HeLa-CCL2 cell heterogeneity studied by single-cell DNA and RNA sequencing

Abstract

The HeLa cells are the earliest and mostly used laboratory human cells for biomedical particularly cancer research. They were derived from a patient’s cervical cancerous tissue, and are known for their heterogeneous cellular origin and variable genomic landscapes. Single-cell sequencing techniques with faithful linear and uniformly amplified genomes (DNA) and transcriptomes (RNA) may facilitate the study of cellular differences at the individual cell level. In this work, we have performed single-cell DNA and RNA sequencing with HeLa-CCL2 cells to study their heterogeneity. We have studied the complexity of copy number variations (CNVs) of HeLa-CCL2 genome at the single cell level, and revealed the transcriptomic heterogeneity of HeLa-CCL2. We also analyzed the relationship between genome and transcriptome at the single-cell level, and found overall correlation between CNV and transcriptome expression patterns. Finally, we concluded that although single-cell sequencing techniques are applicable to study heterogeneous cells such as HeLa-CCL2, the data analyses need to be more careful and well controlled.

Ultra-high sensitivity mass spectrometry quantifies single-cell proteome changes upon perturbation

“…To minimize bias, we selected assays from two widespread scRNA-seq technologies, Drop-seq 41 and the lower throughput SMART-seq2 42 , on the same cellular system. The Drop-seq assay is based on unique molecular identifiers (UMIs) 43 to control for amplification biases in library preparation, whereas the SMART-seq2 assay is not UMI-controlled 44 . Note that MS-based proteomics inherently does not involve any amplification and is not subject to associated artifacts.…”

“…Given our set of more than 430 single-cell proteomes, we compared the T-SCP measurements after filtering with similar single-cell RNA sequencing data (scRNA-seq) 39,40 . To achieve technology-independent insights, we selected assays from two widespread scRNA-seq technologies, Drop-seq 41 and the lower throughput SMART-sSq2 42 , on the same cellular system.…”

Multicellular 3D Models to Study Tumour-Stroma Interactions

“…The broad use of HeLa cells in many labs around the world and their ability to indefinitely grow and overwhelm other cell lines have led to more than 300 different HeLa progeny strains and to a widespread cross-contamination of other cell lines [ 9 , 10 ]. It has been estimated that about 20% of cell lines are falsely identified (mainly due to intraspecies contamination), highlighting the need for proper authentication of the true origin of cell lines, as already suggested by the pioneering work of Walter Nelson-Rees in the 1970s and early 1980s [ 11 ].…”

“…The broad use of HeLa cells in many labs around the world and their abi initely grow and overwhelm other cell lines have led to more than 300 dif progeny strains and to a widespread cross-contamination of other cell lines been estimated that about 20% of cell lines are falsely identified (mainly due cies contamination), highlighting the need for proper authentication of the tr cell lines, as already suggested by the pioneering work of Walter Nelson-Rees and early 1980s [11]. Different strains cultured in different labs show differ and transcriptomic landscapes, mainly due to genotypic drift and accumulatio aberrations due to the extensive chromosome instability characterizing can [10,12,13]. Thus, cancer cells are neither clonal nor genetically stable, and the iment performed on cells cultured in different labs could lead to distinct con irreproducible results.…”

Generation of functional salivary gland tissue from human submandibular gland stem/progenitor cells

“…DNA library was prepared using the NEBNext Ultra DNA Prep Kit and sequenced on the Illumina Hiseq-PE150 platform. And genome copy number analysis was performed as reported previously [23].…”