Targeting immunosuppressive macrophages overcomes PARP inhibitor resistance in BRCA1-associated triple-negative breast cancer

AK Mehta, EM Cheney, CA Hartl, C Pantelidou… - Nature cancer, 2021 - nature.com
Despite objective responses to poly (ADP-ribose) polymerase (PARP) inhibition and
improvements in progression-free survival (PFS) compared to standard chemotherapy in …

Dynamic interactomics by cross-linking mass spectrometry: mapping the daily cell life in postgenomic era

L Santorelli, M Caterino, M Costanzo - OMICS: A Journal of …, 2022 - liebertpub.com
The majority of processes that occur in daily cell life are modulated by hundreds to
thousands of dynamic protein–protein interactions (PPI). The resulting protein complexes …

Advances in quantitative high‐throughput phosphoproteomics with sample multiplexing

JA Paulo, DK Schweppe - Proteomics, 2021 - Wiley Online Library
Eukaryotic protein phosphorylation modulates nearly every major biological process.
Phosphorylation regulates protein activity, mediates cellular signal transduction, and …

Combinatorial selective ER-phagy remodels the ER during neurogenesis

MJ Hoyer, C Capitanio, IR Smith, JC Paoli… - Nature Cell …, 2024 - nature.com
The endoplasmic reticulum (ER) employs a diverse proteome landscape to orchestrate
many cellular functions, ranging from protein and lipid synthesis to calcium ion flux and inter …

Insights into protein post-translational modification landscapes of individual human cells by trapped ion mobility time-of-flight mass spectrometry

BC Orsburn, Y Yuan, NN Bumpus - Nature communications, 2022 - nature.com
Single cell proteomics is a powerful tool with potential for markedly enhancing
understanding of cellular processes. Here we report the development and application of …

The p97-UBXD8 complex regulates ER-Mitochondria contact sites by altering membrane lipid saturation and composition

R Ganji, JA Paulo, Y Xi, I Kline, J Zhu… - Nature …, 2023 - nature.com
The intimate association between the endoplasmic reticulum (ER) and mitochondrial
membranes at ER-Mitochondria contact sites (ERMCS) is a platform for critical cellular …

Mitochondrial fatty acid synthesis coordinates oxidative metabolism in mammalian mitochondria

SM Nowinski, A Solmonson, SF Rusin, JA Maschek… - Elife, 2020 - elifesciences.org
Cells harbor two systems for fatty acid synthesis, one in the cytoplasm (catalyzed by fatty
acid synthase, FASN) and one in the mitochondria (mtFAS). In contrast to FASN, mtFAS is …

UBXN1 maintains ER proteostasis and represses UPR activation by modulating translation

BA Ahlstedt, R Ganji, S Mukkavalli, JA Paulo… - EMBO …, 2024 - embopress.org
ER protein homeostasis (proteostasis) is essential for proper folding and maturation of
proteins in the secretory pathway. Loss of ER proteostasis can lead to the accumulation of …

3D culture models with CRISPR screens reveal hyperactive NRF2 as a prerequisite for spheroid formation via regulation of proliferation and ferroptosis

N Takahashi, P Cho, LM Selfors, HJ Kuiken, R Kaul… - Molecular cell, 2020 - cell.com
Cancer-associated mutations that stabilize NRF2, an oxidant defense transcription factor,
are predicted to promote tumor development. Here, utilizing 3D cancer spheroid models …

Optimized workflow for multiplexed phosphorylation analysis of TMT-labeled peptides using high-field asymmetric waveform ion mobility spectrometry

DK Schweppe, SF Rusin, SP Gygi… - Journal of proteome …, 2019 - ACS Publications
Phosphorylation is a post-translational modification with a vital role in cellular signaling.
Isobaric labeling-based strategies, such as tandem mass tags (TMT), can measure the …