Secondary Analysis of the NCI-60 Whole Exome Sequencing Data Indicates Significant Presence of Propionibacterium acnes Genomic Material in Leukemia (RPMI-8226) and Central Nervous System (SF-295, SF-539, and SNB-19) Cell Lines.

Yuriy Fofanov,B Montgomery Pettitt,Sergei Chumakov,Mark Rojas,Georgiy Golovko,Kamil Khanipov,Levent Albayrak,Alex Y Strongin,Andrew Mcdowell

doi:10.1371/journal.pone.0127799

Abstract

The NCI-60 human tumor cell line panel has been used in a broad range of cancer research over the last two decades. A landmark 2013 whole exome sequencing study of this panel added an exceptional new resource for cancer biologists. The complementary analysis of the sequencing data produced by this study suggests the presence of Propionibacterium acnes genomic sequences in almost half of the datasets, with the highest abundance in the leukemia (RPMI-8226) and central nervous system (SF-295, SF-539, and SNB-19) cell lines. While the origin of these contaminating bacterial sequences remains to be determined, observed results suggest that computational control for the presence of microbial genomic material is a necessary step in the analysis of the high throughput sequencing (HTS) data.

Highlights

Since the late 1980s, the National Cancer Institute's NCI-60 panel representing nine tumor types has been one of the most highly characterized sets of reference cell lines [1], and is considered to be a valuable public resource for cancer research and drug discovery
From the entire collection of bacterial, viral, phage, fungal, and plasmid reference genome sequences used in the analysis, Propionibacterium acnes alone exhibited a significant presence in the NCI-60 cells (Fig 1 and Section B in S1 Text)
The leukemia (RPMI-8226) and central nervous system (SF-295, SF-539, and SNB-19) samples exhibited the highest amount of P. acnes genomic material ranging from 800 subsequences and 290 genes in SNB-19 to over 3000 subsequences and more than 730 genes in RPMI-8226 samples

Summary

Introduction

Since the late 1980s, the National Cancer Institute's NCI-60 panel representing nine tumor types (breast, central nervous system, colon, leukemia, lung, melanoma, ovarian, prostate, and renal) has been one of the most highly characterized sets of reference cell lines [1], and is considered to be a valuable public resource for cancer research and drug discovery. Considering that many laboratories world-wide rely on NCI-60 panel cell lines to identify anticancer agents, PLOS ONE | DOI:10.1371/journal.pone.0127799. NCI-60 Whole Exome Sequencing Data and Presence of P. acnes in the analysis, c) all 80 and 32-base long subsequences mapped to P. acnes genome, and d) the list of names and accession numbers of all microbial reference genomes used in the analysis. We believe that the availability of this data will make it possible to reproduce all the presented results using any mapping algorithm (such as BWA) or perform an exact search for string s, for example, calling in a loop the standard C++ string manipulation function strstr (s1, s2), which returns a pointer to the first occurrence of string s2 in string s1

Methods

Results

Conclusion