Danny Simpson
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View article: Global geographic and socioeconomic disparities in COVID-associated acute kidney injury: a systematic review and meta-analysis.
Global geographic and socioeconomic disparities in COVID-associated acute kidney injury: a systematic review and meta-analysis. Open
Our study shows significant geographic and socioeconomic disparities in the prevalence of COVID-associated AKI, with a higher prevalence in high-income countries and a lower prevalence in low- and lower-middle-income countries. This study …
View article: Inherited mitochondrial genetics as a predictor of immune checkpoint inhibition efficacy in melanoma
Inherited mitochondrial genetics as a predictor of immune checkpoint inhibition efficacy in melanoma Open
Response to immune checkpoint inhibitors (ICIs) in metastatic melanoma (MM) varies among patients, and current baseline biomarkers predicting treatment outcomes are limited. As mitochondrial (MT) metabolism has emerged as an important regu…
View article: A benchmarked, high-efficiency prime editing platform for multiplexed dropout screening
A benchmarked, high-efficiency prime editing platform for multiplexed dropout screening Open
Prime editing installs precise edits into the genome with minimal unwanted byproducts, but low and variable editing efficiencies have complicated application of the approach to high-throughput functional genomics. Here we assembled a prime…
View article: A benchmarked, high-efficiency prime editing platform for multiplexed dropout screening
A benchmarked, high-efficiency prime editing platform for multiplexed dropout screening Open
Prime editing installs precise edits into the genome with minimal unwanted byproducts, but low and variable editing efficiencies have complicated application of the approach to high-throughput functional genomics. Leveraging several recent…
View article: Mapping the Genetic Interaction Network of PARP inhibitor Response
Mapping the Genetic Interaction Network of PARP inhibitor Response Open
SUMMARY Genetic interactions have long informed our understanding of the coordinated proteins and pathways that respond to DNA damage in mammalian cells, but systematic interrogation of the genetic network underlying that system has yet to…
View article: Germline immunomodulatory expression quantitative trait loci (ieQTLs) associated with immune-related toxicity from checkpoint inhibition
Germline immunomodulatory expression quantitative trait loci (ieQTLs) associated with immune-related toxicity from checkpoint inhibition Open
We report that rs7036417 is associated with increased risk of severe irAEs, independent of IPI efficacy. SYK plays an important role in B-cell/T-cell expansion, and increased pSYK has been reported in patients with autoimmune disease. The …
View article: Germline Immunomodulatory Expression Quantitative Trait Loci (ieQTLs) Associated with Immune-Related Toxicity from Checkpoint Inhibition
Germline Immunomodulatory Expression Quantitative Trait Loci (ieQTLs) Associated with Immune-Related Toxicity from Checkpoint Inhibition Open
Robert Ferguson1,2,3*, Vylyny Chat1,2,3*, Leah Morales1,2,3, Danny Simpson1,2,3, Kelsey Monson1,2,3, Elisheva Cohen1,2,3,Sarah Zusin1,2,3, Gabriele Madonna4, Mariaelena Capone4, Ester Simeone4, Anna Pavlick5, Jason Luke6,7, Thomas F Gajews…
View article: Germline Immunomodulatory Expression Quantitative Trait Loci (ieQTLs) Associated with Immune-Related Toxicity from Checkpoint Inhibition
Germline Immunomodulatory Expression Quantitative Trait Loci (ieQTLs) Associated with Immune-Related Toxicity from Checkpoint Inhibition Open
Robert Ferguson1,2,3*, Vylyny Chat1,2,3*, Leah Morales1,2,3, Danny Simpson1,2,3, Kelsey Monson1,2,3, Elisheva Cohen1,2,3,Sarah Zusin1,2,3, Gabriele Madonna4, Mariaelena Capone4, Ester Simeone4, Anna Pavlick5, Jason Luke6,7, Thomas F Gajews…
View article: Mapping the Genetic Landscape of DNA Double-strand Break Repair
Mapping the Genetic Landscape of DNA Double-strand Break Repair Open
SUMMARY Cells repair DNA double-strand breaks (DSBs) through a complex set of pathways that are critical for maintaining genomic integrity. Here we present Repair-seq, a high-throughput screening approach that measures the effects of thous…
View article: Immunomodulatory germline variation associated with the development of multiple primary melanoma (MPM)
Immunomodulatory germline variation associated with the development of multiple primary melanoma (MPM) Open
Multiple primary melanoma (MPM) has been associated with a higher 10-year mortality risk compared to patients with single primary melanoma (SPM). Given that 3–8% of patients with SPM develop additional primary melanomas, new markers predic…
View article: Discovery of novel germline genetic biomarkers of melanoma recurrence impacting exonic and long non-coding RNA (lncRNA) transcripts
Discovery of novel germline genetic biomarkers of melanoma recurrence impacting exonic and long non-coding RNA (lncRNA) transcripts Open
Background: One challenge in clinical management of cutaneous melanoma (CM) is the limited predictability of recurrence and hence the progression to advanced stages that associate with less favorable outcomes. Aggressive follow-up care and…
View article: Immunomodulatory germline variation impacts the development of multiple primary melanoma (MPM)
Immunomodulatory germline variation impacts the development of multiple primary melanoma (MPM) Open
Background: During their lifetime about 8% of patients with single primary cutaneous melanoma (SPM) will develop multiple primary melanomas (MPM), which are associated with significantly higher mortality compared to patients with SPM. Base…
View article: Primary Melanoma Histologic Subtype: Impact on Survival and Response to Therapy
Primary Melanoma Histologic Subtype: Impact on Survival and Response to Therapy Open
Background Two primary histologic subtypes, superficial spreading melanoma (SSM) and nodular melanoma (NM), comprise the majority of all cutaneous melanomas. NM is associated with worse outcomes, which have been attributed to increased thi…
View article: MOESM8 of Baseline antibody profiles predict toxicity in melanoma patients treated with immune checkpoint inhibitors
MOESM8 of Baseline antibody profiles predict toxicity in melanoma patients treated with immune checkpoint inhibitors Open
Additional file 8: Table S7. Functions of protein targets of treatment termination-associated antibodies. Functional analysis of protein targets for top 15 DE toxicity-associated antibodies for each of the anti-CTLA-4, anti-PD-1, and combi…
View article: MOESM6 of Baseline antibody profiles predict toxicity in melanoma patients treated with immune checkpoint inhibitors
MOESM6 of Baseline antibody profiles predict toxicity in melanoma patients treated with immune checkpoint inhibitors Open
Additional file 6: Table S5. Toxicity- and termination-associated antibodies. Lists of differentially expressed, strongly differentially expressed, filtered and curated antibodies associated with severe toxicity for anti-CTLA-4, anti-PD-1,…
View article: MOESM4 of Baseline antibody profiles predict toxicity in melanoma patients treated with immune checkpoint inhibitors
MOESM4 of Baseline antibody profiles predict toxicity in melanoma patients treated with immune checkpoint inhibitors Open
Additional file 4: Table S3. Sample details. Severity and site of toxicity (gastrointestinal (GI), endocrine, skin and/or other) and treatment termination status for baseline sera samples from anti-CTLA-4 (n = 39), anti-PD-1 (n = 28), and …
View article: MOESM7 of Baseline antibody profiles predict toxicity in melanoma patients treated with immune checkpoint inhibitors
MOESM7 of Baseline antibody profiles predict toxicity in melanoma patients treated with immune checkpoint inhibitors Open
Additional file 7: Table S6. Pathway analysis of protein targets of toxicity-associated antibodies. Lists of functional pathways (derived from WikiPathways; http://www.wikipathways.org/ ) enriched for protein targets of filtered toxicity-a…
View article: Are Fireworms Venomous? Evidence for the Convergent Evolution of Toxin Homologs in Three Species of Fireworms (Annelida, Amphinomidae)
Are Fireworms Venomous? Evidence for the Convergent Evolution of Toxin Homologs in Three Species of Fireworms (Annelida, Amphinomidae) Open
Amphinomids, more commonly known as fireworms, are a basal lineage of marine annelids characterized by the presence of defensive dorsal calcareous chaetae, which break off upon contact. It has long been hypothesized that amphinomids are ve…
View article: Apolipoprotein L1 risk variants associate with prevalent atherosclerotic disease in African American systemic lupus erythematosus patients
Apolipoprotein L1 risk variants associate with prevalent atherosclerotic disease in African American systemic lupus erythematosus patients Open
Taken together, the APOL1 RAs associate with prevalent atherosclerotic CVD in this cohort of AA SLE patients, perhaps reflecting a potentiating effect of SLE on APOL1-related cardiovascular phenotypes.
View article: From Mollusks to Medicine: A Venomics Approach for the Discovery and Characterization of Therapeutics from Terebridae Peptide Toxins
From Mollusks to Medicine: A Venomics Approach for the Discovery and Characterization of Therapeutics from Terebridae Peptide Toxins Open
Animal venoms comprise a diversity of peptide toxins that manipulate molecular targets such as ion channels and receptors, making venom peptides attractive candidates for the development of therapeutics to benefit human health. However, id…