Novel functional proteins coded by the human genome discovered in metastases of melanoma patients

Aniel Sanchez; Magdalena Kuras; Jimmy Rodriguez Murillo; Indira Pla; Krzysztof Pawlowski; A. Marcell Szasz; Jeovanis Gil; Fábio C.S. Nogueira; Yasset Perez-Riverol; Jonatan Eriksson; Roger Appelqvist; Tasso Miliotis; Yonghyo Kim; Bo Baldetorp; Christian Ingvar; Håkan Olsson; Lotta Lundgren; Henrik Ekedahl; Peter Horvatovich; Yutaka Sugihara; Charlotte Welinder; Elisabet Wieslander; Ho Jeong Kwon; Gilberto B. Domont; Johan Malm; Melinda Rezeli; Lazaro Hiram Betancourt; György Marko-Varga

doi:10.1007/s10565-019-09494-4

Novel functional proteins coded by the human genome discovered in metastases of melanoma patients

Aniel Sanchez, Magdalena Kuras, Jimmy Rodriguez Murillo, Indira Pla, Krzysztof Pawlowski, A. Marcell Szasz, Jeovanis Gil, Fábio C.S. Nogueira, Yasset Perez-Riverol, Jonatan Eriksson, Roger Appelqvist, Tasso Miliotis, Yonghyo Kim, Bo Baldetorp, Christian Ingvar, Håkan Olsson, Lotta Lundgren, Henrik Ekedahl, Peter Horvatovich, Yutaka SugiharaCharlotte Welinder, Elisabet Wieslander, Ho Jeong Kwon, Gilberto B. Domont, Johan Malm, Melinda Rezeli, Lazaro Hiram Betancourt, György Marko-Varga

Research output: Contribution to journal › Article › peer-review

7 Citations (Scopus)

Abstract

In the advanced stages, malignant melanoma (MM) has a very poor prognosis. Due to tremendous efforts in cancer research over the last 10 years, and the introduction of novel therapies such as targeted therapies and immunomodulators, the rather dark horizon of the median survival has dramatically changed from under 1 year to several years. With the advent of proteomics, deep-mining studies can reach low-abundant expression levels. The complexity of the proteome, however, still surpasses the dynamic range capabilities of current analytical techniques. Consequently, many predicted protein products with potential biological functions have not yet been verified in experimental proteomic data. This category of ‘missing proteins’ (MP) is comprised of all proteins that have been predicted but are currently unverified. As part of the initiative launched in 2016 in the USA, the European Cancer Moonshot Center has performed numerous deep proteomics analyses on samples from MM patients. In this study, nine MPs were clearly identified by mass spectrometry in MM metastases. Some MPs significantly correlated with proteins that possess identical PFAM structural domains; and other MPs were significantly associated with cancer-related proteins. This is the first study to our knowledge, where unknown and novel proteins have been annotated in metastatic melanoma tumour tissue.

Original language	English
Pages (from-to)	261-272
Number of pages	12
Journal	Cell Biology and Toxicology
Volume	36
Issue number	3
DOIs	https://doi.org/10.1007/s10565-019-09494-4
Publication status	Published - 2020 Jun 1

Bibliographical note

Funding Information:
This study was approved by the Regional Ethical Committee at Lund University, Southern Sweden, approval numbers: DNR 191/2007, 101/2013 and 2015/266, 2015/618. All patients involved in the study provided written informed consent. Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Funding Information:
Open access funding provided by Lund University. This study was financially supported by the Berta Kamprad Foundation, ThermoFisher Scientific, Global, and Liconic Biobanking, and was also supported by grants from the National Research Foundation of Korea, funded by the Korean government (2015K1A1A2028365 and 2016K2A9A1A03904900) and Brain Korea 21 Plus Project, Republic of Korea, as well as the NIH/NCI International Cancer Proteogenome Consortium and the Mats and Stefan Paulsson Trust.

Publisher Copyright:
© 2019, The Author(s).

All Science Journal Classification (ASJC) codes

Toxicology
Cell Biology
Health, Toxicology and Mutagenesis

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1007/s10565-019-09494-4

Cite this

Sanchez, A., Kuras, M., Murillo, J. R., Pla, I., Pawlowski, K., Szasz, A. M., Gil, J., Nogueira, F. C. S., Perez-Riverol, Y., Eriksson, J., Appelqvist, R., Miliotis, T., Kim, Y., Baldetorp, B., Ingvar, C., Olsson, H., Lundgren, L., Ekedahl, H., Horvatovich, P., ... Marko-Varga, G. (2020). Novel functional proteins coded by the human genome discovered in metastases of melanoma patients. Cell Biology and Toxicology, 36(3), 261-272. https://doi.org/10.1007/s10565-019-09494-4

@article{b559a45914a84a68b9a6fe3b925777f9,

title = "Novel functional proteins coded by the human genome discovered in metastases of melanoma patients",

abstract = "In the advanced stages, malignant melanoma (MM) has a very poor prognosis. Due to tremendous efforts in cancer research over the last 10 years, and the introduction of novel therapies such as targeted therapies and immunomodulators, the rather dark horizon of the median survival has dramatically changed from under 1 year to several years. With the advent of proteomics, deep-mining studies can reach low-abundant expression levels. The complexity of the proteome, however, still surpasses the dynamic range capabilities of current analytical techniques. Consequently, many predicted protein products with potential biological functions have not yet been verified in experimental proteomic data. This category of {\textquoteleft}missing proteins{\textquoteright} (MP) is comprised of all proteins that have been predicted but are currently unverified. As part of the initiative launched in 2016 in the USA, the European Cancer Moonshot Center has performed numerous deep proteomics analyses on samples from MM patients. In this study, nine MPs were clearly identified by mass spectrometry in MM metastases. Some MPs significantly correlated with proteins that possess identical PFAM structural domains; and other MPs were significantly associated with cancer-related proteins. This is the first study to our knowledge, where unknown and novel proteins have been annotated in metastatic melanoma tumour tissue.",

author = "Aniel Sanchez and Magdalena Kuras and Murillo, {Jimmy Rodriguez} and Indira Pla and Krzysztof Pawlowski and Szasz, {A. Marcell} and Jeovanis Gil and Nogueira, {F{\'a}bio C.S.} and Yasset Perez-Riverol and Jonatan Eriksson and Roger Appelqvist and Tasso Miliotis and Yonghyo Kim and Bo Baldetorp and Christian Ingvar and H{\aa}kan Olsson and Lotta Lundgren and Henrik Ekedahl and Peter Horvatovich and Yutaka Sugihara and Charlotte Welinder and Elisabet Wieslander and Kwon, {Ho Jeong} and Domont, {Gilberto B.} and Johan Malm and Melinda Rezeli and Betancourt, {Lazaro Hiram} and Gy{\"o}rgy Marko-Varga",

note = "Funding Information: This study was approved by the Regional Ethical Committee at Lund University, Southern Sweden, approval numbers: DNR 191/2007, 101/2013 and 2015/266, 2015/618. All patients involved in the study provided written informed consent. Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Funding Information: Open access funding provided by Lund University. This study was financially supported by the Berta Kamprad Foundation, ThermoFisher Scientific, Global, and Liconic Biobanking, and was also supported by grants from the National Research Foundation of Korea, funded by the Korean government (2015K1A1A2028365 and 2016K2A9A1A03904900) and Brain Korea 21 Plus Project, Republic of Korea, as well as the NIH/NCI International Cancer Proteogenome Consortium and the Mats and Stefan Paulsson Trust. Publisher Copyright: {\textcopyright} 2019, The Author(s).",

year = "2020",

month = jun,

day = "1",

doi = "10.1007/s10565-019-09494-4",

language = "English",

volume = "36",

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journal = "Cell Biology and Toxicology",

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Sanchez, A, Kuras, M, Murillo, JR, Pla, I, Pawlowski, K, Szasz, AM, Gil, J, Nogueira, FCS, Perez-Riverol, Y, Eriksson, J, Appelqvist, R, Miliotis, T, Kim, Y, Baldetorp, B, Ingvar, C, Olsson, H, Lundgren, L, Ekedahl, H, Horvatovich, P, Sugihara, Y, Welinder, C, Wieslander, E, Kwon, HJ, Domont, GB, Malm, J, Rezeli, M, Betancourt, LH & Marko-Varga, G 2020, 'Novel functional proteins coded by the human genome discovered in metastases of melanoma patients', Cell Biology and Toxicology, vol. 36, no. 3, pp. 261-272. https://doi.org/10.1007/s10565-019-09494-4

TY - JOUR

T1 - Novel functional proteins coded by the human genome discovered in metastases of melanoma patients

AU - Sanchez, Aniel

AU - Kuras, Magdalena

AU - Murillo, Jimmy Rodriguez

AU - Pla, Indira

AU - Pawlowski, Krzysztof

AU - Szasz, A. Marcell

AU - Gil, Jeovanis

AU - Nogueira, Fábio C.S.

AU - Perez-Riverol, Yasset

AU - Eriksson, Jonatan

AU - Appelqvist, Roger

AU - Miliotis, Tasso

AU - Kim, Yonghyo

AU - Baldetorp, Bo

AU - Ingvar, Christian

AU - Olsson, Håkan

AU - Lundgren, Lotta

AU - Ekedahl, Henrik

AU - Horvatovich, Peter

AU - Sugihara, Yutaka

AU - Welinder, Charlotte

AU - Wieslander, Elisabet

AU - Kwon, Ho Jeong

AU - Domont, Gilberto B.

AU - Malm, Johan

AU - Rezeli, Melinda

AU - Betancourt, Lazaro Hiram

AU - Marko-Varga, György

N1 - Funding Information: This study was approved by the Regional Ethical Committee at Lund University, Southern Sweden, approval numbers: DNR 191/2007, 101/2013 and 2015/266, 2015/618. All patients involved in the study provided written informed consent. Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Funding Information: Open access funding provided by Lund University. This study was financially supported by the Berta Kamprad Foundation, ThermoFisher Scientific, Global, and Liconic Biobanking, and was also supported by grants from the National Research Foundation of Korea, funded by the Korean government (2015K1A1A2028365 and 2016K2A9A1A03904900) and Brain Korea 21 Plus Project, Republic of Korea, as well as the NIH/NCI International Cancer Proteogenome Consortium and the Mats and Stefan Paulsson Trust. Publisher Copyright: © 2019, The Author(s).

PY - 2020/6/1

Y1 - 2020/6/1

N2 - In the advanced stages, malignant melanoma (MM) has a very poor prognosis. Due to tremendous efforts in cancer research over the last 10 years, and the introduction of novel therapies such as targeted therapies and immunomodulators, the rather dark horizon of the median survival has dramatically changed from under 1 year to several years. With the advent of proteomics, deep-mining studies can reach low-abundant expression levels. The complexity of the proteome, however, still surpasses the dynamic range capabilities of current analytical techniques. Consequently, many predicted protein products with potential biological functions have not yet been verified in experimental proteomic data. This category of ‘missing proteins’ (MP) is comprised of all proteins that have been predicted but are currently unverified. As part of the initiative launched in 2016 in the USA, the European Cancer Moonshot Center has performed numerous deep proteomics analyses on samples from MM patients. In this study, nine MPs were clearly identified by mass spectrometry in MM metastases. Some MPs significantly correlated with proteins that possess identical PFAM structural domains; and other MPs were significantly associated with cancer-related proteins. This is the first study to our knowledge, where unknown and novel proteins have been annotated in metastatic melanoma tumour tissue.

AB - In the advanced stages, malignant melanoma (MM) has a very poor prognosis. Due to tremendous efforts in cancer research over the last 10 years, and the introduction of novel therapies such as targeted therapies and immunomodulators, the rather dark horizon of the median survival has dramatically changed from under 1 year to several years. With the advent of proteomics, deep-mining studies can reach low-abundant expression levels. The complexity of the proteome, however, still surpasses the dynamic range capabilities of current analytical techniques. Consequently, many predicted protein products with potential biological functions have not yet been verified in experimental proteomic data. This category of ‘missing proteins’ (MP) is comprised of all proteins that have been predicted but are currently unverified. As part of the initiative launched in 2016 in the USA, the European Cancer Moonshot Center has performed numerous deep proteomics analyses on samples from MM patients. In this study, nine MPs were clearly identified by mass spectrometry in MM metastases. Some MPs significantly correlated with proteins that possess identical PFAM structural domains; and other MPs were significantly associated with cancer-related proteins. This is the first study to our knowledge, where unknown and novel proteins have been annotated in metastatic melanoma tumour tissue.

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ER -

Novel functional proteins coded by the human genome discovered in metastases of melanoma patients

Abstract

Bibliographical note

All Science Journal Classification (ASJC) codes

UN SDGs

Access to Document

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