Biology subjects

Barker, E.

Publications and source records attributed to Barker, E..

4 recordsLinked to original sources

bioRxiv2026

CD56dimCD16dim NK cells are the dominant effector cells against HIV-infected primary T-cells

Despite being rare among circulating natural killer (NK) cells and expressing 10-fold less CD16 than the predominant CD56dimCD16bright population, CD56dimCD16dim NK cells are expanded in HIV long-term elite controllers, yet their capacity to kill HIV-infected cells remained untested. Here, we show that these rare cells are the dominant effectors against HIV-infected T-cells, mediating approximately 4-fold higher direct cytotoxicity and 3-4-fold higher antibody-dependent cellular cytotoxicity (ADCC) than CD56dimCD16bright cells, and serially engaging multiple targets. This advantage is intrinsic, unexplained by cytotoxic granule content or inhibitory receptors recognizing MHC class I. Direct killing depends on NKG2D recognition of Vpr-induced ligands, with NKG2D elevated on CD56dimCD16dim cells; ADCC requires both NKG2D and ADAM17-mediated CD16 turnover for serial engagement. These findings explain the elite-controller reorganization, reveal that NK effector dominance is target-tuned rather than fixed (CD56dimCD16negative cells dominate against K562 cells), and identify high-NKG2D CD56dimCD16dim cells as the effector population HIV therapies should reproduce. Impact StatementA rare natural killer cell subset that makes up only a few percent of circulating NK cells, yet is enriched in the people who control HIV for years without medication, turns out to be the dominant killer of HIV-infected cells, far outperforming the common subset long assumed to do the job, and this work shows how these cells recognize and repeatedly attack infected targets, pointing to the specific effector that future cell-based therapies might use to help people with HIV stay healthy without lifelong drugs.

immunology↗

bioRxiv2024

Dysregulation of cholesterol and bile acid homeostasis across the gut-liver axis following Cryptosporidium intestinal infection

Cryptosporidium spp., an apicomplexan protozoan, is one of the most common pathogens causing moderate-to-severe diarrhea in children under 2 years of age and is also an important opportunistic pathogen for patients with AIDS. There are currently no effective vaccines or therapies available. Infection in children is associated with malnutrition, growth defects, and even impaired cognitive development, but underlying mechanisms remain unclear. We report here that C. parvum infection in neonatal mice impairs bile acid reabsorption in the ileum, disrupts lipid metabolism in the liver, and alters bile acid homeostasis in the enterohepatic circulation. The reduction of bile acid pool further impairs lipid absorption in the small intestine. Additionally, replenishing bile prevents the decline in lipid absorption in infected neonatal mice. Strikingly, bile gavage significantly reduces the infection burden and ameliorates the dysregulated homeostasis of cell proliferation and migration in intestinal epithelium following infection. These findings may guide novel therapeutic approaches for cryptosporidiosis.

microbiology↗

bioRxiv2023

Improvements to the Gulf Pipefish Syngnathus scovelli Genome

The Gulf pipefish Syngnathus scovelli has emerged as an important species in the study of sexual selection, development, and physiology, among other topics. The fish family Syngnathidae, which includes pipefishes, seahorses, and seadragons, has become an increasingly attractive target for comparative research in ecological and evolutionary genomics. These endeavors depend on having a high-quality genome assembly and annotation. However, the first version of the S. scovelli genome assembly was generated by short-read sequencing and annotated using a small set of RNA-sequence data, resulting in limited contiguity and a relatively poor annotation. Here, we present an improved genome assembly and an enhanced annotation, resulting in a new official gene set for S. scovelli. By using PacBio long-read high-fidelity (Hi-Fi) sequences and a proximity ligation (Hi-C) library, we fill small gaps and join the contigs to obtain 22 chromosome-level scaffolds. Compared to the previously published genome, the gaps in our novel genome assembly are smaller, the N75 is much larger (13.3 Mb), and this new genome is around 95% BUSCO complete. The precision of the gene models in the NCBIs eukaryotic annotation pipeline was enhanced by using a large body of RNA-Seq reads from different tissue types, leading to the discovery of 28,162 genes, of which 8,061 were non-coding genes. This new genome assembly and the annotation are tagged as a RefSeq genome by NCBI and thus provide substantially enhanced genomic resources for future research involving S. scovelli.

genomics↗

bioRxiv2019

High-sensitivity monitoring of ctDNA by patient-specific sequencing panels and integration of variant reads

Circulating tumor-derived DNA (ctDNA) can be used to monitor cancer dynamics noninvasively. Patients with small tumors have few copies of ctDNA in plasma, resulting in limited sensitivity to detect low-volume or residual disease. We show that sampling limitations can be overcome and sensitivity for ctDNA detection can be improved by massively parallel sequencing when hundreds to thousands of mutations are identified by tumor genotyping. We describe the INtegration of VAriant Reads (INVAR) analysis pipeline, which combines patient-specific mutation lists with both custom error-suppression methods and signal enrichment based on biological features of ctDNA. In this framework, the sensitivity can be estimated independently for each sample based on the number of informative reads, which is the product of the number of mutations analyzed and the average depth of unique sequencing reads. We applied INVAR to deep sequencing data generated by custom hybrid-capture panels, and showed that when ~106 informative reads were obtained INVAR allowed detection of tumor-derived DNA fractions to parts per million (ppm). In serial samples from patients with advanced melanoma on treatment, we detected ctDNA when imaging confirmed tumor volume of ~1cm3. In patients with resected early-stage melanoma, ctDNA was detected in 40% of patients who later relapsed, with higher rates of detection when more informative reads were obtained. We further demonstrated that INVAR can be generalized and allows improved detection of ctDNA from whole-exome and low-depth whole-genome sequencing data.

cancer biology↗