Multiomic Analysis of Candida albicans Adaptation during Commensal Coexistence with Staphylococcus aureus.

Energy metabolism is subject to reprogramming in the body upon bacterial or virus infection. It is generally believed that immune cells sense the stress signals of infection to mediate the reprogramming of whole-body energy metabolism. However, the key molecules required for the immune cell function remain to be identified. In this study, we addressed the issue by examining the energy metabolism in Lyz2-p65-KO mice, in which p65 (RelA) gene is inactivated in myeloid cells. On Chow diet, the p65-KO mice exhibited no difference to the wild type mice in the energy metabolism. On a high fat diet (HFD), the KO mice gained less adipose tissue and body weight for improved insulin sensitivity and blood lipids along reduction in pro-inflammatory cytokine. This was observed with more energy loss in feces. The KO mice showed a reduction in metabolic rate after LPS challenge for accelerated decrease of oxygen consumption. They had a high mortality rate in the septic shock model with less elevation of serum pro-inflammatory cytokines and more elevation of anti-inflammatory cytokines. In vitro, the KO macrophages expressed less pro-inflammatory cytokines in response to stimulation by palmitic acid, IL-1β and TNF-α. In conclusion, the data suggest that p65 is a key molecule in myeloid cells to mediate the reprogramming of energy metabolism under stress conditions of HFD feeding.

Altered metabolism is a hallmark of cancer, and the reprogramming of energy metabolism has historically been considered a general phenomenon of tumors. It is well recognized that long noncoding RNAs (lncRNAs) regulate energy metabolism in cancer. However, lncRNA‐mediated posttranslational modifications and metabolic reprogramming are unclear at present. In this review, we summarized the current understanding of the interactions between the alterations in cancer‐associated energy metabolism and the lncRNA‐mediated posttranslational modifications of metabolic enzymes, transcription factors, and other proteins involved in metabolic pathways. In addition, we discuss the mechanisms through which these interactions contribute to tumor initiation and progression, and the key roles and clinical significance of functional lncRNAs. We believe that an in‐depth understanding of lncRNA‐mediated cancer metabolic reprogramming can help to identify cellular vulnerabilities that can be exploited for cancer diagnosis and therapy.

Head and neck cancer (HNC) is the sixth cause of cancer-related death worldwide. Head and neck squamous cells carcinoma (HNSCC) is the most frequent subtype of HNC. The development of HNSCC is associated to alcohol consumption, smoking or infection by high-risk human Papillomavirus (HR-HPV). Although the incidence of cancers associated with alcohol and tobacco has diminished, HNSCC associated with HR-HPV has significantly increased in recent years. However, HPV-positive HNSCC responds well to treatment, which includes surgery followed by radiation or chemoradiation therapy. Radiation therapy (RT) is based on ionizing radiation (IR) changing cell physiology. IR can directly interact with deoxyribonucleic acid (DNA) or produce reactive oxygen and nitrogen species (RONS), provoking DNA damage. When DNA damage is not repaired, programmed cell death (apoptosis and/or autophagy) is induced. However, cancer cells can acquire resistance to IR avoiding cell death, where reprogramming of energy metabolism has a critical role and is intimately connected with hypoxia, mitochondrial physiology, oxidative stress (OS) and autophagy. This review is focused on the reprogramming of energy metabolism in response to RT in HPV-positive and HPV-negative HNSCC, showing their differences in cellular metabolism management and the probable direction of treatments for each subtype of HNSCC.

NA-Seq: A Discovery Tool for the Analysis of Chromatin Structure and Dynamics during Differentiation

Reprogramming of energy metabolism is a key for cancer development. Kaposi’s sarcoma-associated herpesvirus (KSHV), a human oncogenic herpesvirus, is tightly associated with several human malignancies by infecting B-lymphocyte or endothelial cells. Cancer cell energy metabolism is mainly dominated by three pathways of central carbon metabolism, including aerobic glycolysis, glutaminolysis, and fatty acid synthesis. Increasing evidence has shown that KSHV infection can alter central carbon metabolic pathways to produce biomass for viral replication, as well as the survival and proliferation of infected cells. In this review, we summarize recent studies exploring how KSHV manipulates host cell metabolism to promote viral pathogenesis, which provides the potential therapeutic targets and strategies for KSHV-associated cancers.

Simple SummaryRecent genomic classification of tumors has stated that clinically refractory cancers aggregate as a distinct molecular subtype associated with epithelial–mesenchymal transition (EMT). EMT subtype tumors are clinically intractable due to shared malignant characteristics such as poor prognosis and metastasis and are resistant to chemotherapy and immune checkpoint blockades. Therefore, there is an urgent clinical need for the identification of potential therapeutic targets for this tumor subtype. Here, we profiled the metabolic signatures of 9452 samples across 31 cancer types based on EMT activity and identified that ~80 to 90% of cancer types had high carbohydrate and energy metabolism associated with the high EMT state. Furthermore, we identified CHST14 as a potential metabolic target for the EMT subtype for stomach cancer associated with reprogramming of energy metabolism. Our analyses identified metabolic reprogramming associated with EMT, suggesting metabolism-associated targets for clinically refractory cancer subtypes.Epithelial–mesenchymal transition (EMT) is critical for cancer development, invasion, and metastasis. Its activity influences metabolic reprogramming, tumor aggressiveness, and patient survival. Abnormal tumor metabolism has been identified as a cancer hallmark and is considered a potential therapeutic target. We profiled distinct metabolic signatures by EMT activity using data from 9452 transcriptomes across 31 different cancer types from The Cancer Genome Atlas. Our results demonstrated that ~80 to 90% of cancer types had high carbohydrate and energy metabolism, which were associated with the high EMT group. Notably, among the distinct EMT activities, metabolic reprogramming in different immune microenvironments was correlated with patient prognosis. Nine cancer types showed a significant difference in survival with the presence of high EMT activity. Stomach cancer showed elevated energy metabolism and was associated with an unfavorable prognosis (p < 0.0068) coupled with high expression of CHST14, indicating that it may serve as a potential drug target. Our analyses highlight the prevalence of cancer type-dependent EMT and metabolic reprogramming activities and identified metabolism-associated genes that may serve as potential therapeutic targets.

Most naturally occurring mammalian cancers and immortalized tissue culture cell lines share a common characteristic, the overexpression of full-length HMGA1 (high mobility group A1) proteins. The HMGA1 protooncogene codes for two closely related isoform proteins, HMGA1a and HMGA1b, and causes cancerous cellular transformation when overexpressed in either transgenic mice or "normal" cultured cell lines. Previous work has suggested that the in vivo types and patterns of the HMGA1 post-translational modifications (PTMs) differ between normal and malignant cells. The present study focuses on the important question of whether HMGA1a and HMGA1b proteins isolated from the same cell type have identical or different PTM patterns and also whether these isoform patterns differ between non-malignant and malignant cells. Two independent mass spectrometry methods were used to identify the types of PTMs found on specific amino acid residues on the endogenous HMGA1a and HMGA1b proteins isolated from a non-metastatic human mammary epithelial cell line, MCF-7, and a malignant metastatic cell line derived from MCF-7 cells that overexpressed the transgenic HMGA1a protein. Although some of the PTMs were the same on both the HMGA1a and HMGA1b proteins isolated from a given cell type, many other modifications were present on one but not the other isoform. Furthermore, we demonstrate that both HMGA1 isoforms are di-methylated on arginine and lysine residues. Most importantly, however, the PTM patterns on the endogenous HMGA1a and HMGA1b proteins isolated from non-metastatic and metastatic cells were consistently different, suggesting that the isoforms likely exhibit differences in their biological functions/activities in these cell types.

Identification of post-translationally modified α-Synuclein protein in biofluids of Parkinson's disease patients using a targeted and quantitative mass spectrometry approach. Celine Vocat1, Bruno Fauvet1, Michel Prudent4, Adrien W. Schmid3, Hilal A. Lashuel1&2. 1 Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, Ecole Polytechnique Federale de Lausanne (EPFL), 1015 Lausanne, Switzerland. 2. Qatar Biomedical Research Institute, 5825 Doha, Qatar. 3. Proteomics Core Facility, Ecole Polytechnique Federale Lausanne (EPFL), Switzerland. 4. Service Regional Vaudois de Transfusion Sanguine, Unite de Recherche et Developpement, Switzerland. Parkinson's disease (PD) is a movement disorder characterized by the progressive loss of dopaminergic neurons and the presence of intracellular protein inclusions (Lewy Bodies) found in the brain of affected patients. Protein aggregation and post-translational modifications (PTMs), such as the site specific phosphorylation of alpha-Synuclein (α-Syn) protein have been reported to be strongly linked to PD pathogenesis. Therefore, pathologically modified α-Syn species represent a primary target for the diagnosis and treatment of PD. In this work, we aimed at conducting a comprehensive study, using multiple mass spectrometry and proteomics based approaches, to assess the chemical heterogeneity of α-Syn and to identify and map the pattern of α-Syn PTMs in plasma and red blood cells from PD and dementia with Lewy bodies (DLB) patients compared to healthy, age-matched control subjects. More specifically, we focused on the pattern of PTMs in the blood in order to identify if these modifications correlate with α-Syn PTM's observed in the brain and cerebrospinal fluid (CSF) during disease progression. The use of full-length, heavy isotope-labelled (15N) α-Syn protein and peptide standards with site-specific modifications, which mirror the key pathological PTMs of α-Syn found in PD, with targeted proteomics and selected reaction monitoring (SRM) mass spectrometry have enabled us to specifically identify and monitor single or multiple site-specific phosphorylations, N-terminal acetylation, truncations and splice variants of α-Syn. We have developed a multiplexed SRM assay which allows us to monitor several PTMs during a single analytical run. The identification of a specific isoform or PTMs pattern that correlate with PD or DLB could provide novel insights into the mechanism of the disease development, contribute to the identification of novel therapeutic targets and most importantly, could provide a diagnostic marker to detect and monitor the progression of PD and related synucleinopathies.

Influence of Combinatorial Histone Modifications on Antibody and Effector Protein Recognition

Cancer is a leading cause of human death worldwide, and the modulation of the metabolic properties of T cells employed in cancer immunotherapy holds great promise for combating cancer. As a crucial factor, energy metabolism influences the activation, proliferation, and function of T cells, and thus metabolic reprogramming of T cells is a unique research perspective in cancer immunology. Special conditions within the tumor microenvironment and high-energy demands lead to alterations in the energy metabolism of T cells. In-depth research on the reprogramming of energy metabolism in T cells can reveal the mechanisms underlying tumor immune tolerance and provide important clues for the development of new tumor immunotherapy strategies as well. Therefore, the study of T cell energy metabolism has important clinical significance and potential applications. In the study, the current achievements in the reprogramming of T cell energy metabolism were reviewed. Then, the influencing factors associated with T cell energy metabolism were introduced. In addition, T cell energy metabolism in cancer immunotherapy was summarized, which highlighted its potential significance in enhancing T cell function and therapeutic outcomes. In summary, energy exhaustion of T cells leads to functional exhaustion, thus resulting in immune evasion by cancer cells. A better understanding of reprogramming of T cell energy metabolism may enable immunotherapy to combat cancer and holds promise for optimizing and enhancing existing therapeutic approaches.

Protein lipoylation, a mitochondria-specific post-translational modification (PTM) evolutionarily conserved from bacteria to mammals, plays critical role in metabolic processes. In humans, four identified lipoylated proteins serve as essential components of key enzymes involved in glycolysis, the tricarboxylic acid (TCA) cycle, and amino acid metabolism. The dynamic addition or removal of lipoylation modifications critically regulates the functional activity of these enzymes, with dysregulation strongly associated with cancers. Notably, cancer-associated metabolic reprogramming frequently coincides with functional impairment of lipoylated proteins, which subsequently modulates tumor growth through metabolic adaptation. In this review, we systematically summarized the biosynthesis of lipoic acid (LA), introduced the basic structure of lipoylated protein and presented the regulation of lipoylation. Since metabolic reprogramming is an important feature of tumorigenesis, we discussed the relationship between protein lipoylation and tumor metabolic reprogramming. Cuproptosis is a novel form of cell death characterized by copper-mediated lipoylation, which disrupts mitochondrial metabolism and induces cell death through the aggregation of lipoylated proteins in the TCA cycle. We highlighted the therapeutic potential of targeting lipoylation to disrupt cancer cell energy metabolism, particularly through cuproptosis. These insights reveal the intricate interplay between lipoylation and cancer progression and open new avenues for developing targeted therapies. Furthermore, we proposed innovative combinatorial strategies leveraging the crosstalk between cuproptosis and ferroptosis to overcome tumor drug resistance. These insights establish lipoylation as a promising therapeutic axis for developing precision cancer therapies targeting metabolic vulnerabilities.

Challenges in Cancer Molecular Targets and Therapeutics

As a hallmark of cancer, metabolic reprogramming adjusts macromolecular synthesis, energy metabolism and redox homeostasis processes to adapt to and promote the complex biological processes of abnormal growth and proliferation. The complexity of metabolic reprogramming lies in its precise regulation by multiple levels and factors, including the interplay of multiple signalling pathways, precise regulation of transcription factors and dynamic adjustments in metabolic enzyme activity. In this complex regulatory network, acetylation and deacetylation, which are important post-translational modifications, regulate key molecules and processes related to metabolic reprogramming by affecting protein function and stability. Dysregulation of acetylation and deacetylation may alter cancer cell metabolic patterns by affecting signalling pathways, transcription factors and metabolic enzyme activity related to metabolic reprogramming, increasing the susceptibility to rapid proliferation and survival. In this review, we focus on discussing how acetylation and deacetylation regulate cancer metabolism, thereby highlighting the central role of these post-translational modifications in metabolic reprogramming, and hoping to provide strong support for the development of novel cancer treatment strategies. KEY POINTS: Protein acetylation and deacetylation are key regulators of metabolic reprogramming in tumour cells. These modifications influence signalling pathways critical for tumour metabolism. They modulate the activity of transcription factors that drive gene expression changes. Metabolic enzymes are also affected, altering cellular metabolism to support tumour growth.

Post-translational modifications (PTMs) play an important role in various biological processes through changing protein structure and function. Some ultramodified proteins (like histones) have multiple PTMs forming PTM patterns that define the functionality of a protein. While bottom-up mass spectrometry (MS) has been successful in identifying individual PTMs within short peptides, it is unable to identify PTM patterns spread along entire proteins in a coordinated fashion. In contrast, top-down MS analyzes intact proteins and reveals PTM patterns along the entire proteins. However, while recent advances in instrumentation have made top-down MS accessible to many laboratories, most computational tools for top-down MS focus on proteins with few PTMs and are unable to identify complex PTM patterns. We propose a new algorithm, MS-Align-E, that identifies both expected and unexpected PTMs in ultramodified proteins. We demonstrate that MS-Align-E identifies many protein forms of histone H4 and benchmark it against the currently accepted software tools.

Background The formation of resistance against trastuzumab deeply affects the treatment of HER2 positive breast cancer. Although studies have demonstrated several possible reasons that cause the trastuzumab resistance, the precise changes of cell process as well as the interaction between cancer cells and tumor microenvironment during the formation of resistance are still poorly understood. Here we figured out several crucial changes including oncogenic signal pathways as well as metabolism processes especially amino acids and polyunsaturated fatty acids (PUFAs) during the establishment of trastuzumab resistance. We further suggested that the inducers of ferroptosis may be promising reagents for trastuzumab resistant HER2 positive breast cancer. Methods The trastuzumab resistant cell was generated from a sensitive cell line SKBR3. To simulate the adaptation process of HER2 positive tumor to anti-tumor drug, the concentration of trastuzumab was changed gently to prevent cell death. After 8 weeks treatment, trastuzumab concentration in medium was raised from 1μg/ml to 6μg/ml, and a “persister” cell line SKBR3_HP was obtained. The original cell line SKBR3 was cultured for 8 weeks as well to exclude any changes that caused by culture condition. And each cell line includes 3 biological repeats. The viability of two cell lines is measured by CCK8 cell proliferation test with different concentration of trastuzumab. Total RNA of both SKBR3 and SKBR3_HP cells were prepared for sequencing. Activity scores of oncogenic signal pathways as well as metabolism processes were defined and calculated as the relative gene expression value averaged over all genes in this pathway in certain cell type. Flow cytometry was applied for reactive oxygen species measurement with BODIPY-C11. Results After 8 weeks treatment of trastuzumab, the persister cell line SKBR3_HP showed a significant higher viability than original sensitive cell line SKBR3. Oncogenic signal pathway analysis revealed that RTK-Ras, MYC and HIPPO pathways turn into a more active state in SKBR3_HP cells, as well as the upregulation of several cell cycle genes, which are all the response to the blockage of HER2 signal cascade and together maintains cell proliferation. Beside signal pathway, the reprogramming of metabolism is also the consequence of cell adaptation to trastuzumab. Minor changes in energy metabolism, such as glycolysis, citrate cycle and oxidative phosphorylation were observed in SKBR3_HP cells. However, amino acid metabolism, including the synthesis of phenylalanine, histidine, arginine, proline, cysteine and methionine, was largely enhanced in SKBR3_HP cells. Fatty acid, specifically the metabolism of PUFAs, such as linoleic acid, alpha-linolenic acid and arachidonic acid, was activated during the formation of trastuzumab resistance, which was confirmed by the lipid metabolomics data that most n-3/n-6 PUFAs decreased in SKBR3_HP cells. As cysteine and PUFAs metabolism might closely associate with cellular redox balances, erastin and RSL3 were applied to interrupt the intake of cysteine and potentiate the lipid peroxidation process, respectively. A situation of higher ferroptosis sensitivity accompanies raising peroxidated lipids could be detected in SKBR3_HP cells. Conclusion By analyzing the transcriptome and metabolomics data of trastuzumab sensitive and persister cell lines, we pointed out that the changes of oncogenic signal pathway, together with metabolism variation, particularly amino acids and PUFAs, are all the cellular adaptations to high trastuzumab environment. And the higher ferroptosis sensitivity of persister cells could be a valuable treatment target. Citation Format: Ningjun Duan, Yijia Hua, Shuang Hu, Yongmei Yin. Reprogramming of oncogenic signal pathways and metabolism during trastuzumab resistance formation of HER2 positive breast cancer [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P1-13-20.