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1.
Int J Mol Sci ; 25(2)2024 Jan 12.
Artigo em Inglês | MEDLINE | ID: mdl-38256049

RESUMO

The incidence and mortality of hepatocellular carcinoma (HCC) in Sub-Saharan Africa is projected to increase sharply by 2040 against a backdrop of limited diagnostic and therapeutic options. Two large South African-based case control studies have developed a serum-based miRNome for Hepatitis B-associated hepatocellular carcinoma (HBV-HCC), as well as identifying their gene targets and pathways. Using a combination of RNA sequencing, differential analysis and filters including a unique molecular index count (UMI) ≥ 10 and log fold change (LFC) range > 2: <-0.5 (p < 0.05), 91 dysregulated miRNAs were characterized including 30 that were upregulated and 61 were downregulated. KEGG analysis, a literature review and other bioinformatic tools identified the targeted genes and HBV-HCC pathways of the top 10 most dysregulated miRNAs. The results, which are based on differentiating miRNA expression of cases versus controls, also develop a serum-based miRNA diagnostic panel that indicates 95.9% sensitivity, 91.0% specificity and a Youden Index of 0.869. In conclusion, the results develop a comprehensive African HBV-HCC miRNome that potentially can contribute to RNA-based diagnostic and therapeutic options.


Assuntos
Carcinoma Hepatocelular , Hepatite B , Neoplasias Hepáticas , MicroRNAs , Humanos , Carcinoma Hepatocelular/genética , Neoplasias Hepáticas/genética , África do Sul/epidemiologia , Hepatite B/complicações , Hepatite B/genética , MicroRNAs/genética
2.
Gut ; 71(6): 1161-1175, 2022 06.
Artigo em Inglês | MEDLINE | ID: mdl-34340996

RESUMO

OBJECTIVE: Hepatocellular carcinoma (HCC) represents a typical inflammation-associated cancer. Tissue resident innate lymphoid cells (ILCs) have been suggested to control tumour surveillance. Here, we studied how the local cytokine milieu controls ILCs in HCC. DESIGN: We performed bulk RNA sequencing of HCC tissue as well as flow cytometry and single-cell RNA sequencing of enriched ILCs from non-tumour liver, margin and tumour core derived from 48 patients with HCC. Simultaneous measurement of protein and RNA expression at the single-cell level (AbSeq) identified precise signatures of ILC subgroups. In vitro culturing of ILCs was used to validate findings from in silico analysis. Analysis of RNA-sequencing data from large HCC cohorts allowed stratification and survival analysis based on transcriptomic signatures. RESULTS: RNA sequencing of tumour, non-tumour and margin identified tumour-dependent gradients, which were associated with poor survival and control of ILC plasticity. Single-cell RNA sequencing and flow cytometry of ILCs from HCC livers identified natural killer (NK)-like cells in the non-tumour tissue, losing their cytotoxic profile as they transitioned into tumour ILC1 and NK-like-ILC3 cells. Tumour ILC composition was mediated by cytokine gradients that directed ILC plasticity towards activated tumour ILC2s. This was liver-specific and not seen in ILCs from peripheral blood mononuclear cells. Patients with high ILC2/ILC1 ratio expressed interleukin-33 in the tumour that promoted ILC2 generation, which was associated with better survival. CONCLUSION: Our results suggest that the tumour cytokine milieu controls ILC composition and HCC outcome. Specific changes of cytokines modify ILC composition in the tumour by inducing plasticity and alter ILC function.


Assuntos
Carcinoma Hepatocelular , Neoplasias Hepáticas , Carcinoma Hepatocelular/metabolismo , Citocinas/metabolismo , Humanos , Imunidade Inata , Células Matadoras Naturais/metabolismo , Leucócitos Mononucleares , Neoplasias Hepáticas/metabolismo , Linfócitos , RNA/metabolismo , Microambiente Tumoral
3.
Cell Rep Med ; 4(6): 101052, 2023 06 20.
Artigo em Inglês | MEDLINE | ID: mdl-37224815

RESUMO

Primary liver cancer is a rising cause of cancer deaths in the US. Although immunotherapy with immune checkpoint inhibitors induces a potent response in a subset of patients, response rates vary among individuals. Predicting which patients will respond to immune checkpoint inhibitors is of great interest in the field. In a retrospective arm of the National Cancer Institute Cancers of the Liver: Accelerating Research of Immunotherapy by a Transdisciplinary Network (NCI-CLARITY) study, we use archived formalin-fixed, paraffin-embedded samples to profile the transcriptome and genomic alterations among 86 hepatocellular carcinoma and cholangiocarcinoma patients prior to and following immune checkpoint inhibitor treatment. Using supervised and unsupervised approaches, we identify stable molecular subtypes linked to overall survival and distinguished by two axes of aggressive tumor biology and microenvironmental features. Moreover, molecular responses to immune checkpoint inhibitor treatment differ between subtypes. Thus, patients with heterogeneous liver cancer may be stratified by molecular status indicative of treatment response to immune checkpoint inhibitors.


Assuntos
Carcinoma Hepatocelular , Neoplasias Hepáticas , Humanos , Inibidores de Checkpoint Imunológico/farmacologia , Inibidores de Checkpoint Imunológico/uso terapêutico , Estudos Retrospectivos , Imunoterapia , Carcinoma Hepatocelular/terapia , Neoplasias Hepáticas/terapia , Genômica
4.
Genome Biol ; 23(1): 255, 2022 12 13.
Artigo em Inglês | MEDLINE | ID: mdl-36514120

RESUMO

BACKGROUND: The cancer genome is commonly altered with thousands of structural rearrangements including insertions, deletions, translocation, inversions, duplications, and copy number variations. Thus, structural variant (SV) characterization plays a paramount role in cancer target identification, oncology diagnostics, and personalized medicine. As part of the SEQC2 Consortium effort, the present study established and evaluated a consensus SV call set using a breast cancer reference cell line and matched normal control derived from the same donor, which were used in our companion benchmarking studies as reference samples. RESULTS: We systematically investigated somatic SVs in the reference cancer cell line by comparing to a matched normal cell line using multiple NGS platforms including Illumina short-read, 10X Genomics linked reads, PacBio long reads, Oxford Nanopore long reads, and high-throughput chromosome conformation capture (Hi-C). We established a consensus SV call set of a total of 1788 SVs including 717 deletions, 230 duplications, 551 insertions, 133 inversions, 146 translocations, and 11 breakends for the reference cancer cell line. To independently evaluate and cross-validate the accuracy of our consensus SV call set, we used orthogonal methods including PCR-based validation, Affymetrix arrays, Bionano optical mapping, and identification of fusion genes detected from RNA-seq. We evaluated the strengths and weaknesses of each NGS technology for SV determination, and our findings provide an actionable guide to improve cancer genome SV detection sensitivity and accuracy. CONCLUSIONS: A high-confidence consensus SV call set was established for the reference cancer cell line. A large subset of the variants identified was validated by multiple orthogonal methods.


Assuntos
Variações do Número de Cópias de DNA , Neoplasias , Humanos , Análise de Sequência de DNA/métodos , Variação Estrutural do Genoma , Tecnologia , Linhagem Celular , Sequenciamento de Nucleotídeos em Larga Escala , Genoma Humano , Neoplasias/genética
5.
Sci Data ; 8(1): 296, 2021 11 09.
Artigo em Inglês | MEDLINE | ID: mdl-34753956

RESUMO

With the rapid advancement of sequencing technologies, next generation sequencing (NGS) analysis has been widely applied in cancer genomics research. More recently, NGS has been adopted in clinical oncology to advance personalized medicine. Clinical applications of precision oncology require accurate tests that can distinguish tumor-specific mutations from artifacts introduced during NGS processes or data analysis. Therefore, there is an urgent need to develop best practices in cancer mutation detection using NGS and the need for standard reference data sets for systematically measuring accuracy and reproducibility across platforms and methods. Within the SEQC2 consortium context, we established paired tumor-normal reference samples and generated whole-genome (WGS) and whole-exome sequencing (WES) data using sixteen library protocols, seven sequencing platforms at six different centers. We systematically interrogated somatic mutations in the reference samples to identify factors affecting detection reproducibility and accuracy in cancer genomes. These large cross-platform/site WGS and WES datasets using well-characterized reference samples will represent a powerful resource for benchmarking NGS technologies, bioinformatics pipelines, and for the cancer genomics studies.


Assuntos
Sequenciamento do Exoma , Genoma Humano , Neoplasias/genética , Sequenciamento Completo do Genoma , Benchmarking , Linhagem Celular Tumoral , Biologia Computacional , Genômica , Humanos , Medicina de Precisão
6.
Nat Biotechnol ; 39(9): 1141-1150, 2021 09.
Artigo em Inglês | MEDLINE | ID: mdl-34504346

RESUMO

Clinical applications of precision oncology require accurate tests that can distinguish true cancer-specific mutations from errors introduced at each step of next-generation sequencing (NGS). To date, no bulk sequencing study has addressed the effects of cross-site reproducibility, nor the biological, technical and computational factors that influence variant identification. Here we report a systematic interrogation of somatic mutations in paired tumor-normal cell lines to identify factors affecting detection reproducibility and accuracy at six different centers. Using whole-genome sequencing (WGS) and whole-exome sequencing (WES), we evaluated the reproducibility of different sample types with varying input amount and tumor purity, and multiple library construction protocols, followed by processing with nine bioinformatics pipelines. We found that read coverage and callers affected both WGS and WES reproducibility, but WES performance was influenced by insert fragment size, genomic copy content and the global imbalance score (GIV; G > T/C > A). Finally, taking into account library preparation protocol, tumor content, read coverage and bioinformatics processes concomitantly, we recommend actionable practices to improve the reproducibility and accuracy of NGS experiments for cancer mutation detection.


Assuntos
Benchmarking , Sequenciamento do Exoma/normas , Neoplasias/genética , Análise de Sequência de DNA/normas , Sequenciamento Completo do Genoma/normas , Linhagem Celular , Linhagem Celular Tumoral , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Mutação , Neoplasias/patologia , Reprodutibilidade dos Testes
7.
Nat Biotechnol ; 39(9): 1151-1160, 2021 09.
Artigo em Inglês | MEDLINE | ID: mdl-34504347

RESUMO

The lack of samples for generating standardized DNA datasets for setting up a sequencing pipeline or benchmarking the performance of different algorithms limits the implementation and uptake of cancer genomics. Here, we describe reference call sets obtained from paired tumor-normal genomic DNA (gDNA) samples derived from a breast cancer cell line-which is highly heterogeneous, with an aneuploid genome, and enriched in somatic alterations-and a matched lymphoblastoid cell line. We partially validated both somatic mutations and germline variants in these call sets via whole-exome sequencing (WES) with different sequencing platforms and targeted sequencing with >2,000-fold coverage, spanning 82% of genomic regions with high confidence. Although the gDNA reference samples are not representative of primary cancer cells from a clinical sample, when setting up a sequencing pipeline, they not only minimize potential biases from technologies, assays and informatics but also provide a unique resource for benchmarking 'tumor-only' or 'matched tumor-normal' analyses.


Assuntos
Benchmarking , Neoplasias da Mama/genética , Análise Mutacional de DNA/normas , Sequenciamento de Nucleotídeos em Larga Escala/normas , Sequenciamento Completo do Genoma/normas , Linhagem Celular Tumoral , Conjuntos de Dados como Assunto , Células Germinativas , Humanos , Mutação , Padrões de Referência , Reprodutibilidade dos Testes
8.
Nat Cancer ; 1(9): 894-908, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-35121952

RESUMO

Argininosuccinate synthase (ASS1) downregulation in different tumors has been shown to support cell proliferation and yet, in several common cancer subsets ASS1 expression associates with poor patient prognosis. Here we demonstrate that ASS1 expression under glucose deprivation is induced by c-MYC, providing survival benefit by increasing nitric oxide synthesis and activating the gluconeogenic enzymes pyruvate carboxylase and phosphoenolpyruvate carboxykinase by S-nitrosylation. The resulting increased flux through gluconeogenesis enhances serine, glycine and subsequently purine synthesis. Notably, high ASS1-expressing breast cancer mice do not respond to immune checkpoint inhibitors and patients with breast cancer with high ASS1 have more metastases. We further find that inhibiting purine synthesis increases pyrimidine to purine ratio, elevates expression of the immunoproteasome and significantly enhances the response of autologous primary CD8+ T cells to anti-PD-1. These results suggest that treating patients with high-ASS1 cancers with purine synthesis inhibition is beneficial and may also sensitize them to immune checkpoint inhibition therapy.


Assuntos
Argininossuccinato Sintase , Neoplasias da Mama , Animais , Argininossuccinato Sintase/metabolismo , Linfócitos T CD8-Positivos/metabolismo , Linhagem Celular Tumoral , Feminino , Humanos , Inibidores de Checkpoint Imunológico , Camundongos , Purinas
9.
Proteins ; 59(2): 205-20, 2005 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-15726586

RESUMO

We developed a pharmacophore-based evolutionary approach for virtual screening. This tool, termed the Generic Evolutionary Method for molecular DOCKing (GEMDOCK), combines an evolutionary approach with a new pharmacophore-based scoring function. The former integrates discrete and continuous global search strategies with local search strategies to expedite convergence. The latter, integrating an empirical-based energy function and pharmacological preferences (binding-site pharmacological interactions and ligand preferences), simultaneously serves as the scoring function for both molecular docking and postdocking analyses to improve screening accuracy. We apply pharmacological interaction preferences to select the ligands that form pharmacological interactions with target proteins, and use the ligand preferences to eliminate the ligands that violate the electrostatic or hydrophilic constraints. We assessed the accuracy of our approach using human estrogen receptor (ER) and a ligand database from the comparative studies of Bissantz et al. (J Med Chem 2000;43:4759-4767). Using GEMDOCK, the average goodness-of-hit (GH) score was 0.83 and the average false-positive rate was 0.13% for ER antagonists, and the average GH score was 0.48 and the average false-positive rate was 0.75% for ER agonists. The performance of GEMDOCK was superior to competing methods such as GOLD and DOCK. We found that our pharmacophore-based scoring function indeed was able to reduce the number of false positives; moreover, the resulting pharmacological interactions at the binding site, as well as ligand preferences, were important to the screening accuracy of our experiments. These results suggest that GEMDOCK constitutes a robust tool for virtual database screening.


Assuntos
Moduladores de Receptor Estrogênico/química , Evolução Molecular , Receptores de Estrogênio/genética , Sítios de Ligação , Bases de Dados Factuais , Bases de Dados de Proteínas , Antagonistas de Estrogênios/farmacologia , Moduladores de Receptor Estrogênico/farmacologia , Estrogênios/farmacologia , Ligantes , Modelos Moleculares , Conformação Proteica , Receptores de Estrogênio/química , Receptores de Estrogênio/efeitos dos fármacos , Interface Usuário-Computador
10.
J Phys Chem B ; 119(3): 1048-61, 2015 Jan 22.
Artigo em Inglês | MEDLINE | ID: mdl-25322200

RESUMO

The biophysical chemistry of macromolecular complexes confer their functional characteristics. We investigate the mechanisms that make the AB5 holotoxin of Vibrio cholerae (CT) a significantly more pathogenic molecule than the enterotoxin of Escherichia coli (LT) with which it shares 88% similarity and whose structure is homologous with a backbone RMSD of 0.84 Å and imposes its deleterious effects though the same process to constitutively ADP-ribosylate adenylate cyclase. We present computational data that characterizes the impact of amino acid variations in the A2 tail, which helps to explain experimental data that demonstrate CT's higher toxicity. A hydrophobic patch on the B pentamer interface and its interactions with the A subdomain are partially disrupted by the substitution of an aspartic acid (LT) for glycine in CT. CT's holotoxin has less solvent accessible surface area (94 Å(2) vs 54 Å(2)) and higher contact area (280 Å(2) vs 241 Å(2)) with S228, which is a gatekeeper, partially controlling the diffusion of water into the pore. CT excludes water from the top of the central pore whereas LT allows much more water to interact. These biophysical properties of the toxins lead to their differential toxicity and resulting impact to human health.


Assuntos
Fenômenos Biofísicos , Toxina da Cólera/química , Toxina da Cólera/toxicidade , Escherichia coli , Temperatura Alta , Simulação de Dinâmica Molecular , Toxina da Cólera/metabolismo , Ligação de Hidrogênio , Porosidade , Conformação Proteica , Solventes/química , Relação Estrutura-Atividade , Propriedades de Superfície , Água/química
11.
PLoS One ; 10(8): e0133751, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26241044

RESUMO

Genome-scale expression data on the absolute numbers of gene isoforms offers essential clues in cellular functions and biological processes. Smooth muscle cells (SMCs) perform a unique contractile function through expression of specific genes controlled by serum response factor (SRF), a transcription factor that binds to DNA sites known as the CArG boxes. To identify SRF-regulated genes specifically expressed in SMCs, we isolated SMC populations from mouse small intestine and colon, obtained their transcriptomes, and constructed an interactive SMC genome and CArGome browser. To our knowledge, this is the first online resource that provides a comprehensive library of all genetic transcripts expressed in primary SMCs. The browser also serves as the first genome-wide map of SRF binding sites. The browser analysis revealed novel SMC-specific transcriptional variants and SRF target genes, which provided new and unique insights into the cellular and biological functions of the cells in gastrointestinal (GI) physiology. The SRF target genes in SMCs, which were discovered in silico, were confirmed by proteomic analysis of SMC-specific Srf knockout mice. Our genome browser offers a new perspective into the alternative expression of genes in the context of SRF binding sites in SMCs and provides a valuable reference for future functional studies.


Assuntos
Proteínas Musculares/genética , Miócitos de Músculo Liso/metabolismo , RNA Mensageiro/genética , Elemento de Resposta Sérica/genética , Fator de Resposta Sérica/metabolismo , Navegador , Animais , Sítios de Ligação , Proteínas de Transporte/genética , Colo/citologia , Simulação por Computador , Biblioteca Gênica , Genes Reporter , Proteínas de Fluorescência Verde , Código das Histonas , Histonas/metabolismo , Canais Iônicos/genética , Jejuno/citologia , Camundongos , Camundongos Knockout , Camundongos Transgênicos , Especificidade de Órgãos , Proteômica , Fator de Resposta Sérica/deficiência , Transcriptoma
12.
J Chem Inf Model ; 45(4): 1134-46, 2005.
Artigo em Inglês | MEDLINE | ID: mdl-16045308

RESUMO

MOTIVATION: Virtual screening of molecular compound libraries is a potentially powerful and inexpensive method for the discovery of novel lead compounds for drug development. The major weakness of virtual screening-the inability to consistently identify true positives (leads)-is likely due to our incomplete understanding of the chemistry involved in ligand binding and the subsequently imprecise scoring algorithms. It has been demonstrated that combining multiple scoring functions (consensus scoring) improves the enrichment of true positives. Previous efforts at consensus scoring have largely focused on empirical results, but they have yet to provide a theoretical analysis that gives insight into real features of combinations and data fusion for virtual screening. RESULTS: We demonstrate that combining multiple scoring functions improves the enrichment of true positives only if (a) each of the individual scoring functions has relatively high performance and (b) the individual scoring functions are distinctive. Notably, these two prediction variables are previously established criteria for the performance of data fusion approaches using either rank or score combinations. This work, thus, establishes a potential theoretical basis for the probable success of data fusion approaches to improve yields in in silico screening experiments. Furthermore, it is similarly established that the second criterion (b) can, in at least some cases, be functionally defined as the area between the rank versus score plots generated by the two (or more) algorithms. Because rank-score plots are independent of the performance of the individual scoring function, this establishes a second theoretically defined approach to determining the likely success of combining data from different predictive algorithms. This approach is, thus, useful in practical settings in the virtual screening process when the performance of at least two individual scoring functions (such as in criterion a) can be estimated as having a high likelihood of having high performance, even if no training sets are available. We provide initial validation of this theoretical approach using data from five scoring systems with two evolutionary docking algorithms on four targets, thymidine kinase, human dihydrofolate reductase, and estrogen receptors of antagonists and agonists. Our procedure is computationally efficient, able to adapt to different situations, and scalable to a large number of compounds as well as to a greater number of combinations. Results of the experiment show a fairly significant improvement (vs single algorithms) in several measures of scoring quality, specifically "goodness-of-hit" scores, false positive rates, and "enrichment". This approach (available online at http://gemdock.life. nctu.edu.tw/dock/download.php) has practical utility for cases where the basic tools are known or believed to be generally applicable, but where specific training sets are absent.


Assuntos
Algoritmos , Bases de Dados Factuais , Desenho de Fármacos , Ligantes , Inibidores Enzimáticos/química , Inibidores Enzimáticos/farmacologia , Antagonistas do Ácido Fólico/química , Antagonistas do Ácido Fólico/farmacologia , Ligação Proteica , Receptores de Estrogênio/antagonistas & inibidores , Tetra-Hidrofolato Desidrogenase/efeitos dos fármacos , Timidina Quinase/antagonistas & inibidores
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