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A Spanish Human Proteome Project (sHPP). La Cristalera, Miraflores de la Sierra, Madrid, August 28-29th, 2012 Juan P Albar, ProteoRed-ISCIII, CNB-CSIC. A SPANISH HUMAN PROTEOME PROJECT (SHPP) Preliminary proposal Index Introduction International context Chromosome/gene centric approach

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a spanish human proteome project shpp

A Spanish Human Proteome Project (sHPP)

La Cristalera, Miraflores de la Sierra, Madrid, August 28-29th, 2012

Juan P Albar, ProteoRed-ISCIII, CNB-CSIC

slide2

A SPANISH HUMAN PROTEOME PROJECT (SHPP)

  • Preliminary proposal
  • Index
  • Introduction
    • International context
    • Chromosome/gene centric approach
    • The HPP technological pillars
    • Protein annotation and database compilation
  • The Spanish Participation in the Human Proteome Project
  • General and Specific Aims
    • General aims
    • Specific aims
  • Members of the Spanish Consortium
    • Description of the groups
    • ProteoRed presence in the Spanish consortium
  • Working Plan
    • Work package list
    • Work package description
  • Financing
  • Spanish Consortium Structure
  • Benefit for Spain
slide3

Spanish HPP Consortium:

Current Developments on the Characterization of the Proteins Encoded by the Chromosome 16"

5th C-HPP Consortium Workshop

The Chromosome-Centric Human Proteome Project

May 5, 2012, Beijing

Juan-Pablo Albar (Chair)

Francisco Blanco (Co-Chair)

Fernando Corrales (Co-Chair)

a spanish human proteome project shpp1

A Spanish Human Proteome Project (sHPP)

Preliminary proposal

San Sebastian, July 9th, 2012

Juan P Albar, ProteoRed-ISCIII, CNB-CSIC

slide5

The Human Proteome Project Launch

Sydney HUPO2010 23 September 2010

Geneva HUPO2011

12 September 2011

Sydney September 23

Human Proteome Project

slide6

The Mission of the HPP

HPP will deliver a comprehensive map of the human proteins in their biological context.

HPP will provide tools for the scientific community that will allow each scientist to design experiments in a better way, as the Human Genome Project did.

HPP will inspire, beyond the scientific community, other stakeholders for diagnosis, prevention, therapy and cure of diseases and improved health worldwide.

Sydney September 23

Human Proteome Project

slide7

A gene-centric proteome project

Map the human proteins (gene by gene):

• Molecular (isoforms)

• Sub-cellular (localization)

• Cells, tissues and organs (expression)

• Interaction networks

• Plasma/serum (abundance)

Use all available technology platforms:

• Mass spectrometry

• Antibodies (immunotechnologies)

• Gene fusions (GFP)

Sydney September 23

Human Proteome Project

hpp technologic pillars
HPP technologic pillars

Legrain et al. MCP 2011

slide16

Spanish HPP Consortium:

Current Developments on the Characterization of the Proteins Encoded by the Chromosome 16"

5th C-HPP Consortium Workshop

The Chromosome-Centric Human Proteome Project

May 5, 2012, Beijing

Juan-Pablo Albar (Chair)

Francisco Blanco (Co-Chair)

Fernando Corrales (Co-Chair)

slide19

16

Chromosome 16 general aims

16

Bioinformaticanalysis of chromosome 16.

Celltype(s) selection. Trascriptomic and proteomicdetailedanalysis.

Expression, purification and characterization of proteinsencodedbychromosome 16 thathavenotbeendescribed so far.

Development of MRM methodsforthequantification of themostabundantproteinspeciesencodedbyeach of thechromosome 16 genes.

Identification, characterization and quantification of proteinvariantsfromchromosome 16 genes.

Definition of SOP

Development of bioinformaticenvironment.

Biobanking.

Configuration of the B-D pilar fortheSpanish HPP consortium.

slide21

16

Genes onChromosome 16

16

More than85 % of proteincoding genes of chromosome 16 are expressed in lymphoidcells, epitelial cells and fibroblasts.

slide22

16

DiseasesmappingonChromosome 16

16

OMIM

CANCER

OBESITY

NEURODEGENERATIVE

AUTOINMUNE DISEASES

Metabolism

Mitochondria

Inflammation

slide23

Development of bioinformatic environment:

Spanish HPP will join the different resources to provide an unique enquiring system

NProt

PRIDE

PAtlas

External repositories

Data standards submission (ProteomeXchange)

Proteomics results

+

+

Emsembl

Upcoming

UProt

GPMDB

slide24

16

Workplanproposal

16

  • Characterize the transcriptome to define the actual chr16’s gen set expressed and most importantly which genes are not expressed in the three selected cell types.
  • Characterize the proteome in detail.
  • Expression, purification, and characterization of 22 unknown proteins available in NAPPA collection.
  • Development of SRM quantitative assays.
      • Proteins (862) will be distributed in known (562) and unknown groups (300) and the study will be performed along 3 years, starting in 2012 (214 proteins).
      • Protein packs will be assigned to each of the 8 MRM groups (24), including equal proportion of known (20, with different range of theoretical difficulty) and unknown proteins (4).
      • Unknown proteins will be first searched by targeted discovery (TD) and relevant information resulting from this studies will be used to design MRM assays. TD groups (9) will analyze 54 proteins the first year.
      • Each group will use the master sample (this might require the use of synthetic peptides during the refinement steps). TD will be done in all three selected cell lines. Regarding MRM, a pool of the three cell lines will be used for the 20 known proteins. Decision on using a pool or a particular cell line for the unknown proteins will be taken in light of the results from TD.
      • Once developed, the assays will be validated by 2 additional groups. Finally, the quantitative assay will be set up using heavy peptides.
  • Definition of Bioinformatic standards and SOPs.
  • Definition of Biobanking strategy, standards... in collaboration with the Spanish Biobanking Platform.
slide25

16

Chromosome 16 timeline

16

2012

2013

2014

Bioinfirmatic study

Master sample

Transcriptomic study

Targeted discovery (300 proteins)

MRM for 204 proteins

MRM for 329 proteins

MRM for 329 proteins

SOP, bioinformatic procedures, formats, data banks, etc.

Validation of MRM assays (3 groups, immunoreagents, correlation with gene expression)

Clinical samples. Disease-related changes on protein abundance. Biomarkers

Biobanking

2015

2016

2017

Validation of MRM assays (3 groups, immunoreagents, correlation with gene expression)

Clinical samples. Disease-related changes on protein abundance. Biomarkers

Biobanking

slide26

SHPP-16

111 Unknow Proteins

735 KnowProteins

Platform

BD-HPP

Platform

C-HPP

BIOBANK/ISCIII

Proteo-Red/ISCIII

Biology

Cells/Tissues

Diseases:

Pathogenesis

Diagnostic

Prognosis

Treatment

who we are

http://www.proteored.org

Who we are
  • ProteoRed, an initiative for the coordination, integration and development of 20 proteomics facilities placed all over Spain.
  • ProteoRed use to organize and participate in multi-centric studies that aims to evaluate the robustness and reproducibility of different proteomics workflows.
  • ProteoRed organization has played an active role in the HUPO-PSI activities, always in close relation with the developments and reviews of different MIAPE modules.
slide28

Geographical organization

Node 2

J. Mato - CIC-bioGUNE

F. Corrales – CIMA

JM. Arizmendi - UPV

Assoc. to node 4

F.J. Blanco - INIBIC

Node 3

J. Abian - LP-CSIC/UAB

J. Arribas - HUVH

S. Martínez - PCB

D. Andreu - UPF

FX. Avilés - IBB UAB

O. Bachs - UB

*

.

Node 4

X. Bustelo - CIC

*

Central Structure

JP. Albar - CNB

J. Mato - CIC-bioGUNE

J. Abian - LP-CSIC/UAB

Geneva

Jean Charles Sanchez - UG

Portugal

Ana Coelho - ITQB

Deborah Penque - ProCura

Node 5

M. Sánchez del Pino – CIPF

R. Bru - UA

Node 1

JP. Albar - CNB

C. Gil - PCM-UCM

A. Marina - CBMSO

-

Assoc. To Node 5

P. Carrasco - UV

Assoc. to Node 1

I. Casal - CIB

Node6

JA. Bárcena - UCO

slide29

CIBER-Obesity

RETIC of

Cancer

RETIC of

Rheumatic

CIBERNed

SHPP-16

BD-HPP Platform

Coordinator: Francisco J. Blanco

ClinicalResearch

Biomarkers (D/P/P/T)

1st Phase: KnownProteins

2nd Phase: UnknownProteins

CAIBER/ISCIII

BIOBANK/ISCIII

Cancer

Chair:

Co-Chair: I. Casal)

RheumaticDiseases:

Chair: FJ. Blanco

Co-Chair: JP Albar

Obesity

Chair: J Prieto

Co-Chair: F. Corrales

NeurologicDisorders

Chair: A. Lopez- Munain

Co-chair:JM Arizmendi

Cardiovascular Diseases:

Chair: L Rodriguez-Padial

Co-Chair: F. Vivanco

InfectiiousDiseases:

Chair: J Fortun

Co-Chair: C. Gil

RETIC-Cardiov.

slide30

HOSPITALES

INSTITUTOS DE INVESTIGACIÓN

CENTROS DE INVESTIGACIÓN

REDES COOPERATIVAS

RHEUMATIC & MUSCLOSKELETAL DISEASES

Dr. F. BLANCO

OBESITY/LIVER DISEASES

Drs J. PRIETO & F. CORRALES

NEUROLOGICAL DISEASES

Dr A. LOPEZ DE MUNAIN

Chr16-HPP Proteomics Platforms

SPANISH NATIONAL BIOBANK NETWORK-ISCIII

Dr M. MORENTE

CARDIOVASCULAR DISEASES

Dr F. VIVANCO & JLR: PADIAL

INFECTIOUS DISEASES

Drs C. GIL & J. FORTÚN

CANCER

Drs C. BELDA & I. CASAL

slide31

HOSPITALES

INSTITUTOS DE INVESTIGACIÓN

CENTROS DE INVESTIGACIÓN

REDES COOPERATIVAS

MINISTERIO DE ECONOMIA Y COMPETITIVIDAD

PLATAFORMAS PROTEÓMICAS

ASOCIACIONES DE PACIENTES

MINISTERIO DE INDUSTRIA

HPP

FARMAINDUSTRIA

MINISTERIO DE SANIDAD

MINISTERIO DE EDUCACIÓN

ASEBIO

EMPRESAS AFINES

COMUNIDADES AUTÓNOMAS

INVERSIÓN PRIVADA

slide32

MINECO

ISCIII

SteeringCommittee

Analytical (C-HPP)

Gene/chromosomecentric

B-D initiatives

Diseasecentric

Bioinformatics

MS andAbbasedquantitativemethods

Open accessrepositories

Hallmarksofdisease

Potentialbiomarkersandtherapeutic targets

Biotechs

MINECO

Designofprototypes

Quantitationoftargetproteins

Pharmas

ISCIII

CNB

UCM

CIB

FJD

CicBiogune

CIMA

CIPF

UAB

PCB

Vall D’Hebron

USAL

La Paz

INIVIC

Clinicaldevices

Personalized medicine

slide33

CHROMOSOME-16 CONSORTIUM STRUCTURE

BoardofDirectors

Project Manager

Executive Committee

Technical Director

Finance Director

WG 1

WG 2

WG 3

WG 5

WG 4

Working Groups

RU1a/1b

RU 2a/2h

RU 3a/3g

RU 4a/4e

RU 5a/5g

Research Units

slide34

WG 1.-Protein Micro Array & Peptide Standard Team

RU1a

(Protein Micro Array and ProteinExpressionTeam)

Dr. Manuel Fuentes

CIC/IBMCC (USAL/CSIC),

Salamanca

RU1b

(Peptide Standard Team)

Dr. Juan P Albar

CNB-CSIC,

ProteoRed, Madrid

Scientific Researchers:

Scientific Researchers:

F. Roncal

M. Lombardía

slide35

WG 2.-S/MRM-Protein Platform Team

RU2a

Dr.

Juan P. Albar

CNB-CSIC,

ProteoRed, Madrid

RU2b

Dr. Fernando Corrales

CIMA-UN

ProteoRed, Pamplona

RU2c

Dr. Francesc Canals

V.H.I.O.

ProteoRed, Barcelona

RU2d

Dr. Concha Gil

PCM-UCM

ProteoRed, Madrid

RU2e

Dr. Manuel Sanchez del Pino

UV

ProteoRed, Valencia

RU2f

Dr. Fernando Vivanco / Dr. M.E Barderas

FJD,Madrid/HNP, Toledo

RU2g

Dr. Francisco Blanco

INIBIC,

ProteoRed, La Coruña

RU2h

Dr. Silvia Barceló

IACS, Zaragoza (Provisional)

  • Scientific Researchers:
  • M. Marcilla
  • S. Gharbi
  • Alpízar
  • C. González

Scientific Researchers:

Scientific Researchers:

Scientific Researchers:

Scientific Researchers:

Scientific Researchers:

Scientific Researchers:

Scientific Researchers:

slide36

WG 3.-Protein Sequencing Team

RU3a

Dr. José M. Mato / Dr. Félix Elortza

CIC-BioGUNE,

ProteoRed, Bilbao

RU3b

Dr. Joaquin Abian

IIBB-CSIC

ProteoRed, Barcelona

RU3c

Dr. Manuel Sanchez del Pino

UV,

ProteoRed, Valencia

RU3d

Dr. Eliandre de Oliveira

PCB,

ProteoRed, Barcelona

RU3e

Dr. Ignacio Casal

CIB-CSIC,

ProteoRed, Madrid

RU3f

Dr. Jesus M. Arizmendi

UPV

ProteoRed, Bilbao

RU3g

Dr.

Juan P. Albar

CNB-CSIC,

ProteoRed, Madrid

Scientific Researchers:

Scientific Researchers:

Scientific Researchers:

Scientific Researchers:

Scientific Researchers:

Scientific Researchers:

  • Scientific Researchers:
  • Paradela
  • R. Navajas
slide37

WG 4.-Bioinformatics Team

RU4a

Dr. Juan P Albar

CNB-CSIC,

ProteoRed, Madrid

RU4b

Dr. Fernando Corrales

CIMA-UN

ProteoRed, Pamplona

RU4c

Dr. Joaquin Abian

IIBB-CSIC

ProteoRed, Barcelona

RU4d

Dr. Concha Gil

PCM-UCM

ProteoRed, Madrid

RU4e

Dr. Jesus M. Arizmendi

UPV

ProteoRed, Bilbao

Scientific Researchers:

  • Scientific Researchers:
  • Medina
  • S. M-Bartolomé

Scientific Researchers:

Scientific Researchers:

Scientific Researchers:

slide38

WG 5.-Clinical Health Care & Biobanking Team (S_B/D-HPP)

RU5a

Dr. Francisco Blanco

INIBIC,

ProteoRed,

La Coruña

RU5b

Dr. Cristobal Belda

FSB, La Paz Hospital, Madrid (Provisional)

RU5c

Dr. Rodríguez Padial/ Dr. Fernando Vivanco / Dr. M.E Barderas

FJD, Madrid/HNP, Toledo

RU5d

Dr. Adolfo López de Munain

Inst. Biodonostia

S. Sebastian

RU5e

Dr. Fernando Corrales

CIMA-UN

ProteoRed, Pamplona

RU5f

Dr. Concha Gil

PCM-UCM

ProteoRed, Madrid

RU5g

Dr. Manuel Morente

SNBN, CNIO, Madrid

(considered for inclusion in the consortium)

Scientific Researchers:

Scientific Researchers:

Scientific Researchers:

Scientific Researchers:

Scientific Researchers:

Scientific Researchers:

Scientific Researchers:

slide39

WG1-Protein Micro Array & Peptide Standard Team

RU1a (Peptide standardization Team):Dr. Manuel Fuentes

Centro de Investigación del Cáncer/IBMCC (USAL/CSIC), Salamanca

RU1b (Protein Micro Array and Protein expression Team): Dr. Juan P Albar

National Center for Biotechnology-CSIC (CNB-CSIC), ProteoRed, Madrid

WG3-Protein Sequencing Team

RU3a-Dr. José M. Mato / Dr. Félix Elortza

CIC-BioGUNE, ProteoRed, Bilbao

RU3b-Dr. Joaquin Abian

IIBB, CSIC ProteoRed, Barcelona

RU3c-Dr. Manuel Sanchez del Pino

University of Valencia, ProteoRed, Valencia

RU3d-Dr. Eliandre de Oliveira

Parc Científic de Barcelona (PCB), ProteoRed, Barcelona

RU3e-Dr. Ignacio Casal

Biology Research Center-CSIC (CIB-CSIC), ProteoRed, Madrid

RU3f-Dr. Jesus M. Arizmendi

Basque Country University ProteoRed, Bilbao

RU3g-Dr. Juan P Albar

National Center for Biotechnology-CSIC (CNB-CSIC), ProteoRed, Madrid

WG2-S/MRM-Protein Platform Team

RU2a-Dr. Juan P Albar

National Center for Biotechnology-CSIC (CNB-CSIC), ProteoRed, Madrid

RU2b-Dr. Fernando Corrales

CIMA-University of Navarra, ProteoRed, Pamplona

RU2c-Dr. Francesc Canals

Vall d\'Hebron Institut d\'Oncologia (V.H.I.O.),ProteoRed, Barcelona

RU2d-Dr. Concha Gil

Madrid Science Park-Computensis University (PCM-UCM), ProteoRed, Madrid

RU2e-Dr. Manuel Sanchez del Pino

Felipe Princess Research Center (CIPF), ProteoRed, Valencia

RU2f-Dr. Fernando Vivanco / Dr. ME Barderas

Jimenez Díaz Foundation (FJD), Madrid /National Paraplegics Hospital, Toledo

RU2g-Dr. Francisco Blanco

Instituto de Investigacion Biomedica (INIBIC), ProteoRed, La Coruña

RU2h-Dr Silvia Barceló

Aragón Health Sciences Institute (IACS), Zaragoza

WG5-Clinical Health Care & Biobanking Team

RU5a-Dr. Francisco Blanco

Instituto de Investigacion Biomedica (INIBIC),

ProteoRed, La Coruña

RU5b-Dr. Cristobal Belda (Provisional)

Severiano Ballesteros Foundation

La Paz Hospital, Madrid

RU5c-Dr. Rodriguez Padial/Dr. Fernando Vivanco/ Dr. ME Barderas

Jimenez Díaz Foundation (FJD), Madrid /National Paraplegics Hospital, Toledo

Ru5d-Dr. Adolfo López de Munain

Instituto Biodonostia, San Sebastian

RU5e-Dr. Fernando Corrales/J. Prieto

CIMA-University of Navarra

RU5f-Dr. Concha Gil

PCM-Computensis University (PCM-UCM), ProteoRed, Madrid

RU5g-Dr. Manuel Morente (considered for inclusion in the consortium)

Spanish National BioBanking Network

CNIO, Madrid

WG4-Bioinformatics Team

RU4a-Dr. Juan P Albar

National Center for Biotechnology-CSIC (CNB-CSIC),

ProteoRed, Madrid

RU4b-Dr. Fernando Corrales

CIMA-University of Navarra

ProteoRed, Pamplona

RU4c-Dr. Joaquin Abian

IIBB, CSIC, ProteoRed, Barcelona

RU4d-Dr. Concha Gil

PCM-Computensis University (PCM-UCM), ProteoRed, Madrid

RU4e-Dr. Jesus M. Arizmendi

Basque Country University, ProteoRed, Bilbao

aims to achieve in the 1st chr 16 consortium meeting
Aims to achieve in the 1st Chr-16 Consortium Meeting
  • Evaluation of the strategy defined in the April 2nd S_HPP Meeting: S/MRM, AIMS, Shotgun, cell culture, protein expression, data base, bioinformatics platform, data workflow
  • Preparation of JPR manuscript, HUPO-Boston Posters…
  • 2012 Working plan (short and medium term)
hupo congress posters i
HUPO CONGRESS POSTERS (I)
  • RE:  Abstract log #322 Your abstract entitled Chromosome 16 Consortium: Current Developments on the Characterization of the Proteins Encoded by the Chromosome 16" (log #322) is formally accepted for poster presentation at the HUPO 11th Annual World Congress, September 9-13, 2012 in Boston, MA (USA).
  • RE:  Abstract log #146 Your abstract entitled Chromosome 16. Transcriptomic profiling of lymphocyte B Ramos cells, MCF-7 epithelial cells and CCD18 fibroblasts (log #146) is formally accepted for poster presentation at the HUPO 11th Annual World Congress, September 9-13, 2012 in Boston, MA (USA).
  • RE:  Abstract log #368  Your abstract entitled Profiling the Chromosome 16 by high-resolution data-dependent Mass Spectrometry (log #368) is formally accepted for poster presentation at the HUPO 11th Annual World Congress, September 9-13, 2012 in Boston, MA (USA). 
hupo congress posters ii
HUPO CONGRESS POSTERS (II)
  • RE: Your abstract log# 758 for the HUPO2012 conference was submitted on 6/30/2012.The log number for your abstract is 758. Chromosome 16 Consortium: The Spanish B/D-C-HPP Initiative Juan P Albar; Jesus Fortun; Jesus Mari Arizmendi; Cristobal Belda; Ignacio Casal; Fernando Corrales; Concha Gil; Adolfo Lopez-Munain; Jesus Prieto; Jesus Rodriguez-Padial; Fernando Vivanco; Francisco J Blanco . Spanish B/D-HPP Consortium, A Coruña, Spain.
  • RE:  Abstract log #217 Your abstract entitled  Automatic reporting and reproducibility analysis of ProteoRed participants in the multi-laboratory studies using  the “MIAPE extractor” tool (log #217) is formally accepted for poster presentation at the HUPO 11th Annual World Congress, September 9-13, 2012 in Boston, MA (USA). 
  • RE: Abstract log# 785 Your abstract entitledReporting and connecting experimental information through proteomics data standards.J. Alberto Medina-Aunon; Salvador Martínez de Bartolomé; Miguel A. López; Juan P. Albar Centro Nacional de Biotecnología - CSIC, Madrid, Spainfor the HUPO2012 conference was submitted on 7/11/2012.
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