Biology subjects

Belay, K.

Publications and source records attributed to Belay, K..

6 recordsLinked to original sources

bioRxiv2025

Conserved Landscape of Chemokine Receptor Co-expression Defines the Functional States of CD8+ T Cells in Melanoma

Cancer immunotherapies, from checkpoint blockade to adoptive cell therapies like tumor-infiltrating lymphocytes (TILs), have revolutionized cancer treatment but are limited by variable efficacy and significant toxicities. A central challenge is identifying ideal T-cell populations that effectively eliminate tumors without causing off-target damage, a distinction not captured by existing biomarkers. We show that co-expression patterns of chemokine receptors (CRs) CXCR3, CCR5, and CXCR6 on CD8+ T cells provide a functional "code" defining subsets with divergent roles in on-target immunity versus off-target inflammation. In mouse and human melanoma, a triple-positive (CXCR3+CCR5+CXCR6+) T-cell subset is essential for tumor control, and its genetic signature correlates with positive clinical response, while a distinct CCR5+CXCR6+ subset drives liver immune-related adverse events (IRAEs). Crucially, this CR code reveals that immunotherapy actively reshapes T-cell trafficking patterns, uncovering profound heterogeneity within conventional populations and distinguishing potent anti-tumor progenitors from cells predisposed to exhaustion or off-target migration. This work establishes CR co-expression as a practical tool, providing a surface marker-based strategy to identify and enrich optimized T cells for adoptive therapies, thereby offering a framework to uncouple efficacy from toxicity. One Sentence SummaryCo-expression of CCR5, CXCR6, and CXCR3 provides a functional code that separates T-cell-mediated anti-tumor efficacy from off-target toxicity, enabling the selection of superior cells for safer and more effective cancer immunotherapies. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC="FIGDIR/small/693486v2_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@19b0f44org.highwire.dtl.DTLVardef@1076129org.highwire.dtl.DTLVardef@17c0be6org.highwire.dtl.DTLVardef@f14893_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LI{middle dot} CXCR6, CXCR3 and CCR5 co-expression signature stratifies patient survival in human melanoma C_LIO_LI{middle dot} CD8+ T cells co-expressing CXCR6, CXCR3 and CCR5 are critical effectors with high proliferative, cytotoxic, and activation profile in human and mice melanoma C_LIO_LI{middle dot} CD8+ T cells co-expressing CXCR6, CXCR3 and CCR5 drive anti-tumoral responses during checkpoint blockade in both human and mice C_LI

immunology↗

bioRxiv2025

Insights gained into Vascular Streak Dieback, an Emerging Disease of Woody Ornamentals in the United States, using Metagenomic Sequencing

Woody ornamentals are integral to urban landscapes and play important roles in habitat restoration and ecological conservation, yet their national and international trade facilitates the spread of plant diseases with significant ecological and economic consequences. Vascular streak dieback (VSD) recently emerged on woody ornamentals in the United States and was found to be associated with the fungal pathogen Ceratobasidium sp. (Csp), but little is known about its genomic diversity and associated microbial communities. We thus applied metagenomic sequencing to 106 symptomatic samples that had tested positive for Csp and had been collected from 34 woody ornamental species in seven states. Taxonomic profiling identified Csp as the only putative pathogen of which we recovered 17 high-quality draft genomes. Phylogenomic and pangenome analyses revealed that U.S. Csp isolates form a tight genetic cluster, distinct in gene content from C. theobromae, a pathogen of cacao, avocado, and cassava in Southeast Asia. Comparative analyses highlighted gene content differences, including candidate effectors and secondary metabolite clusters, which may underlie host interactions and offer diagnostic targets. These findings provide the first genomic insights into the U.S. Csp population, suggest the recent introduction of a single genetic lineage with a broad host range, and establish a framework for improved detection, monitoring, and management of VSD in woody ornamentals. ImportanceIdentification of the pathogen that causes an emerging disease, be it of humans, animals or plants, is a prerequisite to develop effective treatment and/or management practices and to try to control the disease outbreak to prevent further pathogen spread. Vascular Streak Dieback (VSD) is an emerging disease of ornamental bushes and trees in the U.S. Identification of the pathogen has been hindered by the difficulty in growing the fungal pathogen found to be associated with diseased plants in pure culture. Here we succeeded in sequencing DNA of the likely pathogen directly from plant tissue or from the fungal mass growing out of collected plant tissue. The sequences were assembled into genomes, which allowed us to precisely identify the pathogen, compare it to related pathogens of other plants, and to predict how it causes disease. These results can now be used to inform management and control of VSD.

genomics↗

bioRxiv2025

Spatiotemporal Single-Cell Analysis Reveals T Cell Clonal Dynamics and Phenotypic Plasticity in Human Graft-versus-Host Disease

Allogeneic hematopoietic cell transplantation (alloHCT) is curative for various hematologic diseases but often leads to acute graft-versus-host disease (GVHD), a potentially life-threatening complication. We leverage GVHD as a uniquely tractable disease model to dissect complex T-cell-mediated pathology in 27 alloHCT recipients. We integrate pre-transplant identification of alloreactive T-cells with longitudinal tracking across blood and gut, using mixed lymphocyte reaction-based clonal "fingerprinting", TCR clonotyping, single-cell RNA/TCR sequencing, and spatial transcriptomics. Using DecompTCR, a novel computational tool for longitudinal TCR analysis, we uncover clonal expansion programs linked to GVHD severity and TCR features. Multi-omics profiling of gut biopsies reveals enrichment and clonal expansion of CD8 effector and ZNF683(Hobit) resident memory T-cells, cytolytic remodeling of regulatory and unconventional T-cells, and localization of CD8 effector T-cells near intestinal stem cells in crypt loss regions. This framework defines dynamic immune circuit rewiring and phenotypic plasticity with implications for biomarkers and therapies. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=198 SRC="FIGDIR/small/655962v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@178b77dorg.highwire.dtl.DTLVardef@569226org.highwire.dtl.DTLVardef@1951281org.highwire.dtl.DTLVardef@1f1e046_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIPersistent expansion of diverse alloreactive T cell clones is a hallmark of severe GVHD C_LIO_LIDecompTCR reveals dynamic clonal expansion programs linked to GVHD severity and clinical outcome C_LIO_LICD8+ T cell clones exhibit phenotypic plasticity in vivo across intestinal tissue compartments in GVHD C_LIO_LIHigh-resolution spatial profiling shows CD8+ effector T cells localize near intestinal stem cell niches and drive epithelial injury in GVHD C_LI

systems biology↗

bioRxiv2025

Short-term gonadal cultures are sufficient for germline transmission in a songbird

1Primordial germ cells (PGCs) are germline stem cells that develop into sperm or egg cells and are valuable for avian biobanking and the propagation of donor-derived offspring. However, in non-poultry birds the long-term maintenance and self-renewal of PGCs in vitro remains challenging. This limitation hinders biobanking in other avian clades, particularly in the zebra finch and other songbirds that uniquely possess a germline restricted chromosome (GRC). Here, we generated and compared short-term cultures of chicken and zebra finch PGCs from the embryonic gonads or blood, as well as established long-term cultures of chicken PGCs. Using single-cell RNA sequencing, we found that the transcriptome profile of long-term chicken gonadal cultures were exclusively PGCs, whereas the short-term chicken and zebra finch cultures represented a heterogeneous mixture of cell types. The zebra finch culture further included rapidly differentiating PGCs, as well as a germ cell type not previously identified in the embryonic songbird gonad. Although zebra finch short-term gonadal cultures did not yield robust long-term PGC cultures, short-term cultured PGCs were able to integrate into host zebra finch gonads after injection into the dorsal aorta, contribute to gametic populations in adult chimeras, and give rise to phenotypically- and genomically-validated offspring. This study provides a foundation for using short-term gonadal cultures to derive donor and transgenic offspring in songbirds and further explore the unique developmental genetics of PGCs across the avian clade. SummaryBeyond poultry, the long-term culture of self-renewing primordial germ cells (PGCs) remains a challenge. Here, we compare the cell population heterogeneity and reproductive viability of gonadal cultures for the zebra finch, a songbird model of vocal learning, with established chicken PGC protocols. Using single-cell RNA sequencing, we identify the rapid differentiation of zebra finch gonadal germ cells in vitro, including germline identities not previously noted in the embryonic gonad. In comparison, these differentiated cell profiles were also found in zebra finch blood PGC culture conditions, but not identified in short- or long-term chicken PGC cultures. Host embryo injections of these short-term zebra finch gonadal cultures resulted in germline chimeric animals, but at lower rates of gonadal reconstitution compared to chicken. Nonetheless, these cultures allowed for the derivation of zebra finch germline chimeras that yield phenotypically- and genomically-validated offspring from cultured PGCs.

developmental biology↗

bioRxiv2024

Long-read sequencing reveals novel structural variation markers for key agronomic and quality traits of soybean

In plant genomic research, long read sequencing has been widely used to detect structure variations that are not captured by short read sequencing. In this letter, we described an analysis of whole genome re-sequencing of 29 soybean varieties using nanopore long-read sequencing. The compiled germplasm reflects diverse applications, including livestock feeding, soy milk and tofu production, as well as consumption of natto, sprouts, and vegetable soybeans (edamame). We have identified 365,497 structural variations in these newly re-sequenced genomes and found that the newly identified structural variations are associated with important agronomic traits. These traits include seed weight, flowering time, plant height, oleic acid content, methionine content, and trypsin inhibitor content, all of which significantly impact soybean production and quality. Experimental validation supports the roles of predicted candidate genes and structural variant in these biological processes. Our research provides a new source for rapid marker discovery in crop genomes using structural variation and whole genome sequencing.

genomics↗

bioRxiv2023

Pronounced early differentiation underlies zebra finch gonadal germ cell development.

The diversity of germ cell developmental strategies has been well documented across many vertebrate clades. However, much of our understanding of avian primordial germ cell (PGC) specification and differentiation has derived from only one species, the chicken (Gallus gallus). Of the three major classes of birds, chickens belong to Galloanserae, representing less than 4% of species, while nearly 95% of extant bird species belong to Neoaves. This represents a significant gap in our knowledge of germ cell development across avian species, hampering efforts to adapt genome editing and reproductive technologies developed in chicken to other birds. We therefore applied single-cell RNA sequencing to investigate inter-species differences in germ cell development between chicken and zebra finch (Taeniopygia castanotis), a Neoaves songbird species and a common model of vocal learning. Analysis of early embryonic male and female gonads revealed the presence of two distinct early germ cell types in zebra finch and only one in chicken. Both germ cell types expressed zebra finch Germline Restricted Chromosome (GRC) genes, present only in songbirds among birds. One of the zebra finch germ cell types expressed the canonical PGC markers, as did chicken, but with expression differences in several signaling pathways and biological processes. The second zebra finch germ cell cluster was marked by proliferation and fate determination markers, indicating beginning of differentiation. Notably, these two zebra finch germ cell populations were present in both male and female zebra finch gonads as early as HH25. Using additional chicken developmental stages, similar germ cell heterogeneity was identified in the more developed gonads of females, but not males. Overall, our study demonstrates a substantial heterochrony in zebra finch germ cell development compared to chicken, indicating a richer diversity of avian germ cell developmental strategies than previously known.

cell biology↗