bluuebunny/crossref_metadata_2025_split huggingface dataset:
BCL2L1 is associated with γ-globin gene expression
Authors: Dai Yan , Shaikho Elmutaz M. , Perez Jessica , Wilson Carolyn A. , Liu Lesley Y. , White Mitchell R. , Farrell John J. , Chui David H. K. , Sebastiani Paola , Steinberg Martin H. 
Published: October 2019

Key Points
BCL2L1 is associated with HbF gene activation.
Systems biology and big data in asthma and allergy: recent discoveries and emerging challenges
Authors: Tang Howard H.F. , Sly Peter D. , Holt Patrick G. , Holt Kathryn E. , Inouye Michael 
Published: October 2019

Asthma is a common condition caused by immune and respiratory dysfunction, and it is often linked to allergy. A systems perspective may prove helpful in unravelling the complexity of asthma and allergy. Our aim is to give an overview of systems biology approaches used in allergy and asthma research. Specifically, we describe recent “omic”-level findings, and examine how these findings have been systematically integrated to generate further insight.Current research suggests that allergy is driven by genetic and epigenetic factors, in concert with environmental factors such as microbiome and diet, leading to early-life disturbance in immunological development and disruption of balance within key immuno-inflammatory pathways. Variation in inherited susceptibility and exposures causes heterogeneity in manifestations of asthma and other allergic diseases. Machine learning approaches are being used to explore this heterogeneity, and to probe the pathophysiological patterns or “endotypes” that correlate with subphenotypes of asthma and allergy. Mathematical models are being built based on genomic, transcriptomic and proteomic data to predict or discriminate disease phenotypes, and to describe the biomolecular networks behind asthma.The use of systems biology in allergy and asthma research is rapidly growing, and has so far yielded fruitful results. However, the scale and multidisciplinary nature of this research means that it is accompanied by new challenges. Ultimately, it is hoped that systems medicine, with its integration of omics data into clinical practice, can pave the way to more precise, personalised and effective management of asthma.
Peripheral blood leukocyte telomere length is associated with survival of sepsis patients
Authors: Liu Shuo , Wang Chunxue , Green Gary , Zhuo Hanjing , Liu Kathleen D. , Kangelaris Kirsten N. , Gomez Antonio , Jauregui Alejandra , Vessel Kathryn , Ke Serena , Hendrickson Carolyn , Matthay Michael A. , Calfee Carolyn S. , Ware Lorraine B. , Wolters Paul J. 
Published: October 2019

Shorter peripheral blood leukocyte (PBL) telomere length (TL) has been associated with poor outcomes in various chronic lung diseases. Whether PBL-TL is associated with survival from critical illness was tested in this study.We analysed data from a prospective observational cohort study of 937 critically ill patients at Vanderbilt University Medical Center (VUMC). PBL-TL was measured using quantitative PCR of DNA isolated from PBLs. Findings were validated in an independent cohort of 394 critically ill patients with sepsis admitted to the University of California San Francisco (UCSF).In the VUMC cohort, shorter PBL-TL was associated with worse 90-day survival (adjusted hazard ratio (aHR) 1.3, 95% CI 1.1–1.6 per 1 kb TL decrease; p=0.004); in subgroup analyses, shorter PBL-TL was associated with worse 90-day survival for patients with sepsis (aHR 1.5, 95% CI 1.2–2.0 per 1 kb TL decrease; p=0.001), but not trauma. Although not associated with development of acute respiratory distress syndrome (ARDS), among ARDS subjects, shorter PBL-TL was associated with more severe ARDS (OR 1.7, 95% CI 1.2–2.5 per 1 kb TL decrease; p=0.006). The associations of PBL-TL with survival (adjusted HR 1.6, 95% CI 1.2–2.1 per 1 kb TL decrease; p=0.003) and risk for developing severe ARDS (OR 2.5, 95% CI 1.1–6.3 per 1 kb TL decrease; p=0.044) were validated in the UCSF cohort.Short PBL-TL is strongly associated with worse survival and more severe ARDS in critically ill patients, especially patients with sepsis. These findings suggest that telomere dysfunction may contribute to outcomes from critical illness.
Sarcomatoid carcinoma presenting as cancers of unknown primary: a clinicopathological portrait
Authors: Huey Ryan W. , Makawita Shalini , Xiao Lianchun , Matamoros Aurelio , Estrella Jeannelyn S. , Overman Michael J. , Varadhachary Gauri R. , Raghav Kanwal 
Published: October 2019

Abstract

Background
Sarcomatoid carcinoma of unknown primary (SCUP) is a rare entity of either poorly differentiated carcinoma with sarcoma-like differentiation or a true mixed lineage neoplasm. Limited data regarding clinicopathological profile and management exists.

Methods
We retrospectively reviewed the MD Anderson Cancer of Unknown Primary database and tumor registry to identify 48 SCUP patients between 2001 and 2017. Patient characteristics, pathology, molecular diagnostics, treatments, and outcomes were obtained. Kaplan-Meier method was used to estimate overall survival (OS) and compared using log rank test.

Results
Median age at diagnosis was 59 years (range 27–86). Majority of patients were female (58%) and presented with ≥3 metastatic sites (52%), commonly lymph node (50%), bone (42%), lung (27%), and liver (21%). First line treatment included chemotherapy (35%), surgery (27%), and radiation (24%). Gemcitabine and docetaxel (18%) was the most common chemotherapy regimen. Median OS for entire cohort was 11 months (95% CI: 5.6 to 16.4). Poor performance status (PS), > 1 metastatic site, elevated lactate dehydrogenase (LDH), and high neutrophil-to-lymphocyte ratio (NLR) were significantly associated with worse OS on univariate analyses. On multivariate analyses, poor PS (HR 8.7; 95%CI: 3.0–25.0; p <  0.001) and high NLR (HR 3.4; 95%CI: 1.3–8.8; p = 0.011) emerged as independent prognostic factors for OS.

Conclusions
SCUP is a rare presentation with an aggressive clinical course and limited survival. Diagnosis is difficult to make and requires careful review and synthesis of histology, immunohistochemistry, and molecular diagnostics. Chemotherapy resistance remains a challenge. Early mutational profiling is warranted, and clinical trial participation should be encouraged for this subset.
Detection of large rearrangements in a hereditary pan-cancer panel using next-generation sequencing
Authors: Mancini-DiNardo Debora , Judkins Thaddeus , Kidd John , Bernhisel Ryan , Daniels Courtney , Brown Krystal , Meek Kirsten , Craft Jonathan , Holladay Jayson , Morris Brian , Roa Benjamin B. 
Published: October 2019

Abstract

Background
Healthcare providers increasingly use information about pathogenic variants in cancer predisposition genes, including sequence variants and large rearrangements (LRs), in medical management decisions. While sequence variant detection is typically robust, LRs can be difficult to detect and characterize and may be underreported as a cause for hereditary cancer risk. This report describes the outcomes of hereditary cancer genetic testing using a comprehensive strategy that employs next-generation sequencing (NGS) for LR detection, coupled with LR confirmation using repeat hybrid capture NGS, microarray comparative genomic hybridization (microarray-CGH), and/or multiplex ligation-dependent probe amplification (MLPA).

Methods
Sequencing and LR analysis were conducted in a consecutive series of 376,159 individuals who received clinical testing with a hereditary pan-cancer gene panel from September 2013 through May 2017. NGS dosage analysis was used to evaluate potential deletions or duplications, with controls in place to exclude pseudogene reads. Samples positive for a putative LR based on NGS were confirmed using a comprehensive approach that included targeted microarray-CGH and/or MLPA analysis, with further examination as needed to ascertain the nature of the LR.

Results
A total of 3461 LRs were identified and classified as a deleterious mutation (DM), suspected deleterious mutation (SDM) or variant of uncertain significance. Pathogenic LRs (DM/SDM) accounted for the majority of LRs (67.7%), the largest proportion of which were deletions (86.1%), followed by duplications (11.3%), insertions (1.8%), triplications (0.5%), and inversions (0.3%). Several cases presented illustrate that the laboratory approach employed here can ensure consistent identification and accurate characterization of LRs. In the absence of this comprehensive testing strategy, 9% of LRs identified in this testing population might have been missed, potentially leading to inappropriate medical management in as many as 210 individuals referred for hereditary cancer testing.

Conclusions
These data show that copy number analysis using NGS coupled with confirmatory testing reliably detects and characterizes LRs. Further, LRs comprise a substantial proportion (7.2%) of pathogenic variants identified by the test. A robust and accurate LR identification strategy is an essential component of a high-quality genetic testing program, enabling clinicians to optimize patient medical management decisions.
Protein phosphatase 2A (PP2A): a key phosphatase in the progression of chronic obstructive pulmonary disease (COPD) to lung cancer
Authors: Nader Cassandra P. , Cidem Aylin , Verrills Nicole M. , Ammit Alaina J. 
Published: October 2019

AbstractLung cancer (LC) has the highest relative risk of development as a comorbidity of chronic obstructive pulmonary disease (COPD). The molecular mechanisms that mediate chronic inflammation and lung function impairment in COPD have been identified in LC. This suggests the two diseases are more linked than once thought. Emerging data in relation to a key phosphatase, protein phosphatase 2A (PP2A), and its regulatory role in inflammatory and tumour suppression in both disease settings suggests that it may be critical in the progression of COPD to LC. In this review, we uncover the importance of the functional and active PP2A holoenzyme in the context of both diseases. We describe PP2A inactivation via direct and indirect means and explore the actions of two key PP2A endogenous inhibitors, cancerous inhibitor of PP2A (CIP2A) and inhibitor 2 of PP2A (SET), and the role they play in COPD and LC. We explain how dysregulation of PP2A in COPD creates a favourable inflammatory micro-environment and promotes the initiation and progression of tumour pathogenesis. Finally, we highlight PP2A as a druggable target in the treatment of COPD and LC and demonstrate the potential of PP2A re-activation as a strategy to halt COPD disease progression to LC. Although further studies are required to elucidate if PP2A activity in COPD is a causal link for LC progression, studies focused on the potential of PP2A reactivating agents to reduce the risk of LC formation in COPD patients will be pivotal in improving clinical outcomes for both COPD and LC patients in the future.
Induction of LEF1 by MYC activates the WNT pathway and maintains cell proliferation
Authors: Hao Yi-Heng , Lafita-Navarro M. Carmen , Zacharias Lauren , Borenstein-Auerbach Nofit , Kim Min , Barnes Spencer , Kim Jiwoong , Shay Jerry , DeBerardinis Ralph J. , Conacci-Sorrell Maralice 
Published: October 2019

Abstract

Background
While regulated WNT activity is required for normal development and stem cell maintenance, mutations that lead to constitutive activation of the WNT pathway cause cellular transformation and drive colorectal cancer. Activation of the WNT pathway ultimately leads to the nuclear translocation of β-catenin which, in complex with TCF/LEF factors, promotes the transcription of genes necessary for growth. The proto-oncogene MYC is one of the most critical genes activated downstream the WNT pathway in colon cancer. Here, we investigate the converse regulation of the WNT pathway by MYC.

Methods
We performed RNA-seq analyses to identify genes regulated in cells expressing MYC. We validated the regulation of genes in the WNT pathway including LEF1 by MYC using RT-qPCR, Western blotting, and ChIP-seq. We investigated the importance of LEF1 for the viability of MYC-expressing cells in in fibroblasts, epithelial cells, and colon cells. Bioinformatic analyses were utilized to define the expression of MYC-regulated genes in human colon cancer and metabolomics analyses were used to identify pathways regulated by LEF1 in MYC expressing cells.

Results
MYC regulates the levels of numerous WNT-related genes, including the β-catenin co-transcription factor LEF1. MYC activates the transcription of LEF1 and is required for LEF1 expression in colon cancer cells and in primary colonic cells transformed by APC loss of function, a common mutation in colon cancer patients. LEF1 caused the retention of β-catenin in the nucleus, leading to the activation of the WNT pathway in MYC-expressing cells. Consequently, MYC-expressing cells were sensitive to LEF1 inhibition. Moreover, we describe two examples of genes induced in MYC-expressing cells that require LEF1 activity: the peroxisome proliferator activated receptor delta (PPARδ) and the Acyl CoA dehydrogenase 9 (ACAD9).

Conclusions
We demonstrated that MYC is a transcriptional regulator of LEF1 in colonic cells. Our work proposes a novel pathway by which MYC regulates proliferation through activating LEF1 expression which in turn activates the WNT pathway.

Graphical Abstract
Lack of hepatic apoE does not influence early Aβ deposition: observations from a new APOE knock-in model
Authors: Huynh Tien-Phat V. , Wang Chao , Tran Ainsley C. , Tabor G. Travis , Mahan Thomas E. , Francis Caroline M. , Finn Mary Beth , Spellman Rebecca , Manis Melissa , Tanzi Rudolph E. , Ulrich Jason D. , Holtzman David M. 
Published: October 2019

AbstractBackgroundThe apolipoprotein E (APOE) gene is the strongest genetic risk factor for late-onset Alzheimer disease (AD). ApoE is produced by both astrocytes and microglia in the brain, whereas hepatocytes produce the majority of apoE found in the periphery. Studies usingAPOEknock-in and transgenic mice have demonstrated a strong isoform-dependent effect of apoE on the accumulation of amyloid-β (Aβ) deposition in the brain in the form of both Aβ-containing amyloid plaques and cerebral amyloid angiopathy. However, the specific contributions of different apoE pools to AD pathogenesis remain unknown.MethodsWe have begun to address these questions by generating new lines ofAPOEknock-in (APOE-KI) mice (ε2/ε2, ε3/ε3, and ε4/ε4) where the exons in the coding region ofAPOEare flanked by loxP sites, allowing for cell type-specific manipulation of gene expression. We assessed these mice both alone and after crossing them with mice with amyloid deposition in the brain. Using biochemical and histological methods. We also investigated how removal ofAPOEexpression from hepatocytes affected cerebral amyloid deposition.ResultsAs in otherAPOEknock-in mice, apoE protein was present predominantly in astrocytes in the brain under basal conditions and was also detected in reactive microglia surrounding amyloid plaques. Primary cultured astrocytes and microglia from theAPOE-KI mice secreted apoE in lipoprotein particles of distinct size distribution upon native gel analysis with microglial particles being substantially smaller than the HDL-like particles secreted by astrocytes. Crossing of APP/PS1 transgenic mice to the differentAPOE-KI mice recapitulated the previously described isoform-specific effect (ε4 > ε3) on amyloid plaque and Aβ accumulation. Deletion ofAPOEin hepatocytes did not alter brain apoE levels but did lead to a marked decrease in plasma apoE levels and changes in plasma lipid profile. Despite these changes in peripheral apoE and on plasma lipids, cerebral accumulation of amyloid plaques in APP/PS1 mice was not affected.ConclusionsAltogether, these new knock-in strains offer a novel and dynamic tool to study the role ofAPOEin AD pathogenesis in a spatially and temporally controlled manner.
MEIS2C and MEIS2D promote tumor progression via Wnt/β-catenin and hippo/YAP signaling in hepatocellular carcinoma
Authors: Guan Lei , Li Ting , Ai Nanping , Wang Wei , He Bing , Bai Yanxia , Yu Zhaocai , Li Mingyue , Dong Shanshan , Zhu Qingge , Ding Xiao Xiao , Zhang Shiming , li Ming , Tang Guangbo , Xia Xiaochun , Zhao Jing , lin Song , yao Shi , zhang Lei , chen Geng , Liu Fang-E , Li Xinyuan , Zhang Huqin 
Published: October 2019

Abstract

Background
MEIS2 has been identified as one of the key transcription factors in the gene regulatory network in the development and pathogenesis of human cancers. Our study aims to identify the regulatory mechanisms of MEIS2 in hepatocellular carcinoma (HCC), which could be targeted to develop new therapeutic strategies.

Methods
The variation of MEIS2 levels were assayed in a cohort of HCC patients. The proliferation, clone-formation, migration, and invasion abilities of HCC cells were measured to analyze the effects of MEIS2C and MEIS2D (MEIS2C/D) knockdown with small hairpin RNAs in vitro and in vivo. Chromatin immunoprecipitation (ChIP) was performed to identify MEIS2 binding site. Immunoprecipitation and immunofluorescence assays were employed to detect proteins regulated by MEIS2.

Results
The expression of MEIS2C/D was increased in the HCC specimens when compared with the adjacent noncancerous liver (ANL) tissues. Moreover, MEIS2C/D expression negatively correlated with the prognosis of HCC patients. On the other hand, knockdown of MEIS2C/D could inhibit proliferation and diminish migration and invasion of hepatoma cells in vitro and in vivo. Mechanistically, MESI2C activated Wnt/β-catenin pathway in cooperation with Parafibromin (CDC73), while MEIS2D suppressed Hippo pathway by promoting YAP nuclear translocation via miR-1307-3p/LATS1 axis. Notably, CDC73 could directly either interact with MEIS2C/β-catenin or MEIS2D/YAP complex, depending on its tyrosine-phosphorylation status.

Conclusions
Our studies indicate that MEISC/D promote HCC development via Wnt/β-catenin and Hippo/YAP signaling pathways, highlighting the complex molecular network of MEIS2C/D in HCC pathogenesis. These results suggest that MEISC/D may serve as a potential novel therapeutic target for HCC.
Improvement of corn stover fuel properties via hydrothermal carbonization combined with surfactant
Authors: Tu Ren , Sun Yan , Wu Yujian , Fan Xudong , Wang Jiamin , Cheng Shuchao , Jia Zhiwen , Jiang Enchen , Xu Xiwei 
Published: October 2019

Abstract

Background
Biomass fuel has been used to supply heat or crude materials in industry to replace the traditional fossil fuel which was one of the chief causes of climate warming. However, the large-scale utilization of biomass fuel was restricted due to the low density and high hydrophilicity of biomass, which causes the problem of transportation and storage. Therefore, pelletization of biomass was used to improve its fuel density. At present, the biomass pellet was widely used to supply heat, gas or electricity generation via gasification, which supplied clean and sustainable energy for industry. However, the energy consumption during pelletization and high hydrophilicity of pellets were still the problem for the large-scale application of biomass pellet. In this study, hydrothermal carbonization and surfactant played the role of permeation, adsorption and wetting in the solution, which was expected to improve the fuel properties and pelletization effectivity of corn stover.

Results
In the article, surfactant (PEG400, Span80, SDBS) was chosen to be combined with wet torrefaction to overcome the drawbacks and improve the pelletization and combustion properties of Corn stover (CS). Especially, hydrothermal carbonization (HTC) combined with surfactant improves the yield of solid products and reduces the ash content of solid product, which was beneficial for reducing the ashes of furnace during gasification. Meanwhile, surfactant promotes the formation of pseudo-lignin and the absorption for oil with low O and high C during HTC, which improves the energy density of solid product. Furthermore, the oil in solid product plays the role of lubricant and binder, which reduces the negative effect of high energy consumption, low bulk density and weak pellets strength caused by HTC during pelletization. HTC combined with surfactant improved the hydrophobicity of pellet as well as grindability due to the modification of solid product. Moreover, surfactant combined with HTC improved the combustion characteristic of solid product such as ignition and burning temperature as well as kinetic parameters due to the bio-oil absorbed and the improvement of surface and porosity.

Conclusions
The study supplied a new, less-energy intensive and effective method to improve the pelletization and combustion properties of corn stover via hydrothermal carbonization combined with surfactant, and provided a promising alternative fuel from corn stover .
Catalytic valorization of hardwood for enhanced xylose-hydrolysate recovery and cellulose enzymatic efficiency via synergistic effect of Fe3+ and acetic acid
Authors: Huang Kaixuan , Das Lalitendu , Guo Jianming , Xu Yong 
Published: October 2019

Abstract

Background
Poplars are considered suitable dedicated energy crops, with abundant cellulose and hemicellulose, and huge surplus biomass potential in China. Xylan, the major hemicellulosic component, contributes to the structural stability of wood and represents a tremendous quantity of biobased chemicals for fuel production. Monomeric xylose conversion to value-added chemicals such as furfural, xylitol, and xylonic acid could greatly improve the economics of pulp-paper industry and biorefinery. Acetic acid (HAc) is used as a friendly and recyclable selective catalyst amenable to xylan degradation and xylooligosaccharides production from lignocellulosic materials. However, HAc catalyst usually works much feebly at inert woods than agricultural straws. In this study, effects of different iron species in HAc media on poplar xylan degradation were systematically compared, and a preferable Fe3+-assisted HAc hydrolysis process was proposed for comparable xylose-hydrolysate recovery (XHR) and enzymatic saccharification of cellulose.

Results
In presence of 6.5% HAc with 0.17–0.25 wt% Fe3+, xylose yield ranged between 72.5 and 73.9%. Additionally, pretreatment was effective in poplar delignification, with a lignin yield falling between 38.6 and 42.5%. Under similar conditions, saccharification efficiency varied between 60.3 and 65.9%. Starting with 100 g poplar biomass, a total amount of 12.7–12.8 g of xylose and 18.8–22.8 g of glucose were harvested from liquid streams during the whole process of Fe3+-HAc hydrolysis coupled with enzymatic saccharification. Furthermore, the enhancement mechanism of Fe3+ coupled with HAc was investigated after proof-of-concept experiments. Beechwood xylan and xylose were treated under the same condition as poplar sawdust fractionation, giving understanding of the effect of catalysts on the hydrolysis pathway from wood xylan to xylose and furfural by Fe3+-HAc.

Conclusions
The Fe3+-assisted HAc hydrolysis process was demonstrated as an effective approach to the wood xylose and other monosaccharides production. Synergistic effect of Lewis acid site and aqueous acetic acid provided a promising strategy for catalytic valorization of poplar biomass.