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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


A spanish human proteome project shpp

  • 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


A spanish human proteome project shpp

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


A spanish human proteome project shpp

The Human Proteome Project Launch

Sydney HUPO2010 23 September 2010

Geneva HUPO2011

12 September 2011

Sydney September 23

Human Proteome Project


A spanish human proteome project shpp

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


A spanish human proteome project shpp

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


A spanish human proteome project shpp

C-HPP teams by April 24th, 2012. The C-HPP Consortium internal information


Hpp technologic pillars

HPP technologic pillars

Legrain et al. MCP 2011


A spanish human proteome project shpp

Flow of the overall procedures of the C-HPP work


A spanish human proteome project shpp

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 shpp

Chromosome 16


A spanish human proteome project shpp

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.


A spanish human proteome project shpp

Top 15 Biofunctionsrepresented in chromosome 16. IPA analysis


A spanish human proteome project shpp

16

Genes onChromosome 16

16

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


A spanish human proteome project shpp

16

DiseasesmappingonChromosome 16

16

OMIM

CANCER

OBESITY

NEURODEGENERATIVE

AUTOINMUNE DISEASES

Metabolism

Mitochondria

Inflammation


A spanish human proteome project shpp

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


A spanish human proteome project shpp

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.


  • A spanish human proteome project shpp

    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


    A spanish human proteome project shpp

    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.


    A spanish human proteome project shpp

    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


    A spanish human proteome project shpp

    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.


    A spanish human proteome project shpp

    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


    A spanish human proteome project shpp

    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


    A spanish human proteome project shpp

    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


    A spanish human proteome project shpp

    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


    A spanish human proteome project shpp

    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


    A spanish human proteome project shpp

    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:


    A spanish human proteome project shpp

    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


    A spanish human proteome project shpp

    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:


    A spanish human proteome project shpp

    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:


    A spanish human proteome project shpp

    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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