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1.
Proc Natl Acad Sci U S A ; 119(31): e2205412119, 2022 08 02.
Artículo en Inglés | MEDLINE | ID: mdl-35858383

RESUMEN

Camelid single-domain antibodies, also known as nanobodies, can be readily isolated from naïve libraries for specific targets but often bind too weakly to their targets to be immediately useful. Laboratory-based genetic engineering methods to enhance their affinity, termed maturation, can deliver useful reagents for different areas of biology and potentially medicine. Using the receptor binding domain (RBD) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein and a naïve library, we generated closely related nanobodies with micromolar to nanomolar binding affinities. By analyzing the structure-activity relationship using X-ray crystallography, cryoelectron microscopy, and biophysical methods, we observed that higher conformational entropy losses in the formation of the spike protein-nanobody complex are associated with tighter binding. To investigate this, we generated structural ensembles of the different complexes from electron microscopy maps and correlated the conformational fluctuations with binding affinity. This insight guided the engineering of a nanobody with improved affinity for the spike protein.


Asunto(s)
Anticuerpos Neutralizantes , Anticuerpos Antivirales , Afinidad de Anticuerpos , SARS-CoV-2 , Anticuerpos de Dominio Único , Glicoproteína de la Espiga del Coronavirus , Anticuerpos Neutralizantes/química , Anticuerpos Neutralizantes/genética , Anticuerpos Antivirales/química , Anticuerpos Antivirales/genética , Afinidad de Anticuerpos/genética , Microscopía por Crioelectrón , Entropía , Ingeniería Genética , Humanos , Unión Proteica , Dominios Proteicos , SARS-CoV-2/inmunología , Anticuerpos de Dominio Único/química , Anticuerpos de Dominio Único/genética , Glicoproteína de la Espiga del Coronavirus/inmunología
2.
Proteomics ; 24(12-13): e2200436, 2024 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-38438732

RESUMEN

Ion mobility spectrometry-mass spectrometry (IMS-MS or IM-MS) is a powerful analytical technique that combines the gas-phase separation capabilities of IM with the identification and quantification capabilities of MS. IM-MS can differentiate molecules with indistinguishable masses but different structures (e.g., isomers, isobars, molecular classes, and contaminant ions). The importance of this analytical technique is reflected by a staged increase in the number of applications for molecular characterization across a variety of fields, from different MS-based omics (proteomics, metabolomics, lipidomics, etc.) to the structural characterization of glycans, organic matter, proteins, and macromolecular complexes. With the increasing application of IM-MS there is a pressing need for effective and accessible computational tools. This article presents an overview of the most recent free and open-source software tools specifically tailored for the analysis and interpretation of data derived from IM-MS instrumentation. This review enumerates these tools and outlines their main algorithmic approaches, while highlighting representative applications across different fields. Finally, a discussion of current limitations and expectable improvements is presented.


Asunto(s)
Algoritmos , Espectrometría de Movilidad Iónica , Espectrometría de Masas , Programas Informáticos , Espectrometría de Movilidad Iónica/métodos , Espectrometría de Masas/métodos , Proteómica/métodos , Metabolómica/métodos , Humanos
3.
BMC Bioinformatics ; 24(1): 152, 2023 Apr 17.
Artículo en Inglés | MEDLINE | ID: mdl-37069545

RESUMEN

BACKGROUND: The rapid development of synthetic biology relies heavily on the use of databases and computational tools, which are also developing rapidly. While many tool registries have been created to facilitate tool retrieval, sharing, and reuse, no relatively comprehensive tool registry or catalog addresses all aspects of synthetic biology. RESULTS: We constructed SynBioTools, a comprehensive collection of synthetic biology databases, computational tools, and experimental methods, as a one-stop facility for searching and selecting synthetic biology tools. SynBioTools includes databases, computational tools, and methods extracted from reviews via SCIentific Table Extraction, a scientific table-extraction tool that we built. Approximately 57% of the resources that we located and included in SynBioTools are not mentioned in bio.tools, the dominant tool registry. To improve users' understanding of the tools and to enable them to make better choices, the tools are grouped into nine modules (each with subdivisions) based on their potential biosynthetic applications. Detailed comparisons of similar tools in every classification are included. The URLs, descriptions, source references, and the number of citations of the tools are also integrated into the system. CONCLUSIONS: SynBioTools is freely available at https://synbiotools.lifesynther.com/ . It provides end-users and developers with a useful resource of categorized synthetic biology databases, tools, and methods to facilitate tool retrieval and selection.


Asunto(s)
Biología Computacional , Biología Sintética , Biología Computacional/métodos , Sistema de Registros , Bases de Datos Factuales , Programas Informáticos
4.
Mol Biol Evol ; 39(4)2022 04 11.
Artículo en Inglés | MEDLINE | ID: mdl-35298641

RESUMEN

Research over the past two decades has made substantial inroads into our understanding of somatic mutations. Recently, these studies have focused on understanding their presence in homeostatic tissue. In parallel, agent-based mechanistic models have emerged as an important tool for understanding somatic mutation in tissue; yet no common methodology currently exists to provide base-pair resolution data for these models. Here, we present Gattaca as the first method for introducing and tracking somatic mutations at the base-pair resolution within agent-based models that typically lack nuclei. With nuclei that incorporate human reference genomes, mutational context, and sequence coverage/error information, Gattaca is able to realistically evolve sequence data, facilitating comparisons between in silico cell tissue modeling with experimental human somatic mutation data. This user-friendly method, incorporated into each in silico cell, allows us to fully capture somatic mutation spectra and evolution.


Asunto(s)
Genoma Humano , Neoplasias , Evolución Clonal , Humanos , Mutación , Neoplasias/genética
5.
BMC Biol ; 20(1): 159, 2022 07 12.
Artículo en Inglés | MEDLINE | ID: mdl-35820848

RESUMEN

BACKGROUND: Various mammalian species emit ultrasonic vocalizations (USVs), which reflect their emotional state and mediate social interactions. USVs are usually analyzed by manual or semi-automated methodologies that categorize discrete USVs according to their structure in the frequency-time domains. This laborious analysis hinders the effective use of USVs as a readout for high-throughput analysis of behavioral changes in animals. RESULTS: Here we present a novel automated open-source tool that utilizes a different approach towards USV analysis, termed TrackUSF. To validate TrackUSF, we analyzed calls from different animal species, namely mice, rats, and bats, recorded in various settings and compared the results with a manual analysis by a trained observer. We found that TrackUSF detected the majority of USVs, with less than 1% of false-positive detections. We then employed TrackUSF to analyze social vocalizations in Shank3-deficient rats, a rat model of autism, and revealed that these vocalizations exhibit a spectrum of deviations from appetitive calls towards aversive calls. CONCLUSIONS: TrackUSF is a simple and easy-to-use system that may be used for a high-throughput comparison of ultrasonic vocalizations between groups of animals of any kind in any setting, with no prior assumptions.


Asunto(s)
Trastorno Autístico , Ultrasonido , Animales , Emociones , Mamíferos , Ratones , Proteínas de Microfilamentos , Proteínas del Tejido Nervioso , Ratas , Vocalización Animal
6.
J Lipid Res ; 63(7): 100197, 2022 07.
Artículo en Inglés | MEDLINE | ID: mdl-35300982

RESUMEN

Plasma lipid levels are altered in chronic conditions such as type 2 diabetes and cardiovascular disease as well as during acute stresses such as fasting and cold exposure. Advances in MS-based lipidomics have uncovered a complex plasma lipidome of more than 500 lipids that serve functional roles, including as energy substrates and signaling molecules. This plasma lipid pool is maintained through regulation of tissue production, secretion, and uptake. A major challenge in understanding the lipidome complexity is establishing the tissues of origin and uptake for various plasma lipids, which is valuable for determining lipid functions. Using cold exposure as an acute stress, we performed global lipidomics on plasma and in nine tissues that may contribute to the circulating lipid pool. We found that numerous species of plasma acylcarnitines (ACars) and ceramides (Cers) were significantly altered upon cold exposure. Through computational assessment, we identified the liver and brown adipose tissue as major contributors and consumers of circulating ACars, in agreement with our previous work. We further identified the kidney and intestine as novel contributors to the circulating ACar pool and validated these findings with gene expression analysis. Regression analysis also identified that the brown adipose tissue and kidney are interactors with the plasma Cer pool. Taken together, these studies provide an adaptable computational tool to assess tissue contribution to the plasma lipid pool. Our findings have further implications in understanding the function of plasma ACars and Cers, which are elevated in metabolic diseases.


Asunto(s)
Diabetes Mellitus Tipo 2 , Tejido Adiposo Pardo/metabolismo , Frío , Diabetes Mellitus Tipo 2/metabolismo , Ayuno , Humanos , Lipidómica , Lípidos , Termogénesis
7.
BMC Genomics ; 21(Suppl 11): 793, 2020 Dec 29.
Artículo en Inglés | MEDLINE | ID: mdl-33372596

RESUMEN

BACKGROUND: Long-read RNA-Seq techniques can generate reads that encompass a large proportion or the entire mRNA/cDNA molecules, so they are expected to address inherited limitations of short-read RNA-Seq techniques that typically generate < 150 bp reads. However, there is a general lack of software tools for gene fusion detection from long-read RNA-seq data, which takes into account the high basecalling error rates and the presence of alignment errors. RESULTS: In this study, we developed a fast computational tool, LongGF, to efficiently detect candidate gene fusions from long-read RNA-seq data, including cDNA sequencing data and direct mRNA sequencing data. We evaluated LongGF on tens of simulated long-read RNA-seq datasets, and demonstrated its superior performance in gene fusion detection. We also tested LongGF on a Nanopore direct mRNA sequencing dataset and a PacBio sequencing dataset generated on a mixture of 10 cancer cell lines, and found that LongGF achieved better performance to detect known gene fusions over existing computational tools. Furthermore, we tested LongGF on a Nanopore cDNA sequencing dataset on acute myeloid leukemia, and pinpointed the exact location of a translocation (previously known in cytogenetic resolution) in base resolution, which was further validated by Sanger sequencing. CONCLUSIONS: In summary, LongGF will greatly facilitate the discovery of candidate gene fusion events from long-read RNA-Seq data, especially in cancer samples. LongGF is implemented in C++ and is available at https://github.com/WGLab/LongGF .


Asunto(s)
Programas Informáticos , Transcriptoma , Algoritmos , Fusión Génica , Secuenciación de Nucleótidos de Alto Rendimiento , Análisis de Secuencia de ARN
8.
Mol Syst Biol ; 15(4): e8250, 2019 04 12.
Artículo en Inglés | MEDLINE | ID: mdl-30979792

RESUMEN

Identifying hyperactive kinases in cancer is crucial for individualized treatment with specific inhibitors. Kinase activity can be discerned from global protein phosphorylation profiles obtained with mass spectrometry-based phosphoproteomics. A major challenge is to relate such profiles to specific hyperactive kinases fueling growth/progression of individual tumors. Hitherto, the focus has been on phosphorylation of either kinases or their substrates. Here, we combined label-free kinase-centric and substrate-centric information in an Integrative Inferred Kinase Activity (INKA) analysis. This multipronged, stringent analysis enables ranking of kinase activity and visualization of kinase-substrate networks in a single biological sample. To demonstrate utility, we analyzed (i) cancer cell lines with known oncogenes, (ii) cell lines in a differential setting (wild-type versus mutant, +/- drug), (iii) pre- and on-treatment tumor needle biopsies, (iv) cancer cell panel with available drug sensitivity data, and (v) patient-derived tumor xenografts with INKA-guided drug selection and testing. These analyses show superior performance of INKA over its components and substrate-based single-sample tool KARP, and underscore target potential of high-ranking kinases, encouraging further exploration of INKA's functional and clinical value.


Asunto(s)
Neoplasias/enzimología , Fosfotransferasas/análisis , Proteómica/métodos , Biología de Sistemas/métodos , Línea Celular Tumoral , Activación Enzimática , Humanos , Células K562 , Espectrometría de Masas , Fosfoproteínas/análisis
9.
BMC Genomics ; 20(Suppl 1): 78, 2019 Feb 04.
Artículo en Inglés | MEDLINE | ID: mdl-30712508

RESUMEN

BACKGROUND: Recent advances in single-molecule sequencing techniques, such as Nanopore sequencing, improved read length, increased sequencing throughput, and enabled direct detection of DNA modifications through the analysis of raw signals. These DNA modifications include naturally occurring modifications such as DNA methylations, as well as modifications that are introduced by DNA damage or through synthetic modifications to one of the four standard nucleotides. METHODS: To improve the performance of detecting DNA modifications, especially synthetically introduced modifications, we developed a novel computational tool called NanoMod. NanoMod takes raw signal data on a pair of DNA samples with and without modified bases, extracts signal intensities, performs base error correction based on a reference sequence, and then identifies bases with modifications by comparing the distribution of raw signals between two samples, while taking into account of the effects of neighboring bases on modified bases ("neighborhood effects"). RESULTS: We evaluated NanoMod on simulation data sets, based on different types of modifications and different magnitudes of neighborhood effects, and found that NanoMod outperformed other methods in identifying known modified bases. Additionally, we demonstrated superior performance of NanoMod on an E. coli data set with 5mC (5-methylcytosine) modifications. CONCLUSIONS: In summary, NanoMod is a flexible tool to detect DNA modifications with single-base resolution from raw signals in Nanopore sequencing, and will facilitate large-scale functional genomics experiments that use modified nucleotides.


Asunto(s)
Biología Computacional/métodos , ADN , Análisis de Secuencia de ADN/métodos , Programas Informáticos , Algoritmos , Simulación por Computador , ADN/química , ADN/genética , ADN/metabolismo , Escherichia coli/genética , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Humanos , Nanoporos , Reproducibilidad de los Resultados , Flujo de Trabajo
10.
Am J Med Genet A ; 176(12): 2704-2709, 2018 12.
Artículo en Inglés | MEDLINE | ID: mdl-30475443

RESUMEN

The increasing use of next-generation sequencing, especially clinical exome sequencing, has revealed that individuals having two coexisting genetic conditions are not uncommon occurrences. This pilot study evaluates the efficacy of two methodologically distinct computational differential diagnosis generating tools-FindZebra and SimulConsult-in identifying multiple genetic conditions in a single patient. Clinical query terms were generated for each of 15 monogenic disorders that were effective in resulting in the top 10 list of differential diagnoses for each of the 15 monogenic conditions when entered into these bioinformatics tools. Then, the terms of over 125 pairings of these conditions were entered using each tool and the resulting list of diagnoses evaluated to determine how often both diagnoses of a pair were represented in that list. Neither tool was successful in identifying both members of a pair of conditions in greater than 40% of test cases. Disorder detection sensitivity was not homogeneous within a tool, with each tool favoring the identification of a subset of genetic conditions. In view of recent exome sequencing data showing an unexpectedly high prevalence of coexistent monogenic conditions, the results from this pilot study highlight a need for the development of computational tools designed to effectively generate differential diagnoses with consideration of the possibility of coexisting conditions.


Asunto(s)
Diagnóstico por Computador/métodos , Enfermedades Genéticas Congénitas/diagnóstico , Enfermedades Genéticas Congénitas/genética , Pruebas Genéticas/métodos , Preescolar , Biología Computacional/métodos , Diagnóstico por Computador/normas , Diagnóstico Diferencial , Pruebas Genéticas/normas , Humanos , Masculino , Reproducibilidad de los Resultados , Sensibilidad y Especificidad , Programas Informáticos , Navegador Web
11.
Proc Natl Acad Sci U S A ; 111(28): 10263-8, 2014 Jul 15.
Artículo en Inglés | MEDLINE | ID: mdl-24982153

RESUMEN

Transposons make up the bulk of eukaryotic genomes, but are difficult to annotate because they evolve rapidly. Most of the unannotated portion of sequenced genomes is probably made up of various divergent transposons that have yet to be categorized. Helitrons are unusual rolling circle eukaryotic transposons that often capture gene sequences, making them of considerable evolutionary importance. Unlike other DNA transposons, Helitrons do not end in inverted repeats or create target site duplications, so they are particularly challenging to identify. Here we present HelitronScanner, a two-layered local combinational variable (LCV) tool for generalized Helitron identification that represents a major improvement over previous identification programs based on DNA sequence or structure. HelitronScanner identified 64,654 Helitrons from a wide range of plant genomes in a highly automated way. We tested HelitronScanner's predictive ability in maize, a species with highly heterogeneous Helitron elements. LCV scores for the 5' and 3' termini of the predicted Helitrons provide a primary confidence level and element copy number provides a secondary one. Newly identified Helitrons were validated by PCR assays or by in silico comparative analysis of insertion site polymorphism among multiple accessions. Many new Helitrons were identified in model species, such as maize, rice, and Arabidopsis, and in a variety of organisms where Helitrons had not been reported previously to our knowledge, leading to a major upward reassessment of their abundance in plant genomes. HelitronScanner promises to be a valuable tool in future comparative and evolutionary studies of this major transposon superfamily.


Asunto(s)
Elementos Transponibles de ADN/fisiología , Evolución Molecular , Genoma de Planta/fisiología , Plantas/genética , Reacción en Cadena de la Polimerasa/métodos , Análisis de Secuencia de ADN/métodos
12.
Hum Mutat ; 36(12): 1128-34, 2015 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-26333163

RESUMEN

Variations in mismatch repair (MMR) system genes are causative of Lynch syndrome and other cancers. Thousands of variants have been identified in MMR genes, but the clinical relevance is known for only a small proportion. Recently, the InSiGHT group classified 2,360 MMR variants into five classes. One-third of variants, majority of which is nonsynonymous variants, remain to be of uncertain clinical relevance. Computational tools can be used to prioritize variants for disease relevance investigations. Previously, we classified 248 MMR variants as likely pathogenic and likely benign using PON-MMR. We have developed a novel tool, PON-MMR2, which is trained on a larger and more reliable dataset. In performance comparison, PON-MMR2 outperforms both generic tolerance prediction methods as well as methods optimized for MMR variants. It achieves accuracy and MCC of 0.89 and 0.78, respectively, in cross-validation and 0.86 and 0.69, respectively, on an independent test dataset. We classified 354 class 3 variants in InSiGHT database as well as all possible amino acid substitutions in four MMR proteins. Likely harmful variants mainly appear in the protein core, whereas likely benign variants are on the surface. PON-MMR2 is a highly reliable tool to prioritize variants for functional analysis. It is freely available at http://structure.bmc.lu.se/PON-MMR2/.


Asunto(s)
Sustitución de Aminoácidos , Biología Computacional/métodos , Reparación de la Incompatibilidad de ADN/genética , Enzimas Reparadoras del ADN/genética , Mutación , Proteínas Nucleares/genética , Programas Informáticos , Neoplasias Colorrectales Hereditarias sin Poliposis/genética , Enzimas Reparadoras del ADN/química , Bases de Datos Genéticas , Humanos , Aprendizaje Automático , Proteínas Nucleares/química , Reproducibilidad de los Resultados , Navegador Web
13.
Chemosphere ; 358: 142217, 2024 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-38704043

RESUMEN

Long-term exposure to environmental chemicals can detrimentally impact human health, and understanding the relationship between age distribution and levels of external and internal exposure is crucial. Nonetheless, existing methods for assessing population-wide exposure across age groups are limited. To bridge this research gap, we introduced a modeling approach designed to assess both chronic external and internal exposure to chemicals at the population level. The external and internal exposure assessments were quantified in terms of the average daily dose (ADD) and steady-state blood concentration of the environmental chemical, respectively, which were categorized by age and gender groups. The modeling process was presented within a spreadsheet framework, affording users the capability to execute population-wide exposure analyses across a spectrum of chemicals. Our simulation outcomes underscored a salient trend: younger age groups, particularly infants and children, exhibited markedly higher ADD values and blood concentrations of environmental chemicals compared to their older counterparts. This observation is due to the elevated basal metabolic rate per unit of body weight characteristic of younger individuals, coupled with their diminished biotransformation kinetics of xenobiotics within their livers. These factors collectively contribute to increased intake rates of environmental chemicals per unit of body weight through air and food consumption, along with heightened bioaccumulation of these chemicals within their bodies (e.g., blood). Furthermore, we augmented the precision of the external and internal exposure assessment by incorporating the age distribution across the population. The simulation outcomes unveiled that, to estimate the central tendency of the population's exposure levels, employing the baseline value group (age group 21-30) or the surrogate age of 25 serves as a simple yet dependable approach. However, for comprehensive population protection, our recommendation aligns with conducting exposure assessments for the younger age groups (age group 0-11). Future studies should integrate individual-level exposure assessment, analyze vulnerable population groups, and refine population structures within our developed model.


Asunto(s)
Exposición a Riesgos Ambientales , Contaminantes Ambientales , Naftalenos , Exposición a Riesgos Ambientales/estadística & datos numéricos , Humanos , Contaminantes Ambientales/sangre , Niño , Adulto , Preescolar , Naftalenos/sangre , Lactante , Masculino , Femenino , Adulto Joven , Adolescente , Persona de Mediana Edad , Recién Nacido , Anciano
14.
Cell Metab ; 36(5): 1126-1143.e5, 2024 May 07.
Artículo en Inglés | MEDLINE | ID: mdl-38604170

RESUMEN

Cellular senescence underlies many aging-related pathologies, but its heterogeneity poses challenges for studying and targeting senescent cells. We present here a machine learning program senescent cell identification (SenCID), which accurately identifies senescent cells in both bulk and single-cell transcriptome. Trained on 602 samples from 52 senescence transcriptome datasets spanning 30 cell types, SenCID identifies six major senescence identities (SIDs). Different SIDs exhibit different senescence baselines, stemness, gene functions, and responses to senolytics. SenCID enables the reconstruction of senescent trajectories under normal aging, chronic diseases, and COVID-19. Additionally, when applied to single-cell Perturb-seq data, SenCID helps reveal a hierarchy of senescence modulators. Overall, SenCID is an essential tool for precise single-cell analysis of cellular senescence, enabling targeted interventions against senescent cells.


Asunto(s)
COVID-19 , Senescencia Celular , Aprendizaje Automático , Análisis de la Célula Individual , Transcriptoma , Humanos , SARS-CoV-2/metabolismo , Envejecimiento
15.
Methods Cell Biol ; 183: 265-302, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38548414

RESUMEN

Neoantigens have emerged as promising targets for cutting-edge immunotherapies, such as cancer vaccines and adoptive cell therapy. These neoantigens are unique to tumors and arise exclusively from somatic mutations or non-genomic aberrations in tumor proteins. They encompass a wide range of alterations, including genomic mutations, post-transcriptomic variants, and viral oncoproteins. With the advancements in technology, the identification of immunogenic neoantigens has seen rapid progress, raising new opportunities for enhancing their clinical significance. Prediction of neoantigens necessitates the acquisition of high-quality samples and sequencing data, followed by mutation calling. Subsequently, the pipeline involves integrating various tools that can predict the expression, processing, binding, and recognition potential of neoantigens. However, the continuous improvement of computational tools is constrained by the availability of datasets which contain validated immunogenic neoantigens. This review article aims to provide a comprehensive summary of the current knowledge as well as limitations in neoantigen prediction and validation. Additionally, it delves into the origin and biological role of neoantigens, offering a deeper understanding of their significance in the field of cancer immunotherapy. This article thus seeks to contribute to the ongoing efforts to harness neoantigens as powerful weapons in the fight against cancer.


Asunto(s)
Antígenos de Neoplasias , Neoplasias , Humanos , Antígenos de Neoplasias/genética , Neoplasias/genética , Neoplasias/terapia , Inmunoterapia
16.
Artículo en Inglés | MEDLINE | ID: mdl-39013167

RESUMEN

Mass spectrometry is broadly employed to study complex molecular mechanisms in various biological and environmental fields, enabling 'omics' research such as proteomics, metabolomics, and lipidomics. As study cohorts grow larger and more complex with dozens to hundreds of samples, the need for robust quality control (QC) measures through automated software tools becomes paramount to ensure the integrity, high quality, and validity of scientific conclusions from downstream analyses and minimize the waste of resources. Since existing QC tools are mostly dedicated to proteomics, automated solutions supporting metabolomics are needed. To address this need, we developed the software PeakQC, a tool for automated QC of MS data that is independent of omics molecular types (i.e., omics-agnostic). It allows automated extraction and inspection of peak metrics of precursor ions (e.g., errors in mass, retention time, arrival time) and supports various instrumentations and acquisition types, from infusion experiments or using liquid chromatography and/or ion mobility spectrometry front-end separations and with/without fragmentation spectra from data-dependent or independent acquisition analyses. Diagnostic plots for fragmentation spectra are also generated. Here, we describe and illustrate PeakQC's functionalities using different representative data sets, demonstrating its utility as a valuable tool for enhancing the quality and reliability of omics mass spectrometry analyses.

17.
MethodsX ; 12: 102741, 2024 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-38846434

RESUMEN

We present a lightweight tool for clonotyping and measurable residual disease (MRD) assessment in monoclonal lymphoproliferative disorders. It is a translational method that enables computational detection of rearranged immunoglobulin heavy chain gene sequences.•The swigh-score clonotyping tool emphasizes parallelization and applicability across sequencing platforms.•The algorithm is based on an adaptation of the Smith-Waterman algorithm for local alignment of reads generated by 2nd and 3rd generation of sequencers.For method validation, we demonstrate the targeted sequences of immunoglobulin heavy chain genes from diagnostic bone marrow using serial dilutions of CD138+ plasma cells from a patient with multiple myeloma. Sequencing libraries from diagnostic samples were prepared for the three sequencing platforms, Ion S5 (Thermo Fisher Scientific), MiSeq (Illumina), and MinION (Oxford Nanopore), using the LymphoTrack assay. Basic quality filtering was performed, and a Smith-Waterman-based swigh-score algorithm was developed in shell and C for clonotyping and MRD assessment using FASTQ data files. Performance is demonstrated across the three different sequencing platforms.

18.
Genomics Proteomics Bioinformatics ; 21(1): 48-66, 2023 02.
Artículo en Inglés | MEDLINE | ID: mdl-35718270

RESUMEN

Dissecting intercellular epigenetic differences is key to understanding tissue heterogeneity. Recent advances in single-cell DNA methylome profiling have presented opportunities to resolve this heterogeneity at the maximum resolution. While these advances enable us to explore frontiers of chromatin biology and better understand cell lineage relationships, they pose new challenges in data processing and interpretation. This review surveys the current state of computational tools developed for single-cell DNA methylome data analysis. We discuss critical components of single-cell DNA methylome data analysis, including data preprocessing, quality control, imputation, dimensionality reduction, cell clustering, supervised cell annotation, cell lineage reconstruction, gene activity scoring, and integration with transcriptome data. We also highlight unique aspects of single-cell DNA methylome data analysis and discuss how techniques common to other single-cell omics data analyses can be adapted to analyze DNA methylomes. Finally, we discuss existing challenges and opportunities for future development.


Asunto(s)
Metilación de ADN , Epigenoma , Perfilación de la Expresión Génica/métodos , Epigénesis Genética , Transcriptoma , Análisis de la Célula Individual/métodos , Biología Computacional/métodos , Epigenómica/métodos
19.
Genomics Proteomics Bioinformatics ; 21(1): 108-126, 2023 02.
Artículo en Inglés | MEDLINE | ID: mdl-35341983

RESUMEN

The past decade has witnessed a rapid evolution in identifying more versatile clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) nucleases and their functional variants, as well as in developing precise CRISPR/Cas-derived genome editors. The programmable and robust features of the genome editors provide an effective RNA-guided platform for fundamental life science research and subsequent applications in diverse scenarios, including biomedical innovation and targeted crop improvement. One of the most essential principles is to guide alterations in genomic sequences or genes in the intended manner without undesired off-target impacts, which strongly depends on the efficiency and specificity of single guide RNA (sgRNA)-directed recognition of targeted DNA sequences. Recent advances in empirical scoring algorithms and machine learning models have facilitated sgRNA design and off-target prediction. In this review, we first briefly introduce the different features of CRISPR/Cas tools that should be taken into consideration to achieve specific purposes. Secondly, we focus on the computer-assisted tools and resources that are widely used in designing sgRNAs and analyzing CRISPR/Cas-induced on- and off-target mutations. Thirdly, we provide insights into the limitations of available computational tools that would help researchers of this field for further optimization. Lastly, we suggest a simple but effective workflow for choosing and applying web-based resources and tools for CRISPR/Cas genome editing.


Asunto(s)
Sistemas CRISPR-Cas , Edición Génica , ARN Guía de Sistemas CRISPR-Cas , Genoma , Genómica
20.
Curr Drug Deliv ; 20(7): 1015-1029, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-35473527

RESUMEN

BACKGROUND: Chemoresistance continues to limit the recovery of patients with cancer. New strategies, such as combination therapy or nanotechnology, can be further improved. OBJECTIVE: In this study, we applied the computational strategy by exploiting two databases (CellMiner and Prism) to sort out the cell lines sensitive to both anti-cancer drugs, paclitaxel (PTX) and dihydroartemisinin (DHA); both of which are potentially synergistic in several cell lines. METHODS: The combination of PTX and DHA was screened at different ratios to select the optimal ratio that could inhibit lung adenocarcinoma NCI-H23 the most. To further enhance therapeutic efficacy, these combinations of drugs were incorporated into a nanosystem. RESULTS: At a PTX:DHA ratio of 1:2 (w/w), the combined drugs obtained the best combination index (0.84), indicating a synergistic effect. The drug-loaded nanoparticles sized at 135 nm with the drug loading capacity of 15.5 ± 1.34 and 13.8 ± 0.56 corresponding to DHA and PTX, respectively, were used. The nano-sized particles improved drug internalization into the cells, resulting in the significant inhibition of cell growth at all tested concentrations (p < 0.001). Additionally, α-tubulin aggregation, DNA damage suggested the molecular mechanism behind cell death upon PTX-DHA-loaded nanoparticle treatment. Moreover, the rate of apoptosis increased from approximately 5% to more than 20%, and the expression of apoptotic proteins changed 4 and 3 folds corresponding to p-53 and Bcl-2, respectively. CONCLUSION: This study was designed thoroughly by screening cell lines for the optimization of formulations. This novel approach could pave the way for the selection of combined drugs for precise cancer treatment.


Asunto(s)
Antineoplásicos , Nanopartículas , Neoplasias , Humanos , Sinergismo Farmacológico , Detección Precoz del Cáncer , Paclitaxel/farmacología , Antineoplásicos/farmacología , Apoptosis , Nanotecnología , Línea Celular Tumoral , Neoplasias/tratamiento farmacológico
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