Literature Lab: a method of automated literature interrogation to infer biology from microarray analysis

<p>Abstract</p> <p>Background</p> <p>The biomedical literature is a rich source of associative information but too vast for complete manual review. We have developed an automated method of literature interrogation called "Literature Lab" that identifies and ranks associations existing in the literature between gene sets, such as those derived from microarray experiments, and curated sets of key terms (i.e. pathway names, medical subject heading (MeSH) terms, etc).</p> <p>Results</p> <p>Literature Lab was developed using differentially expressed gene sets from three previously published cancer experiments and tested on a fourth, novel gene set. When applied to the genesets from the published data including an <it>in vitro </it>experiment, an <it>in vivo </it>mouse experiment, and an experiment with human tumor samples, Literature Lab correctly identified known biological processes occurring within each experiment. When applied to a novel set of genes differentially expressed between locally invasive and metastatic prostate cancer, Literature Lab identified a strong association between the pathway term "FOSB" and genes with increased expression in metastatic prostate cancer. Immunohistochemistry subsequently confirmed increased nuclear FOSB staining in metastatic compared to locally invasive prostate cancers.</p> <p>Conclusion</p> <p>This work demonstrates that Literature Lab can discover key biological processes by identifying meritorious associations between experimentally derived gene sets and key terms within the biomedical literature.</p

Improvement in Parameters of Hematologic and Immunologic Function and Patient Well-being in the Phase III RESONATE Study of Ibrutinib Versus Ofatumumab in Patients With Previously Treated Chronic Lymphocytic Leukemia/Small Lymphocytic Lymphoma

Background: Ibrutinib compared with ofatumumab significantly improves progression-free and overall survival in patients with previously treated chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL). Patients and Methods: Measures of well-being were assessed in RESONATE, where previously treated patients with CLL/SLL were randomized to receive ibrutinib 420 mg/day (n = 195) or ofatumumab (n = 196) for up to 24 weeks. Endpoints included hematologic function, Functional Assessment of Chronic Illness Therapy–Fatigue (FACIT-F), disease-related symptoms, European Organization for Research and Treatment of Cancer Quality of Life Questionnaires Core 30 (EORTC QLQ-C30), and medical resource utilization. Results: With up to 24 months’ follow-up (median, 16.4 months), 79% of cytopenic patients showed sustained hematologic improvement (82% with improved platelet count, 69% with improved hemoglobin) on ibrutinib versus 43% on ofatumumab (P < .0001). Higher rates of clinically meaningful improvement were demonstrated with ibrutinib versus ofatumumab for FACIT-F and EORTC global health. Greater improvement was observed in disease-related weight loss, fatigue, night sweats, and abdominal discomfort with ibrutinib versus ofatumumab. Hospitalizations in the first 30 days occurred less frequently with ibrutinib than ofatumumab (0.087 vs. 0.184 events/patient; P = .0198). New-onset diarrhea was infrequent with ibrutinib after the first 6 months (47% at ≤6 months vs. 5% at 12-18 months). With ibrutinib, grade ≥ 3 hypertension occurred in 6%, grade ≥ 3 atrial fibrillation in 4%, major hemorrhage in 2%, and tumor lysis syndrome in 1% of patients. Conclusion: Ibrutinib led to significant improvements in hematologic function and disease symptomatology versus ofatumumab, and can restore quality of life while prolonging survival in relapsed/refractory CLL/SLL

Direct photon elliptic flow in Pb-Pb collisions at root s(NN)=2.76 TeV

The elliptic flow of inclusive and direct photons was measured at mid-rapidity in two centrality classes 0-20% and 20-40% in Pb-Pb collisions at root s(NN) = 2.76 TeV by ALICE. Photons were detected with the highly segmented electromagnetic calorimeter PHOS and via conversions in the detector material with the e(broken vertical bar)e pairs reconstructed in the central tracking system. The results of the two methods were combined and the direct-photon elliptic flow was extracted in the transverse momentum range 0.9 < p(T) < 6.2 GeV/c. A comparison to RHIC data shows a similar magnitude of the measured direct-photon elliptic flow. Hydrodynamic and transport model calculations are systematically lower than the data, but are found to be compatible. (C) 2018 The Author. Published by Elsevier B.V.Peer reviewe

Genomic analyses identify hundreds of variants associated with age at menarche and support a role for puberty timing in cancer risk

The timing of puberty is a highly polygenic childhood trait that is epidemiologically associated with various adult diseases. Using 1000 Genomes Project-imputed genotype data in up to similar to 370,000 women, we identify 389 independent signals (P <5 x 10(-8)) for age at menarche, a milestone in female pubertal development. In Icelandic data, these signals explain similar to 7.4% of the population variance in age at menarche, corresponding to similar to 25% of the estimated heritability. We implicate similar to 250 genes via coding variation or associated expression, demonstrating significant enrichment in neural tissues. Rare variants near the imprinted genes MKRN3 and DLK1 were identified, exhibiting large effects when paternally inherited. Mendelian randomization analyses suggest causal inverse associations, independent of body mass index (BMI), between puberty timing and risks for breast and endometrial cancers in women and prostate cancer in men. In aggregate, our findings highlight the complexity of the genetic regulation of puberty timing and support causal links with cancer susceptibility

Genomic analyses identify hundreds of variants associated with age at menarche and support a role for puberty timing in cancer risk

The timing of puberty is a highly polygenic childhood trait that is epidemiologically associated with various adult diseases. Using 1000 Genomes Project–imputed genotype data in up to ~370,000 women, we identify 389 independent signals (P < 5 × 10$^{−8}$) for age at menarche, a milestone in female pubertal development. In Icelandic data, these signals explain ~7.4% of the population variance in age at menarche, corresponding to ~25% of the estimated heritability. We implicate ~250 genes via coding variation or associated expression, demonstrating significant enrichment in neural tissues. Rare variants near the imprinted genes MKRN3 and DLK1 were identified, exhibiting large effects when paternally inherited. Mendelian randomization analyses suggest causal inverse associations, independent of body mass index (BMI), between puberty timing and risks for breast and endometrial cancers in women and prostate cancer in men. In aggregate, our findings highlight the complexity of the genetic regulation of puberty timing and support causal links with cancer susceptibility

Literature Lab: a method of automated literature interrogation to infer biology from microarray analysis-1

<p><b>Copyright information:</b></p><p>Taken from "Literature Lab: a method of automated literature interrogation to infer biology from microarray analysis"</p><p>http://www.biomedcentral.com/1471-2164/8/461</p><p>BMC Genomics 2007;8():461-461.</p><p>Published online 18 Dec 2007</p><p>PMCID:PMC2244637.</p><p></p> treatment in the prostates of transgenic MPAKT mice. B) Association of pathway terms (Squares) with the 64 genes (circles) associated with RAD001 treatment of MPAKT mice. Size of square indicates confidence of associations, thickness of connecting line correlates with the number of abstracts linking any pair of term and gene. C) Protein lysates prepared from the VP of individual MPAKT and WT mice either treated with RAD001 (+) or with placebo (-) for 48 hours were immunoblotted with anti-Hif1α and anti-tubulin as indicated. Lower panel shows the densitometric ratio of Hif1α and tubulin

Literature Lab: a method of automated literature interrogation to infer biology from microarray analysis-4

<p><b>Copyright information:</b></p><p>Taken from "Literature Lab: a method of automated literature interrogation to infer biology from microarray analysis"</p><p>http://www.biomedcentral.com/1471-2164/8/461</p><p>BMC Genomics 2007;8():461-461.</p><p>Published online 18 Dec 2007</p><p>PMCID:PMC2244637.</p><p></p> Heat map of the top 100 genes with increased expression in HL60 cells treated with ATRA compared to untreated HL60 cells (Red – high normalized expression, Blue – low normalized expression). C) Percentage of cells positive for nitro blue tetrazolium (NBT) reduction (Mean +/- St dev). D) Literature Lab ranking, association scores, and confidence calls for cell physiology, metabolism, and pathway terms (Association score is the log of the product of frequency (logPF))

Improvement in Parameters of Hematologic and Immunologic Function and Patient Well-being in the Phase III RESONATE Study of Ibrutinib Versus Ofatumumab in Patients With Previously Treated Chronic Lymphocytic Leukemia/Small Lymphocytic Lymphoma

In the phase III study RESONATE, ibrutinib reduced the risk of progression and improved overall survival versus ofatumumab in previously treated patients with CLL/SLL. In this novel analysis of patient well-being including patient-reported outcomes, ibrutinib reduced disease burden while preserving parameters of hematologic and immunologic function in RESONATE. These results suggest that ibrutinib can improve quality of life while prolonging survival. Ibrutinib compared with ofatumumab significantly improves progression-free and overall survival in patients with previously treated chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL). Measures of well-being were assessed in RESONATE, where previously treated patients with CLL/SLL were randomized to receive ibrutinib 420 mg/day (n = 195) or ofatumumab (n = 196) for up to 24 weeks. Endpoints included hematologic function, Functional Assessment of Chronic Illness Therapy-Fatigue (FACIT-F), disease-related symptoms, European Organization for Research and Treatment of Cancer Quality of Life Questionnaires Core 30 (EORTC QLQ-C30), and medical resource utilization. With up to 24 months' follow-up (median, 16.4 months), 79% of cytopenic patients showed sustained hematologic improvement (82% with improved platelet count, 69% with improved hemoglobin) on ibrutinib versus 43% on ofatumumab (P <.0001). Higher rates of clinically meaningful improvement were demonstrated with ibrutinib versus ofatumumab for FACIT-F and EORTC global health. Greater improvement was observed in disease-related weight loss, fatigue, night sweats, and abdominal discomfort with ibrutinib versus ofatumumab. Hospitalizations in the first 30 days occurred less frequently with ibrutinib than ofatumumab (0.087 vs. 0.184 events/patient; P =.0198). New-onset diarrhea was infrequent with ibrutinib after the first 6 months (47% at ≤6 months vs. 5% at 12-18 months). With ibrutinib, grade ≥ 3 hypertension occurred in 6%, grade ≥ 3 atrial fibrillation in 4%, major hemorrhage in 2%, and tumor lysis syndrome in 1% of patients. Conclusion: Ibrutinib led to significant improvements in hematologic function and disease symptomatology versus ofatumumab, and can restore quality of life while prolonging survival in relapsed/refractory CLL/SLL