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Journal articles on the topic 'Genetic characterization, proteomics'

Author: Grafiati

Published: 25 May 2024

Last updated: 31 July 2025

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1

Yihunie, Fanuel Bizuayehu, Mequanint Addisu Belete, Gizachew Fentahun, Solomon Getachew, and Teshager Dubie. "Diagnostic and Therapeutic Application of Proteomics in Infectious Disease." Advances in Cell and Gene Therapy 2023 (August 24, 2023): 1–6. http://dx.doi.org/10.1155/2023/5510791.

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The study of an organism’s genome, often known as “genomics,” has advanced quickly, producing a wealth of publicly accessible genetic data. Despite how valuable the genome is; proteins essentially control most aspects of cell function. Proteomics, or the comprehensive study of proteins, has emerged as an important technology for disease characterization, diagnosis, prognosis, drug development, and therapy. Proteomics technologies are now used to support the diagnosis and treatment of both infectious and noninfectious diseases. Nevertheless, it is more difficult to describe a proteomic profile

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Van Damme, Petra, Joel Vandekerckhove, and Kris Gevaert. "Disentanglement of protease substrate repertoires." Biological Chemistry 389, no. 4 (2008): 371–81. http://dx.doi.org/10.1515/bc.2008.043.

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Abstract Identification of protease substrates and detailed characterization of processed sites are essential for understanding the biological function of proteases. Because of inherent complexity reasons, this however remains a formidable analytical challenge, illustrated by the fact that the majority of the more than 500 human proteases are uncharacterized to date. Recently, in addition to conventional genetic and biochemical approaches, diverse quantitative peptide-centric proteomics approaches, some of which selectively recover N-terminal peptides, have emerged. These latter proteomic tech

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Agregán, Rubén, Noemí Echegaray, María López-Pedrouso, Radwan Kharabsheh, Daniel Franco, and José M. Lorenzo. "Proteomic Advances in Milk and Dairy Products." Molecules 26, no. 13 (2021): 3832. http://dx.doi.org/10.3390/molecules26133832.

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Proteomics is a new area of study that in recent decades has provided great advances in the field of medicine. However, its enormous potential for the study of proteomes makes it also applicable to other areas of science. Milk is a highly heterogeneous and complex fluid, where there are numerous genetic variants and isoforms with post-translational modifications (PTMs). Due to the vast number of proteins and peptides existing in its matrix, proteomics is presented as a powerful tool for the characterization of milk samples and their products. The technology developed to date for the separation

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Chantada-Vázquez, Maria del Pilar, Susana B. Bravo, Sofía Barbosa-Gouveia, José V. Alvarez, and María L. Couce. "Proteomics in Inherited Metabolic Disorders." International Journal of Molecular Sciences 23, no. 23 (2022): 14744. http://dx.doi.org/10.3390/ijms232314744.

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Inherited metabolic disorders (IMD) are rare medical conditions caused by genetic defects that interfere with the body’s metabolism. The clinical phenotype is highly variable and can present at any age, although it more often manifests in childhood. The number of treatable IMDs has increased in recent years, making early diagnosis and a better understanding of the natural history of the disease more important than ever. In this review, we discuss the main challenges faced in applying proteomics to the study of IMDs, and the key advances achieved in this field using tandem mass spectrometry (MS

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Arauz-Garofalo, Gianluca, Meritxell Jodar, Mar Vilanova, et al. "Protamine Characterization by Top-Down Proteomics: Boosting Proteoform Identification with DBSCAN." Proteomes 9, no. 2 (2021): 21. http://dx.doi.org/10.3390/proteomes9020021.

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Protamines replace histones as the main nuclear protein in the sperm cells of many species and play a crucial role in compacting the paternal genome. Human spermatozoa contain protamine 1 (P1) and the family of protamine 2 (P2) proteins. Alterations in protamine PTMs or the P1/P2 ratio may be associated with male infertility. Top-down proteomics enables large-scale analysis of intact proteoforms derived from alternative splicing, missense or nonsense genetic variants or PTMs. In contrast to current gold standard techniques, top-down proteomics permits a more in-depth analysis of protamine PTMs

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Sun, Claire, Paul Daniel, Nicole Chew, et al. "BIOL-01. GENERATION AND MULTI-OMICS CHARACTERIZATION OF 203 PEDIATRIC CNS TUMOUR MODELS REVEALS NEW THERAPEUTIC VULNERABILITIES." Neuro-Oncology 25, Supplement_1 (2023): i5—i6. http://dx.doi.org/10.1093/neuonc/noad073.020.

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Abstract Pediatric Central Nervous System (CNS) tumors are the leading cause of cancer-related death among children. Identifying new targeted therapies necessitates the use of pediatric cancer models that faithfully recapitulate the patient’s disease. However, the generation and characterization of pediatric cancer models has significantly lagged adult cancers, underscoring the urgent need to develop and characterize pediatric CNS models of disease. Herein, we establish a single-site collection of 233 CNS tumour cell lines, representing 14 distinct brain childhood tumor types. We subjected &am

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Stamatakos, Panagiotis Velissarios, Charalampos Fragkoulis, Ieronymos Zoidakis, Konstantinos Ntoumas, and Athanasios Dellis. "Urinary Bladder Microbiome Identification Protocol with Proteomics in Bladder Cancer Patients and Review of the Literature." Hellenic Urology 33, no. 4 (2021): 111–15. http://dx.doi.org/10.4103/huaj.huaj_3_23.

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Abstract Urine was conventionally thought to be sterile. However, recent evidence about the presence of microorganisms residing the urinary tract has led to an emerging field of investigation about the potential role of urinary microbiome in the pathogenesis of urinary bladder cancer. Urinary microbiota refers to the different microbe populations present in the urinary tract while a variety of genetic, environmental, and experimental parameters have been investigated as predisposing factors of microbial composition. Different methods of urine collection as well as experimental methodology on m

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Wang, Juanjuan, Simone Maarup, Vincent Fougner, et al. "Abstract 1883: Large-scale proteomic analysis of glioblastoma tissues reveals novel molecular insights and potential therapeutic targets." Cancer Research 85, no. 8_Supplement_1 (2025): 1883. https://doi.org/10.1158/1538-7445.am2025-1883.

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Abstract Introduction: Glioblastoma (GBM), classified as WHO grade 4, is a highly aggressive and incurable brain tumor with limited treatment options. Standard treatment consists of maximum safe surgery followed by concurrent chemo/radiation and adjuvant chemotherapy, the Stupp protocol. Despite extensive molecular characterization through DNA sequencing and RNA expression studies, the complex heterogeneity of GBM has yet to translate into improved standard treatments. A key challenge lies in predicting the impact of genetic and transcriptomic alterations at the protein level. Aim: To identify

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Gajadhar, Aaron S., Margaret K. Donovan, Harsharn Auluck, et al. "Abstract 6348: A cloud-scalable software suite for large-cohort proteogenomics data analysis and visualization." Cancer Research 82, no. 12_Supplement (2022): 6348. http://dx.doi.org/10.1158/1538-7445.am2022-6348.

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Abstract Comprehensive assessment of the flow of genetic information through multi-omic data integration can reveal the molecular consequences of genetic variation underlying human disease. Next generation sequencing (NGS) is used to identify genetic variants and characterize gene function (e.g. transcriptome and epigenome), while mass spectrometry is used to assess the proteome through characterization of protein abundances, modifications, and interactions. A new plasma profiling platform, the Proteograph࣪ Product Suite, leverages multiple nanoparticles with distinct physiochemical properties

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Di Narzo, Antonio F., Shannon E. Telesco, Carrie Brodmerkel, et al. "High-Throughput Characterization of Blood Serum Proteomics of IBD Patients with Respect to Aging and Genetic Factors." PLOS Genetics 13, no. 1 (2017): e1006565. http://dx.doi.org/10.1371/journal.pgen.1006565.

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Sudaric, Aleksandra, Marija Vrataric, Snezana Mladenovic-Drinic, and Maja Matosa. "Biotechnology in soybean breeding." Genetika 42, no. 1 (2010): 91–102. http://dx.doi.org/10.2298/gensr1001091s.

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Biotechnology can be defined broadly as a set of tools that allows scientists to genetically characterize or improve living organisms. Several emerging technologies, such as molecular characterization and genetic transformation, are already being used extensively for the purpose of plant improvement. Other emerging sciences, including genomics and proteomics, are also starting to impact plant improvement. Tools provided by biotechnology will not replace classical breeding methods, but rather will help provide new discoveries and contribute to improved nutritional value and yield enhancement th

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Peck Justice, Sarah A., Monica P. Barron, Guihong D. Qi, et al. "Mutant thermal proteome profiling for characterization of missense protein variants and their associated phenotypes within the proteome." Journal of Biological Chemistry 295, no. 48 (2020): 16219–38. http://dx.doi.org/10.1074/jbc.ra120.014576.

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Temperature-sensitive (TS) missense mutants have been foundational for characterization of essential gene function. However, an unbiased approach for analysis of biochemical and biophysical changes in TS missense mutants within the context of their functional proteomes is lacking. We applied MS-based thermal proteome profiling (TPP) to investigate the proteome-wide effects of missense mutations in an application that we refer to as mutant thermal proteome profiling (mTPP). This study characterized global impacts of temperature sensitivity–inducing missense mutations in two different subunits o

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Xu, Zihan, Binchen Mao, Wubin Qian, Xiaobo Chen, and Sheng Guo. "Abstract 5005: Integrative multi-omics characterization of syngeneic tumor models." Cancer Research 85, no. 8_Supplement_1 (2025): 5005. https://doi.org/10.1158/1538-7445.am2025-5005.

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Abstract Background: Mouse syngeneic models are widely used to study tumor-immune interactions and evaluate the efficacy of immunotherapies. Proteins serve as a link between the genetic code and phenotype, and can better reflect the dynamic state of a cell. However, the large-scale profiling of proteomics and phosphoproteomics data using syngeneic models has been limited. This study aims to reveal molecular mechanisms underlying tumor development and therapeutic response using multi-omics data generated from syngeneic models. Methods: Untreated fresh tumor tissues (around 500 mm3) from 12 mous

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La Rosa, Sandra, Chiara Guglielmo, Alessandra Ocello, Concetto Sessa, Giuseppe Seminara, and Antonio Granata. "Dalla medicina reattiva alla medicina di precisione." Giornale di Clinica Nefrologica e Dialisi 33 (September 18, 2021): 112–19. http://dx.doi.org/10.33393/gcnd.2021.2316.

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In recent years, there has been increased awareness of a concept of medicine based on individual differences taking into consideration genetic variability, environment, characteristics of the microbiome and individual lifestyles. It makes use of genomics, transcriptomics, proteomics and metabolomics techniques, obtaining a large amount of information which enables a more precise characterization of the patient. This model expands to the principles of prediction, prevention, personalization and participation, including all medical specialties. In nephrology, the application of precision medicin

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Milton, Ali, Dennis Muhanguzi, Allan Male, et al. "Analysis of Genetic Diversity of Banana Weevils (Cosmopolites sordidus) (Coleoptera: Curculionidae) Using Transcriptome-Derived Simple Sequence Repeat Markers." Journal of Economic Entomology 115, no. 2 (2022): 637–46. http://dx.doi.org/10.1093/jee/toab213.

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Abstract The banana weevil, Cosmopolites sordidus (Germar) (Coleoptera: Curculionidae) is an economically important insect pest of bananas. It causes up to 100% yield losses and substantial lifespan reduction in bananas. Advances in genomics, proteomics, and sequencing technologies have provided powerful pathways to genotyping disastrous pests such as C. sordidus. However, such technologies are often not available to the majority of rural subtropical African banana growers and pest control managers. This study was therefore motivated by the need to create cheap and easily accessible C. sordidu

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Tucholski, Trisha, Wenxuan Cai, Zachery R. Gregorich, et al. "Distinct hypertrophic cardiomyopathy genotypes result in convergent sarcomeric proteoform profiles revealed by top-down proteomics." Proceedings of the National Academy of Sciences 117, no. 40 (2020): 24691–700. http://dx.doi.org/10.1073/pnas.2006764117.

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Hypertrophic cardiomyopathy (HCM) is the most common heritable heart disease. Although the genetic cause of HCM has been linked to mutations in genes encoding sarcomeric proteins, the ability to predict clinical outcomes based on specific mutations in HCM patients is limited. Moreover, how mutations in different sarcomeric proteins can result in highly similar clinical phenotypes remains unknown. Posttranslational modifications (PTMs) and alternative splicing regulate the function of sarcomeric proteins; hence, it is critical to study HCM at the level of proteoforms to gain insights into the m

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Lin, Caijin, Xi Jin, Ding Ma, et al. "Abstract PO1-15-02: Comprehensive characterization of genetic interactions in breast cancer reveals therapeutic vulnerabilities." Cancer Research 84, no. 9_Supplement (2024): PO1–15–02—PO1–15–02. http://dx.doi.org/10.1158/1538-7445.sabcs23-po1-15-02.

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Abstract Background: Genome-informed and genome-targeted precision treatment for breast cancer have achieved remarkable progress in improving clinical outcomes for patients with specific genetic alterations. However, treatment efficacy is compromised by the current practice of basing treatment decision-making solely on single driver alterations, without considering the role of genetic interactions. Consequently, it is of great necessity to conduct systematic investigations to determine the clinical relevance of genetic interactions. Methods: We established a large-scale multi-omics cohort (N=8

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Ramos-Lopez, Omar. "Genotype-based precision nutrition strategies for the prediction and clinical management of type 2 diabetes mellitus." World Journal of Diabetes 15, no. 2 (2024): 142–53. http://dx.doi.org/10.4239/wjd.v15.i2.142.

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Globally, type 2 diabetes mellitus (T2DM) is one of the most common metabolic disorders. T2DM physiopathology is influenced by complex interrelationships between genetic, metabolic and lifestyle factors (including diet), which differ between populations and geographic regions. In fact, excessive consumptions of high fat/high sugar foods generally increase the risk of developing T2DM, whereas habitual intakes of plant-based healthy diets usually exert a protective effect. Moreover, genomic studies have allowed the characterization of sequence DNA variants across the human genome, some of which

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PAPPAS (Φ. ΠΑΠΠΑΣ), F., and M. STEFANIDOU (Μ. ΣΤΕΦΑΝΙΔΟΥ). "Genetically modified food." Journal of the Hellenic Veterinary Medical Society 57, no. 3 (2017): 231. http://dx.doi.org/10.12681/jhvms.15047.

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International consensus has been reached on the principles regarding evaluation of the food safety of genetically modified plants. The concept of substantial equivalence has been developed as part of a safety evaluation framework, based on the idea that existing foods can serve as a basis for comparing the properties of genetically modified foods with the appropriate counterpart. Substantial equivalence is a starting point in the safety evaluation, rather than an endpoint of the assessment. The development and validation of new profiling methods, such as DNA microarray technology, proteomics a

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Chu, Bizhu, An He, Yeteng Tian, et al. "Photoaffinity-engineered protein scaffold for systematically exploring native phosphotyrosine signaling complexes in tumor samples." Proceedings of the National Academy of Sciences 115, no. 38 (2018): E8863—E8872. http://dx.doi.org/10.1073/pnas.1805633115.

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Phosphotyrosine (pTyr)-regulated protein complexes play critical roles in cancer signaling. The systematic characterization of these protein complexes in tumor samples remains a challenge due to their limited access and the transient nature of pTyr-mediated interactions. We developed a hybrid chemical proteomics approach, termed Photo-pTyr-scaffold, by engineering Src homology 2 (SH2) domains, which specifically bind pTyr proteins, with both trifunctional chemical probes and genetic mutations to overcome these challenges. Dynamic SH2 domain-scaffolding protein complexes were efficiently cross-

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Sharma, Vinay, Prateek Gupta, Kagolla Priscilla, et al. "Metabolomics Intervention Towards Better Understanding of Plant Traits." Cells 10, no. 2 (2021): 346. http://dx.doi.org/10.3390/cells10020346.

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The majority of the most economically important plant and crop species are enriched with the availability of high-quality reference genome sequences forming the basis of gene discovery which control the important biochemical pathways. The transcriptomics and proteomics resources have also been made available for many of these plant species that intensify the understanding at expression levels. However, still we lack integrated studies spanning genomics–transcriptomics–proteomics, connected to metabolomics, the most complicated phase in phenotype expression. Nevertheless, for the past few decad

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Bove, Riley, Tanuja Chitnis, Bruce AC Cree, et al. "SUMMIT (Serially Unified Multicenter Multiple Sclerosis Investigation): creating a repository of deeply phenotyped contemporary multiple sclerosis cohorts." Multiple Sclerosis Journal 24, no. 11 (2017): 1485–98. http://dx.doi.org/10.1177/1352458517726657.

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Background: There is a pressing need for robust longitudinal cohort studies in the modern treatment era of multiple sclerosis. Objective: Build a multiple sclerosis (MS) cohort repository to capture the variability of disability accumulation, as well as provide the depth of characterization (clinical, radiologic, genetic, biospecimens) required to adequately model and ultimately predict a patient’s course. Methods: Serially Unified Multicenter Multiple Sclerosis Investigation (SUMMIT) is an international multi-center, prospectively enrolled cohort with over a decade of comprehensive follow-up

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Bizzarri, Nicolò, Camilla Nero, Francesca Sillano, et al. "Building a Personalized Medicine Infrastructure for Gynecological Oncology Patients in a High-Volume Hospital." Journal of Personalized Medicine 12, no. 1 (2021): 3. http://dx.doi.org/10.3390/jpm12010003.

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Gynecological cancers require complex intervention since patients have specific needs to be addressed. Centralization to high-volume centers improves the oncological outcomes of patients with gynecological cancers. Research in gynecological oncology is increasing thanks to modern technologies, from the comprehensive molecular characterization of tumors and individual pathophenotypes. Ongoing studies are focusing on personalizing therapies by integrating information across genomics, proteomics, and metabolomics with the genetic makeup and immune system of the patient. Hence, several challenges

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Roman-Ramos, Henrique, and Paulo Lee Ho. "Current Technologies in Snake Venom Analysis and Applications." Toxins 16, no. 11 (2024): 458. http://dx.doi.org/10.3390/toxins16110458.

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This comprehensive review explores the cutting-edge advancements in snake venom research, focusing on the integration of proteomics, genomics, transcriptomics, and bioinformatics. Highlighting the transformative impact of these technologies, the review delves into the genetic and ecological factors driving venom evolution, the complex molecular composition of venoms, and the regulatory mechanisms underlying toxin production. The application of synthetic biology and multi-omics approaches, collectively known as venomics, has revolutionized the field, providing deeper insights into venom functio

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Meng, Wenshu, and Youhe Gao. "Urinary Proteome Characterization of Stroke-Prone Spontaneously Hypertensive Rats." International Journal of Molecular Sciences 26, no. 1 (2024): 21. https://doi.org/10.3390/ijms26010021.

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Hypertension is a multifactorial and complex disease influenced by genetic and environmental factors, and it has become one of the most serious public health challenges. This study aimed to investigate the changes in hypertension based on urinary proteome. The stroke-prone spontaneously hypertensive rats (SHRSPs) model was used to examined urinary proteome changes during the development of hypertension. Urine proteome profiling was conducted at months 1, 4, 8, 10, 12, and 14 using liquid chromatography coupled with tandem mass spectrometry (LC–MS/MS). Given that the progression of hypertension

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Li, Jinna, Bing Yu, Chunquan Ma, et al. "Functional Characterization of Sugar Beet M14 Antioxidant Enzymes in Plant Salt Stress Tolerance." Antioxidants 12, no. 1 (2022): 57. http://dx.doi.org/10.3390/antiox12010057.

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Salt stress can cause cellular dehydration, which induces oxidative stress by increasing the production of reactive oxygen species (ROS) in plants. They may play signaling roles and cause structural damages to the cells. To overcome the negative impacts, the plant ROS scavenging system plays a vital role in maintaining the cellular redox homeostasis. The special sugar beet apomictic monosomic additional M14 line (BvM14) showed strong salt stress tolerance. Comparative proteomics revealed that six antioxidant enzymes (glycolate oxidase (GOX), peroxiredoxin (PrxR), thioredoxin (Trx), ascorbate p

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Migliozzi, Simona, Kyung-Hee Kim, Harim Koo, et al. "Abstract 4638: Integrated proteogenomic characterization of longitudinal glioblastoma." Cancer Research 84, no. 6_Supplement (2024): 4638. http://dx.doi.org/10.1158/1538-7445.am2024-4638.

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Abstract Glioblastoma multiforme (GBM) is the most aggressive form of primary brain tumor, with no curative treatment options and median patient survival time of almost one year. Despite multi-modal therapy including surgery, irradiation and chemotherapy, all patients experience tumor progression and recurrence. Our group proposed and validated the first single cell guided functional classification of primary GBM in four tumor-intrinsic cell states which informed clinical outcome and delivered therapeutic options. However, recurrent GBM remains therapeutically unresolved due in part to the dif

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Yan, Yuting, Xinzhou Ge, Jian Sun, et al. "Proteogenomic Features Define Novel Subtypes of Mantle Cell Lymphoma." Blood 142, Supplement 1 (2023): 4368. http://dx.doi.org/10.1182/blood-2023-190838.

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Introductions Recent advancements in mass spectrometry-based proteomics have unveiled novel translational and post-translational aspects of tumor biology. The joint characterization of tumor proteomics with genomics and transcriptomics enables proteogenomic analysis, improving our understanding of the molecular mechanisms, identifying new proteome-specific markers associated with clinical outcomes, and discovering novel treatment approaches. However, proteogenomic features remain largely uncharted due to a scarcity of information on MCL proteome. Methods We conducted a proteogenomic profiling

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Pino, James C., Camilo Posso, Setareh Sharzehi, et al. "Abstract 1844: Proteomic characterization of decitabine resistance in acute myeloid leukemia reveals signaling pathway crosstalk dampens the effectiveness of combination therapy." Cancer Research 84, no. 6_Supplement (2024): 1844. http://dx.doi.org/10.1158/1538-7445.am2024-1844.

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Abstract Acute myeloid leukemia (AML) is a deadly form of blood cancer primarily characterized by genetic abnormalities that guide treatment strategies. In recent years, several new therapies have emerged to target these genetic abnormalities such as gilteritinib or quizartinib, which target an internal tandem duplication (ITD) of the FLT3 gene. Additional drugs have been developed to target core cellular processes, such as venetoclax and the decitabine. Despite initial positive responses to these treatments, patients eventually relapse as they develop resistance to the individual drugs. One c

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Tesema, Zeleke, Mengistie Taye, and Desalegn Ayichew. "The role of phenotypic and genetic basis of livestock selection for climate change adaptation and mitigation: A review." Journal of Applied and Advanced Research 4, no. 2 (2019): 66. http://dx.doi.org/10.21839/jaar.2019.v4i2.251.

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Livestock are not only suffering from climate change, but also contribute to climate change through the direct and indirect release of greenhouse gases (CH4, N2O and CO2). Characterization, identification and conservation of heat tolerant livestock breeds are basics for future challenging climate. Properties of the skin, hair, coat color, coat type, sweating, respiration capacity, tissue insulation, surface area relative to body weight, endocrinological profiles and metabolic heat production are important factors involved for heat tolerance. Selection based on these phenotypic characteristics

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Abarrategui-Garrido, Cynthia, Rubén Martínez-Barricarte, Margarita López-Trascasa, Santiago Rodríguez de Córdoba, and Pilar Sánchez-Corral. "Characterization of complement factor H–related (CFHR) proteins in plasma reveals novel genetic variations of CFHR1 associated with atypical hemolytic uremic syndrome." Blood 114, no. 19 (2009): 4261–71. http://dx.doi.org/10.1182/blood-2009-05-223834.

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Abstract The factor H–related protein family (CFHR) is a group of minor plasma proteins genetically and structurally related to complement factor H (fH). Notably, deficiency of CFHR1/CFHR3 associates with protection against age-related macular degeneration and with the presence of anti-fH autoantibodies in atypical hemolytic uremic syndrome (aHUS). We have developed a proteomics strategy to analyze the CFHR proteins in plasma samples from controls, patients with aHUS, and patients with type II membranoproliferative glomerulonephritis. Here, we report on the identification of persons carrying n

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Mahmood, Tahir, Shiguftah Khalid, Muhammad Abdullah, et al. "Insights into Drought Stress Signaling in Plants and the Molecular Genetic Basis of Cotton Drought Tolerance." Cells 9, no. 1 (2019): 105. http://dx.doi.org/10.3390/cells9010105.

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Drought stress restricts plant growth and development by altering metabolic activity and biological functions. However, plants have evolved several cellular and molecular mechanisms to overcome drought stress. Drought tolerance is a multiplex trait involving the activation of signaling mechanisms and differentially expressed molecular responses. Broadly, drought tolerance comprises two steps: stress sensing/signaling and activation of various parallel stress responses (including physiological, molecular, and biochemical mechanisms) in plants. At the cellular level, drought induces oxidative st

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Yubero, Dèlia, Daniel Natera-de Benito, Jordi Pijuan, et al. "The Increasing Impact of Translational Research in the Molecular Diagnostics of Neuromuscular Diseases." International Journal of Molecular Sciences 22, no. 8 (2021): 4274. http://dx.doi.org/10.3390/ijms22084274.

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The diagnosis of neuromuscular diseases (NMDs) has been progressively evolving from the grouping of clinical symptoms and signs towards the molecular definition. Optimal clinical, biochemical, electrophysiological, electrophysiological, and histopathological characterization is very helpful to achieve molecular diagnosis, which is essential for establishing prognosis, treatment and genetic counselling. Currently, the genetic approach includes both the gene-targeted analysis in specific clinically recognizable diseases, as well as genomic analysis based on next-generation sequencing, analyzing

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Cummings, Steven, Thomas Perls, and Evan Hadley. "Complementary and Integrated Studies of Longevity and Healthy Aging." Innovation in Aging 4, Supplement_1 (2020): 851. http://dx.doi.org/10.1093/geroni/igaa057.3126.

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Abstract Five NIH-funded studies, the Long Life Family Study (LLFS, U19), the Longevity Consortium (LC, U19), Longevity Genomics (U24), and Protective Omics Profiles in Centenarians (UH2) work together to triangulate on mechanisms of extreme longevity and healthy aging with the ultimate goal of discovering predictors and targetable pathways. Linkage analyses by LLFS identified extremely strong genetic linkage peaks for cross-sectional as well as longitudinal trajectory rates-of-change phenotypes. Deep sequencing suggests these peaks are driven by rare, protective variants in selected pedigrees

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Halldorsson, Skarphedinn, Siri Fløgstad Svensson, Henriette Engen Berg, et al. "OTEH-7. Molecular characterization of tumor stiffness in glioblastoma." Neuro-Oncology Advances 3, Supplement_2 (2021): ii11—ii12. http://dx.doi.org/10.1093/noajnl/vdab070.046.

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Abstract Tumor heterogeneity is one of the hallmarks of glioblastoma multiforme (GBM). Morphology within a given GBM tumor can be extremely variable where some regions of the tumor have a soft, gel-like structure while other areas are dense and fibrous. Abnormal mechanical stress and tissue stiffening caused by cancer proliferation are believed to affect vascularity by compressing structurally weak blood vessels and restricting the supply of nutrients and oxygen to the tissue. These effects contribute to a hypoxic microenvironment that promotes disease progression and chemoresistance. The gene

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Faith, Dominick R., Margie Kinnersley, Diane M. Brooks та ін. "Characterization and genomic analysis of the Lyme disease spirochete bacteriophage ϕBB-1". PLOS Pathogens 20, № 4 (2024): e1012122. http://dx.doi.org/10.1371/journal.ppat.1012122.

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Lyme disease is a tick-borne infection caused by the spirochete Borrelia (Borreliella) burgdorferi. Borrelia species have highly fragmented genomes composed of a linear chromosome and a constellation of linear and circular plasmids some of which are required throughout the enzootic cycle. Included in this plasmid repertoire by almost all Lyme disease spirochetes are the 32-kb circular plasmid cp32 prophages that are capable of lytic replication to produce infectious virions called ϕBB-1. While the B. burgdorferi genome contains evidence of horizontal transfer, the mechanisms of gene transfer b

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Guzman, Norberto A., and Daniel E. Guzman. "Immunoaffinity Capillary Electrophoresis in the Era of Proteoforms, Liquid Biopsy and Preventive Medicine: A Potential Impact in the Diagnosis and Monitoring of Disease Progression." Biomolecules 11, no. 10 (2021): 1443. http://dx.doi.org/10.3390/biom11101443.

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Over the years, multiple biomarkers have been used to aid in disease screening, diagnosis, prognosis, and response to therapy. As of late, protein biomarkers are gaining strength in their role for early disease diagnosis and prognosis in part due to the advancements in identification and characterization of a distinct functional pool of proteins known as proteoforms. Proteoforms are defined as all of the different molecular forms of a protein derived from a single gene caused by genetic variations, alternative spliced RNA transcripts and post-translational modifications. Monitoring the structu

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Roychowdhury, Rajib, Soumya Prakash Das, Amber Gupta, et al. "Multi-Omics Pipeline and Omics-Integration Approach to Decipher Plant’s Abiotic Stress Tolerance Responses." Genes 14, no. 6 (2023): 1281. http://dx.doi.org/10.3390/genes14061281.

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The present day’s ongoing global warming and climate change adversely affect plants through imposing environmental (abiotic) stresses and disease pressure. The major abiotic factors such as drought, heat, cold, salinity, etc., hamper a plant’s innate growth and development, resulting in reduced yield and quality, with the possibility of undesired traits. In the 21st century, the advent of high-throughput sequencing tools, state-of-the-art biotechnological techniques and bioinformatic analyzing pipelines led to the easy characterization of plant traits for abiotic stress response and tolerance

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Ogden, Aaron J., Wardatou Boukari, Alba Nava, et al. "Characterization of Local and Systemic Impact of Whitefly (Bemisia tabaci) Feeding and Whitefly-Transmitted Tomato Mottle Virus Infection on Tomato Leaves by Comprehensive Proteomics." International Journal of Molecular Sciences 21, no. 19 (2020): 7241. http://dx.doi.org/10.3390/ijms21197241.

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Tomato mottle virus (ToMoV) is a single-stranded DNA (ssDNA) begomovirus transmitted to solanaceous crops by the whitefly species complex (Bemisia tabaci), causing stunted growth, leaf mottling, and reduced yield. Using a genetic repertoire of seven genes, ToMoV pathogenesis includes the manipulation of multiple plant biological processes to circumvent antiviral defenses. To further understand the effects of whitefly feeding and whitefly-transmitted ToMoV infection on tomato plants (Solanum lycopersicum ‘Florida Lanai’), we generated comprehensive protein profiles of leaves subjected to feedin

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Martins Rodrigues, Fernanda, Qingsong Gao, Kuan-lin Huang, et al. "Characterization of Germline Variants in Multiple Myeloma." Blood 132, Supplement 1 (2018): 4499. http://dx.doi.org/10.1182/blood-2018-99-118673.

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Abstract Multiple myeloma (MM) is an incurable hematological malignancy characterized by the clonal proliferation of malignant plasma cells in the bone marrow. Like other cancers, MM is a genetically complex and heterogeneous disease. One of its distinctive characteristics is that it is preceded by a pre-malignant condition known as monoclonal gammopathy of undetermined significance (MGUS), which then progresses to asymptomatic (smoldering) multiple myeloma (SMM) and, ultimately, to late-stage MM. Its progression through these stages is determined by a sequence of genomic aberrations, starting

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Cairo, Stefano, Mara Gilardi, Marianna Zipeto, Michael Ritchie, and Gilad Silberberg. "Abstract 2849: Comparative analysis of mutational signatures in TumorGraft PDX bank and TCGA dataset to improve patient tumor modeling." Cancer Research 85, no. 8_Supplement_1 (2025): 2849. https://doi.org/10.1158/1538-7445.am2025-2849.

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Abstract Mutational signatures are unique patterns of DNA alterations that arise from specific mutagenic processes, such as exposure to genotoxic agents or DNA repair deficiencies. Tumors with common mutational signatures can harbor defects in specific DNA repair pathways that may underlie common genetic vulnerabilities. Furthermore, exposure patterns of mutational signatures can vary among clinical types of cancer. Champions’ TumorGraft platform, a collection of 1500 patient-derived xenografts generated from more than 50 different types of cancer, is one of the most comprehensive preclinical

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Pino, James C., Camilo Posso, Sunil K. Joshi, et al. "Abstract 3172: Mapping the molecular landscape of acute myeloid leukemia enables prediction of drug response from proteogenomic data." Cancer Research 83, no. 7_Supplement (2023): 3172. http://dx.doi.org/10.1158/1538-7445.am2023-3172.

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Abstract Acute myeloid leukemia (AML) is a deadly blood cancer that remains largely classified by genetic aberrations, which inform therapy stratification. However, therapeutic response cannot be predicted or explained by genetic abnormalities alone. The integration of multiple omics, consisting of genomic, transcriptomic, proteomic, and phosphoproteomic measurements, offers a holistic view to resolve the underlying pathophysiology of AML that influences response to therapy. In this work, we pair multi-omic characterization together with ex vivo drug sensitivity assays accrued with 145 small m

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Sakura, Fumiaki, Kosuke Noma, Takaki Asano, et al. "A complementary approach for genetic diagnosis of inborn errors of immunity using proteogenomic analysis." PNAS Nexus, March 28, 2023. http://dx.doi.org/10.1093/pnasnexus/pgad104.

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Advances in next-generation sequencing technology have identified many genes responsible for inborn errors of immunity (IEI). However, there is still room for improvement in the efficiency of genetic diagnosis. Recently, RNA sequencing and proteomics using peripheral blood mononuclear cells (PBMCs) have gained attention, but only some studies have integrated these analyses in IEI. Moreover, previous proteomic studies for PBMCs have achieved limited coverage (approximately 3000 proteins). More comprehensive data are needed to gain valuable insights into the molecular mechanisms underlying IEI.

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Sun, Benjamin B., Joshua Chiou, Matthew Traylor, et al. "Plasma proteomic associations with genetics and health in the UK Biobank." Nature, October 4, 2023. http://dx.doi.org/10.1038/s41586-023-06592-6.

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AbstractThe Pharma Proteomics Project is a precompetitive biopharmaceutical consortium characterizing the plasma proteomic profiles of 54,219 UK Biobank participants. Here we provide a detailed summary of this initiative, including technical and biological validations, insights into proteomic disease signatures, and prediction modelling for various demographic and health indicators. We present comprehensive protein quantitative trait locus (pQTL) mapping of 2,923 proteins that identifies 14,287 primary genetic associations, of which 81% are previously undescribed, alongside ancestry-specific p

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Zhang, Minzhe, Thomas Sheffield, Xiaowei Zhan, et al. "Spatial molecular profiling: platforms, applications and analysis tools." Briefings in Bioinformatics, August 6, 2020. http://dx.doi.org/10.1093/bib/bbaa145.

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Abstract Molecular profiling technologies, such as genome sequencing and proteomics, have transformed biomedical research, but most such technologies require tissue dissociation, which leads to loss of tissue morphology and spatial information. Recent developments in spatial molecular profiling technologies have enabled the comprehensive molecular characterization of cells while keeping their spatial and morphological contexts intact. Molecular profiling data generate deep characterizations of the genetic, transcriptional and proteomic events of cells, while tissue images capture the spatial l

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Chen, Chengxuan, Yuan Liu, Qiang Li, et al. "The genetic, pharmacogenomic, and immune landscapes associated with protein expression across human cancers." Cancer Research, August 7, 2023. http://dx.doi.org/10.1158/0008-5472.can-23-0758.

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Abstract Proteomics is a powerful approach that can rapidly enhance our understanding of cancer development. Detailed characterization of the genetic, pharmacogenomic, and immune landscape in relation to protein expression in cancer patients could provide new insights into the functional roles of proteins in cancer. By taking advantage of the genotype data from The Cancer Genome Atlas (TCGA) and protein expression data from The Cancer Proteome Atlas (TCPA), we characterized the effects of genetic variants on protein expression across 31 cancer types and identified approximately 100,000 protein

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Wang, Juanjuan, Annelaura Bach Nielsen, Filip Mundt, et al. "Integrating deep proteomics into precision oncology for multi-omics characterization of metastatic cancer." Journal of Clinical Oncology 43, no. 16_suppl (2025). https://doi.org/10.1200/jco.2025.43.16_suppl.e15065.

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e15065 Background: Precision oncology is enhancing cancer treatment by tailoring therapies to specific genetic and molecular profiles. However, identifying suitable treatment targets and resistance mechanisms remains challenging in many cases. In Denmark, Rigshospitalet's Phase 1 Unit is conducting the Copenhagen Prospective Personalized Oncology (CoPPO) study to provide comprehensive sequencing for metastatic cancer patients, helping with targeted treatments [1]. Our study enables the integration of multi-omics information from the same biopsy, facilitating a comprehensive molecular understan

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Bhardwaj, Sonali, Mitchell Bulluss, Ana D'Aubeterre, et al. "Integrating the analysis of human biopsies using post‐translational modifications proteomics." Protein Science 33, no. 4 (2024). http://dx.doi.org/10.1002/pro.4979.

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AbstractProteome diversities and their biological functions are significantly amplified by post‐translational modifications (PTMs) of proteins. Shotgun proteomics, which does not typically survey PTMs, provides an incomplete picture of the complexity of human biopsies in health and disease. Recent advances in mass spectrometry‐based proteomic techniques that enrich and study PTMs are helping to uncover molecular detail from the cellular level to system‐wide functions, including how the microbiome impacts human diseases. Protein heterogeneity and disease complexity are challenging factors that

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Hasan, Saadia, Michael S. Fernandopulle, Stewart W. Humble, et al. "Multi-modal proteomic characterization of lysosomal function and proteostasis in progranulin-deficient neurons." Molecular Neurodegeneration 18, no. 1 (2023). http://dx.doi.org/10.1186/s13024-023-00673-w.

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Abstract Background Progranulin (PGRN) is a lysosomal glycoprotein implicated in various neurodegenerative diseases, including frontotemporal dementia and neuronal ceroid lipofuscinosis. Over 70 mutations discovered in the GRN gene all result in reduced expression of the PGRN protein. Genetic and functional studies point toward a regulatory role for PGRN in lysosome functions. However, the detailed molecular function of PGRN within lysosomes and the impact of PGRN deficiency on lysosomes remain unclear. Methods We developed multifaceted proteomic techniques to characterize the dynamic lysosoma

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Noberini, Roberta, and Tiziana Bonaldi. "Proteomics contributions to epigenetic drug discovery." PROTEOMICS, September 19, 2023. http://dx.doi.org/10.1002/pmic.202200435.

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AbstractThe combined activity of epigenetic features, which include histone post‐translational modifications, DNA methylation, and nucleosome positioning, regulates gene expression independently from changes in the DNA sequence, defining how the shared genetic information of an organism is used to generate different cell phenotypes. Alterations in epigenetic processes have been linked with a multitude of diseases, including cancer, fueling interest in the discovery of drugs targeting the proteins responsible for writing, erasing, or reading histone and DNA modifications. Mass spectrometry (MS)

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