A metastasis map of human cancer cell lines.

Most deaths from cancer are explained by metastasis, and yet large-scale metastasis research has been impractical owing to the complexity of in vivo models. Here we introduce an in vivo barcoding strategy that is capable of determining the metastatic potential of human cancer cell lines in mouse xenografts at scale. We validated the robustness, scalability and reproducibility of the method and applied it to 500 cell lines1,2 spanning 21 types of solid tumour. We created a first-generation metastasis map (MetMap) that reveals organ-specific patterns of metastasis, enabling these patterns to be associated with clinical and genomic features. We demonstrate the utility of MetMap by investigating the molecular basis of breast cancers capable of metastasizing to the brain-a principal cause of death in patients with this type of cancer. Breast cancers capable of metastasizing to the brain showed evidence of altered lipid metabolism. Perturbation of lipid metabolism in these cells curbed brain metastasis development, suggesting a therapeutic strategy to combat the disease and demonstrating the utility of MetMap as a resource to support metastasis research.

Systematic identification of biomarker-driven drug combinations to overcome resistance.

The ability to understand and predict variable responses to therapeutic agents may improve outcomes in patients with cancer. We hypothesized that the basal gene-transcription state of cancer cell lines, coupled with cell viability profiles of small molecules, might be leveraged to nominate specific mechanisms of intrinsic resistance and to predict drug combinations that overcome resistance. We analyzed 564,424 sensitivity profiles to identify candidate gene-compound pairs, and validated nine such relationships. We determined the mechanism of a novel relationship, in which expression of the serine hydrolase enzymes monoacylglycerol lipase (MGLL) or carboxylesterase 1 (CES1) confers resistance to the histone lysine demethylase inhibitor GSK-J4 by direct enzymatic modification. Insensitive cell lines could be sensitized to GSK-J4 by inhibition or gene knockout. These analytical and mechanistic studies highlight the potential of integrating gene-expression features with small-molecule response to identify patient populations that are likely to benefit from treatment, to nominate rational candidates for combinations and to provide insights into mechanisms of action.

A Middle Pleistocene abrading tool from Tabun Cave, Israel: A search for the roots of abrading technology in human evolution.

During the reanalysis of the finds from Jelinek's and Ronen's excavations at Tabun Cave, Israel, we encountered a cobble bearing traces of mechanical alterations similar to those recorded on grinding tools. However, the artifact derives from the early layers of the Acheulo-Yabrudian complex of the late Lower Paleolithic (ca. 350 ka), a time with no evidence for grinding or abrasion. Accordingly, we sought to determine whether the traces on the artifact can be attributed to purposeful human action. We conducted a detailed use-wear analysis of the cobble and implemented an experimental program, gaining positive results for the hypothesis of purposeful human practice. We argue that the significance and novelty of early abrading technology is that it marks a new mode of raw material manipulation-one that is categorically different from other modes of tool use observed among earlier hominins or other primates and animals. Throughout the Early Pleistocene, use of stone tools was associated with vertical motions (battering, pounding, striking) or with the application of a thin or narrow working edge, leveled at cutting or scraping. Conversely, abrading consists in applying a wide working surface in a continuous sequence of horizontal motions, geared to modify or reduce the surfaces of a targeted material. The emergence of this technology joins additional behavioral changes recently identified and attributed to the Middle Pleistocene, illustrating the growing and diversifying capabilities of early hominins to harness technology to shape their environment.

Earliest floral grave lining from 13,700-11,700-y-old Natufian burials at Raqefet Cave, Mt. Carmel, Israel.

Flowering plants possess mechanisms that stimulate positive emotional and social responses in humans. It is difficult to establish when people started to use flowers in public and ceremonial events because of the scarcity of relevant evidence in the archaeological record. We report on uniquely preserved 13,700-11,700-y-old grave linings made of flowers, suggesting that such use began much earlier than previously thought. The only potentially older instance is the questionable use of flowers in the Shanidar IV Neanderthal grave. The earliest cemeteries (ca. 15,000-11,500 y ago) in the Levant are known from Natufian sites in northern Israel, where dozens of burials reflect a wide range of inhumation practices. The newly discovered flower linings were found in four Natufian graves at the burial site of Raqefet Cave, Mt. Carmel, Israel. Large identified plant impressions in the graves include stems of sage and other Lamiaceae (Labiatae; mint family) or Scrophulariaceae (figwort family) species; accompanied by a plethora of phytoliths, they provide the earliest direct evidence now known for such preparation and decoration of graves. Some of the plant species attest to spring burials with a strong emphasis on colorful and aromatic flowers. Cave floor chiseling to accommodate the desired grave location and depth is also evident at the site. Thus, grave preparation was a sophisticated planned process, embedded with social and spiritual meanings reflecting a complex preagricultural society undergoing profound changes at the end of the Pleistocene.

The earliest cotton fibers and Pan-regional contacts in the Near East.

Fiber technology (cordage and textile) has played a central role in all human societies for thousands of years, and its production, application and exchange have deep roots in prehistory. However, fiber remains have only rarely been observed in prehistoric sites because they tend to decay quickly in normal environmental conditions. To overcome preservation problems of macroscopic remains, we employed microbotanical analysis on soils from anthropogenic sediments in activity areas at Tel Tsaf in the Jordan Valley, Israel (ca. 5,200-4,700 cal BC), and recovered fiber microremains. This includes at least two types of bast fibers and the earliest evidence of cotton in the Near East, some of which were dyed in various colors. Some of these fibers likely represent the remnants of ancient clothing, fabric containers, cordage, or other belongings. The cotton remains, probably derived from wild species originating in South Asia, predate the oldest known cotton domestication in the Indus Valley by about two millennia. Tel Tsaf played a pivotal role in trans-regional trade and exchange networks in the southern Levant, and the presence of cotton at the site points to possible connections with the Indus Valley as early as 7,200 years ago.

Long-distance trade in the Middle Chalcolithic of the southern Levant: The case of the olivine beads from Tel Tsaf, Jordan Valley, Israel.

Eight olivine beads found at the Middle Chalcolithic site of Tel Tsaf (ca. 5,200-4,700 cal. BC), Jordan Valley, Israel, underscore a new facet of interregional exchange for this period. The current paper presents the olivine beads assemblage, its morphometric and technological characteristics, and chemical composition. The results of the chemical analysis suggest that all eight beads derive from the same source. By means of comparison with the chemical characteristics of known olivine sources, we argue for a northeastern African-western Arabian provenience and cautiously suggest Ethiopia as a probable origin. Finally, we discuss the significance of the assemblage, its possible origin, and the mechanisms that may have brought the beads to the site.

Massively parallel pooled screening reveals genomic determinants of nanoparticle delivery.

To accelerate the translation of cancer nanomedicine, we used an integrated genomic approach to improve our understanding of the cellular processes that govern nanoparticle trafficking. We developed a massively parallel screen that leverages barcoded, pooled cancer cell lines annotated with multiomic data to investigate cell association patterns across a nanoparticle library spanning a range of formulations with clinical potential. We identified both materials properties and cell-intrinsic features that mediate nanoparticle-cell association. Using machine learning algorithms, we constructed genomic nanoparticle trafficking networks and identified nanoparticle-specific biomarkers. We validated one such biomarker: gene expression of SLC46A3, which inversely predicts lipid-based nanoparticle uptake in vitro and in vivo. Our work establishes the power of integrated screens for nanoparticle delivery and enables the identification and utilization of biomarkers to rationally design nanoformulations.

The function of the south-Levantine Late Chalcolithic and Early Bronze Age basalt vessels bearing circumferential depressions: Insights from use-wear analyses.

One of the most characteristic aspects of the Late Chalcolithic and Early Bronze Age periods in the southern Levant is the appearance of large assemblages of basalt vessels. These vessels, frequently meticulously made, appear sometimes a considerable distance from the raw material sources and are found mainly at habitation sites. While these and their prestigious value have been widely discussed in the past, their function is still obscure. In the current paper, we address their functionality through microscopic use-wear analysis. Emphasis was placed on basalt vessels with a distinct wear pattern-circumferential depressions, which appear along the perimeter of their interior bases. The documented traces were compared to results of an experimental study we conducted to characterize the effects of abrasion, grinding, and lubrication on basalt surfaces. The results of the comparative experimental study suggest that the circumferential depression was formed from a repetitive rotational activity using a narrow-ended tool. Further, it seems that two material types acted in combination as the circling device and processed material. One was hard and abrasive, such as stone, and the other was semi-resilient, such as wood or mineral powder. Water was likely used as a lubricant in the rotational process. While the actual function of the bowls bearing the circumferential depressions is not entirely clear, the use-wear analyses suggest that they may have been devices involved in craft industries, used for processing materials unrelated to food (minerals in particular). Whatever the exact function was, it clear that this use continued from the Chalcolithic through the Early Bronze Age, providing evidence for functional continuity between these two periods.

Exploring exchange and direct procurement strategies for Natufian food processing tools of el-Wad Terrace, Israel.

We present the results of a detailed geochemical provenance study of 54 Natufian (ca. 15,000-11,700 cal. BP) basalt pestles from the site of el-Wad Terrace (EWT), Israel. It is the first time precise locations from where basalt raw materials were derived are provided. The results indicate that the Natufian hunter-gatherers used multiple sources of basaltic rocks, distributed over a large area surrounding the Sea of Galilee. This area is located at a considerable distance from EWT, ca. 60-120 km away, in a region where contemporaneous Natufian basecamps are few. We consider two possible models that suggest vehicles for the transportation of these artifacts to EWT, namely the exchange obtaining model (EOM) and the direct procurement model (DPM). We argue that these mechanisms are not mutually exclusive and may have operated together. We also suggest that at a time of increasing Natufian territoriality, a large area around the Sea of Galilee remained unclaimed. The paper concludes with a brief discussion of the implications for the two models. In particular, we note that the DPM implies that technological know-how for pestle production was maintained within the EWT community.

Bee products in the prehistoric southern levant: evidence from the lipid organic record.

Beehive products have a rich global history. In the wider Levantine region, bees had a significant role in Egypt and Mesopotamia, and intensive beekeeping was noted in Israel during the Biblical period when apiaries were first identified. This study investigates the origins of this extensive beekeeping through organic residue analysis of pottery from prehistoric sites in the southern Levant. The results suggest that beehive products from likely wild bees were used during the Chalcolithic period as a vessel surface treatment and/or as part of the diet. These functions are reinforced by comparison to the wider archaeological record. While the true frequency of beeswax use may be debated, alternatives to beehive products were seemingly preferred as wild resources contrasted with the socio-economic system centred on domesticated resources, controlled production and standardization. Bee products only became an important part of the economic canon in the southern Levant several millennia later.

7,200 years old constructions and mudbrick technology: The evidence from Tel Tsaf, Jordan Valley, Israel.

The history of mudbrick production and construction in the southern Levant may be dated as far back to the Pre-Pottery Neolithic A. However, at many of the sites where mudbrick remains were noted, their preservation was poor, so investigation of their production and the related construction techniques in antiquity was precluded. The 7,200 year old (cal BP) site of Tel Tsaf, located in the Jordan Valley, is distinguished by outstanding preservation of mudbrick architecture, which enables us to delve into various issues related to mudbrick technology, construction and preservation. The present paper discusses some of the mudbrick features at Tel Tsaf and their characteristics and offers a comprehensive analytical study of the mudbricks from multiple contexts and phases. These demonstrate consistency in three of the four measured variables: magnetic susceptibility, organic content and calcium carbonate equivalent. The results of our study suggest that while we can identify morphometric variability between bricks and walls, by and large, a uniform composition characterized the tested assemblages without any temporal or spatial variability. This indicates that a single locally-sourced raw material was used and that recycling of old decayed mudbricks was likely practiced. The consistency of mudbrick-production during all phases of the occupation at Tel Tsaf and the absence of multiple recipes implies that a shared production and technological know-how was maintained for at least 500 years at the site.

SUMO targeting of a stress-tolerant Ulp1 SUMO protease.

SUMO proteases of the SENP/Ulp family are master regulators of both sumoylation and desumoylation and regulate SUMO homeostasis in eukaryotic cells. SUMO conjugates rapidly increase in response to cellular stress, including nutrient starvation, hypoxia, osmotic stress, DNA damage, heat shock, and other proteotoxic stressors. Nevertheless, little is known about the regulation and targeting of SUMO proteases during stress. To this end we have undertaken a detailed comparison of the SUMO-binding activity of the budding yeast protein Ulp1 (ScUlp1) and its ortholog in the thermotolerant yeast Kluyveromyces marxianus, KmUlp1. We find that the catalytic UD domains of both ScUlp1 and KmUlp1 show a high degree of sequence conservation, complement a ulp1Δ mutant in vivo, and process a SUMO precursor in vitro. Next, to compare the SUMO-trapping features of both SUMO proteases we produced catalytically inactive recombinant fragments of the UD domains of ScUlp1 and KmUlp1, termed ScUTAG and KmUTAG respectively. Both ScUTAG and KmUTAG were able to efficiently bind a variety of purified SUMO isoforms and bound immobilized SUMO1 with nanomolar affinity. However, KmUTAG showed a greatly enhanced ability to bind SUMO and SUMO-modified proteins in the presence of oxidative, temperature and other stressors that induce protein misfolding. We also investigated whether a SUMO-interacting motif (SIM) in the UD domain of KmULP1 that is not conserved in ScUlp1 may contribute to the SUMO-binding properties of KmUTAG. In summary, our data reveal important details about how SUMO proteases target and bind their sumoylated substrates, especially under stress conditions. We also show that the robust pan-SUMO binding features of KmUTAG can be exploited to detect and study SUMO-modified proteins in cell culture systems.

The beginning of metallurgy in the southern Levant: a late 6th millennium CalBC copper awl from Tel Tsaf, Israel.

The beginning of metallurgy in the ancient Near East attracts much attention. The southern Levant, with the rich assemblage of copper artifacts from the Nahal Mishmar cave and the unique gold rings of the Nahal Qanah cave, is regarded as a main center of early metallurgy during the second half of the 5th millennium CalBC. However, a recently discovered copper awl from a Middle Chalcolithic burial at Tel Tsaf, Jordan Valley, Israel, suggests that cast metal technology was introduced to the region as early as the late 6th millennium CalBC. This paper examines the chemical composition of this item and reviews its context. The results indicate that it was exported from a distant source, probably in the Caucasus, and that the location where it was found is indicative of the social status of the buried individual. This rare finding indicates that metallurgy was first diffused [corrected] to the southern Levant through exchange networks and only centuries later involved local productionThis copper awl, the earliest metal artifact found in the southern Levant, indicates that the elaborate Late Chalcolithic metallurgy developed from a more ancient tradition.