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Inherited disorders of mitochondrial metabolism, including isolated methylmalonic aciduria, present unique challenges to energetic homeostasis by disrupting energy-producing pathways. To better understand global responses to energy shortage, we investigated a hemizygous mouse model of methylmalonyl-CoA mutase (Mmut)–type methylmalonic aciduria. We found Mmut mutant mice to have reduced appetite, energy expenditure and body mass compared with littermate controls, along with a relative reduction in lean mass but increase in fat mass. Brown adipose tissue showed a process of whitening, in line with lower body surface temperature and lesser ability to cope with cold challenge. Mutant mice had dysregulated plasma glucose, delayed glucose clearance and a lesser ability to regulate energy sources when switching from the fed to fasted state, while liver investigations indicated metabolite accumulation and altered expression of peroxisome proliferator–activated receptor and Fgf21-controlled pathways. Together, these shed light on the mechanisms and adaptations behind energy imbalance in methylmalonic aciduria and provide insight into metabolic responses to chronic energy shortage, which may have important implications for disease understanding and patient management.

Cells are continuously exposed to potentially dangerous compounds. Progressive accumulation of damage is suspected to contribute to neurodegenerative diseases and aging, but the molecular identity of the damage remains largely unknown. Here we report that PARK7, an enzyme mutated in hereditary Parkinson's disease, prevents damage of proteins and metabolites caused by a metabolite of glycolysis. We found that the glycolytic metabolite 1,3-bisphosphoglycerate (1,3-BPG) spontaneously forms a novel reactive intermediate that avidly reacts with amino groups. PARK7 acts by destroying this intermediate, thereby preventing the formation of proteins and metabolites with glycerate and phosphoglycerate modifications on amino groups. As a consequence, inactivation of PARK7 (or its orthologs) in human cell lines, mouse brain, and leads to the accumulation of these damaged compounds, most of which have not been described before. Our work demonstrates that PARK7 function represents a highly conserved strategy to prevent damage in cells that metabolize carbohydrates. This represents a fundamental link between metabolism and a type of cellular damage that might contribute to the development of Parkinson's disease.

During liver development, the formation of the bile ducts, hepatic arteries and periportal mesenchyme is interdependent. However, how bile duct development is coordinated with morphogenesis of the vasculature and mesenchyme, and how bile duct lumina form and connect with the canaliculi remains unclear. By combining molecular biology, transgene technology and computational modelling, we found that Slit-Robo signalling, which is active in the mesenchyme, is required for hepatic artery morphogenesis. Furthermore, we propose that the orientation of cholangiocyte division, the dynamics of cholangiocyte differentiation, and osmotic effects are the main drivers of biliary lumen formation. Finally, we provide a first description of how bile duct lumina connect with canaliculi in embryonic livers, and identified Claudin7 as a marker of the cells delineating these junctions., (BIFA - Sciences biomédicales et pharmaceutiques) -- UCL, 2022

SARS-CoV-2 causes major disturbances in serum metabolite levels, associated with severity of the immune response. Despite the numerous advantages of urine for biomarker discovery, the potential association between urine metabolites and disease severity has not been investigated in coronavirus disease 2019 (COVID-19). In a proof-of-concept study, we performed quantitative urine metabolomics in patients hospitalized with COVID-19 and controls using LC-MS/MS. We assessed whether metabolites alterations were associated with COVID-19, disease severity, and inflammation. The study included 56 patients hospitalized with COVID-19 (26 non-critical and 30 critical disease); 16 healthy controls; and 3 controls with proximal tubule dysfunction unrelated to SARS-CoV-2. Metabolomic profiling revealed a major urinary increase of tryptophan metabolites kynurenine (P < 0.001), 3-hydroxykynurenine (P < 0.001) and 3-hydroxyanthranilate (P < 0.001) in SARS-CoV-2 infected patients. Urine levels of kynurenines were associated with disease severity and systemic inflammation (kynurenine, r 0.43, P = 0.001; 3-hydroxykynurenine, r 0.44, P < 0.001). Increased urinary levels of neutral amino acids and imino acid proline were also common in COVID-19, suggesting specific transport defects. Urine metabolomics identified major alterations in the tryptophan-kynurenine pathway, consistent with changes in host metabolism during SARS-CoV-2 infection. The association between increased urinary levels of kynurenines, inflammation and COVID-19 severity supports further evaluation of these easily available biomarkers.

Tumor development is characterized by both genetic and epigenetic alterations that lead to gene expression changes. One of such transcriptomic changes is the aberrant activation of a group of germline-specific genes in a variety of tumors of somatic origin. The spurious activation of this group of genes is due to the DNA demethylation of their promoter region in tumor cells, a phenomenon associated with the global loss of DNA methylation that often accompanies tumorigenesis. Several of these “cancer-germline” genes were found to exert pro-tumoral functions, or evoke an immune response. Cancer-germline genes are therefore attracting much interest, as they constitute promising targets for anti-cancer therapies with the hope of limited side effects due to their highly restricted pattern of expression. Whether additional tissue-specific gene clusters become activated in tumors, be it by DNA demethylation or not, remains unanswered. Most studies, indeed, have used transcriptomic approaches that were biased towards testis-specific genes. In the present work, we aimed to fill this gap by combining omics data of lung adenocarcinoma (LUAD) tissues and cell lines, as well as normal lung and alveolar type II cells (AT2), the cells of origin of LUAD, without imposing any criteria of expression specificity to the ectopically activated genes we were looking for. We divided our work in two complementary axes. In the first part, we asked whether the global loss of DNA demethylation in tumors is also associated with the ectopic activation of somatic-specific gene clusters in LUAD. We found that, indeed, promoter DNA demethylation in these cells leads to the transcriptional induction of genes displaying selective expression in gastro-intestinal tissues (colon and small intestine), and of genes specific to stratified squamous epithelia (esophagus, skin and vagina). Interestingly, our data show that ectopic activation of this latter group of genes in LUAD is associated with poor progno, (BIFA - Sciences biomédicales et pharmaceutiques) -- UCL, 2022

Endometriosis is an inflammatory gynecological pathology that affects approximately 10% of women worldwide and can cause subfertility. In 30% of patients, the endometriotic tissue is resistant to progestin treatment. The objective of my thesis was to characterize and define the potential role of the protein Progesterone Receptor Membrane Component 1 (PGRMC1), described as a "fertility stabilizer", in the human endometrium and endometriosis. A spatiotemporal regulation of PGRMC1 was identified with a predominant expression on the surface of the proliferative endometrium and potentially reduced in endometriosis. My results (i) discredit the AG-205 inhibitor, a major tool in the study of PGRMC1, (ii) demonstrate the repressive activity of PGRMC1 towards MMP-3 and (iii) suggest that it regulates cell proliferation during the menstrual cycle. PGRMC1 could thus control endometrial tissue remodeling, which is crucial for fertility., (BIFA - Sciences biomédicales et pharmaceutiques) -- UCL, 2022

This thesis aims to study extracellular vesicles (EVs) in thyroid cancer (TC) hoping to understand their role in cancer progression and to identify new biomarkers for the differential diagnosis between TC and benign nodules. Using a mouse model mimicking human TC, we isolated and characterized EVs from control and cancerous thyroid tissues. We identified tumor-derived EV-miRNAs by sequencing. More abundant EV-miRNAs were mostly deregulated in tumor cells and could affect immune-related pathways. We thus propose that tumor cells secrete more EVs containing a deregulated miRNA signature and that this could affect the immune microenvironment. Finally, the diagnostic value of a few miRNA candidates was assessed by quantifying their levels in plasma-EVs from patients with thyroid diseases, suggesting the diagnostic potential of EV-enclosed miR-146b-5p and miR-21a-5p, (BIFA - Sciences biomédicales et pharmaceutiques) -- UCL, 2022

Intestinal T cells are key in gut barrier function. Their role in early stages of alcohol-associated liver disease (ALD) remain unknown. To explore the links between intestinal T cells, microbial translocation and ALD METHODS: Patients with alcohol use disorder (AUD) following a rehabilitation programme were compared to subjects with non-alcoholic fatty liver disease (NAFLD) and healthy controls. Clinical and laboratory data (liver stiffness, controlled attenuation parameter, AST, ALT, K18-M65) served to identify AUD patients with isolated steatosis (minimal liver disease) or steatohepatitis/fibrosis (ALD). Serum microbial translocation markers were measured by ELISA, duodenal and plasma levels of sphingolipids by targeted LC-MS. T lymphocytes in duodenal biopsies were characterised by immunohistochemistry, flow cytometry and RNA sequencing on FACS-sorted cells. Mechanisms for T-cell alterations were assessed in vitro. Patients with ALD, but not those with minimal liver disease, showed reduced numbers of duodenal CD8+ T resident memory (TRM) cells compared to controls or patients with NAFLD. TRM transcriptomic analysis, in vitro analyses and pharmacological inhibition of cathepsin B confirmed TRM apoptosis driven by lysosomal membrane permeabilisation and cathepsin B release into the cytosol. Altered lipid metabolism and increased duodenal and plasma sphingolipids correlated with apoptosis. Dihydroceramide dose-dependently reduced viability of TRM. Duodenal TRM phenotypic changes, apoptosis and transcriptomic alterations correlated with increased levels of microbial translocation markers. Short-term abstinence did not reverse TRM cell death in patients with ALD. Duodenal CD8+ TRM apoptosis related to functional changes in lysosomes and lipid metabolism points to impaired gut adaptive immunity specifically in patients with AUD who developed early ALD.

Telomeres protect the ends of our chromosomes. The replicative immortality of cancer cells depends on the activation of a telomere maintenance mechanism: the telomerase or an alternative lengthening of telomeres (ALT) mechanism. ALT is activated in about 10% of tumors but this prevalence increases greatly in pediatric tumors. The latter are in need of targeted therapies but, to date, there is still no therapy targeting ALT. In this thesis, we identified TSPYL5 (testis-specific Y-encoded-like protein 5) as a critical protein for ALT+ cell viability, opening new perspectives for anti-ALT targeted therapies. We also established a mouse xenograft model with human ALT+ cancer cells to test the efficiency of future anti-ALT compounds. The lack of good tools for the diagnosis of ALT also led us to the development of a new robust test on tumor sections. Finally, we provided additional evidence that replicative stress induces some characteristics of ALT telomeres., (BIFA - Sciences biomédicales et pharmaceutiques) -- UCL, 2022

The cytosolic enzyme ethylmalonyl-CoA decarboxylase (ECHDC1) decarboxylates ethyl- or methyl-malonyl-CoA, two side products of acetyl-CoA carboxylase. These CoA derivatives can be used to synthesize a subset of branched-chain fatty acids (FAs). We previously found that ECHDC1 limits the synthesis of these abnormal FAs in cell lines, but its effects in vivo are unknown. To further evaluate the effects of ECHDC1 deficiency, we generated knockout mice. These mice were viable, fertile, showed normal postnatal growth, and lacked obvious macroscopic and histologic changes. Surprisingly, tissues from wild-type mice already contained methyl-branched FAs due to methylmalonyl-CoA incorporation, but these FAs were only increased in the intraorbital glands of ECHDC1 knockout mice. In contrast, ECHDC1 knockout mice accumulated 16-20-carbon FAs carrying ethyl-branches in all tissues, which were undetectable in wild-type mice. Ethyl-branched FAs were incorporated into different lipids, including acylcarnitines, phosphatidylcholines, plasmanylcholines, and triglycerides. Interestingly, we found a variety of unusual glycine-conjugates in the urine of knockout mice, which included adducts of ethyl-branched compounds in different stages of oxidation. This suggests that the excretion of potentially toxic intermediates of branched-chain FA metabolism might prevent a more dramatic phenotype in these mice. Curiously, ECHDC1 knockout mice also accumulated 2,2-dimethylmalonyl-CoA. This indicates that the broad specificity of ECHDC1 might help eliminate a variety of potentially dangerous branched-chain dicarboxylyl-CoAs. We conclude that ECHDC1 prevents the formation of ethyl-branched FAs and that urinary excretion of glycine-conjugates allows mice to eliminate potentially deleterious intermediates of branched-chain FA metabolism.