MethodsPub Date : 2025-02-12DOI: 10.1016/j.ymeth.2025.02.003
Nishant S. Kulkarni , Alexander Josowitz , Roshan James , Yang Liu , Bindhu Rayaprolu , Botir Sagdullaev , Amardeep S. Bhalla , Mohammed Shameem
{"title":"Latest trends & strategies in ocular drug delivery","authors":"Nishant S. Kulkarni , Alexander Josowitz , Roshan James , Yang Liu , Bindhu Rayaprolu , Botir Sagdullaev , Amardeep S. Bhalla , Mohammed Shameem","doi":"10.1016/j.ymeth.2025.02.003","DOIUrl":"10.1016/j.ymeth.2025.02.003","url":null,"abstract":"<div><div>Ocular drug delivery is one of the most challenging routes of administration, and this may be attributed to the complex interplay of ocular barriers and clearance mechanisms that restrict therapeutic payload residence. Most of the currently approved products that ameliorate ocular disease conditions are topical, i.e., delivering therapeutics to the outside anterior segment of the eye. This site of administration works well for certain conditions such as local infections but due to the presence of numerous ocular barriers, the permeation of therapeutics to the posterior segment of the eye is limited. Conditions such as age-related macular degeneration and diabetic retinopathy that contribute to an extreme deterioration of vision acuity require therapeutic interventions at the posterior segment of the eye. This necessitates development of intraocular delivery systems such as intravitreal injections, implants, and specialized devices that deliver therapeutics to the posterior segment of the eye. Frequent dosing regimens and high concentration formulations have been strategized and developed to achieve desired therapeutic outcomes by overcoming some of the challenges of drug clearance and efficacy. Correspondingly, development of suitable delivery platforms such as biodegradable and non-biodegradable implants, nano delivery systems, and implantable devices have been explored. This article provides an overview of the current trends in the development of suitable formulations & delivery systems for ocular drug delivery with an emphasis on late-stage clinical and approved product. Moreover, this work aims to summarize current challenges and highlights exciting pre-clinical developments, and future opportunities in cell and gene therapies that may be explored for effective ocular therapeutic outcomes.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"235 ","pages":"Pages 100-117"},"PeriodicalIF":4.2,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143403229","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
MethodsPub Date : 2025-02-09DOI: 10.1016/j.ymeth.2025.02.002
Linna Han, Z. Begum Yagci, Albert J. Keung
{"title":"A high sensitivity assay of UBE3A ubiquitin ligase activity","authors":"Linna Han, Z. Begum Yagci, Albert J. Keung","doi":"10.1016/j.ymeth.2025.02.002","DOIUrl":"10.1016/j.ymeth.2025.02.002","url":null,"abstract":"<div><div>UBE3A is an E3 ubiquitin ligase associated with several neurodevelopmental disorders. The development of several preclinical therapeutic approaches involving UBE3A, such as gene therapy, enzyme replacement therapy, and epigenetic reactivation, require the detection of its ubiquitin ligase activity. Prior commercial assays leveraged Western Blotting to detect shifts in substrate size due to ubiquitination, but these suffered from long assay times and have also been discontinued. Here we develop a new assay that quantifies UBE3A activity. It measures the fluorescence intensity of ubiquitinated p53 substrates with a microplate reader, eliminating the need for Western Blot antibodies and instruments, and enables detection in just 1 h. The assay is fast, cost-effective, low noise, and uses components with long shelf lives. Importantly, it is also highly sensitive, detecting UBE3A levels as low as 1 nM, similar to that observed in human and mouse cerebrospinal fluid. It also differentiates the activity of wild-type UBE3A and catalytic mutants. We also design a p53 substrate with a triple-epitope tag HIS-HA-CMYC on the N terminus, which allows for versatile detection of UBE3A activity from diverse natural and engineered sources. This new assay provides a timely solution for growing needs in preclinical validation, quality control, endpoint measurements for clinical trials, and downstream manufacturing testing and validation.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"235 ","pages":"Pages 92-99"},"PeriodicalIF":4.2,"publicationDate":"2025-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143394412","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
MethodsPub Date : 2025-02-08DOI: 10.1016/j.ymeth.2025.02.001
Rentao Luo, Jiawei Liu, Lixin Guan, Mengshan Li
{"title":"HybProm: An attention-assisted hybrid CNN-BiLSTM model for the interpretable prediction of DNA promoter","authors":"Rentao Luo, Jiawei Liu, Lixin Guan, Mengshan Li","doi":"10.1016/j.ymeth.2025.02.001","DOIUrl":"10.1016/j.ymeth.2025.02.001","url":null,"abstract":"<div><div>Promoter prediction is essential for analyzing gene structures, understanding regulatory networks, transcription mechanisms, and precisely controlling gene expression. Recently, computational and deep learning methods for promoter prediction have gained attention. However, there is still room to improve their accuracy. To address this, we propose the HybProm model, which uses DNA2Vec to transform DNA sequences into low-dimensional vectors, followed by a CNN-BiLSTM-Attention architecture to extract features and predict promoters across species, including E. coli, humans, mice, and plants. Experiments show that HybProm consistently achieves high accuracy (90%-99%) and offers good interpretability by identifying key sequence patterns and positions that drive predictions.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"235 ","pages":"Pages 71-80"},"PeriodicalIF":4.2,"publicationDate":"2025-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143377724","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
MethodsPub Date : 2025-02-05DOI: 10.1016/j.ymeth.2025.01.019
Weihong Zhang , Fan Hu , Peng Yin , Yunpeng Cai
{"title":"A transferability-guided protein-ligand interaction prediction method","authors":"Weihong Zhang , Fan Hu , Peng Yin , Yunpeng Cai","doi":"10.1016/j.ymeth.2025.01.019","DOIUrl":"10.1016/j.ymeth.2025.01.019","url":null,"abstract":"<div><div>Accurate prediction of protein–ligand interaction (PLI) is crucial for drug discovery and development. However, existing methods often struggle with effectively integrating heterogeneous protein and ligand data modalities and optimizing knowledge transfer from pretraining to the target task. This paper proposes a novel transferability-guided PLI prediction method that maximizes knowledge transfer by deeply integrating protein and ligand representations through a cross-attention mechanism and incorporating transferability metrics to guide fine-tuning. The cross-attention mechanism facilitates interactive information exchange between modalities, enabling the model to capture intricate interdependencies. Meanwhile, the transferability-guided strategy quantifies transferability from pretraining tasks and incorporates it into the training objective, ensuring the effective utilization of beneficial knowledge while mitigating negative transfer. Extensive experiments demonstrate significant and consistent improvements over traditional fine-tuning, validated by statistical tests. Ablation studies highlight the pivotal role of cross-attention, and quantitative analysis reveals the method’s ability to reduce harmful transfer. Our guided strategy provides a paradigm for more comprehensive utilization of pretraining knowledge, offering prospects for enhancing other PLI prediction approaches. This method advances PLI prediction via innovative modality fusion and guided knowledge transfer, paving the way for accelerated drug discovery pipelines. Code and data are freely available at <span><span>https://github.com/brian-zZZ/Guided-PLI</span><svg><path></path></svg></span>.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"235 ","pages":"Pages 64-70"},"PeriodicalIF":4.2,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143350880","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
MethodsPub Date : 2025-02-03DOI: 10.1016/j.ymeth.2025.01.020
Amit Phogat , Sowmya Ramaswamy Krishnan , Medha Pandey , M. Michael Gromiha
{"title":"ZFP-CanPred: Predicting the effect of mutations in zinc-finger proteins in cancers using protein language models","authors":"Amit Phogat , Sowmya Ramaswamy Krishnan , Medha Pandey , M. Michael Gromiha","doi":"10.1016/j.ymeth.2025.01.020","DOIUrl":"10.1016/j.ymeth.2025.01.020","url":null,"abstract":"<div><div>Zinc-finger proteins (ZNFs) constitute the largest family of transcription factors and play crucial roles in various cellular processes. Missense mutations in ZNFs significantly alter protein-DNA interactions, potentially leading to the development of various types of cancers. This study presents ZFP-CanPred, a novel deep learning-based model for predicting cancer-associated driver mutations in ZNFs. The representations derived from protein language models (PLMs) from the structural neighbourhood of mutated sites were utilized to train ZFP-CanPred for differentiating between cancer-causing and neutral mutations. ZFP-CanPred, achieved a superior performance with an accuracy of 0.72, F1-score of 0.79, and area under the Receiver Operating Characteristics (ROC) Curve (AUC) of 0.74, on an independent test set. In a comparative analysis against 11 existing prediction tools using a curated dataset of 331 mutations, ZFP-CanPred demonstrated the highest AU-ROC of 0.74, outperforming both generic and cancer-specific methods. The model’s balanced performance across specificity and sensitivity addresses a significant limitation of current methodologies. The source code and other related files are available on GitHub at <span><span>https://github.com/amitphogat/ZFP-CanPred.git</span><svg><path></path></svg></span>. We envisage that the present study contributes to understand the oncogenic processes and developing targeted therapeutic strategies.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"235 ","pages":"Pages 55-63"},"PeriodicalIF":4.2,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143254023","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
MethodsPub Date : 2025-02-01DOI: 10.1016/j.ymeth.2024.11.010
Chengxin He , Zhenjiang Zhao , Xinye Wang , Huiru Zheng , Lei Duan , Jie Zuo
{"title":"Exploring drug-target interaction prediction on cold-start scenarios via meta-learning-based graph transformer","authors":"Chengxin He , Zhenjiang Zhao , Xinye Wang , Huiru Zheng , Lei Duan , Jie Zuo","doi":"10.1016/j.ymeth.2024.11.010","DOIUrl":"10.1016/j.ymeth.2024.11.010","url":null,"abstract":"<div><div>Predicting drug-target interaction (DTI) is of great importance for drug discovery and development. With the rapid development of biological and chemical technologies, computational methods for DTI prediction are becoming a promising approach. However, there are few solutions to the cold-start problem in DTI prediction scenarios, as these methods rely on existing interaction information to support their modeling. Consequently, they are unable to effectively predict DTIs for new drugs or targets with limited interaction data in the existing work. To this end, we propose a graph transformer method based on meta-learning named MGDTI (short for <u>M</u>eta-learning-based <u>G</u>raph Transformer for <u>D</u>rug-<u>T</u>arget <u>I</u>nteraction prediction) to fill this gap. Technically, we employ drug-drug similarity and target-target similarity as additional information to mitigate the scarcity of interactions. Besides, we trained MGDTI via meta-learning to be adaptive to cold-start tasks. Moreover, we employed graph transformer to prevent over-smoothing by capturing long-range dependencies. Extensive results on the benchmark dataset demonstrate that MGDTI is effective on DTI prediction under cold-start scenarios.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"234 ","pages":"Pages 10-20"},"PeriodicalIF":4.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142643674","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
MethodsPub Date : 2025-02-01DOI: 10.1016/j.ymeth.2024.12.002
Karen Ofuji Osiro , Harry Morales Duque , Kamila Botelho Sampaio de Oliveira , Nadielle Tamires Moreira Melo , Letícia Ferreira Lima , Hugo Costa Paes , Octavio Luiz Franco
{"title":"Cleaving the way for heterologous peptide production: An overview of cleavage strategies","authors":"Karen Ofuji Osiro , Harry Morales Duque , Kamila Botelho Sampaio de Oliveira , Nadielle Tamires Moreira Melo , Letícia Ferreira Lima , Hugo Costa Paes , Octavio Luiz Franco","doi":"10.1016/j.ymeth.2024.12.002","DOIUrl":"10.1016/j.ymeth.2024.12.002","url":null,"abstract":"<div><div>One of the main bottlenecks for recombinant peptide production is choosing the proper cleavage method to remove fusion protein tags from target peptides. While these tags are crucial for inhibiting the activity of the target peptide during heterologous expression, incorporating a cleavage site is essential for their later removal, ensuring the pure sequencing of the peptide. This review evaluates different cleavage methods, including protease-mediated, self-cleavable protein, and chemical-mediated sites, regarding their advantages and limitations. For instance, intein, N<sup>pro</sup> EDDIE, enterokinase, factor Xa, SUMO, and CNBr are options for residue-free cleavage. Although protease-mediated cleavage is widely used, it can be expensive, due to its own cost added to the whole process. As an alternative, self-cleavable sites eliminate the requirement for proteinases. Another crucial step in defining the proper cleavage method is cost consideration, which relates to the purpose of peptide production. Here, we explore a range of cleavage approaches, meeting the needs of both cost-constrained applications and a more flexible budget. Overall, selecting the most suitable cleavage method should be based on careful consideration of toxicity, cost, accuracy, and specific application requirements to ensure a state-of-the-art approach.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"234 ","pages":"Pages 36-44"},"PeriodicalIF":4.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142783791","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
MethodsPub Date : 2025-02-01DOI: 10.1016/j.ymeth.2024.12.003
Chiara Urbinati , Giulia Pezzoni , Patrizia Cavadini , Vittoria Di Giovanni , Lorenzo Capucci , Marco Rusnati
{"title":"Validation of plasmonic-based biosensors for rapid and in depth characterization of monoclonal antibodies directed against rabbit haemorrhagic and foot-and-mouth disease viruses in biological samples","authors":"Chiara Urbinati , Giulia Pezzoni , Patrizia Cavadini , Vittoria Di Giovanni , Lorenzo Capucci , Marco Rusnati","doi":"10.1016/j.ymeth.2024.12.003","DOIUrl":"10.1016/j.ymeth.2024.12.003","url":null,"abstract":"<div><div>ELISA and RT-PCR represent the standard tools for the sensitive identification of viruses in biological samples, but they lack the capacity to finely characterize the binding of viruses or viral antigens to monoclonal antibodies (MAbs). Biosensing technologies are gaining increasing importance as powerful MAb characterization tools in the field of virology. Surface plasmon resonance (SPR) is an optical biosensing technology already used for the in depth characterization of MAbs of diagnostic and therapeutic value. Rabbit haemorrhagic disease virus (RHDV) and foot-and-mouth disease virus (FMDV) are top veterinary issues for which the development of novel methods aimed at the characterization of antiviral MAbs represents a priority with important livestock healthcare and economic implications. With these premises in mind, here we prepared a series of SPR biosensors by immobilizing RHDV2 or its 6S subunit by different strategies that were then used to characterize the binding capacity of a panel of anti-RHDV2 MAbs. From the comparison of the results obtained, the biosensor composed of intact RHDV2 captured with catcher-MAb covalently immobilized to the surface showed the best analytical performances. To evaluate the versatility of the biosensor, the same strategy was then adopted using FMVD in cell extracts. The results obtained are discussed in view of the exploitation of SPR in the rapid and resilient fine characterization of antiviral MAbs for diagnostic or therapeutic purposes in the field of animal virology.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"234 ","pages":"Pages 85-92"},"PeriodicalIF":4.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142799033","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
MethodsPub Date : 2025-02-01DOI: 10.1016/j.ymeth.2024.12.007
Lauren N. McKinley , Philip C. Bevilacqua
{"title":"CHiTA: A scarless high-throughput pipeline for characterization of ribozymes","authors":"Lauren N. McKinley , Philip C. Bevilacqua","doi":"10.1016/j.ymeth.2024.12.007","DOIUrl":"10.1016/j.ymeth.2024.12.007","url":null,"abstract":"<div><div>Small self-cleaving ribozymes are catalytic RNAs that cleave their phosphodiester backbone rapidly and site-specifically, without the assistance of proteins. Their catalytic properties make them ideal targets for applications in RNA pharmaceuticals and bioengineering. Consequently, computational pipelines that predict or design thousands of self-cleaving ribozyme candidates have been developed. Traditional experimental techniques for verifying the activity of these putative ribozymes, however, are low-throughput and time intensive. High-throughput (HT) pipelines that employ next-generation sequencing (NGS) analyze the activity of these thousands of ribozymes simultaneously. Until recently, the application of these HT pipelines has been limited to studying all single and double mutants of a select representative ribozyme. Unfortunately, this prevents the exploration of candidates having different lengths, circular permutations, and auxiliary stem-loops. Moreover, pipelines that analyze ribozymes <em>en masse</em> often include transcription of non-native flanking sequences that preclude accurate assessment of the intrinsic rate of ribozyme self-cleavage. To overcome these limitations, we developed a HT pipeline, “<em>C</em>leavage <em>Hi</em>gh-<em>T</em>hroughput <em>A</em>ssay (CHiTA)”, which employs NGS and massively parallel oligonucleotide synthesis (MPOS) to characterize ribozyme activity for thousands of candidates in a scarless fashion. Herein, we describe detailed strategies and protocols to implement CHiTA to measure the activity of putative ribozymes from a wide range of ribozyme classes.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"234 ","pages":"Pages 120-130"},"PeriodicalIF":4.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142811777","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
MethodsPub Date : 2025-02-01DOI: 10.1016/j.ymeth.2024.12.015
Clarence Todd , Lingling Jin , Ian McQuillan
{"title":"SV-JIM, detailed pairwise structural variant calling using long-reads and genome assemblies","authors":"Clarence Todd , Lingling Jin , Ian McQuillan","doi":"10.1016/j.ymeth.2024.12.015","DOIUrl":"10.1016/j.ymeth.2024.12.015","url":null,"abstract":"<div><div>This paper proposes a detailed process for SV calling that permits a data-driven assessment of multiple SV callers that uses both genome assemblies and long-reads. The process is implemented as a software pipeline named Structural Variant − Jaccard Index Measure, or SVJIM, using the Snakemake <span><span>[20]</span></span> workflow management system. Like most state-of-the-art SV callers, SV-JIM detects the presence of variations between pairs of genomes, but it streamlines the numerous SV calling stages into a single process for user convenience and evaluates the multiple SV sets produced using the Jaccard index measure to identify those with the highest consistency among the included SV callers. SV-JIM then produces aggregated SV results based on how many callers supported the reported SVs. For validation, SV-JIM was assessed through three case studies on the Homo sapiens genome and two plant genomes – Brassica nigra and Arabidopsis thaliana. Executing SV-JIM identified a significant amount of inter-caller variance which varied by tens of thousands of results on the larger Brassica nigra and Homo sapiens genomes. Further, aggregating the SV sets helped simplify better retention of the less frequently occurring SV types by requiring a level of minimum support rather than from a specific SV caller combination. Finally, these case studies identified a potential for inflated precision reporting that can occur during evaluation. SV-JIM is available publicly under MIT license at <span><span>https://github.com/USask-BINFO/SV-JIM</span><svg><path></path></svg></span>.</div></div>","PeriodicalId":390,"journal":{"name":"Methods","volume":"234 ","pages":"Pages 305-313"},"PeriodicalIF":4.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142997939","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}