Single-cell deconvolution of head and neck squamous cell carcinoma

Complexities in cell-type composition have rightfully led to skepticism and caution in the interpretation of bulk transcriptomic analyses. Recent studies have shown that deconvolution algorithms can be utilized to computationally estimate cell-type proportions from the gene expression data of bulk blood samples, but their performance when applied to tumor tissues, including those from head and neck, remains poorly characterized. Here, we use single-cell data (~6000 single cells) collected from 21 head and neck squamous cell carcinoma (HNSCC) samples to generate cell-type-specific gene expression signatures. We leverage bulk RNA-seq data from \u3e500 HNSCC samples profiled by The Cancer Genome Atlas (TCGA), and using single-cell data as a reference, apply two newly developed deconvolution algorithms (CIBERSORTx and MuSiC) to the bulk transcriptome data to quantitatively estimate cell-type proportions for each tumor in TCGA. We show that these two algorithms produce similar estimates of constituent/major cell-type proportions and that a high T-cell fraction correlates with improved survival. By further characterizing T-cell subpopulations, we identify that regulatory T-cells (

Thermal structure of the crust during granulite metamorphism: petrological speculations and geodynamic implications

It is shown on a basis of generalization of lateral and vertical distribution of P-T parameters in granulite-gneiss belts of various ages that the thermal gradient within the lower crust during granulite metamorphism is rather low, ca. 5-10℃/km. Two extreme types of granulitic crustal sections are recognized. First type (GM1) corresponds to normal and especially to thinned (25-40km) crust. High and ultra-high temperatures (up to 1050℃) are characteristic for the deepest granulites of this type. Second type (GM2) corresponds to thickened (50-55km) crust. It is characterized by moderately high temperatures in the lower crust (from 700-800℃ at crust-mantle boundary). GM1 is generally connected with settings related to the hot mantle upwelling to crust-mantle boundary accompanied by heat and penetrating fluid fluxes and crustal extension or crustal thinning. Maximal heating is characteristic for the most thinned crust, i.e., for riftogenic environment including extension zones in back areas of active continental margins and in the crust of epi-continental sedimentary basins. Metamorphism of GM2 type is related to compression conditions and collision crustal stacking

Mesoarchean Kola-Karelia continent

Mesoarchean Kola-Karelia continent in the eastern Fennoscandian Shield includes three tectonic provinces, Kola, Karelia and Belomoria, that were formed by the Paleoarchean and Mesoarchean microcontinents. Traces of Mesoarchean tonalite-trondhjemite-granodiorite (TTG)-type early crust were documented in all of the most ancient units of the Kola-Karelia continent. Ancient crust was revealed and dated in the Ranua and Iisalmi microcontinents, 3.5-3.4 Ga; Vodlozero and Khetolambina microcontinents, 3.25-3.15 Ga; Kuhmo-Segozero microcontinent, ~3.0 Ga; Murmansk and Inari-Kola microcontinents, 2.93 Ga; and Kianta microcontinent, 2.83-2.81 Ga. In the older (>3.0 Ga) tectonic units and microcontinents, the ancient crust was possibly formed in brief bursts of endogenic activity. In younger microcontinents (3.0–2.93 Ga), these processes could continue until 2.8 and even 2.72 Ga. The tectonic settings in which early TTG crust has been produced are largely uncertain. The primary melt glassy inclusions with a glass phase in cores of prismatic zircon crystals from TTG gneisses provide evidence for the volcanic origin of gneiss protolith. Suggested genetic modeling of TTG-type complexes assumes that felsic K-Na melts with positive Eu anomaly are a product of dry high-temperature partial melting of the previously formed mafic-to-felsic crustal rocks and/or thick older TTG crust. Positive Eu anomaly in the eutectic is directly related to the predominance of plagioclase and K-feldspar in the melt. TTG-type crust melted to produce granite-granodiorite (GG) rocks. Earliest microcontinents are separated by Mesoarchean greenstone belts (mainly 3.05-2.85 Ga, in some cases up to 2.75 Ga), which are fragments of paleo-island-arc systems accreted to their margins: the Kolmozero-Voronya, Central Belomorian, Vedlozero-Segozero, Sumozero-Kenozero, and Tipasjärvi-Kuhmo-Suomussalmi belts; and the mature island arcs (microcontinents): Khetolambina and Kovdozero. These structural units are characterized by significant extent, close to rectilinear trend, localization along the boundaries between Archean microcontinents, and a specific set of petrotectonic assemblages (basalt-andesite-rhyolite, komatiite-tholeiite, and andesite-dacite associations). The recently discovered Meso-Neoarchean Belomorian eclogite province that is structurally linked with the Central Belomorian greenstone belt contains two eclogite associations distributed within TTG gneisses: the subduction-type Salma association and the Gridino eclogitized mafic dikes. The protolith of the Salma eclogites is thought to have been a sequence of gabbro, Fe-Ti gabbro, and troctolite, formed at ca. 2.9 Ga in a slow-spreading ridge (similar to the Southwest Indian Ridge). The main subduction and eclogite-facies events occurred between ca. 2.87 and ca. 2.82 Ga. Mafic magma injections into the crust of the active margin that led to formation of the Grigino dike swarm were associated with emplacement of a mid-ocean ridge in a subduction zone, beginning at ca. 2.87 Ga. Crustal delamination of the active margin and subsequent involvement of the lower crust in subduction 2.87–2.82 Ga ago led to high-pressure metamorphism of the Gridino dikes that reached eclogite-facies conditions during a collision event between 2.82 and 2.78 Ga. This collision resulted in consolidation of the Karelia, Kola, and Khetolamba blocks and formation of the Mesoarchean Belomorian accretionary-collisional orogen. To date, the subduction-related Salma eclogites provide the most complete and meaningful information on the nature of plate tectonics in the Archean, from ocean-floor spreading to subduction and collision. The Kovdozero granite-greenstone terrain that separates the Khetolambina nd Kuhmo-Segozero microcontinents is formed by TTG granitoids and gneisses hosting metasediments and metavolcanics of several greenstone belts, which belonged to the Parandovo-Tiksheozero island arc that existed from ca. 2.81 to 2.77 Ga. The Iringora greenstone belt includes the ophiolite complex of the same name with an age of 2.78 Ga. The collision of microcontinents resulted in the upward squeezing of the island arc and the obduction of its marginal portions onto surrounding structures.74 page(s

Archaean to Palaeoproterozoic high-grade evolution of the Belomorian eclogite province in the Gridino area, Fennoscandian Shield : geochronological evidence

The Belomorian eclogite province was repeatedly affected by multiple deformation episodes and metamorphism under moderate to high pressure. Within the Gridino area, high pressure processes developed in a continental crust of tonalite-trondhjemite-granodiorite (TTG) affinity that contains mafic pods and dykes, in which products of these processes are most clearly evident. New petrological, geochemical and geochronological data on mafic and felsic rocks, including PT-estimates, mineral chemistry, bulk rock chemistries, REE composition of the rocks and zircons and U-Pb and Lu-Hf geochronology presented in the paper make it possible to reproduce the magmatic and high-grade metamorphic evolution in the study area. In the framework of the extremely long-lasting geologic history recorded in the Belomorian province (3-1.7. Ga), new geochronological data enabled us to define the succession of events that includes mafic dyke emplacement between 2.87 and 2.82. Ga and eclogite facies metamorphism of the mafic dykes between ~ 2.82 and ~ 2.72. Ga (most probably in the time span of 2.79-2.73. Ga). The clockwise PT path of the Gridino association crosses the granulite- and amphibolite-facies PT fields during the time period of 2.72. Ga to 2.64. Ga. A special aspect of this work concerns the superposed subisobaric heating (thermal impact) with an increase in the temperature to granulite facies conditions at 2.4. Ga. Later amphibolite facies metamorphism occurred at 2.0-1.9. Ga. Our detailed geochronological and petrological studies reveal a complicated Mesoarchaean-Palaeoproterozoic history that involved deep subduction of the continental crust and a succession of plume-related events.29 page(s

The Salma eclogites of the Belomorian Province, Russia : HP/UHP metamorphism through the subduction of Mesoarchean oceanic crust

42 page(s

Secular changes in sedimentation systems and sequence stratigraphy

The ephemeral nature of most sedimentation processes and the fragmentary character of the sedimentary record are of first-order importance. Despite a basic uniformity of external controls on sedimentation resulting in markedly similar lithologies, facies, facies associations and depositional elements within the rock record across time, there are a number of secular changes, particularly in rates and intensities of processes that resulted in contrasts between preserved Precambrian and Phanerozoic successions. Secular change encompassed (1) variations in mantle heat, rates of plate drift and of continental crustal growth, the gravitational effects of the Moon, and in rates of weathering, erosion, transport, deposition and diagenesis; (2) a decreasing planetary rotation rate over time; (3) no vegetation in the Precambrian, but prolific microbial mats, with the opposite pertaining to the Phanerozoic; (4) the long-term evolution of the hydrosphere-atmosphere-biosphere system. A relatively abrupt and sharp turning point was reached in the Neoarchaean, with spikes in mantle plume flux and tectonothermal activity and possibly concomitant onset of the supercontinent cycle. Substantial and irreversible change occurred subsequently in the Palaeoproterozoic, whereby the dramatic change from reducing to oxidizing volcanic gases ushered in change to an oxic environment, to be followed at ca. 2.4-2.3. Ga by the "Great Oxidation Event" (GOE); rise in atmospheric oxygen was accompanied by expansion of oxygenic photosynthesis in the cyanobacteria. A possible global tectono-thermal "slowdown" from ca. 2.45-2.2. Ga may have separated a preceding plate regime which interacted with a higher energy mantle from a ca. 2.2-2.0. Ga Phanerozoic-style plate tectonic regime; the "slowdown" period also encompassed the first known global-scale glaciation and overlapped with the GOE. While large palaeodeserts emerged from ca. 2.0-1.8. Ga, possibly associated with the evolution of the supercontinent cycle, widespread euxinia by ca. 1.85. Ga ushered in the "boring billion" year period. A second time of significant and irreversible change, in the Neoproterozoic, saw a second major oxidation event and several low palaeolatitude Cryogenian (740-630. Ma) glaciations. With the veracity of the "Snowball Earth" model for Neoproterozoic glaciation being under dispute, genesis of Pre-Ediacaran low-palaeolatitude glaciation remains enigmatic. Ediacaran (635-542. Ma) glaciation with a wide palaeolatitudinal range contrasts with the circum-polar nature of Phanerozoic glaciation. The observed change from low latitude to circum-polar glaciation parallels advent and diversification of the Metazoa and the Neoproterozoic oxygenation (ca. 580. Ma), and was succeeded by the Ediacaran-Cambrian transition which ushered in biomineralization, with all its implications for the chemical sedimentary record. © 2012 International Association for Gondwana Research.Patrick G. Eriksson, Santanu Banerjee, Octavian Catuneanu, Patricia L. Corcoran, Kenneth A. Eriksson, Eric E. Hiatt, Marc Laflamme, Nils Lenhardt, Darrel G.F. Long, Andrew D. Miall, Michael V. Mints, Peir K. Pufahl, Subir Sarkar, Edward L. Simpson, George E. William