commun Biol 2024; 7:200. [PMID: 38368460 PMCID: PMC10874445 DOI: 10.1038/s42003-024-05877-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 01/31/2024] [Indexed: 02/19/2024] Open
Abstract
Common mitochondrial DNA (mtDNA) deletions are large structural variants in the mitochondrial genome that accumulate in metabolically active tissues with age and have been investigated in various diseases. We applied the Splice-Break2 pipeline (designed for high-throughput quantification of mtDNA deletions) to human RNA-Seq datasets and describe the methodological considerations for evaluating common deletions in bulk, single-cell, and spatial transcriptomics datasets. A robust evaluation of 1570 samples from 14 RNA-Seq studies showed: (i) the abundance of some common deletions detected in PCR-amplified mtDNA correlates with levels observed in RNA-Seq data; (ii) RNA-Seq library preparation method has a strong effect on deletion detection; (iii) deletions had a significant, positive correlation with age in brain and muscle; (iv) deletions were enriched in cortical grey matter, specifically in layers 3 and 5; and (v) brain regions with dopaminergic neurons (i.e., substantia nigra, ventral tegmental area, and caudate nucleus) had remarkable enrichment of common mtDNA deletions.
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Affiliation(s)
- Audrey A Omidsalar
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Carmel G McCullough
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Lili Xu
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Stanley Boedijono
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Daniel Gerke
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Michelle G Webb
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Zarko Manojlovic
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Adolfo Sequeira
- Department of Psychiatry and Human Behavior, University of California - Irvine (UCI) School of Medicine, Irvine, CA, USA
| | - Mark F Lew
- Department of Neurology, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Marco Santorelli
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Geidy E Serrano
- Banner Sun Health Research Institute (BSHRI), Sun City, AZ, USA
| | - Thomas G Beach
- Banner Sun Health Research Institute (BSHRI), Sun City, AZ, USA
| | - Agenor Limon
- Mitchell Center for Neurodegenerative Diseases, Department of Neurology, School of Medicine, University of Texas Medical Branch, Galveston, TX, USA
| | - Marquis P Vawter
- Department of Psychiatry and Human Behavior, University of California - Irvine (UCI) School of Medicine, Irvine, CA, USA
| | - Brooke E Hjelm
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA.
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McCullough CG, Szelinger S, Belnap N, Ramsey K, Schrauwen I, Claasen AM, Burke LW, Siniard AL, Huentelman MJ, Narayanan V, Craig DW. Front Cover, Volume 41, Issue 2. Hum Mutat 2020. [DOI: 10.1002/humu.23982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Carmel G. McCullough
- Department of Translational GenomicsUniversity of Southern CaliforniaLos Angeles California
| | - Szabolcs Szelinger
- Center for Rare Childhood Disorders, Neurogenomics DivisionTranslational Genomics Research InstitutePhoenix Arizona
| | - Newell Belnap
- Center for Rare Childhood Disorders, Neurogenomics DivisionTranslational Genomics Research InstitutePhoenix Arizona
| | - Keri Ramsey
- Center for Rare Childhood Disorders, Neurogenomics DivisionTranslational Genomics Research InstitutePhoenix Arizona
| | - Isabelle Schrauwen
- Center for Rare Childhood Disorders, Neurogenomics DivisionTranslational Genomics Research InstitutePhoenix Arizona
| | - Ana M. Claasen
- Center for Rare Childhood Disorders, Neurogenomics DivisionTranslational Genomics Research InstitutePhoenix Arizona
| | - Leah W. Burke
- Department of Pediatrics, Larner College of MedicineUniversity of VermontBurlington Vermont
| | - Ashley L. Siniard
- Center for Rare Childhood Disorders, Neurogenomics DivisionTranslational Genomics Research InstitutePhoenix Arizona
| | - Matthew J. Huentelman
- Center for Rare Childhood Disorders, Neurogenomics DivisionTranslational Genomics Research InstitutePhoenix Arizona
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders, Neurogenomics DivisionTranslational Genomics Research InstitutePhoenix Arizona
| | - David W. Craig
- Department of Translational GenomicsUniversity of Southern CaliforniaLos Angeles California
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McCullough CG, Szelinger S, Belnap N, Ramsey K, Schrauwen I, Claasen AM, Burke LW, Siniard AL, Huentelman MJ, Narayanan V, Craig DW. Utilizing RNA and outlier analysis to identify an intronic splice-altering variant in AP4S1 in a sibling pair with progressive spastic paraplegia. Hum Mutat 2019; 41:412-419. [PMID: 31660686 DOI: 10.1002/humu.23939] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 10/10/2019] [Accepted: 10/24/2019] [Indexed: 01/05/2023]
Abstract
We report a likely pathogenic splice-altering AP4S1 intronic variant in two sisters with progressive spastic paraplegia, global developmental delay, shy character, and foot deformities. Sequencing was completed on whole-blood messenger RNA (mRNA) and analyzed for gene expression outliers after exome sequencing analysis failed to identify a causative variant. AP4S1 was identified as an outlier and contained a rare homozygous variant located three bases upstream of exon 5 (NC_000014.8(NM_007077.4):c.295-3C>A). Confirmed by additional RNA-seq, reverse-transcription polymerase chain reaction, and Sanger sequencing, this variant corresponded with exon 5, including skipping, altered isoform usage, and loss of expression from the canonical isoform 2 (NM_001128126.3). Previously, loss-of-function variants within AP4S1 were associated with a quadriplegic cerebral palsy-6 phenotype, AP-4 Deficiency Syndrome. In this study, the inclusion of mRNA-seq allowed for the identification of a previously missed splice-altering variant, and thereby expands the mutational spectrum of AP-4 Deficiency Syndrome to include impacts to some tissue-dependent isoforms.
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Affiliation(s)
- Carmel G McCullough
- Department of Translational Genomics, University of Southern California, Los Angeles, California
| | - Szabolcs Szelinger
- Center for Rare Childhood Disorders, Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Newell Belnap
- Center for Rare Childhood Disorders, Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Keri Ramsey
- Center for Rare Childhood Disorders, Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Isabelle Schrauwen
- Center for Rare Childhood Disorders, Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Ana M Claasen
- Center for Rare Childhood Disorders, Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Leah W Burke
- Department of Pediatrics, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Ashley L Siniard
- Center for Rare Childhood Disorders, Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Matthew J Huentelman
- Center for Rare Childhood Disorders, Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders, Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona
| | - David W Craig
- Department of Translational Genomics, University of Southern California, Los Angeles, California
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