Review
Oncology
Nicholas Bradley Larson, Ann L. Oberg, Alex A. Adjei, Liguo Wang
Summary: Next-generation sequencing (NGS) technologies, widely used in cancer research, generate vast and diverse data that require sophisticated computational methods and bioinformatics expertise. This review provides background details of NGS technology and basic bioinformatics concepts for clinicians interested in cancer research applications, with a focus on DNA-based approaches. It introduces principles of library preparation, alignment, variant calling, variant annotations, and NGS applications for other molecular data types. The review also discusses the utility of NGS methods in NSCLC research and study design considerations for leveraging NGS technologies in clinical care.
JOURNAL OF THORACIC ONCOLOGY
(2023)
Review
Immunology
Ryuhjin Ahn, Yufei Cui, Forest M. White
Summary: Effective T cell antitumor immunity is essential for successful cancer immunotherapy. Mass spectrometry-based survey of tumor antigens (immunopeptidomics) combined with other omics platforms has contributed to the identification and quantification of T cell antigens. This review discusses the types of tumor antigens for targeted cancer immunotherapy and the importance of immunopeptidomics methods in MHC peptide identification. It also highlights the integration of mass spectrometry-driven approaches with other technologies in the discovery of targetable T cell antigens for cancer immunotherapy.
SEMINARS IN IMMUNOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Rupert L. Mayer, Francis Impens
Summary: Immunopeptidomics is a promising approach for discovering bacterial epitopes presented on infected cells, which can be utilized in the development of next-generation vaccines, especially for intracellular bacterial pathogens. Challenges remain in the selection of bacterial antigens as vaccine candidates.
TRENDS IN MICROBIOLOGY
(2021)
Review
Chemistry, Physical
Bauer L. LeSavage, Riley A. Suhar, Nicolas Broguiere, Matthias P. Lutolf, Sarah C. Heilshorn
Summary: The translation discusses how organotypic models of patient-specific tumors are changing our understanding of cancer heterogeneity and personalized medicine. These models can preserve genetic, proteomic, morphological, and pharmacotypic features of the parent tumor in vitro, and offer genomic and environmental manipulation. However, current cancer organoid culture techniques are uncontrolled and irreproducible, hindering the acceleration of insights into patient care.
Article
Medicine, Research & Experimental
Katarina Madunic, Oleg A. Mayboroda, Tao Zhang, Julia Weber, Geert-Jan Boons, Hans Morreau, Ronald van Vlierberghe, Tom van Wezel, Guinevere S. M. Lageveen-Kammeijer, Manfred Wuhrer
Summary: Cells are covered with a dense layer of carbohydrates, some of which are solely present on neoplastic cells. The so-called tumor-associated carbohydrate antigens (TACAs) are increasingly recognized as promising targets for immunotherapy. These carbohydrates differ from those of the surrounding non-cancerous tissues and contribute to the malignant phenotype of the cancer cells by promoting proliferation, metastasis, and immunosuppression. However, due to tumor tissue heterogeneity and technological limitations, TACAs are insufficiently explored. In this study, a workflow was established to analyze the colorectal cancer (CRC)-associated O-linked glycans. Distinctive O-glycosylation features were found in cancerous, stromal, and normal colon mucosal regions. Over 100 O-linked glycans were detected in cancerous regions with absence in normal mucosa. A novel panel of highly specific TACAs, based upon differences in the glycomic profiles between CRC and healthy colon mucosa, were identified. These TACAs could be potential targets for innovative cancer immune target therapies and lay the foundation for the targeted treatment of CRC.
Editorial Material
Multidisciplinary Sciences
Ewen Callaway
Summary: New technologies may offer stronger or wider immunity, but they will face competition for market share.
Article
Oncology
Chul Seung Lee, Hoon Seok Kim, Jeoffrey Schageman, In Kyu Lee, Myungshin Kim, Yonggoo Kim
Summary: Circulating tumor DNA (ctDNA) is a minimally invasive biomarker that can be analyzed using next-generation sequencing (NGS) to evaluate its clinical and analytical performance in colorectal cancer (CRC) patients. Postoperative ctDNA detection can serve as a valuable marker for identifying the risk of recurrence or persistent tumor lesions in patients with CRC.
Review
Biology
Heena Satam, Kandarp Joshi, Upasana Mangrolia, Sanober Waghoo, Gulnaz Zaidi, Shravani Rawool, Ritesh P. Thakare, Shahid Banday, Alok K. Mishra, Gautam Das, Sunil K. Malonia
Summary: Next-generation sequencing (NGS) is a powerful tool that can sequence millions of DNA fragments simultaneously, providing detailed information about genomes, genetic variations, gene activity, and changes in gene behavior. Recent advancements have focused on improving sequencing speed and accuracy, reducing costs, and enhancing data analysis. These advancements have great potential for advancing genomics research and improving our understanding of diseases and personalized healthcare.
Review
Oncology
Victoria Klepsch, Kerstin Siegmund, Gottfried Baier
Summary: The text explores the potential of NR2F6 as an emerging target for cancer immunotherapy, aiming to increase patient response rates and extend treatment options. Future therapies may combine surface receptor and intracellular protein targets.
Article
Oncology
Patrick Metzger, Maria Elena Hess, Andreas Blaumeiser, Thomas Pauli, Vincent Schipperges, Ralf Mertes, Jan Christoph, Philipp Unberath, Niklas Reimer, Raphael Scheible, Anna L. L. Illert, Hauke Busch, Geoffroy Andrieux, Melanie Boerries
Summary: Next-generation sequencing (NGS) is a powerful technology that allows for fast and high-throughput sequencing of DNA and RNA, enabling the identification of genetic mutations, gene fusions, and other alterations related to cancer growth. In the context of Molecular Tumor Boards (MTBs), multidisciplinary teams of experts utilize NGS and bioinformatics tools to analyze patients' genetic profiles and develop personalized treatment recommendations for cancer patients. MIRACUM-Pipe provides a standardized solution to analyze NGS data, including quality control, variant calling, copy number estimation, annotation, visualization, and report generation, making it an essential tool for MTB decision-making.
Article
Biochemical Research Methods
Brian C. Searle, Ariana E. Shannon, Damien Beau Wilburn
Summary: Scribe is a new library search engine that uses deep learning fragmentation prediction software to predict fragmentation and retention times for peptides in a FASTA database, outperforming traditional database searching tools in terms of sensitivity and quantitative precision.
JOURNAL OF PROTEOME RESEARCH
(2023)
Review
Oncology
Youngjun Park, Dominik Heider, Anne-Christin Hauschild
Summary: In recent years, advancements in next-generation sequencing and artificial intelligence have led to the development of various algorithms and applications. Integrating systems biology and machine learning has been crucial in addressing challenges posed by big data. Machine learning algorithms and network-based models play a key role in analyzing NGS data effectively.
Review
Biology
Calin Cainap, Ovidiu Balacescu, Simona Sorana Cainap, Laura-Ancuta Pop
Summary: Lung cancer remains one of the most commonly diagnosed and deadly cancers in the world. Early diagnosis is crucial for improving the standard of care. Next generation sequencing has been proven as a helpful tool in early cancer detection, including lung cancer, due to its advantages of low cost, speed, efficacy, low sample usage, and diversity.
Review
Spectroscopy
Hsin-Hsiang Chung, Penghsuan Huang, Chih-Lin Chen, Chuping Lee, Cheng-Chih Hsu
Summary: This review summarizes the applications of mass spectrometry imaging (MSI) techniques in pathological research, including disease diagnosis, microbiology, and drug discovery. It also describes the improvements in MSI, such as the accumulation of imaging data sets and identification of significant molecules, that have enhanced its capabilities in pathology practices.
MASS SPECTROMETRY REVIEWS
(2023)
Article
Biochemistry & Molecular Biology
Andrey Kechin, Ulyana Boyarskikh, Viktoriya Borobova, Evgeniy Khrapov, Sergey Subbotin, Maxim Filipenko
Summary: This study developed a new tool, called BRACNAC, for detecting CNVs and CNAs in the BRCA1 and BRCA2 genes. The tool showed high sensitivity and specificity and could be applied to NGS data of different origins. The study also identified the limitations of the tool.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Tanushree Halder, Elke Stroeher, Hui Liu, Yinglong Chen, Guijun Yan, Kadambot H. M. Siddique
Summary: Improving the root system of wheat is crucial for enhancing grain yield and climate resilience. This study identified proteins associated with root length and root mass in wheat using label-free quantitative proteomics. The findings revealed potential biomarkers that could be used for improving the root system of wheat.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Yinhua Pan, Quanqing Zou, Wu Yin, Zhen Huang, Yingzhu Zhao, Zongming Mo, Lihui Li, Jianrong Yang
Summary: A prognostic model of BC based on LNM-related genes was established in this study, providing guidance for prognosis evaluation and precise treatment of BC. The genes related to lymph node metastasis in BC are largely unknown and need further exploration. Searching for potential lymph node metastasis-related genes of BC will provide meaningful biomarkers for BC treatment. Our model, based on TCGA-BRCA data, effectively predicted patient outcomes and classified BC patients. The identified feature genes might have a predictive function in immunotherapy. The results of this study provide a new reference for the prognosis and treatment of BC patients with lymph node metastasis.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Qiushi Liang, Joon M. Pijnenburg, Erikjan Rijkers, Arnold G. Vulto, Ans T. van der Ploeg, Niek P. van Til, Eva C. Vlaar, Jeroen A. A. Demmers, W. W. M. Pim Pijnappel
Summary: Pompe disease is a lysosomal storage disorder characterized by glycogen accumulation in skeletal muscle, leading to profound pathology. This study showed that lentiviral gene therapy with LV-IGF2.GAAco can nearly completely correct disease-associated proteomic changes, supporting its future clinical development as a new treatment option for Pompe disease.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Chuang Liu, Wenjing Zhang, Qianli Dong, Haipeng Liu
Summary: This study fills the knowledge gap about the matrix proteins involved in the formation of mineralized exoskeletons in decapod crustaceans. By comparing with well-studied molluscan biomineralization proteins, it is proposed that decapod crustaceans evolved novel proteins while sharing some proteins with molluscs. This study provides insights into the evolution and adaptation of crustaceans and molluscs in forming their exoskeletons.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Rania D. Baka, Josipa Kules, Angelo Beletic, Vladimir Farkas, Dina Resetar Maslov, Blanka Beer Ljubic, Ivana Rubic, Vladimir Mrljak, Mark McLaughlin, David Eckersall, Zoe Polizopoulou
Summary: This study analyzed serum samples from dogs with epilepsy and identified potential markers of epilepsy, proteins involved in nerve tissue regeneration, and proteins altered by antiepileptic medication. The findings provide insight into the pathogenesis of epilepsy and the effects of medication on extracellular matrix proteins.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Viviane M. Codognoto, Fabiana F. de Souza, Thais R. Cataldi, Carlos A. Labate, Laiza S. de Camargo, Pedro H. Esteves Trindade, Roberto R. da Rosa Filho, Diego J. B. de Oliveira, Eunice Oba
Summary: This study aimed to compare urine proteomics from non- and pregnant buffaloes to identify potential biomarkers of early pregnancy. A total of 798 proteins were reported in the urine considering all groups, and the differential proteins play essential roles during pregnancy.
JOURNAL OF PROTEOMICS
(2024)
