Genome-wide association studies (GWAS) have ascertained numerous trait-associated common genetic variants, frequently localized to regulatory DNA. We find that common genetic variation at BCL11A associated with fetal hemoglobin (HbF) level lies in noncoding sequences decorated by an erythroid enhancer chromatin signature. Fine-mapping uncovers a motif-disrupting common variant associated with reduced transcription factor binding, modestly diminished BCL11A expression and elevated HbF. The surrounding sequences function in vivo as a developmental stage-specific lineage-restricted enhancer. Genome engineering reveals the enhancer is required in erythroid but not B-lymphoid cells for BCL11A expression. These findings illustrate how GWAS may expose functional variants of modest impact within causal elements essential for appropriate gene expression. We propose the GWAS-marked BCL11A enhancer represents an attractive target for therapeutic genome engineering for the β-hemoglobinopathies.

Increasing thyroid nodule size impacts cancer risk in a nonlinear fashion. A threshold is detected at 2.0 cm, beyond which cancer risk is unchanged. However, the risk of follicular carcinomas and other rare thyroid malignancies increases as nodules enlarge.

IntroductionHemoglobinopathies are among the most common inherited recessive diseases. 1 Globin gene mutations occurred numerous times during human history and have been selected to high frequencies in malarial endemic regions. Although many of these globin mutations in the heterozygous state afford modest protection against malaria, the coinheritance of 2 mutant ␤-globin alleles (in homozygous or compound heterozygous combination) produces the common ␤-globin disorders. Sickle cell disease (SCD) and the ␤-thalassemias are chronic diseases with considerable morbidity and mortality. In low-income countries, most affected individuals die in early childhood. Nearly 300 000 infants are estimated born with SCD each year (the majority in Africa), and another 40 000 severely affected with ␤-thalassemia. 2 In the United States alone, the annual medical costs for the approximately 75 000 individuals with SCD are estimated at more than $1 billion. 3 Although genetic screening and prenatal diagnosis have reduced the incidence of ␤-thalassemia in selected countries, such as Sardinia and Cyprus, ␤-thalassemia remains common in many areas of Asia and the Middle East with limited resources for treatment. Children with ␤-globin disorders are at particular risk of life-threatening infections. As childhood infectious diseases are brought under better control in the developing world, the ␤-globin disorders will undoubtedly take on intensified public health significance. Given anticipated population growth, the worldwide prevalence of these diseases is expected to rise dramatically over the next century. 4 Since the initial hematologic descriptions of SCD and ␤-thalassemia by Herrick and Cooley, respectively, in the early 20th century, studies of the hemoglobinopathies have been at the forefront of human genetics and molecular biology. Sickle cell disease, distinguished by its unique hemoglobin structure because of the characteristic glutamate-to-valine substitution of ␤ S , was heralded as the first "molecular disease." 5page543 The subsequent demonstration of globin chain imbalance as the pathophysiologic underpinning of the thalassemias presaged the molecular biology era in which various thalassemia mutations were dissected, illuminating fundamental aspects of gene regulation. 6 Fetal hemoglobinTwo gene clusters encode the various globins-the ␣ cluster on chromosome 16 contains the embryonic gene, and adult ␣1 and ␣2 genes, and the ␤ cluster on chromosome 11 the embryonic ⑀, the fetal G ␥ and A ␥, and adult ␦ and ␤ genes (Figure 1). 7 During early embryonic development, erythropoiesis is yolk-sac-derived, transitioning to the fetal liver midway through the first trimester. Approaching the time of birth, the bone marrow becomes the dominant site of erythropoiesis. Two accompanying switches occur in the expression of genes from the ␤-globin cluster-a switch from embryonic-to-fetal globins early in gestation, and then from fetal-to-adult globins around the time of birth. Thus HbF (␣ 2 ␥ 2 ) constitutes the major hemoglobin during...

Nasopharyngeal carcinoma is uncommon in the United States, with only 0.2 to 0.5 cases per 100,00 people; this is in contrast to southern China and Hong Kong, where the incidence is 25 to 50 per 100,000 people. There is a potential link between Epstein-Barr virus and the development of nasopharyngeal carcinoma. Radiotherapy alone as a single modality leads to similar 10-year survival rates in United States, Denmark, and Hong Kong (34%, 37%, and 43%, respectively). Multiple studies have shown an advantage to concurrent chemoradiation in the treatment of advanced disease. Radiation therapy remains the mainstay of salvage therapy, and modern techniques have allowed clinicians to achieve adequate local control without excessive toxicity.

RNA interference (RNAi) technology using short hairpin RNAs (shRNAs) expressed via RNA polymerase (pol) III promoters has been widely exploited to modulate gene expression in a variety of mammalian cell types. For certain applications, such as lineage-specific knockdown, embedding targeting sequences into pol II-driven microRNA (miRNA) architecture is required. Here, using the potential therapeutic target BCL11A, we demonstrate that pol III-driven shRNAs lead to significantly increased knockdown but also increased cytotoxcity in comparison to pol II-driven miRNA adapted shRNAs (shRNA(miR)) in multiple hematopoietic cell lines. We show that the two expression systems yield mature guide strand sequences that differ by a 4 bp shift. This results in alternate seed sequences and consequently influences the efficacy of target gene knockdown. Incorporating a corresponding 4 bp shift into the guide strand of shRNA(miR)s resulted in improved knockdown efficiency of BCL11A. This was associated with a significant de-repression of the hemoglobin target of BCL11A, human γ-globin or the murine homolog Hbb-y. Our results suggest the requirement for optimization of shRNA sequences upon incorporation into a miRNA backbone. These findings have important implications in future design of shRNA(miR)s for RNAi-based therapy in hemoglobinopathies and other diseases requiring lineage-specific expression of gene silencing sequences.

IMPORTANCE Precision oncology is revolutionizing cancer care, allowing for personalized treatments to improve outcomes. Cancer research has benefitted from well-designed studies incorporating precision medicine objectives, but it is unclear if these studies are representative of the diverse cancer population. OBJECTIVETo evaluate racial and ethnic representation in breast, prostate, lung, and colorectal cancer studies incorporating precision oncology objectives in the Clinicaltrials.gov registry and compare with the incidence of these cancer types in racial and ethnic minority groups in the US population. DESIGN, SETTING, AND PARTICIPANTSThis cross-sectional study identified US-based breast, prostate, lung, and colorectal cancer studies incorporating precision oncology objectives for reporting of race and ethnicity. The Surveillance, Epidemiology, and End Results and US Census databases were used to determine cancer incidence by race and ethnicity, linked with cancer type and median year of enrollment for each trial. Data were collected and analyzed between December 2020 and April 2021. MAIN OUTCOMES AND MEASURESThe expected number of participants per study by each racial and ethnic group was calculated based on the corresponding US-based proportion. Under-and overrepresentation was defined as the ratio of the actual number of enrolled cases to the expected number of cases for each trial by cancer type. Ratios above 1 indicated overrepresentation while a ratio below 1 indicated underrepresentation. Random-effects meta-analysis of representation ratios of individual trials was performed to weigh each individual study. RESULTSOf 93 studies encompassing 5867 enrollees with race and ethnicity data; 4826 participants (82.3%) were non-Hispanic White, 587 (10.0%) were Black, and 238 (4.1%) were Asian.Per observed-to-expected ratios, White participants were overrepresented in all studies, with a ratio of 1.35 (95% CI, 1.30-1.37), as well as Asian participants, with a ratio of 1.46 (95% CI, 1.28-1.66), while Black participants (ratio, 0.49; 95% CI, 0.45-0.54), Hispanic participants (ratio, 0.24; 95% CI, 0.20-0.28), and American Indian and Alaskan Native participants (ratio, 0.43; 95% CI, 0.24-0.78) were underrepresented. By individual cancer site, White participants were consistently overrepresented in all studies, while Black and Hispanic participants were underrepresented.CONCLUSIONS AND RELEVANCE This analysis found that precision oncology studies for breast, lung, prostate, and colorectal cancers vastly underrepresent racial and ethnic minority populations relative to their cancer incidence in the US population. It is imperative to increase diversity among enrollees so that all individuals may benefit from cancer research breakthroughs and personalized treatments.

Purpose: Molecular properties associated with complete response or acquired resistance to concurrent chemotherapy and radiation therapy (CRT) are incompletely characterized. Experimental Design:We performed integrated whole exome/transcriptome sequencing and immune infiltrate analysis on rectal adenocarcinoma tumors prior to neoadjuvant CRT (pre-CRT) and at time of resection (post-CRT) in 17 patients (8 complete/partial responders [R], 9 nonresponders [NR]).Results: CRT was not associated with increased tumor mutational burden or neoantigen load and did not alter the distribution of established somatic tumor mutations in rectal cancer. Concurrent KRAS/TP53 mutations (KP) associated with NR tumors and were enriched for an epithelialmesenchymal transition transcriptional program. Furthermore, NR was associated with reduced CD4/CD8 T-cell infiltrates and a post-CRT M2 macrophage phenotype. Absent any local tumor recurrences, KP/NR status predicted worse progression-free survival, suggesting that local

Radiation has long been associated with carcinogenesis. Nevertheless, it is an important part of multimodality therapy for many malignancies. It is critical to assess the risk of secondary malignant neoplasms (SMNs) after radiation treatment. The authors reviewed the literature with a focus on radiation and associated SMNs for primary hematologic, breast, gynecologic, and pediatric tumors. Radiation appeared to increase the risk of SMN in all of these; however, this risk was found to be associated with age, hormonal influences, chemotherapy use, environmental influences, genetic predisposition, infection, and immunosuppression. The risk also appears to be altered with modern radiotherapy techniques. Practitioners of all specialties who treat cancer survivors in follow‐up should be aware of this potential risk. Cancer 2016;122:1809–21. © 2016 American Cancer Society.