Biology subjects

Fenyö, D.

Publications and source records attributed to Fenyö, D..

9 recordsLinked to original sources

bioRxiv2022

Proteogenomic Characterization Reveals Therapeutic Opportunities Related to Mitochondrial Function in Melanoma

The dynamics of more than 1900 mitochondrial proteins was explored through quantitative proteomics in 151 melanoma-related tissue samples of both surgical and autopsy origin. Dysregulation of mitochondrial pathways in primary tumors, metastases, and peritumoral tissues was correlated with age and survival of patients, as well as with tumor cell proliferation and the BRAF mutation status of the tumors. The outlined proteomic landscape confirmed the central role of a pathologically upregulated mitochondrial translation machinery and oxidative phosphorylation (OXPHOS) in the development, proliferation, and progression of melanomas. Our results from different melanoma cell lines confirmed our findings and we could document that treatments with selected OXPHOS inhibitors and antibiotics successfully impaired tumor cell proliferation. In addition, we provided proteomic evidence on the mechanism-of-action of the different treatments. These observations could contribute to the development of therapeutic approaches targeting the mitochondrial pathology in melanoma. TOC figure O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC="FIGDIR/small/513481v1_ufig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@11f21e2org.highwire.dtl.DTLVardef@e98c64org.highwire.dtl.DTLVardef@100145forg.highwire.dtl.DTLVardef@399284_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIMitochondrial proteome landscape outlined in 151 melanoma-related samples C_LIO_LIMitochondrial Translation and OXPHOS impact disease severity and survival C_LIO_LIBRAF V600E mutation correlates with upregulation of mitochondrial energy production C_LIO_LITargeting the mitochondrial OXPHOS and ribosomes impairs tumor cell proliferation C_LIO_LITherapeutic opportunities complementary to the standard of care are proposed C_LI In briefMitochondrial proteome profiling of melanomas reveals dysregulation in major metabolic pathways, suggesting a central role of the mitochondria within the development and progression of melanoma. Targeting mitochondrial pathways has the potential to impact the course of the disease, which provides opportunities for complementary drug interventions.

cancer biology↗

bioRxiv2022

PTK7 is a positive allosteric modulator of GPR133 (ADGRD1) signaling in GBM

GPR133 (ADGRD1), an adhesion G protein-coupled receptor, supports growth of glioblastoma, a brain malignancy. We demonstrated that GPR133 is intramolecularly cleaved, and that dissociation of its N-terminal and C-terminal fragments (NTF and CTF) at the plasma membrane correlates with increased receptor signaling. However, how the extracellular interactome of GPR133 in glioblastoma modulates signaling remains unknown. Here, we use affinity purification and mass spectrometry to identify extracellular binding partners of GPR133 in patient-derived glioblastoma cells. We show that the transmembrane protein PTK7 binds the GPR133 NTF and its expression in trans increases GPR133 signaling. This effect requires the intramolecular cleavage of GPR133 and PTK7s anchoring in the plasma membrane. The GPR133-PTK7 interaction facilitates orthosteric activation of GPR133 by soluble peptide mimicking the endogenous tethered Stachel agonist, suggesting PTK7 binding allosterically enhances accessibility of GPR133s orthosteric Stachel binding pocket. GPR133 and PTK7 are expressed in adjacent cells in glioblastoma, where their knockdown phenocopies each other. We propose that this novel ligand-receptor interaction is relevant to the pathogenesis of glioblastoma, as well as physiological processes in several tissues.

cell biology↗

bioRxiv2021

Proteogenomics Reveals how Metastatic Melanoma Modulates the Immune System to Allow Immune Evasion

Malignant melanoma (MM) develops from the melanocytes and in its advanced stage is the most aggressive type of skin cancer. Here we report a comprehensive analysis on a prospective cohort study, including non-tumor, primary and metastasis tissues (n=77) with the corresponding plasma samples (n=56) from patients with malignant melanoma. The tumors and surrounding tissues were characterized with a combination of high-throughput analyses including quantitative proteomics, phosphoproteomics, acetylomics, and whole exome sequencing (WES) combined with in-depth histopathology analysis. Melanoma cell proliferation highly correlates with dysregulation at the proteome, at the posttranslational- and at the transcriptome level. Some of the changes were also verified in the plasma proteome. The metabolic reprogramming in melanoma includes upregulation of the glycolysis and the oxidative phosphorylation, and an increase in glutamine consumption, while downregulated proteins involved in the degradation of amino acids, fatty acids, and the extracellular matrix (ECM) receptor interaction. The pathways most dysregulated in MM including the MAP kinases-, the PI3K-AKT signaling, and the calcium homeostasis, are among the most affected by mutations, thus, dysregulation in these pathways can be manifested as drivers in melanoma development and progression. The phosphoproteome analysis combined with target-based prediction mapped 75% of the human kinome. Melanoma cell proliferation was driven by two key factors: i) metabolic reprogramming leading to upregulation of the glycolysis and oxidative phosphorylation, supported by HIF-1 signaling pathway and mitochondrial translation; and ii) a dysregulation of the immune system response, which was mirrored by immune system processes in the plasma proteome. Regulation of the melanoma acetylome and expression of deacetylase enzymes discriminated between groups based on tissue origin and proliferation, indicating a way to guide the successful use of HDAC inhibitors in melanoma. The disease progression toward metastasis is driven by the downregulation of the immune system response, including MHC class I and II, which allows tumors to evade immune surveillance. Altogether, new evidence is provided at different molecular levels to allow improved understanding of the melanoma progression, ultimately contributing to better treatment strategies. TOC figure O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=157 SRC="FIGDIR/small/439245v1_ufig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@937db9org.highwire.dtl.DTLVardef@1230b57org.highwire.dtl.DTLVardef@1bd889eorg.highwire.dtl.DTLVardef@547d90_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2021

Nanobody Repertoires for Exposing Vulnerabilities of SARS-CoV-2

Despite the great promise of vaccines, the COVID-19 pandemic is ongoing and future serious outbreaks are highly likely, so that multi-pronged containment strategies will be required for many years. Nanobodies are the smallest naturally occurring single domain antigen binding proteins identified to date, possessing numerous properties advantageous to their production and use. We present a large repertoire of high affinity nanobodies against SARS-CoV-2 Spike protein with excellent kinetic and viral neutralization properties, which can be strongly enhanced with oligomerization. This repertoire samples the epitope landscape of the Spike ectodomain inside and outside the receptor binding domain, recognizing a multitude of distinct epitopes and revealing multiple neutralization targets of pseudoviruses and authentic SARS-CoV-2, including in primary human airway epithelial cells. Combinatorial nanobody mixtures show highly synergistic activities, and are resistant to mutational escape and emerging viral variants of concern. These nanobodies establish an exceptional resource for superior COVID-19 prophylactics and therapeutics.

biochemistry↗

bioRxiv2021

LINE-1 Retrotransposon expression in cancerous, epithelial and neuronal cells revealed by 5'-single cell RNA-Seq

LINE-1 retrotransposons are sequences capable of copying themselves to new genomic loci via an RNA intermediate. New studies implicate LINE-1 in a range of diseases, especially in the context of aging, but without an accurate understanding of where and when LINE-1 is expressed, a full accounting of its role in health and disease is not possible. We therefore developed a method - 5 scL1seq - that makes use of a widely available library preparation method (10x Genomics 5 single cell RNA-seq) to measure LINE-1 expression in tens of thousands of single cells. We recapitulated the known pattern of LINE-1 expression in tumors - present in cancer cells, absent from immune cells - and identified hitherto undescribed LINE-1 expression in human epithelial cells and mouse hippocampal neurons. In both cases, we saw a modest increase with age, supporting recent research connecting LINE-1 to age related diseases.

bioinformatics↗

bioRxiv2020

LINE-1 ORF1p RIP-seq reveals widespread association with p-body enriched mRNAs

BackgroundLong INterspersed Element-1 (LINE-1) is an autonomous retroelement able to "copy-and-paste" itself into new loci of the host genome through a process called retrotransposition. The LINE-1 bicistronic mRNA codes for two proteins, ORF1p, a nucleic acid chaperone, and ORF2p, a protein with endonuclease and reverse transcriptase activity. Both proteins bind LINE-1 mRNA in cis and are necessary for retrotransposition. While LINE-1 transcription is usually repressed in most healthy somatic cells through a plethora of mechanisms, ORF1p expression has been observed in nearly 50% of tumors, and new LINE-1 insertions have been documented in a similar fraction of tumors, including prostate cancer. ResultsHere, we utilized RNA ImmunoPrecipitation (RIP) and the L1EM analysis software to identify ORF1p bound RNA in prostate cancer cells. We identified LINE-1 loci that were expressed in androgen sensitive and androgen independent cells, that we show are representative of LINE-1 copies expressed in prostate cancer before and after treatment. In all androgen independent cells, we found higher levels of LINE-1 RNA, as well as unique expression patterns of LINE-1 loci. Interestingly, we observed that ORF1p bound many non-LINE-1 mRNA in all prostate cancer cell lines evaluated, and polyA RNA, and RNA localized in p-bodies were especially enriched. Furthermore, the expression levels of many of the identified ORF1p bound mRNAs also correlated with expression of LINE-1 RNA in prostate tumors from The Cancer Genome Atlas (TCGA). ConclusionOur results show a significant remodeling of LINE-1 loci expression in androgen independent cell lines when compared to parental androgen dependent cells, suggesting an evolution of LINE-1 expression during prostate cancer progression. Additionally, our finding that ORF1p bound a significant amount of non-LINE-1 mRNA, and that the enriched ORF1p bound mRNAs are also amplified in LINE-1 expressing TCGA prostate tumors, suggest that ORF1p may play a role in non-LINE-1 RNA processing and regulation of specific transcripts in prostate tumors.

cell biology↗

bioRxiv2020

Predicting Endometrial Cancer Subtypes and Molecular Features from Histopathology Images Using Multi-resolution Deep Learning Models

The determination of endometrial carcinoma histological subtypes, molecular subtypes, and mutation status is a critical diagnostic process that directly affects patients prognosis and treatment options. Compared to the histopathological approach, however, the availability of molecular subtyping is limited as it can only be accurately obtained by genomic sequencing, which may be cost prohibitive. Here, we implemented a customized multi-resolution deep convolutional neural network, Panoptes, that predicts not only the histological subtypes, but also molecular subtypes and 18 common gene mutations based on digitized H&E stained pathological images. The model achieved high accuracy and generalized well on independent datasets. Our results suggest that Panoptes has potential clinical application of helping pathologists determine molecular subtypes and mutations of endometrial carcinoma without sequencing. SignificanceRecently, molecular subtyping and mutation status are increasingly utilized in clinical practice as they offer better-informed prognosis and the possibility of individualized therapies for endometrial carcinoma patients. Taking advantage of the multi-resolution nature of the whole slide digital histopathology images, our Panoptes models integrate features of different magnification and make accurate predictions of histological subtypes, molecular subtypes, and key mutations in much faster workflows compared to conventional sequencing-based analyses. Feature extraction and visualization revealed that the model relied on human-interpretable patterns. Overall, our multi-resolution deep learning model is capable of assisting pathologists determine molecular subtypes of endometrial carcinoma, which can potentially accelerate diagnosis process.

bioinformatics↗

bioRxiv2020

Predicting and Visualizing STK11 Mutation in Lung Adenocarcinoma Histopathology Slides Using Deep Learning

Studies have shown that STK11 mutation plays a critical role in affecting the lung adenocarcinoma (LUAD) tumor immune environment. By training an Inception-Resnet-v2 deep convolutional neural network model, we were able to classify STK11-mutated and wild type LUAD tumor histopathology images with a promising accuracy (per slide AUROC=0.795). Dimensional reduction of the activation maps before the output layer of the test set images revealed that fewer immune cells were accumulated around cancer cells in STK11-mutation cases. Our study demonstrated that deep convolutional network model can automatically identify STK11 mutations based on histopathology slides and confirmed that the immune cell density was the main feature used by the model to distinguish STK11-mutated cases.

bioinformatics↗

bioRxiv2018

The ULK1-FBXW5-SEC23B nexus controls autophagy

In response to nutrient deprivation, the cell needs to mobilize an extensive amount of membrane to form and grow the autophagosome, allowing the progression of autophagy. By providing membranes and a source for LC3 lipidation, COPII (Coat Protein Complex II) localizes to the endoplasmic reticulum (ER)-Golgi intermediate compartment (ERGIC) and promotes autophagosome biogenesis. However, the molecular mechanisms that, in response to starvation, divert COPII from the secretory pathway to the autophagic pathway are largely unknown. Here, we show that the F-box protein FBXW5 targets SEC23B, a component of COPII, for proteasomal degradation and that this event limits the autophagic flux in the presence of nutrients. In response to starvation, ULK1 phosphorylates SEC23B on Serine 186, preventing the interaction of SEC23B with FBXW5 and, therefore, inhibiting its degradation. Phosphorylated and stabilized SEC23B associates with SEC24A and SEC24B, but not SEC24C and SEC24D, and they re-localize to the ERGIC, promoting autophagic flux. Induction of autophagy and localization of both SEC23B and SEC24B to the ERGIC in response to nutrient deprivation are significantly reduced in SEC23B(S186A) knock-in cells. We propose that, in the presence of nutrients, FBXW5 limits COPII-mediated autophagosome biogenesis. Inhibition of this event by ULK1 ensures efficient execution of the autophagic cascade in response to nutrient starvation.

cell biology↗