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1.
J Hum Kinet ; 90: 89-100, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-38380301

RESUMO

High-intensityintervaltraining (HIIT) issuperiortoothertrainingstrategies in both male andfemalehealthyindividuals. Understanding sex-specificdifferences in cardiac auto-regulation maycontributetothe optimal trainingstrategiesfor HIIT. The presentstudyaimedtoidentifysexdifferences in heart rate variability (HRV) andvascularfunctionfollowing HIIT in youngadults. Twenty-fourphysicallyactiveyoung male andfemaleadults (M: 12, F: 12, age: 19.5 yr, BMI: 22.1 kg·m-2) volunteeredtoparticipate in thestudy. Participantsperformed 10 boutsof HIIT including 20 s of high-intensitycycling at 115-130% Wmaxfollowedby 100 s ofrecovery. The cardiac auto-regulationsincluding HRV andvascularfunctionweremeasured at five different time points. The R-R interval, rMSSD, and SDNN wererecoveredfaster in malesthan in females after 15 min of HIIT. Thereweresexdifferences in theautonomicnervoussystemwhereln LF andln HF activitiesalongwithsympathovagalbalance (ln LF/HF) weregreater in femalescomparedwithmalesimmediatelyand 15 min after HIIT. However, nosignificantdifferences in bloodpressureand brachial-ankle pulse wavevelocitywereobservedbetween male andfemaleparticipants. Overall, HRV was moreactivated in femalesthan in malesfollowing HIIT, but theacuteresponse in vascularfunction was not different betweensexes. In futurestudies, sex-specificadaptationsofcardiacautoregulationfollowingrepeated HIIT mayneedtobeperformed.

2.
Brain Tumor Res Treat ; 12(1): 40-49, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-38317487

RESUMO

BACKGROUND: For patients diagnosed with asymptomatic, non-functional pituitary incidentaloma (PI), periodic follow-up is generally proposed. However, the recommended follow-up period differs among existing guidelines and consensus is lacking. Thus, this study aimed to suggest follow-up periods for PI based on MRI characteristics. METHODS: Between 2007 and 2023, 245 patients who were diagnosed with PI were retrospectively assessed. Their mean clinical and neuroradiological follow-up periods were 74.2 and 27.3 months, respectively. Their baseline clinical and neuroradiological characteristics were analyzed. These 245 patients were divided into two groups: those with PI size progression and those without PI size progression. Additionally, neuroradiological features of each group were analyzed according to presumptive diagnoses of PI. RESULTS: PI size increased in 33 of 245 patients. For the remaining 212 patients, PI size decreased or stayed unchanged. Of the 33 patients with PI size progression, ten underwent surgery. Stalk deviation (p<0.001) and lesion enhancement (p=0.001) were significantly more observed in those with PI size progression than in those without PI size progression. MRI morphological factors were not related to changes in PI size in the presumptive Rathke's cleft cyst group. In the presumptive pituitary adenoma group, absence of tumor enhancement (p<0.001) and stalk deviation (p<0.001) were significantly associated with tumor reduction and progression, respectively. CONCLUSION: Our findings support an additional guideline for patients with asymptomatic non-functional PI without stalk deviation and enhancement. For these patients, the clinical and neuroradiological follow-up periods could be reduced.

3.
Investig Clin Urol ; 65(1): 69-76, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-38197753

RESUMO

PURPOSE: To investigate the prevalence of lower urinary tract symptoms/benign prostatic hyperplasia in a Korean population. MATERIALS AND METHODS: The Korean Prostate & Voiding Health Association provided free prostate-related community health care and conducted surveys in all regions of Korea from 2001 to 2022 with the cooperation of local government public health centers. A total of 72,068 males older than 50 were surveyed and analyzed. History taking, International Prostate Symptom Score (IPSS), transrectal ultrasonography, prostate-specific antigen (PSA) testing, uroflowmetry, and urine volume testing were performed. RESULTS: The mean prostate volumes in males in their 50s, 60s, 70s, and 80s or above were 24.7 g, 27.7 g, 31 g, and 33.7 g, respectively. The proportion of males with high PSA greater than 3 ng/mL was 3.8% among males in their 50s, 7.7% among males in their 60s, 13.1% among males in their 70s, and 17.9% among males 80 years of age or older. The mean IPSS total scores in males in their 50s, 60s, 70s, and 80s or above were 10.7, 12.7, 14.5, and 16, respectively. Severe symptoms were reported by 27.3% of males, whereas 51.7% reported moderate symptoms. The mean Qmax in males in their 50s, 60s, 70s, and 80s or above were 20 mL/s, 17.4 mL/s, 15.4 mL/s, and 13.8 mL/s, respectively. CONCLUSIONS: In this population-based study, mean prostate volume, IPSS, PSA, and Qmax were 30.6±15.1 g, 14.8±8.2, 1.9±4.7 ng/mL, and 15.6±6.5 mL/s, respectively. Aging was significantly associated with increased prostate volume, PSA levels, and IPSS scores, and with decreased Qmax and urine volume.


Assuntos
Sintomas do Trato Urinário Inferior , Hiperplasia Prostática , Masculino , Humanos , Hiperplasia Prostática/complicações , Hiperplasia Prostática/epidemiologia , Antígeno Prostático Específico , Próstata , Sintomas do Trato Urinário Inferior/epidemiologia , Sintomas do Trato Urinário Inferior/etiologia , República da Coreia/epidemiologia
4.
Cell Genom ; 4(2): 100484, 2024 Feb 14.
Artigo em Inglês | MEDLINE | ID: mdl-38232733

RESUMO

The epigenetic landscape of cancer is regulated by many factors, but primarily it derives from the underlying genome sequence. Chromothripsis is a catastrophic localized genome shattering event that drives, and often initiates, cancer evolution. We characterized five esophageal adenocarcinoma organoids with chromothripsis using long-read sequencing and transcriptome and epigenome profiling. Complex structural variation and subclonal variants meant that haplotype-aware de novo methods were required to generate contiguous cancer genome assemblies. Chromosomes were assembled separately and scaffolded using haplotype-resolved Hi-C reads, producing accurate assemblies even with up to 900 structural rearrangements. There were widespread differences between the chromothriptic and wild-type copies of chromosomes in topologically associated domains, chromatin accessibility, histone modifications, and gene expression. Differential epigenome peaks were most enriched within 10 kb of chromothriptic structural variants. Alterations in transcriptome and higher-order chromosome organization frequently occurred near differential epigenetic marks. Overall, chromothripsis reshapes gene regulation, causing coordinated changes in epigenetic landscape, transcription, and chromosome conformation.


Assuntos
Adenocarcinoma , Cromotripsia , Neoplasias Esofágicas , Humanos , Haplótipos , Cromatina , Genoma , Adenocarcinoma/genética
5.
J Pathol ; 262(1): 10-21, 2024 01.
Artigo em Inglês | MEDLINE | ID: mdl-37792584

RESUMO

Wilms tumors (WTs) are histologically diverse childhood cancers with variable contributions of blastema, stroma, and epithelia. A variety of cancer genes operate in WTs, including the tripartite-motif-containing-28 gene (TRIM28). Case reports and small case series suggest that TRIM28 mutations are associated with epithelial morphology and WT predisposition. Here, we systematically investigated the prevalence of TRIM28 inactivation and predisposing mutations in a cohort of 126 WTs with >2/3 epithelial cells, spanning 20 years of biobanking in the German SIOP93-01/GPOH and SIOP2001/GPOH studies. Overall, 44.4% (56/126) cases exhibited loss of TRIM28 by immunohistochemical staining. Of these, 48 could be further analyzed molecularly, revealing TRIM28 sequence variants in each case - either homozygous (~2/3) or heterozygous with epigenetic silencing of the second allele (~1/3). The majority (80%) of the mutations resulted in premature stops and frameshifts. In addition, we detected missense mutations and small deletions predicted to destabilize the protein through interference with folding of key structural elements such as the zinc-binding clusters of the RING, B-box-2, and PHD domains or the central coiled-coil region. TRIM28-mutant tumors otherwise lacked WT-typical IGF2 alterations or driver events, except for rare TP53 progression events that occurred with expected frequency. Expression profiling identified TRIM28-mutant tumors as a homogeneous subset of epithelial WTs that mostly present with stage I disease. There was a high prevalence of perilobar nephrogenic rests, putative precursor lesions, that carried the same biallelic TRIM28 alterations in 7/7 cases tested. Importantly, 46% of the TRIM28 mutations were present in blood cells or normal kidney tissue, suggesting germline events or somatic mosaicism, partly supported by family history. Given the high prevalence of predisposing variants in TRIM28-driven WT, we suggest that immunohistochemical testing of TRIM28 be integrated into diagnostic practice as the management of WT in predisposed children differs from that with sporadic tumors. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.


Assuntos
Neoplasias Renais , Tumor de Wilms , Criança , Humanos , Neoplasias Renais/patologia , Bancos de Espécimes Biológicos , Tumor de Wilms/metabolismo , Rim/patologia , Mutação em Linhagem Germinativa , Suscetibilidade a Doenças/patologia , Proteína 28 com Motivo Tripartido/genética
6.
Nat Med ; 29(12): 3175-3183, 2023 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-37973947

RESUMO

Gene therapy (GT) provides a potentially curative treatment option for patients with sickle cell disease (SCD); however, the occurrence of myeloid malignancies in GT clinical trials has prompted concern, with several postulated mechanisms. Here, we used whole-genome sequencing to track hematopoietic stem cells (HSCs) from six patients with SCD at pre- and post-GT time points to map the somatic mutation and clonal landscape of gene-modified and unmodified HSCs. Pre-GT, phylogenetic trees were highly polyclonal and mutation burdens per cell were elevated in some, but not all, patients. Post-GT, no clonal expansions were identified among gene-modified or unmodified cells; however, an increased frequency of potential driver mutations associated with myeloid neoplasms or clonal hematopoiesis (DNMT3A- and EZH2-mutated clones in particular) was observed in both genetically modified and unmodified cells, suggesting positive selection of mutant clones during GT. This work sheds light on HSC clonal dynamics and the mutational landscape after GT in SCD, highlighting the enhanced fitness of some HSCs harboring pre-existing driver mutations. Future studies should define the long-term fate of mutant clones, including any contribution to expansions associated with myeloid neoplasms.


Assuntos
Anemia Falciforme , Neoplasias , Humanos , Hematopoese/genética , Filogenia , Mutação/genética , Células-Tronco Hematopoéticas/patologia , Células Clonais , Anemia Falciforme/genética , Anemia Falciforme/terapia , Anemia Falciforme/patologia , Terapia Genética , Neoplasias/patologia
7.
Nat Genet ; 55(2): 246-254, 2023 02.
Artigo em Inglês | MEDLINE | ID: mdl-36702998

RESUMO

APOBEC mutational signatures SBS2 and SBS13 are common in many human cancer types. However, there is an incomplete understanding of its stimulus, when it occurs in the progression from normal to cancer cell and the APOBEC enzymes responsible. Here we whole-genome sequenced 342 microdissected normal epithelial crypts from the small intestines of 39 individuals and found that SBS2/SBS13 mutations were present in 17% of crypts, more frequent than most other normal tissues. Crypts with SBS2/SBS13 often had immediate crypt neighbors without SBS2/SBS13, suggesting that the underlying cause of SBS2/SBS13 is cell-intrinsic. APOBEC mutagenesis occurred in an episodic manner throughout the human lifespan, including in young children. APOBEC1 mRNA levels were very high in the small intestine epithelium, but low in the large intestine epithelium and other tissues. The results suggest that the high levels of SBS2/SBS13 in the small intestine are collateral damage from APOBEC1 fulfilling its physiological function of editing APOB mRNA.


Assuntos
Apolipoproteínas B , Citidina Desaminase , Criança , Humanos , Pré-Escolar , Apolipoproteínas B/genética , Citidina Desaminase/genética , Mutagênese/genética , RNA Mensageiro/genética , Desaminase APOBEC-1/genética , Intestino Delgado
8.
Nat Commun ; 13(1): 4272, 2022 08 11.
Artigo em Inglês | MEDLINE | ID: mdl-35953478

RESUMO

Germ cell tumours (GCTs) are a collection of benign and malignant neoplasms derived from primordial germ cells. They are uniquely able to recapitulate embryonic and extraembryonic tissues, which carries prognostic and therapeutic significance. The developmental pathways underpinning GCT initiation and histogenesis are incompletely understood. Here, we study the relationship of histogenesis and clonal diversification in GCTs by analysing the genomes and transcriptomes of 547 microdissected histological units. We find no correlation between genomic and histological heterogeneity. However, we identify unifying features including the retention of fetal developmental transcripts across tissues, expression changes on chromosome 12p, and a conserved somatic evolutionary sequence of whole genome duplication followed by clonal diversification. While this pattern is preserved across all GCTs, the developmental timing of the duplication varies between prepubertal and postpubertal cases. In addition, tumours of younger children exhibit distinct substitution signatures which may lend themselves as potential biomarkers for risk stratification. Our findings portray the extensive diversification of GCT tissues and genetic subclones as randomly distributed, while identifying overarching transcriptional and genomic features.


Assuntos
Neoplasias Embrionárias de Células Germinativas , Neoplasias Testiculares , Criança , Genômica , Humanos , Masculino , Neoplasias Embrionárias de Células Germinativas/genética , Neoplasias Testiculares/genética , Transcriptoma/genética
9.
Nat Commun ; 13(1): 3949, 2022 07 08.
Artigo em Inglês | MEDLINE | ID: mdl-35803914

RESUMO

Cellular DNA damage caused by reactive oxygen species is repaired by the base excision repair (BER) pathway which includes the DNA glycosylase MUTYH. Inherited biallelic MUTYH mutations cause predisposition to colorectal adenomas and carcinoma. However, the mechanistic progression from germline MUTYH mutations to MUTYH-Associated Polyposis (MAP) is incompletely understood. Here, we sequence normal tissue DNAs from 10 individuals with MAP. Somatic base substitution mutation rates in intestinal epithelial cells were elevated 2 to 4-fold in all individuals, except for one showing a 31-fold increase, and were also increased in other tissues. The increased mutation burdens were of multiple mutational signatures characterised by C > A changes. Different mutation rates and signatures between individuals are likely due to different MUTYH mutations or additional inherited mutations in other BER pathway genes. The elevated base substitution rate in normal cells likely accounts for the predisposition to neoplasia in MAP. Despite ubiquitously elevated mutation rates, individuals with MAP do not display overt evidence of premature ageing. Thus, accumulation of somatic mutations may not be sufficient to cause the global organismal functional decline of ageing.


Assuntos
Polipose Adenomatosa do Colo , Neoplasias Colorretais , DNA Glicosilases/genética , Polipose Adenomatosa do Colo/genética , Polipose Adenomatosa do Colo/patologia , Neoplasias Colorretais/genética , Neoplasias Colorretais/patologia , DNA Glicosilases/metabolismo , Predisposição Genética para Doença , Mutação em Linhagem Germinativa , Humanos , Mutação , Taxa de Mutação
10.
Nature ; 606(7913): 343-350, 2022 06.
Artigo em Inglês | MEDLINE | ID: mdl-35650442

RESUMO

Age-related change in human haematopoiesis causes reduced regenerative capacity1, cytopenias2, immune dysfunction3 and increased risk of blood cancer4-6, but the reason for such abrupt functional decline after 70 years of age remains unclear. Here we sequenced 3,579 genomes from single cell-derived colonies of haematopoietic cells across 10 human subjects from 0 to 81 years of age. Haematopoietic stem cells or multipotent progenitors (HSC/MPPs) accumulated a mean of 17 mutations per year after birth and lost 30 base pairs per year of telomere length. Haematopoiesis in adults less than 65 years of age was massively polyclonal, with high clonal diversity and a stable population of 20,000-200,000 HSC/MPPs contributing evenly to blood production. By contrast, haematopoiesis in individuals aged over 75 showed profoundly decreased clonal diversity. In each of the older subjects, 30-60% of haematopoiesis was accounted for by 12-18 independent clones, each contributing 1-34% of blood production. Most clones had begun their expansion before the subject was 40 years old, but only 22% had known driver mutations. Genome-wide selection analysis estimated that between 1 in 34 and 1 in 12 non-synonymous mutations were drivers, accruing at constant rates throughout life, affecting more genes than identified in blood cancers. Loss of the Y chromosome conferred selective benefits in males. Simulations of haematopoiesis, with constant stem cell population size and constant acquisition of driver mutations conferring moderate fitness benefits, entirely explained the abrupt change in clonal structure in the elderly. Rapidly decreasing clonal diversity is a universal feature of haematopoiesis in aged humans, underpinned by pervasive positive selection acting on many more genes than currently identified.


Assuntos
Envelhecimento , Hematopoiese Clonal , Células Clonais , Longevidade , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Envelhecimento/genética , Criança , Pré-Escolar , Hematopoiese Clonal/genética , Células Clonais/citologia , Feminino , Neoplasias Hematológicas/genética , Neoplasias Hematológicas/patologia , Células-Tronco Hematopoéticas/citologia , Humanos , Lactente , Recém-Nascido , Masculino , Pessoa de Meia-Idade , Células-Tronco Multipotentes/citologia , Adulto Jovem
11.
Nat Commun ; 12(1): 880, 2021 02 09.
Artigo em Inglês | MEDLINE | ID: mdl-33563981

RESUMO

L1 retrotransposons can pose a threat to genome integrity. The host has evolved to restrict L1 replication. However, mechanisms underlying L1 propagation out of the host surveillance remains unclear. Here, we propose an evolutionary survival strategy of L1, which exploits RNA m6A modification. We discover that m6A 'writer' METTL3 facilitates L1 retrotransposition, whereas m6A 'eraser' ALKBH5 suppresses it. The essential m6A cluster that is located on L1 5' UTR serves as a docking site for eukaryotic initiation factor 3 (eIF3), enhances translational efficiency and promotes the formation of L1 ribonucleoprotein. Furthermore, through the comparative analysis of human- and primate-specific L1 lineages, we find that the most functional m6A motif-containing L1s have been positively selected and became a distinctive feature of evolutionarily young L1s. Thus, our findings demonstrate that L1 retrotransposons hijack the RNA m6A modification system for their successful replication.


Assuntos
Adenosina/análogos & derivados , Evolução Molecular , Elementos Nucleotídeos Longos e Dispersos/genética , RNA/metabolismo , Regiões 5' não Traduzidas , Adenosina/genética , Adenosina/metabolismo , Homólogo AlkB 5 da RNA Desmetilase/metabolismo , Animais , Células HeLa , Humanos , Metilação , Metiltransferases/metabolismo , Primatas/classificação , Primatas/genética , Biossíntese de Proteínas , RNA/química , Ribonucleoproteínas/metabolismo
12.
Oncogene ; 40(7): 1347-1361, 2021 02.
Artigo em Inglês | MEDLINE | ID: mdl-33420369

RESUMO

Previous studies studying mis-splicing mutations were based on exome data and thus our current knowledge is largely limited to exons and the canonical splice sites. To comprehensively characterise intronic mis-splicing mutations, we analysed 1134 pan-cancer whole genomes and transcriptomes together with 3022 normal control samples. The ratio-based splicing analysis resulted in 678 somatic intronic mutations, with 46% residing in deep introns. Among the 309 deep intronic single nucleotide variants, 245 altered core splicing codes, with 38% activating cryptic splice sites, 12% activating cryptic polypyrimidine tracts, and 36% and 12% disrupting authentic polypyrimidine tracts and branchpoints, respectively. All the intronic cryptic splice sites were created at pre-existing GT/AG dinucleotides or by GC-to-GT conversion. Notably, 85 deep intronic mutations indicated gain of splicing enhancers or loss of splicing silencers. We found that 64 tumour suppressors were affected by intronic mutations and blood cancers showed higher proportion of deep intronic mutations. In particular, a telomere maintenance gene, POT1, was recurrently mis-spliced by deep intronic mutations in blood cancers. We validated a pseudoexon activation involving a splicing silencer in POT1 by CRISPR/Cas9. Our results shed light on previously unappreciated mechanisms by which noncoding mutations acting on splicing codes in deep introns contribute to tumourigenesis.


Assuntos
Carcinogênese/genética , Neoplasias Hematológicas/genética , Splicing de RNA/genética , Proteínas de Ligação a Telômeros/genética , Sistemas CRISPR-Cas/genética , Linhagem Celular Tumoral , Éxons/genética , Neoplasias Hematológicas/patologia , Humanos , Íntrons/genética , Mutação/genética , Polimorfismo de Nucleotídeo Único/genética , Sítios de Splice de RNA/genética , Complexo Shelterina
13.
Clin Epigenetics ; 12(1): 119, 2020 08 06.
Artigo em Inglês | MEDLINE | ID: mdl-32762727

RESUMO

BACKGROUND: It is crucial to unravel molecular determinants of responses to immune checkpoint blockade (ICB) therapy because only a small subset of advanced non-small cell lung cancer (NSCLC) patients responds to ICB therapy. Previous studies were concentrated on genomic and transcriptomic markers (e.g., mutation burden and immune gene expression). However, these markers are not sufficient to accurately predict a response to ICB therapy. RESULTS: Here, we analyzed DNA methylomes of 141 advanced NSCLC samples subjected to ICB therapy (i.e., anti-programmed death-1) from two independent cohorts (60 and 81 patients from our and IDIBELL cohorts). Integrative analysis of patients with matched transcriptome data in our cohort (n = 28) at pathway level revealed significant overlaps between promoter hypermethylation and transcriptional repression in nonresponders relative to responders. Fifteen immune-related pathways, including interferon signaling, were identified to be enriched for both hypermethylation and repression. We built a reliable prognostic risk model based on eight genes using LASSO model and successfully validated the model in independent cohorts. Furthermore, we found 30 survival-associated molecular interaction networks, in which two or three hypermethylated genes showed significant mutual exclusion across nonresponders. CONCLUSIONS: Our study demonstrates that methylation patterns can provide insight into molecular determinants underlying the clinical benefit of ICB therapy.


Assuntos
Carcinoma Pulmonar de Células não Pequenas/tratamento farmacológico , Metilação de DNA/genética , Estudo de Associação Genômica Ampla/métodos , Inibidores de Checkpoint Imunológico/uso terapêutico , Imunoterapia/métodos , Neoplasias Pulmonares/tratamento farmacológico , Carcinoma Pulmonar de Células não Pequenas/genética , Humanos , Neoplasias Pulmonares/genética
14.
Cell ; 182(3): 672-684.e11, 2020 08 06.
Artigo em Inglês | MEDLINE | ID: mdl-32697969

RESUMO

Inflammatory bowel disease (IBD) is a chronic inflammatory disease associated with increased risk of gastrointestinal cancers. We whole-genome sequenced 446 colonic crypts from 46 IBD patients and compared these to 412 crypts from 41 non-IBD controls from our previous publication on the mutation landscape of the normal colon. The average mutation rate of affected colonic epithelial cells is 2.4-fold that of healthy colon, and this increase is mostly driven by acceleration of mutational processes ubiquitously observed in normal colon. In contrast to the normal colon, where clonal expansions outside the confines of the crypt are rare, we observed widespread millimeter-scale clonal expansions. We discovered non-synonymous mutations in ARID1A, FBXW7, PIGR, ZC3H12A, and genes in the interleukin 17 and Toll-like receptor pathways, under positive selection in IBD. These results suggest distinct selection mechanisms in the colitis-affected colon and that somatic mutations potentially play a causal role in IBD pathogenesis.


Assuntos
Evolução Clonal/genética , Colite/genética , Doenças Inflamatórias Intestinais/genética , Taxa de Mutação , Adulto , Idoso , Idoso de 80 Anos ou mais , Envelhecimento/genética , Evolução Clonal/imunologia , Colite/metabolismo , Colite Ulcerativa/genética , Colite Ulcerativa/metabolismo , Doença de Crohn/genética , Doença de Crohn/metabolismo , Proteínas de Ligação a DNA/genética , Células Epiteliais/metabolismo , Células Epiteliais/patologia , Proteína 7 com Repetições F-Box-WD/genética , Feminino , Humanos , Mutação INDEL , Doenças Inflamatórias Intestinais/imunologia , Doenças Inflamatórias Intestinais/metabolismo , Doenças Inflamatórias Intestinais/patologia , Interleucina-17/metabolismo , Mucosa Intestinal/metabolismo , Mucosa Intestinal/patologia , Masculino , Pessoa de Meia-Idade , Filogenia , Mutação Puntual , Receptores de Superfície Celular/genética , Ribonucleases/genética , Receptores Toll-Like/genética , Fatores de Transcrição/genética , Sequenciamento Completo do Genoma
15.
Nat Commun ; 11(1): 951, 2020 02 19.
Artigo em Inglês | MEDLINE | ID: mdl-32075964

RESUMO

Neoantigen burden is regarded as a fundamental determinant of response to immunotherapy. However, its predictive value remains in question because some tumours with high neoantigen load show resistance. Here, we investigate our patient cohort together with a public cohort by our algorithms for the modelling of peptide-MHC binding and inter-cohort genomic prediction of therapeutic resistance. We first attempt to predict MHC-binding peptides at high accuracy with convolutional neural networks. Our prediction outperforms previous methods in > 70% of test cases. We then develop a classifier that can predict resistance from functional mutations. The predictive genes are involved in immune response and EGFR signalling, whereas their mutation patterns reflect positive selection. When integrated with our neoantigen profiling, these anti-immunogenic mutations reveal higher predictive power than known resistance factors. Our results suggest that the clinical benefit of immunotherapy can be determined by neoantigens that induce immunity and functional mutations that facilitate immune evasion.


Assuntos
Algoritmos , Antígenos de Neoplasias/genética , Neoplasias/imunologia , Neoplasias/terapia , Antígenos de Neoplasias/imunologia , Antígenos de Neoplasias/metabolismo , Estudos de Coortes , Receptores ErbB/genética , Receptores ErbB/imunologia , Genoma Humano/genética , Antígenos de Histocompatibilidade Classe I/metabolismo , Humanos , Evasão da Resposta Imune/genética , Evasão da Resposta Imune/imunologia , Imunoterapia , Mutação , Neoplasias/genética , Neoplasias/patologia , Redes Neurais de Computação , Fragmentos de Peptídeos/metabolismo , Ligação Proteica
16.
Acta Biomater ; 101: 285-292, 2020 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-31610340

RESUMO

Recently, endovascular coil embolization has been introduced to treat intracranial aneurysms because it has lower morbidity and mortality than surgical clipping. The endovascular coils prevent the extravasation of blood by decreasing the permeability of an aneurysm flow governed by Darcy's law. Here, we developed and explored Pt-coated micro-ropes for potential use as endovascular coils. Electrospinning with subsequent electroplating were employed to fabricate Pt-coated nanofibers, which were tightly twisted to form micro-ropes. The compatibility of Pt micro-ropes with commercial delivery catheters was verified and their performance was experimentally explored in an in vitro experimental model. The developed Pt-coated micro-ropes demonstrated feasibility as efficient and low-cost endovascular coils. STATEMENT OF SIGNIFICANCE: The use of Platinum (Pt)-coated polymer nanofibers to prevent blood extravasation has been demonstrated. These Pt nanofibers were installed within a microfluidic channel, and the resulting reduced permeability was evaluated using a fluid similar to blood. Based on the obtained results, these newly developed nanofibers are expected to decrease the operation cost for aneurysmal subarachnoid hemorrhage (SAH), owing their reduced size and low material cost. Overall, the use of this new material should reduce the operational risk associated with the multiple steps required to place the Pt coils at the SAH site. The compatibility of Pt micro-ropes with commercial delivery catheters was verified and their performance was experimentally explored in an in vitro experimental model. The developed Pt-coated micro-ropes demonstrated feasibility as efficient and low-cost endovascular coils.


Assuntos
Materiais Revestidos Biocompatíveis/farmacologia , Embolização Terapêutica , Procedimentos Endovasculares , Nanofibras/química , Platina/farmacologia , Resinas Acrílicas/química , Catéteres , Galvanoplastia , Humanos , Nanofibras/ultraestrutura , Permeabilidade , Reologia , Bexiga Urinária/efeitos dos fármacos
17.
Nat Commun ; 10(1): 4278, 2019 09 19.
Artigo em Inglês | MEDLINE | ID: mdl-31537801

RESUMO

Mitotic cell division increases tumour mutation burden and copy number load, predictive markers of the clinical benefit of immunotherapy. Cell division correlates also with genomic demethylation involving methylation loss in late-replicating partial methylation domains. Here we find that immunomodulatory pathway genes are concentrated in these domains and transcriptionally repressed in demethylated tumours with CpG island promoter hypermethylation. Global methylation loss correlated with immune evasion signatures independently of mutation burden and aneuploidy. Methylome data of our cohort (n = 60) and a published cohort (n = 81) in lung cancer and a melanoma cohort (n = 40) consistently demonstrated that genomic methylation alterations counteract the contribution of high mutation burden and increase immunotherapeutic resistance. Higher predictive power was observed for methylation loss than mutation burden. We also found that genomic hypomethylation correlates with the immune escape signatures of aneuploid tumours. Hence, DNA methylation alterations implicate epigenetic modulation in precision immunotherapy.


Assuntos
Metilação de DNA/genética , Neoplasias/genética , Neoplasias/imunologia , Evasão Tumoral/genética , Evasão Tumoral/imunologia , Aneuploidia , Biomarcadores Tumorais/genética , Proliferação de Células/genética , Ilhas de CpG/genética , Variações do Número de Cópias de DNA/genética , Epigênese Genética , Regulação Neoplásica da Expressão Gênica/genética , Humanos , Taxa de Mutação , Regiões Promotoras Genéticas/genética
19.
Genome Res ; 28(8): 1136-1146, 2018 08.
Artigo em Inglês | MEDLINE | ID: mdl-29970450

RESUMO

Long interspersed nuclear element-1 (LINE-1 or L1) retrotransposons are normally suppressed in somatic tissues mainly due to DNA methylation and antiviral defense. However, the mechanism to suppress L1s may be disrupted in cancers, thus allowing L1s to act as insertional mutagens and cause genomic rearrangement and instability. Whereas the frequency of somatic L1 insertions varies greatly among individual tumors, much remains to be learned about underlying genetic, cellular, or environmental factors. Here, we report multiple correlates of L1 activity in stomach, colorectal, and esophageal tumors through an integrative analysis of cancer whole-genome and matched RNA-sequencing profiles. Clinical indicators of tumor progression, such as tumor grade and patient age, showed positive association. A potential L1 expression suppressor, TP53, was mutated in tumors with frequent L1 insertions. We characterized the effects of somatic L1 insertions on mRNA splicing and expression, and demonstrated an increased risk of gene disruption in retrotransposition-prone cancers. In particular, we found that a cancer-specific L1 insertion in an exon of MOV10, a key L1 suppressor, caused exon skipping and decreased expression of the affected allele due to nonsense-mediated decay in a tumor with a high L1 insertion load. Importantly, tumors with high immune activity, for example, those associated with Epstein-Barr virus infection or microsatellite instability, tended to carry a low number of L1 insertions in genomes with high expression levels of L1 suppressors such as APOBEC3s and SAMHD1 Our results indicate that cancer immunity may contribute to genome stability by suppressing L1 retrotransposition in gastrointestinal cancers.


Assuntos
Neoplasias Gastrointestinais/genética , Elementos Nucleotídeos Longos e Dispersos/genética , Retroelementos/genética , Proteína Supressora de Tumor p53/genética , Desaminase APOBEC-3G/genética , Linhagem Celular Tumoral , Metilação de DNA/genética , Neoplasias Gastrointestinais/imunologia , Neoplasias Gastrointestinais/patologia , Regulação Neoplásica da Expressão Gênica/imunologia , Instabilidade Genômica/genética , Instabilidade Genômica/imunologia , Humanos , Elementos Nucleotídeos Longos e Dispersos/imunologia , Mutagênese Insercional/genética , Proteínas de Neoplasias/genética , Proteínas de Neoplasias/imunologia , RNA Helicases/genética , RNA Helicases/imunologia , Splicing de RNA/genética , Retroelementos/imunologia
20.
ACS Appl Mater Interfaces ; 10(25): 21213-21223, 2018 Jun 27.
Artigo em Inglês | MEDLINE | ID: mdl-29911866

RESUMO

CO2 capture using polyethyleneimine (PEI)-impregnated silica adsorbents has been receiving a lot of attention. However, the absence of physical stability (evaporation and leaching of amine) and chemical stability (urea formation) of the PEI-impregnated silica adsorbent has been generally established. Therefore, in this study, a double-layer impregnated structure, developed using modified PEI, is newly proposed to enhance the physical and chemical stabilities of the adsorbent. Epoxy-modified PEI and diepoxide-cross-linked PEI were impregnated via a dry impregnation method in the first and second layers, respectively. The physical stability of the double-layer structured adsorbent was noticeably enhanced when compared to the conventional adsorbents with a single layer. In addition to the enhanced physical stability, the result of simulated temperature swing adsorption cycles revealed that the double-layer structured adsorbent presented a high potential working capacity (3.5 mmol/g) and less urea formation under CO2-rich regeneration conditions. The enhanced physical and chemical stabilities as well as the high CO2 working capacity of the double-layer structured adsorbent were mainly attributed to the second layer consisting of diepoxide-cross-linked PEI.

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