Publications by authors named "Drew Bergman"
Background: The field of radiation oncology (RO) is frequently overlooked by medical students due to limited exposure during traditional medical school curricula. Initiatives aimed at increasing exposure while creating opportunities for medical student engagement are vital. Here, we present the inception, 1.
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- Visiting electives in radiation oncology (RO) can impact medical students' residency match outcomes, but high costs deter some, particularly underrepresented students, from participating.
- A review identified 92 RO electives, with 40 offering scholarships for underrepresented in medicine (URiM) students; the median stipend was $2000, but financial support is not evenly distributed across the U.S.
- The geographical disparities in scholarship availability suggest a need for interventions to improve access to these valuable training opportunities for all medical students.
Enhancers are key drivers of gene regulation thought to act via 3D physical interactions with the promoters of their target genes. However, genome-wide depletions of architectural proteins such as cohesin result in only limited changes in gene expression, despite a loss of contact domains and loops. Consequently, the role of cohesin and 3D contacts in enhancer function remains debated.
View Article and Find Full Text PDFLinking variants from genome-wide association studies (GWAS) to underlying mechanisms of disease remains a challenge. For some diseases, a successful strategy has been to look for cases in which multiple GWAS loci contain genes that act in the same biological pathway. However, our knowledge of which genes act in which pathways is incomplete, particularly for cell-type-specific pathways or understudied genes.
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- Hepatocellular carcinoma (HCC) is usually diagnosed late, making it hard to treat effectively, as seen in a case of a 77-year-old man whose HCC presented as a lung tumor.
- The patient's genomic profile showed common mutations (TERT, TP53, and ATM) associated with HCC, revealing a complex biology to the cancer.
- Despite receiving palliative treatment and targeted therapy, the patient passed away six months after diagnosis, underscoring the urgency for better treatment options for aggressive and unresectable HCC cases.
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- Gene regulation in humans involves distal enhancers activating nearby promoters, with a proposed model suggesting that promoters have specific sequence preferences for certain enhancers mediated by transcription factors.
- A new high-throughput assay called ExP STARR-seq was developed to analyze the compatibility between 1,000 enhancer and 1,000 promoter sequences in human K562 cells, revealing that enhancers generally activate promoters similarly and their combined effects determine RNA output.
- The study found that housekeeping gene promoters, which have activating motifs, are less responsive to enhancers, while promoters of variably expressed genes are more responsive, indicating a nuanced model of gene transcription control based on enhancer-promoter compatibility.
Acquired melanocytic nevi grow and persist in a stable form into adulthood. Using genome-wide methylation profiling, we evaluated 32 histopathologically and dermoscopically characterized nevi to identify the key epigenetic regulatory mechanisms involved in nevogenesis. Benign (69% globular and 31% nonspecific dermoscopic pattern) and dysplastic (95% reticular/nonspecific dermoscopic pattern) nevi were dissimilar, with only two shared differentially methylated loci.
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- Genome-wide association studies (GWAS) have found many noncoding regions related to diseases, but translating these findings into functional insights is challenging due to insufficient maps of enhancers and target genes.
- The activity-by-contact (ABC) model was developed to predict enhancer-gene interactions and applied across 131 human cell types, linking over 5,000 GWAS signals to nearly 2,250 unique genes with implications for various diseases.
- Specifically for inflammatory bowel disease (IBD), ABC model identified risk variants in enhancers that regulate gene expression, offering a new understanding of disease mechanisms and providing a blueprint for future connections between genetic variants and their functions.
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- HyPR-seq is a new method for quantifying gene expression at the single-cell level, improving sensitivity for individual RNA transcripts compared to existing methods.
- It works by hybridizing DNA probes to RNA, then amplifying and sequencing these probes, allowing researchers to profile over 100,000 single cells efficiently.
- This technique not only identifies rare transcripts and measures gene expression changes but also significantly reduces costs, making it a practical choice for targeted RNA analysis in various biological applications.
Genome-wide association studies have associated thousands of genetic variants with complex traits and diseases, but pinpointing the causal variant(s) among those in tight linkage disequilibrium with each associated variant remains a major challenge. Here, we use seven experimental assays to characterize all common variants at the multiple disease-associated TNFAIP3 locus in five disease-relevant immune cell lines, based on a set of features related to regulatory potential. Trait/disease-associated variants are enriched among SNPs prioritized based on either: (1) residing within CRISPRi-sensitive regulatory regions, or (2) localizing in a chromatin accessible region while displaying allele-specific reporter activity.
View Article and Find Full Text PDFEnhancer elements in the human genome control how genes are expressed in specific cell types and harbor thousands of genetic variants that influence risk for common diseases. Yet, we still do not know how enhancers regulate specific genes, and we lack general rules to predict enhancer-gene connections across cell types. We developed an experimental approach, CRISPRi-FlowFISH, to perturb enhancers in the genome, and we applied it to test >3,500 potential enhancer-gene connections for 30 genes.
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