Biology subjects

Miragaia, R.

Publications and source records attributed to Miragaia, R..

3 recordsLinked to original sources

bioRxiv2026

Comparative Single-Cell Profiling of CRISPR Knockout and Interference Defines Modality-Specific Strengths in Functional Genomics

Pooled CRISPR screens coupled with single-cell RNA sequencing enable high-throughput functional interrogation of gene regulatory networks, yet systematic comparisons of CRISPR knockout (CRISPRko) and CRISPR interference (CRISPRi) remain limited. We established a single-cell CRISPRko workflow and benchmarked it against CRISPRi using 87 sgRNAs targeting 29 unfolded protein response genes. CRISPRko generated transcriptional phenotypes are highly concordant with CRISPRi, and induced comparable pathway-level responses. While CRISPRi allows direct assessment of target gene repression, CRISPRko provides an effective complementary approach for complete loss-of-function studies, expanding the toolkit for single-cell functional genomics.

genomics↗

bioRxiv2025

Integrated single-cell analyses of affinity-tested B-cells enable the identification of a gene signature to predict antibody affinity.

Advancements in single-cell technologies and deep sequencing have revealed the vast B-cell repertoire arising from immunisation, enhancing the number of antibodies available for testing. However, selecting the highest affinity antibodies from many sequences is not a straightforward feat, as mechanisms sustaining affinity maturation and related markers remain under-studied. Here, we generated datasets of antigen-specific B-cells after mouse immunisation as well as re-analysed public data to identify a novel transcriptomic signature, "High Signature" (HS), with predictive power for high-affinity antibodies. HS, derived by integrating antibody sequences, gene expression, and affinity measurements, enabled sub-nanomolar affinity antibody selection without sequence pre-analysis. Notably, HS-expressing B-cells were 2.5 times more likely to yield high-affinity antibodies than randomly picked cells. Mechanistically, we identified RUVBL2, an AAA+ ATPase, as a primary HS modulator, suggesting its involvement in affinity maturation. Furthermore, HS applied to human PBMC data enriched high-affinity antibody expression, underscoring its potential in antibody discovery.

immunology↗

bioRxiv2017

An unbiased reconstruction of the T helper cell type 2 differentiation network

T helper type 2 (Th2) cells are important regulators of our adaptive immune response, particularly the response against parasites, and have relevance for auto-immunity as well as tumour progression. This classic T helper type has been studied intensively, but not systematically. Using newly developed, genome-wide retroviral CRISPR knock-out (KO) technology, combined with RNA-seq, ATAC-seq and ChIP-seq, we have dissected the regulatory circuitry governing differentiation in these cells. During Th2 activation/differentiation approximately 4000 genes are perturbed, with at least 200 genes specifically associated with the Th2 program in mouse and human. We confirm previously known Th2 driver genes and have discovered several novel genes, including transcription factors, metabolic genes and potential receptors/cytokines, critical for Th2 function. Our study provides an atlas for, but not limited to, the Th2 regulatory network, pinpointing the key players of Th2 differentiation.

immunology↗