Reply: Evidence that APP gene copy number changes reflect recombinant vector contamination

• Published in: bioRxiv
• Main Authors: Ming-Hsiang, Lee, Liu, Christine S, Zhu, Yunjiao, Kaeser, Gwendolyn E, Rivera, Richard, Romanow, William J, Kihara, Yasuyuki, Chun, Jerold
• Format: Paper
• Language: English
• Published: Cold Spring Harbor Cold Spring Harbor Laboratory Press 09.07.2020
• Subjects: Alzheimer's disease; Amyloid precursor protein; Contaminants; Contamination; Copy number; Neurodegenerative diseases; Recombination; United States > US
• DOI: 10.1101/730291

In the accompanying comment1, Kim et al. concluded that somatic gene recombination (SGR) and amyloid precursor protein (APP) genomic complementary DNAs (gencDNAs) in brain are contamination artifacts and do not naturally exist. We disagree. Here we address the three types of analyses used by Kim et al. to reach their conclusions: informatic contaminant identification, plasmid PCR, and single-cell sequencing. Additionally, Kim et al. requested "reads supporting novel APP insertion breakpoints", and we now provide 10 different examples that support APP gencDNA insertion within eight chromosomes beyond wildtype APP on chromosome 21 from Alzheimer's disease (AD) samples. If SGR exists as experimentally supported here and previously2,3, contamination scenarios become moot. Our informatic analyses of data generated by an independent laboratory (Park et al.)4, complement and are entirely consistent with what Lee et al.2 presented via nine distinct lines of evidence, in addition to three from a prior publication3. Plasmid contamination was identified in a single pull-down dataset after publication of Lee et al.2; however subsequent analyses did not alter any of our conclusions including those of our prior publications3,5 and plasmid contamination-free replication of this approach by ourselves and others supported the original conclusions. Novel retro-insertion sites, alterations of APP gencDNA number and form with cell type from the same brain and pathogenic SNVs occurring only in AD, all support the existence of APP gencDNAs produced by SGR. Competing Interest Statement Sanford Burnham Prebys Medical Discovery Institute has filed the following patent applications on the subject matter of this publication: (1) PCT application number PCT/US2018/030520 entitled, "Methods of diagnosing and treating Alzheimer's disease" filed 1 May 2018, which claims priority to US provisional application 62/500,270 filed 2 May 2017; and (2) US provisional application number 62/687,428 entitled, "Anti-retroviral therapies and reverse transcriptase inhibitors for treatment of Alzheimer's disease" filed 20 June 2018. JC is a co-founder of Mosaic Pharmaceuticals.