Angioimmunoblastic T-cell lymphoma contains multiple clonal T-cell populations derived from a common TET2 mutant progenitor cell

Angioimmunoblastic T-cell lymphoma (AITL) is a neoplastic proliferation of T follicular helper cells with clinical and histological presentations suggesting a role of antigenic drive in its development. Genetically, it is characterized by a step-wise acquisition of somatic mutations, with early mutations involving epigenetic regulators (TET2, DNMT3A) and occurring in haematopoietic stem cells, while subsequent changes involving signaling molecules (RHOA, VAV1, PLCG1, CD28) critical for T-cell biology. To search for evidence of potential oncogenic cooperation between genetic changes and intrinsic TCR signaling, we investigated somatic mutations and T-cell receptor β (TRB) rearrangement in 119 AITL, 11 peripheral T-cell lymphomas with T follicular helper phenotype (PTCL-TFH) and 25 PTCL-NOS by Fluidigm PCR and Illumina MiSeq sequencing. We confirmed frequent TET2, DNMT3A and RHOA mutations in AITL (72%, 34%, 61%) and PTCL-TFH (73%, 36%, 45%) and showed multiple TET2 mutations (2-3) in 57% of the involved AITL and PTCL-TFH. Clonal TRB rearrangement was seen in 73 cases with multiple functional rearrangements (2-4) in 18 cases (24%). On selected cases, we confirmed bi-clonal T-cell populations and further demonstrated that these independent T-cell populations harbored identical TET2 mutations by BaseScope in situ hybridization, suggesting their derivation from a common TET2 mutant progenitor cell population. Furthermore, both T-cell populations express CD4. Finally, in comparison with tonsillar TFH cells, both AITL and PTCL-TFH showed a significant over-representation of several TRB variable family members, particularly TRBV19*01. Our findings suggest the presence of parallel neoplastic evolutions from a common TET2 mutant haematopoietic progenitor pool in AITL and PTCL-TFH albeit to be confirmed in a large series of cases. The biased TRBV usage in these lymphomas suggests that antigenic stimulation may play an important role in predilection of T-cells to clonal expansion and malignant transformation.Bloodwise (13006, 15019) UK, Kay Kendal Leukemia Fund (KKL582) UK, and Pathological Society of Great Britain and Ireland, UK

Diffuse large B-cell lymphoma: sub-classification by massive parallel quantitative RT-PCR.

Diffuse large B-cell lymphoma (DLBCL) is a heterogeneous entity with remarkably variable clinical outcome. Gene expression profiling (GEP) classifies DLBCL into activated B-cell like (ABC), germinal center B-cell like (GCB), and Type-III subtypes, with ABC-DLBCL characterized by a poor prognosis and constitutive NF-κB activation. A major challenge for the application of this cell of origin (COO) classification in routine clinical practice is to establish a robust clinical assay amenable to routine formalin-fixed paraffin-embedded (FFPE) diagnostic biopsies. In this study, we investigated the possibility of COO-classification using FFPE tissue RNA samples by massive parallel quantitative reverse transcription PCR (qRT-PCR). We established a protocol for parallel qRT-PCR using FFPE RNA samples with the Fluidigm BioMark HD system, and quantified the expression of the COO classifier genes and the NF-κB targeted-genes that characterize ABC-DLBCL in 143 cases of DLBCL. We also trained and validated a series of basic machine-learning classifiers and their derived meta classifiers, and identified SimpleLogistic as the top classifier that gave excellent performance across various GEP data sets derived from fresh-frozen or FFPE tissues by different microarray platforms. Finally, we applied SimpleLogistic to our data set generated by qRT-PCR, and the ABC and GCB-DLBCL assigned showed the respective characteristics in their clinical outcome and NF-κB target gene expression. The methodology established in this study provides a robust approach for DLBCL sub-classification using routine FFPE diagnostic biopsies in a routine clinical setting.The research in Du lab was supported by research grants (LLR10006 & LLR13006) from Leukaemia & Lymphoma Research, U.K. XX was supported by a visiting fellowship from the China Scholarship Council, Ministry of Education, P.R. China.This is the accepted manuscript. The final version is available from NPG at http://www.nature.com/labinvest/journal/v95/n1/full/labinvest2014136a.html

Identification of novel prognostic markers in cervical intraepithelial neoplasia using LDMAS (LOH Data Management and Analysis Software).

BACKGROUND: Detection of Loss of Heterozygosity (LOH) is one of the most common molecular applications in the study of human diseases, in particular cancer. The technique is commonly used to examine whether a known tumour suppressor gene is inactivated or to map unknown tumour suppressor gene(s). However, with the increasing number of samples analysed using different software, no tool is currently available to integrate and facilitate the extensive and efficient data retrieval and analyses, such as correlation of LOH data with various clinical data sets. RESULTS: An algorithm to identify prognostic disease markers is devised and implemented as novel software called LDMAS. LDMAS is a software suite designed for data retrieval, management and integrated analysis of the clinico-pathological data and molecular results from independent databases. LDMAS is used in stratification of disease stages according to clinical stage or histological features and correlation of various clinico-pathological features with molecular findings to obtain relevant prognostic markers such as those used in predicting the outcome of cervical intraepithelial neoplasia (CIN). This approach lead to the identification of novel prognostic cervical cancer markers and extraction of useful clinical information such as correlation of Human Papilloma Virus (HPV) status with CIN lesions. CONCLUSIONS: A novel software called LDMAS is implemented and used to extract and identify prognostic disease markers. The software is used to successfully identify 4 novel prognostic markers that can be used to predict the outcome of CIN. LDMAS provides an essential platform for the extraction of useful information from large amount of data generated by LOH studies. LDMAS provides three unique and novel features for LOH analysis: (1) automatic extraction of relevant data from patient records and reports (2) correlation of LOH data with clinico-pathological data and (3) storage of complex data in flexible format. The first feature automates the creation of database of clinically relevant information from huge amount of data, the second feature extracts useful biomedical information such as prognostic markers in CIN and the third feature simplifies the statistical analyses of the data and allows non-statisticians to carry out the analysis. Additionally, LDMAS can be used to extract clinically useful markers from other diseases and interface to high throughput genotyping analysis software such as GDAS used to generate LOH data from Affymetrix GeneChip Mapping arrays.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Screening and analysis of soda saline-alkali stress induced up- regulated genes in sugar sorghum

Soil salinization severely constrains the growth of crops, which ultimately leads to reduced yields. Because Sorghum dochna (common name sugar sorghum) has the advantageous properties of excellent salt stress resis- tance, high biomass, and tremendous flexibility for utilization as food, livestock feed, and industrial products, this species holds great potential to be further developed as a primary alternative crop. To elucidate the molecular mechanism that governs sugar sorghum’s adaptation to high salinity environments, we constructed a suppression subtractive hybridization (SSH) cDNA library from sugar sorghum transcripts that contains the soda saline-alkali induced up-regulated genes from the resistant variety M-81E. The SSH cDNA library was screened by using the colony hybridization method, and the ESTs obtained were sequenced and analyzed. A total of 200 EST clones were identified, representing 127 unigenes (6 contigs and 121 singlets). A Blast analysis showed that 48 ESTs (46.6%) have annotated functions in GenBank, 55 ESTs (53.4%) have unknown functions (or encode hypothetical proteins), and 24 ESTs (18.9%) have no blast hits. The majority of the hypothetical ESTs from the cDNA library displayed very high sequence similarity with their homologs found through GenBank. A clustering analysis of the ESTs with known functions indicated that a wide variety of genes were induced during the salt stress treatment. These genes were found to function in photosynthesis, material and energy metabolism (carbohydrates, lipids, amino acids, co-enzymes, ions, etc.), synthesis or maintenance of constituents of the cell wall and cell membrane, signal transduction, transcriptional regulation, and as water channels. This indicates that sugar sorghum tolerance to soda saline-alkali stress results from the coordinated functions of many genes

Objective assessment of urban built environment related to physical activity — development, reliability and validity of the China Urban Built Environment Scan Tool (CUBEST)

Background: Some aspects of the neighborhood built environment may influence residents’ physical activity, which in turn, affects their health. This study aimed to develop an urban built environment evaluation tool and conduct necessary reliability and validity tests. Methods: A 41-item urban built environment scan tool was developed to objectively assess the neighborhood built environment features related to physical activity. Six neighborhoods in Hangzhou were selected from three types of administrative planning units. A pair of auditors independently assessed all of the 205 street segments at the same time. Half of the segments (n = 104) were audited twice by the same auditor after a two-week time interval. Inter-rater reliability was assessed by comparing the audits of paired observers, while intra-rater reliability was evaluated by comparing an auditor’s repeated assessments of the same segments. The construct validity was tested using factor analysis. Results: The inter-rater reliability for most items was above 0.8. The intra-rater reliability for most items was above 0.4, and was lower than corresponding inter-rater reliability. Six factors were extracted by factor analysis and the factor loading matrix showed good construct validity. Conclusions: The CUBEST is a reliable and valid instrument that can be used to assess the physical activity-related built environment in Hangzhou, and potentially other cities in China

Hydrodynamic modelling of modularized floating photovoltaics arrays

Large arrays of floating photovoltaics (FPV) are emerging to be an attractive solution to renewable energy production and ocean space utilization. FPV arrays are typically buoyed by hundreds of modularized floating bases arranged in ocean surface. The total performance of the FPV arrays is significantly affected by the hydrodynamic interactions between these individual floaters. As the size of the array increases, more time will be required to calculate the entire hydrodynamic properties. From the engineering point of view, it is a challenging task to fully consider the radiation interactions among the modularized FPV floaters. In fact, when the distance between two floating bodies is large enough, their interaction will gradually vanish. The present study developed a cut-off scheme to improve the computational efficiency while providing a reliable prediction of the interaction effects in engineering practice. A cut-off radius is introduced in this scheme to determine the coupling range in which the radiation hydrodynamic interactions should be considered. The cut-off radius is determined by three parameters, including the modular shape, wave frequency and accuracy requirement. Several arrays of rectangular FPV bases were taken as examples to show how to quantify the radiation interactions and find an optimal cut-off radius. The effect of wave direction, gap distance, and connection type were also investigated. The results from the validation case showed that the hydrodynamic interaction can be well predicted using the proposed cut-off scheme, while more than half of the computational time can be saved

Auto-Ubiquitination-Induced Degradation of MALT1-API2 Prevents BCL10 Destabilization in t(11;18)(q21;q21)-Positive MALT Lymphoma

BACKGROUND: The translocation t(11;18)(q21;q21) is the most frequent chromosomal aberration associated with MALT lymphoma and results in constitutive NF-kappaB activity via the expression of an API2-MALT1 fusion protein. The properties of the reciprocal MALT1-API2 were never investigated as it was reported to be rarely transcribed. PRINCIPAL FINDINGS: Our data indicate the presence of MALT1-API2 transcripts in the majority of t(11;18)(q21;q21)-positive MALT lymphomas. Based on the breakpoints in the MALT1 and API2 gene, the MALT1-API2 protein contains the death domain and one or both immunoglobulin-like domains of MALT1 (approximately 90% of cases)--mediating the possible interaction with BCL10--fused to the RING domain of API2. Here we show that this RING domain enables MALT1-API2 to function as an E3 ubiquitin ligase for BCL10, inducing its ubiquitination and proteasomal degradation in vitro. Expression of MALT1-API2 transcripts in t(11;18)(q21;q21)-positive MALT lymphomas was however not associated with a reduction of BCL10 protein levels. CONCLUSION: As we observed MALT1-API2 to be an efficient target of its own E3 ubiquitin ligase activity, our data suggest that this inherent instability of MALT1-API2 prevents its accumulation and renders a potential effect on MALT lymphoma development via destabilization of BCL10 unlikely

Conversion of the LIMA1 tumour suppressor into an oncogenic LMO-like protein by API2-MALT1 in MALT lymphoma.

MALT1 is the only known paracaspase and is a critical mediator of B- and T-cell receptor signalling. The function of the MALT1 gene is subverted by oncogenic chimeric fusions arising from the recurrent t(11;18)(q21;q21) aberration, which is the most frequent translocation in mucosa-associated lymphoid tissue (MALT) lymphoma. API2-MALT1-positive MALT lymphomas manifest antibiotic resistance and aggressive clinical behaviour with poor clinical outcome. However, the mechanisms underlying API2-MALT1-induced MALT lymphomagenesis are not fully understood. Here we show that API2-MALT1 induces paracaspase-mediated cleavage of the tumour suppressor protein LIMA1. LIMA1 binding by API2-MALT1 is API2 dependent and proteolytic cleavage is dependent on MALT1 paracaspase activity. Intriguingly, API2-MALT1-mediated proteolysis generates a LIM domain-only (LMO)-containing fragment with oncogenic properties in vitro and in vivo. Importantly, primary MALT lymphomas harbouring the API2-MALT1 fusion uniquely demonstrate LIMA1 cleavage fragments. Our studies reveal a novel paracaspase-mediated oncogenic gain-of-function mechanism in the pathogenesis of MALT lymphoma.This work was supported in part by NIH grants R01 DE119249 and R01 CA136905 (K.S.J.E-J.), R01 CA140806 (M.S.L.) and the Department of Pathology at the University of Michigan.This is the accepted manuscript. The final version is available from Nature at http://www.nature.com/ncomms/2015/150108/ncomms6908/full/ncomms6908.html

Exchange-biased hybrid gamma-Fe2O3/NiO core-shell nanostructures:three-step synthesis, microstructure, and magnetic properties

A two-step solvothermal method combining a calcination process was conducted to synthesize gamma-Fe2O3/NiO core-shell nanostructures with controlled microstructure. The formation mechanism of this binary system has been discussed, and the influence of microstructures on magnetic properties has been analyzed in detail. Microstructural characterizations reveal that the NiO shells consisted of many irregular nanosheets with disordered orientations and monocrystalline structures, packed on the surface of the gamma-Fe2O3 microspheres. Both the grain size and NiO content of nanostructures increase with the increasing calcination temperature from 300 degrees C to 400 degrees C, accompanied by an enhancement of the compactness of NiO shells. Magnetic studies indicate that their magnetic properties are determined by four factors: the size effect, NiO phase content, interface microstructure, i.e. contact mode, area, roughness and compactness, and FM-AFM (where FM and AFM denote the ferromagnetic gamma-Fe2O3 and the antiferromagnetic NiO components, respectively) coupling effect. At 5 K, the gamma-Fe2O3/NiO core-shell nanostructures display certain exchange bias (H-E = 60 Oe) and enhanced coercivity (H-C = 213 Oe)