Biological projects

1.1. Chromosome 1

1.2. Chromosome 2

Identification of missing proteins in sperm samples, in collaboration with Chromosome 14 team
Functional characterization of unknown proteins

1.3. Chromosome 3

1.4. Chromosome 4

1.5. Chromosome 5

  • Chromosome 5 consortium has COPD, asthma and lung cancer research project performed in the laboratory of Dirkje Postma.

1.6. Chromosome 6

1.7. Chromosome 7

1.8. Chromosome 8

1.9. Chromosome 9

1.10. Chromosome 10

1.11. Chromosome 11

1.12. Chromosome 12

1.13. Chromosome 13

  • Identification of missing protein-driven bio-signature for cancer, metabolic disease and other biological regulations.

1.14. Chromosome 14

  • Proteomics for testicular pathophysiology, reproductive toxicology and male infertility research projects; contact: charles.pineau at inserm.fr
  • Targeted MS-based assays for a multiplex quantification of liver injury biomarkers candidates in plasma; contact: virginie.brun at cea.fr
  • Infectious diseases (malaria, toxoplasma, lyme disease); contact: ccarapito at unistra.fr

1.15. Chromosome 15

1.16. Chromosome 16

1.17. Chromosome 17

Contact person William Hancock.
In view of the importance of EGFR/ERBB2 heterodimer signaling in breast cancer, it is of interest to explore the transcriptomic and proteomic analysis of two primary cell lines isolated from inflammatory breast cancer patients, one (SUM149) that expresses high levels of EGFR transcript with much lower levels of ERBB2 (1/4), while the other expresses very high levels of ERBB2 transcript (SUM190) and no detectable EGFR transcript. As a control we used a SKBR3 cell line that expressed high levels of ERBB2 transcript and low levels of EGFR. Analysis of the transcript levels indicated that the most likely signaling pathway for SUM190 involved the ERBB2/ERBB3 heterodimer, while SUM149 had several possibilities with involvement of EGFR dimers, ERBB2 heterodimers with EGFR and ERBB2 or ERBB3. We then explored the proteome of the two cell lines in terms of correlations between the transcriptome and proteomic measurements, identification of a panel of 21 oncogenes expressed in the two cell lines, interaction analysis of the observed proteins with this panel of oncogenes and selection of relevant cancer pathways. The analysis resulted in 4 pathways in addition to ERBB2 signaling (EGFR, integrin, MYC signaling, and PI3K signaling that contained many of the oncogene interacting proteins. In general there was reasonable agreement between the RNA-Seq and proteomic values shown in these tables except for some housekeeping proteins. In this study we have demonstrated that one of the goals of the chromosome-centric human proteome project (C-HPP), which is to integrate RNA-Seq with proteomics measurement.

1.18. Chromosome 18

The ongoing Plasma master proteome project is aimed on establishment of the normal levels concentration for each protein using blood plasma of healthy volunteers (astronaut candidates). Creation of the multiplex SRM assay for 200 plasma protein associated with diseases is planned within the project. The clinical proof-of-principal study is based on meta-analysis and our SRM-analysis of the following collections of clinical samples:

  1. glioblastoma
  2. colorectal cancer
  3. risk of stroke

1.19. Chromosome 19

1.20. Chromosome 20

1.21. Chromosome 21

1.22. Chromosome 22

1.23. Chromosome X

1.24. Chromosome Y

1.25. Mitochondrial Chromosome