111 Works

Data from: Th2 cytokines inhibit lymphangiogenesis

Ira L. Savetsky, Swapna Ghanta, Jason C. Gardenier, Jeremy S. Torrisi, Gabriela D. Garcia Nores, Geoffrey E. Hespe, Matthew D. Nitti, Raghu P. Kataru & Babak J. Mehrara
Lymphangiogenesis is the process by which new lymphatic vessels grow in response to pathologic stimuli such as wound healing, inflammation, and tumor metastasis. It is well-recognized that growth factors and cytokines regulate lymphangiogenesis by promoting or inhibiting lymphatic endothelial cell (LEC) proliferation, migration and differentiation. Our group has shown that the expression of T-helper 2 (Th2) cytokines is markedly increased in lymphedema, and that these cytokines inhibit lymphatic function by increasing fibrosis and promoting changes...

Data from: Lymph node transplantation decreases swelling and restores immune responses in a transgenic model of lymphedema

Jung-Ju Huang, Jason C. Gardenier, Geoffrey E. Hespe, Gabriela D. García Nores, Raghu P. Kataru, Catherine L. Ly, Inés Martínez-Corral, Sagrario Ortega & Babak J. Mehrara
Introduction: Secondary lymphedema is a common complication of cancer treatment and recent studies have demonstrated that lymph node transplantation (LNT) can decrease swelling, as well as the incidence of infections. However, although these results are exciting, the mechanisms by which LNT improves these pathologic findings of lymphedema remain unknown. Using a transgenic mouse model of lymphedema, this study sought to analyze the effect of LNT on lymphatic regeneration and T cell-mediated immune responses. Methods: We...

Data from: Splicing factor SF3B1K700E mutant dysregulates erythroid differentiation via aberrant alternative splicing of transcription factor TAL1

Shuiling Jin, Hairui Su, Ngoc-Tung Tran, Jing Song, Sydney S. Lu, Ying Li, Suming Huang, Omar Abdel-Wahab, Yanyan Liu & Xinyang Zhao
More than 60% of myeloid dysplasia syndrome (MDS) contains mutations in genes encoding for splicing factors such as SF3B1, U2AF, SRSF2 and ZRSR2. Mutations in SF3B1 are associated with 80% cases of refractory anemia with ring sideroblast (RARS), a subtype of MDS. SF3B1K700E is the most frequently mutated site among mutations on SF3B1. Yet the molecular mechanisms on how mutations of splicing factors lead to defective erythropoiesis are not clear. SF3B1K700E mutant binds to an...

Additional file 1 of COVID-19 vaccine update: vaccine effectiveness, SARS-CoV-2 variants, boosters, adverse effects, and immune correlates of protection

Wei-Yu Chi, Yen-Der Li, Hsin-Che Huang, Timothy En Haw Chan, Sih-Yao Chow, Jun-Han Su, Louise Ferrall, Chien-Fu Hung & T.-C. Wu
Additional file 1: Table S1. Vaccine effectiveness against viral variants. Studies of vaccine effectiveness against viral variants. Related to Table 2.

Additional file 2 of COVID-19 vaccine update: vaccine effectiveness, SARS-CoV-2 variants, boosters, adverse effects, and immune correlates of protection

Wei-Yu Chi, Yen-Der Li, Hsin-Che Huang, Timothy En Haw Chan, Sih-Yao Chow, Jun-Han Su, Louise Ferrall, Chien-Fu Hung & T.-C. Wu
Additional file 2: Table S2. Vaccine efficacy and effectiveness in children and adolescents

Bile acid distributions, sex-specificity, and prognosis in colorectal cancer

Yuping Cai, Xinyi Shen, Lingeng Lu, Hong Yan, Huang Huang, Patricia Gaule, Engjel Muca, Casey M. Theriot, Zahra Rattray, Nicholas J. W. Rattray, Jun Lu, Nita Ahuja, Yawei Zhang, Philip B. Paty, Sajid A. Khan & Caroline H. Johnson
Abstract Background Bile acids are known to be genotoxic and contribute to colorectal cancer (CRC). However, the link between CRC tumor bile acids to tumor location, patient sex, microbiome, immune-regulatory cells, and prognosis is not clear. Methods We conducted bile acid analysis using targeted liquid chromatography–mass spectrometry (LC–MS) on tumor tissues from CRC patients (n = 228) with survival analysis. We performed quantitative immunofluorescence (QIF) on tumors to examine immune cells. Results Twelve of the...

Additional file 1 of Bile acid distributions, sex-specificity, and prognosis in colorectal cancer

Yuping Cai, Xinyi Shen, Lingeng Lu, Hong Yan, Huang Huang, Patricia Gaule, Engjel Muca, Casey M. Theriot, Zahra Rattray, Nicholas J. W. Rattray, Jun Lu, Nita Ahuja, Yawei Zhang, Philip B. Paty, Sajid A. Khan & Caroline H. Johnson
Additional file 1: Table S1. Names of the bile acids measured in tumor tissues. Table S2. Demographics of colon cancer patients from samples used within this study. Table S4. Comparison of bile acid abundance between RCCs and LCCs by sex and age. Table S5. Pearson correlation of glucuronic acid to bile acid abundances in patients with LCC ≥ 55 years old (n=99). Table S6. Correlations between prognosis-linked bile acid and T regulatory cell abundances in...

Additional file 10 of DNA methylation predicts the outcome of COVID-19 patients with acute respiratory distress syndrome

Martina Bradic, Sarah Taleb, Binitha Thomas, Omar Chidiac, Amal Robay, Nessiya Hassan, Joel Malek, Ali Ait Hssain & Charbel Abi Khalil
Additional file 10: Table S10. Description of the eight genes that are predictors of mortality. Data were collected from Gene Ontology (GO) to identify the functional annotation of each gene and recently published COVID-19 related articles to highlight the role of each gene in relation to COVID-19.

Additional file 2 of DNA methylation predicts the outcome of COVID-19 patients with acute respiratory distress syndrome

Martina Bradic, Sarah Taleb, Binitha Thomas, Omar Chidiac, Amal Robay, Nessiya Hassan, Joel Malek, Ali Ait Hssain & Charbel Abi Khalil
Additional file 2: Table S2. Summary of different models tested for estimating differences between controls and COVID-19 patients for immune cell proportions. Adjusted R2, residual standard error (sigma), AIC, and p.value for each tested model for each cell type are shown. The following models were tested, mod1; Age and ethnicity as covariates, mod2; age as a covariate, mod3; ethnicity as a covariate, mod4; no covariates.

Additional file 3 of DNA methylation predicts the outcome of COVID-19 patients with acute respiratory distress syndrome

Martina Bradic, Sarah Taleb, Binitha Thomas, Omar Chidiac, Amal Robay, Nessiya Hassan, Joel Malek, Ali Ait Hssain & Charbel Abi Khalil
Additional file 3: Table S3. Summary of identified differentially methylated CpGs between COVID-19 patients and controls. A. All significant CpGs B. Variable description from Table S2A. C. Significant CpGs from genes previously described as COVID-19 important [1]. D. Functional annotation of genes from Supplemental table 3C.

Additional file 4 of DNA methylation predicts the outcome of COVID-19 patients with acute respiratory distress syndrome

Martina Bradic, Sarah Taleb, Binitha Thomas, Omar Chidiac, Amal Robay, Nessiya Hassan, Joel Malek, Ali Ait Hssain & Charbel Abi Khalil
Additional file 4: Table S4. Summary of differentially methylated pathways detected between COVID-19 patients and controls based on CpG sites.

Additional file 6 of DNA methylation predicts the outcome of COVID-19 patients with acute respiratory distress syndrome

Martina Bradic, Sarah Taleb, Binitha Thomas, Omar Chidiac, Amal Robay, Nessiya Hassan, Joel Malek, Ali Ait Hssain & Charbel Abi Khalil
Additional file 6: Table S6. Analysis of dead and recovered+A3 COVID-19 patients for immune cell proportions. A. Summary of different models tested for immune cell proportions. Adjusted R2, residual standard error (sigma), AIC, and p-value for each tested model for each cell type are shown. The following models were tested, mod1; Age + MV days + Gender + ICU LoS + ECMO + Nosocomial infections, mod2; Age + Gender + ICU LoS + ECMO +...

Additional file 8 of DNA methylation predicts the outcome of COVID-19 patients with acute respiratory distress syndrome

Martina Bradic, Sarah Taleb, Binitha Thomas, Omar Chidiac, Amal Robay, Nessiya Hassan, Joel Malek, Ali Ait Hssain & Charbel Abi Khalil
Additional file 8: Table S8. Description of 27 genes from 49 differentially methylated CpGs between survived and dead patients over four time points. A summarized description of the 27 genes obtained from Supplementary Table 7B, collected from Gene Ontology (GO) to identify the functional annotation of each gene and recently published COVID-19-related articles to highlight the role of each gene in relation to COVID-19.

Additional file 8 of DNA methylation predicts the outcome of COVID-19 patients with acute respiratory distress syndrome

Martina Bradic, Sarah Taleb, Binitha Thomas, Omar Chidiac, Amal Robay, Nessiya Hassan, Joel Malek, Ali Ait Hssain & Charbel Abi Khalil
Additional file 8: Table S8. Description of 27 genes from 49 differentially methylated CpGs between survived and dead patients over four time points. A summarized description of the 27 genes obtained from Supplementary Table 7B, collected from Gene Ontology (GO) to identify the functional annotation of each gene and recently published COVID-19-related articles to highlight the role of each gene in relation to COVID-19.

Additional file 2 of Genomic and transcriptomic analysis of a diffuse pleural mesothelioma patient-derived xenograft library

Michael Offin, Jennifer L. Sauter, Sam E. Tischfield, Jacklynn V. Egger, Shweta Chavan, Nisargbhai S. Shah, Parvathy Manoj, Katia Ventura, Viola Allaj, Elisa de Stanchina, William Travis, Marc Ladanyi, Andreas Rimner, Valerie W. Rusch, Prasad S. Adusumilli, John T. Poirier, Marjorie G. Zauderer, Charles M. Rudin & Triparna Sen
Additional file 2: Figure S1. Clinical outcomes of patients based on histology

Additional file 1 of Genomic and transcriptomic analysis of a diffuse pleural mesothelioma patient-derived xenograft library

Michael Offin, Jennifer L. Sauter, Sam E. Tischfield, Jacklynn V. Egger, Shweta Chavan, Nisargbhai S. Shah, Parvathy Manoj, Katia Ventura, Viola Allaj, Elisa de Stanchina, William Travis, Marc Ladanyi, Andreas Rimner, Valerie W. Rusch, Prasad S. Adusumilli, John T. Poirier, Marjorie G. Zauderer, Charles M. Rudin & Triparna Sen
Additional file 1: Table S1. Patient demographics at the time of PDX collection by histology.

Additional file 3 of Modelling multiple time-scales with flexible parametric survival models

Nurgul Batyrbekova, Hannah Bower, Paul W. Dickman, Anna Ravn Landtblom, Malin Hultcrantz, Robert Szulkin, Paul C. Lambert & Therese M-L. Andersson
Additional file 3: Supplementary Figure 2.

Prognostic markers for the clinical course in the blood of patients with SARS-CoV-2 infection

Johannes C. Fischer, Vera Balz, Danny Jazmati, Edwin Bölke, Noemi F. Freise, Verena Keitel, Torsten Feldt, Björn-Erik Ole Jensen, Johannes Bode, Tom Lüdde, Dieter Häussinger, Ortwin Adams, E. Marion Schneider, Jürgen Enczmann, Jutta M. Rox, Derik Hermsen, Karin Schulze-Bosse, Detlef Kindgen-Milles, Wolfram Trudo Knoefel, Martijn van Griensven, Jan Haussmann, Balint Tamaskovics, Christian Plettenberg, Kathrin Scheckenbach, Stefanie Corradini … & Christiane Matuschek
Abstract Background The presentation of peptides and the subsequent immune response depend on the MHC characteristics and influence the specificity of the immune response. Several studies have found an association between HLA variants and differential COVID-19 outcomes and have shown that HLA genotypes are associated with differential immune responses against SARS-CoV-2, particularly in severely ill patients. Information, whether HLA haplotypes are associated with the severity or length of the disease in moderately diseased individuals is...

Prognostic markers for the clinical course in the blood of patients with SARS-CoV-2 infection

Johannes C. Fischer, Vera Balz, Danny Jazmati, Edwin Bölke, Noemi F. Freise, Verena Keitel, Torsten Feldt, Björn-Erik Ole Jensen, Johannes Bode, Tom Lüdde, Dieter Häussinger, Ortwin Adams, E. Marion Schneider, Jürgen Enczmann, Jutta M. Rox, Derik Hermsen, Karin Schulze-Bosse, Detlef Kindgen-Milles, Wolfram Trudo Knoefel, Martijn van Griensven, Jan Haussmann, Balint Tamaskovics, Christian Plettenberg, Kathrin Scheckenbach, Stefanie Corradini … & Christiane Matuschek
Abstract Background The presentation of peptides and the subsequent immune response depend on the MHC characteristics and influence the specificity of the immune response. Several studies have found an association between HLA variants and differential COVID-19 outcomes and have shown that HLA genotypes are associated with differential immune responses against SARS-CoV-2, particularly in severely ill patients. Information, whether HLA haplotypes are associated with the severity or length of the disease in moderately diseased individuals is...

Data from: Sequence co-evolution gives 3D contacts and structures of protein complexes

Thomas A. Hopf, Charlotta P. I. Schärfe, João P. G. L. M. Rodrigues, Anna G. Green, Chris Sander, Alexandre M. J. J. Bonvin, Debora S. Marks & Oliver Kohlbacher
Protein-protein interactions are fundamental to many biological processes. Experimental screens have identified tens of thousands of interactions and structural biology has provided detailed functional insight for select 3D protein complexes. An alternative rich source of information about protein interactions is the evolutionary sequence record. Building on earlier work, we show that analysis of correlated evolutionary sequence changes across proteins identifies residues that are close in space with sufficient accuracy to determine the three-dimensional structure of...

Data from: Alternative splicing substantially diversifies the transcriptome during early photomorphogenesis and correlates with the energy availability in Arabidopsis

Lisa Hartmann, Philipp Drewe-Boß, Theresa Wießner, Gabriele Wagner, Sascha Geue, Hsin-Chieh Lee, Dominik M. Obermüller, André Kahles, Jonas Behr, Fabian H. Sinz, Gunnar Rätsch & Andreas Wachter
Plants use light as source of energy and information to detect diurnal rhythms and seasonal changes. Sensing changing light conditions is critical to adjust plant metabolism and to initiate developmental transitions. Here we analyzed transcriptome-wide alterations in gene expression and alternative splicing (AS) of etiolated seedlings undergoing photomorphogenesis upon exposure to blue, red, or white light. Our analysis revealed massive transcriptome reprograming as reflected by differential expression of ~20% of all genes and changes in...

Data from: Reflectance confocal microscopy features of BRAF V600E mutated thin melanomas detected by immunohistochemistry

Ana Claudia Urvanegia, Juliana Casagrande Tavoloni Braga, Danielle Shitara, Jose Humberto Fregnani, Jose Ivanildo Neves, Clovis Antonio Pinto, Ashfaq A. Marghoob, Joao Pedreira Duprat & Gisele Gargantini Rezze
The classification of melanoma into four histological subtypes has been questioned regarding its clinical validity in providing relevant information for treatment for metastatic tumors. Specific genetic alterations are associated with particular clinical and histopathological features, suggesting that these could be helpful in refining existing melanoma classification schemes. We analyzed BRAF V600E mutated melanomas to explore the Reflectance confocal microscopy (RCM) utility as a screening aid in the evaluation of the most appropriate patients for genetic...

USP8 and TP53 drivers are associated with CNV in a corticotroph adenoma cohort enriched for aggressive tumors

Andrew Uzilov & Eliza Geer
Context: Pituitary corticotroph adenomas are rare tumors that can be associated with excess adrenocorticotropic hormone (ACTH) and adrenal cortisol production, resulting in the clinically debilitating endocrine condition Cushing disease. A subset of corticotroph tumors behave aggressively, and genomic drivers behind the development of these tumors are largely unknown. Objective: To investigate genomic drivers of corticotroph tumors at risk for aggressive behavior. Design: Whole-exome sequencing of patient-matched corticotroph tumor and normal DNA from a patient cohort...

SUVfdg: a standard-uptake-value (SUV) body habitus normalizer specific to fluorodeoxyglucose (FDG) in humans

Bradley Beattie, Tim Akhurst, Finn Augensen & John Humm
In PET, several different Standard Uptake Value (SUV) metrics have been proposed utilizing different normalizers in an attempt to take into consideration the patient to patient differences in radionuclide uptake due to differences in body habitus (body weight, surface area, lean body mass). These normalizers are to some extent aribitrary in that they are selected from the list of proposed body habitus metrics, none of which necessarily describes well the distribution volume into which a...

COVID-19 vaccine update: vaccine effectiveness, SARS-CoV-2 variants, boosters, adverse effects, and immune correlates of protection

Wei-Yu Chi, Yen-Der Li, Hsin-Che Huang, Timothy En Haw Chan, Sih-Yao Chow, Jun-Han Su, Louise Ferrall, Chien-Fu Hung & T.-C. Wu
Abstract Coronavirus Disease 2019 (COVID-19) has been the most severe public health challenge in this century. Two years after its emergence, the rapid development and deployment of effective COVID-19 vaccines have successfully controlled this pandemic and greatly reduced the risk of severe illness and death associated with COVID-19. However, due to its ability to rapidly evolve, the SARS-CoV-2 virus may never be eradicated, and there are many important new topics to work on if we...

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