Identification of Genes and Pathways Differentially Expressed in Progestin Responsive Endometrial Cancer and Hyperplasia

Abstract One of the oldest and most common therapies for endometrial complex atypical hyperplasia (CAH) and low-stage, low-grade endometrioid endometrial carcinoma (EEC) is the use of progestins. Importantly, the use of progestins remains the only fertility-sparing treatment available. Despite frequent initial response to progestins, relapse rates are high (35-50%). Currently, there are no biomarkers available for predicting a woman’s likelihood of successful progestin therapy. Primary samples (n = 63) were obtained from a total of 31 patients with either CAH or EEC who underwent progestin therapy and were acquired pre- and post-treatment with progestins. Pathological review of the FFPE samples was performed to identify regions of high hyperplastic or neoplastic content for core punches and RNA extraction. RNA-seq was then performed on the FFPE RNA using the TruSeq RNA Exome approach, a method that uses targeted capture to improve sequencing from fragmented samples. Differential expression analysis was performed using two methods: DESeq2 a parametric method and Noiseq a non-parametric method. Both methods were used to obtain an overlapping subset of genes to reduce spurious results due to samples with outlier expression. Analysis of all samples identified 137 genes significantly associated with outcome. These 137 genes were largely increased in post-treatment samples from progestin responders and were highly enriched for progestogen and estrogen responsive genes, indicating a strong hormonal gene expression response to progestin therapy. Importantly, post-treatment samples from non-responding patients did not show this expression pattern, demonstrating that this set of genes may indicate successful hormone response in post-treatment samples. We also identified a 61 gene signature that remains high in non-responders after treatment compared to responders. Overall, we find that responders show a coordinated change in expression during progestin therapy that is missing from non-responders and this signature could be used in the early evaluation of progestin treatment success. Focusing solely on pre-treatment samples, we identified more variable expression differences across tumors, suggesting multiple reasons for progestin success/failure. We found that the combined expression of estrogen receptor alpha and progesterone receptor was predictive of progestin therapy success. In addition, non-responding tumors had increased expression of several immune-related genes that we are currently exploring. Overall, these results show that progestin therapy response could be predicted using gene expression signatures and that multiple factors may underlie progestin success/failure.

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Impact of therapy on gene expression in high-risk prostate cancer (PCA) treated with neoadjuvant docetaxel and androgen deprivation therapy.

Journal of Clinical Oncology ◽

10.1200/jco.2016.34.2_suppl.8 ◽

2016 ◽

Vol 34 (2_suppl) ◽

pp. 8-8

Author(s):

Himisha Beltran ◽

Alexander Wyatt ◽

Edmund Chedgy ◽

Ladan Fazli ◽

Andrea Sboner ◽

...

Keyword(s):

Gene Expression ◽

High Risk ◽

Hormone Receptors ◽

Dna Analysis ◽

Rna Extraction ◽

Post Treatment ◽

Rna Seq ◽

Sequencing Data ◽

Quantitative Expression ◽

High Risk Prostate Cancer

8 Background: Molecular analyses of neoadjuvant post-treatment radical prostatectomy (RP) specimens has been challenging as often times only microscopic foci remain present at time of RP precluding RNA-seq. DNA analysis alone in the absence of expression may be suboptimal in elucidating complex mechanisms of resistance and/or prognostic risk stratification. We therefore set out to develop an assay that could quantify mRNA expression in treated and untreated PCA using formalin fixed paraffin embedded (FFPE) tissues. Methods: We evaluated 40 untreated and post-treatment FFPE specimens as well as patient-matched pre-treated needle biopsies and baseline clinical data from patients enrolled on CALGB 90203: a randomized phase 3 trial comparing noeadjuvant docetaxel and ADT followed by RP vs RP alone for men with high risk localized PCA. High-density tumor areas were selected for RNA extraction (min 50ng RNA). We used NanoString nCounter to quantify gene expression of a custom panel of 75 genes including AR and androgen regulated, neural/neuroendocrine (NE), EMT, cell cycle, hormone receptors, TMPRSS-ERG, ARv7 splice variant, and housekeeper genes. mRNA data was integrated with matched whole exome sequencing data. Frozen specimens and RNA-Seq (n = 7) were used for QC and comparative analysis. Results: Quantitative expression using Nanostring showed high correlation with RNA-seq of patient-matched frozen tissue (Spearman coefficient 0.9). There was significant upregulation of AR and the ARv7 expression following treatment, as well as a subset of NE and EMT genes; three high chromogranin A outlier cases were identified in the treatment arm. There was an overall higher AR score in treated cases (based on expression of 30 AR signaling genes) compared to untreated, along the spectrum of CRPC. Conclusions: These data support the feasibility of quantifying gene expression in neoadjuvant-treated PCA cases with limited FFPE tissue requirement. Extensive characterization of AR status and NE/EMT genes identifies molecular outliers that can arise post-treatment and provides new insight into the heterogeneity of treatment response and potential early markers of resistance. Clinical trial information: NCT00430183.

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GAA Trinucleotide Repeat Region Regulates M9/pMGA Gene Expression in Mycoplasma gallisepticum

Infection and Immunity ◽

10.1128/iai.68.2.871-876.2000 ◽

2000 ◽

Vol 68 (2) ◽

pp. 871-876 ◽

Cited By ~ 34

Author(s):

Li Liu ◽

Kevin Dybvig ◽

Victor S. Panangala ◽

Vicky L. van Santen ◽

Christopher T. French

Keyword(s):

Gene Expression ◽

Trinucleotide Repeat ◽

Mycoplasma Gallisepticum ◽

Avian Host ◽

Phase Variable ◽

Repeat Region ◽

Chromosomal Dna ◽

Promoter Regions ◽

Variable Expression ◽

Gaa Repeats

ABSTRACT Mycoplasma gallisepticum, the cause of chronic respiratory infections in the avian host, possesses a family of M9/pMGA genes encoding an adhesin(s) associated with hemagglutination. Nucleotide sequences of M9/pMGA gene family members indicate extensive sequence similarity in the promoter regions of both the transcribed and silent genes. The mechanism that regulates M9/pMGA gene expression is unknown, but studies have revealed an apparent correlation between gene expression and the number of tandem GAA repeat motifs located upstream of the putative promoter. In this study, transposon Tn4001was used as a vector with the Escherichia coli lacZ gene as the reporter system to examine the role of the GAA repeats in M9/pMGA gene expression in M. gallisepticum. A 336-bp M9 gene fragment (containing the GAA repeat region, the promoter, and the translation start codon) was amplified by PCR, ligated with alacZ gene from E. coli, and inserted into the Tn4001-containing plasmid pISM2062. This construct was transformed into M. gallisepticum PG31. Transformants were filter cloned on agar supplemented with 5-bromo-4-chloro-3-indolyl-β-d-galactopyranoside (X-Gal) to monitor lacZ gene expression on the basis of blue/white color selection. Several cycles of filter cloning resulted in cell lineages in which lacZ gene expression alternated between the On and Off states in successive generations of progeny clones. The promoter regions of the M9-lacZ hybrid genes of individual progeny clones were amplified by PCR and sequenced. The only differences between the promoter regions of the blue and white colonies were in the number of GAA repeats. Clones that expressedlacZ had exactly 12 tandem copies of the GAA repeat. Clones that did not express lacZ invariably had either more than 12 (14 to 16) or fewer than 12 (5 to 11) GAA repeats. Southern analysis of M. gallisepticum chromosomal DNA confirmed that the phase-variable expression of the lacZ reporter gene was not caused by Tn4001 transposition. These data strongly indicate that changes in the length of the GAA repeat region are responsible for regulating M9/pMGA gene expression.

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A Single-Center Trial to Evaluate the Efficacy and Tolerability of Four Microneedling Treatments on Fine Lines and Wrinkles of Facial and Neck Skin in Subjects With Fitzpatrick Skin Types I-IV: An Objective Assessment Using Non-Invasive Devices and 0.33mm Microbiopsies

Aesthetic Surgery Journal ◽

10.1093/asj/sjab052 ◽

2021 ◽

Author(s):

Christine E Wamsley ◽

Mikaela Kislevitz ◽

Jennifer Barillas ◽

Deniz Basci ◽

Vishal Kandagatla ◽

...

Keyword(s):

Gene Expression ◽

Objective Assessment ◽

Standard Of Care ◽

Transepidermal Water Loss ◽

Post Treatment ◽

Non Invasive ◽

Muscle Formation ◽

The Face ◽

High Resolution Ultrasonography ◽

Elastin Gene

Abstract Background While ablative techniques have been standard of care for the treatment of fine lines and wrinkles, microneedling is a minimally invasive alternative. Objectives The purpose of this study was to assess the efficacy of microneedling on facial and neck fine lines and wrinkles. Methods 35 subjects between 44 and 65 years old with Fitzpatrick skin types I-IV received four monthly microneedling treatments over the face and neck. Subjects returned one and three months post-treatment. At every visit, high-resolution ultrasonography, optical coherence tomography, transepidermal water loss and BTC-2000 were performed. 0.33mm microbiopsies were collected pre-treatment, before the fourth treatment and three months post-treatment. Results 32 subjects (93.75% female, 6.25% male) completed all seven visits. Facial dermal and epidermal density increased 101.86% and 19.28%, respectively from baseline at three months post-treatment. Facial elasticity increased 28.2% from baseline three months post-treatment. Facial attenuation coefficient increased 15.65% and 17.33% one and three months post-treatment. At study completion, blood flow 300µm deep decreased 25.8% in the face and 42.3% in the neck. Relative collagen type III and elastin gene expression was statistically higher three months post-treatment. However, total elastin protein levels unchanged compared to baseline. 58% of biopsies extracted three months post-treatment showed dermal muscle formation, compared to baseline 15.3%. Conclusions The results illustrate the effects of microneedling treatments. Non-invasive measurements and biopsy data showed changes in skin architecture and collagen/elastin gene expression suggesting skin rejuvenation, with new extracellular matrix production and muscle formation.

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DIPG-40. TARGETING MASTER REGULATOR DEPENDENCIES IN DIFFUSE INTRINSIC PONTINE GLIOMA (DIPG)

Neuro-Oncology ◽

10.1093/neuonc/noaa222.087 ◽

2020 ◽

Vol 22 (Supplement_3) ◽

pp. iii294-iii295

Author(s):

Jovana Pavisic ◽

Chankrit Sethi ◽

Chris Jones ◽

Stergios Zacharoulis ◽

Andrea Califano

Keyword(s):

Gene Expression ◽

Expression Profiles ◽

Treatment Options ◽

Diffuse Intrinsic Pontine Glioma ◽

Low Grade ◽

Precision Oncology ◽

Pontine Glioma ◽

Convection Enhanced Delivery ◽

Master Regulator

Abstract Diffuse intrinsic pontine glioma (DIPG) remains a fatal disease with no effective drugs to date. Mutation-based precision oncology approaches are limited by lack of targetable mutations and genetic heterogeneity. We leveraged systems biology methodologies to discover common targetable disease drivers—master regulator proteins (MRs)—in DIPG to expand treatment options. Using the metaVIPER algorithm, we interrogated an integrated low grade glioma and GBM gene regulatory network with 31 DIPG-gene expression signatures to identify tumor-specific MRs by differential expression of their transcriptional targets. Unsupervised clustering identified MR signatures of upregulated activity in RRM2/TOP2A in 13 patients, CD3D in 5 patients, and MMP7, TACSTD2, RAC2 and SLC15A1/SLC34A2 in individual patients, all of which can be targeted. Notably, intratumoral administration of etoposide by convection enhanced delivery was effective in murine proneural gliomas in which TOP2 was identified as a MR while RRM2—targetable by drugs such as cladribine—has been shown to be a positive regulator of glioma progression whose knock-down inhibits tumor growth. We also prioritized drugs by their ability to reverse MR-activity signatures using a large drug-perturbation database. Patients clustered by predicted drug sensitivities with distinct groups of tumors predicted to respond to proteasome inhibitors, Thiotepa or Volasertib all of which have early evidence in treating gliomas. We will refine this analysis in a multi-institutional study of >100 patient gene expression profiles to define MR signatures driving known biological/molecular disease subtypes, use DIPG cell lines recapitulating common MR architectures to optimize therapy prioritization, and validate our findings in vivo.

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Gene Expression Profile and Co-Expression Network of Pearl Gentian Grouper under Cold Stress by Integrating Illumina and PacBio Sequences

Animals ◽

10.3390/ani11061745 ◽

2021 ◽

Vol 11 (6) ◽

pp. 1745

Author(s):

Ben-Ben Miao ◽

Su-Fang Niu ◽

Ren-Xie Wu ◽

Zhen-Bang Liang ◽

Bao-Gui Tang ◽

...

Keyword(s):

Gene Expression ◽

Cold Stress ◽

Differential Expression Analysis ◽

Endocrine System ◽

Control Group ◽

Regulation Mechanism ◽

Rna Seq ◽

Cold Tolerant ◽

Stress Signals ◽

Membrane Changes

Pearl gentian grouper (Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂) is a fish of high commercial value in the aquaculture industry in Asia. However, this hybrid fish is not cold-tolerant, and its molecular regulation mechanism underlying cold stress remains largely elusive. This study thus investigated the liver transcriptomic responses of pearl gentian grouper by comparing the gene expression of cold stress groups (20, 15, 12, and 12 °C for 6 h) with that of control group (25 °C) using PacBio SMRT-Seq and Illumina RNA-Seq technologies. In SMRT-Seq analysis, a total of 11,033 full-length transcripts were generated and used as reference sequences for further RNA-Seq analysis. In RNA-Seq analysis, 3271 differentially expressed genes (DEGs), two low-temperature specific modules (tan and blue modules), and two significantly expressed gene sets (profiles 0 and 19) were screened by differential expression analysis, weighted gene co-expression networks analysis (WGCNA), and short time-series expression miner (STEM), respectively. The intersection of the above analyses further revealed some key genes, such as PCK, ALDOB, FBP, G6pC, CPT1A, PPARα, SOCS3, PPP1CC, CYP2J, HMGCR, CDKN1B, and GADD45Bc. These genes were significantly enriched in carbohydrate metabolism, lipid metabolism, signal transduction, and endocrine system pathways. All these pathways were linked to biological functions relevant to cold adaptation, such as energy metabolism, stress-induced cell membrane changes, and transduction of stress signals. Taken together, our study explores an overall and complex regulation network of the functional genes in the liver of pearl gentian grouper, which could benefit the species in preventing damage caused by cold stress.

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389 Combining transcriptomic- and tissue-based immune biomarkers to evaluate GB1275, a CD11b modulator, as a single agent or with pembrolizumab in patients with advanced solid tumors

Journal for ImmunoTherapy of Cancer ◽

10.1136/jitc-2020-sitc2020.0389 ◽

2020 ◽

Vol 8 (Suppl 3) ◽

pp. A414-A414

Author(s):

Wells Messersmith ◽

Drew Rasco ◽

Johann De Bono ◽

Andrea Wang-Gillam ◽

Wungki Park ◽

...

Keyword(s):

Gene Expression ◽

Solid Tumors ◽

Peripheral Blood ◽

Post Treatment ◽

Transcriptomic Analysis ◽

Gene Set Enrichment Analysis ◽

Cancer Center ◽

Advanced Solid Tumors ◽

Core Tissue ◽

Dose Dependent

BackgroundGB1275 is a first-in-class CD11b modulator in development as monotherapy and in combination with pembrolizumab or chemotherapy for the treatment of advanced solid tumors. Nonclinical data show that GB1275 reduced influx of tumor-associated myeloid-derived suppressor cells (MDSCs) and macrophages (TAMs), and repolarized M2 immuno-suppressive TAMs towards an M1 phenotype. We hypothesize that GB1275 administration can alleviate myeloid cell-mediated immunosuppressive effects and improve cancer treatment outcomes. A phase 1 trial evaluating GB1275 as monotherapy and in combination with pembrolizumab in specified advanced tumors in ongoing (NCT04060342).MethodsBlood gene expression variations as well as core tissue biopsies pre- and post-treatment were assessed following GB1275 monotherapy and combination with pembrolizumab. After obtaining informed consent, peripheral blood for MDSCs was collected from 21 patients pre- and two weeks post-treatment; core tissue biopsies were collected from 13 patients pre- and post-treatment. The frequency of MDSCs in whole blood was measured using the Serametrix MDSC FACS Assay. Gene expression transcriptome profiles were generated using NovaSeq platform. CD8 staining was performed at Neogenomics, and tumor infiltrating lymphocyte (TIL) quantification was performed by an independent pathologist.ResultsPreliminary statistical analysis of MDSC immunophenotyping pre- and post- treatment is consistent with the proposed mechanism of GB1275, showing modulation of peripheral blood MDSCs in some patients. Preliminary gene expression analysis in the blood showed dose-dependent clusters following treatment with GB1275 alone. Moreover, the transcriptomic analysis revealed two unique expression patterns for patients treated with GB1275 monotherapy or in combination with pembrolizumab. Gene Set Enrichment Analysis showed that the CD11b pathway is downregulated in patients treated with GB1275. Analyses of TIL count revealed an increase in lymphocyte trafficking into the tumor after treatment with GB1275 alone or in combination with pembrolizumab. CD8 expression and transcriptomic analysis are underway and will be presented.ConclusionsGB1275 alone or in combination with pembrolizumab demonstrates biological activity, which may be dose dependent. The observed increase in TILs after treatment is supportive of the mechanism of action of GB1275. Further biomarker analyses in blood and tissues are ongoing and will be correlated with clinical activity in a larger number of patients.Ethics ApprovalThis ongoing study is being conducted in accordance with the the Declaration of Helsinki and Council for International Organizations of Medical Sciences (CIOMS) International Ethical Guidelines. The study was approved by the Ethics Boards of University of Colorado Hospital, Washington University School of Medicine - Siteman Cancer Center, Memorial Sloan Kettering Cancer Center, The Sarah Cannon Research Institute/Tennessee Oncology, South Texas Accelerated Research Therapeutics, and The Royal Marsden NHS Foundation Trust.

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Impact of aging on gene expression response to x-ray irradiation using mouse blood

Scientific Reports ◽

10.1038/s41598-021-89682-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Constantinos G. Broustas ◽

Axel J. Duval ◽

Sally A. Amundson

Keyword(s):

Gene Expression ◽

Differentially Expressed Genes ◽

Differentially Expressed ◽

X Rays ◽

Gene Expression Response ◽

X Ray ◽

The Impact ◽

Old Mice ◽

Radiation Biodosimetry ◽

Young Mice

AbstractAs a radiation biodosimetry tool, gene expression profiling is being developed using mouse and human peripheral blood models. The impact of dose, dose-rate, and radiation quality has been studied with the goal of predicting radiological tissue injury. In this study, we determined the impact of aging on the gene expression profile of blood from mice exposed to radiation. Young (2 mo) and old (21 mo) male mice were irradiated with 4 Gy x-rays, total RNA was isolated from whole blood 24 h later, and subjected to whole genome microarray analysis. Pathway analysis of differentially expressed genes revealed young mice responded to x-ray exposure by significantly upregulating pathways involved in apoptosis and phagocytosis, a process that eliminates apoptotic cells and preserves tissue homeostasis. In contrast, the functional annotation of senescence was overrepresented among differentially expressed genes from irradiated old mice without enrichment of phagocytosis pathways. Pathways associated with hematologic malignancies were enriched in irradiated old mice compared with irradiated young mice. The fibroblast growth factor signaling pathway was underrepresented in older mice under basal conditions. Similarly, brain-related functions were underrepresented in unirradiated old mice. Thus, age-dependent gene expression differences should be considered when developing gene signatures for use in radiation biodosimetry.

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Pancreatic Cancers with High Grade Tumor Budding Exhibit Hallmarks of Diminished Anti-Tumor Immunity

Cancers ◽

10.3390/cancers13051090 ◽

2021 ◽

Vol 13 (5) ◽

pp. 1090

Author(s):

Hassan Sadozai ◽

Animesh Acharjee ◽

Thomas Gruber ◽

Beat Gloor ◽

Eva Karamitopoulou

Keyword(s):

Gene Expression ◽

Pancreatic Cancer ◽

Disease Progression ◽

Immune Escape ◽

Epithelial Mesenchymal Transition ◽

Tumor Budding ◽

Ductal Adenocarcinoma ◽

Low Grade ◽

High Grade ◽

Mesenchymal Transition

Tumor budding is associated with epithelial-mesenchymal transition and diminished survival in a number of cancer types including pancreatic ductal adenocarcinoma (PDAC). In this study, we dissect the immune landscapes of patients with high grade versus low grade tumor budding to determine the features associated with immune escape and disease progression in pancreatic cancer. We performed immunohistochemistry-based quantification of tumor-infiltrating leukocytes and tumor bud assessment in a cohort of n = 111 PDAC patients in a tissue microarray (TMA) format. Patients were divided based on the ITBCC categories of tumor budding as Low Grade (LG: categories 1 and 2) and High Grade (HG: category 3). Tumor budding numbers and tumor budding grade demonstrated a significant association with diminished overall survival (OS). HG cases exhibit notably reduced densities of stromal (S) and intratumoral (IT) T cells. HG cases also display lower M1 macrophages (S) and increased M2 macrophages (IT). These findings were validated using gene expression data from TCGA. A published tumor budding gene signature demonstrated a significant association with diminished survival in PDAC patients in TCGA. Immune-related gene expression revealed an immunosuppressive TME in PDAC cases with high expression of the budding signature. Our findings highlight a number of immune features that permit an improved understanding of disease progression and EMT in pancreatic cancer.

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The role of epigenetic modifications, long-range contacts, enhancers and topologically associating domains in the regulation of glioma grade-specific genes

Scientific Reports ◽

10.1038/s41598-021-95009-3 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Ilona E. Grabowicz ◽

Bartek Wilczyński ◽

Bożena Kamińska ◽

Adria-Jaume Roura ◽

Bartosz Wojtaś ◽

...

Keyword(s):

Gene Expression ◽

Long Range ◽

Genetic Alterations ◽

Chromatin Organization ◽

Open Chromatin ◽

Low Grade ◽

Strong Impact ◽

Cell Matrix ◽

Topologically Associating Domains ◽

Genome Wide

AbstractGenome-wide studies have uncovered specific genetic alterations, transcriptomic patterns and epigenetic profiles associated with different glioma types. We have recently created a unique atlas encompassing genome-wide profiles of open chromatin, histone H3K27ac and H3Kme3 modifications, DNA methylation and transcriptomes of 33 glioma samples of different grades. Here, we intersected genome-wide atlas data with topologically associating domains (TADs) and demonstrated that the chromatin organization and epigenetic landscape of enhancers have a strong impact on genes differentially expressed in WHO low grade versus high grade gliomas. We identified TADs enriched in glioma grade-specific genes and/or epigenetic marks. We found the set of transcription factors, including REST, E2F1 and NFKB1, that are most likely to regulate gene expression in multiple TADs, containing specific glioma-related genes. Moreover, many genes associated with the cell–matrix adhesion Gene Ontology group, in particular 14 PROTOCADHERINs, were found to be regulated by long-range contacts with enhancers. Presented results demonstrate the existence of epigenetic differences associated with chromatin organization driving differential gene expression in gliomas of different malignancy.

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Fertility preservation in women with early ovarian cancer

Hormone Molecular Biology and Clinical Investigation ◽

10.1515/hmbci-2020-0026 ◽

2020 ◽

Vol 0 (0) ◽

Author(s):

Daniel Necula ◽

Daria Istrate ◽

Jérôme Mathis

Keyword(s):

Ovarian Cancer ◽

Fertility Preservation ◽

Low Grade ◽

Term Survival ◽

Organizational Issues ◽

Fertility Sparing Surgery ◽

Fertility Sparing ◽

Early Ovarian Cancer ◽

Reproductive Techniques

AbstractFertility preservation is an important option to consider for young women with low-grade early ovarian cancer. Fertility-sparing surgery (“FSS”) permits the conservation of the uterus and one of the ovaries. This technique is considered safe for stages IA G1, G2 and probably safe for IC G1 epithelial and non-epithelial ovarian cancers. There are still uncertainties and FSS is not fully accepted for stage IC G1, G2 and clear cell carcinoma. The difficulty in choosing the best option lies in the fact that there is a lack of prospective randomized studies, due to ethical and organizational issues. Retrospective studies and reviews showed reassuring results for FSS in terms of relapse and long term survival. The spontaneous pregnancy rate seems to decrease after FSS, but chemotherapy does not seem to have an impact on fertility rates. Compared with the general population, assisted reproductive techniques are considered safe and with similar fertility results.

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