2025 Hyper Recent •CC0 1.0 Universal

This work is dedicated to the public domain. No rights reserved.

Access Preprint From Server
April 10th, 2025
Version: 1
Cornell University
genomics
biorxiv

Minimal Correlation but Complementary Diagnostic Utility for Plasma Cell-free RNA and Proteins

Bliss, A.Open in Google Scholar•Loy, C. J.Open in Google Scholar•Kim, J.Open in Google Scholar•Shimizu, C.Open in Google Scholar•Lenz, J. S.Open in Google Scholar•Belcher, E.Open in Google Scholar•Tremoulet, A. H.Open in Google Scholar•Burns, J. C.Open in Google Scholar•De Vlaminck, I.Open in Google Scholar

Proteins and RNA circulate in plasma and can offer insights into human physiology. Yet, despite their clinical importance, direct comparisons between these analytes remain unexplored. Here, we measured and compared plasma cell-free RNA (cfRNA) and protein levels for 263 children diagnosed with inflammatory diseases by RNA-sequencing (n=155) and SomaScan proteomics (n=171). Remarkably, cfRNA and protein levels were largely uncorrelated across samples (feature-by-sample r=0.052; median feature-level r=0.009). Nonetheless, machine learning models based on either modality distinguished Kawasaki Disease (KD) from Multisystem Inflammatory Syndrome in Children (MIS-C) with similar high accuracy (median AUC > 0.93). Analysis of KD subtypes revealed distinct cfRNA and protein signatures, with one group showing molecular similarity to MIS-C. These findings underscore the complementary nature of cfRNA and protein profiling and highlight the utility of integrating multiple blood analytes to improve disease classification and deepen our understanding of complex inflammatory conditions.

Similar Papers

biorxiv
Sat Apr 12 2025
A DNA methylation-based clock for age estimates in the wood mouse (Apodemus sylvaticus)
Although short-lived, easily manipulated wild systems could be useful for studying ageing, developing epigenetic clocks for them is challenging because their chronological age is often unknown. Here, we present a multi-tissue epigenetic clock for the wood mouse (Apodemus sylvaticus) that was developed in a laboratory colony and then applied to wild individuals. We used the mammalian methylation ar...
Wolf, S. E.
•
Babayan, S. A.
•
Marioni, R. A.
•
Chandra, T.
...•
Pedersen, A. B.
biorxiv
Fri Apr 11 2025
Dissecting the genetic basis of drought escape across multiple traits in colonizing Arabidopsis thaliana lineages
Drought response in plants is complex, involving integration across a range of physiological processes. However, our knowledge of how different aspects of drought response are linked at the genetic level is limited. We investigated multi-trait adaptation in Arabidopsis thaliana from the Cape Verde Islands (CVI). Using a high-throughput phenotyping platform that minimizes spatial heterogeneity, we ...
Elfarargi, A. F.
•
Gilbault, E.
•
Doring, N.
•
Dinis, H.
...•
Hancock, A. M.
biorxiv
Fri Apr 11 2025
Shift augmentation improves DNA convolutional neural network indel effect predictions
Determining genetic variant effects on molecular phenotypes like gene expression is a task of paramount importance to medical genetics. DNA convolutional neural networks (CNNs) attain state-of-the-art performance at predicting variant effects on gene regulation. However, most applications of such models focus on single nucleotide polymorphisms (SNPs), as technical challenges limit their applicatio...
Korsakova, A.
•
Srivastava, D.
•
Kelley, D. R.
biorxiv
Thu Apr 10 2025
Development of a Comprehensive Analytical Workflow for eDNA Analysis of Vertebrates, Arthropods, and Mollusks
Environmental DNA (eDNA) analysis is a powerful tool for biodiversity monitoring, but conventional methods are often limited to specific taxonomic groups and short-read sequencing. This study aimed to enhance species detection using Oxford Nanopore long-read sequencing and 16Sar/br primers. Our results showed that MiFish primers effectively detected fish species, while COI primers primarily detect...
Omino, M.
•
Sugawara, I.
•
Takada, K.
•
Yoshitake, K.
biorxiv
Thu Apr 10 2025
A modified methyl transferase cofactor to selectively disable gene expression in E. coli
Artificial control of gene expression in bacteria offers interesting prospects for influencing bacterial pathogenicity and antibiotic resistance. We show that the methyl-transferase cofactor, AdoHcy azide, can disable gene expression in modified plasmids in some strains of E. coli, where ampicillin and kanamycin resistance as well as eGFP genes were selectively and independently disabled. The disa...
Irving, O. J.
•
Stone, S.
•
Neely, R. K.
•
Albrecht, T.
biorxiv
Thu Apr 10 2025
Two telomere-to-telomere, gap-free genome assemblies and comparisons revealed the conserved key genes associated with sugar accumulation in Rubus genus
Two telomere-to-telomere, gap-free genome for Rubus species were sequenced and assembled by using an integrative approach that combined ultra-long reads from Oxford Nanopore Technology (ONT), PacBio high-fidelity (HiFi) long reads, Illumina paired-end short reads, and High-throughput Chromosome Conformation Capture (Hi-C) data, resulted in the first gap-free reference genomes of the Rubus genus. B...
Li, X.
•
Han, X.
•
Liu, S.
•
Zhang, Q.
...•
Zhou, J.
biorxiv
Thu Apr 10 2025
Genetic structure of mesophotic and shallow Acropora aculeus on isolated atolls of Eastern Australia
Acropora is the most diverse and widespread coral genus in the world. Although known for its critical ecological role in shallow-water habitats, its abundance and diversity at upper mesophotic depths have only recently been uncovered. Consequently, little is known about the genetic structuring of mesophotic Acropora populations and their potential ecological and evolutionary relationships with sha...
Hernandez-Agreda, A.
•
Hoey, J. A.
•
van Hulten, D.
•
Hernandez, P.
...•
Bongaerts, P.
biorxiv
Thu Apr 10 2025
MENDELSEEK: An algorithm that predicts Mendelian Genes and elucidates what makes them special
While individual Mendelian diseases (diseases caused by a single gene) are rare, their aggregate number is significant. Discovering which gene causes a Mendelian disease is crucial for accurate diagnosis and treatment. Despite decades of effort, the genetic cause driving over half of identified Mendelian diseases is unknown. To address this, we describe MENDELSEEK, a machine learning approach that...
Zhou, H.
•
Skolnick, J.
biorxiv
Thu Apr 10 2025
distQTL: Distribution Quantitative Trait Loci Identification by Population-Scale Single-Cell Data
Mapping expression quantitative trait loci (eQTLs) is a powerful method to study how genetic variation influences gene expression. Traditional bulk eQTL methods rely on averaged gene expression across a possibly heterogeneous mixture of cells, which can obscure underlying regulatory heterogeneity. Single-cell eQTL methods circumvent the averaging artifacts, providing an immense opportunity to inte...
Coulter, A.
•
Tong, C. Y.
•
Ni, Y.
•
Jiang, Y.