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Henrich, A.

Publications and source records attributed to Henrich, A..

2 recordsLinked to original sources

Inflammatory proteostasis reprogramming creates a lysosomal bottleneck for microglial aggregate clearance

Efficient clearance of extracellular protein aggregates by microglia is essential for maintaining brain homeostasis and limiting the accumulation of pathological proteins during neurodegeneration. However, how inflammatory activation affects the ability of microglia to internalize and degrade these aggregates remains incompletely understood. Here, we show that lipopolysaccharide (LPS)-induced inflammatory activation impairs the degradation of extracellularly-acquired -synuclein (-Syn) and Tau aggregates while largely preserving their uptake. Mechanistically, Toll-like receptor 4 (TLR4) activation induces translational reprogramming and increases intracellular proteostatic demand, while inhibition of protein synthesis restores -Syn degradation without preventing inflammatory Nuclear factor kappa-light-chain-enhancer of activated B cells (NF-{kappa}B) activation. Despite largely preserved canonical autophagic flux, inflammatory stimulation is associated with reduced expression of lysosomal proteins, including cathepsin D, suggesting insufficient lysosomal adaptation to increased intracellular demand. Consistent with this model, pharmacological activation of transcription factor EB (TFEB) restores aggregate degradation, indicating that the impairment can be overcome by enhancing lysosomal function. Supporting its potential relevance to human disease, microglial -Syn deposits in brain tissue from patients with dementia with Lewy bodies show limited spatial association with cathepsin D-positive structures. Together, our findings identify a demand-driven lysosomal bottleneck through which inflammatory activation compromises aggregate degradation without substantially affecting uptake, highlighting lysosomal adaptation as a critical determinant of microglial aggregate clearance during neuroinflammation.

cell biology↗

Prediction of tumor-specific splicing from somatic mutations as a source of neoantigen candidates

Splicing is dysregulated in many tumors and may result in tumor-specific transcripts that can encode neoantigens, which are promising targets for cancer immunotherapy. Detecting tumor-specific splicing is challenging because many non-canonical splice junctions identified in tumor transcriptomes also appear in healthy tissues. Here, we developed splice2neo to integrate the predicted splice effects from somatic mutations with splice junctions detected in tumor RNA-seq for individual cancer patients. Splice2neo excludes splice junctions from healthy tissue samples, annotates resulting transcript and peptide sequences, and provides targeted re-quantification of supporting RNA-seq reads. We developed a stringent detection rule to predict splice junctions as mutation-derived targets and identified 1.7 target splice junctions per tumor with a false discovery rate below 5% in a melanoma cohort. We confirmed tumor-specificity using independent, healthy tissue samples. Furthermore, using tumor-derived RNA, we confirmed individual exon skipping events experimentally. Most target splice junctions encoded neoepitope candidates with predicted MHC-I or MHC-II binding. Compared to neoepitope candidates derived from non-synonymous point mutations, the splicing-derived MHC-I neoepitope candidates had a lower self-similarity to corresponding wild-type peptides. In conclusion, we demonstrate that identifying mutation-derived and tumor-specific splice junctions can lead to additional neoantigen candidates to expand the target repertoire for cancer immunotherapies. Key PointsO_LIsplice2neo is a versatile tool for identifying and analyzing of splice junctions as a source of neoantigen candidates C_LIO_LIWe identified mutation-retrieved splice junctions supported by RNA-seq in melanoma samples C_LIO_LIThe predicted target splice junctions exhibited a strong tumor-specificity as they were absent in healthy tissues. C_LIO_LITarget splice junctions often lead to frame-shift peptides and encode promising neoantigen candidates C_LI

bioinformatics↗