HUPO 2015 C-HPP Poster Abstracts

Chromosome 1

Chromosome 2

Title: Exploring the ‘missing proteome’ in testis: why and how?
Authors: Charles Pineau¹, Lydie Lane^2,3, Yves Vandenbrouck⁴, Jérôme Garin⁴ and ProFi consortium⁵
Affiliations: ¹ Protim, Inserm U1085 - Irset, Campus de Beaulieu, 35042 Rennes - France
²Department of Human Protein Sciences, Faculty of medicine, University of Geneva, 1211 Geneva 4, Switzerland
³SIB Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland
⁴CEA, DSV, iRTSV, Laboratoire de Biologie à Grande Echelle, INSERM U1038, Université Grenoble, F-38054, France
⁵http://www.profiproteomics.fr
Abstract: It was suggested that the production of proteins that have been systematically missed might be restricted to unusual organs or cell types, for example the testis. Testicular function, and spermatogenesis in particular, is conditioned by the successive activation and/or repression of thousands of genes and proteins, including numerous germ cell- and testis-specific products. A recent study from the Human Protein Atlas confirmed that the largest number of tissue-enriched genes is found in the testis, this organ being considered as an outlier when looking for protein-coding genes. This is in accordance with an in-depth analysis of human RNA-seq data showing that certain organs such as the brain and especially the testis, express more protein-coding genes than others. Indeed, substantially more genic regions are transcribed in the testis than in other organs. A relatively small number of testis-specific transcripts were identified in the premeiotic germ cell lineage or somatic testicular cells (i.e., Sertoli and Leydig cells). Therefore, we believe that post-meiotic germ cells, including mature spermatozoa, are potentially fruitful sites to search for missing proteins.

Chromosome 3

Chromosome 4

Chromosome 5

Title: Identification of protein biomarkers for colorectal cancer by proteogenomic analysis
Authors: Malgorzata A Komor¹, Thang V Pham², Annemieke C Hiemstra¹, Sander R Piersma², Beatriz Carvalho¹, Gerrit A Meijer¹, Connie R Jimenez², Remond JA Fijneman¹
Affiliations: ¹ Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
² Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
Contact: Malgorzata A Komor
Abstract: The abstract in pdf is available here.

Chromosome 6

Chromosome 7

Chromosome 8

Chromosome 9

Chromosome 10

Chromosome 11

Chromosome 12

Chromosome 13

Chromosome 14

Chromosome 15

Chromosome 16

Title: Missing proteins in Chromosome 16 Spanish HPP
Author: F. Clemente¹, M.L. Hernáez¹, I. Zapico¹, M. Gonzalez-Gonzalez², L. Odriozola³, P. Fernandez⁴, C. Ruiz⁴, I. Orera⁵, S. Barcelo⁶, M. Marcilla⁷, S. Gharbi⁷, E. Perez⁶, A. Paradela⁷, E. Sabido⁸, M. Fuentes², F. Corrales³, C. Gil¹.
Affiliations: ¹UCM Madrid/Spain
²CIC-USAL Salamanca/Spain
³CIMA Pamplona/Spain
⁴INIBIC A Coruña/Spain
⁵IACS Zaragoza/Spain
⁶IDIBELL Barcelona/Spain
⁷CNB Madrid/Spain
⁸CRG/UPF Barcelona/Spain
Abstarct: According to neXtProt database annotation, there are still proteins without conclusive experimental evidence, which are termed “missing proteins”. This lack of information could be due to either the low level of the protein expression or the specific cell line/tissue in which is expressed or the specifically development step of their turn up. To overcome this problem, in the Spanish HPP consortium we are trying to get the spectral and the MRM data from the unknown proteins for its detection later in human samples. To get this information, we analyzed the Chr.16 proteins from which there is not spectral information. Moreover, for most of them there is not empirical evidence in the Swissprot database, or the evidence exists only at transcript level.
The Spanish HPP consortium has developed a specific protocol for unknown proteins encoded in chromosome 16, in order to get proteomic information for the MRM method, which is based on the expression of recombinant proteins in a cell free translation system. Upon method optimization we use synthetic labelled peptides to search the missing proteins on different biological samples, including biofluids and cell lines.

Chromosome 17

Chromosome 18

Chromosome 19

Title: Single Amino Acid Variant Analysis in Glioma Stem Cells Derived from Chromosomes 7, 10, 19 and 20
Authors: E. Mostovenko, Á. Végvári, M. Rezeli, C.F. Lichti, D. Fenyö, E.P. Sulman, G. Marko-‐Varga, C.L. Nilsson
Abstract: Recently, glioma derived stem cells (GSCs), one cause of recurrence of glioblastoma tumors, were studied from the chromosomal perspective of frequency of DNA copy number variants (CNV) and chromosomal location of single amino acid variant proteins. Chromosomes 7, 19, and 20 show elevated CNV in samples, whereas chromosome 10 shows the lowest frequency of variation. We applied a combined transcriptomic-proteomic approach to identify SAV peptides in GSCs, followed by validation with SRM. Finally, structural modelling of SAV proteins may guide us in the identification of novel protein targets.
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Title: Single amino acid variants in proteins derived from glioma stem cells and brain metastatic tumor cells as analyzed by quantitative mass spectrometry
Authors: K. Barbara Sahlin*, Melinda Rezeli, Akos Vegvari, Ekaterina Mostovenko, Carol Nilsson, György Marko-Varga
Abstract:
Background
Primary brain cancer tumors (glioblastoma, GBM) have high mortality rates. We analyzed biobanked GSCs from MD Anderson Cancer Center (Houston, Texas, USA). GSCs are strongly implicated as tumor-imitiating cells and an important cause of tumor recurrence. Current standard-of-care treatments fail in 98% of GBM patients, partly due to the aggressive, resistant nature of the GSCs. The GSC lines were established by isolating neurosphere-forming cells from surgical specimens of human GBM using a method described previously¹.
Materials and methods
Proteins were extracted from all cell lines, and prepared for mass spectrometric analysis as previously described². By use of a proprietary database that includes all known protein variants, we identified hundreds of variant peptides in our samples³.

Results
Branched chain amino acid transferase 2 (BCAT2) T186R (a threonine 186 to arginine variant, SAV) has been identified as a target in glioma stem cells (GSCs). BCAT2 T186R is a germline variant with prevalence of 25% in patient tumor-derived GSCs, compared to 9.6% of the general population. This mitochondrial enzyme metabolizes branched amino acids, which are easily absorbed through the blood-brain barrier, and produces glutamate and alpha-ketoacids. GSCs that express the BCAT2 variant therefore may have an energetic advantage to grow in the brain environment. Another 225 SAV-containing peptides were targeted for analysis by single reaction monitoring (SRM), in amultiplexed approach. Our results to date indicate that mutant forms of Nestin (V130 A), Vigilin (S61A), and IDH1 (V178I) are expressed in all GSC lines studied.

Conclusion
We suspect that these SAVs, along with BCAT2 T186R, may be oncogenic “drivers”, and that they also may be expressed in brain metastatic tumors of non-neuronal origin. In the continued study, we will quantify the SAVs in six brain-metastic and six non-brain metastatic cell lines derived from patient melanoma tumors.
Acknowledgments. We thank Dr. Erik Sulman, MDACC, for providing GSCs for this study. Support from the Cancer Prevention and Research Institute of Texas (RML1122 to CLN) and the University of Texas Medical Branch (CLN) is gratefully acknowledged.

References
1. Bhat, K. P. L.; Salazar, K. L.; Balasubramaniyan, V.; Wani, K.; Heathcock, L.; Hollingsworth, F.; James, J. D.; Gumin, J.; Diefes, K. L.; Kim, S. H.; Turski, A.; Azodi, Y.; Yang, Y.; Doucette, T.; Colman, H.; Sulman, E. P.; Lang, F. F.; Rao, G.; Copray, S.; Vaillant, B. D.; Aldape, K. D., Genes & Development 2011, 25 (24), 2594-2609.
2. Lichti, C. F.; Liu, H.; Shavkunov, A. S.; Mostovenko, E.; Sulman, E. P.; Ezhilarasan, R.; Wang, Q.; Kroes, R. A.; Moskal, J. C.; Fenyö, D.; Oksuz, B. A.; Conrad, C. A.; Lang, F. F.; Berven, F. S.; Végvári, Á.; Rezeli, M.; Marko-Varga, G.; Hober, S.; Nilsson, C. L., Journal of Proteome Research 2014, 13 (1), 191-199.
3. Lichti, C. F.; Mostovenko, E.; Wadsworth, P. A.; Lynch, G. C.; Pettitt, B. M.; Sulman, E. P.; Wang, Q.; Lang, F. F.; Rezeli, M.; Marko-Varga, G.; Végvári, Á.; Nilsson, C. L., Systematic Journal of Proteome Research 2015, 14 (2), 778-786.

C-HPP

Chromosome-Centric Human Proteome Project