27 results on '"Loayza-Puch, F."'
Search Results
2. Gene and protein sequence features augment HLA class I ligand predictions.
- Author
-
Bresser K, Nicolet BP, Jeko A, Wu W, Loayza-Puch F, Agami R, Heck AJR, Wolkers MC, and Schumacher TN
- Published
- 2024
- Full Text
- View/download PDF
3. DNMT and HDAC inhibition induces immunogenic neoantigens from human endogenous retroviral element-derived transcripts.
- Author
-
Goyal A, Bauer J, Hey J, Papageorgiou DN, Stepanova E, Daskalakis M, Scheid J, Dubbelaar M, Klimovich B, Schwarz D, Märklin M, Roerden M, Lin YY, Ma T, Mücke O, Rammensee HG, Lübbert M, Loayza-Puch F, Krijgsveld J, Walz JS, and Plass C
- Subjects
- Humans, Histone Deacetylase Inhibitors pharmacology, T-Lymphocytes, Histocompatibility Antigens Class I, Endogenous Retroviruses genetics, Neoplasms
- Abstract
Immunotherapies targeting cancer-specific neoantigens have revolutionized the treatment of cancer patients. Recent evidence suggests that epigenetic therapies synergize with immunotherapies, mediated by the de-repression of endogenous retroviral element (ERV)-encoded promoters, and the initiation of transcription. Here, we use deep RNA sequencing from cancer cell lines treated with DNA methyltransferase inhibitor (DNMTi) and/or Histone deacetylase inhibitor (HDACi), to assemble a de novo transcriptome and identify several thousand ERV-derived, treatment-induced novel polyadenylated transcripts (TINPATs). Using immunopeptidomics, we demonstrate the human leukocyte antigen (HLA) presentation of 45 spectra-validated treatment-induced neopeptides (t-neopeptides) arising from TINPATs. We illustrate the potential of the identified t-neopeptides to elicit a T-cell response to effectively target cancer cells. We further verify the presence of t-neopeptides in AML patient samples after in vivo treatment with the DNMT inhibitor Decitabine. Our findings highlight the potential of ERV-derived neoantigens in epigenetic and immune therapies., (© 2023. Springer Nature Limited.)
- Published
- 2023
- Full Text
- View/download PDF
4. Breast Cancer Metastatic Progression Requires mRNA Posttranscriptional Suppression.
- Author
-
Amaya Ramirez CC and Loayza-Puch F
- Abstract
Cancer cell survival is highly dependent on its metabolic reprogramming, which supports not only cell growth but also confers to the tumor cells characteristics to initiate migration and colonization. Among the different mechanisms that are involved, translational control plays a significant role in oncogenesis; however, its impact on cancer progression still remains poorly understood. A study by Navickas and colleagues revealed that the RNA-binding protein heterogeneous nuclear ribonucleoprotein C (HNRNPC) functions as a translational regulator, and its downregulation in highly metastatic cells leads to the lengthening of 3' untranslated regions in HNRNPC-bound mRNAs, resulting in translational repression mediated by the AGO-miRNA RNA-induced silencing complex., (©2023 American Association for Cancer Research.)
- Published
- 2023
- Full Text
- View/download PDF
5. An adverse tumor-protective effect of IDO1 inhibition.
- Author
-
Kenski JCN, Huang X, Vredevoogd DW, de Bruijn B, Traets JJH, Ibáñez-Molero S, Schieven SM, van Vliet A, Krijgsman O, Kuilman T, Pozniak J, Loayza-Puch F, Terry AM, Müller J, Logtenberg MEW, de Bruijn M, Levy P, Körner PR, Goding CR, Schumacher TN, Marine JC, Agami R, and Peeper DS
- Subjects
- Humans, Interferon-gamma metabolism, T-Lymphocytes metabolism, Indoleamine-Pyrrole 2,3,-Dioxygenase genetics, Tryptophan, Melanoma pathology
- Abstract
By restoring tryptophan, indoleamine 2,3-dioxygenase 1 (IDO1) inhibitors aim to reactivate anti-tumor T cells. However, a phase III trial assessing their clinical benefit failed, prompting us to revisit the role of IDO1 in tumor cells under T cell attack. We show here that IDO1 inhibition leads to an adverse protection of melanoma cells to T cell-derived interferon-gamma (IFNγ). RNA sequencing and ribosome profiling shows that IFNγ shuts down general protein translation, which is reversed by IDO1 inhibition. Impaired translation is accompanied by an amino acid deprivation-dependent stress response driving activating transcription factor-4 (ATF4)
high /microphtalmia-associated transcription factor (MITF)low transcriptomic signatures, also in patient melanomas. Single-cell sequencing analysis reveals that MITF downregulation upon immune checkpoint blockade treatment predicts improved patient outcome. Conversely, MITF restoration in cultured melanoma cells causes T cell resistance. These results highlight the critical role of tryptophan and MITF in the melanoma response to T cell-derived IFNγ and uncover an unexpected negative consequence of IDO1 inhibition., Competing Interests: Declaration of interests D.S.P. is co-founder, shareholder, and advisor of Immagene, which is unrelated to this study., (Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved.)- Published
- 2023
- Full Text
- View/download PDF
6. Alternative cleavage and polyadenylation generates downstream uncapped RNA isoforms with translation potential.
- Author
-
Malka Y, Alkan F, Ju S, Körner PR, Pataskar A, Shulman E, Loayza-Puch F, Champagne J, Wenzel C, Faller WJ, Elkon R, Lee C, and Agami R
- Subjects
- 5' Untranslated Regions, 3' Untranslated Regions genetics, Proto-Oncogene Proteins c-bcl-2 genetics, Exonucleases genetics, Polyadenylation, RNA Isoforms genetics
- Abstract
The use of alternative promoters, splicing, and cleavage and polyadenylation (APA) generates mRNA isoforms that expand the diversity and complexity of the transcriptome. Here, we uncovered thousands of previously undescribed 5' uncapped and polyadenylated transcripts (5' UPTs). We show that these transcripts resist exonucleases due to a highly structured RNA and N6-methyladenosine modification at their 5' termini. 5' UPTs appear downstream of APA sites within their host genes and are induced upon APA activation. Strong enrichment in polysomal RNA fractions indicates 5' UPT translational potential. Indeed, APA promotes downstream translation initiation, non-canonical protein output, and consistent changes to peptide presentation at the cell surface. Lastly, we demonstrate the biological importance of 5' UPTs using Bcl2, a prominent anti-apoptotic gene whose entire coding sequence is a 5' UPT generated from 5' UTR-embedded APA sites. Thus, APA is not only accountable for terminating transcripts, but also for generating downstream uncapped RNAs with translation potential and biological impact., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)
- Published
- 2022
- Full Text
- View/download PDF
7. Roles of eIF5A in the immunosurveillance of cellular senescence.
- Author
-
Jiang X and Loayza-Puch F
- Subjects
- Cellular Senescence
- Abstract
Competing Interests: No potential conflicts of interest are disclosed.
- Published
- 2022
- Full Text
- View/download PDF
8. Author Correction: Cancer-associated fibroblasts require proline synthesis by PYCR1 for the deposition of pro-tumorigenic extracellular matrix.
- Author
-
Kay EJ, Paterson K, Riera-Domingo C, Sumpton D, Däbritz JHM, Tardito S, Boldrini C, Hernandez-Fernaud JR, Athineos D, Dhayade S, Stepanova E, Gjerga E, Neilson LJ, Lilla S, Hedley A, Koulouras G, McGregor G, Jamieson C, Johnson RM, Park M, Kirschner K, Miller C, Kamphorst JJ, Loayza-Puch F, Saez-Rodriguez J, Mazzone M, Blyth K, Zagnoni M, and Zanivan S
- Published
- 2022
- Full Text
- View/download PDF
9. Cancer-associated fibroblasts require proline synthesis by PYCR1 for the deposition of pro-tumorigenic extracellular matrix.
- Author
-
Kay EJ, Paterson K, Riera-Domingo C, Sumpton D, Däbritz JHM, Tardito S, Boldrini C, Hernandez-Fernaud JR, Athineos D, Dhayade S, Stepanova E, Gjerga E, Neilson LJ, Lilla S, Hedley A, Koulouras G, McGregor G, Jamieson C, Johnson RM, Park M, Kirschner K, Miller C, Kamphorst JJ, Loayza-Puch F, Saez-Rodriguez J, Mazzone M, Blyth K, Zagnoni M, and Zanivan S
- Subjects
- Carcinogenesis metabolism, Carcinogenesis pathology, Collagen metabolism, Extracellular Matrix metabolism, Female, Glutamine metabolism, Humans, Proline, delta-1-Pyrroline-5-Carboxylate Reductase, Breast Neoplasms metabolism, Cancer-Associated Fibroblasts metabolism, Cancer-Associated Fibroblasts pathology, Pyrroline Carboxylate Reductases metabolism
- Abstract
Elevated production of collagen-rich extracellular matrix is a hallmark of cancer-associated fibroblasts (CAFs) and a central driver of cancer aggressiveness. Here we find that proline, a highly abundant amino acid in collagen proteins, is newly synthesized from glutamine in CAFs to make tumour collagen in breast cancer xenografts. PYCR1 is a key enzyme for proline synthesis and highly expressed in the stroma of breast cancer patients and in CAFs. Reducing PYCR1 levels in CAFs is sufficient to reduce tumour collagen production, tumour growth and metastatic spread in vivo and cancer cell proliferation in vitro. Both collagen and glutamine-derived proline synthesis in CAFs are epigenetically upregulated by increased pyruvate dehydrogenase-derived acetyl-CoA levels. PYCR1 is a cancer cell vulnerability and potential target for therapy; therefore, our work provides evidence that targeting PYCR1 may have the additional benefit of halting the production of a pro-tumorigenic extracellular matrix. Our work unveils new roles for CAF metabolism to support pro-tumorigenic collagen production., (© 2022. The Author(s).)
- Published
- 2022
- Full Text
- View/download PDF
10. Proteomic patterns associated with response to breast cancer neoadjuvant treatment.
- Author
-
Shenoy A, Belugali Nataraj N, Perry G, Loayza Puch F, Nagel R, Marin I, Balint N, Bossel N, Pavlovsky A, Barshack I, Kaufman B, Agami R, Yarden Y, Dadiani M, and Geiger T
- Subjects
- Breast Neoplasms pathology, CRISPR-Cas Systems genetics, Cell Line, Tumor, Cell Proliferation, Citric Acid Cycle, Female, Gene Regulatory Networks, Humans, Neoplasm Invasiveness, Neoplasm Proteins metabolism, Prognosis, Protein Interaction Maps, Pyrroline Carboxylate Reductases metabolism, Recurrence, Survival Analysis, delta-1-Pyrroline-5-Carboxylate Reductase, Breast Neoplasms metabolism, Breast Neoplasms therapy, Neoadjuvant Therapy, Proteomics
- Abstract
Tumor relapse as a consequence of chemotherapy resistance is a major clinical challenge in advanced stage breast tumors. To identify processes associated with poor clinical outcome, we took a mass spectrometry-based proteomic approach and analyzed a breast cancer cohort of 113 formalin-fixed paraffin-embedded samples. Proteomic profiling of matched tumors before and after chemotherapy, and tumor-adjacent normal tissue, all from the same patients, allowed us to define eight patterns of protein level changes, two of which correlate to better chemotherapy response. Supervised analysis identified two proteins of proline biosynthesis pathway, PYCR1 and ALDH18A1, that were significantly associated with resistance to treatment based on pattern dominance. Weighted gene correlation network analysis of post-treatment samples revealed that these proteins are associated with tumor relapse and affect patient survival. Functional analysis showed that knockdown of PYCR1 reduced invasion and migration capabilities of breast cancer cell lines. PYCR1 knockout significantly reduced tumor burden and increased drug sensitivity of orthotopically injected ER-positive tumor in vivo, thus emphasizing the role of PYCR1 in resistance to chemotherapy., (© 2020 The Authors. Published under the terms of the CC BY 4.0 license.)
- Published
- 2020
- Full Text
- View/download PDF
11. A fragment-like approach to PYCR1 inhibition.
- Author
-
Milne K, Sun J, Zaal EA, Mowat J, Celie PHN, Fish A, Berkers CR, Forlani G, Loayza-Puch F, Jamieson C, and Agami R
- Subjects
- Antineoplastic Agents chemical synthesis, Antineoplastic Agents chemistry, Cell Line, Tumor, Cell Proliferation drug effects, Dose-Response Relationship, Drug, Drug Screening Assays, Antitumor, Enzyme Inhibitors chemical synthesis, Enzyme Inhibitors chemistry, Humans, Molecular Structure, Pargyline chemical synthesis, Pargyline chemistry, Pyrroline Carboxylate Reductases metabolism, Small Molecule Libraries chemical synthesis, Small Molecule Libraries chemistry, Structure-Activity Relationship, delta-1-Pyrroline-5-Carboxylate Reductase, Antineoplastic Agents pharmacology, Enzyme Inhibitors pharmacology, Pargyline pharmacology, Pyrroline Carboxylate Reductases antagonists & inhibitors, Small Molecule Libraries pharmacology
- Abstract
Pyrroline-5-carboxylate reductase 1 (PYCR1) is the final enzyme involved in the biosynthesis of proline and has been found to be upregulated in various forms of cancer. Due to the role of proline in maintaining the redox balance of cells and preventing apoptosis, PYCR1 is emerging as an attractive oncology target. Previous PYCR1 knockout studies led to a reduction in tumor growth. Accordingly, a small molecule inhibitor of PYCR1 could lead to new treatments for cancer, and a focused screening effort identified pargyline as a fragment-like hit. We report the design and synthesis of the first tool compounds as PYCR1 inhibitors, derived from pargyline, which were assayed to assess their ability to attenuate the production of proline. Structural activity studies have revealed the key determinants of activity, with the most potent compound (4) showing improved activity in vitro in enzyme (IC
50 = 8.8 µM) and pathway relevant effects in cell-based assays., (Copyright © 2019 Elsevier Ltd. All rights reserved.)- Published
- 2019
- Full Text
- View/download PDF
12. Translatome analysis reveals altered serine and glycine metabolism in T-cell acute lymphoblastic leukemia cells.
- Author
-
Kampen KR, Fancello L, Girardi T, Rinaldi G, Planque M, Sulima SO, Loayza-Puch F, Verbelen B, Vereecke S, Verbeeck J, Op de Beeck J, Royaert J, Vermeersch P, Cassiman D, Cools J, Agami R, Fiers M, Fendt SM, and De Keersmaecker K
- Subjects
- Animals, Cell Line, Gene Expression Profiling, Mice, Phosphoric Monoester Hydrolases, Polyribosomes genetics, Polyribosomes metabolism, Protein Biosynthesis, RNA, Messenger genetics, Ribosomal Protein L10, Ribosomal Proteins genetics, Ribosomal Proteins metabolism, Ribosomes metabolism, Sequence Analysis, RNA, Glycine metabolism, Mutation, Precursor T-Cell Lymphoblastic Leukemia-Lymphoma genetics, Precursor T-Cell Lymphoblastic Leukemia-Lymphoma metabolism, Serine metabolism
- Abstract
Somatic ribosomal protein mutations have recently been described in cancer, yet their impact on cellular transcription and translation remains poorly understood. Here, we integrate mRNA sequencing, ribosome footprinting, polysomal RNA sequencing and mass spectrometry datasets from a mouse lymphoid cell model to characterize the T-cell acute lymphoblastic leukemia (T-ALL) associated ribosomal RPL10 R98S mutation. Surprisingly, RPL10 R98S induces changes in protein levels primarily through transcriptional rather than translation efficiency changes. Phosphoserine phosphatase (PSPH), encoding a key serine biosynthesis enzyme, was the only gene with elevated transcription and translation leading to protein overexpression. PSPH upregulation is a general phenomenon in T-ALL patient samples, associated with elevated serine and glycine levels in xenograft mice. Reduction of PSPH expression suppresses proliferation of T-ALL cell lines and their capacity to expand in mice. We identify ribosomal mutation driven induction of serine biosynthesis and provide evidence supporting dependence of T-ALL cells on PSPH.
- Published
- 2019
- Full Text
- View/download PDF
13. LncRNA-OIS1 regulates DPP4 activation to modulate senescence induced by RAS.
- Author
-
Li L, van Breugel PC, Loayza-Puch F, Ugalde AP, Korkmaz G, Messika-Gold N, Han R, Lopes R, Barbera EP, Teunissen H, de Wit E, Soares RJ, Nielsen BS, Holmstrøm K, Martínez-Herrera DJ, Huarte M, Louloupi A, Drost J, Elkon R, and Agami R
- Subjects
- Dipeptidyl Peptidase 4 metabolism, Gene Expression, Genes, ras, Genome, HEK293 Cells, Humans, Neoplasms genetics, Neoplasms metabolism, Cellular Senescence genetics, Dipeptidyl Peptidase 4 genetics, RNA, Long Noncoding metabolism
- Abstract
Oncogene-induced senescence (OIS), provoked in response to oncogenic activation, is considered an important tumor suppressor mechanism. Long non-coding RNAs (lncRNAs) are transcripts longer than 200 nt without a protein-coding capacity. Functional studies showed that deregulated lncRNA expression promote tumorigenesis and metastasis and that lncRNAs may exhibit tumor-suppressive and oncogenic function. Here, we first identified lncRNAs that were differentially expressed between senescent and non-senescent human fibroblast cells. Using RNA interference, we performed a loss-function screen targeting the differentially expressed lncRNAs, and identified lncRNA-OIS1 (lncRNA#32, AC008063.3 or ENSG00000233397) as a lncRNA required for OIS. Knockdown of lncRNA-OIS1 triggered bypass of senescence, higher proliferation rate, lower abundance of the cell-cycle inhibitor CDKN1A and high expression of cell-cycle-associated genes. Subcellular inspection of lncRNA-OIS1 indicated nuclear and cytosolic localization in both normal culture conditions as well as following oncogene induction. Interestingly, silencing lncRNA-OIS1 diminished the senescent-associated induction of a nearby gene (Dipeptidyl Peptidase 4, DPP4) with established role in tumor suppression. Intriguingly, similar to lncRNA-OIS1, silencing DPP4 caused senescence bypass, and ectopic expression of DPP4 in lncRNA-OIS1 knockdown cells restored the senescent phenotype. Thus, our data indicate that lncRNA-OIS1 links oncogenic induction and senescence with the activation of the tumor suppressor DPP4.
- Published
- 2018
- Full Text
- View/download PDF
14. FcαRI co-stimulation converts human intestinal CD103 + dendritic cells into pro-inflammatory cells through glycolytic reprogramming.
- Author
-
Hansen IS, Krabbendam L, Bernink JH, Loayza-Puch F, Hoepel W, van Burgsteden JA, Kuijper EC, Buskens CJ, Bemelman WA, Zaat SAJ, Agami R, Vidarsson G, van den Brink GR, de Jong EC, Wildenberg ME, Baeten DLP, Everts B, and den Dunnen J
- Subjects
- Cellular Reprogramming, Glycolysis, Humans, Immunoglobulin A immunology, Interleukin-1beta immunology, Interleukin-23 immunology, Intestines cytology, Th17 Cells immunology, Antigens, CD immunology, Dendritic Cells immunology, Integrin alpha Chains immunology, Intestines immunology, Receptors, Fc immunology
- Abstract
CD103
+ dendritic cells (DC) are crucial for regulation of intestinal tolerance in humans. However, upon infection of the lamina propria this tolerogenic response is converted to an inflammatory response. Here we show that immunoglobulin A (IgA) immune complexes (IgA-IC), which are present after bacterial infection of the lamina propria, are important for the induction of inflammation by the human CD103+ SIRPα+ DC subset. IgA-IC, by recognition through FcαRI, selectively amplify the production of proinflammatory cytokines TNF, IL-1β and IL-23 by human CD103+ DCs. These cells then enhance inflammation by promoting Th17 responses and activating human intestinal innate lymphoid cells 3. Moreover, FcαRI-induced cytokine production is orchestrated via upregulation of cytokine translation and caspase-1 activation, which is dependent on glycolytic reprogramming mediated by kinases Syk, PI3K and TBK1-IKKε. Our data suggest that the formation of IgA-IC in the human intestine provides an environmental cue for the conversion of a tolerogenic to an inflammatory response.- Published
- 2018
- Full Text
- View/download PDF
15. Using mitoribosomal profiling to investigate human mitochondrial translation.
- Author
-
Gao F, Wesolowska M, Agami R, Rooijers K, Loayza-Puch F, Lawless C, Lightowlers RN, and Chrzanowska-Lightowlers ZMA
- Abstract
Background : Gene expression in human mitochondria has various idiosyncratic features. One of these was recently revealed as the unprecedented recruitment of a mitochondrially-encoded tRNA as a structural component of the large mitoribosomal subunit. In porcine particles this is mt-tRNA
Phe whilst in humans it is mt-tRNAVal . We have previously shown that when a mutation in mt-tRNAVal causes very low steady state levels, there is preferential recruitment of mt-tRNAPhe . We have investigated whether this altered mitoribosome affects intra-organellar protein synthesis. Methods : By using mitoribosomal profiling we have revealed aspects of mitoribosome behaviour with its template mt-mRNA under both normal conditions as well as those where the mitoribosome has incorporated mt-tRNAPhe . Results : Analysis of the mitoribosome residency on transcripts under control conditions reveals that although mitochondria employ only 22 mt-tRNAs for protein synthesis, the use of non-canonical wobble base pairs at codon position 3 does not cause any measurable difference in mitoribosome occupancy irrespective of the codon. Comparison of the profile of aberrant mt-tRNAPhe containing mitoribosomes with those of controls that integrate mt-tRNAVal revealed that the impaired translation seen in the latter was not due to stalling on triplets encoding either of these amino acids. The alterations in mitoribosome interactions with start codons was not directly attributable to the either the use of non-cognate initiation codons or the presence or absence of 5' leader sequences, except in the two bicistronic RNA units, RNA7 and RNA14 where the initiation sites are internal. Conclusions : These data report the power of mitoribosomal profiling in helping to understand the subtleties of mammalian mitochondrial protein synthesis. Analysis of profiles from the mutant mt-tRNAVal cell line suggest that despite mt-tRNAPhe being preferred in the porcine mitoribosome, its integration into the human counterpart results in a suboptimal structure that modifies its interaction with mt-mRNAs., Competing Interests: No competing interests were disclosed.- Published
- 2017
- Full Text
- View/download PDF
16. Transcription Impacts the Efficiency of mRNA Translation via Co-transcriptional N6-adenosine Methylation.
- Author
-
Slobodin B, Han R, Calderone V, Vrielink JAFO, Loayza-Puch F, Elkon R, and Agami R
- Subjects
- Adenosine metabolism, Humans, Methylation, Peptide Chain Initiation, Translational, RNA Polymerase II metabolism, TATA Box, Adenosine analogs & derivatives, Gene Expression Regulation, Protein Biosynthesis, RNA Processing, Post-Transcriptional, RNA, Messenger metabolism, Transcription, Genetic
- Abstract
Transcription and translation are two main pillars of gene expression. Due to the different timings, spots of action, and mechanisms of regulation, these processes are mainly regarded as distinct and generally uncoupled, despite serving a common purpose. Here, we sought for a possible connection between transcription and translation. Employing an unbiased screen of multiple human promoters, we identified a positive effect of TATA box on translation and a general coupling between mRNA expression and translational efficiency. Using a CRISPR-Cas9-mediated approach, genome-wide analyses, and in vitro experiments, we show that the rate of transcription regulates the efficiency of translation. Furthermore, we demonstrate that m
6 A modification of mRNAs is co-transcriptional and depends upon the dynamics of the transcribing RNAPII. Suboptimal transcription rates lead to elevated m6 A content, which may result in reduced translation. This study uncovers a general and widespread link between transcription and translation that is governed by epigenetic modification of mRNAs., (Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.)- Published
- 2017
- Full Text
- View/download PDF
17. TGFβ1-induced leucine limitation uncovered by differential ribosome codon reading.
- Author
-
Loayza-Puch F, Rooijers K, Zijlstra J, Moumbeini B, Zaal EA, Oude Vrielink JF, Lopes R, Ugalde AP, Berkers CR, and Agami R
- Subjects
- Breast Neoplasms genetics, Breast Neoplasms metabolism, Cell Line, Tumor, Female, Fusion Regulatory Protein 1, Heavy Chain genetics, Fusion Regulatory Protein 1, Heavy Chain metabolism, Gene Expression Regulation, Neoplastic drug effects, Humans, Signal Transduction, Transforming Growth Factor beta1 pharmacology, Codon, Leucine genetics, Leucine metabolism, Protein Biosynthesis drug effects, Ribosomes metabolism, Transforming Growth Factor beta1 metabolism
- Abstract
Cancer cells modulate their metabolic networks to support cell proliferation and a higher demand of building blocks. These changes may restrict the availability of certain amino acids for protein synthesis, which can be utilized for cancer therapy. However, little is known about the amino acid demand changes occurring during aggressive and invasive stages of cancer. Recently, we developed diricore, an approach based on ribosome profiling that can uncover amino acid limitations. Here, we applied diricore to a cellular model in which epithelial breast cells respond rapidly to TGFβ1, a cytokine essential for cancer progression and metastasis, and uncovered shortage of leucine. Further analyses indicated that TGFβ1 treatment of human breast epithelial cells reduces the expression of SLC3A2, a subunit of the leucine transporter, which diminishes leucine uptake and inhibits cell proliferation. Thus, we identified a specific amino acid limitation associated with the TGFβ1 response, a vulnerability that might be associated with aggressiveness in cancer., (© 2017 The Authors.)
- Published
- 2017
- Full Text
- View/download PDF
18. Monitoring amino acid deficiencies in cancer.
- Author
-
Loayza-Puch F and Agami R
- Subjects
- Amino Acids, Humans, Neoplasms
- Published
- 2016
- Full Text
- View/download PDF
19. BRCA1185delAG tumors may acquire therapy resistance through expression of RING-less BRCA1.
- Author
-
Drost R, Dhillon KK, van der Gulden H, van der Heijden I, Brandsma I, Cruz C, Chondronasiou D, Castroviejo-Bermejo M, Boon U, Schut E, van der Burg E, Wientjens E, Pieterse M, Klijn C, Klarenbeek S, Loayza-Puch F, Elkon R, van Deemter L, Rottenberg S, van de Ven M, Dekkers DH, Demmers JA, van Gent DC, Agami R, Balmaña J, Serra V, Taniguchi T, Bouwman P, and Jonkers J
- Subjects
- Alleles, Animals, Antineoplastic Agents pharmacology, Cisplatin pharmacology, Crosses, Genetic, DNA Damage, Drug Screening Assays, Antitumor, Female, Founder Effect, Frameshift Mutation, Genetic Engineering, Humans, Male, Mammary Neoplasms, Animal drug therapy, Mice, Mutation, Neoplasm Transplantation, Phthalazines pharmacology, Piperazines pharmacology, Poly(ADP-ribose) Polymerases metabolism, Recombination, Genetic, BRCA1 Protein genetics, Breast Neoplasms genetics, Drug Resistance, Neoplasm, Gene Deletion, Mammary Neoplasms, Animal genetics
- Abstract
Heterozygous germline mutations in breast cancer 1 (BRCA1) strongly predispose women to breast cancer. BRCA1 plays an important role in DNA double-strand break (DSB) repair via homologous recombination (HR), which is important for tumor suppression. Although BRCA1-deficient cells are highly sensitive to treatment with DSB-inducing agents through their HR deficiency (HRD), BRCA1-associated tumors display heterogeneous responses to platinum drugs and poly(ADP-ribose) polymerase (PARP) inhibitors in clinical trials. It is unclear whether all pathogenic BRCA1 mutations have similar effects on the response to therapy. Here, we have investigated mammary tumorigenesis and therapy sensitivity in mice carrying the Brca1185stop and Brca15382stop alleles, which respectively mimic the 2 most common BRCA1 founder mutations, BRCA1185delAG and BRCA15382insC. Both the Brca1185stop and Brca15382stop mutations predisposed animals to mammary tumors, but Brca1185stop tumors responded markedly worse to HRD-targeted therapy than did Brca15382stop tumors. Mice expressing Brca1185stop mutations also developed therapy resistance more rapidly than did mice expressing Brca15382stop. We determined that both murine Brca1185stop tumors and human BRCA1185delAG breast cancer cells expressed a really interesting new gene domain-less (RING-less) BRCA1 protein that mediated resistance to HRD-targeted therapies. Together, these results suggest that expression of RING-less BRCA1 may serve as a marker to predict poor response to DSB-inducing therapy in human cancer patients.
- Published
- 2016
- Full Text
- View/download PDF
20. Tumour-specific proline vulnerability uncovered by differential ribosome codon reading.
- Author
-
Loayza-Puch F, Rooijers K, Buil LC, Zijlstra J, Oude Vrielink JF, Lopes R, Ugalde AP, van Breugel P, Hofland I, Wesseling J, van Tellingen O, Bex A, and Agami R
- Subjects
- Animals, Asparaginase metabolism, Asparagine genetics, Asparagine metabolism, Aspartate-Ammonia Ligase metabolism, Breast Neoplasms pathology, Carcinoma, Ductal, Breast metabolism, Carcinoma, Ductal, Breast pathology, Cell Line, Tumor, Cell Proliferation, Female, Gene Knockout Techniques, Humans, Kidney Neoplasms pathology, Mice, Proline biosynthesis, Proline deficiency, Pyrroline Carboxylate Reductases deficiency, Pyrroline Carboxylate Reductases genetics, Pyrroline Carboxylate Reductases metabolism, delta-1-Pyrroline-5-Carboxylate Reductase, Breast Neoplasms metabolism, Codon genetics, Kidney Neoplasms metabolism, Proline metabolism, Protein Biosynthesis genetics, Ribosomes metabolism
- Abstract
Tumour growth and metabolic adaptation may restrict the availability of certain amino acids for protein synthesis. It has recently been shown that certain types of cancer cells depend on glycine, glutamine, leucine and serine metabolism to proliferate and survive. In addition, successful therapies using L-asparaginase-induced asparagine deprivation have been developed for acute lymphoblastic leukaemia. However, a tailored detection system for measuring restrictive amino acids in each tumour is currently not available. Here we harness ribosome profiling for sensing restrictive amino acids, and develop diricore, a procedure for differential ribosome measurements of codon reading. We first demonstrate the functionality and constraints of diricore using metabolic inhibitors and nutrient deprivation assays. Notably, treatment with L-asparaginase elicited both specific diricore signals at asparagine codons and high levels of asparagine synthetase (ASNS). We then applied diricore to kidney cancer and discover signals indicating restrictive proline. As for asparagine, this observation was linked to high levels of PYCR1, a key enzyme in proline production, suggesting a compensatory mechanism allowing tumour expansion. Indeed, PYCR1 is induced by shortage of proline precursors, and its suppression attenuated kidney cancer cell proliferation when proline was limiting. High PYCR1 is frequently observed in invasive breast carcinoma. In an in vivo model system of this tumour, we also uncover signals indicating restrictive proline. We further show that CRISPR-mediated knockout of PYCR1 impedes tumorigenic growth in this system. Thus, diricore has the potential to reveal unknown amino acid deficiencies, vulnerabilities that can be used to target key metabolic pathways for cancer treatment.
- Published
- 2016
- Full Text
- View/download PDF
21. Myc coordinates transcription and translation to enhance transformation and suppress invasiveness.
- Author
-
Elkon R, Loayza-Puch F, Korkmaz G, Lopes R, van Breugel PC, Bleijerveld OB, Altelaar AF, Wolf E, Lorenzin F, Eilers M, and Agami R
- Subjects
- Apoptosis, Cell Line, Tumor, Cell Movement genetics, Cell Proliferation, Gene Expression Profiling, Genes, myc, Humans, Protein Biosynthesis, Signal Transduction, TOR Serine-Threonine Kinases genetics, TOR Serine-Threonine Kinases metabolism, Cell Transformation, Neoplastic genetics, Gene Expression Regulation, Neoplastic, Neoplasm Invasiveness, Neoplasm Metastasis genetics, Neoplasms genetics, Proto-Oncogene Proteins c-myc genetics, Proto-Oncogene Proteins c-myc metabolism
- Abstract
c-Myc is one of the major human proto-oncogenes and is often associated with tumor aggression and poor clinical outcome. Paradoxically, Myc was also reported as a suppressor of cell motility, invasiveness, and metastasis. Among the direct targets of Myc are many components of the protein synthesis machinery whose induction results in an overall increase in protein synthesis that empowers tumor cell growth. At present, it is largely unknown whether beyond the global enhancement of protein synthesis, Myc activation results in translation modulation of specific genes. Here, we measured Myc-induced global changes in gene expression at the transcription, translation, and protein levels and uncovered extensive transcript-specific regulation of protein translation. Particularly, we detected a broad coordination between regulation of transcription and translation upon modulation of Myc activity and showed the connection of these responses to mTOR signaling to enhance oncogenic transformation and to the TGFβ pathway to modulate cell migration and invasiveness. Our results elucidate novel facets of Myc-induced cellular responses and provide a more comprehensive view of the consequences of its activation in cancer cells., (© 2015 The Netherlands Cancer Institute. Published under the terms of the CC BY NC ND 4.0 license.)
- Published
- 2015
- Full Text
- View/download PDF
22. Exposure to arginine analog canavanine induces aberrant mitochondrial translation products, mitoribosome stalling, and instability of the mitochondrial proteome.
- Author
-
Konovalova S, Hilander T, Loayza-Puch F, Rooijers K, Agami R, and Tyynismaa H
- Subjects
- Cell Line, Tumor, Humans, Protein Biosynthesis, Arginine metabolism, Canavanine pharmacology, Mitochondria drug effects, Mitochondria metabolism, Mitochondrial Proteins metabolism, Proteome metabolism, Ribosomes metabolism
- Abstract
Impairment of mitochondrial protein homeostasis disrupts mitochondrial function and causes human diseases and aging, but the molecular mechanisms of protein synthesis and quality control in mammalian mitochondria are not fully understood. Here we demonstrate in human cells that misincorporation of an arginine analog, canavanine, during mitochondrial protein synthesis, induced aberrant translation products and destabilized the mtDNA-encoded proteome, leading to loss of mitochondrial respiratory chain complexes. Furthermore, in the presence of a high concentration of canavanine, mitoribosome stalling could be demonstrated. The stalling did not, however, occur at arginine codons, but downstream of those codons. In particular, two adjacent arginines induced the most prominent downstream stalling effect, with the distance between the arginine codons and the stalling peak corresponding roughly to the length of the ribosomal exit tunnel. These results suggest that misincorporated canavanine disrupted the proper folding of the hydrophobic nascent polypeptides within the exit tunnel or while being inserted into the inner mitochondrial membrane. The canavanine treatment provides a model system for studying the consequences of mitoribosome stalling and the responses to misfolded proteins exiting the mitochondrial ribosome., (Copyright © 2015 Elsevier Ltd. All rights reserved.)
- Published
- 2015
- Full Text
- View/download PDF
23. Lncing protein translation to metastasis.
- Author
-
Loayza-Puch F and Agami R
- Subjects
- Animals, Female, Humans, Gene Expression Regulation, Neoplastic, Neoplasm Metastasis genetics, Protein Biosynthesis genetics, RNA, Long Noncoding metabolism, Ribonucleoproteins physiology
- Published
- 2013
- Full Text
- View/download PDF
24. p53 induces transcriptional and translational programs to suppress cell proliferation and growth.
- Author
-
Loayza-Puch F, Drost J, Rooijers K, Lopes R, Elkon R, and Agami R
- Subjects
- Apoptosis, Carcinogenesis genetics, Carcinogenesis metabolism, Cell Line, Cellular Senescence, Humans, Protein Biosynthesis, Proteome genetics, TOR Serine-Threonine Kinases metabolism, Transcription, Genetic, Tumor Suppressor Protein p53 genetics, Cell Proliferation, Gene Expression Regulation, Neoplastic, Proteome metabolism, Transcriptome, Tumor Suppressor Protein p53 metabolism
- Abstract
Background: Cell growth and proliferation are tightly connected to ensure that appropriately sized daughter cells are generated following mitosis. Energy stress blocks cell growth and proliferation, a critical response for survival under extreme conditions. Excessive oncogenic stress leads to p53 activation and the induction of senescence, an irreversible state of cell-cycle arrest and a critical component in the suppression of tumorigenesis. Nutrient-sensing and mitogenic cues converge on a major signaling node, which regulates the activity of the mTOR kinase. Although transcriptional responses to energy and oncogenic stresses have been examined by many gene-expression experiments, a global exploration of the modulation of mRNA translation in response to these conditions is lacking., Results: We combine RNA sequencing and ribosomal profiling analyses to systematically delineate modes of transcriptional and translational regulation induced in response to conditions of limited energy, oncogenic stress and cellular transformation. We detect a key role for mTOR and p53 in these distinct physiological states, and provide the first genome-wide demonstration that p53 activation results in mTOR inhibition and a consequent global repression of protein translation. We confirm the role of the direct p53 target genes Sestrin1 and Sestrin2 in this response, as part of the broad modulation of gene expression induced by p53 activation., Conclusions: We delineate a bimodal tumor-suppressive regulatory program activated by p53, in which cell-cycle arrest is imposed mainly at the transcriptional level, whereas cell growth inhibition is enforced by global repression of the translation machinery.
- Published
- 2013
- Full Text
- View/download PDF
25. Ribosome profiling reveals features of normal and disease-associated mitochondrial translation.
- Author
-
Rooijers K, Loayza-Puch F, Nijtmans LG, and Agami R
- Subjects
- Cell Line, Humans, Mitochondria metabolism, Mitochondrial Proteins metabolism, RNA, Transfer, Trp genetics, RNA, Transfer, Trp metabolism, Ribosomes metabolism, Transcriptome, Disease genetics, Mitochondria genetics, Mitochondrial Proteins genetics, Protein Biosynthesis, Ribosomes genetics
- Abstract
Mitochondria are essential cellular organelles for generation of energy and their dysfunction may cause diabetes, Parkinson's disease and multi-systemic failure marked by failure to thrive, gastrointestinal problems, lactic acidosis and early lethality. Disease-associated mitochondrial mutations often affect components of the mitochondrial translation machinery. Here we perform ribosome profiling to measure mitochondrial translation at nucleotide resolution. Using a protocol optimized for the retrieval of mitochondrial ribosome protected fragments (RPFs) we show that the size distribution of wild-type mitochondrial RPFs follows a bimodal distribution peaking at 27 and 33 nucleotides, which is distinct from the 30-nucleotide peak of nuclear RPFs. Their cross-correlation suggests generation of mitochondrial RPFs during ribosome progression. In contrast, RPFs from patient-derived mitochondria mutated in tRNA-Tryptophan are centered on tryptophan codons and reduced downstream, indicating ribosome stalling. Intriguingly, long RPFs are enriched in mutated mitochondria, suggesting they characterize stalled ribosomes. Our findings provide the first model for translation in wild-type and disease-triggering mitochondria.
- Published
- 2013
- Full Text
- View/download PDF
26. The poly(A)-binding protein nuclear 1 suppresses alternative cleavage and polyadenylation sites.
- Author
-
Jenal M, Elkon R, Loayza-Puch F, van Haaften G, Kühn U, Menzies FM, Oude Vrielink JA, Bos AJ, Drost J, Rooijers K, Rubinsztein DC, and Agami R
- Subjects
- 3' Untranslated Regions, Animals, Base Sequence, Cell Line, Gene Expression Regulation, Humans, Mice, Molecular Sequence Data, Muscular Dystrophy, Oculopharyngeal genetics, Muscular Dystrophy, Oculopharyngeal metabolism, Mutation, Poly(A)-Binding Protein II genetics, RNA-Binding Proteins metabolism, Poly(A)-Binding Protein II metabolism, Polyadenylation, RNA Processing, Post-Transcriptional
- Abstract
Alternative cleavage and polyadenylation (APA) is emerging as an important layer of gene regulation. Factors controlling APA are largely unknown. We developed a reporter-based RNAi screen for APA and identified PABPN1 as a regulator of this process. Genome-wide analysis of APA in human cells showed that loss of PABPN1 resulted in extensive 3' untranslated region shortening. Messenger RNA transcription, stability analyses, and in vitro cleavage assays indicated enhanced usage of proximal cleavage sites (CSs) as the underlying mechanism. Using Cyclin D1 as a test case, we demonstrated that enhanced usage of proximal CSs compromises microRNA-mediated repression. Triplet-repeat expansion in PABPN1 (trePABPN1) causes autosomal-dominant oculopharyngeal muscular dystrophy (OPMD). The expression of trePABPN1 in both a mouse model of OPMD and human cells elicited broad induction of proximal CS usage, linked to binding to endogenous PABPN1 and its sequestration in nuclear aggregates. Our results elucidate a novel function for PABPN1 as a suppressor of APA., (Copyright © 2012 Elsevier Inc. All rights reserved.)
- Published
- 2012
- Full Text
- View/download PDF
27. 3'UTR-mediated gene silencing of the Mixed Lineage Leukemia (MLL) gene.
- Author
-
Gomez-Benito M, Loayza-Puch F, Oude Vrielink JA, Odero MD, and Agami R
- Subjects
- Cell Line, Tumor, Female, Gene Expression Regulation, Neoplastic genetics, Gene Fusion genetics, Histone-Lysine N-Methyltransferase, Humans, Leukemia genetics, Leukemia pathology, Male, Translocation, Genetic genetics, 3' Untranslated Regions genetics, Gene Silencing, Myeloid-Lymphoid Leukemia Protein deficiency, Myeloid-Lymphoid Leukemia Protein genetics
- Abstract
Translocations involving the Mixed Lineage Leukemia (MLL) gene generate in-frame fusions of MLL with more than 50 different partner genes (PGs). Common to all MLL translocations is the exchange not only of coding regions, but also of MLL and PG 3'-untranslated regions (3'UTRs). As a result, the MLL-PG fusion is normally highly expressed and considered the main driver of leukemia development, whereas the function of the PG-MLL fusions in leukemic disease is unclear. As 3'UTRs have been recognized as determinant regions for regulation of gene expression, we hypothesized that loss of the MLL 3'UTR could have a role in generating high MLL-PG levels and leukemia development. Here, we first tested the MLL-PG and PG-MLL mRNA levels in different leukemic cells and tumours and uncovered differential expression that indicates strong repression by the MLL-3'UTR. Reporter assays confirmed that the 3'UTR of MLL, but not of its main PGs, harbours a region that imposes a strong gene silencing effect. Gene suppression by the MLL 3'UTR was largely microRNA independent and did not affect mRNA stability, but inhibited transcription. This effect can at least partially be attributed to a tighter interaction of the MLL 3'UTR with RNA polymerase II than PG 3'UTRs, affecting its phosphorylation state. Altogether, our findings indicate that MLL translocations relieve oncogenic MLL-PG fusions from the repressive MLL 3'UTR, contributing to higher activity of these genes and leukaemia development.
- Published
- 2011
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.