Comprehensive phage display viral antibody profiling using VirScan: potential applications in chronic immune-mediated disease DOI
Jed Valentiner Shrewsbury,

Evangelin Shaloom Vitus,

Adam Koziol

et al.

Journal of Virology, Journal Year: 2024, Volume and Issue: 98(11)

Published: Oct. 21, 2024

ABSTRACT Phage immunoprecipitation sequencing (PhIP-Seq) is a high-throughput platform that uses programmable phage display for serology. VirScan, specific PhIP-Seq library encoding viral peptides from all known human viruses, enables comprehensive quantification of past exposures. We review its use in immune-mediated diseases (IMDs), highlighting utility identifying exposures the context IMD development. Finally, we evaluate potential precision medicine by integrating it with other large-scale omics data sets.

Language: Английский

Alcohol-associated liver cancer DOI
Yaojie Fu, Luca Maccioni, Xin Wei Wang

et al.

Hepatology, Journal Year: 2024, Volume and Issue: 80(6), P. 1462 - 1479

Published: April 12, 2024

Heavy alcohol intake induces a wide spectrum of liver diseases ranging from steatosis, steatohepatitis, cirrhosis, and HCC. Although consumption is well-known risk factor for the development, morbidity, mortality HCC globally, alcohol-associated hepatocellular carcinoma (A-HCC) poorly characterized compared to viral hepatitis–associated Most A-HCCs develop after cirrhosis (AC), but direct carcinogenesis ethanol its metabolites A-HCC remains obscure. The differences between HCCs caused by other etiologies have not been well investigated in terms clinical prognosis, genetic or epigenetic landscape, molecular mechanisms, heterogeneity. Moreover, there huge gap basic research practice due lack preclinical models A-HCC. In current review, we discuss pathogenesis, heterogeneity, approaches, epigenetic, profiles A-HCC, insights into prospects future on potential effect cholangiocarcinoma metastasis also discussed.

Language: Английский

Citations

11

Pan-serological antibodies and liver cancer risk: a nested case-control analysis DOI Creative Commons
Cody Z. Watling,

Xing Hua,

Jessica L. Petrick

et al.

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: Feb. 14, 2025

Abstract Recently, studies have reported that pan-viral serology signatures may be predictive for liver cancer development. However, whether these same findings are observed prospective has not been previously investigated. The nested case-control analysis included 191 persons who developed and 382 controls from the PLCO cohort. presence of circulating antibodies, measured by VirScan, was determined in serum samples obtained at study recruitment. antibodies compared between cases using multivariable conditional logistic regressions, prediction models were used to estimate exposures predicted No significant associations found viruses, bacteria or allergens risk after adjustment multiple testing. agent most significantly associated with hepatitis C virus (HCV), but it only detected among 23 participants (odds ratio (OR): 3.98; 95% confidence intervals (CI):1.59–9.99; p = 0.0032, False Discovery Rate (FDR) 0.35). In based on 109 antibody features, no (area under curve [AUC]: 0.52–0.54). analyses restricted common type cancer, hepatocellular carcinoma, association HCV stronger (OR: 23.16, CI: 4.55-117.68; FDR p-value 0.0016), although all similar (AUC 0.55; CI:0.43–0.68). Antibodies infectious agents, other than HCV, prospectively risk. utility an exposure signature development needs further explored.

Language: Английский

Citations

0

Clinical value of blood routine and tumor markers in differentiating hepatocellular carcinoma from intrahepatic cholangiocarcinoma DOI Creative Commons
Wei Shi, Jin Wen,

Lang Hong

et al.

Medicine, Journal Year: 2025, Volume and Issue: 104(12), P. e41899 - e41899

Published: March 21, 2025

Hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (ICC) are the 2 major types of primary liver cancer, differing significantly in etiology, treatment strategies, prognosis despite their common hepatic origin. Accurate preoperative differentiation between HCC ICC is critical for optimizing improving patient outcomes. However, traditional diagnostic methods, including imaging tumor markers, have limitations sensitivity specificity, necessitating exploration novel approaches. This retrospective study included 165 patients diagnosed with (n = 87) or 78) January 2023 2024. Preoperative data, routine blood tests markers (e.g., alpha-fetoprotein [AFP], carbohydrate antigen 19-9 [CA19-9], carcinoembryonic [CEA]), were collected. Blood parameters, such as white cell count (WBC), neutrophil-to-lymphocyte ratio (NLR), lymphocyte-to-monocyte (LMR), analyzed. Univariate multivariate logistic regression analyses conducted to identify independent factors. A predictive model was constructed its performance evaluated using receiver operating characteristic curves. Subgroup performed investigate efficiency different subsets. AFP CA19-9 emerged key differentiating ICC. levels higher (P < .001), whereas markedly elevated .001). Among WBC monocyte .005), NLR .02), .012) associated an increased risk ICC, while a LMR protective against .006). The demonstrated robust accuracy, area under curve (AUC) 0.791. revealed superior at (≥200 ng/mL, AUC 0.90) (≥37 U/mL, 0.91). combination parameters demonstrates high efficacy preoperatively Key CA19-9, along inflammatory immune-related WBC, NLR, LMR, enhance accuracy. provides valuable insights into refining strategies supports individualized planning cancer.

Language: Английский

Citations

0

Revamping Hepatocellular Carcinoma Immunotherapy: The Advent of Microbial Neoantigen Vaccines DOI Creative Commons

Junze Liang,

Yanxia Liao,

Zhiwei Tu

et al.

Vaccines, Journal Year: 2024, Volume and Issue: 12(8), P. 930 - 930

Published: Aug. 21, 2024

Immunotherapy has revolutionized the treatment paradigm for hepatocellular carcinoma (HCC). However, its efficacy varies significantly with each patient's genetic composition and complex interactions their microbiome, both of which are pivotal in shaping anti-tumor immunity. The emergence microbial neoantigens, a novel class tumor vaccines, heralds transformative shift HCC therapy. This review explores untapped potential neoantigens as innovative poised to redefine current modalities. For instance, derived from microbiome have demonstrated capacity enhance immunity colorectal cancer, suggesting similar applications HCC. By harnessing these unique we propose framework personalized immunotherapeutic response, aiming deliver more precise potent strategy Leveraging could advance medicine, potentially revolutionizing patient outcomes

Language: Английский

Citations

1

Phage immunoprecipitation and sequencing—a versatile technique for mapping the antibody reactome DOI Creative Commons
Gustav N. Sundell, Sheng‐ce Tao

Molecular & Cellular Proteomics, Journal Year: 2024, Volume and Issue: 23(9), P. 100831 - 100831

Published: Aug. 19, 2024

Characterizing the antibody reactome for circulating antibodies provide insight into pathogen exposure, allergies, and autoimmune diseases. This is important biomarker discovery, clinical diagnosis, prognosis of disease progression, as well population-level insights immune system. The emerging technology phage display immunoprecipitation sequencing (PhIP-seq) a high-throughput method identifying antigens/epitopes reactome. In PhIP-seq, libraries with sequences defined lengths overlapping segments are bioinformatically designed using naturally occurring proteins cloned genomes to be displayed on surface. These used in experiments antibodies. can done parallel samples from multiple sources, DNA inserts bound phages barcoded subjected next-generation hit determination. PhIP-seq powerful technique characterizing that has undergone rapid advances recent years. this review, we comprehensively describe history discuss library design applications.

Language: Английский

Citations

0

PhIP-Seq: methods, applications and challenges DOI Creative Commons

Ziru Huang,

Samarappuli Mudiyanselage Savini Gunarathne,

Wenwen Liu

et al.

Frontiers in Bioinformatics, Journal Year: 2024, Volume and Issue: 4

Published: Sept. 4, 2024

Phage-immunoprecipitation sequencing (PhIP-Seq) technology is an innovative, high-throughput antibody detection method. It enables comprehensive analysis of individual profiles. This shows great potential, particularly in exploring disease mechanisms and immune responses. Currently, PhIP-Seq has been successfully applied various fields, such as the exploration biomarkers for autoimmune diseases, vaccine development, allergen detection. A variety bioinformatics tools have facilitated development this process. However, still faces many challenges room improvement. Here, we review methods, applications, discuss its future directions immunological research clinical applications. With continuous progress optimization, expected to play even more important role biomedical research, providing new ideas methods prevention, diagnosis, treatment.

Language: Английский

Citations

0

Comprehensive phage display viral antibody profiling using VirScan: potential applications in chronic immune-mediated disease DOI
Jed Valentiner Shrewsbury,

Evangelin Shaloom Vitus,

Adam Koziol

et al.

Journal of Virology, Journal Year: 2024, Volume and Issue: 98(11)

Published: Oct. 21, 2024

ABSTRACT Phage immunoprecipitation sequencing (PhIP-Seq) is a high-throughput platform that uses programmable phage display for serology. VirScan, specific PhIP-Seq library encoding viral peptides from all known human viruses, enables comprehensive quantification of past exposures. We review its use in immune-mediated diseases (IMDs), highlighting utility identifying exposures the context IMD development. Finally, we evaluate potential precision medicine by integrating it with other large-scale omics data sets.

Language: Английский

Citations

0