Exploring the metabolic landscape and resulting vulnerabilities of minimal residual disease in breast cancer

Despite overall improvements in breast cancer management, breast cancer continues to be a major health challenge worldwide, with high mortality rates. Following initially successful therapies, some cells are able to evade the treatment and remain in the body at undetectable levels (known as minimal residual disease) and could eventually lead to a lethal tumor recurrence. Understanding the nature of this elusive cell population is of a great importance in tumor eradication and relapse prevention. Nevertheless, the intricate mechanistic details about these processes and the nature of these cells remain poorly understood, mainly due to difficulties in obtaining patient material of MRD and being able to study them over the course of treatment. To characterize MRD in breast cancer, we employed an inducible TetO-MYC/TetO-Neu/MMTV-rtTA mouse model and primary 3D cultures of mammary organoids that yield a correlate of MRD upon oncogene silencing. A combination of immunofluorescence, RNA sequencing, lipidomics and metabolomics revealed the unique nature of the residual cells. Despite the phenotypic similarity to the normal population, the residual cells exhibited a distinct transcriptional profile. This profile was also different when compared to the tumor, highlighting the unique properties of the residual cell population. In addition, lipid profiles of the residual cells were also distinguished from both normal and tumor populations. Surprisingly, despite the inactivated oncogenes and seemingly normal phenotype of the residual structures, the residual cells bore a metabolic resemblance to tumor cells. They retained some tumor metabolic hallmarks, which persevered long after the oncogenes were silenced and tumors had regressed. This was demonstrated in our 3D cultures and verified in vivo on histological sections and fresh samples of the mammary glands following tumor regression. Enhanced glycolysis, the urea cycle and NOS2 activity were the most prominent features preserved in the residual cells. As shown in correlation with publicly available microarray datasets of patient samples following neoadjuvant treatment, these traits could be particularly important in MRD of the basal-like HER2 positive and HER2 negative breast cancer subtypes. In conclusion, our findings suggest vast and profound effects of the changes happening over the course of tumor progression, which result in an altered metabolic network even in the absence of oncogene signaling, implying the existence of a “metabolic memory” probably imprinted through the changes in the epigenetic landscape. This phenomenon, particularly its potential driver(s), remains to be investigated. Furthermore, enhanced glycolysis, urea cycle and NOS2 activity in the residual cells compared to the normal, could provide an opportunity to interfere with MRD, offering the potential of preventing tumor recurrences

Metabolic memory underlying minimal residual disease in breast cancer.

Funder: European Molecular Biology LaboratoryFunder: European Molecular Biology Laboratory (EMBL)Tumor relapse from treatment-resistant cells (minimal residual disease, MRD) underlies most breast cancer-related deaths. Yet, the molecular characteristics defining their malignancy have largely remained elusive. Here, we integrated multi-omics data from a tractable organoid system with a metabolic modeling approach to uncover the metabolic and regulatory idiosyncrasies of the MRD. We find that the resistant cells, despite their non-proliferative phenotype and the absence of oncogenic signaling, feature increased glycolysis and activity of certain urea cycle enzyme reminiscent of the tumor. This metabolic distinctiveness was also evident in a mouse model and in transcriptomic data from patients following neo-adjuvant therapy. We further identified a marked similarity in DNA methylation profiles between tumor and residual cells. Taken together, our data reveal a metabolic and epigenetic memory of the treatment-resistant cells. We further demonstrate that the memorized elevated glycolysis in MRD is crucial for their survival and can be targeted using a small-molecule inhibitor without impacting normal cells. The metabolic aberrances of MRD thus offer new therapeutic opportunities for post-treatment care to prevent breast tumor recurrence

Genetic code expansion for multiprotein complex engineering

We present a baculovirus-based protein engineering method that enables site-specific introduction of unique functionalities in a eukaryotic protein complex recombinantly produced in insect cells. We demonstrate the versatility of this efficient and robust protein production platform, \u2018MultiBacTATAG\u2019, (i) for the fluorescent labeling of target proteins and biologics using click chemistries, (ii) for glycoengineering of antibodies, and (iii) for structure\u2013function studies of novel eukaryotic complexes using single-molecule F\uf6rster resonance energy transfer as well as site-specific crosslinking strategies

Petrological and organic geochemical properties of lignite from the Kolubara and Kostolac basins, Serbia: Implication on Grindability Index (Reprinted)

The influence of different coal lithotypes on grindability has been investigated using lignite from two of the most important Upper Miocene lignite basins in Serbia (Kolubara and Kostolac). Yellow xylite-rich types demonstrated the most negative impact on Hardgrove Grindability Index (HGI). All different types of xylite-rich coal, as well as total xylite-rich coal from the Kolubara basin have a negative influence on the grindability properties, while only the yellow type of xylite-rich coal from the Kostolac showed a negative impact on HGI. Matrix coal does not show a clear effect on HGI. A negative correlation between textinite content and HGI is observed in both basins, whereas contents of other macerals do not show influence on grindability properties. Content of total organic carbon demonstrated the negative impact on HGI. Correlation analysis indicates that the negative impact of the yellow type of xylite-rich coal and the sum of total xylite-rich coal on the grindability properties partly can be related to content of total organic carbon and high amount of soluble organic matter. Matrix lithotype does not show any significant correlation with bulk geochemical parameters in both basins. The peat-forming vegetation of all samples from both basins were dominated by decay-resistant gymnosperm (coniferous) plants, belonging to one or several of the families Taxodiaceae, Podocarpaceae, Cupressaceae, Araucariaceae, Phyllocladaceae and Pinaceae. Lignite from the Kolubara basin is characterized by a higher contribution of angiosperm vegetation than coal from the Kostolac basin. Peatification of the Kolubara coal occurred under more oxic conditions than the Kostolac one. Analysis of biomarkers indicated that the negative impact of all types of xylite-rich coal from the Kolubara on HGI can be related to the higher proportion of angiosperms, abundance of mid-chain n-alkanes and sesquiterpenoids, aromatization of non-hopanoid triterpenoids and hopanoids, and intense degradation of wood tissues in a more oxic environment. The positive impact of matrix coal on HGI in the Kolubara samples can be attributed to elevated content of non-aromatic hopanoids and low amounts of aromatic non-hopanoid triterpenoids and sesquiterpenoids, which seems to hinder the grindability properties

Petrological and organic geochemical properties of lignite from the Kolubara and Kostolac basins, Serbia: Implication on Grindability Index

The influence of different coal lithotypes on grindability has been investigated using lignite from two of the most important Upper Miocene lignite basins in Serbia (Kolubara and Kostolac). Yellow xylite-rich types demonstrated the most negative impact on Hardgrove Grindability Index (HGI). All different types of xylite-rich coal, as well as total xylite-rich coal from the Kolubara basin have a negative influence on the grindability properties, while only the yellow type of xylite-rich coal from the Kostolac showed a negative impact on HGI. Matrix coal does not show a clear effect on HGI. A negative correlation between textinite content and HGI is observed in both basins, whereas contents of other macerals do not show influence on grindability properties. Content of total organic carbon demonstrated the negative impact on HGI. Correlation analysis indicates that the negative impact of the yellow type of xylite-rich coal and the sum of total xylite-rich coal on the grindability properties partly can be related to content of total organic carbon and high amount of soluble organic matter. Matrix lithotype does not show any significant correlation with bulk geochemical parameters in both basins. The peat-forming vegetation of all samples from both basins were dominated by decay-resistant gymnosperm (coniferous) plants, belonging to one or several of the families Taxodiaceae, Podocarpaceae, Cupressaceae, Araucariaceae, Phyllocladaceae and Pinaceae. Lignite from the Kolubara basin is characterized by a higher contribution of angiosperm vegetation than coal from the Kostolac basin. Peatification of the Kolubara coal occurred under more oxic conditions than the Kostolac one. Analysis of biomarkers indicated that the negative impact of all types of xylite-rich coal from the Kolubara on HGI can be related to the higher proportion of angiosperms, abundance of mid-chain n-alkanes and sesquiterpenoids, aromatization of non-hopanoid triterpenoids and hopanoids, and intense degradation of wood tissues in a more oxic environment. The positive impact of matrix coal on HGI in the Kolubara samples can be attributed to elevated content of non-aromatic hopanoids and low amounts of aromatic non-hopanoid triterpenoids and sesquiterpenoids, which seems to hinder the grindability properties. (C) 2014 Elsevier B.V. All rights reserved