Pan-cancer application of a lung-adenocarcinoma-derived gene-expression-based prognostic predictor.

Gene-expression profiling can be used to classify human tumors into molecular subtypes or risk groups, representing potential future clinical tools for treatment prediction and prognostication. However, it is less well-known how prognostic gene signatures derived in one malignancy perform in a pan-cancer context. In this study, a gene-rule-based single sample predictor (SSP) called classifier for lung adenocarcinoma molecular subtypes (CLAMS) associated with proliferation was tested in almost 15 000 samples from 32 cancer types to classify samples into better or worse prognosis. Of the 14 malignancies that presented both CLAMS classes in sufficient numbers, survival outcomes were significantly different for breast, brain, kidney and liver cancer. Patients with samples classified as better prognosis by CLAMS were generally of lower tumor grade and disease stage, and had improved prognosis according to other type-specific classifications (e.g. PAM50 for breast cancer). In all, 99.1% of non-lung cancer cases classified as better outcome by CLAMS were comprised within the range of proliferation scores of lung adenocarcinoma cases with a predicted better prognosis by CLAMS. This finding demonstrates the potential of tuning SSPs to identify specific levels of for instance tumor proliferation or other transcriptional programs through predictor training. Together, pan-cancer studies such as this may take us one step closer to understanding how gene-expression-based SSPs act, which gene-expression programs might be important in different malignancies, and how to derive tools useful for prognostication that are efficient across organs.

Features of increased malignancy in eosinophilic clear cell renal cell carcinoma.

Clear cell renal cell carcinoma (ccRCC) is the most common form of renal cancer. Due to inactivation of the von Hippel-Lindau tumour suppressor, the hypoxia-inducible transcription factors (HIFs) are constitutively activated in these tumours, resulting in a pseudo-hypoxic phenotype. The HIFs induce the expression of genes involved in angiogenesis and cell survival, but they also reset the cellular metabolism to protect cells from oxygen and nutrient deprivation. ccRCC tumours are highly vascularized and the cytoplasm of the cancer cells is filled with lipid droplets and glycogen, resulting in the histologically distinctive pale (clear) cytoplasm. Intratumoural heterogeneity may occur, and in some tumours, areas with granular, eosinophilic cytoplasm are found. Little is known regarding these traits and how they relate to the coexistent clear cell component, yet eosinophilic ccRCC is associated with higher grade and clinically more aggressive tumours. In this study, we have for the first time performed RNA sequencing comparing histologically verified clear cell and eosinophilic areas from ccRCC tissue, aiming to analyse the characteristics of these cell types. Findings from RNA sequencing were confirmed by immunohistochemical staining of biphasic ccRCC. We found that the eosinophilic phenotype displayed a higher proliferative drive and lower differentiation, and we confirmed a correlation to tumours of higher stage. We further identified mutations of the tumour suppressor p53 (TP53) exclusively in the eosinophilic ccRCC component, where mTORC1 activity was also elevated. Also, eosinophilic areas were less vascularized, yet harboured more abundant infiltrating immune cells. The cytoplasm of clear cell ccRCC cells was filled with lipids but had very low mitochondrial content, while the reverse was found in eosinophilic tissue. We herein suggest possible transcriptional mechanisms behind these phenomena. © 2020 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.

Localization and Regulation of Polymeric Ig Receptor in Healthy and Diseased Human Kidney.

The polymeric Ig receptor (PIgR) constitutes an important part of the immune system by mediating transcytosis of dimeric IgA into mucosal fluids. Although well studied in organs such as the intestine, the regulation and localization of PIgR in human kidney are incompletely characterized. Herein, using immunohistochemistry, we show that in healthy human kidneys, PIgR is expressed by the progenitor-like tubular scattered cells of the proximal tubules and by parietal epithelial cells of glomeruli. We further show that proximal tubular expression of PIgR becomes widespread during kidney disease, correlating to elevated levels of urinary secretory IgA. Urinary secretory IgA levels also correlated to the degree of tubular fibrosis, plasma creatinine, and urea levels. In addition, primary tubular cells were cultured to study the function and regulation of PIgR in vitro. Cellular PIgR expression was induced by conditioned medium from activated human leukocytes, as well as by inflammatory cytokines, whereas transforming growth factor-ß1 caused decreased expression. Furthermore, interferon-γ increased the transcytosis of dimeric IgA in cultured tubular cells. Finally, a correlation study of mRNA data from the Genotype-Tissue Expression portal indicated that PIGR mRNA expression in kidney correlates to the expression of TNFSF13, a cytokine involved in plasma cell class switching to IgA. These results indicate that PIgR induction is an integral part of the injury phenotype of renal tubular cells.

Activin receptor-like kinase 1 is associated with immune cell infiltration and regulates CLEC14A transcription in cancer.

Cancer cells sustain their metabolic needs through nutrients and oxygen supplied by the bloodstream. The requirement for tumor angiogenesis has been therapeutically exploited in the clinical setting mainly by means of inhibition of the vascular endothelial growth factor family of ligands and receptors. Despite promising results in preclinical models, the benefits for patients proved to be limited. Inadequate efficacy similarly halted the development of agents impinging on the activity of the activin receptor-like kinase (ALK)1, a member of the transforming growth factor-ß superfamily. Notwithstanding its characterization as an endothelial cell marker, the full spectrum of biological processes associated with ALK1 is essentially unexplored. Here, we present data revealing the genetic network associated with ACVRL1 (the gene encoding for ALK1) expression in human cancer tissues. Computational analysis unveiled a hitherto unknown role for ACVRL1 in relation to genes modulating the functionality of the immune cell compartment. Moreover, we generated a signature of 8 genes co-expressed with ACVRL1 across different tumor types and characterized the c-type lectin domain containing protein (CLEC)14A as a potential downstream target of ACVRL1. Considering the lack of reagents for ALK1 detection that has hampered the field to date, our work provides the opportunity to validate the 8-gene signature and CLEC14A as biomarkers for ALK1 activity. Ultimately, this may help revisit the clinical development of already existing ALK1-blocking compounds as precision medicines for cancer.

Continuous gas-phase synthesis of nanowires with tunable properties.

Semiconductor nanowires are key building blocks for the next generation of light-emitting diodes, solar cells and batteries. To fabricate functional nanowire-based devices on an industrial scale requires an efficient methodology that enables the mass production of nanowires with perfect crystallinity, reproducible and controlled dimensions and material composition, and low cost. So far there have been no reports of reliable methods that can satisfy all of these requirements. Here we show how aerotaxy, an aerosol-based growth method, can be used to grow nanowires continuously with controlled nanoscale dimensions, a high degree of crystallinity and at a remarkable growth rate. In our aerotaxy approach, catalytic size-selected Au aerosol particles induce nucleation and growth of GaAs nanowires with a growth rate of about 1 micrometre per second, which is 20 to 1,000 times higher than previously reported for traditional, substrate-based growth of nanowires made of group III-V materials. We demonstrate that the method allows sensitive and reproducible control of the nanowire dimensions and shape--and, thus, controlled optical and electronic properties--through the variation of growth temperature, time and Au particle size. Photoluminescence measurements reveal that even as-grown nanowires have good optical properties and excellent spectral uniformity. Detailed transmission electron microscopy investigations show that our aerotaxy-grown nanowires form along one of the four equivalent〈111〉B crystallographic directions in the zincblende unit cell, which is also the preferred growth direction for III-V nanowires seeded by Au particles on a single-crystal substrate. The reported continuous and potentially high-throughput method can be expected substantially to reduce the cost of producing high-quality nanowires and may enable the low-cost fabrication of nanowire-based devices on an industrial scale.

Room-temperature InP/InAsP Quantum Discs-in-Nanowire Infrared Photodetectors.

The possibility to engineer nanowire heterostructures with large bandgap variations is particularly interesting for technologically important broadband photodetector applications. Here we report on a combined study of design, fabrication, and optoelectronic properties of infrared photodetectors comprising four million n+-i-n+ InP nanowires periodically ordered in arrays. The nanowires were grown by metal-organic vapor phase epitaxy on InP substrates, with either a single or 20 InAsP quantum discs embedded in the i-segment. By Zn compensation of the residual n-dopants in the i-segment, the room-temperature dark current is strongly suppressed to a level of pA/NW at 1 V bias. The low dark current is manifested in the spectrally resolved photocurrent measurements, which reveal strong photocurrent contributions from the InAsP quantum discs at room temperature with a threshold wavelength of about 2.0 µm and a bias-tunable responsivity reaching 7 A/W@1.38 µm at 2 V bias. Two different processing schemes were implemented to study the effects of radial self-gating in the nanowires induced by the nanowire/SiOx/ITO wrap-gate geometry. Summarized, our results show that properly designed axial InP/InAsP nanowire heterostructures are promising candidates for broadband photodetectors.

Papillary renal cell carcinoma-derived chemerin, IL-8, and CXCL16 promote monocyte recruitment and differentiation into foam-cell macrophages.

Papillary renal cell carcinoma (pRCC) is the second most common type of renal cell carcinoma. The only curative treatment available for pRCC is radical surgery. If the disease becomes widespread, neither chemo- nor radiotherapy will have therapeutic effect, hence further research on pRCC is of utmost importance. Histologically, pRCC is characterized by a papillary growth pattern with focal aggregation of macrophages of the foam cell phenotype. In other forms of cancer, a clear role for tumor-associated macrophages during cancer growth and progression has been shown. Although the presence of foamy macrophages is a histological hallmark of pRCC tumors, little is known regarding their role in pRCC biology. In order to study the interaction between pRCC tumor and myeloid cells, we established primary cultures from pRCC tissue. We show that human pRCC cells secrete the chemokines IL-8, CXCL16, and chemerin, and that these factors attract primary human monocytes in vitro. RNAseq data from The Cancer Genome Atlas confirmed a high expression of these factors in pRCC tissue. Conditioned medium from pRCC cultures induced a shift in human monocytes toward the M2 macrophage phenotype. In extended cultures, these macrophages became enlarged and loaded with lipids, adopting the foam cell morphology found in pRCC tissue. These results show for the first time that pRCC primary tumor cells secrete factors that attract and differentiate monocytes into anti-inflammatory tumor-associated macrophages with foam cell histology.

Direct regulation of GAS6/AXL signaling by HIF promotes renal metastasis through SRC and MET.

Dysregulation of the von Hippel-Lindau/hypoxia-inducible transcription factor (HIF) signaling pathway promotes clear cell renal cell carcinoma (ccRCC) progression and metastasis. The protein kinase GAS6/AXL signaling pathway has recently been implicated as an essential mediator of metastasis and receptor tyrosine kinase crosstalk in cancer. Here we establish a molecular link between HIF stabilization and induction of AXL receptor expression in metastatic ccRCC. We found that HIF-1 and HIF-2 directly activate the expression of AXL by binding to the hypoxia-response element in the AXL proximal promoter. Importantly, genetic and therapeutic inactivation of AXL signaling in metastatic ccRCC cells reversed the invasive and metastatic phenotype in vivo. Furthermore, we define a pathway by which GAS6/AXL signaling uses lateral activation of the met proto-oncogene (MET) through SRC proto-oncogene nonreceptor tyrosine kinase to maximize cellular invasion. Clinically, AXL expression in primary tumors of ccRCC patients correlates with aggressive tumor behavior and patient lethality. These findings provide an alternative model for SRC and MET activation by growth arrest-specific 6 in ccRCC and identify AXL as a therapeutic target driving the aggressive phenotype in renal clear cell carcinoma.

An integrated genomics analysis of epigenetic subtypes in human breast tumors links DNA methylation patterns to chromatin states in normal mammary cells.

BACKGROUND: Aberrant DNA methylation is frequently observed in breast cancer. However, the relationship between methylation patterns and the heterogeneity of breast cancer has not been comprehensively characterized. METHODS: Whole-genome DNA methylation analysis using Illumina Infinium HumanMethylation450 BeadChip arrays was performed on 188 human breast tumors. Unsupervised bootstrap consensus clustering was performed to identify DNA methylation epigenetic subgroups (epitypes). The Cancer Genome Atlas data, including methylation profiles of 669 human breast tumors, was used for validation. The identified epitypes were characterized by integration with publicly available genome-wide data, including gene expression levels, DNA copy numbers, whole-exome sequencing data, and chromatin states. RESULTS: We identified seven breast cancer epitypes. One epitype was distinctly associated with basal-like tumors and with BRCA1 mutations, one epitype contained a subset of ERBB2-amplified tumors characterized by multiple additional amplifications and the most complex genomes, and one epitype displayed a methylation profile similar to normal epithelial cells. Luminal tumors were stratified into the remaining four epitypes, with differences in promoter hypermethylation, global hypomethylation, proliferative rates, and genomic instability. Specific hyper- and hypomethylation across the basal-like epitype was rare. However, we observed that the candidate genomic instability drivers BRCA1 and HORMAD1 displayed aberrant methylation linked to gene expression levels in some basal-like tumors. Hypomethylation in luminal tumors was associated with DNA repeats and subtelomeric regions. We observed two dominant patterns of aberrant methylation in breast cancer. One pattern, constitutively methylated in both basal-like and luminal breast cancer, was linked to genes with promoters in a Polycomb-repressed state in normal epithelial cells and displayed no correlation with gene expression levels. The second pattern correlated with gene expression levels and was associated with methylation in luminal tumors and genes with active promoters in normal epithelial cells. CONCLUSIONS: Our results suggest that hypermethylation patterns across basal-like breast cancer may have limited influence on tumor progression and instead reflect the repressed chromatin state of the tissue of origin. On the contrary, hypermethylation patterns specific to luminal breast cancer influence gene expression, may contribute to tumor progression, and may present an actionable epigenetic alteration in a subset of luminal breast cancers.

Structural Properties of wurtzite InP-InGaAs nanowire core-shell heterostructures.

We report on growth and characterization of wurtzite InP-In(1-x)Ga(x)As core-shell nanowire heterostructures. A range of nanowire structures with different Ga concentration in the shell was characterized with transmission electron microscopy and X-ray diffraction. We found that the main part of the nanowires has a pure wurtzite crystal structure, with occasional stacking faults occurring only at the top and bottom. This allowed us to determine the structural properties of wurtzite In(1-x)Ga(x)As. The InP-In(1-x)Ga(x)As core-shell nanowires show a triangular and hexagonal facet structure of {1100} and {101̅0} planes. X-ray diffraction measurements showed that the core and the shell are pseudomorphic along the c-axis, and the strained axial lattice constant is closer to the relaxed In(1-x)Ga(x)As shell. Microphotoluminescence measurements of the nanowires show emission in the infrared regime, which makes them suitable for applications in optical communication.

Individual patient risk stratification of high-risk neuroblastomas using a two-gene score suited for clinical use.

Several gene expression-based prognostic signatures have been described in neuroblastoma, but none have successfully been applied in the clinic. Here we have developed a clinically applicable prognostic gene signature, both with regards to number of genes and analysis platform. Importantly, it does not require comparison between patients and is applicable amongst high-risk patients. The signature is based on a two-gene score (R-score) with prognostic power in high-stage tumours (stage 4 and/or MYCN-amplified diagnosed after 18 months of age). QPCR-based and array-based analyses of matched cDNAs confirmed cross platform (array-qPCR) transferability. We also defined a fixed cut-off value identifying prognostically differing subsets of high-risk patients on an individual patient basis. This gene expression signature independently contributes to the current neuroblastoma classification system, and if prospectively validated could provide further stratification of high-risk patients, and potential upfront identification of a group of patients that are in need of new/additional treatment regimens.

Study of carrier concentration in single InP nanowires by luminescence and Hall measurements.

The free electron carrier concentrations in single InP core-shell nanowires are determined by micro-photoluminescence, cathodoluminescence (CL) and Hall effect measurements. The results from luminescence measurements were obtained by solving the Fermi-Dirac integral, as well as by analyzing the peak full width at half maximum (FWHM). Furthermore, the platform used for Hall effect measurements, combined with spot mode CL spectroscopy, is used to determine the carrier concentrations at specific positions along single nanowires. The results obtained via luminescence measurements provide an accurate and rapid feedback technique for the epitaxial development of doping incorporation in nanowires. The technique has been employed on several series of samples in which growth parameters, such as V/III-ratio, temperature and dopant flows, were investigated in an optimization procedure. The correlation between the Hall effect and luminescence measurements for extracting the carrier concentration of different samples were in excellent agreement.

Synthesis of doped InP core-shell nanowires evaluated using hall effect measurements.

InP core-shell nanowire pn-junctions doped with Zn and Sn have been investigated in terms of growth morphology and shell carrier concentration. The carrier concentrations were evaluated using spatially resolved Hall effect measurements and show improved homogeneity compared to previous investigations, attributed to the use of Sn as the n-type dopant. Anisotropies in the growth rate of different facets are found for different doping levels that in turn affects the migration of Sn and In on the nanowire surface. A route for increasing the In migration length to obtain a more homogeneous shell thickness is presented.

Toward a molecular pathologic classification of urothelial carcinoma.

We recently defined molecular subtypes of urothelial carcinomas according to whole genome gene expression. Herein we describe molecular pathologic characterization of the subtypes using 20 genes and IHC of 237 tumors. In addition to differences in expression levels, the subtypes show important differences in stratification of protein expression. The selected genes included biological features central to bladder cancer biology, eg, cell cycle activity, cellular architecture, cell-cell interactions, and key receptor tyrosine kinases. We show that the urobasal (Uro) A subtype shares features with normal urothelium such as keratin 5 (KRT5), P-cadherin (P-Cad), and epidermal growth factor receptor (EGFR) expression confined to basal cells, and cell cycle activity (CCNB1) restricted to the tumor-stroma interface. In contrast, the squamous cell cancer-like (SCCL) subtype uniformly expresses KRT5, P-Cad, EGFR, KRT14, and cell cycle genes throughout the tumor parenchyma. The genomically unstable subtype shows proliferation throughout the tumor parenchyma and high ERBB2 and E-Cad expression but absence of KRT5, P-Cad, and EGFR expression. UroB tumors demonstrate features shared by both UroA and SCCL subtypes. A major transition in tumor progression seems to be loss of dependency of stromal interaction for proliferation. We present a simple IHC/histology-based classifier that is easy to implement as a standard pathologic evaluation to differentiate the three major subtypes: urobasal, genomically unstable, and SCCL. These three major subtypes exhibit important prognostic differences.

Analysis of Nanowire pn-Junction with Combined Current-Voltage, Electron-Beam-Induced Current, Cathodoluminescence, and Electron Holography Characterization.

We present the characterization of a pn-junction GaAs nanowire. For the characterization, current-voltage, electron-beam-induced current, cathodoluminescence, and electron holography measurements are used. We show that by combining information from these four methods, in combination with drift-diffusion modelling, we obtain a detailed picture of how the nanowire pn-junction is configured and how the recombination lifetime varies axially in the nanowire. We find (i) a constant doping concentration and 600 ps recombination lifetime in the n segment at the top part of the nanowire; (ii) a 200-300 nm long gradient in the p doping next to the pn-junction; and (iii) a strong gradient in the recombination lifetime on the p side, with 600 ps lifetime at the pn-junction, which drops to 10 ps at the bottom of the p segment closest to the substrate. We recommend such complementary characterization with multiple methods for nanowire-based optoelectronic devices.

Effects of TGF-ß signaling in clear cell renal cell carcinoma cells.

Clear cell renal cell carcinoma (ccRCC) is by far the most common type of kidney cancer and is characterized by loss of the tumor suppressor gene von Hippel-Lindau (VHL). ccRCC patients with metastatic disease has poor prognosis and today's therapy is insufficient. The cytokine Transforming Growth Factor-ß (TGF-ß) has been extensively studied in tumor biology and is believed to serve a variety of functions in tumor progression. We have previously shown that inhibition of NOTCH signaling causes a reduced migratory and invasive capacity of ccRCC cells, at least partly by a cross-talk with the TGF-ß pathway. In the present study we aimed to further clarify the role of TGF-ß signaling in ccRCC. We investigated the effects of TGF-ß pathway modulation and showed that TGF-ß inhibition attenuates the invasive capacity of ccRCC cells. By performing expression profiling we obtained a gene signature of the TGF-ß induced response in ccRCC cells. The expression analyses revealed an extensive overlap between the TGF-ß response and genes regulated by the hypoxia inducible factor (HIF). The link between the hypoxic and the TGF-ß pathways was further corroborated by functional experiments, which demonstrated that TGF-ß pathway activity was attenuated upon reintroduction of functional VHL in ccRCC.

Optical characterization of InAs quantum wells and dots grown radially on wurtzite InP nanowires.

Correlated micro-photoluminescence (µPL) and cathodoluminescence (CL) measurements are reported for single core-shell InP-InAs wurtzite nanowires grown using metal-organic vapor phase epitaxy. Samples covering a radial InAs shell thickness of 1-12 ML were investigated. The effective masses for the wurtzite material were determined from the transition energy dependence of the InAs shell thickness, using a model based on linear deformation potential theory. InP cores with segments of mixed zincblende and wurtzite, on which quantum dots nucleated selectively, were also investigated. Narrow peaks were observed by µPL and the spatial origin of the emission was identified with CL imaging.

Generation of trisomies in cancer cells by multipolar mitosis and incomplete cytokinesis.

One extra chromosome copy (i.e., trisomy) is the most common type of chromosome aberration in cancer cells. The mechanisms behind the generation of trisomies in tumor cells are largely unknown, although it has been suggested that dysfunction of the spindle assembly checkpoint (SAC) leads to an accumulation of trisomies through failure to correctly segregate sister chromatids in successive cell divisions. By using Wilms tumor as a model for cancers with trisomies, we now show that trisomic cells can form even in the presence of a functional SAC through tripolar cell divisions in which sister chromatid separation proceeds in a regular fashion, but cytokinesis failure nevertheless leads to an asymmetrical segregation of chromosomes into two daughter cells. A model for the generation of trisomies by such asymmetrical cell division accurately predicted several features of clones having extra chromosomes in vivo, including the ratio between trisomies and tetrasomies and the observation that different trisomies found in the same tumor occupy identical proportions of cells and colocalize in tumor tissue. Our findings provide an experimentally validated model explaining how multiple trisomies can occur in tumor cells that still maintain accurate sister chromatid separation at metaphase-anaphase transition and thereby physiologically satisfy the SAC.

A previously uncharacterized Factor Associated with Metabolism and Energy (FAME/C14orf105/CCDC198/1700011H14Rik) is related to evolutionary adaptation, energy balance, and kidney physiology.

In this study we use comparative genomics to uncover a gene with uncharacterized function (1700011H14Rik/C14orf105/CCDC198), which we hereby name FAME (Factor Associated with Metabolism and Energy). We observe that FAME shows an unusually high evolutionary divergence in birds and mammals. Through the comparison of single nucleotide polymorphisms, we identify gene flow of FAME from Neandertals into modern humans. We conduct knockout experiments on animals and observe altered body weight and decreased energy expenditure in Fame knockout animals, corresponding to genome-wide association studies linking FAME with higher body mass index in humans. Gene expression and subcellular localization analyses reveal that FAME is a membrane-bound protein enriched in the kidneys. Although the gene knockout results in structurally normal kidneys, we detect higher albumin in urine and lowered ferritin in the blood. Through experimental validation, we confirm interactions between FAME and ferritin and show co-localization in vesicular and plasma membranes.

Isolation and characterization of progenitor-like cells from human renal proximal tubules.

The tubules of the kidney display a remarkable capacity for self-renewal on damage. Whether this regeneration is mediated by dedifferentiating surviving cells or, as recently suggested, by stem cells has not been unequivocally settled. Herein, we demonstrate that aldehyde dehydrogenase (ALDH) activity may be used for isolation of cells with progenitor characteristics from adult human renal cortical tissue. Gene expression profiling of the isolated ALDH(high) and ALDH(low) cell fractions followed by immunohistochemical interrogation of renal tissues enabled us to delineate a tentative progenitor cell population scattered through the proximal tubules (PTs). These cells expressed CD24 and CD133, previously described markers for renal progenitors of Bowman's capsule. Furthermore, we show that the PT cells, and the glomerular progenitors, are positive for KRT7, KRT19, BCL2, and vimentin. In addition, tubular epithelium regenerating on acute tubular necrosis displayed long stretches of CD133(+)/VIM(+) cells, further substantiating that these cells may represent a progenitor cell population. Furthermore, a potential association of these progenitor cells with papillary renal cell carcinoma was discovered. Taken together, our data demonstrate the presence of a previously unappreciated subset of the PT cells that may be endowed with a more robust phenotype, allowing increased resistance to acute renal injury, enabling rapid repopulation of the tubules.