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Zamboni, N.

Publications and source records attributed to Zamboni, N..

23 records · Page 2Linked to original sources

Spatial heterogeneity of glioblastoma cells reveals sensitivity to NAD+ depletion at tumor edge

Even after total resection of glioblastoma core lesions by surgery and aggressive post-surgical treatments, life-threatening tumors inevitably recur. A characteristic obstacle in effective treatment is high intratumoral heterogeneity, both longitudinally and spatially. Recurrence occurs predominantly at the brain parenchyma-tumor core interface, a region termed tumor edge. Given the difficulty of accessing it surgically, the composition of the tumor edge, harboring both cancerous and non-cancerous cells, remains largely unknown. Here, to identify phenotypic diversity among heterogeneous glioblastoma core and edge lesions, we uncovered the existence of three phenotypically-distinct clonal subpopulations within individual tumors from glioblastoma patients. Clones from the tumor core shared the same phenotype, exclusively generating tumor-core cells. In contrast, two distinct clonal subtypes were identified at the tumor edge: one generated only edge-lesion cells and the other expanded more broadly to establish both edge- and core-lesions. Using multiple xenograft experimental models in mouse brains, tumor edge development was found to require that both somatic and tumor cells express the NADase CD38, combinedly elevating glioblastoma malignancy. In vitro data suggested that intracellular NADase activity at the edge was provoked through intercellular communication between edge clones and normal astrocytes. Systemic treatment of tumor-bearing mice with 78c, a small-molecule CD38 inhibitor, attenuated the formation of glioblastoma edge lesions, suggesting its clinical potential to pharmacologically eliminate tumor-edge lesions. Collectively, these findings provide novel phenotypic and mechanistic insights into clonal heterogeneity within glioblastoma, particularly in the surgically unresectable, currently understudied tumor edge.

cancer biology↗

Dynamic analysis of sugar metabolism reveals the mechanisms of action of synthetic sugar analogs

Synthetic sugar analogs are widely applied in metabolic oligosaccharide engineering (MOE) and as novel drugs to interfere with glycoconjugate biosynthesis. However, mechanistic insights on their exact metabolism in the cell and over time are mostly lacking. We developed sensitive ion-pair UHPLC-QqQ mass spectrometry methodology for analysis of sugar metabolites in organisms and in model cells and identified novel low abundant nucleotide sugars in human cells, such as ADP-glucose and UDP-arabinose, and CMP-sialic acid (CMP-NeuNAc) in Drosophila. Dynamic tracing of propargyloxycarbonyl (Poc) labeled analogs, commonly used for MOE, revealed that ManNPoc is metabolized to both CMP-NeuNPoc and UDP-GlcNPoc. Finally, combined treatment of B16-F10 melanoma cells with antitumor compound 3Fax-NeuNAc and 13C-labeled GlcNAc revealed that endogenous CMP-NeuNAc levels started to decrease before a subsequent decrease of ManNAc 6-phosphate was observed. This implicates 3Fax-NeuNAc first acts as a substrate for cytosolic CMP-sialic acid synthetase and subsequently its product CMP-3Fax-NeuNAc functions as a feed-back inhibitor for UDP-GlcNAc 2-epimerase/N-acetylmannosamine kinase. Thus, dynamic analysis of sugar metabolites provides key insights into the time-dependent metabolism of synthetic sugars, which is important for the rational design of analogs with optimized effects.

biochemistry↗

The Molecular Landscape of the Aging Mouse Liver

Systems biology approaches often use inferred networks of gene expression and metabolite data to identify regulatory factors and pathways connected with phenotypic variance. Generally, study-specific multi-layer "Omics" datasets are used to contextualize generic molecular networks. In this regard separating upstream causal mechanisms, downstream biomarkers, and incidental correlations remains a significant challenge, yet it is essential for designing mechanistic experiments. To address this, we designed a study following a population of 2157 individuals from 89 isogenic BXD mouse strains across their lifespan to identify molecular interactions among genotype, environment, age (GxExA) and metabolic fitness. Each strain was separated into two cohorts, one fed low fat (6% cal/fat) and the other high fat (60% cal/fat) diets. Tissues were collected for 662 individuals (309 cohorts) diverging across age (7, 12, 18, and 24 months), diet, sex, and strain. Transcriptome, proteome, and metabolome data were generated for liver. Of these we identified linear relations among these molecular data with lifespan for the same genomes of mice (Roy et al. 2020), and we defined [~]1100 novel protein-coding genes associated with longevity. We knocked down the ortholog of Ctsd in C. elegans. The treatment reduced longevity both in wildtype and in mutant long-lived strains, thus validating the prediction. Next, to assess the molecular impact of GxExA on gene expression, the multi-omics data was parsed into metabolic networks where connectivity varied due to the independent variables. Differences in edge strengths connecting nodes in these molecular networks according to each variable enabled causal inference by using stability selection, with roughly 21% of novel gene-pathway connections being causally affected by diet and/or age. For instance, Chchd2 is activated by aging and drives changes in the proteasome, oxidative phosphorylation, and mitochondrial translation transcriptional networks. Together, we have developed a large multi-omics resource for studying aging in the liver, and a resource for turning standard associations into causal networks.

systems biology↗

Characterization of HIF-dependent alternative isoforms in pancreatic cancer

Intra-tumor hypoxia is a common feature in many solid cancers. Although transcriptional targets of hypoxia-inducible factors (HIFs) have been well characterized, alternative splicing or processing of pre-mRNA transcripts which occurs during hypoxia and subsequent HIF stabilization is much less understood. Here, we identify HIF-dependent alternative splicing events after whole transcriptome sequencing in pancreatic cancer cells exposed to hypoxia with and without downregulation of the aryl hydrocarbon receptor nuclear translocator (ARNT), a protein required for HIFs to form a transcriptionally active dimer. We correlate the discovered hypoxia-driven events with available sequencing data from pan-cancer TCGA patient cohorts to select a narrow set of putative biologically relevant splice events for experimental validation. We validate a small set of candidate HIF-dependent alternative splicing events in multiple human cancer cell lines as well as patient-derived human pancreatic cancer organoids. Lastly, we report the discovery of a HIF-dependent mechanism to produce a hypoxia-dependent, long and coding isoform of the UDP-N-acetylglucosamine transporter SLC35A3.

cell biology↗

A novel mode of communication between blood and the germline for the inheritance of paternal experiences

In many species, environmental stimuli can affect the germline and contribute to phenotypic changes in the offspring, without altering the genetic code1-5. So far, little is known about which biological signals can link exposure to germ cells. Using a mouse model of postnatal trauma with transgenerational effects, we show that exposure alters lipid-based metabolites in blood of males and their non-exposed offspring. Comparable alterations are validated in serum and saliva of orphan children exposed to trauma. Peroxisome proliferator-activated receptor (PPAR) is identified as mediating the effects of metabolites alterations. Mimicking PPAR activation with a dual PPAR/{gamma} agonist in vivo induces changes in the sperm transcriptome similarly to trauma, and reproduces metabolic phenotypes in the offspring. Injecting serum collected from adult males exposed to postnatal trauma into controls recapitulates metabolic phenotypes in the offspring. These results suggest conserved effects of early life adversity on blood metabolites, and causally involve paternal blood factors and PPAR nuclear receptor in phenotype heritability.

molecular biology↗