Dataset Information

SARS-CoV-2 variants evolve convergent strategies to remodel the host response: Infection proteomics

ABSTRACT: We sought to compare differences in the human cellular response to distinct SARS-CoV-2 variants of concern. Here, we infected Calu-3 lung epithelial cells with each of the SARS-CoV-2 variants of concern (Alpha, Beta, Gamma, Delta, and Omicron) compared to two early-lineage controls (VIC and IC19). We performed global abundance proteomics and phosphoproteomics at 10, 24, and, for certain samples, 48 hours post infection to comprehensively characterize the host response to infection.

INSTRUMENT(S): Orbitrap Fusion Lumos, Orbitrap Exploris 480

ORGANISM(S): Severe Acute Respiratory Syndrome Coronavirus 2

TISSUE(S): Lung, Epithelial Cell

DISEASE(S): Covid-19

SUBMITTER: Mehdi Bouhaddou

LAB HEAD: Nevan J

PROVIDER: PXD036968 | Pride | 2024-02-16

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	2022-03-22_HomoSapiens_uniprot-proteome_UP000005640.fasta	Fasta
	2022-04-27_SARSCoV2WT_SARSCoV2VOC.fasta	Fasta
	20220428_100713_2022-04-27_UK6_AB_Report.csv	Csv
	20220428_110043_2022-04-27_UK5_AB_Report_directDIA.csv	Csv
	20220428_110145_2022-04-27_UK4_AB_Report.csv	Csv

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SARS-CoV-2 variants evolve convergent strategies to remodel the host response.

Bouhaddou Mehdi M Reuschl Ann-Kathrin AK Polacco Benjamin J BJ Thorne Lucy G LG Ummadi Manisha R MR Ye Chengjin C Rosales Romel R Pelin Adrian A Batra Jyoti J Jang Gwendolyn M GM Xu Jiewei J Moen Jack M JM Richards Alicia L AL Zhou Yuan Y Harjai Bhavya B Stevenson Erica E Rojc Ajda A Ragazzini Roberta R Whelan Matthew V X MVX Furnon Wilhelm W De Lorenzo Giuditta G Cowton Vanessa V Syed Abdullah M AM Ciling Alison A Deutsch Noa N Pirak Daniel D Dowgier Giulia G Mesner Dejan D Turner Jane L JL McGovern Briana L BL Rodriguez M Luis ML Leiva-Rebollo Rocio R Dunham Alistair S AS Zhong Xiaofang X Eckhardt Manon M Fossati Andrea A Liotta Nicholas F NF Kehrer Thomas T Cupic Anastasija A Rutkowska Magdalena M Mena Ignacio I Aslam Sadaf S Hoffert Alyssa A Foussard Helene H Olwal Charles Ochieng' CO Huang Weiqing W Zwaka Thomas T Pham John J Lyons Molly M Donohue Laura L Griffin Aliesha A Nugent Rebecca R Holden Kevin K Deans Robert R Aviles Pablo P Lopez-Martin Jose A JA Jimeno Jose M JM Obernier Kirsten K Fabius Jacqueline M JM Soucheray Margaret M Hüttenhain Ruth R Jungreis Irwin I Kellis Manolis M Echeverria Ignacia I Verba Kliment K Bonfanti Paola P Beltrao Pedro P Sharan Roded R Doudna Jennifer A JA Martinez-Sobrido Luis L Patel Arvind H AH Palmarini Massimo M Miorin Lisa L White Kris K Swaney Danielle L DL Garcia-Sastre Adolfo A Jolly Clare C Zuliani-Alvarez Lorena L Towers Greg J GJ Krogan Nevan J NJ

Cell 20230921 21

SARS-CoV-2 variants of concern (VOCs) emerged during the COVID-19 pandemic. Here, we used unbiased systems approaches to study the host-selective forces driving VOC evolution. We discovered that VOCs evolved convergent strategies to remodel the host by modulating viral RNA and protein levels, altering viral and host protein phosphorylation, and rewiring virus-host protein-protein interactions. Integrative computational analyses revealed that although Alpha, Beta, Gamma, and Delta ultimately conv ...[more]

PMID: 37738970

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