SOLID TUMOR scRNAseq

PREVENTING BIAS IN scRNAseq PERFORMED ON SOLID TUMORS

Key Takeaways

  • Samples stored, shipped and processed using the HIVE™ scRNAseq Solution precisely match flow cytometry from freshly
    dissociated tissue without sample bias.
  • HIVE™ scRNAseq Solution captures the complete tumor miccroenvironment in solid tissue biopsies.
  • Sequencing of samples stored, shipped and processed using the HIVE™ scRNAseq Solution is consistent across Illumina® platforms.
Solid Tumor scRNAseq Preventing Bias in scRNAseq Performed on Solid Tumors

Check out our application note:
Solid Tumor scRNAseq: Preventing Bias in scRNAseq Performed on Solid Tumors

Request more information about the HIVE™ scRNAseq Solution

In this study, an established biospecimen provider to processed a biopsy from a renal cell carcinoma (RCC) tumor using their established SOPs to dissociate fresh tumor tissue, perform flow cytometry, and cryopreserve the sample or capture single cells with the HIVE™ scRNAseq Solution for single cell RNA sequencing. The HIVE™ scRNAseq protocol was easily adopted into their standardized operations.

Samples stored, shipped and processed using the HIVE™ scRNAseq Solution precisely matched flow cytometry from freshly dissociated tissue without any sample bias. The HIVE™ stabilized all cells in the sample and yielded high integrity scRNAseq data through 20 weeks’ storage. Cryopreservation immediately damaged the sample and destroyed precious immune cells, including T cells, monocytes, and macrophages through 20 weeks’ storage, biasing scRNAseq data obtained from solid tumor tissues.

HONEYCOMB™ SUPPORTS ONCOLOGY

Sample Types

  • Tumor tissues, biopsies
  • Fine needle aspirates
  • Blood, bone marrow
  • Lavages, urine, CSF, swabs

Supporting Scale-up

  • Easily adopted by biospecimen providers, biobanks, and satellite labs
  • Highly reliable for longitudinal studies
  • Enables access to global sample distribution
The HIVE™ scRNAseq device enables pharma studies that rely on remotely collected samples by facilitating their storage and shipping while retaining the complexity of the sample.

HIVE™ scRNAseq SOLUTION CAPTURES THE COMPLETE TUMOR MICROENVIRONMENT IN SOLID TISSUE BIOPSIES

Sample processed by Discovery Life Sciences,1 a third-party biospecimen provider

  • RCC tumor biopsy:
    • Adult male
    • Pre-treatment
  • SOPs performed on the sample:
    • Fresh tissue dissociation
    • Flow cytometry
    • HIVE™ processing
    • Cryopreservation of the remaining cells
    • scRNAseq at remote core facility
The HIVE™ scRNAseq device enables reproducible performance with minimal intersample variability between samples before and after shipping internationally.
(Left) UMAP of all samples; each dot is a cell, and each color represents a cell-type. (Right) Dot plot showing the specificity (percent cells expressing) and robustness (average expression) of scRNAseq marker genes.

HIVE™ SAMPLE COMPOSITION PRECISELY MATCHES FRESH FLOW CYTOMETRY

Flow Cytometry

  • Differentiates relevant immune cells and tumor cells
  • Uses freshly dissociated tissue and established SOPs

HIVE™ scRNAseq

  • Acquires molecular insight for tumor dynamics & microenvironment
  • Stabilizes single cell RNA for storage
  • No sample bias with the HIVE™ scRNAseq Solution, same composition as orthologous method
The HIVE™ scRNAseq device enables reproducible performance with minimal intersample variability between samples before and after shipping internationally.
Sample composition based on (Left) flow cytometry antibody panel and (Right) HIVE™ scRNAseq marker genes

HIVE™ SEQUENCING IS CONSISTENT ACROSS ILLUMINA® PLATFORMS

Sequencing Platforms

  • Illumina® NextSeq® 2000 platform is a benchtop sequencer with 360 GB output in 11–48 hours
  • Illumina® NovaSeq® 6000 is production-scale with 6000 GB output in 13–44 hours
  • See Illumina’s blog post2 on sequencing HIVE™ libraries

HIVE™ Sequencing Recommendations3

  • Libraries compatible with ≥100-cycle kits:
    • Read1: 25 cycles; Index1: 8 cycles;
    • Index2: 8 cycles; Read2: 75 cycles
The HIVE™ scRNAseq device enables reproducible performance with minimal intersample variability between samples before and after shipping internationally.
Data from both sequencing platforms represents all samples

THE HIVE™ SINGLE-CELL RNAseq SOLUTION STABILIZES SAMPLES FOR LONG-TERM STORAGE

Cryopreservation Immediately Damages Cells and Degrades Sample Quality while in Storage

  • The HIVE™ scRNAseq Solution yielded 2–3× more cells from the same sample with higher number of cells, genes per cell, and transcripts per cell
  • Samples processed using the HIVE™ scRNAseq Solution were stable through 20 weeks, while the sample progressively degraded in cryopreservation
The HIVE™ scRNAseq device enables reproducible performance with minimal intersample variability between samples before and after shipping internationally.

CRYOPRESERVATION CAUSES DRAMATIC LOSS OF T CELLS AND OTHER IMMUNE CELLS

The HIVE™ scRNAseq Soltuion Preserves Critical Immune Cells and Prevents Biological Bias4

  • Long-term cryopreservation damages T cells, monocytes, and macrophages
  • The HIVE™ scRNAseq Solution accurately captures immune dynamics and prevents sample bias
The HIVE™ scRNAseq device enables robust and specific expression across various cell types.

References

  1. Discovery Life Sciences. https://www.dls.com/biospecimens
  2. llumina BaseSpace Sequence Hub: Demo Data. NextSeq 2000: HIVE single cell RNAseq libraries from Honeycomb Biotechnologies on P3 100 cycles kit. https://basespace.illumina.com/datacentral
  3. HIVE™ sequencer compatibility and recommendations. https://honeycombbio.zendesk.com/hc/en-us/articles/4738507106587-Recommended-Sequencers-
  4. https://honeycomb.bio/resources/clinical-study-pilottop-10-pharma-uses-hive-for-research/?resource_id=9b698eb3105bd82528f23d0c92dedfc0
Request more information about the HIVE™ scRNAseq Solution

For research use only. Not for use in diagnostic procedures.