Paleoproteomic study of the Iceman's brain tissue

Curated cauldrons: Preserved proteins from early copper-alloy vessels illuminate feasting practices in the Caucasian steppe

Large metal and metal-alloy cauldrons first appear on the far western steppe and Caucasus region during the Maykop period (3700-2900 BCE); however, the types of foods or beverages cooked in and served from these vessels have remained mysterious. Here, we present proteomic analysis of nine residues from copper-alloy cauldrons from Maykop burial contexts where we identify muscle, blood, and milk proteins specific to domesticated, and possibly wild, ruminants. This study clearly demonstrates that the earliest, large-volume feasting vessels contained both primary and secondary animal products, likely prepared in the form of a stew.

Paleoproteomics

Paleoproteomics, the study of ancient proteins, is a rapidly growing field at the intersection of molecular biology, paleontology, archaeology, paleoecology, and history. Paleoproteomics research leverages the longevity and diversity of proteins to explore fundamental questions about the past. While its origins predate the characterization of DNA, it was only with the advent of soft ionization mass spectrometry that the study of ancient proteins became truly feasible. Technological gains over the past 20 years have allowed increasing opportunities to better understand preservation, degradation, and recovery of the rich bioarchive of ancient proteins found in the archaeological and paleontological records. Growing from a handful of studies in the 1990s on individual highly abundant ancient proteins, paleoproteomics today is an expanding field with diverse applications ranging from the taxonomic identification of highly fragmented bones and shells and the phylogenetic resolution of extinct species to the exploration of past cuisines from dental calculus and pottery food crusts and the characterization of past diseases. More broadly, these studies have opened new doors in understanding past human-animal interactions, the reconstruction of past environments and environmental changes, the expansion of the hominin fossil record through large scale screening of nondiagnostic bone fragments, and the phylogenetic resolution of the vertebrate fossil record. Even with these advances, much of the ancient proteomic record still remains unexplored. Here we provide an overview of the history of the field, a summary of the major methods and applications currently in use, and a critical evaluation of current challenges. We conclude by looking to the future, for which innovative solutions and emerging technology will play an important role in enabling us to access the still unexplored "dark" proteome, allowing for a fuller understanding of the role ancient proteins can play in the interpretation of the past.

[The Iceman : Life scenarios and pathological findings from 30 years of research on the glacier mummy "Ötzi"]

The comprehensive investigation of the excellently preserved mummy of Ötzi, the Iceman, and his equipment over the last 30 years has provided a wealth of information about the life and disease of this late Neolithic individual. This research has indicated that his origin was from a local southern Alpine population, that he grew up in the valleys of the Southern Alps, and that he had considerable local mobility. He had well-balanced nutrition with a mixed vegetable and animal diet. He was very mobile in the alpine terrain and of athletic constitution. The Iceman suffered from mild to moderate degenerative joint disease primarily of the right hip joint, slight spondylosis of the cervical and lumbar spine, a minor focal (premature) arteriosclerosis, lung anthracosis and possibly silicosis, previous pleuritic inflammation (possibly of post-specific origin), intestinal infections of the stomach by Helicobacter pylori and Trichuris trichiura worm infestation in the intestines, a mild osteomalacia of cancellous bone, and diverse pathologies of his teeth with dental caries and periodontitis, as well as hair anomalies. The presence of borreliosis is still under debate. As potential remedies, the Iceman carried some anthelmintic substances with him: a birch polypore and an anthelmintic fern. The numerous tattoos may also have had therapeutic effects. Finally, the last days of Ötzi could be reconstructed quite precisely: his gastrointestinal content indicates that the Iceman moved from Alpine heights to a lower location and then again up to the glacier region where he died. During this journey he encountered two attacks: the first, several days before his death, lead to a stabbing wound in his right hand; the second was an arrow hit that wounded the Iceman lethally at his left axilla by laceration of the subclavian artery.

Ancient protein analysis in archaeology

The analysis of ancient proteins from paleontological, archeological, and historic materials is revealing insights into past subsistence practices, patterns of health and disease, evolution and phylogeny, and past environments. This review tracks the development of this field, discusses some of the major methodological strategies used, and synthesizes recent developments in archeological applications of ancient protein analysis. Moreover, this review highlights some of the challenges faced by the field and potential future directions, arguing that the development of minimally invasive or nondestructive techniques, strategies for protein authentication, and the integration of ancient protein analysis with other biomolecular techniques are important research strategies as this field grows.

Protein sequence comparison of human and non-human primate tooth proteomes

In the context of human evolution, the study of proteins may overcome the limitation of the high degradation of ancient DNA over time to provide biomolecular information useful for the phylogenetic reconstruction of hominid taxa. In this study, we used a shotgun proteomics approach to compare the tooth proteomes of extant human and non-human primates (gorilla, chimpanzee, orangutan and baboon) in order to search for a panel of peptides able to discriminate between taxa and further help reconstructing the evolutionary relationships of fossil primates. Among the 25 proteins shared by the five genera datasets, we found a combination of peptides with sequence variations allowing to differentiate the hominid taxa in the proteins AHSG, AMBN, APOA1, BGN, C9, COL11A2, COL22A1, COL3A1, DSPP, F2, LUM, OMD, PCOLCE and SERPINA1. The phylogenetic tree confirms the placement of the samples in the appropriate genus branches. Altogether, the results provide experimental evidence that a shotgun proteomics approach on dental tissue has the potential to detect taxonomic variation, which is promising for future investigations of uncharacterized and/or fossil hominid/hominin specimens. SIGNIFICANCE: A shotgun proteomics approach on human and non-human primate teeth allowed to identify peptides with taxonomic interest, highlighting the potential for future studies on hominid fossils.

Helicobacter pylori in ancient human remains

The bacterium Helicobacter pylori (H. pylori) infects the stomachs of approximately 50% of all humans. With its universal occurrence, high infectivity and virulence properties it is considered as one of the most severe global burdens of modern humankind. It has accompanied humans for many thousands of years, and due to its high genetic variability and vertical transmission, its population genetics reflects the history of human migrations. However, especially complex demographic events such as the colonisation of Europe cannot be resolved with population genetic analysis of modern H. pylori strains alone. This is best exemplified with the reconstruction of the 5300-year-old H. pylori genome of the Iceman, a European Copper Age mummy. Our analysis provided precious insights into the ancestry and evolution of the pathogen and underlined the high complexity of ancient European population history. In this review we will provide an overview on the molecular analysis of H. pylori in mummified human remains that were done so far and we will outline methodological advancements in the field of ancient DNA research that support the reconstruction and authentication of ancient H. pylori genome sequences.

The Current Situation of the Tyrolean Iceman

The Tyrolean Iceman, commonly known as Ötzi, is the world's oldest glacier mummy and one of the best investigated ancient human remains in the world. Since the discovery of the 5,300-year-old Copper Age individual in 1991, in a glacier in the Eastern Italian Alps, a variety of morphological, biochemical, and molecular analyses have been performed that revealed important insights into his origin, his life habits, and the circumstances surrounding his demise. In more recent research, the mummy was subjected to cutting-edge modern research methodologies currently focusing on high-throughput sequence analysis of ancient biomolecules (DNA, proteins, lipids) that are still preserved in the mummified tissues. This application of innovative "-omics" technologies revealed novel insights on the ancestry, disease predisposition, diet, and the presence of pathogens in the glacier mummy. In this review, the most important and actual results of the molecular studies will be highlighted.

Investigation of the archeological remains using ultrahigh resolution mass spectrometry

Investigation of the archeological material at the molecular level can reveal the composition of ancient paint, balsamic material, reveal cooking recipes, etc. High-resolution mass spectrometry is a powerful technique with underestimated potential for archeology. Here, we present the investigation of the 3000-year-old archeological remains, identified as parts of internal organs of an Egyptian mummy, using high-resolution Orbitrap mass spectrometry. We observed a diverse number of oxidized classes of compounds: O, O₂, O₃, O₄, O₅, N, NO, NO₂, NO₃, NO₄, NO₅, N₂O, N₂O₂. Such chemical composition is unusual and we never observed it in our previous studies of petroleum, humic substances, products of wood pyrolysis or other natural complex mixtures. It is possible that such compounds are formed via biodegradation of lipids and other organic material used for funeral rites. We did not observe evidence of the presence of mineral bitumen, although there are many historical records of the use of mineral bitumen for mummification.

Possible evidence for care and treatment in the Tyrolean Iceman

The Tyrolean Iceman is the world's oldest glacier mummy. He was found in September 1991 in the Italian part of the Ötztal Alps. Since his discovery a variety of morphological, radiological and molecular analyses have been performed that revealed detailed insights into his state of health. Despite the various pathological conditions found in the Iceman, little is known about possible forms of care and treatment during the Copper Age in Northern Italy. A possible approach to this topic is the presence of tattoos on the mummified body. In previous work, it was already believed that the tattoos were administered as a kind of treatment for his lower back pain and degenerative joint disease of his knees, hip and wrist. In other studies, the tattoos of the Iceman have been related to an early form of acupuncture. We carefully re-evaluated the various health issues of the Iceman, including joint diseases, gastrointestinal problems and arterial calcifications and compared them to the location and number of tattoos. Together with the finding of medically effective fungi and plants, such as the birch polypore or fern in his equipment and intestines, we suggest that care and treatment was already common during the Iceman's time.

Fossilised Biomolecules and Biomarkers in Carbonate Concretions from Konservat-Lagerstätten

In the vast majority of fossils, the organic matter is degraded with only an impression or cast of the organism remaining. In rare cases, ideal burial conditions result in a rapid fossilisation with an exceptional preservation of soft tissues and occasionally organic matter. Such deposits are known as Lagerstätten and have been found throughout the geological record. Exceptional preservation is often associated with finely crystalline quartz (e.g., cherts), fine sediments (e.g., muds) or volcanic ashes. Other mechanisms include burial in anoxic/euxinic sediments and in the absence of turbidity or scavenging. Exceptional preservation can also occur when an organism is encapsulated in carbonate cement, forming a concretion. This mechanism involves complex microbial processes, resulting in a supersaturation in carbonate, with microbial sulfate reduction and methane cycling the most commonly suggested processes. In addition, conditions of photic zone euxinia are often found to occur during concretion formation in marine environments. Concretions are ideal for the study of ancient and long-extinct organisms, through both imaging techniques and biomolecular approaches. These studies have provided valuable insights into the evolution of organisms and their environments through the Phanerozoic and have contributed to increasing interest in fields including chemotaxonomy, palaeobiology, palaeoecology and palaeophysiology.

The Iceman's Last Meal Consisted of Fat, Wild Meat, and Cereals

The history of humankind is marked by the constant adoption of new dietary habits affecting human physiology, metabolism, and even the development of nutrition-related disorders. Despite clear archaeological evidence for the shift from hunter-gatherer lifestyle to agriculture in Neolithic Europe [1], very little information exists on the daily dietary habits of our ancestors. By undertaking a complementary -omics approach combined with microscopy, we analyzed the stomach content of the Iceman, a 5,300-year-old European glacier mummy [2, 3]. He seems to have had a remarkably high proportion of fat in his diet, supplemented with fresh or dried wild meat, cereals, and traces of toxic bracken. Our multipronged approach provides unprecedented analytical depth, deciphering the nutritional habit, meal composition, and food-processing methods of this Copper Age individual.

A guide to ancient protein studies

Palaeoproteomics is an emerging neologism used to describe the application of mass spectrometry-based approaches to the study of ancient proteomes. As with palaeogenomics (the study of ancient DNA), it intersects evolutionary biology, archaeology and anthropology, with applications ranging from the phylogenetic reconstruction of extinct species to the investigation of past human diets and ancient diseases. However, there is no explicit consensus at present regarding standards for data reporting, data validation measures or the use of suitable contamination controls in ancient protein studies. Additionally, in contrast to the ancient DNA community, no consolidated guidelines have been proposed by which researchers, reviewers and editors can evaluate palaeoproteomics data, in part due to the novelty of the field. Here we present a series of precautions and standards for ancient protein research that can be implemented at each stage of analysis, from sample selection to data interpretation. These guidelines are not intended to impose a narrow or rigid list of authentication criteria, but rather to support good practices in the field and to ensure the generation of robust, reproducible results. As the field grows and methodologies change, so too will best practices. It is therefore essential that researchers continue to provide necessary details on how data were generated and authenticated so that the results can be independently and effectively evaluated. We hope that these proposed standards of practice will help to provide a firm foundation for the establishment of palaeoproteomics as a viable and powerful tool for archaeologists, anthropologists and evolutionary biologists.

Integrated quantitative proteomic and transcriptomic analysis of lung tumor and control tissue: a lung cancer showcase

Proteomics analysis of paired cancer and control tissue can be applied to investigate pathological processes in tumors. Advancements in data-independent acquisition mass spectrometry allow for highly reproducible quantitative analysis of complex proteomic patterns. Optimized sample preparation workflows enable integrative multi-omics studies from the same tissue specimens.We performed ion mobility enhanced, data-independent acquisition MS to characterize the proteome of 21 lung tumor tissues including adenocarcinoma and squamous cell carcinoma (SCC) as compared to control lung tissues of the same patient each. Transcriptomic data were generated for the same specimens. The quantitative proteomic patterns and mRNA abundances were subsequently analyzed using systems biology approaches.We report a significantly (p = 0.0001) larger repertoire of proteins in cancer tissues. 12 proteins were higher in all tumor tissues as compared to matching control tissues. Three proteins, CAV1, CAV2, and RAGE, were vice versa higher in all controls. We also identified characteristic SCC and adenocarcinoma protein patterns. Principal Component Analysis provided evidence that not only cancer from control tissue but also tissue from adenocarcinoma and SCC can be differentiated. Transcriptomic levels of key proteins measured from the same matched tissue samples correlated with the observed protein patterns.The applied study set-up with paired lung tissue specimens of which different omics are measured, is generally suited for an integrated multi-omics analysis.

Paleoproteomics of the Dental Pulp: The plague paradigm

Chemical decomposition and fragmentation may limit the detection of ancient host and microbial DNA while some proteins can be detected for extended periods of time. We applied paleoproteomics on 300-year-old dental pulp specimens recovered from 16 individuals in two archeological funeral sites in France, comprising one documented plague site and one documented plague-negative site. The dental pulp paleoproteome of the 16 teeth comprised 439 peptides representative of 30 proteins of human origin and 211 peptides representative of 27 proteins of non-human origin. Human proteins consisted of conjunctive tissue and blood proteins including IgA immunoglobulins. Four peptides were indicative of three presumable Yersinia pestis proteins detected in 3/8 dental pulp specimens from the plague-positive site but not in the eight dental pulp specimens collected in the plague-negative site. Paleoproteomics applied to the dental pulp is a new and innovative approach to screen ancient individuals for the detection of blood-borne pathogens and host inflammatory response.

Identification of proteins from 4200-year-old skin and muscle tissue biopsies from ancient Egyptian mummies of the first intermediate period shows evidence of acute inflammation and severe immune response

We performed proteomics analysis on four skin and one muscle tissue samples taken from three ancient Egyptian mummies of the first intermediate period, approximately 4200 years old. The mummies were first dated by radiocarbon dating of the accompany-\break ing textiles, and morphologically examined by scanning electron microscopy of additional skin samples. Proteins were extracted, separated on SDS-PAGE (sodium dodecyl sulfate polyacrylamide gel electrophoresis) gels, and in-gel digested with trypsin. The resulting peptides were analysed using nanoflow high-performance liquid chromatography-mass spectrometry. We identified a total of 230 unique proteins from the five samples, which consisted of 132 unique protein identifications. We found a large number of collagens, which was confirmed by our microscopy data, and is in agreement with previous studies showing that collagens are very long-lived. As expected, we also found a large number of keratins. We identified numerous proteins that provide evidence of activation of the innate immunity system in two of the mummies, one of which also contained proteins indicating severe tissue inflammation, possibly indicative of an infection that we can speculate may have been related to the cause of death.This article is part of the themed issue 'Quantitative mass spectrometry'.

The mummified brain of a pleistocene woolly mammoth (Mammuthus primigenius) compared with the brain of the extant African elephant (Loxodonta africana)

This study presents the results of an examination of the mummified brain of a pleistocene woolly mammoth (Mammuthus primigenius) recovered from the Yakutian permafrost in Siberia, Russia. This unique specimen (from 39,440-38,850 years BP) provides the rare opportunity to compare the brain morphology of this extinct species with a related extant species, the African elephant (Loxodonta africana). An anatomical description of the preserved brain of the woolly mammoth is provided, along with a series of quantitative analyses of various brain structures. These descriptions are based on visual inspection of the actual specimen as well as qualitative and quantitative comparison of computed tomography imaging data obtained for the woolly mammoth in comparison with magnetic resonance imaging data from three African elephant brains. In general, the brain of the woolly mammoth specimen examined, estimated to weigh between 4,230 and 4,340 g, showed the typical shape, size, and gross structures observed in extant elephants. Quantitative comparative analyses of various features of the brain, such as the amygdala, corpus callosum, cerebellum, and gyrnecephalic index, all indicate that the brain of the woolly mammoth specimen examined has many similarities with that of modern African elephants. The analysis provided here indicates that a specific brain type representative of the Elephantidae is likely to be a feature of this mammalian family. In addition, the extensive similarities between the woolly mammoth brain and the African elephant brain indicate that the specializations observed in the extant elephant brain are likely to have been present in the woolly mammoth.

Glycosylated proteins preserved over millennia: N-glycan analysis of Tyrolean Iceman, Scythian Princess and Warrior

An improved understanding of glycosylation will provide new insights into many biological processes. In the analysis of oligosaccharides from biological samples, a strict regime is typically followed to ensure sample integrity. However, the fate of glycans that have been exposed to environmental conditions over millennia has not yet been investigated. This is also true for understanding the evolution of the glycosylation machinery in humans as well as in any other biological systems. In this study, we examined the glycosylation of tissue samples derived from four mummies which have been naturally preserved: – the 5,300 year old “Iceman called Oetzi”, found in the Tyrolean Alps; the 2,400 year old “Scythian warrior” and “Scythian Princess”, found in the Altai Mountains; and a 4 year old apartment mummy, found in Vienna/Austria. The number of N-glycans that were identified varied both with the age and the preservation status of the mummies. More glycan structures were discovered in the contemporary sample, as expected, however it is significant that glycan still exists in the ancient tissue samples. This discovery clearly shows that glycans persist for thousands of years, and these samples provide a vital insight into ancient glycosylation, offering us a window into the distant past.