Adaptive Cell Responses Research Articles

α-Tocopherol Long-Chain Metabolite α-T-13'-COOH Exhibits Biphasic Effects on Cell Viability, Induces ROS-Dependent DNA Damage, and Modulates Redox Status in Murine RAW264.7 Macrophages.

The α-tocopherol long-chain metabolite α-tocopherol-13'-hydroxy-chromanol (α-T-13'-COOH) is a proposed regulatory intermediate of endogenous vitamin E metabolism. Effects of α-T-13'-COOH on cell viability and adaptive stress response are not well understood. The present study aims to investigate the concentration-dependent effects of α-T-13'-COOH on cellular redox homeostasis, genotoxicity, and cytotoxicity in murine RAW264.7 macrophages as a model system. Murine RAW264.7 macrophages are exposed to various dosages of α-T-13'-COOH to determine its regulatory effects on reactive oxygen species (ROS) production, DNA damage, expression of stress-related markers, and the activity of ROS scavenging enzymes including superoxide dismutases, catalase, and glutathione-S-transferases. The impact on cell viability is assessed by analyzing cell proliferation, cell cycle arrest, and cell apoptosis. α-T-13'-COOH influences ROS production and induces DNA damage in a dose-dependent manner. The metabolite modulates the activity of ROS-scavenging enzymes, with significant changes observed in the activities of antioxidant enzymes. A biphasic response affecting cell viability is noted: sub-micromolar doses of α-T-13'-COOH promote cell proliferation and enhance DNA synthesis, whereas supraphysiological doses lead to DNA damage and cytotoxicity. It hypothesizes an adaptive stress response, characterized by upregulation of ROS detoxification mechanisms, enhanced cell cycle arrest, and increased apoptosis, indicating a correlation with oxidative stress and subsequent cellular damage.

Abstract A004: RNA splicing alterations in the development of acquired MAPKi resistance in melanoma

Abstract The standard treatment for melanoma with a BRAF mutation involves Mitogen-Activated Protein Kinase inhibitors (MAPKi), which target the aberrant MAPK signaling pathway. Although patients initially respond well to this therapy, many develop acquired resistance over time. This resistance can be attributed to various altered signaling pathways, including the reactivation of the MAPK pathway, activation of alternative survival pathways like PI3K/PTEN/AKT, engagement of receptor tyrosine kinases (RTKs) such as PDGFRβ and EGFR, and developmental pathways. Despite extensive omics studies aimed at deciphering the mechanisms behind acquired resistance, the specific alterations within these pathways remain poorly understood. To gain further insights into acquired MAPKi resistance in melanoma, we explored the role of RNA splicing events by analyzing publicly available datasets of pre- and post-MAPKi treated melanoma from patient-derived cell lines and in vitro studies using PDX models. We investigated differential transcript usage (DTU) to detect specific splice variants altered during the development of resistance. Our analysis revealed significant transcript alterations during on-treatment that reverted to baseline states once resistance was established, underscoring the dynamic and adaptive nature of these changes. Genes with DTU were enriched in pathways related to MAPKi resistance, such as the MAPKi signaling pathway, PI3K/AKT pathway, and signaling by RTKs. Furthermore, the DTU-centered analysis provided better insights into MAPKi resistance mechanisms compared to standard differential gene expression (DEG) analysis, with DTUs showing higher enrichment scores in MAPKi resistance-related pathways. Further, identifying developmental splicing signatures highlights the complexity of MAPKi resistance, as it reveals significant upregulation of transcripts associated with embryonic melanoblast stem cells (MSCs) among the altered transcripts in on-treatment cell lines. This reprogramming through RNA splicing may confer an adaptive advantage, enabling melanoma cells to revert to a more plastic, stem-like state, with developmental splicing events playing a crucial role in the adaptive response to MAPKi therapy. Next, using a regulatory model based on the expression of splicing factors (SFs), we accurately predicted transcript alterations in on-treatment samples and identified key SFs. Our study highlights the crucial role of RNA splicing in the adaptive response of melanoma cells to MAPKi treatment. These insights pave the way for future research and therapeutic strategies focusing on RNA splicing to combat drug resistance in cancer. Citation Format: Sumit Mukherjee, Arashdeep Singh, Hyunjeong Joo, Sumeet Patiyal, Hyungsoo Kim, Lipika R. Pal, Kun Wang, Chi-Ping Day, Ze’ev A Ronai, Eytan Ruppin, Sridhar Hannenhalli. RNA splicing alterations in the development of acquired MAPKi resistance in melanoma [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: RNAs as Drivers, Targets, and Therapeutics in Cancer; 2024 Nov 14-17; Bellevue, Washington. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(11_Suppl):Abstract nr A004.

Hydrogel Elastic Energy: A Stressor Triggering an Adaptive Stress-Mediated Cell Response.

The crosstalk between the cells and the extracellular matrix (ECM) is bidirectional and consists of a pushing/pulling stretch exerted by the cells and a mechanical resistance counteracted by the surrounding microenvironment. It is widely recognized that the stiffness of the ECM, its viscoelasticity, and its overall deformation are the most important traits influencing the response of the cells. Here these three parameters are combined into a concept of elastic energy, which in biological terms represents the mechanical feedback that cells perceive when the ECM is deformed. It is shown that elastic energy is a stress factor that influences the response of cells in three-dimensional (3D) cultures. Strikingly, the higher the elastic energy of the matrix and thus the mechanical feedback, the higher the stress state of the cells, which correlates with the formation of G3BP-mediated stress granules. This condition is associated with an increase in alkaline phosphatase (ALP) activity but a decrease in gene expression and is mediated by the nuclear translocation of Yes-associated protein (YAP). This work supports the importance of considering the elastic energy as mechano-controller in regulating cellular stress state in 3D cultures.

An integrated proteomics and metabolomics analysis of methylglyoxal-induced neurotoxicity in a human neuroblastoma cell line

This study aimed to highlight the molecular and biochemical changes induced by methylglyoxal (MGO) exposure in SH-SY5Y human neuroblastoma cells, and to explore how these changes contribute to its neurotoxicity, utilizing an integrated proteomics and metabolomics approach. Using label-free quantitative nanoLC-MS/MS proteomics and targeted LC-TQ-MS/MS-based metabolomics, the results revealed that MGO exposure, particularly at cytotoxic levels, significantly altered the proteome and metabolome of SH-SY5Y cells. Analysis of proteomics data showed significant alterations in cellular functions including protein synthesis, cellular structural integrity, mitochondrial function, and oxidative stress responses. Analysis of metabolomics and integration of metabolomics and proteomics data highlighted significant changes in key metabolic pathways including arginine biosynthesis, glutathione metabolism, cysteine and methionine metabolism, and the tricarboxylic acid cycle. These results suggest that MGO exposure induced both toxic effects and adaptive responses in cells. MGO exposure led to increased endoplasmic reticulum stress, disruptions in cellular adhesion and extracellular matrix integrity, mitochondrial dysfunction, and amino acid metabolism disruption, contributing to cellular toxicity. Conversely, cells exhibited adaptive responses by upregulating protein synthesis, activating the Nrf2 pathway, and reprogramming metabolism to counteract dicarbonyl stress and maintain energy levels. Furthermore, a set of key proteins and metabolites associated with these changes were shown to exhibit a significant concentration-dependent decrease or increase in their expression levels with increasing MGO concentrations, suggesting their potential as biomarkers for MGO exposure. Taken together, these findings provide insight into the molecular mechanisms underlying MGO-induced neurotoxicity and potential targets for therapeutic intervention.

Abstract A036: The role of hypoxia in CD8+ T cell localization and function in pancreatic cancer

Abstract Pancreatic ductal adenocarcinoma (PDAC) is a deadly malignancy characterized by poor response to existing therapeutic options. This resistance to treatment is partly due to its extensive inflammatory, desmoplastic stromal response, along with a hypoxic microenvironment. Although tumor hypoxia induces adaptive responses in both cancer cells and the surrounding stroma, most studies on the role of hypoxia in tumorigenesis have focused on cancer cell-intrinsic properties. The impact of hypoxia on stromal cells themselves and their interactions with cancer cells has remained largely unknown. We previously showed that inflammatory cancer-associated fibroblasts (iCAFs), which express high levels of cytokines and chemokines, are preferentially located in hypoxic regions of PDAC, and that hypoxia promotes an inflammatory fibroblast phenotype. The iCAF phenotype has been correlated with highly immunosuppressive features of PDAC. These findings and our preliminary observation that CD8+ T cells are largely excluded from hypoxic PDAC regions, raise the possibility that hypoxia suppresses the infiltration and activation of CD8+ T cells by modulating their interactions with inflammatory fibroblasts. By culturing CD8+ T cells under hypoxia with conditioned media from co-cultures of pancreatic cancer cells and fibroblasts, we have found that cancer cells and fibroblasts decrease CD8+ T cell proliferation and cytotoxic activity under low oxygen conditions. We are working to elucidate the mechanism by which hypoxia regulates CD8+ T cell infiltration and activation through cancer cell-fibroblast crosstalk. Citation Format: Ashley M. Mello, Tenzin Ngodup, Katelyn L. Donahue, Marina Pasca Di Magliano, Kyoung Eun Lee. The role of hypoxia in CD8+ T cell localization and function in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr A036.

Multi-omics profiling combined with molecular docking reveals immune-inflammatory proteins as potential drug targets in colorectal cancer

Colorectal cancer is globally ranked as the third most common malignant tumor. Its development involves a complex biological process driven by various genetic and epigenetic alterations. To elucidate the biological significance of the extensive omics data, we conducted comparative multi-omics studies on colorectal cancer patients at different clinical stages. Bioinformatics methods were applied to analyze multi-omics datasets and explore the molecular landscape. Drug prediction and molecular docking also were conducted to assess potential therapeutic interventions. In vitro experiments were used to validate the inhibitory effect on the migration and proliferation of cell lines. The results indicate up-regulated proteins involved in immune-inflammatory related pathways, while biomarkers related to muscular contraction and cell adhesion are significantly down-regulated. Drug prediction, coupled with in vitro experiments, suggests that AZ-628 may act as a potential drug to inhibit the proliferation and migration of CRC cell lines HCT-116 and HT-29 by regulating the aforementioned key biological pathways or proteins. Complementing these findings, metabolomics analysis unveiled a down-regulation of key carbon metabolism pathways, alongside an up-regulation in amino acid metabolism, particularly proline metabolism. This metabolic shift may reflect an adaptive response in cancer cells, favoring specific amino acids to support their growth. Together, these integrated results provide valuable insights into the intricate landscape of tumor development, highlighting the crossroads of immune regulation, cellular structure, and metabolic reprogramming in the tumorigenic process and providing valuable insights into cancer pathology.

Mitochondria-Associated Membranes in Aging and Senescence.

Although the pursuit of eternal youth remains elusive, progress in the fields of medicine and science has greatly extended the human lifespan. Nevertheless, the rising incidence of diseases and their economic impact present notable obstacles. Mitochondria-associated membranes (MAMs), essential sites for close interaction between mitochondria and the endoplasmic reticulum (ER), are increasingly recognized for their involvement in both normal cellular processes and the development of diseases. Studies suggest that MAMs undergo dynamic alterations, particularly pertinent in the investigation of age-related illnesses. This review highlights the significance of MAMs in age-related conditions, elucidating the morphological and functional alterations in mitochondria and ER during aging. By emphasizing the complex interaction between these organelles, it demonstrates the cell's adaptive responses to combat age-related deterioration. Suggesting MAMs as potential targets for therapeutic interventions holds the potential for attenuating the progression of age-related diseases.

Vorinostat Treatment of Gastric Cancer Cells Leads to ROS-Induced Cell Inhibition and a Complex Pattern of Molecular Alterations in Nrf2-Dependent Genes.

Histone deacetylase inhibitors (HDACi) show high antineoplastic potential in preclinical studies in various solid tumors, including gastric carcinoma; however, their use in clinical studies has not yet yielded convincing efficacies. Thus, further studies on cellular/molecular effects of HDACi are needed, for improving clinical efficacy and identifying suitable combination partners. Here, we investigated the role of oxidative stress in gastric cancer cells upon treatment with HDACi. A particular focus was laid on the role of the Nrf2 pathway, which can mediate resistance to cell-inhibitory effects of reactive oxidative species (ROS). Using fluorescence-based ROS sensors, oxidative stress was measured in human gastric cancer cell lines. Activation of the Nrf2 pathway was monitored in luciferase reporter assays as well as by mRNA and proteomic expression analyses of Nrf2 regulators and Nrf2-induced genes. Furthermore, the effects of ROS scavenger N-acetyl-L-cysteine (NAC) and Nrf2-knockdown on HDACi-dependent antiproliferative effects were investigated in colorimetric formazan-based and clonogenic survival assays. HDACi treatment led to increased oxidative stress levels and consequently, treatment with NAC reduced cytotoxicity of HDACi. In addition, vorinostat treatment stimulated expression of a luciferase reporter under the control of an antioxidative response element, indicating activation of the Nrf2 system. This Nrf2 activation was only partially reversible by treatment with NAC, suggesting ROS independent pathways to contribute to HDACi-promoted Nrf2 activation. In line with its cytoprotective role, Nrf2 knockdown led to a sensitization against HDACi. Accordingly, the expression of antioxidant and detoxifying Nrf2 target genes was upregulated upon HDACi treatment. In conclusion, oxidative stress induction upon HDAC inhibition contributes to the antitumor effects of HDAC inhibitors, and activation of Nrf2 represents a potentially important adaptive response of gastric cancer cells in this context.

Nuclear factor of activated T-cells 5 is indispensable for a balanced adaptive transcriptional response of lung endothelial cells to hypoxia.

Chronic hypoxia causes detrimental structural alterations in the lung, which may cause pulmonary hypertension and are partially mediated by the endothelium. While its relevance for the development of hypoxia-associated lung diseases is well known, determinants controlling the initial adaptation of the lung endothelium to hypoxia remain largely unexplored. We revealed that hypoxia activates the transcription factor nuclear factor of activated T-cells 5 (NFAT5) and studied its regulatory function in murine lung endothelial cells (MLECs). EC-specific knockout of Nfat5 (Nfat5(EC)-/-) in mice exposed to normobaric hypoxia (10% O2) for 21 days promoted vascular fibrosis and aggravated the increase in pulmonary right ventricular systolic pressure as well as right ventricular dysfunction as compared with control mice. Microarray- and single-cell RNA-sequencing-based analyses revealed an impaired growth factor-, energy-, and protein-metabolism-associated gene expression in Nfat5-deficient MLEC after exposure to hypoxia for 7 days. Specifically, loss of NFAT5 boosted the expression and release of platelet-derived growth factor B (Pdgfb)-a hypoxia-inducible factor 1 alpha (HIF1α)-regulated driver of vascular smooth muscle cell (VSMC) growth-in capillary MLEC of hypoxia-exposed Nfat5(EC)-/- mice, which was accompanied by intensified VSMC coverage of distal pulmonary arteries. Collectively, our study shows that early and transient subpopulation-specific responses of MLEC to hypoxia may determine the degree of organ dysfunction in later stages. In this context, NFAT5 acts as a protective transcription factor required to rapidly adjust the endothelial transcriptome to cope with hypoxia. Specifically, NFAT5 restricts HIF1α-mediated Pdgfb expression and consequently limits muscularization and resistance of the pulmonary vasculature.

70 Circulating leptin and immune-related transcriptomic patterns in clear cell renal cell carcinoma

Abstract Background Obesity has been associated with better outcomes in localized and metastatic clear cell renal cell carcinoma (ccRCC), as well as improved survival on immunotherapy treatment. However, the mechanisms underlying this association remain unclear. Leptin is an adipokine secreted by adipocytes, and circulating levels of leptin are higher in individuals with obesity. Additionally, leptin promotes inflammation and angiogenesis and has been proposed as pro-tumorigenic in colorectal and breast cancer. In this study, we examined how circulating leptin levels relate to both tumor and perinephric fat transcriptomic patterns in a cohort of ccRCC patients by evaluating the associations with body mass index (BMI), sex, and immune-related gene expression patterns. Methods We conducted a retrospective cohort study of 92 treatment-naïve ccRCC patients undergoing nephrectomy at Memorial Sloan Kettering Cancer Center. Available data included circulating leptin from fasting blood samples, clinical characteristics from medical records, and, in a subset of patients, RNA sequencing from tumor and perinephric fat specimens. We analyzed differentially expressed genes (DEG) according to circulating leptin levels using Gene Set Enrichment Analysis (GSEA) to describe pathways that were enriched in patients with high levels of leptin. We performed analysis for the whole cohort and stratified by sex based on differences in leptin levels. Results From the 92 patients with available peripheral leptin measurements, 51 and 44 had available tumor and perinephric fat RNA sequencing data, respectively. Of these, 64 (70%) were male, the median age was 60 years old, and most tumors were low grade and stage. Leptin distribution was significantly different in males than females, with circulating leptin levels of 7 ng/ml (IQR 4-14) and 22 ng/ml (IQR 9-52), respectively. Higher BMI was associated with higher leptin levels, with a correlation coefficient of 0.63 (p<0.001) in males and 0.77 (p<0.001) in females. GSEA of tumor DEGs by circulating leptin, showed upregulation of pathways related to adaptive immune activity in patients with higher leptin levels across sexes, although this association was attenuated in females. Strikingly, in the perinephric fat there were stark differences in opposite directions in female and male specimens, with females showing significantly enriched transcription of genes associated with B cell signaling, humoral and adaptive immune responses. Conclusions Higher leptin levels were associated with a modest increase of immune-related gene expression in the tumors in both males and females, but significantly different directional changes were observed in the perinephric fat. Circulating leptin may be involved in peritumoral immune responses which may link host factors to sex related tumor outcomes. Further studies should aim to address the relationship between leptin activity and the tumor and fat microenvironment. DOD CDMRP Funding: yes

A 5-ALA mediated photodynamic therapy increases natural killer cytotoxicity against oral squamous cell carcinoma cell lines.

Oral squamous cell carcinoma (OSCC) constitutes over 90% of oral cancers, known for its aggressiveness and poor prognosis. Photodynamic therapy (PDT) has emerged as a promising adjuvant therapy and is linked to immunogenic cell death, activating innate and adaptive anti-tumor responses. Natural Killer (NK) cells, key players in malignant cell elimination, have not been extensively studied in PDT. This study evaluates whether PDT increases OSCC cell lines' susceptibility to NK cell cytotoxicity. PDT, using 5-aminolevulinic acid (5-ALA) and LED irradiation, was applied to Ca1 and Luc4 cell lines. Results showed a dose-dependent viability decrease post-PDT. Gene expression analysis revealed upregulation of NK cell-activating ligands (ULBP1-4, MICA/B) and decreased MHC class I expression in Ca1, suggesting increased NK cell susceptibility. Enhanced NK cell cytotoxicity was confirmed in Ca1 but not in Luc4 cells. These findings indicate that PDT may enhance NK cell-mediated cytotoxicity in OSCC, offering potential for improved treatment strategies.

Scanpro is a tool for robust proportion analysis of single-cell resolution data

In higher organisms, individual cells respond to signals and perturbations by epigenetic regulation and transcriptional adaptation. However, in addition to shifting the expression level of individual genes, the adaptive response of cells can also lead to shifts in the proportions of different cell types. Recent methods such as scRNA-seq allow for the interrogation of expression on the single-cell level, and can quantify individual cell type clusters within complex tissue samples. In order to identify clusters showing differential composition between different biological conditions, differential proportion analysis has recently been introduced. However, bioinformatics tools for robust proportion analysis of both replicated and unreplicated single-cell datasets are critically missing. In this manuscript, we present Scanpro, a modular tool for proportion analysis, seamlessly integrating into widely accepted frameworks in the Python environment. Scanpro is fast, accurate, supports datasets without replicates, and is intended to be used by bioinformatics experts and beginners alike.

P-596 Impaired fatty acid desaturation in COV434 human granulosa cells leads to increased omega-6 phospholipid abundance

Abstract Study question How does fatty acid desaturation in COV434 granulosa cells influence their lipogenic pathway? Summary answer Suppressing fatty acid desaturation in human granulosa cells leads to a depletion of polyunsaturated phospholipids and an increase in omega-6 fatty acid-containing lipids. What is known already Maintaining the balance between saturated and unsaturated lipids in oocyte-surrounding granulosa cells is crucial to supporting oocyte maturation. We have shown the link between the de novo production of oleic acid through fatty acid desaturation and the main functional parameters of granulosa cells, such as cell proliferation and steroid production. A potential contributor to the observed pathophysiological outcomes lies in the dysregulation of cellular lipids as a consequence of insufficient intracellular oleic acid availability. This lipidomic study investigates the adaptive lipogenic response of granulosa cells to deficient fatty acid desaturation. Study design, size, duration We tested the influence of a chemical inhibitor against stearoyl-CoA desaturase 1 (SCD1), a major fatty acid desaturase enzyme, on cell membrane lipid packing, lipidome, and lipogenic-related genes in immortalized granulosa cells, COV434. We applied free oleic acid to conduct a rescue experiment. Three independent technical replicates were performed for each experimental condition, and mean values were compared among test conditions using one-way ANOVA analysis. Participants/materials, setting, methods The level of membrane fluidity was estimated using the membrane polarity-sensitive dye Laurdan. We used liquid chromatography–mass spectrometry to investigate the lipidome profiles. Data were obtained by calculating the peak areas of intact lipid species. We used quantitative PCR with TaqMan primers to assess the expression of mechanistic target of rapamycin (mTOR), diacylglycerol acyltransferase 1 (DGAT1), and fatty acid synthase (FASN), with 18S ribosomal RNA as the internal control. Main results and the role of chance Reduced oleic acid availability increased cholesterol content 1.2-fold (p = 0.007) and membrane packing, representing intended modifications in de novo desaturation. We used data comprising 459 lipid species. SCD1 inhibition caused a significant increase in dipalmitoyl phosphatidic acid 32:0 (7.4-fold increase vs. untreated controls, p < 0.001) and a substantial decrease in dioleoyl phosphatidic acid 36:2 (-38% reduction, p < 0.001). SCD1 inhibition also led to an elevation of omega-6 phospholipids (e.g., 38:4, 40:4), but conversely, a depletion of polyunsaturated lipids (e.g., 34:2, 36:2). In contrast, oleic acid supplementation resulted in an enrichment of oleic acid-containing lipids (e.g. 34:1, 36:1) but also caused a significant depletion of all polyunsaturated lipids, including omega-6 species (e.g., 20:3, 20:4). These findings indicate that the de novo generation of oleic acid intricately modulates polyunsaturated phospholipid metabolism, especially that of omega-6 phospholipids.Although the reductions in the expression levels of lipogenic-related genes due to SCDinhib treatment were not statistically significant, the addition of oleic acid significantly enhanced the suppression of FASN by 67% (p = 0.022). This suggests the presence of an interaction effect that potentiates the downregulation of the de novo fatty acid synthesis and diverts metabolic pathways away from omega-6 fatty acid production. Limitations, reasons for caution Examining lipidomic profile in isolated primary ovarian cells is crucial for a better understanding of their biological significance. Wider implications of the findings We identified that the role of de novo oleic acid generation in polyunsaturated phospholipid metabolism has significance for cellular physiology in oocyte-surrounding granulosa cells. Potential future applications include targeted metabolic interventions for reproductive disorders impacting oogenesis. Trial registration number not

Development of a major histocompatibility complex class II conditional knockout mouse to study cell-specific and time-dependent adaptive immune responses in peripheral nerves.

The precise relationship between molecular mimicry and tissue-specific autoimmunity is unknown. Major histocompatibility complex (MHC) class II antigen presenting cell-CD4+ T-cell receptor complex interactions are necessary for adaptive immunity. This study aimed to determine the role of endoneurial endothelial cell MHC class II in autoimmune polyneuropathy. Cryopreserved Guillain-Barré syndrome (GBS) patient sural nerve biopsies and sciatic nerves from the severe murine experimental autoimmune neuritis (sm-EAN) GBS model were studied. Cultured conditional ready MHC Class II antigen A-alpha chain (H2-Aa) embryonic stem cells were used to generate H2-Aaflox/+ C57BL/6 mice. Mice were backcrossed and intercrossed to the SJL background to generate H2-Aaflox/flox SJL mice, bred with hemizygous Tamoxifen-inducible von Willebrand factor Cre recombinase (vWF-iCre/+) SJL mice to generate H2-Aaflox/flox; vWF-iCre/+ mice to study microvascular endothelial cell adaptive immune responses. Sm-EAN was induced in Tamoxifen-treated H2-Aaflox/flox; vWF-iCre/+, H2-Aaflox/flox; +/+, H2-Aa+/+; vWF-iCre/+ and untreated H2-Aaflox/flox; vWF-iCre/+ adult female SJL mice. Neurobehavioral, electrophysiological and histopathological assessments were performed at predefined time points. Endoneurial endothelial cell MHC class II expression was observed in normal and inflamed human and mouse peripheral nerves. Tamoxifen-treated H2-Aaflox/flox; vWF-iCre/+ mice were resistant to sm-EAN despite extensive MHC class II expression in lymphoid and non-lymphoid tissues. A conditional MHC class II knockout mouse to study cell- and time-dependent adaptive immune responses in vivo was developed. Initial studies show microvascular endothelial cell MHC class II expression is necessary for peripheral nerve specific autoimmunity, as advocated by human in vitro adaptive immunity and ex vivo transplant rejection studies.

The potential role of liquid-liquid phase separation in the cellular fate of the compartments for unconventional protein secretion.

Eukaryotic cells have developed intricate mechanisms for biomolecule transport, particularly in stressful conditions. This interdisciplinary study delves into unconventional protein secretion (UPS) pathways activated during starvation, facilitating the export of proteins bypassing most of the components of the classical secretory machinery. Specifically, we focus on the underexplored mechanisms of the GRASP's role in UPS, particularly in biogenesis and cargo recruitment for the vesicular-like compartment for UPS. Our results show that liquid-liquid phase separation (LLPS) plays a key role in the coacervation of Grh1, the GRASP yeast homologue, under starvation-like conditions. This association seems a precursor to the Compartment for Unconventional Protein Secretion (CUPS) biogenesis. Grh1's self-association is regulated by electrostatic, hydrophobic, and hydrogen-bonding interactions. Importantly, our study demonstrates that phase-separated states of Grh1 can recruit UPS cargo under starvation-like situations. Additionally, we explore how the coacervate liquid-to-solid transition could impact cells' ability to return to normal post-stress states. Our findings offer insights into intracellular protein dynamics and cell adaptive responses to stress.

SARS-CoV-2 infection induces adaptive NK cell responses by spike protein-mediated induction of HLA-E expression

ABSTRACT HLA-E expression plays a central role for modulation of NK cell function by interaction with inhibitory NKG2A and stimulatory NKG2C receptors on canonical and adaptive NK cells, respectively. Here, we demonstrate that infection of human primary lung tissue with SARS-CoV-2 leads to increased HLA-E expression and show that processing of the peptide YLQPRTFLL from the spike protein is primarily responsible for the strong, dose-dependent increase of HLA-E. Targeting the peptide site within the spike protein revealed that a single point mutation was sufficient to abrogate the increase in HLA-E expression. Spike-mediated induction of HLA-E differentially affected NK cell function: whereas degranulation, IFN-γ production, and target cell cytotoxicity were enhanced in NKG2C+ adaptive NK cells, effector functions were inhibited in NKG2A+ canonical NK cells. Analysis of a cohort of COVID-19 patients in the acute phase of infection revealed that adaptive NK cells were induced irrespective of the HCMV status, challenging the paradigm that adaptive NK cells are only generated during HCMV infection. During the first week of hospitalization, patients exhibited a selective increase of early NKG2C+CD57− adaptive NK cells whereas mature NKG2C+CD57+ cells remained unchanged. Further analysis of recovered patients suggested that the adaptive NK cell response is primarily driven by a wave of early adaptive NK cells during acute infection that wanes once the infection is cleared. Together, this study suggests that NK cell responses to SARS-CoV-2 infection are majorly influenced by the balance between canonical and adaptive NK cells via the HLA-E/NKG2A/C axis.

Network-based elucidation of colon cancer drug resistance mechanisms by phosphoproteomic time-series analysis

Aberrant signaling pathway activity is a hallmark of tumorigenesis and progression, which has guided targeted inhibitor design for over 30 years. Yet, adaptive resistance mechanisms, induced by rapid, context-specific signaling network rewiring, continue to challenge therapeutic efficacy. Leveraging progress in proteomic technologies and network-based methodologies, we introduce Virtual Enrichment-based Signaling Protein-activity Analysis (VESPA)—an algorithm designed to elucidate mechanisms of cell response and adaptation to drug perturbations—and use it to analyze 7-point phosphoproteomic time series from colorectal cancer cells treated with clinically-relevant inhibitors and control media. Interrogating tumor-specific enzyme/substrate interactions accurately infers kinase and phosphatase activity, based on their substrate phosphorylation state, effectively accounting for signal crosstalk and sparse phosphoproteome coverage. The analysis elucidates time-dependent signaling pathway response to each drug perturbation and, more importantly, cell adaptive response and rewiring, experimentally confirmed by CRISPR knock-out assays, suggesting broad applicability to cancer and other diseases.

New regulatory role of Znf1 in transcriptional control of pentose phosphate pathway and ATP synthesis for enhanced isobutanol and acid tolerance.

To develop a cost-effective microbial cell factory for the production of biofuels and biochemicals, an understanding of tolerant mechanisms is vital for the construction of robust host strains. Here, we characterized a new function of a key metabolic transcription factor named Znf1 and its involvement in stress response in Saccharomyces cerevisiae to enhance tolerance to advanced biofuel, isobutanol. RNA-sequencing analysis of the wild-type versus the znf1Δ deletion strains in glucose revealed a new role for transcription factor Znf1 in the pentose phosphate pathway (PPP) and energy generation. The gene expression analysis confirmed that isobutanol induces an adaptive cell response, resulting in activation of ATP1-3 and COX6 expression. These genes were Znf1 targets that belong to the electron transport chain, important to produce ATPs. Znf1 also activated PPP genes, required for the generation of key amino acids, cellular metabolites, and maintenance of NADP/NADPH redox balance. In glucose, Znf1 also mediated the upregulation of valine biosynthetic genes of the Ehrlich pathway, namely ILV3, ILV5, and ARO10, associated with the generation of key intermediates for isobutanol production.Using S. cerevisiae knockout collection strains, cells with deleted transcriptional regulatory gene ZNF1 or its targets displayed hypersensitivity to isobutanol and acid inhibitors; in contrast, overexpression of ZNF1 enhanced cell survival. Thus, the transcription factor Znf1 functions in the maintenance of energy homeostasis and redox balance at various checkpoints of yeast metabolic pathways. It ensures the rapid unwiring of gene transcription in response to toxic products/by-products generated during biofuel production. Importantly, we provide a new approach to enhance strain tolerance during the conversion of glucose to biofuels.

Abstract PO5-16-02: Investigating survivin as a novel target for immunotherapy in diverse breast cancer patients

Abstract Background: The BIRC5 gene encodes survivin, a tumor-specific antigen associated with aggressive tumor features, Black race and poor prognosis in breast cancer (BC). Recent studies have shown that anti-survivin vaccines stimulate a strong anti-tumor immune response in multiple tumor types. However, the relationship between BIRC5/survivin and immune response in BC is poorly understood, particularly among diverse patients. In this analysis, we sought to investigate the relationship between BIRC5/survivin and the BC immune microenvironment across clinical tumor features and RNA-based risk scores for genomic instability. Methods: We leveraged the Carolina Breast Cancer Study (CBCS), a large population-based study that oversampled young (≤50 years) and Black women with invasive BC. NanoString mRNA expression profiling was used to evaluate breast tumor expression for 10 major immune cell types, adaptive and innate immune response, TP53 and homologous recombination deficiency (HRD) pathways, and BIRC5/survivin from 1952 BC patients, including 1,030 (53%) Black and 922 (47%) non-Black women from the CBCS, with additional comparison in The Cancer genome Atlas (TCGA) (n=1,095 breast tumors). BIRC5 was evaluated both as a continuous and categorical variable, using the third expression quartile as a cut point for BIRC5-high, with the lower three quartiles categorized as BIRC5-low. We used generalized linear models to estimate beta values and adjusted p-values as the measure of association between BIRC5 status and immune-related expression in strata defined by estrogen receptor (ER) status, tumor stage, TP53 and HRD status. All analyses were adjusted for multiple comparisons with the Benjamini-Hochberg procedure. Results: In an analysis of continuous BIRC5 expression and global classes of immune response, BIRC5 mRNA expression was highest among tumors with an adaptive-enriched immune class (p< 0.001) in both CBCS and TCGA. However, when investigating immune gene expression according to BIRC5 status (i.e., BIRC5-high relative to BIRC5-low), multivariate differential expression analysis revealed significantly decreased immune cell-related expression scores among BIRC5-high tumors relative to BIRC5-low, and this relationship persisted in analysis stratified on stage (I/II vs III/IV), ER status, TP53 and HRD status. Across all strata, the strongest relationship between BIRC5-high and the immune microenvironment was observed for adaptive immune response (Beta: -0.14; p=0.005), with decreased immune gene expression related to B cells (Beta: -0.16; p=0.01), T cells (Beta: -0.14; p=0.007), Cytotoxic cells (Beta: -0.14; p=0.005), and PD-L1 (Beta: -0.15; p=0.005), relative to BIRC5-low. Conclusion: High BIRC5/survivin expression is associated with decreased immune-related gene expression in both ER-positive and ER-negative disease, and across all tumor stages. Anti-survivin therapies may be beneficial for boosting immune response in breast tumors with low immunogenicity, offering promise for BC subtypes previously ineligible for immunotherapy. Citation Format: Alina Hamilton, Qichen Wang, Sarah Soppe, Melissa Troester, Yara Abdou. Investigating survivin as a novel target for immunotherapy in diverse breast cancer patients [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO5-16-02.

Iron Supplementation Increases Tumor Burden and Alters Protein Expression in a Mouse Model of Human Intestinal Cancer.

Iron supplements are widely consumed. However, excess iron may accelerate intestinal tumorigenesis. To determine the effect of excess iron on intestinal tumor burden and protein expression changes between tumor and normal tissues, ApcMin/+ mice were fed control (adequate) and excess iron (45 and 450 mg iron/kg diet, respectively; n = 9/group) for 10 wk. Tumor burden was measured, and two-dimensional fluorescence difference gel electrophoresis was used to identify differentially expressed proteins in tumor and normal intestinal tissues. There was a significant increase (78.3%; p ≤ 0.05) in intestinal tumor burden (mm2/cm) with excess iron at wk 10. Of 980 analyzed protein spots, 69 differentially expressed (p ≤ 0.05) protein isoforms were identified, representing 55 genes. Of the isoforms, 56 differed (p ≤ 0.05) between tumor vs. normal tissues from the adequate iron group and 23 differed (p ≤ 0.05) between tumors from the adequate vs. excess iron. Differentially expressed proteins include those involved in cell integrity and adaptive response to reactive oxygen species (including, by gene ID: ANPEP, DPP7, ITGB1, PSMA1 HSPA5). Biochemical pathway analysis found that iron supplementation modulated four highly significant (p ≤ 0.05) functional networks. These findings enhance our understanding of interplay between dietary iron and intestinal tumorigenesis and may help develop more specific dietary guidelines regarding trace element intake.