Alu insertion variants alter gene transcript levels.

Alu are high copy number interspersed repeats that have accumulated near genes during primate and human evolution. They are a pervasive source of structural variation in modern humans. Impacts that Alu insertions may have on gene expression are not well understood, although some have been associated with expression quantitative trait loci (eQTLs). Here, we directly test regulatory effects of polymorphic Alu insertions in isolation of other variants on the same haplotype. To screen insertion variants for those with such effects, we used ectopic luciferase reporter assays and evaluated 110 Alu insertion variants, including more than 40 with a potential role in disease risk. We observed a continuum of effects with significant outliers that up- or down-regulate luciferase activity. Using a series of reporter constructs, which included genomic context surrounding the Alu, we can distinguish between instances in which the Alu disrupts another regulator and those in which the Alu introduces new regulatory sequence. We next focused on three polymorphic Alu loci associated with breast cancer that display significant effects in the reporter assay. We used CRISPR to modify the endogenous sequences, establishing cell lines varying in the Alu genotype. Our findings indicate that Alu genotype can alter expression of genes implicated in cancer risk, including PTHLH, RANBP9, and MYC These data show that commonly occurring polymorphic Alu elements can alter transcript levels and potentially contribute to disease risk.

Structural variants caused by Alu insertions are associated with risks for many human diseases.

Interspersed repeat sequences comprise much of our DNA, although their functional effects are poorly understood. The most commonly occurring repeat is the Alu short interspersed element. New Alu insertions occur in human populations, and have been responsible for several instances of genetic disease. In this study, we sought to determine if there are instances of polymorphic Alu insertion variants that function in a common variant, common disease paradigm. We cataloged 809 polymorphic Alu elements mapping to 1,159 loci implicated in disease risk by genome-wide association study (GWAS) (P < 10-8). We found that Alu insertion variants occur disproportionately at GWAS loci (P = 0.013). Moreover, we identified 44 of these Alu elements in linkage disequilibrium (r2 > 0.7) with the trait-associated SNP. This figure represents a >20-fold increase in the number of polymorphic Alu elements associated with human phenotypes. This work provides a broader perspective on how structural variants in repetitive DNAs may contribute to human disease.

Periocular infantile hemangiomas: Characteristics, ocular sequelae, and outcomes.

OBJECTIVES: To identify clinical factors associated with complications of periocular infantile hemangioma (IH) and monitor improvement in complication rates post-treatment. METHODS: Retrospective cohort study. Eighty-nine patients diagnosed with periocular IH at a pediatric dermatology clinic of a tertiary care center between 2001 and 2013 were included with parental approval. Parents were interviewed by telephone between July and September of 2015, then again in January 2018 to inquire about ophthalmologic follow-up. Electronic medical records were reviewed from January 2001 through January 2018. RESULTS: Sixty percent of patients demonstrated ocular sequelae, including astigmatism (33%), visual axis obstruction (29%), nasolacrimal duct obstruction (7%), ptosis (4%), amblyopia (3%), and strabismus (1%). Compared with superficial IH, deep and mixed IH had higher odds, 3.4 (P = 0.025) and 3.8 (P = 0.034), respectively, of developing ocular sequelae. All patients with astigmatism prior to involution of IH received systemic therapy, with a significant post-treatment decrease in the proportion of patients with astigmatism (40% to 18%, P = 0.027). Three-quarters of patients experienced complete IH involution by time of enrollment in kindergarten. Fifty-one (57.3%) patients received formal ophthalmologic evaluation confirmed through chart review or phone interview, with average follow-up duration of 51.2 months (range: 1.9, 99.3). CONCLUSION: Deep and mixed IH were more likely to demonstrate ocular complications than superficial IH. Rate of astigmatism decreased with systemic therapy. Our study suggests that patients with periocular IH have a lower rate of amblyopia now compared with the prepropranolol era and emphasizes the importance of early treatment of periocular IH to prevent permanent visual sequelae.

Retrospective Study of Nasal Infantile Hemangiomas: Characteristics, Complications, and Outcomes.

BACKGROUND/OBJECTIVES: Nasal infantile hemangiomas (IHs) pose serious medical complications and psychosocial stress if tumor involution is incomplete or prolonged. The objective was to determine which IH characteristics are associated with complications and are predictive of outcome, assessed as the presence of IHs or residual skin changes upon kindergarten entry, to better manage these lesions and counsel families. METHODS: A retrospective chart review of all patients seen in the Division of Pediatric Dermatology at Johns Hopkins Medicine between 2001 and 2014 for nasal IHs (N = 89) was performed. A follow-up telephone interview with parents was conducted in June and July 2014. RESULTS: Complications were observed in 39% of patients. Segmental and indeterminate IHs were more likely to have complications than focal IHs (p = 0.01). Mixed IHs were more likely to ulcerate than deep or superficial IHs (p = 0.01). Eighty percent of patients had treatment and 19% had surgery. Although IHs regressed by kindergarten entry in 70% of patients, 78% of these patients had residual skin changes. Mixed and superficial IHs left more residua than deep IHs (p = 0.04). A statistical comparison of treatments with respect to outcome at kindergarten entry could not be made because subgroups were too small and heterogeneous. CONCLUSION: Nasal IHs had higher rates of complications and treatment than previous reports of IHs at all body sites. Lesions of segmental and indeterminate type and mixed depth should be identified as high risk and treated accordingly. Parents may be counseled that most nasal IHs involute by kindergarten but leave residua and that early referral for treatment may be important for the best outcome.

Older age associated with better antidepressant response to H1-coil transcranial magnetic stimulation in female patients.

BACKGROUND: TMS is increasingly used to treat depression, but predictors of treatment outcomes remain unclear. We assessed the association between age and TMS response given inconsistent prior reports limited by small sample size, heterogeneity, outdated TMS parameters, lack of assessment of H1-coil TMS, and lack of an a priori hypothesis. We hypothesized that older age would be associated with better treatment response based on trends in recent large exploratory analyses. METHODS: We conducted a naturalistic retrospective analysis of patients (n = 378) ages 18-80 with depression (baseline Quick Inventory of Depressive Symptomatology Self-Report (QIDS-SR) > 5) who received 29-35 sessions of TMS between 2014 and 2021. Response was assessed using percent reduction of QIDS-SR. The relationship between percent response or remission and age group was assessed using the chi-square test. RESULTS: 85 % of patients received the standard protocol of H1-coil TMS to the left DLPFC. Percent response and remission rates for the entire study sample increased with age (response: p = .026; remission: p = .0023). This finding was stronger in female patients (response: p = .0033; remission: p = .00098) and was not observed in male patients (response: p = .73; remission: p = .26). This was confirmed in a sub-analysis of patients who only received the standard protocol with the H1-coil for the entire treatment course. LIMITATIONS: Naturalistic retrospective analysis from one academic center. CONCLUSIONS: Older age is associated with a better antidepressant response to H1-coil TMS in female patients. This was demonstrated in a hypothesis-driven confirmation of prior exploratory findings in a large sample size with a homogeneous data collection protocol across all participants.

Ultrasound-Guided Transthoracic Fine-Needle Aspiration: A Reliable Tool in Diagnosis and Molecular Profiling of Lung Masses.

INTRODUCTION: Pulmonary adenocarcinoma is a major cause of mortality worldwide. The majority of patients present with advanced stage disease, and minimally invasive procedures are desirable for diagnosis and treatment plans. Herein, we report our experience with percutaneous/transthoracic needle aspiration (TT-NA) in the cytologic diagnosis of pulmonary adenocarcinoma. MATERIAL AND METHODS: After institutional review board approval, the cytopathology electronic data system was searched for all consecutive TT-NA of the lung masses from January 2011 to November 2015. Patients' medical records were reviewed and cytologic materials were evaluated. RESULTS: A total of 151 specimens were identified, with a mean age of 62.8 years; 62.9% of the patients had a prior history of malignancy. Carcinoma/adenocarcinoma was the most common (80%) diagnosis. The targeted lesions were predominantly located in the lung (56.3%, 81/151) and pleural based (27.8%, 42/151). The mean size of the lesions was 3.6 cm. Cytology specimens were adequate in 70.9% of the cases, while 72.8% (110/151) of the cases also had concurrent core biopsy. A malignant diagnosis was rendered in the majority of the cases (64.9%). In 71% of the cases, immunohistochemistry/histochemistry studies were successfully performed. Molecular/genetic studies were requested in 80% of the cases and had adequate material. Complications of the procedure were seen in 9.9% of the patients including pneumothorax (7.9%) and hemoptysis (1.9%). CONCLUSION: TT-NA is a relatively safe and reliable technique in the assessment of pulmonary lesions.

Insertion and deletion polymorphisms of the ancient AluS family in the human genome.

BACKGROUND: Polymorphic Alu elements account for 17% of structural variants in the human genome. The majority of these belong to the youngest AluY subfamilies, and most structural variant discovery efforts have focused on identifying Alu polymorphisms from these currently retrotranspositionally active subfamilies. In this report we analyze polymorphisms from the evolutionarily older AluS subfamily, whose peak activity was tens of millions of years ago. We annotate the AluS polymorphisms, assess their likely mechanism of origin, and evaluate their contribution to structural variation in the human genome. RESULTS: Of 52 previously reported polymorphic AluS elements ascertained for this study, 48 were confirmed to belong to the AluS subfamily using high stringency subfamily classification criteria. Of these, the majority (77%, 37/48) appear to be deletion polymorphisms. Two polymorphic AluS elements (4%) have features of non-classical Alu insertions and one polymorphic AluS element (2%) likely inserted by a mechanism involving internal priming. Seven AluS polymorphisms (15%) appear to have arisen by the classical target-primed reverse transcription (TPRT) retrotransposition mechanism. These seven TPRT products are 3' intact with 3' poly-A tails, and are flanked by target site duplications; L1 ORF2p endonuclease cleavage sites were also observed, providing additional evidence that these are L1 ORF2p endonuclease-mediated TPRT insertions. Further sequence analysis showed strong conservation of both the RNA polymerase III promoter and SRP9/14 binding sites, important for mediating transcription and interaction with retrotransposition machinery, respectively. This conservation of functional features implies that some of these are fairly recent insertions since they have not diverged significantly from their respective retrotranspositionally competent source elements. CONCLUSIONS: Of the polymorphic AluS elements evaluated in this report, 15% (7/48) have features consistent with TPRT-mediated insertion, thus suggesting that some AluS elements have been more active recently than previously thought, or that fixation of AluS insertion alleles remains incomplete. These data expand the potential significance of polymorphic AluS elements in contributing to structural variation in the human genome. Future discovery efforts focusing on polymorphic AluS elements are likely to identify more such polymorphisms, and approaches tailored to identify deletion alleles may be warranted.

Dermatology in the North American Indian/Alaska Native population.

Dermatology is greatly understudied in the American Indian/Alaska Native (AIAN) population. This topic deserves attention in light of the changing demographics of the United States and the healthcare disparities faced by AIAN, including access to dermatologic care. In this review, we discuss disorders that are more prevalent or otherwise important in the AIAN population, such as cutaneous malignancies, photodermatoses, acanthosis nigricans, connective tissue disorders, cutaneous infections, hypertrophic scar formation, and Heck's disease. We aim to provide an updated review and increase awareness of the dermatologic needs of the AIAN population.