Search

Reverse phase protein microarray analysis was used to identify cell signaling derangements in squamous cell carcinoma (SCC) compared with actinic keratosis (AK) and upper inner arm (UIA). We analyzed two independent tissue sets with isolation and enrichment of epithelial cells by laser capture microdissection. Set 1 served as a pilot and a means to identify protein pathway activation alterations that could be further validated in a second independent set. Set 1 was comprised of 4 AK, 13 SCC, and 20 UIA. Set 2 included 15 AK, 9 SCCs, and 20 UIAs. Activation of 51 signaling proteins, known to be involved in tumorigenesis, were assessed for set 1 and showed that the MEK–ERK [mitogen-activated protein (MAP)/extracellular signal-regulated (ERK; MEK)] pathway was activated in SCC compared with AK and UIA, and that epidermal growth factor receptor (EGFR) and mTOR pathways were aberrantly activated in SCC. Unsupervised two-way hierarchical clustering revealed that AK and UIA shared a common signaling network activation architecture while SCC was dramatically different. Statistical analysis found that prosurvival signaling through phosphorylation of ASK and 4EBP1 as well as increased Bax and Bak expression was higher in AK compared with UIA. We expanded pathway network activation mapping in set 2 to 101 key signaling proteins, which corroborated activation of MEK–ERK, EGFR, and mTOR pathways through discovery of a number of upstream and downstream signaling molecules within these pathways to conclude that SCC is indeed a pathway activation–driven disease. Pathway activation mapping of SCC compared with AK revealed several interconnected networks that could be targeted with drug therapy for potential chemoprevention and therapeutic applications. Cancer Prev Res; 5(3); 403–13. ©2012 AACR.

PDF file - 83K

Objective To find indicators of disease severity and factors of early remission in patients with deficiency of adenosine deaminase 2 (DADA2). Methods We enrolled six DADA2 patients from six families. Direct sequencing of adenosine deaminase 2 gene (ADA2) was performed by Sanger analysis. A literature review was conducted for articles regarding paediatric DADA2. Results We found that more organs were involved in early-onset (≤1 year of age) than in late-onset (>1 year of age) DADA2 patients had high level inflammatory responses, such as elevated ESR, SF, serum amyloid A and CRP. Disease severity was not significantly different from missense and frameshift mutation. Early administration of TNF inhibitor might result in better remission and reduce recurrence. In the literature, four articles describing 51 paediatric DADA2 patients were identified. We also found that fever, stroke, peripheral nervous system involvement, hypogammaglobulinaemia and hypertension were more frequent in early onset DADA2 patients. Conclusion Early-onset DADA2 may be more severe. Early administration of TNF inhibitor can effectively reduce recurrence and quickly alleviate the disease.

XLSX file - 128K, Reverse Phase Protein Microarray data for the cell lines with high HGF vs. cell lines with low HGF

Purpose: The receptor tyrosine kinase (RTK) c-MET and its ligand hepatocyte growth factor (HGF) are deregulated and promote malignancy in cancer and brain tumors. Consequently, clinically applicable c-MET inhibitors have been developed. The purpose of this study was to investigate the not-well-known molecular determinants that predict responsiveness to c-MET inhibitors and to explore new strategies for improving inhibitor efficacy in brain tumors.Experimental Design: We investigated the molecular factors and pathway activation signatures that determine sensitivity to c-MET inhibitors in a panel of glioblastoma and medulloblastoma cells, glioblastoma stem cells, and established cell line–derived xenografts using functional assays, reverse protein microarrays, and in vivo tumor volume measurements, but validation with animal survival analyses remains to be done. We also explored new approaches for improving the efficacy of the inhibitors in vitro and in vivo.Results: We found that HGF coexpression is a key predictor of response to c-MET inhibition among the examined factors and identified an ERK/JAK/p53 pathway activation signature that differentiates c-MET inhibition in responsive and nonresponsive cells. Surprisingly, we also found that short pretreatment of cells and tumors with exogenous HGF moderately but statistically significantly enhanced the antitumor effects of c-MET inhibition. We observed a similar ligand-induced sensitization effect to an EGF receptor small-molecule kinase inhibitor.Conclusions: These findings allow the identification of a subset of patients that will be responsive to c-MET inhibition and propose ligand pretreatment as a potential new strategy for improving the anticancer efficacy of RTK inhibitors. Clin Cancer Res; 19(6); 1433–44. ©2013 AACR.

XLSX file - 108K, Primary tumor group statistics.

XLSX file - 33K, List of primary antibodies used to probe RPMA slides.

XLSX file - 351K, Spearman's Rho correlation analysis results for the short-survivor group, using RPMA data.

PDF file - 103K, Validation of the reproducibility of the RPMA for HER2 and pHER2 analysis from FFPE-tissues

XLSX file - 242K, Spearman's Rho correlation analysis results for the entire study set, using RPMA data.

PDF file - 60K, Methods for cell and tissue culture and Reverse Phase Protein Microarray Construction and Analysis

Purpose: There is an urgent need for therapies that will reduce the mortality of patients with bone metastasis. In this study, we profiled the protein signal pathway networks of the human bone metastasis microenvironment. The goal was to identify sets of interacting proteins that correlate with survival time following the first diagnosis of bone metastasis.Experimental Design: Using Reverse Phase Protein Microarray technology, we measured the expression of 88 end points in the bone microenvironment of 159 bone metastasis tissue samples derived from patients with primary carcinomas and sarcomas.Results: Metastases originating from different primary tumors showed similar levels of cell signaling across tissue types for the majority of proteins analyzed, suggesting that the bone microenvironment strongly influences the metastatic tumor signaling profiles. In a training set (72 samples), TNF receptor 1, alone (P = 0.0013) or combined with serotonin (P = 0.0004), TNFα (P = 0.0214), and RANK (P = 0.0226), was associated with poor survival, regardless of the primary tumor of origin. Results were confirmed by (i) analysis of an independent validation set (71 samples) and (ii) independent bioinformatic analysis using a support vector machine learning model. Spearman rho analysis revealed a highly significant number of interactions intersecting with ERα S118, serotonin, TNFα, RANKL, and matrix metalloproteinase in the bone metastasis signaling network, regardless of the primary tumor. The interaction network pattern was significantly different in the short versus long survivors.Conclusions: TNF receptor 1 and neuroendocrine-regulated protein signal pathways seem to play an important role in bone metastasis and may constitute a novel drug-targetable mechanism of seed-soil cross talk in bone metastasis. Clin Cancer Res; 19(9); 2473–85. ©2013 AACR.

PDF file - 54K, Antibodies used for Array and Western Blot Immunostaining

PDF file - 58K, Machine learning dataset characteristics.

Purpose: Targeting of the HER2 protein in human breast cancer represents a major advance in oncology but relies on measurements of total HER2 protein and not HER2 signaling network activation. We used reverse-phase protein microarrays (RPMA) to measure total and phosphorylated HER2 in the context of HER family signaling to understand correlations between phosphorylated and total levels of HER2 and downstream signaling activity.Experimental Design: Three independent study sets, comprising a total of 415 individual patient samples from flash-frozen core biopsy samples and formalin-fixed and paraffin-embedded (FFPE) surgical and core samples, were analyzed via RPMA. The phosphorylation and total levels of the HER receptor family proteins and downstream signaling molecules were measured in laser capture microdissected (LCM) enriched tumor epithelium from 127 frozen pretreatment core biopsy samples and whole-tissue lysates from 288 FFPE samples and these results were compared with FISH and immunohistochemistry (IHC).Results: RPMA measurements of total HER2 were highly concordant (>90% all sets) with FISH and/or IHC data, as was phosphorylation of HER2 in the FISH/IHC+ population. Phosphorylation analysis of HER family signaling identified HER2 activation in some FISH/IHC− tumors and, identical to that seen with FISH/IHC+ tumors, the HER2 activation was concordant with EGF receptor (EGFR) and HER3 phosphorylation and downstream signaling endpoint activation.Conclusions: Molecular profiling of HER2 signaling of a large cohort of human breast cancer specimens using a quantitative and sensitive functional pathway activation mapping technique reveals IHC−/FISH−/pHER2+ tumors with HER2 pathway activation independent of total HER2 levels and functional signaling through HER3 and EGFR. Clin Cancer Res; 18(23); 6426–35. ©2012 AACR.

XLSX file - 60K, Bone metastasis specimen study set.

PDF file - 3431K, Anti-TNFR1 antibody validation by western blot. Area Under the Curve (AUC) value changes with the data set size in the machine learning model. Anti-Serotonin antibody validation by competition assay using reverse phase protein microarray (RPMA).

XLSX file - 350K, Spearman's Rho correlation analysis results for the long-survivor group, using RPMA data.

PDF file - 296K, Short-time exogenous HGF treatment enhances the in vivo anti-tumor effects of METi

PDF file - 54K, Regression and Spearman (rank-based) correlation analyses between the molecular parameters and cell responsiveness to METi

The mechanism of crustal recycling in subduction zones has been a heated debate, and Mg–Fe isotopes may provide new constraints for this debate. This study reported the Fe–Mg isotope data for mafic plutonic rocks from the eastern and central Gangdese arc and their associated trench sediments in southern Tibet. The δ26Mg (–0.32 to –0.20‰) and δ56Fe (0.04 to 0.12‰) values of the eastern Gangdese arc rocks show negative and positive correlations with (87Sr/86Sr)i and (206Pb/204Pb)i values, but positive and negative correlations with εNd(t) and εHf(t) values, respectively. The Mg and Fe isotopic compositions (δ26Mg = –0.28 to –0.15‰; δ56Fe = 0.02 to 0.12‰) of the central Gangdese arc rocks are comparable with the eastern ones, but they are not covariant with Sr–Pb–Nd–Hf isotopes. More importantly, the Fe–Mg isotopes for most of the arc rocks fall in between local trench sediments (δ26Mg = –0.61 to –0.30‰; δ56Fe = 0.00 to 0.17‰) and the normal mantle. Integrated qualitative analyses and quantitative simulations suggest that while the Mg–Fe isotope variations in the eastern Gangdese arc rocks revealed the important role of source mixing between sediment-derived melts and peridotite, their variations in the central Gangdese arc rocks reflected the controlling effects of source mixing between carbonated serpentinite-derived Mg-rich fluid and peridotite and source melting. The good covariant relationships between Mg–Fe isotope and traditional geochemical tracers provide further evidence for the recycling of crustal materials in subduction zones via various types of slab-derived fluids and melts.

Cerebral venous sinus thrombosis (CVST) is a rare complication of childhood-onset SLE (cSLE) and is potentially fatal to the patient. In order to better define the characteristics of CVST in cSLE, we analysed a single-centre study of cSLE presenting with CVST.Clinical characteristics and laboratory findings of cSLE patients complicated with CVST from January 2006 to December 2019 were analysed through this retrospective, single-centre study.A total of 1395 records of cSLE patients were reviewed. Five patients (0.36%) had CVST. Headache (80%) was the most frequent symptom. The transverse sinus (45%) was the most frequent location of thrombus, followed by the sigmoid sinus (27%). The SLE disease activity index (SLEDAI) at the time of CVST was 11±3. The D-dimer was elevated in all 5 cases, only one patient was positive for ACL and anti-β2GP-I IgM. All the patients underwent MRV screen to confirm the diagnosis. All the patients had a favourable outcome after receiving glucocorticoid and immunosuppressant treatment, as well as anticoagulant therapy.CVST is relatively rare in cSLE and tends to occur in active lupus patients. Severe and persistent headache is an index of CVST. Early diagnosis and more intensive therapy for SLE, combined with anticoagulation therapy, could significantly improve the prognosis of CVST in cSLE.

Lupus nephritis is one of the most common and severe systemic lupus erythematosus complications. However, the pathogenesis of lupus nephritis is still poorly understood. Increasing evidence has shown that microRNAs (miRNAs) are extensively involved in the pathophysiology of autoimmune diseases. NZBWF1 is the classical mouse model of lupus nephritis. The present study aimed to investigate the expression profiling of mRNA and miRNAs of NZBWF1 mice with lupus nephritis using microarray, and explored the potential molecular mechanism of miRNA. miRNA and mRNA microarrays were performed to identify miRNA and mRNA expression changes between pre-diseased (8-week-old) NZBWF1 mice and diseased NZBWF1 mice with lupus nephritis (28-week-old). Quantitative polymerase chain reaction (qPCR) validated these results. The target of miRNA was confirmed through a dual-luciferase reporter and stimulated mesangial cells experiment. The combined miRNA and mRNA analysis identified 43 differentially expressed miRNAs and 1796 differentially expressed mRNAs between pre-disease (8-week-old) (n = 4) and diseased (28-week-old) NZBWF1 mice. We found that miR-1968-5p was significantly decreased, and csf1 mRNA was significantly increased in lupus nephritis mouse and verified by RT-PCR. csf1 has been demonstrated to play important roles in SLE. Bioinformatics analysis predicted that the csf1 was a potential target gene of miR-1968-5p. A dual-luciferase reporter assay confirmed the target binding. In cell experiments, overexpression or knockdown of miR resulted in a decrease or increase of csf1 expression, respectively. These results suggest that miR-1968-5p may be involved in the pathogenesis of lupus nephritis of NZBWF1 mice by targeting csf1.

Hydrous minerals in the hybridized zone at the slab-mantle interface play a critical role in retaining and transporting fluid mobile elements in subduction zones. The observed high B and As concentrations and high δ11B values in arc magmas were previously thought to have been resulted from the mechanical transport of forearc serpentinites down to subarc depths by mantle corner flows or through subduction channels because B, As, and Sb are mostly released during early stages of subduction. This study provides new insights into the recycling of B, As, and Sb in subduction zones via an in-situ study on a set of carbonate-bearing serpentinite samples from the Mianlue melange complex in the Qinling Orogen. Petrological observations and bulk-rock Sr-Pb isotopes reveal that the Jianchaling serpentinites were formed by interactions between forearc peridotites and sediment-derived fluids at a shallow depth in the subduction channel. Some Jianchaling serpentinites experienced the lizardite to antigorite transition at 300–400 °C with infiltrations of CO2-rich fluids. In contrast, the Liangyazi antigorite serpentinites were produced at a greater depth. Antigorite grains in the Jianchaling serpentinites have lower Feapfu than those in the Liangyazi serpentinites and most antigorite with geochemical data in the literature. Meanwhile, B, As, and Sb concentrations of Fe-poor antigorite from the Jianchaling serpentines (385–653 ppm B, 198–334 ppm As, and 6.24–8.01 ppm Sb) are not only higher than those of the Fe-rich antigorite from the Liangyazi serpentinites but also 2–3.5 times higher than those of the surrounding lizardite. The lower modal percentage of spinel and ferritchromite in antigorite veinlets, together with the lower bulk-rock FeO content of antigorite-lizardite serpentinites than that of lizardite serpentinites from the Jianchaling region, indicates that some FeO might be lost during the lizardite to antigorite transition. The presence of carbonate minerals in the antigorite veinlets and the remarkably high B, As, and Sb concentrations in the Jianchaling antigorite indicate that the penetrating fluids during the lizardite to antigorite transition are most likely derived from sediment and metabasite decarbonations at

Early-onset Systemic lupus erythematosus (SLE) is a heterogeneous disease with more variable symptoms than other types of SLE. It can begin as early as 12 months after birth, and the clinical process appears to be more severe. The common clinical manifestations of early-onset SLE are skin and mucosal lesions, renal involvement, central nervous system diseases and hematological system abnormalities. Although the disease is well described in the literature, diagnosis is often difficult due to its insidious onset, early onset, and atypical symptoms. Here, we present four cases of early-onset SLE. Next-generation sequencing were performed and detected mutations were confirmed by Sanger sequencing in all four cases. In addition, glucocorticoid, propyl, cyclophosphamide, and other drugs were significantly improved after treatment. Conclusion: To our knowledge, this is the first case study in China describing early-onset SLE. With the research progress and knowledge integration of basic disciplines such as genomics, epigenetics and immunology, the pathogenesis of early-onset SLE and other rheumatoid immune diseases will be revealed, which will bring more hope for the diagnosis and treatment of early-onset SLE.

The black rock series in the Qiongzhusi Formation contains important geochemical information about the early Cambrian tectonic and ecological environment of the southwestern Yangtze Block. In this paper, major, trace, and rare earth element data are presented in an attempt to reveal the sediment source during the deposition of the early Cambrian Qiongzhusi Formation and to reconstruct the sedimentary tectonic environment and weathering intensity during that time. The basin primarily received continental clastic material with neutral-acidic igneous rocks from a stable source and with a moderate level of maturity during the depositional period of the Qiongzhusi Formation. Furthermore, the strata were weakly influenced by submarine hydrothermal fluids during diagenesis. The reconstruction of the sedimentary environment and weathering intensity shows that P2O5 enrichment and water body stratification occurred due to the effects of upwelling ocean currents during the depositional period of the Qiongzhusi Formation. The combination of upwelling and bottom-water hydrothermal fluids led to environmental changes in the study area, from dry and hot to moist and warm. Last, the reconstruction of the tectonic environment of the Qiongzhusi Formation indicates that deposition occurred in continental slope and marginal marine environments associated with a continental arc tectonic system. These findings provide an essential basis for the comprehensive reconstruction of the early Cambrian sedimentary environment of the Yangtze Block.

The Paleogene Niubao formation is mainly exposed in the central part of the Lunpola basin in the hinterland of the Tibetan Plateau and has high potential for oil and gas exploration and development. The biomarkers of source rocks are systematically studied by selecting representative samples. The middle and upper Niubao formation contain rhythmically inter-bedded mudstone and sandstone that show periodic variations characteristic of the lake water environment. Additionally, the large volumes of muddy dolomite in the upper Niubao formation (UNF) are associated with high salinity in the lake environment under a hot and arid climate. The organic geochemical analysis shows that the middle Niubao formation (MNF) and UNF have high organic abundance (total organic carbon (TOC) contents of 1.48–8.96% in the MNF and 1.52–12.83% in the UNF) and type I–II kerogen. The analysis shows that the UNF was deposited in a persistent, anoxic, stratified and highly saline paleo-lake environment, which was beneficial to the preservation of organic matter. The high phytoalkane and γ-paraffin contents in the UNF indicate a strongly reducing and highly saline lacustrine depositional environment. The high pregnane contents and ascending sterane in the source rocks in the MNF indicate high maturity, and the distribution of n-alkanes and regular sterane indicates the input of some terrestrial organic matter. The high maturity indicates that the source rock in the MNF may represent the main hydrocarbon-generating layer in the basin.

In this study, we aimed to explore the expression of the Aicardi-Goutières syndrome (AGS) mutant gene SAMHD1 in paediatric-onset systemic lupus erythematosus (pSLE), its correlations with clinical and laboratory parameters, and the relationship between its expression and the type 1 interferon (IFN) signalling pathway.Peripheral blood from 98 pSLE patients and 44 gender and age-matched healthy individuals were examined. Gene expression levels of SAMDH1 and interferon-stimulated genes (ISGs; MxA, IRF3 and IRF7) were evaluated using real-time RT-PCR assays.SAMHD1 levels in pSLE patients were significantly increased compared to those in healthy donors (p0.001). SAMHD1 was associated with serum ferritin (r=0.221, p=0.042) in pSLE patients. SAMHD1 levels were significantly increased (p0.05) in pSLE patients with butterfly erythema, alopecia, and photosensitivity. SAMHD1 was positively correlated with MxA, IRF3 and IRF7 levels, indicating that SAMHD1 was associated with the type 1 IFN signalling pathway.SAMHD1 was significantly increased and correlated with MxA, IRF3 and IRF7 in pSLE patients.

Childhood-onset systemic lupus erythematosus (cSLE) is a multisystem autoimmune disease characterised and presents partially differently from adults. A large cSLE cohort study is lacking in China. The present study aimed to determine the clinical characteristics in a large population of patients with cSLE, and compare with adult-onset SLE (aSLE) in an SLE cohort of China.The retrospective study included patients with cSLE diagnosed at the Beijing Children's hospital between July 2006 and October 2020. All patients met at least 4 of ACR classification criteria for SLE. In addition, data including demographic, clinical and serologic data were collected. Our data were compared with other cSLE cohorts and Chinese aSLE cohorts.A total of 1020 patients were included in this study, comprising 808 female and 212 male patients (female to male ratio, 3.8:1). The mean age at diagnosis of lupus was 11.1 years (range 1.0-17.2). It took on average 6 months (range 0.1-132) from first symptoms to cSLE diagnosis and over 12 months in 12% of patients. The most common primary manifestations at onset were rash (37.2%), fever (33.4%), nephropathy (14.2%) and arthritis (13.6%). The most common clinical manifestations were rash (67.9%) and fever (57.5%). 59.4% of patients had haematological involvement, 46.0% had lupus nephritis, 33.2% had arthritis. cSLE was more active and associated with more inflammation than aSLE patients.This study is a large single-centre study on cSLE from China and clarifies the clinical phenotype and autoantibody spectrum of cSLE. The clinical manifestations and autoantibody spectrum of cSLE are diverse, with regional and populational differences.

The Duolong mineral district in western Tibet is one of the largest porphyry Cu–Au deposit fields with significant metallogenic potential in China. Its tectonic environment relevant to Early Cretaceous Cu–Au mineralization remains controversial. Here we report new whole-rock major and trace element, and Sr-Nd-Hf-Pb isotopic data for the newly discovered basalt in the Nadun area, Duolong mineral district, to decipher their genesis and further constrain the tectonic environment. A contemporaneous rhyolite sample interbedded with the basalt in the lower part of the volcanic section in the Nadun area yields an LA-ICP-MS zircon U–Pb age of 122.5 ± 1.2 Ma. The basalt samples exhibit high-K calc-alkaline/shoshonite properties and are enriched in high field strength elements, e.g., high TiO2 (1.43–1.79 wt.%) and Nb (14.6–19.5 ppm) contents, with high Nb/La ratios (0.4–0.6), which are compositionally comparable to those of Nb-enriched arc basalts (NEABs). The (87Sr/86Sr)i ratios of 0.7052 to 0.7056, negative eNd(t) (− 0.7 to − 0.2) and eHf(t) values (+ 6.0 to + 6.5), and high (206Pb/204Pb)i, (207Pb/204Pb)i, (208Pb/204Pb)i and ratios (18.522 to 18.561, 15.641 to 15.645 and 38.679 to 38.730, respectively) suggest that the Nadun NEABs are more enriched than those of the island arc basalts (IABs) in the area. The slightly enriched radiogenic isotopes for the Nadun NEABs indicate that the subducting sediments play an important role in the source. Furthermore, their high Nb, Ti, and Cu contents indicate that the source mantle wedge was metasomatized by slab melts. The Nadun NEAB and other coeval magmatic rocks in the Duolong mineral district, including adakite, OIB-like basalt, MORB-type basalt, A-type rhyolite, and common IAB, are typical rock assemblages of ridge subduction. We infer that the Duolong mineral district were formed by ridge subduction in the Early Cretaceous.

The westward subduction of the Pacific plate interacted with the northward subduction of the eastern Neo-Tethys plate in the Early Cretaceous. However, the subduction polarities between these two plates in the Early Cretaceous is not well constrained. The proto-Philippine arc is suggested to have originated at the Pacific – Neo-Tethys intersection in the SW Pacific in the latest Jurassic – Early Cretaceous, and can provide information about the ancient interaction between these two plates. In this study, the oldest known Early Cretaceous mantle-derived arc volcanic rocks and slab-melting generated adakites occurring in the Philippine arc have been studied for Pb, Sr, Nd and Hf isotopes to discriminate the provenance of their mantle sources and/or subduction components. The 126–118 Ma Kansi island arc volcanics have Pacific-type Pb isotopes, suggesting that the subduction components in the source are mainly from the subducted Pacific plate. Their Hf-Nd isotopes give support to a mantle source that is isotopically transitional Pacific-Indian type. The formation of the Kansi volcanics dates the subduction of the Pacific plate under the transitional Pacific-Indian mantle as Early Cretaceous. The subsequent generation of the 110 Ma Kansi adakitic diorites with the similar Pacific-type Pb isotopes indicates further partial melting of the subducted Pacific plate. In contrast, the post-110 Ma Lutopan adakitic diorites have Indian-type Pb isotopes, indicating the subsequent subduction of an Indian-type oceanic slab in the eastern Neo-Tethys tectonic regime. Therefore, the proto-Philippine arc is constrained to have originated at the intersection between Indian-type and Pacific-type oceanic crusts and mantle domains. The successive generation of these Early Cretaceous arc rocks in the Philippines indicates that a transformation of the tectonic regime from southwestward Pacific subduction to northeastward subduction of the eastern Neo-Tethys plate in the SW Pacific Ocean occurred at ca. 110 Ma, due to the abrupt change in drifting direction of the Pacific plate.