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1.
Nature ; 592(7854): 450-456, 2021 04.
Artigo em Inglês | MEDLINE | ID: mdl-33762733

RESUMO

Hepatocellular carcinoma (HCC) can have viral or non-viral causes1-5. Non-alcoholic steatohepatitis (NASH) is an important driver of HCC. Immunotherapy has been approved for treating HCC, but biomarker-based stratification of patients for optimal response to therapy is an unmet need6,7. Here we report the progressive accumulation of exhausted, unconventionally activated CD8+PD1+ T cells in NASH-affected livers. In preclinical models of NASH-induced HCC, therapeutic immunotherapy targeted at programmed death-1 (PD1) expanded activated CD8+PD1+ T cells within tumours but did not lead to tumour regression, which indicates that tumour immune surveillance was impaired. When given prophylactically, anti-PD1 treatment led to an increase in the incidence of NASH-HCC and in the number and size of tumour nodules, which correlated with increased hepatic CD8+PD1+CXCR6+, TOX+, and TNF+ T cells. The increase in HCC triggered by anti-PD1 treatment was prevented by depletion of CD8+ T cells or TNF neutralization, suggesting that CD8+ T cells help to induce NASH-HCC, rather than invigorating or executing immune surveillance. We found similar phenotypic and functional profiles in hepatic CD8+PD1+ T cells from humans with NAFLD or NASH. A meta-analysis of three randomized phase III clinical trials that tested inhibitors of PDL1 (programmed death-ligand 1) or PD1 in more than 1,600 patients with advanced HCC revealed that immune therapy did not improve survival in patients with non-viral HCC. In two additional cohorts, patients with NASH-driven HCC who received anti-PD1 or anti-PDL1 treatment showed reduced overall survival compared to patients with other aetiologies. Collectively, these data show that non-viral HCC, and particularly NASH-HCC, might be less responsive to immunotherapy, probably owing to NASH-related aberrant T cell activation causing tissue damage that leads to impaired immune surveillance. Our data provide a rationale for stratification of patients with HCC according to underlying aetiology in studies of immunotherapy as a primary or adjuvant treatment.


Assuntos
Carcinoma Hepatocelular/patologia , Carcinoma Hepatocelular/terapia , Imunoterapia , Neoplasias Hepáticas/imunologia , Neoplasias Hepáticas/terapia , Hepatopatia Gordurosa não Alcoólica/complicações , Hepatopatia Gordurosa não Alcoólica/imunologia , Animais , Antígeno B7-H1/imunologia , Antígeno B7-H1/metabolismo , Linfócitos T CD8-Positivos/imunologia , Linfócitos T CD8-Positivos/metabolismo , Carcinogênese/imunologia , Carcinoma Hepatocelular/complicações , Carcinoma Hepatocelular/imunologia , Progressão da Doença , Humanos , Fígado/imunologia , Fígado/patologia , Neoplasias Hepáticas/complicações , Neoplasias Hepáticas/patologia , Masculino , Camundongos , Hepatopatia Gordurosa não Alcoólica/patologia , Receptor de Morte Celular Programada 1/antagonistas & inibidores , Receptor de Morte Celular Programada 1/imunologia , Receptor de Morte Celular Programada 1/metabolismo , Fator de Necrose Tumoral alfa/imunologia
2.
Nature ; 592(7854): 444-449, 2021 04.
Artigo em Inglês | MEDLINE | ID: mdl-33762736

RESUMO

Nonalcoholic steatohepatitis (NASH) is a manifestation of systemic metabolic disease related to obesity, and causes liver disease and cancer1,2. The accumulation of metabolites leads to cell stress and inflammation in the liver3, but mechanistic understandings of liver damage in NASH are incomplete. Here, using a preclinical mouse model that displays key features of human NASH (hereafter, NASH mice), we found an indispensable role for T cells in liver immunopathology. We detected the hepatic accumulation of CD8 T cells with phenotypes that combined tissue residency (CXCR6) with effector (granzyme) and exhaustion (PD1) characteristics. Liver CXCR6+ CD8 T cells were characterized by low activity of the FOXO1 transcription factor, and were abundant in NASH mice and in patients with NASH. Mechanistically, IL-15 induced FOXO1 downregulation and CXCR6 upregulation, which together rendered liver-resident CXCR6+ CD8 T cells susceptible to metabolic stimuli (including acetate and extracellular ATP) and collectively triggered auto-aggression. CXCR6+ CD8 T cells from the livers of NASH mice or of patients with NASH had similar transcriptional signatures, and showed auto-aggressive killing of cells in an MHC-class-I-independent fashion after signalling through P2X7 purinergic receptors. This killing by auto-aggressive CD8 T cells fundamentally differed from that by antigen-specific cells, which mechanistically distinguishes auto-aggressive and protective T cell immunity.


Assuntos
Linfócitos T CD8-Positivos/imunologia , Fígado/imunologia , Fígado/patologia , Hepatopatia Gordurosa não Alcoólica/imunologia , Hepatopatia Gordurosa não Alcoólica/patologia , Receptores CXCR6/imunologia , Acetatos/farmacologia , Animais , Linfócitos T CD8-Positivos/efeitos dos fármacos , Linfócitos T CD8-Positivos/patologia , Morte Celular/efeitos dos fármacos , Morte Celular/imunologia , Dieta Hiperlipídica/efeitos adversos , Modelos Animais de Doenças , Humanos , Interleucina-15/imunologia , Interleucina-15/farmacologia , Fígado/efeitos dos fármacos , Masculino , Camundongos , Camundongos Endogâmicos C57BL
3.
Hum Mol Genet ; 31(15): 2483-2497, 2022 08 17.
Artigo em Inglês | MEDLINE | ID: mdl-35157032

RESUMO

Cervical cancer is among the leading causes of cancer-related death in females worldwide. Infection by human papillomavirus (HPV) is an established risk factor for cancer development. However, genetic factors contributing to disease risk remain largely unknown. We report on a genome-wide association study (GWAS) on 375 German cervical cancer patients and 866 healthy controls, followed by a replication study comprising 658 patients with invasive cervical cancer, 1361 with cervical dysplasia and 841 healthy controls. Functional validation was performed for the top GWAS variant on chromosome 14q12 (rs225902, close to PRKD1). After bioinformatic annotation and in silico predictions, we performed transcript analysis in a cervical tissue series of 317 samples and demonstrate rs225902 as an expression quantitative trait locus (eQTL) for FOXG1 and two tightly co-regulated long non-coding RNAs at this genomic region, CTD-2251F13 (lnc-PRKD1-1) and CTD-2503I6 (lnc-FOXG1-6). We also show allele-specific effects of the 14q12 variants via luciferase assays. We propose a combined effect of genotype, HPV status and gene expression at this locus on cervical cancer progression. Taken together, this work uncovers a potential candidate locus with regulatory functions and contributes to the understanding of genetic susceptibility to cervical cancer.


Assuntos
Infecções por Papillomavirus , Neoplasias do Colo do Útero , Feminino , Seguimentos , Fatores de Transcrição Forkhead/genética , Fatores de Transcrição Forkhead/metabolismo , Predisposição Genética para Doença , Estudo de Associação Genômica Ampla , Humanos , Proteínas do Tecido Nervoso/genética , Papillomaviridae/genética , Papillomaviridae/metabolismo , Infecções por Papillomavirus/complicações , Infecções por Papillomavirus/genética , Polimorfismo de Nucleotídeo Único/genética , Neoplasias do Colo do Útero/genética
4.
Nature ; 542(7639): 119-123, 2017 02 02.
Artigo em Inglês | MEDLINE | ID: mdl-28099419

RESUMO

The genome of pancreatic ductal adenocarcinoma (PDAC) frequently contains deletions of tumour suppressor gene loci, most notably SMAD4, which is homozygously deleted in nearly one-third of cases. As loss of neighbouring housekeeping genes can confer collateral lethality, we sought to determine whether loss of the metabolic gene malic enzyme 2 (ME2) in the SMAD4 locus would create cancer-specific metabolic vulnerability upon targeting of its paralogous isoform ME3. The mitochondrial malic enzymes (ME2 and ME3) are oxidative decarboxylases that catalyse the conversion of malate to pyruvate and are essential for NADPH regeneration and reactive oxygen species homeostasis. Here we show that ME3 depletion selectively kills ME2-null PDAC cells in a manner consistent with an essential function for ME3 in ME2-null cancer cells. Mechanistically, integrated metabolomic and molecular investigation of cells deficient in mitochondrial malic enzymes revealed diminished NADPH production and consequent high levels of reactive oxygen species. These changes activate AMP activated protein kinase (AMPK), which in turn directly suppresses sterol regulatory element-binding protein 1 (SREBP1)-directed transcription of its direct targets including the BCAT2 branched-chain amino acid transaminase 2) gene. BCAT2 catalyses the transfer of the amino group from branched-chain amino acids to α-ketoglutarate (α-KG) thereby regenerating glutamate, which functions in part to support de novo nucleotide synthesis. Thus, mitochondrial malic enzyme deficiency, which results in impaired NADPH production, provides a prime 'collateral lethality' therapeutic strategy for the treatment of a substantial fraction of patients diagnosed with this intractable disease.


Assuntos
Carcinoma Ductal Pancreático/genética , Deleção de Genes , Malato Desidrogenase/deficiência , Neoplasias Pancreáticas/genética , Proteínas Quinases Ativadas por AMP/metabolismo , Aminoácidos de Cadeia Ramificada/metabolismo , Animais , Biocatálise , Carcinoma Ductal Pancreático/enzimologia , Carcinoma Ductal Pancreático/psicologia , Carcinoma Ductal Pancreático/terapia , Humanos , Ácidos Cetoglutáricos/metabolismo , Malato Desidrogenase/genética , Masculino , Camundongos , Antígenos de Histocompatibilidade Menor/biossíntese , Antígenos de Histocompatibilidade Menor/genética , Mitocôndrias/enzimologia , Mitocôndrias/patologia , NADP/biossíntese , NADP/metabolismo , Neoplasias Pancreáticas/enzimologia , Neoplasias Pancreáticas/patologia , Neoplasias Pancreáticas/terapia , Proteínas da Gravidez/biossíntese , Proteínas da Gravidez/genética , Espécies Reativas de Oxigênio/metabolismo , Proteína de Ligação a Elemento Regulador de Esterol 1/metabolismo , Transaminases/biossíntese , Transaminases/genética
5.
Nature ; 542(7641): 362-366, 2017 02 16.
Artigo em Inglês | MEDLINE | ID: mdl-28178232

RESUMO

Malignant neoplasms evolve in response to changes in oncogenic signalling. Cancer cell plasticity in response to evolutionary pressures is fundamental to tumour progression and the development of therapeutic resistance. Here we determine the molecular and cellular mechanisms of cancer cell plasticity in a conditional oncogenic Kras mouse model of pancreatic ductal adenocarcinoma (PDAC), a malignancy that displays considerable phenotypic diversity and morphological heterogeneity. In this model, stochastic extinction of oncogenic Kras signalling and emergence of Kras-independent escaper populations (cells that acquire oncogenic properties) are associated with de-differentiation and aggressive biological behaviour. Transcriptomic and functional analyses of Kras-independent escapers reveal the presence of Smarcb1-Myc-network-driven mesenchymal reprogramming and independence from MAPK signalling. A somatic mosaic model of PDAC, which allows time-restricted perturbation of cell fate, shows that depletion of Smarcb1 activates the Myc network, driving an anabolic switch that increases protein metabolism and adaptive activation of endoplasmic-reticulum-stress-induced survival pathways. Increased protein turnover renders mesenchymal sub-populations highly susceptible to pharmacological and genetic perturbation of the cellular proteostatic machinery and the IRE1-α-MKK4 arm of the endoplasmic-reticulum-stress-response pathway. Specifically, combination regimens that impair the unfolded protein responses block the emergence of aggressive mesenchymal subpopulations in mouse and patient-derived PDAC models. These molecular and biological insights inform a potential therapeutic strategy for targeting aggressive mesenchymal features of PDAC.


Assuntos
Mesoderma/patologia , Neoplasias Pancreáticas/patologia , Animais , Carcinoma Ductal Pancreático/tratamento farmacológico , Carcinoma Ductal Pancreático/metabolismo , Carcinoma Ductal Pancreático/patologia , Desoxicitidina/análogos & derivados , Desoxicitidina/farmacologia , Desoxicitidina/uso terapêutico , Estresse do Retículo Endoplasmático/genética , Feminino , Genes myc , Genes ras , Humanos , MAP Quinase Quinase 4/metabolismo , Sistema de Sinalização das MAP Quinases , Masculino , Mesoderma/metabolismo , Camundongos , Mosaicismo , Proteína Oncogênica p55(v-myc)/metabolismo , Neoplasias Pancreáticas/tratamento farmacológico , Neoplasias Pancreáticas/metabolismo , Proteólise , Proteínas Proto-Oncogênicas p21(ras)/genética , Proteínas Proto-Oncogênicas p21(ras)/metabolismo , Proteína SMARCB1/deficiência , Proteína SMARCB1/metabolismo , Transcriptoma/genética , Gencitabina
6.
Mar Drugs ; 21(4)2023 Apr 06.
Artigo em Inglês | MEDLINE | ID: mdl-37103372

RESUMO

Palytoxin is considered one of the most potent biotoxins. As palytoxin-induced cancer cell death mechanisms remain to be elucidated, we investigated this effect on various leukemia and solid tumor cell lines at low picomolar concentrations. As palytoxin did not affect the viability of peripheral blood mononuclear cells (PBMC) from healthy donors and did not create systemic toxicity in zebrafish, we confirmed excellent differential toxicity. Cell death was characterized by a multi-parametric approach involving the detection of nuclear condensation and caspase activation assays. zVAD-sensitive apoptotic cell death was concomitant with a dose-dependent downregulation of antiapoptotic Bcl-2 family proteins Mcl-1 and Bcl-xL. Proteasome inhibitor MG-132 prevented the proteolysis of Mcl-1, whereas the three major proteasomal enzymatic activities were upregulated by palytoxin. Palytoxin-induced dephosphorylation of Bcl-2 further exacerbated the proapoptotic effect of Mcl-1 and Bcl-xL degradation in a range of leukemia cell lines. As okadaic acid rescued cell death triggered by palytoxin, protein phosphatase (PP)2A was involved in Bcl-2 dephosphorylation and induction of apoptosis by palytoxin. At a translational level, palytoxin abrogated the colony formation capacity of leukemia cell types. Moreover, palytoxin abrogated tumor formation in a zebrafish xenograft assay at concentrations between 10 and 30 pM. Altogether, we provide evidence of the role of palytoxin as a very potent and promising anti-leukemic agent, acting at low picomolar concentrations in cellulo and in vivo.


Assuntos
Leucemia , Leucócitos Mononucleares , Animais , Humanos , Leucócitos Mononucleares/metabolismo , Peixe-Zebra/metabolismo , Regulação para Baixo , Proteína de Sequência 1 de Leucemia de Células Mieloides , Proteínas Proto-Oncogênicas c-bcl-2/metabolismo , Apoptose , Proteínas Reguladoras de Apoptose/metabolismo , Linhagem Celular Tumoral , Proteína bcl-X/metabolismo , Proteína bcl-X/farmacologia
7.
Anal Chem ; 94(28): 10045-10053, 2022 07 19.
Artigo em Inglês | MEDLINE | ID: mdl-35792073

RESUMO

The phosphonate group is a key pharmacophore in many antiviral, antimicrobial, and antineoplastic drugs. Due to its high polarity and short retention time, detecting and quantifying such phosphonate-containing drugs with LC/MS-based methods are challenging and require derivatization with hazardous reagents. Given the emerging importance of phosphonate-containing drugs, developing a practical, accessible, and safe method for their quantitation in pharmacokinetics (PK) studies is desirable. NMR-based methods are often employed in drug discovery but are seldom used for compound quantitation in PK studies. Here, we show that proton-phosphorous (1H-31P) heteronuclear single quantum correlation (HSQC) NMR allows for the quantitation of the phosphonate-containing enolase inhibitor HEX in plasma and tissues at micromolar concentrations. Although mice were shown to rapidly clear HEX from circulation (over 95% in <1 h), the plasma half-life of HEX was more than 1 h in rats and nonhuman primates. This slower clearance rate affords a significantly higher exposure of HEX in rat models compared to that in mouse models while maintaining a favorable safety profile. Similar results were observed for the phosphonate-containing antibiotic, fosfomycin. Our study demonstrates the applicability of the 1H-31P HSQC method to quantify phosphonate-containing drugs in complex biological samples and illustrates an important limitation of mice as preclinical model species for phosphonate-containing drugs.


Assuntos
Antineoplásicos , Organofosfonatos , Animais , Antineoplásicos/farmacocinética , Antivirais , Camundongos , Organofosfonatos/química , Primatas , Prótons , Ratos
9.
J Sports Sci ; 40(18): 2028-2036, 2022 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-36227924

RESUMO

Grounded in social facilitation theory, this study examined the impact of co-acting competitors (i.e., opponents) on elite biathletes' shooting performance based on World Cup competition data. To this end, the impact of the number as well as the mean overlapping time with co-acting competitors at the shooting range on both shooting time and shooting accuracy was assessed. Competition data of World Cup races from 2005 to 2020 were analysed. This included 115 mass start and 195 pursuit events of a total of 758 elite biathletes amounting to 57.251 shooting bouts equivalent to a total of 286.255 shots. Data was analysed using a fixed effects model. Results revealed two main findings: First, the more co-acting opponents were present at the shooting range, the shorter (i.e., better) was shooting time. However, more co-acting opponents were also associated with decreased shooting accuracy in mass start, but not in pursuit. Second, a longer temporal overlap with co-acting opponents negatively affected biathletes' shooting time. There was no effect on shooting accuracy. To conclude, the present study provides first evidence for a link between co-acting competitors and shooting performance in elite biathletes by analysing ecologically valid, real world data.


Assuntos
Desempenho Atlético , Armas de Fogo , Esqui , Futebol , Humanos
10.
Int J Cancer ; 2021 Apr 27.
Artigo em Inglês | MEDLINE | ID: mdl-33905146

RESUMO

Cervical malignancy is triggered by human papillomavirus infection but the risk for cervical cancer has a hereditary component. From a recent Genome Wide Association Study meta-analysis, 2q14.1 (PAX8) and 6p21.32 (PBX2) have been proposed as novel cervical cancer susceptibility loci. We investigated the two main signals at these loci in an independent case-control series of 2578 cases with cervical dysplasia or carcinoma and 1483 healthy females. We find significant associations for both variants, rs10175462 at PAX8 and rs2856437 at PBX2, with overall cervical disease (rs10175462: odds ratio [OR] 0.82, 95% confidence interval [CI] 0.74-0.91, P = 2.4 × 10-4 ; rs2856437: OR 1.52, 95% CI 1.14-2.02, P = .004). Both variants showed evidence of association with invasive squamous cervical cancer (rs10175462: OR 0.80, 95% CI 0.68-0.94, P = .006; rs2856437: OR 1.56, 95% CI 1.03-2.36, P = .036) and with high-grade dysplasia (rs10175462: OR 0.79, 95%CI 0.70-0.90, P = 1.9 × 10-4 ; rs2856437: OR 1.58, 95% CI 1.15-2.17, P = .005). A combined analysis of high-grade dysplasia and invasive cervical cancer also showed significant associations for both variants (rs10175462: OR 0.81, 95% CI 0.73-0.91, P = 2.4 × 10-4 ; rs2856437: OR 1.57, 95% CI 1.18-2.10, P = .002). No association was detected for rs2856437 with low-grade dysplasia, while rs10175462 showed weak evidence of association (P = .05). RNA analyses in cervical samples revealed that PAX8 transcripts were upregulated in HPV-positive lesions (P = .008) but this was not observed in the presence of the protective minor allele of rs10175462. The rs10175462 genotype also correlated with reduced levels of the lncRNA PAX8-AS1 (P < .001). Taken together, our results extend the evidence for a link between genomic risk variants at the HLA region (PBX2) with cervical disease and support PAX8 as the first consistent non-HLA cervical cancer susceptibility locus.

11.
Antimicrob Agents Chemother ; 65(10): e0111721, 2021 09 17.
Artigo em Inglês | MEDLINE | ID: mdl-34252308

RESUMO

Remdesivir is a nucleoside monophosphoramidate prodrug that has been FDA approved for coronavirus disease 2019 (COVID-19). However, the clinical efficacy of remdesivir for COVID-19 remains contentious, as several trials have not found statistically significant differences in either time to clinical improvement or mortality between remdesivir-treated and control groups. Similarly, the inability of remdesivir to provide a clinically significant benefit above other investigational agents in patients with Ebola contrasts with strong, curative preclinical data generated in rhesus macaque models. For both COVID-19 and Ebola, significant discordance between the robust preclinical data and remdesivir's lackluster clinical performance have left many puzzled. Here, we critically evaluate the assumptions of the models underlying remdesivir's promising preclinical data and show that such assumptions overpredict efficacy and minimize toxicity of remdesivir in humans. Had the limitations of in vitro drug efficacy testing and species differences in drug metabolism been considered, the underwhelming clinical performance of remdesivir for both COVID-19 and Ebola would have been fully anticipated.


Assuntos
Tratamento Farmacológico da COVID-19 , Doença pelo Vírus Ebola , Monofosfato de Adenosina/análogos & derivados , Monofosfato de Adenosina/uso terapêutico , Alanina/análogos & derivados , Alanina/uso terapêutico , Animais , Antivirais/farmacologia , Antivirais/uso terapêutico , Doença pelo Vírus Ebola/tratamento farmacológico , Humanos , Macaca mulatta , SARS-CoV-2 , Resultado do Tratamento
12.
Cancer Immunol Immunother ; 70(4): 1101-1113, 2021 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-33123754

RESUMO

Although immunotherapy has achieved impressive durable clinical responses, many cancers respond only temporarily or not at all to immunotherapy. To find novel, targetable mechanisms of resistance to immunotherapy, patient-derived melanoma cell lines were transduced with 576 open reading frames, or exposed to arrayed libraries of 850 bioactive compounds, prior to co-culture with autologous tumor-infiltrating lymphocytes (TILs). The synergy between the targets and TILs to induce apoptosis, and the mechanisms of inhibiting resistance to TILs were interrogated. Gene expression analyses were performed on tumor samples from patients undergoing immunotherapy for metastatic melanoma. Finally, the effect of inhibiting the top targets on the efficacy of immunotherapy was investigated in multiple preclinical models. Aurora kinase was identified as a mediator of melanoma cell resistance to T-cell-mediated cytotoxicity in both complementary screens. Aurora kinase inhibitors were validated to synergize with T-cell-mediated cytotoxicity in vitro. The Aurora kinase inhibition-mediated sensitivity to T-cell cytotoxicity was shown to be partially driven by p21-mediated induction of cellular senescence. The expression levels of Aurora kinase and related proteins were inversely correlated with immune infiltration, response to immunotherapy and survival in melanoma patients. Aurora kinase inhibition showed variable responses in combination with immunotherapy in vivo, suggesting its activity is modified by other factors in the tumor microenvironment. These data suggest that Aurora kinase inhibition enhances T-cell cytotoxicity in vitro and can potentiate antitumor immunity in vivo in some but not all settings. Further studies are required to determine the mechanism of primary resistance to this therapeutic intervention.


Assuntos
Aurora Quinase A/metabolismo , Aurora Quinase B/metabolismo , Resistencia a Medicamentos Antineoplásicos/imunologia , Imunoterapia/métodos , Linfócitos do Interstício Tumoral/imunologia , Melanoma/imunologia , Linfócitos T Citotóxicos/transplante , Animais , Apoptose , Aurora Quinase A/antagonistas & inibidores , Aurora Quinase A/genética , Aurora Quinase B/antagonistas & inibidores , Aurora Quinase B/genética , Proliferação de Células , Feminino , Humanos , Melanoma/genética , Melanoma/metabolismo , Melanoma/terapia , Camundongos , Prognóstico , Taxa de Sobrevida , Linfócitos T Citotóxicos/imunologia , Células Tumorais Cultivadas , Microambiente Tumoral/imunologia , Ensaios Antitumorais Modelo de Xenoenxerto
13.
RNA ; 25(10): 1229-1241, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31266821

RESUMO

Polyadenylation at the 3'-end is a major regulator of messenger RNA and its length is known to affect nuclear export, stability, and translation, among others. Only recently have strategies emerged that allow for genome-wide poly(A) length assessment. These methods identify genes connected to poly(A) tail measurements indirectly by short-read alignment to genetic 3'-ends. Concurrently, Oxford Nanopore Technologies (ONT) established full-length isoform-specific RNA sequencing containing the entire poly(A) tail. However, assessing poly(A) length through base-calling has so far not been possible due to the inability to resolve long homopolymeric stretches in ONT sequencing. Here we present tailfindr, an R package to estimate poly(A) tail length on ONT long-read sequencing data. tailfindr operates on unaligned, base-called data. It measures poly(A) tail length from both native RNA and DNA sequencing, which makes poly(A) tail studies by full-length cDNA approaches possible for the first time. We assess tailfindr's performance across different poly(A) lengths, demonstrating that tailfindr is a versatile tool providing poly(A) tail estimates across a wide range of sequencing conditions.


Assuntos
Nanoporos , Poli A/metabolismo , Análise de Sequência de DNA/métodos , Análise de Sequência de RNA/métodos , Poli T/metabolismo , Poliadenilação
14.
Bioorg Med Chem Lett ; 30(24): 127656, 2020 12 15.
Artigo em Inglês | MEDLINE | ID: mdl-33130289

RESUMO

Phosphate and phosphonates containing a single PN bond are frequently used pro-drug motifs to improve cell permeability of these otherwise anionic moieties. Upon entry into the cell, the PN bond is cleaved by phosphoramidases to release the active agent. Here, we apply a novel mono-amidation strategy to our laboratory's phosphonate-containing glycolysis inhibitor and show that a diverse panel of phosphonoamidates may be rapidly generated for in vitro screening. We show that, in contrast to the canonical l-alanine or benzylamine moieties which have previously been reported as efficacious pro-drug moieties, small and long-chain aliphatic amines demonstrate greater drug release efficacy for our phosphonate inhibitor. These results expand the scope of possible amine pro-drugs that can be used as second pro-drug leave groups for phosphate or phosphonate-containing drugs.


Assuntos
Aminas/química , Hidrocarbonetos/química , Organofosfatos/química , Organofosfonatos/química , Pró-Fármacos/química , Amidas/química
15.
Nature ; 514(7524): 628-32, 2014 Oct 30.
Artigo em Inglês | MEDLINE | ID: mdl-25119024

RESUMO

Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest cancers in western countries, with a median survival of 6 months and an extremely low percentage of long-term surviving patients. KRAS mutations are known to be a driver event of PDAC, but targeting mutant KRAS has proved challenging. Targeting oncogene-driven signalling pathways is a clinically validated approach for several devastating diseases. Still, despite marked tumour shrinkage, the frequency of relapse indicates that a fraction of tumour cells survives shut down of oncogenic signalling. Here we explore the role of mutant KRAS in PDAC maintenance using a recently developed inducible mouse model of mutated Kras (Kras(G12D), herein KRas) in a p53(LoxP/WT) background. We demonstrate that a subpopulation of dormant tumour cells surviving oncogene ablation (surviving cells) and responsible for tumour relapse has features of cancer stem cells and relies on oxidative phosphorylation for survival. Transcriptomic and metabolic analyses of surviving cells reveal prominent expression of genes governing mitochondrial function, autophagy and lysosome activity, as well as a strong reliance on mitochondrial respiration and a decreased dependence on glycolysis for cellular energetics. Accordingly, surviving cells show high sensitivity to oxidative phosphorylation inhibitors, which can inhibit tumour recurrence. Our integrated analyses illuminate a therapeutic strategy of combined targeting of the KRAS pathway and mitochondrial respiration to manage pancreatic cancer.


Assuntos
Carcinoma Ductal Pancreático/metabolismo , Carcinoma Ductal Pancreático/patologia , Mitocôndrias/metabolismo , Neoplasias Pancreáticas/metabolismo , Neoplasias Pancreáticas/patologia , Proteínas Proto-Oncogênicas p21(ras)/genética , Animais , Autofagia , Carcinoma Ductal Pancreático/tratamento farmacológico , Carcinoma Ductal Pancreático/genética , Respiração Celular/efeitos dos fármacos , Sobrevivência Celular/efeitos dos fármacos , Modelos Animais de Doenças , Feminino , Regulação Neoplásica da Expressão Gênica , Genes p53/genética , Glicólise , Lisossomos/metabolismo , Camundongos , Mitocôndrias/efeitos dos fármacos , Mutação/genética , Recidiva Local de Neoplasia/prevenção & controle , Células-Tronco Neoplásicas/efeitos dos fármacos , Células-Tronco Neoplásicas/metabolismo , Células-Tronco Neoplásicas/patologia , Fosforilação Oxidativa/efeitos dos fármacos , Neoplasias Pancreáticas/tratamento farmacológico , Neoplasias Pancreáticas/genética , Proteínas Proto-Oncogênicas p21(ras)/metabolismo , Recidiva , Transdução de Sinais , Neoplasias Pancreáticas
16.
Molecules ; 24(13)2019 Jul 09.
Artigo em Inglês | MEDLINE | ID: mdl-31324042

RESUMO

We recently reported that SF2312 ((1,5-dihydroxy-2-oxopyrrolidin-3-yl)phosphonic acid), a phosphonate antibiotic with a previously unknown mode of action, is a potent inhibitor of the glycolytic enzyme, Enolase. SF2312 can only be synthesized as a racemic-diastereomeric mixture. However, co-crystal structures with Enolase 2 (ENO2) have consistently shown that only the (3S,5S)-enantiomer binds to the active site. The acidity of the alpha proton at C-3, which deprotonates under mildly alkaline conditions, results in racemization; thus while the separation of four enantiomeric intermediates was achieved via chiral High Performance Liquid Chromatography (HPLC) of the fully protected intermediate, deprotection inevitably nullified enantiopurity. To prevent epimerization of the C-3, we designed and synthesized MethylSF2312, ((1,5-dihydroxy-3-methyl-2-oxopyrrolidin-3-yl)phosphonic acid), which contains a fully-substituted C-3 alpha carbon. As a racemic-diastereomeric mixture, MethylSF2312 is equipotent to SF2312 in enzymatic and cellular systems against Enolase. Chiral HPLC separation of a protected MethylSF2312 precursor resulted in the efficient separation of the four enantiomers. After deprotection and inevitable re-equilibration of the anomeric C-5, (3S)-MethylSF2312 was up to 2000-fold more potent than (3R)-MethylSF2312 in an isolated enzymatic assay. This observation strongly correlates with biological activity in both human cancer cells and bacteria for the 3S enantiomer of SF2312. Novel X-ray structures of human ENO2 with chiral and racemic MethylSF2312 show that only (3S,5S)-enantiomer occupies the active site. Enolase inhibition is thus a direct result of binding by the (3S,5S)-enantiomer of MethylSF2312. Concurrent with these results for MethylSF2312, we contend that the (3S,5S)-SF2312 is the single active enantiomer of inhibitor SF2312.


Assuntos
Inibidores Enzimáticos/farmacologia , Organofosfonatos/farmacologia , Fosfopiruvato Hidratase/antagonistas & inibidores , Fosfopiruvato Hidratase/química , Pirrolidinonas/farmacologia , Sítios de Ligação , Ativação Enzimática/efeitos dos fármacos , Inibidores Enzimáticos/química , Modelos Moleculares , Conformação Molecular , Estrutura Molecular , Organofosfonatos/química , Ligação Proteica , Pirrolidinonas/química , Análise Espectral , Estereoisomerismo , Relação Estrutura-Atividade
17.
Genome Res ; 25(3): 316-27, 2015 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-25650244

RESUMO

Glioblastoma (GBM) is a prototypical heterogeneous brain tumor refractory to conventional therapy. A small residual population of cells escapes surgery and chemoradiation, resulting in a typically fatal tumor recurrence ∼ 7 mo after diagnosis. Understanding the molecular architecture of this residual population is critical for the development of successful therapies. We used whole-genome sequencing and whole-exome sequencing of multiple sectors from primary and paired recurrent GBM tumors to reconstruct the genomic profile of residual, therapy resistant tumor initiating cells. We found that genetic alteration of the p53 pathway is a primary molecular event predictive of a high number of subclonal mutations in glioblastoma. The genomic road leading to recurrence is highly idiosyncratic but can be broadly classified into linear recurrences that share extensive genetic similarity with the primary tumor and can be directly traced to one of its specific sectors, and divergent recurrences that share few genetic alterations with the primary tumor and originate from cells that branched off early during tumorigenesis. Our study provides mechanistic insights into how genetic alterations in primary tumors impact the ensuing evolution of tumor cells and the emergence of subclonal heterogeneity.


Assuntos
Neoplasias Encefálicas/genética , Neoplasias Encefálicas/patologia , Exoma , Genoma Humano , Glioblastoma/genética , Glioblastoma/patologia , Sequenciamento de Nucleotídeos em Larga Escala , Adulto , Fatores Etários , Idoso , Idoso de 80 Anos ou mais , Neoplasias Encefálicas/metabolismo , Neoplasias Encefálicas/mortalidade , Neoplasias Encefálicas/terapia , Evolução Clonal/genética , Variações do Número de Cópias de DNA , Metilação de DNA , Genômica/métodos , Glioblastoma/metabolismo , Glioblastoma/mortalidade , Glioblastoma/terapia , Humanos , Pessoa de Meia-Idade , Mutação , Taxa de Mutação , Gradação de Tumores , Recidiva Local de Neoplasia , Polimorfismo de Nucleotídeo Único , Transdução de Sinais , Resultado do Tratamento , Proteína Supressora de Tumor p53/genética , Proteína Supressora de Tumor p53/metabolismo , Adulto Jovem
18.
Nat Chem Biol ; 12(12): 1053-1058, 2016 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-27723749

RESUMO

Despite being crucial for energy generation in most forms of life, few if any microbial antibiotics specifically inhibit glycolysis. To develop a specific inhibitor of the glycolytic enzyme enolase 2 (ENO2) for the treatment of cancers with deletion of ENO1 (encoding enolase 1), we modeled the synthetic tool compound inhibitor phosphonoacetohydroxamate (PhAH) into the active site of human ENO2. A ring-stabilized analog of PhAH, in which the hydroxamic nitrogen is linked to Cα by an ethylene bridge, was predicted to increase binding affinity by stabilizing the inhibitor in a bound conformation. Unexpectedly, a structure-based search revealed that our hypothesized backbone-stabilized PhAH bears strong similarity to SF2312, a phosphonate antibiotic of unknown mode of action produced by the actinomycete Micromonospora, which is active under anaerobic conditions. Here, we present multiple lines of evidence, including a novel X-ray structure, that SF2312 is a highly potent, low-nanomolar inhibitor of enolase.


Assuntos
Inibidores Enzimáticos/farmacologia , Organofosfonatos/farmacologia , Fosfopiruvato Hidratase/antagonistas & inibidores , Pirrolidinonas/farmacologia , Relação Dose-Resposta a Droga , Inibidores Enzimáticos/química , Humanos , Modelos Moleculares , Estrutura Molecular , Organofosfonatos/química , Fosfopiruvato Hidratase/metabolismo , Pirrolidinonas/química , Relação Estrutura-Atividade
19.
Horm Behav ; 99: 9-13, 2018 03.
Artigo em Inglês | MEDLINE | ID: mdl-29408015

RESUMO

Most migrating birds make stopovers to replenish fuel stores. The decision to resume migration from stopover to a large extent shapes the temporal organization of migration. This decision is known to be shaped by a suite of intrinsic and extrinsic factors such as the bird's fuel stores and current weather conditions. However, how departures from stopover are physiologically regulated is largely unknown. We here present data that strongly indicate that corticosterone, a hormone with a stimulatory effect on locomotion, acts as a mediator between fuel stores and departure from stopover. In migrating northern wheatears (Oenanthe oenanthe) temporarily caged at stopover, we observed a positive relationship between the change in fuel stores and the concurrent change in glucocorticoid metabolite (GCM) levels measured in the birds' droppings. We also found a positive relationship between the change in GCM levels and the change in the intensity of nocturnal migratory restlessness. As in northern wheatears nocturnal migratory restlessness is an accurate proxy for stopover departure likelihood, our results indicate that corticosterone mediates between fuel stores and the decision to resume migration. Our unique longitudinal study represents a considerable advance in our understanding of the endocrine regulation of avian migration.


Assuntos
Migração Animal/fisiologia , Hormônios/fisiologia , Passeriformes/fisiologia , Descanso/fisiologia , Animais , Corticosterona/metabolismo , Metabolismo Energético/efeitos dos fármacos , Metabolismo Energético/fisiologia , Glucocorticoides/metabolismo , Hormônios/farmacologia , Estudos Longitudinais , Movimento/efeitos dos fármacos , Movimento/fisiologia , Agitação Psicomotora/metabolismo , Descanso/psicologia
20.
J Anim Ecol ; 87(4): 1102-1115, 2018 07.
Artigo em Inglês | MEDLINE | ID: mdl-29504627

RESUMO

Most migratory songbirds travel between their breeding areas and wintering grounds through a series of nocturnal flights. The timing of their departures defines the potential flight duration and thus the distance covered during a migratory night. Yet, migratory songbirds show substantial variation in their nocturnal departure timing. With this study, we aim to assess whether the respective challenges of the migration route, namely its distance and nature, help to explain this variation. At a stopover site, we caught Northern Wheatears (Oenanthe oenanthe) of two subspecies that differ in distance and nature of their onward migration route in spring, but not in autumn. We determined the start of their nocturnal migratory restlessness during short-term captivity, and radiotracked their nocturnal departure timing after release in both migration seasons. Northern Wheatears started their nocturnal migratory restlessness earlier when facing a long remaining migration distance and an extended sea barrier in spring. Individual departure directions generally affected the nocturnal departure timing with early departures being directed towards the respective migratory destination. In spring, this pattern was predominantly found in birds carrying relatively large fuel stores, but was absent in lean birds. At the same time, birds facing a short remaining migration distance and no extended sea barrier strongly reacted to relatively large fuel stores by an early start of nocturnal migratory behaviour (migratory restlessness and departure timing), whereas this reaction was not found in birds facing a long remaining migration distance and sea barrier. These results suggest that the basic diel schedule of birds' migratory activity is adapted to the onward migration route. Further, they suggest that birds adjust their behavioural response, that is start of nocturnal migratory behaviour, to fuel stores in relation to their impending migratory challenges. This is a substantial step in understanding variation of nocturnal departure timing and its adjustments in migratory songbirds. Further, it emphasizes the importance of interpreting birds' nocturnal migratory behaviour in the respective ecological context.


Assuntos
Distribuição Animal , Migração Animal , Aves Canoras/fisiologia , Animais , Alemanha , Estações do Ano , Fatores de Tempo
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