Biology subjects

Kifer, D.

Publications and source records attributed to Kifer, D..

4 recordsLinked to original sources

bioRxiv2026

Reconstructing N-Glycan Profiles of Individual Glycoproteins from the Total Blood Plasma N-Glycome: Implications for Immunoglobulin G N-Glycosylation GWAS

The genetic regulation of the plasma N-glycome variation in human populations is not fully characterized, partly due to the limited sample size in glyco-genetics studies. Here, we aimed to demonstrate that protein-specific N-glycan profiles, like those of immunoglobulin G (IgG), can be accurately reconstructed from the total plasma N-glycome (TPNG), enabling us to find new regulators of this complex process re-analysing existing datasets. By testing multiple linear and non-linear machine learning approaches we built a model to reconstruct IgG N-glycans from TPNG data, training on the TwinsUK cohort and validating on CEDAR. We reconstruct GWAS summary statistics for IgG N-glycans by applying the trained linear model to plasma glycan GWAS summary statistics, i.e., as GWAS of linear combinations of plasma glycan traits. The majority of the identified loci had been implicated in IgG N-glycosylation GWAS. Additionally, we found four new loci and suggested the role of FCRLA, KDELR2, HHEX, and TCF3 in the regulation of IgG N-glycosylation. In conclusion, we showed that our method enables the creation of protein-specific N-glycome datasets, allowing for powerful meta-analyses without the need to profile new samples.

genetics↗

bioRxiv2025

High-Throughput Site-Specific N-Glycosylation Profiling of Human Fibrinogen in Atrial Fibrillation

Fibrinogen is a major plasma glycoprotein involved in blood coagulation and inflammatory responses. Alterations in its glycosylation have been implicated in various pathological conditions, yet its site-specific N-glycosylation profile remains largely unexplored in a clinical context. Here, we present a high-throughput LC-MS workflow for site-specific analysis of fibrinogen N-glycosylation using a cost-effective ethanol precipitation enrichment method. The method demonstrated good intra- and inter-plate repeatability (CV: 5% and 12%, respectively) and was validated through the first assessment of intraindividual temporal stability in healthy individuals, revealing consistent glycosylation patterns within individuals. Application to 181 atrial fibrillation (AF) patients and 52 healthy controls identified three gamma chain glycoforms significantly associated with AF. Most notably, increased levels of the asialylated N4H5, known to enhance fibrin bundle thickness and promote clot formation, suggest a potential mechanism linking glycosylation changes to the prothrombotic state in AF. Furthermore, fibrinogen sialylation showed strong associations with cardiovascular risk factors, including triglycerides, BMI, and glucose levels. Longitudinal analysis of 108 AF patients six months post-catheter ablation showed stability in the AF-associated glycan profile. Our findings establish fibrinogen glycosylation as a potential biomarker for cardiovascular conditions and demonstrate the utility of site-specific glycosylation analysis for clinical applications.

molecular biology↗

bioRxiv2024

Contrasting macroevolutionary patterns in the human N-glycosylation pathway

Building on coding mutations and splicing variants, post-translational modifications add a final layer to protein diversity that operates at developmental and physiological timescales. Although protein glycosylation is one of the most common post-translational modifications, its evolutionary origin remains largely unexplored. Here, we performed a phylostratigraphic tracking of glycosylation machinery genes and their targets -- glycosylated proteins -- in a broad phylogenetic context. Our results show that the vast majority of human glycosylation machinery genes trace back to two evolutionary periods: the origin of all cellular organisms and the origin of all eukaryotes. This indicates that protein glycosylation is an ancient process likely common to all life, further elaborated in early eukaryotes. In contrast, human glycoproteins exhibited prominent enrichment signals in more recent evolutionary periods, suggesting an important role in the transition from metazoans to vertebrates. Focusing specifically on the N-glycosylation pathway, we noted that the majority of N-glycosylation genes acting on the cytoplasmic side of the endoplasmic reticulum (ER) trace back to the origin of cellular organisms. This sharply contrasts with the rest of the N-glycosylation pathway, which is oriented toward the ER lumen, where genes of eukaryotic origin predominate. In the Golgi, we also identified an analogous binary evolutionary origin of glycosylation machinery genes. We discuss these findings in the context of the evolutionary emergence of the eukaryotic endomembrane system and propose that the ER evolved through the invagination of a prokaryotic cell membrane containing an N-glycosylation pathway.

evolutionary biology↗

bioRxiv2020

Embryo-like features in developing Bacillus subtilis biofilms

Correspondence between evolution and development has been discussed for more than two centuries1. Recent work reveals that phylogeny-ontogeny correlations are indeed present in developmental transcriptomes of eukaryotic clades with complex multicellularity2-10. Nevertheless, it has been largely ignored that the pervasive presence of phylogeny-ontogeny correlations is a hallmark of development in eukaryotes6, 10-12. This perspective opens a possibility to look for similar parallelisms in biological settings where developmental logic and multicellular complexity are more obscure13-16. For instance, it has been increasingly recognized that multicellular behaviour underlies biofilm formation in bacteria13, 14, 17-19. However, it remains unclear whether bacterial biofilm growth shares some basic principles with development in complex eukaryotes14-16, 18, 20. Here we show that the ontogeny of growing Bacillus subtilis biofilms recapitulates phylogeny at the expression level. Using time-resolved transcriptome and proteome profiles, we found that biofilm ontogeny correlates with the evolutionary measures, in a way that evolutionary younger and more diverged genes were increasingly expressed towards later timepoints of biofilm growth. Molecular and morphological signatures also revealed that biofilm growth is highly regulated and organized into discrete ontogenetic stages, analogous to those of eukaryotic embryos11, 21. Together, this suggests that biofilm formation in Bacillus is a bona fide developmental process comparable to organismal development in animals, plants and fungi. Given that most cells on Earth reside in the form of biofilms22 and that biofilms represent the oldest known fossils23, we anticipate that the widely-adopted vision of the first life as a single-cell and free-living organism needs rethinking.

evolutionary biology↗