TY - THES A1 - Lopes Fernando, Raquel Sofia T1 - The impact of aging on proteolytic systems, transcriptome and metabolome of slow and fast muscle fiber types N2 - Aging is a complex process characterized by several factors, including loss of genetic and epigenetic information, accumulation of chronic oxidative stress, protein damage and aggregates and it is becoming an emergent drug target. Therefore, it is the utmost importance to study aging and agerelated diseases, to provide treatments to develop a healthy aging process. Skeletal muscle is one of the earliest tissues affected by age-related changes with progressive loss of muscle mass and function from 30 years old, effect known as sarcopenia. Several studies have shown the accumulation of protein aggregates in different animal models, as well as in humans, suggesting impaired proteostasis, a hallmark of aging, especially regarding degradation systems. Thus, different publications have explored the role of the main proteolytic systems in skeletal muscle from rodents and humans, like ubiquitin proteasomal system (UPS) and autophagy lysosomal system (ALS), however with contradictory results. Yet, most of the published studies are performed in muscles that comprise more than one fiber type, that means, muscles composed by slow and fast fibers. These fiber types, exhibit different metabolism and contraction speed; the slow fibers or type I display an oxidative metabolism, while fast fibers function towards a glycolytic metabolism ranging from fast oxidative to fast glycolytic fibers. To this extent, the aim of this thesis sought to understand on how aging impacts both fiber types not only regarding proteostasis but also at a metabolome and transcriptome network levels. Therefore, the first part of this thesis, presents the differences between slow oxidative (from Soleus muscle) and fast glycolytic fibers (Extensor digitorum longus, EDL) in terms of degradation systems and how they cope with oxidative stress during aging, while the second part explores the differences between young and old EDL muscle transcriptome and metabolome, unraveling molecular features. More specifically, the results from the present work show that slow oxidative muscle performs better at maintaining the function of UPS and ALS during aging than EDL muscle, which is clearly affected, accounting for the decline in the catalytic activity rates and accumulation of autophagy-related proteins. Strinkingly, transcriptome and metabolome analyses reveal that fast glycolytic muscle evidences significant downregulation of mitochondrial related processes and damaged mitochondria morphology during aging, despite of having a lower oxidative metabolism compared to oxidative fibers. Moreover, predictive analyses reveal a negative association between aged EDL gene signature and lifespan extending interventions such as caloric restriction (CR). Although, CR intervention does not alter the levels of mitochondrial markers in aged EDL muscle, it can reverse the higher mRNA levels of muscle damage markers. Together, the results from this thesis give new insights about how different metabolic muscle fibers cope with age-related changes and why fast glycolytic fibers are more susceptible to aging than slow oxidative fibers. N2 - Altern ist ein komplexer Prozess, der durch mehrere Faktoren gekennzeichnet ist, darunter der Verlust genetischer und epigenetischer Informationen, oxidativer Stress, sowie die Anhäufung von Proteinschäden und Aggregaten. Daher ist es von größter Bedeutung, das Altern und altersbedingte Krankheiten zu erforschen, um Arzneimittel und andere Behandlungen für einen gesunden Alterungsprozess zu entwickeln. Die Skelettmuskulatur ist eines der ersten Gewebe, das von altersbedingten Veränderungen betroffen ist. Ab einem Alter von 30 Jahren kommt es zu einem fortschreitenden Verlust der Muskelmasse und -funktion, der auch als Sarkopenie bezeichnet wird. Mehrere Studien haben die Anhäufung von Proteinaggregaten beim Altern in verschiedenen Tiermodellen und auch beim Menschen gezeigt, was auf eine gestörte Proteostase, insbesondere hinsichtlich der Abbauprozesse schließen lässt. Demnach wurde weiterführend die Rolle der wichtigsten proteolytischen Systeme, das Ubiquitin Proteasom System (UPS) und AutophagieLysosomale System (ALS), im alternden Skelettmuskel von Nagetieren und Menschen untersucht. Die Ergebnisse waren widersprüchlich, jedoch wurden die meisten der veröffentlichten Studien an Muskeln durchgeführt, die aus mehr als einem Muskelfasertyp bestehen, d.h. Muskeln, die aus langsamen und schnellen Muskelfasern zusammengesetzt sind. Diese Muskelfasertypen unterscheiden sich hinsichtlich des Stoffwechsels und der Kontraktionsgeschwindigkeit. Die langsamen Fasern oder der Typ I haben einen oxidativen Stoffwechsel, während die schnellen Fasern einen glykolytischen Stoffwechsel aufweisen und aus schnellen oxidativen bis zu schnellen glykolytischen Fasern bestehen können. Insofern war es das Ziel dieser Arbeit zu verstehen, wie sich das Altern auf beide Fasertypen auswirkt, und zwar nicht nur im Hinblick auf die Proteostase, sondern auch auf das Metabolom und Transkriptom. Im ersten Teil dieser Arbeit werden die Unterschiede zwischen langsamen oxidativen (Soleus-Muskel) und schnellen glykolytischen Fasern (Extensor digitorum longus-Muskel; EDL) in Bezug auf die Proteinabbausysteme und die Art und Weise, wie sie mit oxidativem Stress während des Alterns umgehen, dargestellt. Im zweiten Teil werden die Unterschiede zwischen dem Transkriptom und dem Metabolom des jungen und alten EDL-Muskels untersucht, um die molekularen Merkmale zu entschlüsseln. Im Einzelnen zeigen die Ergebnisse der vorliegenden Arbeit, dass der langsam oxidierende Muskel im Vergleich zum EDL-Muskel besser in der Lage ist, die Funktion von UPS und ALS während des Alterns aufrechtzuerhalten. Die Funktionalität des UPS und ALS ist im alternden EDL-Muskels vermindert, was durch den Rückgang der katalytischen Aktivitätsraten und die Anhäufung von mit Autophagie-assoziierten Proteinen gezeigt wurde. Transkriptom- und Metabolomanalysen zeigen, dass schnelle glykolytische Muskeln eine signifikante Herabregulierung mitochondrialer Prozesse und eine geschädigte Mitochondrienmorphologie während des Alterns aufweisen, obwohl sie im Vergleich zu oxidativen Fasern durch einen geringeren oxidativen Stoffwechsel charakterisiert sind. Darüber hinaus ergeben prädiktive Analysen einen negativen Zusammenhang zwischen der Gensignatur des gealterten EDL-Muskels und lebensverlängernden Maßnahmen wie der kalorischenRestriktion. Obwohl die kalorischen Restriktion Intervention die Werte der mitochondrialen Marker im gealterten EDL-Muskel nicht verändert, kann sie die höheren mRNA-Werte der Muskelschädigungsmarker umkehren. Zusammenfassend liefern die Ergebnisse dieser Arbeit neue Erkenntnisse darüber, wie verschiedene metabolische Muskelfasern mit altersbedingten. Veränderungen umgehen und warum schnelle glykolytische Fasern anfälliger für die Alterung als langsame oxidative Fasern sind. KW - skeletal muscle aging KW - proteostasis KW - slow and fast fiber types KW - transcriptomics KW - metabolomics KW - sarcopenia KW - Skelettmuskelalterung KW - Proteostase KW - langsame und schnelle Fasertypen KW - Transkriptom KW - Metabolom KW - ubiquitin proteasomal system KW - autophagy lysosomal system KW - Ubiquitin Proteasom System KW - Autophagie Lysosomale System Y1 - 2023 U6 - https://doi.org/10.25932/publishup-60579 ER - TY - JOUR A1 - Aga-Barfknecht, Heja A1 - Soultoukis, George A. A1 - Stadion, Mandy A1 - Garcia-Carrizo, Francisco A1 - Jähnert, Markus A1 - Gottmann, Pascal A1 - Vogel, Heike A1 - Schulz, Tim Julius A1 - Schürmann, Annette T1 - Distinct adipogenic and fibrogenic differentiation capacities of mesenchymal stromal cells from pancreas and white adipose tissue JF - International journal of molecular sciences N2 - Pancreatic steatosis associates with beta-cell failure and may participate in the development of type-2-diabetes. Our previous studies have shown that diabetes-susceptible mice accumulate more adipocytes in the pancreas than diabetes-resistant mice. In addition, we have demonstrated that the co-culture of pancreatic islets and adipocytes affect insulin secretion. The aim of this current study was to elucidate if and to what extent pancreas-resident mesenchymal stromal cells (MSCs) with adipogenic progenitor potential differ from the corresponding stromal-type cells of the inguinal white adipose tissue (iWAT). miRNA (miRNome) and mRNA expression (transcriptome) analyses of MSCs isolated by flow cytometry of both tissues revealed 121 differentially expressed miRNAs and 1227 differentially expressed genes (DEGs). Target prediction analysis estimated 510 DEGs to be regulated by 58 differentially expressed miRNAs. Pathway analyses of DEGs and miRNA target genes showed unique transcriptional and miRNA signatures in pancreas (pMSCs) and iWAT MSCs (iwatMSCs), for instance fibrogenic and adipogenic differentiation, respectively. Accordingly, iwatMSCs revealed a higher adipogenic lineage commitment, whereas pMSCs showed an elevated fibrogenesis. As a low degree of adipogenesis was also observed in pMSCs of diabetes-susceptible mice, we conclude that the development of pancreatic steatosis has to be induced by other factors not related to cell-autonomous transcriptomic changes and miRNA-based signals. KW - MSCs KW - fatty pancreas KW - WAT KW - lineage commitment KW - transcriptomics KW - miRNAs Y1 - 2022 U6 - https://doi.org/10.3390/ijms23042108 SN - 1422-0067 VL - 23 IS - 4 PB - Molecular Diversity Preservation International CY - Basel ER - TY - JOUR A1 - Aga-Barfknecht, Heja A1 - Hallahan, Nicole A1 - Gottmann, Pascal A1 - Jähnert, Markus A1 - Osburg, Sophie A1 - Schulze, Gunnar A1 - Kamitz, Anne A1 - Arends, Danny A1 - Brockmann, Gudrun A1 - Schallschmidt, Tanja A1 - Lebek, Sandra A1 - Chadt, Alexandra A1 - Al-Hasani, Hadi A1 - Joost, Hans-Georg A1 - Schürmann, Annette A1 - Vogel, Heike T1 - Identification of novel potential type 2 diabetes genes mediating beta-cell loss and hyperglycemia using positional cloning JF - Frontiers in genetics N2 - Type 2 diabetes (T2D) is a complex metabolic disease regulated by an interaction of genetic predisposition and environmental factors. To understand the genetic contribution in the development of diabetes, mice varying in their disease susceptibility were crossed with the obese and diabetes-prone New Zealand obese (NZO) mouse. Subsequent whole-genome sequence scans revealed one major quantitative trait loci (QTL),Nidd/DBAon chromosome 4, linked to elevated blood glucose and reduced plasma insulin and low levels of pancreatic insulin. Phenotypical characterization of congenic mice carrying 13.6 Mbp of the critical fragment of DBA mice displayed severe hyperglycemia and impaired glucose clearance at week 10, decreased glucose response in week 13, and loss of beta-cells and pancreatic insulin in week 16. To identify the responsible gene variant(s), further congenic mice were generated and phenotyped, which resulted in a fragment of 3.3 Mbp that was sufficient to induce hyperglycemia. By combining transcriptome analysis and haplotype mapping, the number of putative responsible variant(s) was narrowed from initial 284 to 18 genes, including gene models and non-coding RNAs. Consideration of haplotype blocks reduced the number of candidate genes to four (Kti12,Osbpl9,Ttc39a, andCalr4) as potential T2D candidates as they display a differential expression in pancreatic islets and/or sequence variation. In conclusion, the integration of comparative analysis of multiple inbred populations such as haplotype mapping, transcriptomics, and sequence data substantially improved the mapping resolution of the diabetes QTLNidd/DBA. Future studies are necessary to understand the exact role of the different candidates in beta-cell function and their contribution in maintaining glycemic control. KW - type 2 diabetes KW - beta-cell loss KW - insulin KW - positional cloning KW - transcriptomics KW - haplotype Y1 - 2020 U6 - https://doi.org/10.3389/fgene.2020.567191 SN - 1664-8021 VL - 11 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Witzel, Katja A1 - Neugart, Susanne A1 - Ruppel, Silke A1 - Schreiner, Monika A1 - Wiesner, Melanie A1 - Baldermann, Susanne T1 - Recent progress in the use of 'omics technologies in brassicaceous vegetables JF - Frontiers in plant science N2 - Continuing advances in 'omics methodologies and instrumentation is enhancing the understanding of how plants cope with the dynamic nature of their growing environment. 'Omics platforms have been only recently extended to cover horticultural crop species. Many of the most widely cultivated vegetable crops belong to the genus Brassica: these include plants grown for their root (turnip, rutabaga/swede), their swollen stem base (kohlrabi), their leaves (cabbage, kale, pak choi) and their inflorescence (cauliflower, broccoli). Characterization at the genome, transcript, protein and metabolite levels has illustrated the complexity of the cellular response to a whole series of environmental stresses, including nutrient deficiency, pathogen attack, heavy metal toxicity, cold acclimation, and excessive and sub optimal irradiation. This review covers recent applications of omics technologies to the brassicaceous vegetables, and discusses future scenarios in achieving improvements in crop end-use quality. KW - genomics KW - transcriptomics KW - metabolomics KW - proteomics KW - crop KW - microbiomics Y1 - 2015 U6 - https://doi.org/10.3389/fpls.2015.00244 SN - 1664-462X VL - 6 PB - Frontiers Research Foundation CY - Lausanne ER -