Eggleston, Heather, Njoya, Kimani, Anderson, Cameron E., Holm, Inge, Eiglmeier, Karin, Liang, Jiangtao, Sharakhov, Igor V., Vernick, Kenneth D., Riehle, Michelle M., Medical College of Wisconsin [Milwaukee] (MCW), Génétique et Génomique des Insectes Vecteurs - Genetics and Genomics of Insect Vectors, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Virginia Polytechnic Institute and State University [Blacksburg], Institut Pasteur [Paris] (IP), This work received financial support to KDV from the European Commission, Horizon 2020 Infrastructures #731060 Infravec2, European Research Council, Support for frontier research, Advanced Grant #323173 AnoPath, Agence Nationale de la Recherche, #ANR-19-CE35-0004 ArboVec, National Institutes of Health, NIAID #AI145999, and French Laboratoire d'Excellence 'Integrative Biology of Emerging Infectious Diseases' #ANR-10-LABX-62-IBEID, to RJN from National Science Foundation, IIS#194727, and to MMR from National Institutes of Health, NIAID #AI145999, ANR-19-CE35-0004,ArboVEC,Barrières d'hôtes dans la spécificité des interactions entre moustiques vecteurs et arbovirus(2019), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), European Project: 731060,INFRAVEC2(2017), and European Project: 323173,EC:FP7:ERC,ERC-2012-ADG_20120314,ANOPATH(2013)
Background Anopheles cell lines are used in a variety of ways to better understand the major vectors of malaria in sub-Saharan Africa. Despite this, commonly used cell lines are not well characterized, and no tools are available for cell line identification and authentication. Methods Utilizing whole genome sequencing, genomes of 4a-3A and 4a-3B ‘hemocyte-like’ cell lines were characterized for insertions and deletions (indels) and SNP variation. Genomic locations of distinguishing sequence variation and species origin of the cell lines were also examined. Unique indels were targeted to develop a PCR-based cell line authentication assay. Mitotic chromosomes were examined to survey the cytogenetic landscape for chromosome structure and copy number in the cell lines. Results The 4a-3A and 4a-3B cell lines are female in origin and primarily of Anopheles coluzzii ancestry. Cytogenetic analysis indicates that the two cell lines are essentially diploid, with some relatively minor chromosome structural rearrangements. Whole-genome sequence was generated, and analysis indicated that SNPs and indels which differentiate the cell lines are clustered on the 2R chromosome in the regions of the 2Rb, 2Rc and 2Ru chromosomal inversions. A PCR-based authentication assay was developed to fingerprint three indels unique to each cell line. The assay distinguishes between 4a-3A and 4a-3B cells and also uniquely identifies two additional An. coluzzii cell lines tested, Ag55 and Sua4.0. The assay has the specificity to distinguish four cell lines and also has the sensitivity to detect cellular contamination within a sample of cultured cells. Conclusions Genomic characterization of the 4a-3A and 4a-3B Anopheles cell lines was used to develop a simple diagnostic assay that can distinguish these cell lines within and across research laboratories. A cytogenetic survey indicated that the 4a-3A and Sua4.0 cell lines carry essentially normal diploid chromosomes, which makes them amenable to CRISPR/Cas9 genome editing. The presented simple authentication assay, coupled with screening for mycoplasma, will allow validation of the integrity of experimental resources and will promote greater experimental reproducibility of results. Graphical abstract