Biology subjects

Follonier, O.

Publications and source records attributed to Follonier, O..

4 recordsLinked to original sources

bioRxiv2026

Capabilities, specificity gaps and training-data dependence of AlphaFold3 across diverse application areas

Structure prediction models have moved from single proteins to assemblies that include diverse biomolecules and their modifications. AlphaFold3 (AF3) and related models extended structural modelling via an all-atom framework, opening many new potential applications in structural biology. We evaluate how well the new capabilities of AF3 translate into application tasks in diverse areas: prediction of ubiquitinated protein structures, T-cell receptor (TCR)-epitope recognition, antibody-antigen complexes, protein-RNA and protein-lipid interactions. We find that, while AF3 can perform well in favourable settings, this performance is uneven across applications. In RNA-target predictions, the model confidence fails to separate genuine from decoy interaction partners and in several tasks accuracy depends on the presence of related complexes in the training set. Taken together, our assessment is more cautious than for AF2, whose gains in modelling monomers and complexes were clear and broadly generalisable. AF3s extension to new biomolecule types shows less consistent performance and generalisation. AF3 can be a powerful tool for hypothesis generation and prioritisation, but its predictions and use of confidence metrics will depend strongly on the specific application area and must be interpreted with respect to training-set overlap. We expect that the benchmarks provided here will serve for testing of future developments in the structure prediction field.

bioinformatics↗

bioRxiv2026

OFF-Target Effects of Mycophenolic Acid on BK Polyomavirus Replication in Primary Human Renal Proximal Tubular Epithelial Cells

Tacrolimus (TAC) and mycophenolic acid (MPA) effectively reduce allograft rejection in kidney transplant recipients by inhibiting donor-specific lymphocyte activation and proliferation, respectively. However, this desired on-target effect is associated with uncontrolled BK polyomavirus (BKPyV)-replication and premature kidney allograft failure in 10%-20% of recipients. Besides impairing BKPyV-specific immunity, TAC also stimulates BKPyV-replication directly in renal proximal tubule epithelial cells (RPTECs) as an off-target effect. We now investigated off-target effects of MPA on BKPyV-replication in RPTECs. Following BKPyV exposure for 2 h, MPA inhibited BKPyV replication as shown by reduced supernatant BKPyV loads (IC50 0.65 M), number of infected cells, and viral protein expression at 72 hours post-infection (hpi). Notably, MPA inhibition of the viral large tumor antigen (LTag) was associated with the appearance of a truncated Tag of [~]17 kDa (truncTag-17). Adding guanosine (GUO) reversed MPA inhibition of BKPyV replication and viral protein expression, while truncTag-17 disappeared. Time course studies indicated that MPA inhibition was operative from 24 h before up to 24 h after BKPyV infection. GUO reversed MPA inhibition when administered from 24 h before to 24 h after BKPyV infection. Deep sequencing of passaged supernatant BKPyV genomes revealed more guanine-replacement (C[->]T or G[->]A) mutations for MPA compared to MPA/GUO (35% versus 10%, read threshold >0.5%). Thus, MPA can exert direct off-target effects on BKPyV replication in RPTECs linked to truncTag-17 expression, which can be partially reversed by exogenous GUO. ImportanceReducing immunosuppression is currently recommended for kidney transplant recipients with BKPyV-DNAemia and nephropathy to improve virus-specific immune control, but increases the risk of T-cell and antibody-mediated rejection. Although TAC and MPA synergize in their on-target effects on lymphocytes, they differ in their off-target effects on RPTECs. Unlike TAC, MPA inhibits BKPyV replication in an uncompetitive dose-dependent manner. MPA inhibition can be partially reversed by exogenous GUO using the purine salvage pathway that is lacking in lymphocytes. MPA acts during the early viral replication phase that depends on LTag promoting cellular G1[->]S-phase progression. MPA-mediated GUO depletion not only reduces rapid cell proliferation similar to the well-known gastrointestinal or hematopoietic toxicities, but also slows viral replication, induces expression of a truncTag-17, and increases GC-mutation rates in progeny virus genomes. We discuss the relevance of these off-target characteristics of MPA in the optimized management of kidney transplant recipients with BKPyV-DNAemia and -nephropathy.

microbiology↗

bioRxiv2024

TCR clustering by contrastive learning on antigen specificity.

Effective clustering of T-cell receptor (TCR) sequences could be used to predict their antigen-specificities. TCRs with highly dissimilar sequences can bind to the same antigen, thus making their clustering into a common antigen group a central challenge. Here, we develop TouCAN, a method that relies on contrastive learning and pre-trained protein language models to perform TCR sequence clustering and antigen-specificity predictions. Following training, TouCAN demonstrates the ability to cluster highly dissimilar TCRs into common antigen groups. Additionally, TouCAN demonstrates TCR clustering performance and antigen-specificity predictions comparable to other leading methods in the field.

bioinformatics↗

bioRxiv2023

Structural implications of BK polyomavirus sequence variations in the major viral capsid protein Vp1 and large T-antigen: a computational study

BK polyomavirus (BKPyV) is a double-stranded DNA virus causing nephropathy, hemorrhagic cystitis, and urothelial cancer in transplant patients. The BKPyV-encoded capsid protein Vp1 and large T-antigen (LTag) are key targets of neutralizing antibodies and cytotoxic T-cells, respectively. Our single-center data suggested that variability in Vp1 and LTag may contribute to failing BKPyV-specific immune control, and impact vaccine design. We therefore analyzed all available entries in GenBank (1516 VP1; 742 LTAG) and explored potential structural effects using computational approaches. BKPyV-genotype (gt)1 was found in 71.18% of entries, followed by BKPyV-gt4 (19.26%), BKPyV-gt2 (8.11%) and BKPyV-gt3 (1.45%), but rates differed according to country and specimen type. Vp1-mutations matched a serotype different than the assigned one or were serotype-independent in 43%, 18% affected more than one amino acid. Notable Vp1-mutations altered antibody-binding domains, interactions with sialic acid receptors, or were predicted to change conformation. LTag-sequences were more conserved, with only 16 mutations detectable in more than one entry and without significant effects on LTag-structure or interaction domains. However, LTag changes were predicted to affect HLA-class I presentation of immunodominant 9mers to cytotoxic T-cells. These global data strengthen single center observations and specifically our earlier findings revealing mutant 9mer epitopes conferring immune escape from HLA-I cytotoxic T cells. We conclude that variability of BKPyV-Vp1 and LTag may have important implications for diagnostic assays assessing BKPyV-specific immune control and for vaccine design. IMPORTANCEType and rate of amino acid variations in BKPyV may provide important insights into BKPyV diversity in human populations and an important step towards defining determinants of BKPyV-specific immunity needed to protect vulnerable patients from BKPyV diseases. Our analysis of BKPyV sequences obtained from human specimens reveals an unexpectedly high genetic variability for this double-stranded DNA virus that strongly relies on host cell DNA replication machinery with its proof reading and error correction mechanisms. BKPyV variability and immune escape should be taken into account when designing further approaches to antivirals, monoclonal antibodies and vaccines for patients at risk of BKPyV diseases.

microbiology↗