Allochthonous resources are less important for faunal communities on highly productive, small tropical islands

Ecosystems are interconnected by energy fluxes that provide resources for the inhabiting organisms along the transition zone. Especially where in situ resources are scarce, ecosystems can become highly dependent on external resources. The dependency on external input becomes less pronounced in systems with elevated in situ production, where only consumer species close to the site of external input remain subsidized, whereas species distant to the input site rely on the in situ production of the ecosystem. It is largely unclear though if this pattern is consistent over different consumer species and trophic levels in one ecosystem, and whether consumer species that occur both proximate to and at a distance from the input site differ in their dependency on external resource inputs between sites. Using stable isotope analysis, we investigated the dependency on external marine input for common ground-associated consumer taxa on small tropical islands with high in situ production. We show that marine input is only relevant for strict beach-dwelling taxa, while the terrestrial vegetation is the main carbon source for inland-dwelling taxa. Consumer species that occurred both close (beach) and distant (inland) to the site of marine input showed similar proportions of marine input in their diets. This supports earlier findings that the relevance of external resources becomes limited to species close to the input site in systems with sufficient in situ production. However, it also indicates that the relevance of external input is also species-dependent, as consumers occurring close and distant to the input site depended equally strong or weak on marine input.

Multi-omics discovery of exome-derived neoantigens in hepatocellular carcinoma

BACKGROUND

Although mutated HLA ligands are considered ideal cancer-specific immunotherapy targets, evidence for their presentation is lacking in hepatocellular carcinomas (HCCs). Employing a unique multi-omics approach comprising a neoepitope identification pipeline, we assessed exome-derived mutations naturally presented as HLA class I ligands in HCCs.

METHODS

In-depth multi-omics analyses included whole exome and transcriptome sequencing to define individual patient-specific search spaces of neoepitope candidates. Evidence for the natural presentation of mutated HLA ligands was investigated through an in silico pipeline integrating proteome and HLA ligandome profiling data.

RESULTS

The approach was successfully validated in a state-of-the-art dataset from malignant melanoma, and despite multi-omics evidence for somatic mutations, mutated naturally presented HLA ligands remained elusive in HCCs. An analysis of extensive cancer datasets confirmed fundamental differences of tumor mutational burden in HCC and malignant melanoma, challenging the notion that exome-derived mutations contribute relevantly to the expectable neoepitope pool in malignancies with only few mutations.

CONCLUSIONS

This study suggests that exome-derived mutated HLA ligands appear to be rarely presented in HCCs, inter alia resulting from a low mutational burden as compared to other malignancies such as malignant melanoma. Our results therefore demand widening the target scope for personalized immunotherapy beyond this limited range of mutated neoepitopes, particularly for malignancies with similar or lower mutational burden.

Multi-omics discovery of exome-derived neoantigens in hepatocellular carcinoma

BACKGROUND

Although mutated HLA ligands are considered ideal cancer-specific immunotherapy targets, evidence for their presentation is lacking in hepatocellular carcinomas (HCCs). Employing a unique multi-omics approach comprising a neoepitope identification pipeline, we assessed exome-derived mutations naturally presented as HLA class I ligands in HCCs.

METHODS

In-depth multi-omics analyses included whole exome and transcriptome sequencing to define individual patient-specific search spaces of neoepitope candidates. Evidence for the natural presentation of mutated HLA ligands was investigated through an in silico pipeline integrating proteome and HLA ligandome profiling data.

RESULTS

The approach was successfully validated in a state-of-the-art dataset from malignant melanoma, and despite multi-omics evidence for somatic mutations, mutated naturally presented HLA ligands remained elusive in HCCs. An analysis of extensive cancer datasets confirmed fundamental differences of tumor mutational burden in HCC and malignant melanoma, challenging the notion that exome-derived mutations contribute relevantly to the expectable neoepitope pool in malignancies with only few mutations.

CONCLUSIONS

This study suggests that exome-derived mutated HLA ligands appear to be rarely presented in HCCs, inter alia resulting from a low mutational burden as compared to other malignancies such as malignant melanoma. Our results therefore demand widening the target scope for personalized immunotherapy beyond this limited range of mutated neoepitopes, particularly for malignancies with similar or lower mutational burden.