With the AACR Virtual Annual Meeting scheduled to reach more than 60,000 researchers from June 22 – 24, 2020, innovative cancer research is taking the spotlight again. Transcriptome analysis has become a key method in cancer diagnosis, in drug mechanisms research, and in the understanding of responses of organisms, tissues, and cells to cancer development. As a true transcriptome analysis company Lexogen is offering a comprehensive product portfolio for transcriptome research, which is reflected in the large number of cancer-related publications citing the use of Lexogen products.

Gene Expression profiling

The QuantSeq 3’ mRNA-Seq library preparation kit is the kit of choice for the characterization of gene expression changes due to its exceptional cost-efficiency, high-throughput suitability, and the protocol-inherent optimized handling of FFPE and biopsy samples. Complimentary data evaluation (up to differential gene expression) is included in the kit price, and the comprehensive QuantSeq portfolio includes globin mRNA blocking and Unique Molecular Indexing (UMI) modules as well as 384 12-nt UDI library barcoding options. The method has been automated on a large range of liquid handling platforms and is available worldwide as a service at Lexogen and numerous NGS core facilities.

Selected Publications:

  • Merril et al. (2019) used QuantSeq to screen for gene expression changes as a molecular determinant of drug response in triple-negative breast cancer (TNBC) cell lines.
  • Hiller et al. (2020) could show with the help of QuantSeq that pre-operative b-blockade independently reduces biomarkers of metastasis in breast cancer.
  • In a more general approach, Manavalan et al. (2019) used QuantSeq-derived 3’ mRNA reads to map polyadenylation sites revealing that depletion of CDK12, a protein frequently mutated in cancer, results in alternative adenylation.
  • Similarly, in Fischl et al. (2019) QuantSeq helped to show that specific alternative adenylation profiles are established during cancer progression.

Whole Transcriptome Analysis

Whole Transcriptome Analysis with excellent uniform transcript coverage and transcript discovery rates can be performed using Lexogen’s CORALL RNA-Seq Library Preparation Kit, either by using total RNA, poly(A)-selected RNAs or total RNA depleted for ribosomal RNAs (e.g. by using Lexogen’s RiboCop rRNA Depletion Kit for Human/Mouse/Rat) as input.

Selected Publication:

  • RiboCop rRNA depletion was used in Müller et a. (2018) to show that the oncofetal mRNA-binding protein IGF2BP1 promotes the expression of the transcriptional regulator SRF in cancer cells.

Metabolic Labeling

The SLAMseq metabolic labeling Kit enables the labeling of newly synthesized RNA, which allows for measuring transcriptome-wide RNA synthesis and decay rates as well as the determination of direct transcriptional targets of transcription factors and regulatory pathways.

Selected Publication:

  • Muhar et al. (2018) validated SLAMseq in human K562 leukemia cells for basic cancer research by degrading key proteins by chemical-genetic perturbation and by adding small molecule inhibitors. The combination of SLAMseq and QuantSeq 3’ mRNA-Seq enabled the authors to determine that BRD4 acts as a global transcriptional activator, MYC controls only selected processes, and BET bromodomain inhibitors (BETi) deregulate a small set of hypersensitive targets including MYC.

RNA Extraction & Functional sRNA Isolation

The brand-new TraPR Small RNA Isolation Kit presents a gel- and bias-free, column-based method for isolation of functional small RNAs from RNA-induced silencing complexes (RISCs) of all organisms (Grentzinger et al., 2020). Within 15 minutes, TraPR enables purification of RISC fractions even from challenging or inconsistent samples, cell types, tissues, and bio-fluids. The TraPR Small RNA Isolation Kit generates high-quality sRNA preparations suitable for Next Generation Sequencing (NGS) applications and thus provides a highly reproducible, time-saving method to obtain all functional, regulatory sRNAs, a key advantage when profiling miRNAs, siRNAs etc in cancer research.

Complementing the portfolio, Lexogen’s SPLIT RNA Extraction Kit delivers RNA of highest quality and virtually DNA free for all kinds of downstream analysis including RNA-Seq and RT-qPCR. The RNA can be recovered as total RNA or split into two fractions, large RNA and small RNA, facilitating the analysis of e.g., mRNA and miRNA from the same sample. The new SPLIT RNA Extraction Kit for Blood enables concomitant depletion of globin mRNAs from human blood samples.

Selected Publication:

  • Total RNA from gastric cancer tissue was extracted with the help of the SPLIT RNA Extraction Kit in Xiao et al. (2018).

References

Chirackal Manavalan, A.P., Pilarova, K., Kluge, M., et al. (2019). CDK12 controls G1/S progression by regulating RNAPII processivity at core DNA replication genes. EMBO Reports 20, e47592. DOI: 10.15252/embr.201847592.

Fischl, H., Neve, J., Wang, Z., et al. (2019). hnRNPC regulates cancer-specific alternative cleavage and polyadenylation profiles. Nucleic Acids Research. DOI: 10.1093/nar/gkz461.

Grentzinger, T., Oberlin, S., Schott, G., et al. (2020). A universal method for the rapid isolation of all known classes of functional silencing small RNAs. Nucleic Acids Research. DOI: 10.1093/nar/gkaa472.

Hiller, J.G., Cole, S.W., Crone, E.M., et al. (2020). Preoperative β-Blockade with Propranolol Reduces Biomarkers of Metastasis in Breast Cancer: A Phase II Randomized Trial. Clinical Cancer Research. 26, 1803-1811. DOI: 10.1158/1078-0432.CCR-19-2641.

Merrill, N.M., Lachacz, E.J., Vandecan, N.M., et al. (2019). Molecular determinants of drug response in TNBC cell lines. Breast Cancer Research and Treatment. DOI: 10.1007/s10549-019-05473-9.

Mueller, S., Glaß, M., Singh, A.K., et al. (2018). IGF2BP1 promotes SRF-dependent transcription in cancer in a m6A- and miRNA-dependent manner. Nucleic Acids Research. DOI: 10.1093/nar/gky1012.

Muhar, M., Ebert, A., Neumann, T., et al. (2018). SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis. Science. DOI: 10.1126/science.aao2793.

Xiao, C., Hong, H., Yu, H., Yuan, Jet, et al. (2018). MiR-340 affects gastric cancer cell proliferation, cycle, and apoptosis through regulating SOCS3/JAK-STAT signaling pathway. Immunopharmacology and Immunotoxicology, 1-6. DOI: 10.1080/08923973.2018.1455208.