Single Cell Genomics Team

CNAG-CRG

TEAM LEADER:
Holger Heyn

POSTDOCTORAL FELLOWS:
Amy Guillaumet (until July), Catia Moutinho (from July), Gustavo Rodriguez, Giovanni Iacono (from March)

DATA ANALYST:
Elisabetta Mereu

PhD STUDENT:
Atefeh Lafzi, Davide Polizzi (until September)

Summary

The Single Cell Genomics Team focuses on the systematic integration of genomic data from individual cells to elucidate causalities underlying phenotype formation. The mission of the group is the implementation of single-cell sequencing technologies and their application in a research and translational context. We established single-cell RNA sequencing processes for MARS-seq and SMART-seq and high-throughput protocols in microfluidic systems. Newly developed computational pipelines include methods to deconvolute tissue composition, identify cell type markers and track transcriptional dynamics. We are joining computational, statistical and biological knowledge in order to establish and apply best practices in single-cell research. The group combines collaborative research, development activities and follows an independent research line on translational cancer research. In 2017, we critically enlarged the scope of single-cell methods by implementing cryopreservation for sample transfer and archiving. A systematic comparison of different protocols pointed to large differences in sensitivity of molecule capture, with a high degree of accuracy across the methods. We applied single-cell RNA sequencing for cellular phenotyping, among others, during development, tumor evolution and aging. We are member of the Human Cell Atlas Project.

Our single-cell RNA sequencing experimental workflow: From sample processing to data interpretation.

Fig. 1

Our single-cell RNA sequencing experimental workflow: From sample processing to data interpretation.

Research lines

  • Single-cell technologies
  • Computational pipeline development
  • Cancer Heterogeneity Dynamics
  • Human cell atlas

Selected Publications

Guillaumet-Adkins A, Rodríguez-Esteban G, Mereu E, Mendez-Lago M, Jaitin DA, Villanueva A, Vidal A, Martinez-Marti A, Felip E, Vivancos A, Keren-Shaul H, Heath S, Gut M, Amit I, Gut I, Heyn H.
“Single-cell transcriptome conservation in cryopreserved cells and tissues.”
Genome Biol, 18(1):45 (2017).

Vidal E, Sayols S, Moran S, Guillaumet-Adkins A, Schroeder MP, Royo R, Orozco M, Gut M, Gut I, Lopez-Bigas N, Heyn H, Esteller M.
“A DNA methylation map of human cancer at single base-pair resolution.”
Oncogene, 36(40):5648-5657 (2017).

Barriga FM, Montagni E, Mana M, Mendez-Lago M, Hernando-Momblona X, Sevillano M, Guillaumet-Adkins A, Rodriguez-Esteban G, Buczacki SJA, Gut M, Heyn H, Winton DJ, Yilmaz OH, Attolini CS, Gut I, Batlle E.
“Mex3a Marks a Slowly Dividing Subpopulation of Lgr5+ Intestinal Stem Cells.”
Cell Stem Cell, 20(6):801-816.e7 (2017).

Martinez-Marti A, Felip E, Matito J, Mereu E, Navarro A, Cedrés S, Pardo N, Martinez de Castro A, Remon J, Miquel JM, Guillaumet-Adkins A, Nadal E, Rodriguez-Esteban G, Arqués O, Fasani R, Nuciforo P, Heyn H, Villanueva A, Palmer HG, Vivancos A
“Dual MET and ERBB inhibition overcomes intratumor plasticity in osimertinib-resistant-advanced non-small-cell lung cancer (NSCLC).”
Ann Oncol, 28(10):2451-2457 (2017).

Ziegenhain C, Vieth B, Parekh S, Reinius B, Guillaumet-Adkins A, Smets M, Leonhardt H, Heyn H, Hellmann I, Enard W.
“Comparative Analysis of Single-Cell RNA Sequencing Methods.”
Mol Cell, 65(4):631-643.e4 (2017).