A Bird’s Eye View of Quantitative Proteome of Tumor Tissues from Lung Cancer Patients by a High Precision Mass Spectrometry Method

Abstract

Lung cancer produces a high incidence of malignant tumors. There have been many studies on lung cancer using mass spectrometry (MS) technologies. However, most studies have focused on humoral samples. In this work, 26 pairs of tissue samples (tumor vs. para-tumor) from patients with lung cancer were analyzed using liquid chromatography-tandem MS (LC-MS/MS) with data-independent acquisition mode. In total, 3152 proteins were quantified from tissue samples with high confidence, including 189 up-regulated and 522 down-regulated proteins (tumor vs. para-tumor). In addition, 79 and 690 proteins were identified only in para-cancerous samples and cancerous samples, respectively. The results from bio-informatics tools indicated that altered proteins like PEBP1, HRG and LYZ could be ideal reservoirs for screening the potential biomarkers for lung cancer. It is believed these tissue-specific proteomics results will assist in the studies of lung cancer.

Keywords

Lung cancer / Proteome / Data-independent aquisition

References

[1] Krist A H, Davidson K W, Mangione C M, Barry M J, Cabana M, Caughey A B, Davis E M, Donahue K E, Doubeni C A, Kubik M, Landefeld C S, Li L, Ogedegbe G, Owens D K, Pbert L, Silverstein M, Stevermer J, Tseng C W, Wong J B. JAMA, 2021, 325: 962.

[2] Song S Y, Tang W J, Yu S Y, Liu H W, Bai Y. Chem. Res. Chinese Universities, 2022, 38(3): 809.

[3] Chang H R, Ding Q J, Wang H L. Chem. Res. Chinese Universities, 2023, 39(3): 395.

[4] Xie Y, Meng W Y, Li R Z, Wang Y W, Qian X, Chan C, Yu Z F, Fan X X, Pan H D, Xie C, Wu Q B, Yan P Y, Liu L, Tang Y J, Yao X J, Wang M F, Leung E L. Translational Oncology, 2021, 14: 100907.

[5] Nooreldeen R, Bach H. International Journal of Molecular Science, 2021, 22: 18.

[6] Liu L, Zhu B, Fang Z, Zhang N, Qin H, Guo Z, Liang X, Yao Z, Ye M. Analytical Chemistry, 2021, 93: 7473.

[7] Zhang X, Wang Q, Li Y, Ruan C, Wang S, Hu L, Ye M. Analytical Chemistry, 2019, 92: 1363.

[8] Sun Y, Huo C, Qiao Z, Shang Z, Uzzaman A, Liu S, Jiang X, Fan L-Y, Ji L, Guan X, Cao C-X, Xiao H. Journal of Proteome Research, 2018, 17: 1101.

[9] Zhang C, Leng W, Sun C, Lu T, Chen Z, Men X, Wang Y, Wang G, Zhen B, Qin J. EBioMedicine, 2018, 30: 120.

[10] Boccellino M, Pinto F, Ieluzzi V, Giovane A, Quagliuolo L, Fariello C, Coppola M, Carlucci A, Santini M, Ferati K, Bexheti-Ferati A, Giordano A, Di Domenico M. Journal of Cellular Physiology, 2019, 234: 23798.

[11] Blume J E, Manning W C, Troiano G, Hornburg D, Figa M, Hesterberg L, Platt T L, Zhao X, Cuaresma R A, Everley P A, Ko M, Liou H, Mahoney M, Ferdosi S, Elgierari E M, Stolarczyk C, Tangeysh B, Xia H, Benz R, Siddiqui A, Carr S A, Ma P, Langer R, Farias V, Farokhzad O C. Nature Communications, 2020, 11: 3662.

[12] Tirumalai R S, Chan K C, Prieto D A, Issaq H J, Conrads T P, Veenstra T D. Molecular & Cellular Proteomics, 2003, 2: 1096.

[13] Hu A, Noble W S, Wolf-Yadlin A. F1000Research, 201, 5: 12.

[14] Huang D W, Sherman B T, Lempicki R A. Nature Protocol, 2009, 4: 44.

[15] Hanahan D, Weinberg Robert A. Cell, 2011, 144: 646.

[16] Alvarez-Curto E, Inoue A, Jenkins L, Raihan S Z, Prihandoko R, Tobin A B, Milligan G. Journal of Biological Chemistry, 201, 291: 27147.

[17] Wang T, Wang Z, Niu R, Wang L. Cancer Biology & Medicine, 2019, 16: 671.

[18] Theek B, Baues M, Gremse F, Pola R, Pechar M, Negwer I, Koynov K, Weber B, Barz M, Jahnen-Dechent W, Storm G, Kiessling F, Lammers T. Journal of Controlled Release, 2018, 282: 25.

[19] Winiarska A, Zareba L, Krolczyk G, Czyzewicz G, Zabczyk M, Undas A. Disease Markers, 2019, 2019: 8170759.

[20] Rath O, Park S, Tang H-H, Banfield M J, Brady R L, Lee Y C, Dignam J D, Sedivy J M, Kolch W, Yeung K C. Cellular Signalling, 2008, 20: 935.

[21] Yang X, Wang Y, Lu P, Shen Y, Zhao X, Zhu Y, Jiang Z, Yang H, Pan H, Zhao L, Zhong Y, Wang J, Liang Z, Shen X, Lu D, Jiang S, Xu J, Wu H, Lu H, Jiang G, Zhu H. EMBO reports, 2020, 21: 13.

[22] Ghimire K, Li Y, Chiba T, Julovi S M, Li J, Ross M A, Straub A C, O’Connell P J, Rüegg C, Pagano P J, Isenberg J S, Rogers N M. Cells, 2020, 9: 1695.

[23] Meijles D N, Sahoo S, Al Ghouleh I, Amaral J H, Bienes-Martinez R, Knupp H E, Attaran S, Sembrat J C, Nouraie S M, Rojas M M, Novelli E M, Gladwin M T, Isenberg J S, Cifuentes-Pagano E, Pagano P J. Science Signaling, 2017, 10: 14.

[24] Jia J, Arif A, Terenzi F, Willard B, Plow Edward F, Hazen Stanley L, Fox Paul L. Cell, 2014, 159: 623.

[25] Koike A, Arai S, Yamada S, Nagae A, Saita N, Itoh H, Uemoto S, Totani M, Ikemoto M. Inflammation, 2011, 35: 409.

[26] Wang Y, Tian Y, Liu X, Dong J, Wang L, Ye M. Journal of Proteome Research, 2020, 19: 3807.

[27] Saltzman A, Stone M, Franks C, Searfoss G, Munro R, Jaye M, Ivashchenko Y. Biochemical and Biophysical Research Communications, 1998, 246: 627.