TALKIEN: crossTALK IntEraction Network. A web-based tool for deciphering molecular communication through ligand–receptor interactions DOI
Ferrán Moratalla-Navarro, Vı́ctor Moreno, Rebeca Sanz‐Pamplona

et al.

Molecular Omics, Journal Year: 2023, Volume and Issue: 19(9), P. 688 - 696

Published: Jan. 1, 2023

Molecular crosstalk, the dialogue between different cell types, is attracting more attention in cancer research. On one hand, communication tumor and non-tumor cells microenvironment or clones has influential consequences for progression spread of tumors response to treatment. other novel techniques such as single-cell sequencing spatial transcriptomics provide detailed information that needs be interpreted. TALKIEN: crossTALK IntEraction Network a simple intuitive online R/shiny application visualize molecular crosstalk through construction analysis protein-protein interaction network. Taking two lists genes proteins input, which are representative lineages, TALKIEN extracts about ligand-receptor interactions, builds network analyzes it using systems biology centrality measures component analysis, among others. Moreover, expands displaying pathways downstream receptors. The allows users select graphical layouts, performs functional gives drugs targeting In conclusion, detect interactions generating new silico predictions cell-cell thus providing translational rationale future experiments. It freely available at https://www.odap-ico.org/talkien.

Language: Английский

CAPTURE: Comprehensive anti-cancer peptide predictor with a unique amino acid sequence encoder DOI
Hina Ghafoor, Muhammad Nabeel Asim, Muhammad Ali Ibrahim

et al.

Computers in Biology and Medicine, Journal Year: 2024, Volume and Issue: 176, P. 108538 - 108538

Published: May 3, 2024

Language: Английский

Citations

5
Protein network analysis and functional enrichment via computational biotechnology unravel molecular and pathogenic mechanisms of kidney stone disease DOI Creative Commons

Paleerath Peerapen,

Visith Thongboonkerd

Biomedical Journal, Journal Year: 2023, Volume and Issue: 46(2), P. 100577 - 100577

Published: Jan. 13, 2023

Mass spectrometry-based proteomics has been extensively applied to current biomedical research. From such large-scale identification of proteins, several computational tools have developed for determining protein–protein interactions (PPI) network and functional significance the identified proteins their complex. Analyses PPI enrichment widely various fields Herein, we summarize commonly used analysis in kidney stone research discuss applications disease (KSD). Such approach mainly investigate networks derived from urine patients with (stone formers), matrix, Randall's plaque, renal papilla, tubular cells, mitochondria immune cells. The data obtained biotechnology leads experimental validation investigations that offer new knowledge on formation processes. Moreover, may also lead defining therapeutic targets preventive strategies better outcome KSD management.

Language: Английский

Citations

12
Extracellular matrix re-normalization to improve cold tumor penetration by oncolytic viruses DOI Creative Commons
Geofrey F. Soko,

Benson Kiprono Kosgei,

Stephene S. Meena

et al.

Frontiers in Immunology, Journal Year: 2025, Volume and Issue: 15

Published: Jan. 8, 2025

Immunologically inert or cold tumors pose a substantial challenge to the effectiveness of immunotherapy. The use oncolytic viruses (OVs) induce immunogenic cell death (ICD) in tumor cells is well-established strategy for initiating cancer immunity cycle (CIC). This process promotes trafficking and infiltration CD8+ T into tumors, thereby eliciting tumor-specific immune response. Despite potential OVs handling clinical outcomes have fallen short expectations. To better understand obstacles faced by virus immunotherapy (OVI), we would like revisit OV issue. Growing evidence indicates that limited intratumoral penetration inadequate distribution are critical factors contributing suboptimal response OVI. Aberrant expressions matrix proteins cancer-associated fibroblasts (CAFs) alter mechanical properties extracellular (ECM). results increased ECM desmoplasia elevated interstitial fluid pressure (IFP), creating physical barriers impede dissemination within tumors. review explores latest advancements strategies designed improve facilitate tumor-infiltrating lymphocytes (TILs) Additionally, investigated current trials challenges associated with translating these practice patient outcomes.

Language: Английский

Citations

0
Characterization of 53 Multiplexed Targeted Proteomics Assays for Verification Studies in Cancer Cell Lines DOI Creative Commons
Constance A. Sobsey, Gerald Batist, Christoph H. Borchers

et al.

Journal of Proteome Research, Journal Year: 2025, Volume and Issue: 24(2), P. 459 - 471

Published: Jan. 13, 2025

The National Cancer Institute's Clinical Proteomics Tumor Analysis Consortium (CPTAC) was established to address the need for improved design, standardization, and validation of proteomics assays enable better translation biomarkers from analytical lab clinic. Here, we applied CPTAC guidelines characterize quantitative mass spectrometry (MS) in a new multiple reaction monitoring (MRM) panel. panel 50 proteins developed response previous study that identified proteomic profile altered translational control associated with cancer drug. MRM-MS 53 peptides interest were developed, optimized, characterized on UPLC system coupled triple-quadrupole spectrometer (QQQ-MS) using synthetic proteotypic corresponding stable-isotope labeled internal standard (SIS) peptides. Most found be fit-for-purpose biomarker verification they precisely reproducibly quantify at levels endogenous concentration desired cell lines. Of these, 28 peptide represent previously had no published database. targeted this publicly deposited validated multiplexed may use research applications cancer, cellular stress, neurology, cardiology, metabolism.

Language: Английский

Citations

0
HarmonizR: blocking and singular feature data adjustment improve runtime efficiency and data preservation DOI Creative Commons
Simon Schlumbohm, Julia E. Neumann, Philipp Neumann

et al.

BMC Bioinformatics, Journal Year: 2025, Volume and Issue: 26(1)

Published: Feb. 11, 2025

Abstract Background Data adjustment is an essential tool for increasing statistical power during analysis, example in case of complex multi-experiment data from (single-cell) RNA, proteomics and other omics data. Despite its benefits, integration introduces internal biases—so-called batch effects. Due to the inherent presence missing values by such methods their additional introduction means integration, renowned algorithms as ComBat limma are unable perform effect adjustment. Recently, HarmonizR framework was presented these cases, which a value tolerant Results In this contribution, we provide significant improvements approach. A novel blocking strategy introduced severely reduce runtime, while still supporting parallel architectures. Additionally, “unique removal” has been integrated into maintain even more features datasets, showing feature rescue up 103.9% our tested datasets. work, show (1) improved runtime both small large, real datasets (2) ability retain dataset adjustment, Conclusion The proposed tackle previous shortcomings published version. Since mainly developed on rare tumor entities, it did not include beyond parallelization, addressed update. An additionally welcome update regarding furthermore enhances quickly robustly reduction.

Language: Английский

Citations

0
Mass Spectrometry‐Based Proteomics for Next‐Generation Precision Oncology DOI
Kuen‐Tyng Lin, Gul Muneer, Peirong Huang

et al.

Mass Spectrometry Reviews, Journal Year: 2025, Volume and Issue: unknown

Published: April 23, 2025

ABSTRACT Cancer is the leading cause of death worldwide characterized by patient heterogeneity and complex tumor microenvironment. While genomics‐based testing has transformed modern medicine, challenge diverse clinical outcomes highlights unmet needs for precision oncology. As functional molecules regulating cellular processes, proteins hold great promise as biomarkers drug targets. Mass spectrometry (MS)‐based proteomics illuminated molecular features cancers facilitated discovery or therapeutic targets, paving way innovative strategies that enhance personalized treatment. In this article, we introduced tools current achievements MS‐based proteomics, choice targeted MS from to validation phases, profiling sensitivity bulk samples single‐cell level tissue liquid biopsy specimens, regulatory landscape protein laboratory‐developed tests (LDTs). The challenges, success future perspectives in translating research assay into applications are also discussed. With well‐designed studies demonstrate benefits meet requirements both analytical performance, assays promising with numerous opportunities improve cancer diagnosis, treatment, monitoring.

Language: Английский

Citations

0
Nanotechnology‐Enabled Blood Test for Oral Epithelial Disorders Management: A Proof‐of‐Concept Study DOI Creative Commons
Erica Quagliarini, Giulio Caracciolo, Francesca Giulimondi

et al.

Oral Diseases, Journal Year: 2025, Volume and Issue: unknown

Published: May 6, 2025

ABSTRACT Objective To address the limitations and complexities associated with tissue biopsy, emerging nanotechnology methods show promise in enhancing detection management of oral squamous cell carcinoma potential malignant disorders. Among them, characterization protein corona, biomolecular layer that envelops materials when exposed to biological fluids, has recently emerged as a powerful tool for distinguishing oncological patients from healthy people. Materials Methods Building upon recent insights, here we formulated new diagnostic method potentially disorders based on personalized corona formed graphene oxide nanosheets plasma patients. Results The findings highlighted discernible distinction between subjects ones, resulting an overall accuracy 87%. Subsequently, applied this monitor progression diseases undergoing treatment, observed trend indicating convergence profiles throughout treatment course. Conclusion If further confirmed larger prospective studies, approach could discriminate can be considered these diseases.

Language: Английский

Citations

0
De moleculaire biologie van urologische tumoren DOI
Guido Jenster

Published: Jan. 1, 2025

Citations

0
Protein Biomarker Discovery Studies on Urinary sEV Fractions Separated with UF-SEC for the First Diagnosis and Detection of Recurrence in Bladder Cancer Patients DOI Creative Commons
Stephanie Jordaens, Eline Oeyen, Hanny Willems

et al.

Biomolecules, Journal Year: 2023, Volume and Issue: 13(6), P. 932 - 932

Published: June 1, 2023

Urinary extracellular vesicles (EVs) are an attractive source of bladder cancer biomarkers. Here, a protein biomarker discovery study was performed on the content small urinary EVs (sEVs) to identify possible biomarkers for primary diagnosis and recurrence non-muscle-invasive (NMIBC). The sEVs were isolated by ultrafiltration (UF) in combination with size-exclusion chromatography (SEC). first part compared healthy individuals NMIBC patients diagnosis. second tumor-free recurrent separated size range 40 200 nm. Based manually curated high quality mass spectrometry (MS) data, statistical analysis revealed 69 proteins that differentially expressed these sEV fractions tumor vs. age- gender-matched control group. When discriminating power between is taken into account, most potential MASP2, C3, A2M, CHMP2A NHE-RF1. Additionally, two (HBB HBA1) samples patients, but their biological relevance very limited.

Language: Английский

Citations

9
Advances in the Clinical Application of High-throughput Proteomics DOI Open Access
Miao Cui, Fei Deng, Mary L. Disis

et al.

Exploratory Research and Hypothesis in Medicine, Journal Year: 2024, Volume and Issue: 000(000), P. 000 - 000

Published: July 3, 2024

High-throughput proteomics has become an exciting field and a potential frontier of modern medicine since the early 2000s. While significant progress been made in technical aspects field, translating to clinical applications challenging. This review summarizes recent advances high-throughput discusses associated challenges, advantages, future directions. We focus on research breast cancer, bladder laryngeal squamous cell carcinoma, gastric colorectal coronavirus disease 2019. The application will face challenges such as varying protein properties, limitations statistical modeling, logistical difficulties data deposition, integration, harmonization, well regulatory requirements for validation considerations. However, there are several noteworthy advantages proteomics, including identification novel global networks, discovery new proteins, synergistic incorporation with other omic data. look forward participating embracing proteomics-based single-cell biology its applications, individualized pathology informatics, digital pathology, deep learning models proteomics. Several proteomic technologies noteworthy, data-independent acquisition mass spectrometry, nanopore-based 4-D secondary ion spectrometry. In summary, we believe drastically shift paradigm translational research, practice, public health near future.

Language: Английский

Citations

3