Sequential trypsin and ProAlanase digestions unearth immunological protein biomarkers shrouded by skeletal collagen

Deep palaeoproteomic profiling of archaeological human brains

Palaeoproteomics leverages the persistence, diversity, and biological import of ancient proteins to explore the past, and answer fundamental questions about phylogeny, environment, diet, and disease. These insights are largely gleaned from hard tissues like bone and teeth, as well-established protocols exist for extracting ancient proteins from mineralised tissues. No such method, however, exists for the soft tissues, which are underexplored in palaeoproteomics given permission for destructive analysis routinely depends on a proven methodology. Considering less than one-tenth of all human proteins are expressed in bone, compared to three-quarters in the internal organs, the amount of biological information presently inaccessible is substantial. We address this omission with an optimised LC-FAIMS-MS/MS workflow yielding the largest, most diverse palaeoproteome yet described. Using archaeological human brains, we test ten protocols with varied chemistries and find that urea lysis effectively disrupts preserved membrane regions to expose low-abundant, intracellular analytes. Further, we show that ion mobility spectrometry improves unique protein identification by as much as 40%, and represents a means of "cleaning" dirty archaeological samples. Our methodology will be useful for improving protein recovery from a range of ancient tissues and depositional environments.

A male Denisovan mandible from Pleistocene Taiwan

Denisovans are an extinct hominin group defined by ancient genomes of Middle to Late Pleistocene fossils from southern Siberia. Although genomic evidence suggests their widespread distribution throughout eastern Asia and possibly Oceania, so far only a few fossils from the Altai and Tibet are confidently identified molecularly as Denisovan. We identified a hominin mandible (Penghu 1) from Taiwan (10,000 to 70,000 years ago or 130,000 to 190,000 years ago) as belonging to a male Denisovan by applying ancient protein analysis. We retrieved 4241 amino acid residues and identified two Denisovan-specific variants. The increased fossil sample of Denisovans demonstrates their wider distribution, including warm and humid regions, as well as their shared distinct robust dentognathic traits that markedly contrast with their sister group, Neanderthals.

Clothomics: a practical guide to understand the opportunities and challenges of omics-based methods in archaeological cloth research

Since the first studies in the early 2000s, an increasing number of articles have used biomolecular tools for studying archaeological and historical cloth materials, produced by animal and plant fibres, leather and furs. Genomic and proteomic studies have particularly contributed to prior visual and microscopic methods to broaden complex themes such as society, identity, technology, economy and trade. We have termed this new interdisciplinary field "clothomics", as it applies diverse omics methodologies, such as genomics and proteomics, to expand the horizons of cloth research. This paper aims at providing users with a set of practical step-by-step guides for the most widely applied omics analyses of cloth, proteomics and genomics, in animal-based materials. The paper reviews current applications, provides recommendations for selecting the right analytical strategy, focusing on practical considerations like how to sample, how to choose between proteomic and genomic methodological approaches, and where we see the current limitations. We are optimistic with the field of clothomics as we see it receives more attention scientifically and from the funding bodies. Although it faces several technical challenges, we also experience attempts to overcome these by recovering and detecting more biomolecules and becoming a more inclusive field through data sharing and participatory science. With a close collaboration between scholars of different disciplines, clothomics will provide a better understanding of human-animal interactions and the use of animal products beyond subsistence.

Tracing Leprosy: The paleopathological study of the individuals excavated from the Sant Llàtzer leprosarium in Barcelona, Spain (12th-18th c.)

OBJECTIVE

Our objectives are twofold: to analyse the frequency of leprosy-related pathological lesions in the cemetery of Sant Llàtzer Hospital (12th-18th c.); and to examine how individuals affected by the disease were perceived and integrated into society during that period in Barcelona.

MATERIALS

The skeletal remains of 87 individuals recovered from the cemetery.

METHODS

All remains were analysed macroscopically and, when required, radiographed.

RESULTS

Of the total number of individuals (n=87), 21 (24.1 %) showed evidence indicative of leprosy. Notably, the frequency of leprosy cases was lower in the 13th-15th c. (10 %; n = 50), the only period for which multi-person graves were documented.

CONCLUSIONS

The frequency of leprosy-related lesions in Sant Llàtzer is similar to that observed in other European Christian leprosaria, although it varies across the centuries. There is no funerary evidence that leprosy sufferers were treated differently than other citizens.

SIGNIFICANCE

The cemetery of Sant Llàtzer, the first in Spain directly linked to a leprosarium, uniquely spans a significant period of activity. Its exceptionally preserved remains and rich records have offered unparalleled insight into the disease and its profound social implications.

LIMITATIONS

Leprosy affects the bone in only a small percentage of untreated cases. Moreover, poor preservation of skeletal remains may prevent diagnosis.

SUGGESTIONS FOR FURTHER RESEARCH

Biochemistry, genomics, and proteomics might provide new insights into the disease, the origin and migrations of the individuals buried in Sant Llàtzer, as well as other aspects of their daily lives.