Comparison of Multiple Myeloma Donor Patient Samples and Derived Cell Lines Identifies a Confirmed Hyperdiploid Myeloma Cell Line and Demonstrates Remarkable Genetic Similarity Between Cell Lines and Patient Samples
Authors: Keats Jonathan J , Arendt Bonnie K. , Braggio Esteban , Barrett Michael , Price-Troska Tammy , Fonseca Rafael , Bergsagel P. Leif , Jelinek Diane F. 
Published: April 2020

Abstract
Our understanding of the molecular pathogenesis of myeloma is largely based on observations made from the available human myeloma cell lines. Cell lines have proved invaluable to the characterization of the known immunoglobulin translocations, recurrent deletions and amplifications, and the development of novel therapies. However, it has long been perceived that the cell lines are not representative of patient samples as they often have complex genomes and not even a single cell line has been described with a typical hyperdiploid karyotype. The absence of a hyperdiploid model system is significant as conventional cytogenetic studies of myeloma patient samples has established that patients can be almost evenly split into two broad categories of hyperdiploid and non-hyperdiploid based on their chromosome counts, with the hyperdiploid patients having recurrent trisomies of chromosomes 3, 5, 7, 9, 11, 15, 19, and 21 plus periodic gains of 1q, 18, 20 and loss of 13. Though all of the cell lines have abnormal genomes none of the previously tested cell lines had the characteristic pattern of chromosomal gains seen in hyperdiploid patients and the majority have immunoglobulin translocations, which are more commonly associated with non-hyperdiploid patients. These observations have provided the basis for the assumption that the cell lines are only representative of the non-hyperdiploid patient population. Furthermore, even though very few cell lines have been directly compared to the patient sample from which they were derived it is widely believed that the cell line genomes are unstable and have diverged significantly from the patient samples from which they were derived.
Therefore, we decided to compare patient-cell line pairs available from the Mayo Clinic using Agilent 244k array-based comparative genomic hybridization (aCGH) and Affymetrix U133Plus2.0 gene expression profiling and repeated the analysis of our previously studied 46 cell lines on the higher resolution Agilent 244k platform. To date we have completed the analysis of four patient cell line pairs (ALMC-1; ALMC-2; KP-6; KAS-6/1, KAS-6/2) and have repeated our entire cell line panel on the higher resolution array. Four additional patient-cell line pairs (DP-6, JMW-1, SPMC, and VPC-6) are currently being completed.
The first compelling observation from this study was that the patient sample from which KP-6 was derived is a perfect match to the characteristic hyperdiploid karyotype with a CGH defined karyotype (51, XY, −1p, +1q, +3, +7, +11, −13, +15, −16q, −17p, +19, +21). The KP-6 cell line showed a similar aCGH defined karyotype (50, X, −Y, −1p, +1q, +3q, +7, −8p, +9p, +11, +15, −16q, −17p, +17q, +19, +21) with the most significant changes occurring on the trisomic chromosomes as many transitioned from trisomies to single arm gains. Therefore, KP-6 appears to be the first myeloma cell line derived from a patient with a characteristic hyperdiploid phenotype. The ALMC patient cell line series is comprised of patient samples at diagnosis and relapse and cell lines derived from both stages. The two patient-cell line pairs only show five and two aCGH definable changes, respectively. In comparison the two matched patient sample pairs have diverged at six regions in the genome. The KAS patient-cell line series is actually two cell lines derived from pre- (KAS-6/1) and post-transplant (KAS-6/2) samples and the KAS-6/2 matching post-transplant patient sample. The comparison of the paired patient sample and derived cell line shows only four aCGH detectable changes. Similarly, there are only three changes between the KAS-6/1 cell line and post-transplant patient sample suggesting that the evolution of this tumor in both the patient and tissue culture is very limited.
In conclusion, this study has identified the first bona fide hyperdiploid cell line, thereby providing a valuable investigative tool to better understand the biological differences between the two broad genetic categories of myeloma. Moreover, we demonstrate that the genomes of myeloma cell lines are typically stable and highly representative of the patient sample that was placed into culture to establish the cell line thereby validating their use in the study of this disease.