IL-33-binding HpARI family homologues with divergent effects in suppressing or enhancing type 2 immune responses.

HpARI is an immunomodulatory protein secreted by the intestinal nematode Heligmosomoides polygyrus bakeri, which binds and blocks IL-33. Here, we find that the H. polygyrus bakeri genome contains three HpARI family members and that these have different effects on IL-33-dependent responses in vitro and in vivo, with HpARI1+2 suppressing and HpARI3 amplifying these responses. All HpARIs have sub-nanomolar affinity for mouse IL-33; however, HpARI3 does not block IL-33-ST2 interactions. Instead, HpARI3 stabilizes IL-33, increasing the half-life of the cytokine and amplifying responses to it in vivo. Together, these data show that H. polygyrus bakeri secretes a family of HpARI proteins with both overlapping and distinct functions, comprising a complex immunomodulatory arsenal of host-targeted proteins.

The impact of FASTQ and alignment read order on structural variant calling from long-read sequencing data.

Background: Structural variant (SV) calling from DNA sequencing data has been challenging due to several factors, including the ambiguity of short-read alignments, multiple complex SVs in the same genomic region, and the lack of "truth" datasets for benchmarking. Additionally, caller choice, parameter settings, and alignment method are known to affect SV calling. However, the impact of FASTQ read order on SV calling has not been explored for long-read data. Results: Here, we used PacBio DNA sequencing data from 15 Caenorhabditis elegans strains and four Arabidopsis thaliana ecotypes to evaluate the sensitivity of different SV callers on FASTQ read order. Comparisons of variant call format files generated from the original and permutated FASTQ files demonstrated that the order of input data affected the SVs predicted by each caller. In particular, pbsv was highly sensitive to the order of the input data, especially at the highest depths where over 70% of the SV calls generated from pairs of differently ordered FASTQ files were in disagreement. These demonstrate that read order sensitivity is a complex, multifactorial process, as the differences observed both within and between species varied considerably according to the specific combination of aligner, SV caller, and sequencing depth. In addition to the SV callers being sensitive to the input data order, the SAMtools alignment sorting algorithm was identified as a source of variability following read order randomization. Conclusion: The results of this study highlight the sensitivity of SV calling on the order of reads encoded in FASTQ files, which has not been recognized in long-read approaches. These findings have implications for the replication of SV studies and the development of consistent SV calling protocols. Our study suggests that researchers should pay attention to the input order sensitivity of read alignment sorting methods when analyzing long-read sequencing data for SV calling, as mitigating a source of variability could facilitate future replication work. These results also raise important questions surrounding the relationship between SV caller read order sensitivity and tool performance. Therefore, tool developers should also consider input order sensitivity as a potential source of variability during the development and benchmarking of new and improved methods for SV calling.

Corrigendum: Trickle infection with Heligmosomoides polygyrus results in decreased worm burdens but increased intestinal inflammation and scarring.

[This corrects the article DOI: 10.3389/fimmu.2022.1020056.].