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PubMed2025

GCLC desuccinylation regulated by oxidative stress protects human cancer cells from ferroptosis.

Tumor cells evolve strong antioxidant capacities to counteract the abnormal high level of reactive oxygen species (ROS) in the tumor microenvironment. Glutamate-cysteine ligase catalyzing subunit (GCLC) for synthesis of antioxidant glutathione (GSH) represents the key enzyme to maintain redox homeostasis of tumor cells, however, whether its activity is regulated by posttranslational modifications, such as succinylation, remains to be clarified. Here, we demonstrate the existence of succinylation modification on GCLC by in vitro and in vivo assays. NAD-dependent deacetylase Sirtuin-2 (SIRT2) serves as the desuccinylase and catalyzes GCLC desuccinylation at sites of K38, K126, and K326. Specifically, GCLC directly interacts with SIRT2, which can be substantially enhanced upon ROS treatment. This strengthened association results in GCLC desuccinylation and activation, consequently promoting GSH synthesis and rendering cancer cells resistant to ferroptosis induction. Depletion of SIRT2 decreases total GSH level and meanwhile increases the cellular susceptibility to ferroptosis, which can mostly be rescued by introducing wild-type GCLC, but not its 3K-E mutant. We further demonstrated that histone acetyltransferase P300 serves as the succinyltransferase of GCLC, and their association is remarkably decreased after ROS treatment. Thus, SIRT2-regulated GCLC succinylation represents an essential signaling axis for cancer cells to maintain their redox balance in coping with oxidative stress-induced ferroptosis.

Humans↗
PubMed2025

A novel feedback loop between DYRK2 and USP28 regulates cancer homeostasis and DNA damage signaling.

Posttranslational modifications, such as ubiquitination and phosphorylation, play pivotal roles in regulating protein stability in response to cellular stress. Dual-specificity tyrosine phosphorylation-regulated kinase 2 (DYRK2) and ubiquitin-specific peptidase 28 (USP28) are critical regulators of cell cycle progression, DNA damage response, and oncogenic signaling. However, their functional interplay remains largely unexplored. Here, we describe a novel bidirectional regulatory mechanism between DYRK2 and USP28 that integrates DNA damage response and ubiquitin-mediated protein degradation. We demonstrate that DYRK2 phosphorylates USP28, promoting its ubiquitination and proteasomal degradation in a kinase activity-independent manner, thereby contributing to the maintenance of oncogenic protein homeostasis. Conversely, USP28 functions as a deubiquitinase for DYRK2, stabilizing its protein levels and enhancing its kinase activity. Notably, we show that DYRK2 interacts and co-localizes with USP28, with the 521-541 DYRK2 region, particularly residue T525, playing a crucial role in USP28-mediated DYRK2 stabilization. Functionally, this reciprocal regulation modulates p53 signaling, influencing apoptotic responses to DNA damage. DYRK2-mediated phosphorylation of p53 at S46 is significantly reduced upon USP28 depletion, suggesting that USP28 facilitates DYRK2-dependent apoptosis. Additionally, our results highlight a complex regulatory axis involving USP28 and DYRK2, with implications for oncogenic cell death and genomic stability. Overall, our findings uncover a novel feedback loop in which DYRK2 and USP28 dynamically regulate each other to control proto-oncoprotein homeostasis and DNA damage signaling. This interplay offers potential therapeutic opportunities for targeting cancers with dysregulated ubiquitination and genomic instability.

Dyrk Kinases↗
PubMed2025

Malonate promotes CD8+ T cell memory formation via protein malonylation.

Protein malonylation represents a recently identified posttranslational modification whose role in CD8+ T cell differentiation and functionality remains incompletely understood. In this study, we demonstrate that enhancing protein malonylation through sodium malonate (SM) treatment promotes CD8+ T cell memory formation in response to bacterial infection, subsequently potentiating recall responses. Comparative metabolomic analysis between SM-treated and control CD8+ T cells revealed significant metabolic alterations associated with protein malonylation. We present the first comprehensive proteomic analysis of lysine malonylation in murine CD8+ T cells, identifying 77 malonylation sites across 64 proteins involved in diverse cellular processes, particularly metabolic pathways. Malonylation of STAT6 was confirmed via the use of a specific chemical probe. Notably, we established that malonylation at the lysine 374 site of STAT6 results in increased TCF1 expression, due to alleviated transcriptional repression of TCF1 by STAT6. Collectively, our findings provide compelling evidence that protein malonylation plays a significant role in regulating CD8+ T cell memory formation.

Animals↗
PubMed2026

Bacterial stress responses lower mRNA-protein level correlations.

Diverse bacterial pathogens have evolved complex regulatory mechanisms to adapt to various environmental stresses during infection. The uncertainty in mRNA-protein levels in response to environmental stressors complicates our understanding of bacterial physiology and their adaptation to stressful environments. To examine this issue, we have integrated transcriptomics and proteomics data on three human bacterial pathogens: Salmonella enterica Typhimurium, Yersinia pseudotuberculosis, and Staphylococcus aureus under 10 infection-relevant stress conditions. We observed positive correlations between mRNA and protein levels, which were decreased under different stress conditions. Essential genes exhibited higher expression levels with lower variation across the conditions and stronger mRNA-protein correlations compared to nonessential genes, highlighting their critical role in bacterial adaptability and survival. Moreover, we identified a substantial number of genes with stress-induced noncorrelating mRNA-protein levels, particularly under conditions triggering strong stress responses. Particularly this level was dramatically lowered for osmotic stress-specific genes affected by impaired translational activity under osmotic stress. Our findings highlight the prevalence of noncorrelating mRNA-protein levels and the potential role of posttranslational modifications in modulating protein levels in response to environmental stressors during infection. This study provides a comprehensive framework for integrating transcriptomics and proteomics data and identifies potential gene products that might significantly impact the ability of diverse bacterial pathogens to adapt to hostile infection environments.

RNA, Messenger↗
PubMed1979

Synthesis and processing of molecules bearing thymus leukemia antigen.

Thymus-leukemia (TL) antigens are expressed in murine lymphocytes under strict developmental regulation. To elucidate the molecular basis of TL expression, we have identified the molecular species that react with TL antiserum. At least three species can be resolved by metabolic radiolabeling of thymocytes and ASL1 leukemia cells, lysis, immune precipitation, and sodium dodecyl sulfate-polyacrylamide. After a brief incubation with [35S]methionine, the only radioactive molecule recognized by TL antiserum is a homogeneous species with an apparent Mr of 45,000 daltons. This molecule, 45K TL, includes high-mannose-type carbohydrate attached to a 45,000 dalton glycosidase-resistant backbone. In this form, 45K, it is never exposed on the cell surface. If pulse-labeled cells are further incubated with nonradioactive methionine before lysis, however, radioactivity disappears from the 45K TL species and appears in the slower migrating species 46K and 48K TL. Thus, 46K and 48K appear to represent products generated from the 45K TL precursor by posttranslational modification. These TL forms are displayed on the cell surface; they lack high-mannose carbohydrate but evidently include acidic complex-type carbohydrate. Normal thymocytes from Qa:Tla-negative mice lack not only the surface forms of TL but also the intracellular 45K TL form. Peripheral lymphoid cells of Qa:Tla-positive mice synthesize none of these TL species. But the TL antiserum, which contains Qa antibody, recognizes a distinct gene product in spleen and thymus of Qa-Tla-positive mice. In its pulse-labeled form, this molecule, which may represent Qa-1, has an apparent Mr of 44,000 daltons, and consists of a glycosidase-resistant polypeptide core of only 35,000 daltons linked to more high mannose carbohydrate than 45K TL.

Animals↗
PubMed2026

Genomes of the ex-type strains of Elsinoë mangiferae and E. perseae, the causal agents of scab on mango and avocado.

Elsinoë species are slow-growing, hemibiotrophic to necrotrophic fungi that cause scab diseases on economically important fruit crops. Genome resources for many host-specific species remain limited. We report high-quality draft genome assemblies for the ex-type strains of Elsinoë mangiferae (CBS 226.50) and E. perseae (CBS 406.34), causal agents of mango and avocado scab, respectively. Among 5 approaches tested, a Nanopore-only NextDenovo assembly produced the most contiguous genomes, yielding 24.5 Mb (E. mangiferae) and 25.1 Mb (E. perseae) assemblies with 13 and 18 contigs, respectively, BUSCO completeness scores of ∼94%, and multiple putative telomere-to-telomere chromosomes. Gene prediction identified 9,134 and 9,243 genes, respectively. Functional annotation revealed enrichment of metabolic and regulatory pathways, including those involved in posttranslational modification, protein transport, and secondary metabolism. Carbohydrate-active enzyme repertoires were small but conserved, consistent with stealth pathogenicity strategies and low plant cell wall degradation. Both genomes encoded large secretomes (>850 proteins), diverse protease repertoires (>300 proteins), Ecp2-like effector proteins, and multiple biosynthetic gene clusters, including clusters with similarity to those associated with elsinochrome and ACT-toxin II biosynthesis, some of which may contribute to host-pathogen interactions and disease development. A large fraction of genes lacked functional characterization, suggesting incomplete databases and/or the presence of lineage-specific genes potentially involved in virulence or host adaptation. These genome resources fill critical gaps for underrepresented Elsinoë species and provide taxonomically anchored references essential for diagnostics, comparative genomics, and research into the molecular basis of host specificity and pathogenicity in scab-causing fungi.

Persea↗
PubMed1977

Synthesis of lens protein in vitro: formation of beta-crystallin.

Upon addition of lens polyribosomes to a reticulocyte-cell-free system, alpha, beta L-, and gamma crystallin are synthesized, while beta H crystallin is not formed. This phenomenon is comparable to the biosynthetic events in the lens-cell-free system and in tissue culture. It is shown that beta H crystallin formation depends upon the presence of a polypeptide beta B1 b which arises by posttranslational modification. The putative precursor for beta B1 b is a polypeptide beta BU a of which the messenger with a sedimentation coefficient of 12.5 S has been isolated.

Animals↗
PubMed2024

The Lrs14 family of DNA-binding proteins as nucleoid-associated proteins in the Crenarchaeal order Sulfolobales.

Organization of archaeal chromatin combines bacterial, eukaryotic, and unique characteristics. Many archaeal lineages harbor a wide diversity of small and highly expressed nucleoid-associated proteins, which are involved in DNA structuring. In Sulfolobales, representing model organisms within the Crenarchaeota, Sul7d, Cren7, Sul10a, and Sul12a are well-characterized nucleoid-associated proteins. Here, we combine evidence that the Lrs14 family of DNA binders is part of the repertoire of nucleoid-associated proteins in Sulfolobales. Lrs14-encoding genes are widespread within genomes of different members of the Sulfolobales, typically encoded as four to nine homologs per genome. The Lrs14 proteins harbor a winged helix-turn-helix DNA-binding domain and are typified by a coiled-coil dimerization. They are characterized by distinct sequence- and structure-based features, including redox-sensitive motifs and residues targeted for posttranslational modification, allowing a further classification of the family into five conserved clusters. Lrs14-like proteins have unique DNA-organizing properties. By binding to the DNA nonsequence specifically and in a highly cooperative manner, with a slight preference for AT-rich promoter regions, they introduce DNA kinks and are able to affect transcription of adjacent transcription units either positively or negatively. Genes encoding Lrs14-type proteins display considerable differential expression themselves in response to various stress conditions, with certain homologs being specific to a particular stressor. Taken together, we postulate that members of the Lrs14 family can be considered nucleoid-associated proteins in Sulfolobales, combining a DNA-structuring role with a global gene expression role in response to stress conditions.

DNA-Binding Proteins↗
PubMed1977

Possible molecular mechanisms of ageing.

While the error theory of ageing has attracted most interest in recent times it cannot yet be regarded as being demonstrated. Posttranslational modifications of proteins genetic theory appears loical but has little in vivo evidence to prove it. Basic mechanisms of ageing probably involve the interaction of several processes.

Aging↗
PubMed1976

The biosynthesis of human hemoglobin A1c. Slow glycosylation of hemoglobin in vivo.

Hemoglobin A1c, the most abundant minor hemoglobin component in human erythrocytes, is formed by the condensation of glucose with the N-terminal amino groups of the beta-chains of Hb A. The biosynthesis of this glycosylated hemoglobin was studied in vitro by incubating suspensions of reticulocytes and bone marrow cells with [3H]leucine or 59Fe-bound transferrin. In all experiments, the specific activity of Hb A1c was significantly lower than that of Hb A, suggesting that the formation of Hb A1c is a posttranslational modification. The formation of Hb A1c in vivo was determined in two individuals who were given an infusion of 59Fe-labeled transferrin. As expected, the specific activity of Hb A rose promptly to a maximum during the 1st week and remained nearly constant thereafter. In contrast, the specific activity of Hb A1c and also of Hbs A1a and A1b rose slowly, reaching that of Hb A by about day 60. These results indicate that Hb A1c is slowly formed during the 120-day life-span of the erythrocyte, probably by a nonenzymatic process. Patients with shortened erythrocyte life-span due to hemolysis had markedly decreased levels of Hb A1c.

Anemia, Hemolytic↗
PubMed1977

Postsynthetic deamidation of hemoglobin Providence (beta 82 Lys replaced by Asn, Asp) and its effect on oxygen transport.

Carriers of hemoglobin Providence have three types of beta chain in their hemolysates. The two abnormal chains have asparagine (Providence N, Prov N) or aspartic acid (Providence D) at position beta 82, instead of lysine. In vitro, only two beta chains are synthesized by reticulocytes of carriers, betaA and betaProv N. In vivo studies showed that the specific activity of Providence N was initially 10-fold higher than that of Providence D; the specific activities of the two labeled hemoglobins were approximately equal 5 wk after injection of isotope. Oxygen affinity of carriers' blood was somewhat increased, but they were not polycythemic. The affinity of the purified hemoglobins Providence was decreased. Addition of 2, 3 diphosphoglycerate had little effect on the affinity of either hemoglobin component, and addition of inositol hexaphosphate produced no change in the affinity of Providence D. These studies demonstrate that Providence N is deamidated to Providence D during the life span of the erythrocyte, and suggest this finding may represent only an easily observed prototype of posttranslational modification of proteins in general. Despite and abnormal P50 of the blood, oxygen transport is probably normal in carriers of the abnormal hemoglobins.

Adolescent↗
PubMed1978

Large molecular weight TSH-beta: the sole immunoactive form of TSH-beta in certain human sera.

The beta subunit of TSH (TSH-beta) usually cannot be detected (less than 0.2 ng/ml) in the serum of normal individuals, whereas patients with primary hypothyroidism exhibit elevated TSH-beta levels (0.2-9.3 ng/ml), which increase further after the administration of TRH. Two patients were found to have large TSH-beta as the only form of serum TSH-beta immunoactivity. Patient A was a euthyroid woman with a goiter; TSH and alpha subunit levels were normal (1 microU/ml and 0.6 ng/ml, respectively); TSH-beta was elevated (8-24 ng/ml). Patient B was a woman with borderline hypothyroidism, an elevated serum TSH level (19 microunits/ml), a normal serum alpha level (2.4 ng/ml), and an elevated serum TSH-beta level (1.8-3.6 ng/ml). Dilutions of both patients' sera demonstrated nonparallelism of their serum TSH-beta to standard TSH-beta. The elevated serum TSH-beta levels did not increase after TRH, although TSH and alpha subunit increased appropriately. After the administration of dexamethasone or T4 to patient B, serum TSH-beta did not decrease, although TSH and alpha decreased. Gel chromatography and rechromatography of the patients' sera on a Sephadex G-100 column showed elution of all TSH-beta immunoactivity in or near the void volume (Vo; greater than 150,000 mol wt), whereas sera of hypothyroid patients demonstrated less than 7% of TSH-beta immunoactivity in the Vo. By chromatography on a Sephadex G-200 column, the TSH-beta immunoactivity had a 160,000 mol wt in patient A and 200,000 mol wt in patient B. Incubation of labeled or unlabeled TSH-beta with serum or gamma-globulin fractions from both patients resulted in no significant increase in the binding of TSH-beta to serum components, as determined by both gel chromatography and precipitation with antihuman gamma-globulin. Large TSH-beta was stable after incubation with 6 M guanidine. Ribonuclease failed to affect the large TSH-beta. Inter-chain disulfide bonding was not demonstrated in large TSH-beta after treatment with three different reducing agents (mercaptoethanol, sodium sulfite, and dithioerythritol). Treatment with trypsin did not convert the large TSH-beta immunoactivity to standard TSH-beta. These experiments demonstrated that the large TSH-beta immunoactivity was not caused by binding of TSH-beta to an immunoglobulin or other serum protein or by aggregation of TSH-beta molecules. The significance of these apparently covalently bonded large forms of TSH-beta immunoactivity is not yet known; the presence of small amounts of a large molecular weight form in the serum of hypothyroid patients and normal pituitary extracts raises the possibility that they may be components of normal TSH biosynthesis or represent posttranslational modifications.

Adult↗
PubMed2024

Reversion from basal histone H4 hypoacetylation at the replication fork increases DNA damage in FANCA deficient cells.

The FA/BRCA pathway safeguards DNA replication by repairing interstrand crosslinks (ICL) and maintaining replication fork stability. Chromatin structure, which is in part regulated by histones posttranslational modifications (PTMs), has a role in maintaining genomic integrity through stabilization of the DNA replication fork and promotion of DNA repair. An appropriate balance of PTMs, especially acetylation of histones H4 in nascent chromatin, is required to preserve a stable DNA replication fork. To evaluate the acetylation status of histone H4 at the replication fork of FANCA deficient cells, we compared histone acetylation status at the DNA replication fork of isogenic FANCA deficient and FANCA proficient cell lines by using accelerated native immunoprecipitation of nascent DNA (aniPOND) and in situ protein interactions in the replication fork (SIRF) assays. We found basal hypoacetylation of multiple residues of histone H4 in FA replication forks, together with increased levels of Histone Deacetylase 1 (HDAC1). Interestingly, high-dose short-term treatment with mitomycin C (MMC) had no effect over H4 acetylation abundance at the replication fork. However, chemical inhibition of histone deacetylases (HDAC) with Suberoylanilide hydroxamic acid (SAHA) induced acetylation of the FANCA deficient DNA replication forks to levels comparable to their isogenic control counterparts. This forced permanence of acetylation impacted FA cells homeostasis by inducing DNA damage and promoting G2 cell cycle arrest. Altogether, this caused reduced RAD51 foci formation and increased markers of replication stress, including phospho-RPA-S33. Hypoacetylation of the FANCA deficient replication fork, is part of the cellular phenotype, the perturbation of this feature by agents that prevent deacetylation, such as SAHA, have a deleterious effect over the delicate equilibrium they have reached to perdure despite a defective FA/BRCA pathway.

Histones↗
PubMed1978

Difference between mammary epithelial cells from mature virgin and primiparous mice.

Mammary epithelial cells from mature virgin mice are similar to those from primiparous mice in several respects. However, there is one known difference. The cells from the mature virgin must traverse the cell cycle in order to become competent to make casein and enzymatically active alpha-lactalbumin in vitro; those from the primiparous animal can make these proteins without first traversing the cycle. In this regard, cells from human placental lactogen- and prolactin-treated mature virgins are, after involution, similar to those from primiparous mice. The developemental block in the cells from the mature virgin, imposed by preventing cell cycle traversal, has been partially delineated. It does not appear to reside at the levels of ultrastructural maturation or the formation of casein messenger RNA. Rather, the lesion is postranscriptional and may be at the level of translation, or posttranslational modification, or both.

Animals↗
PubMed1979

Biosynthesis of glycosylated hemoglobins in the monkey.

We have investigated the in vivo biosynthesis of the minor hemoglobin components in the rhesus monkey. The elution profile of rhesus hemolysate on BioRex 70 cation exchange resin was analogous to that of human hemolysate. The rhesus Hb Alc peak was identified with the TBA test, which revealed a carbohydrate content identical to that of human Hb A1c. A rhesus monkey was injected with autologous 55Fe-bound transferrin, and the specific activity of each of the minor and major components was followed for over 70 days. As previously shown in man, rhesus Hb alc accumulated specific activity almost linearly over the erythrocyte life-span, indicative of slow and continuous conversion of Hb A0 to Hb Alc. This study revealed two new findings. (1) The specific activity of rhesus Hb Alb was always significantly less than that of Hb Alc. This result suggested that HB Alb is made by further posttranslational modification of Hb Alc. (2) The first portion of rhesus Hb A0 to be eluted on BioRex 70 contained a significant amount of carbohydrate and lower initial specific radioactivity than did the latter portion. This unexpected heterogeneity in the major hemoglobin component reflects slow, nonenzymatic glycosylation at sites other than at the N-terminus of the beta-chain.

Animals↗
PubMed1979

Tubulin tyrosylation in vivo and changes accompanying differentiation of cultured neuroblastoma-glioma hybrid cells.

Changes in a posttranslational modification of tubulin, which accompany differentiation, have been studied in neuroblastoma-glioma hybrid cultured cells. The modification consists of the reversible enzymatic addition of a tyrosine to the COOH terminus of the alpha chain. Cytoplasmic tubulin purified from undifferentiated cells resembled that from adult mammalian brain in that half was in a form which can not accept tyrosine; of the remainder, which is a substrate for tubulin-tyrosine ligase, a higher proportion had COOH-terminal tyrosine. In the tubulin from differentiated cells, in which there had been extensive assembly of axonal microtubules from a preformed pool of subunits, the nonsubstrate tubulin was almost entirely replaced by the species with COOH-terminal tyrosine. In living cells, in the absence of protein synthesis, there was fixation of labeled tyrosine into cytoplasmic alpha chains which was extensive enough to be consistent with turnover, during the course of an hour, of the pre-existing COOH-terminal tyrosine. The alpha chain in the particulate fraction of the cells was comparably labeled, along with some unidentified low molecular weight components.

Animals↗
PubMed2025

Chemoproteomic Profiling of Reactive Cysteines in Response to Oxidative Stress Induced by 6-Hydroxydopamine.

Although oxidative stress is a well-established driver of neurodegeneration, it remains poorly understood as to how the global cysteine (Cys) proteome is remodeled under oxidative stress conditions. Proteins with aberrantly modified cysteines in response to oxidative stress can induce and exacerbate neurodegeneration, contributing to disorders like Alzheimer's, Parkinson's, frontotemporal dementia, and amyotrophic lateral sclerosis. In this study, we induced oxidative stress in SH-SY5Y neuronal cells by subjecting them to the neurotoxin 6-hydroxydopamine (6-OHDA). To identify proteins with altered cysteine oxidation or PTM status, we used a desthiobiotin iodoacetamide (DBIA) probe, which selectively labels cysteines with unmodified and preserved thiols. Using these unbiased chemoproteomic strategies, we identified proteins with reduced Cys reactivity to DBIA in response to 6-OHDA-induced oxidative stress. Many of these proteins are critically involved in biological processes linked to cell stress responses (e.g., mitochondrial oxidative stress and apoptosis). Furthermore, we found that two key Cys on UCHL1 (a deubiquitinase critically involved in neurodegeneration) exhibited enhanced reactivity under oxidative stress conditions. Our study defines the remodeling of the Cys proteome under 6-OHDA-induced oxidative stress conditions. Furthermore, these findings suggest potential cysteine-mediated regulatory mechanisms in response to oxidative stress, providing a valuable resource for further exploration of cysteine modifications in the context of neurodegenerative signaling.

Oxidopamine↗
PubMed2026

Elucidating the In Vitro Adverse Effect of Functionalized Single-Walled Carbon Nanotubes Against Breast Cancer Cells at the Proteomics Level.

The tremendous therapeutic potential of carbon-based nanomaterials (CNMs) has been limited by inconsistent data regarding the nanotoxicity assessment. Although a bulk of studies have been performed to assess the in vitro cytotoxicity mechanism of CNMs, the exact factors responsible for the cytotoxicity of CNMs have not been fully understood. With the rapid advancement of mass spectrometry technologies, proteomics has emerged as a powerful strategy for systematically investigating the molecular and cellular mechanisms underlying toxicity induced by nanomaterials. This study examined the in vitro cytotoxicity of single-walled carbon nanotubes (SWCNTs) in human MCF-7 breast cancer cells by conducting a comparative proteome-level analysis using mass spectrometry. Initially, the characterized SWCNTs were incubated with MCF-7 cells for 3, 6, and 24 h. Proteins were subsequently extracted from each treatment group and subjected to nano-liquid chromatography-tandem mass spectrometry (nLC-MS/MS) analysis. The relative abundance of the identified proteins was determined by comparison with the control group, and differential expression patterns, including upregulated and downregulated proteins, were assessed. A total of 3482 unique protein groups were identified across all exposure periods. Among these, 3466 protein groups were detected following 3 h of exposure, 3469 following 6 h of exposure, and 3480 following 24 h of exposure. Compared with the control group, the identified differentially expressed proteins exhibited fold changes ranging from 2-fold to 20-fold across the incubation periods. In total, 70 proteins were found to be significantly regulated following SWCNT exposure. Of the differentially expressed proteins, 45 were significantly upregulated, whereas 25 were significantly downregulated. Visualization of these regulations over time was shown in a heatmap of log2-transformed fold-change values to explore time-specific proteomic alterations. Functional enrichment analysis of these proteins also showed that the regulated proteins were significantly associated with Reactome pathways, including ER-to-Golgi anterograde transport, Golgi-to-ER retrograde transport, COPI-mediated vesicle trafficking, regulation of insulin-like growth factor transport and uptake by insulin-like growth factor-binding proteins, protein metabolism, and posttranslational protein modification. Furthermore, a systematic comparison of previous studies within the present findings was provided to situate our study within the broader context of understanding CNT-induced cellular toxicity. Collectively, these findings provided an important proteomic evidence of the adverse effects of SWCNTs on MCF-7 cells. Furthermore, this study showed a comprehensive proteomic landscape of cellular responses to SWCNT exposure, contributing to a better understanding of the molecular mechanisms underlying SWCNT-induced cytotoxicity and bridging the gap between protein regulation and the resulting cellular responses. In this study, we characterized the proteomic landscape of MCF-7 cells following SWCNT exposure, revealing molecular mechanisms associated with cellular responses and cytotoxicity. The identified differentially expressed proteins established a link between altered protein regulation and SWCNT-induced cellular effects. Moreover, these proteins need to be further validated in different cell models and would potentially represent promising candidates for the identification of novel molecular targets involved in SWCNT-induced cytotoxicity.

MCF‐7 cells↗