Marinos Velarde, A. | Search bioRxiv

bioRxiv2026

T cell repertoire diversity measurement; inferences from a dynamical systems model, Fourier Analysis of the T cell repertoire

T cell repertoire sequencing has unveiled a vast, complex array of T cells responsible for the human immune responses. Traditional analytic methodology fails to fully characterize and quantify the diversity of T cell receptors constituting the T cell repertoire. T cell receptor clonal frequency measured in terms of T cell receptor beta (TRB) V gene segment usage when arrayed in correspondence with the respective V gene segment positions on the TRB loci yields a periodic, undulating curve in the spatial domain of the TRB genomic locus. Using the genomic distance from the TRB-D1 segment to the TRB-V1-29 segments, Fourier analysis was performed utilizing Lomb-Scargle periodogram to obtain Spectral Power curves quantifying the TRB V clonal frequencies from 6 allogeneic stem cell transplant donors (baseline) and recipients (>/=100 days) using a variety of analytic software. Spectral Power curves revealed dominant spectral peaks at wavelengths ranging from 4-9 kb (113-252 millicycles/kb) in the six donors, with consistent frequency domain spectral patterns. This is consistent with similar use of V segments across healthy individuals. Recipients on the other hand demonstrated more dispersed spectra, with a spectral centroid shifted towards higher frequencies compared to donors (260 vs. 247 millicycles/kb). Consistent with this observation, the Low Frequency Index was lower in the recipients (0.18 vs 0.20). Power was concentrated in the <3 kb and 3-12 kb wavelengths in both groups. The analyses reported here demonstrate that the healthy SCT donors have a remarkably similar spectral signature occupying short to intermediate wavelegnths in the frequency domain, whereas recipients tend to shift towards higher frequencies. These findings are consistent with a normal organized distribution of TRB V segment usage in healthy individuals (by analogy other loci), and a more diffuse and disorderly usage in recipients, consistent with the notion of T cell responses constituting a dynamical system which evolves as a function of time. Fourier analysis of TRB (and potentially TRA) sequencing data provides a repertoire wide summary of T cell clonal distribution.

immunology↗

bioRxiv2025

Molecular and cellular dynamics of measurable residual disease progression in myelodysplastic syndromes

Cancer relapse after treatment invariably proceeds from the persistence and progression of measurable residual disease (MRD), an ultrasmall malignant population. Despite the poor prognostic impact established by increasingly sensitive MRD detection methods, the molecular pathways defining MRD remain unknown. To identify the unique features of MRD and the molecular forces shaping its progression, we performed single-cell multi-omic profiling on DNA, RNA and protein layers for a longitudinal patient cohort with relapsed myelodysplastic syndromes (MDS) after stem cell transplantation (SCT), the only curative modality for MDS. We provide a comprehensive molecular portrait of MRD cells with novel markers, shared across genetically heterogeneous patients. MDS relapse after SCT manifested universally with marked phenotypic evolution. Genotype and phenotype analyses revealed MRD progression as a dynamic, evolutionary process rather than a static expansionary one, driven by both subclonal sweeping and cell state transitions. Malignant cells adapted to infiltrating T cells by rewiring IFN-{gamma} responses to activate a key immunoevasive pathway. Our study demonstrates the power of longitudinal, single-cell multi-omic analysis for identifying, tracking, and understanding MRD cells, opening new avenues to target MRD persistence and progression.

cancer biology↗