Examining the Roles of H3K4 Methylation States with Systematically Characterized Antibodies.

Histone post-translational modifications (PTMs) are important genomic regulators often studied by chromatin immunoprecipitation (ChIP), whereby their locations and relative abundance are inferred by antibody capture of nucleosomes and associated DNA. However, the specificity of antibodies within these experiments has not been systematically studied. Here, we use histone peptide arrays and internally calibrated ChIP (ICeChIP) to characterize 52 commercial antibodies purported to distinguish the H3K4 methylforms (me1, me2, and me3, with each ascribed distinct biological functions). We find that many widely used antibodies poorly distinguish the methylforms and that high- and low-specificity reagents can yield dramatically different biological interpretations, resulting in substantial divergence from the literature for numerous H3K4 methylform paradigms. Using ICeChIP, we also discern quantitative relationships between enhancer H3K4 methylation and promoter transcriptional output and can measure global PTM abundance changes. Our results illustrate how poor antibody specificity contributes to the "reproducibility crisis," demonstrating the need for rigorous, platform-appropriate validation.

Fatty acid binding protein 5 inhibition attenuates pronociceptive cytokine/chemokine expression and suppresses osteoarthritis pain: A comparative human and rat study.

OBJECTIVE: Osteoarthritis (OA) is often accompanied by debilitating pain that is refractory to available analgesics due in part to the complexity of signaling molecules that drive OA pain and our inability to target these in parallel. Fatty acid binding protein 5 (FABP5) is a lipid chaperone that regulates inflammatory pain; however, its contribution to OA pain has not been characterized. DESIGN: This combined clinical and pre-clinical study utilized synovial tissues obtained from subjects with end-stage OA and rats with monoiodoacetate-induced OA. Cytokine and chemokine release from human synovia incubated with a selective FABP5 inhibitor was profiled with cytokine arrays and ELISA. Immunohistochemical analyses were conducted for FABP5 in human and rat synovium. The efficacy of FABP5 inhibitors on pain was assessed in OA rats using incapacitance as an outcome. RNA-seq was then performed to characterize the transcriptomic landscape of synovial gene expression in OA rats treated with FABP5 inhibitor or vehicle. RESULTS: FABP5 was expressed in human synovium and FABP5 inhibition reduced the secretion of pronociceptive cytokines (interleukin-6 [IL6], IL8) and chemokines (CCL2, CXCL1). In rats, FABP5 was upregulated in the OA synovium and its inhibition alleviated incapacitance. The transcriptome of the rat OA synovium exhibited >6000 differentially expressed genes, including the upregulation of numerous pronociceptive cytokines and chemokines. FABP5 inhibition blunted the upregulation of the majority of these pronociceptive mediators. CONCLUSIONS: FABP5 is expressed in the OA synovium and its inhibition suppresses pronociceptive signaling and pain, indicating that FABP5 inhibitors may constitute a novel class of analgesics to treat OA.

A critical role for Macrophage-derived Cysteinyl-Leukotrienes in HIV-1 induced neuronal injury.

Macrophages (MΦ) infected with human immunodeficiency virus (HIV)-1 or activated by its envelope protein gp120 exert neurotoxicity. We found previously that signaling via p38 mitogen-activated protein kinase (p38 MAPK) is essential to the neurotoxicity of HIVgp120-stimulated MΦ. However, the associated downstream pathways remained elusive. Here we show that cysteinyl-leukotrienes (CysLT) released by HIV-infected or HIVgp120 stimulated MΦ downstream of p38 MAPK critically contribute to neurotoxicity. SiRNA-mediated or pharmacological inhibition of p38 MAPK deprives MΦ of CysLT synthase (LTC4S) and, pharmacological inhibition of the cysteinyl-leukotriene receptor 1 (CYSLTR1) protects cerebrocortical neurons against toxicity of both gp120-stimulated and HIV-infected MΦ. Components of the CysLT pathway are differentially regulated in brains of HIV-infected individuals and a transgenic mouse model of NeuroHIV (HIVgp120tg). Moreover, genetic ablation of LTC4S or CysLTR1 prevents neuronal damage and impairment of spatial memory in HIVgp120tg mice. Altogether, our findings suggest a novel critical role for cysteinyl-leukotrienes in HIV-associated brain injury.

Extramammary Paget Disease. Part II. Evidence-based Approach to Management.

Extramammary Paget disease is a rare cutaneous malignancy that most commonly affects the genitals, perianal area, and axilla of elderly patients. Delays in care often lead to high levels of disease burden for patients. Thus, evidence-based recommendations are paramount in mitigating morbidity and mortality for this unique patient population. This 2-part continuing medical education series provides a complete picture of extramammary Paget disease. Part 2 of this continuing medical education series focuses on the complex management of extramammary Paget disease including surgical and non-invasive therapies, as well as novel approaches for advanced disease.

Extramammary Paget Disease. Part I. Epidemiology, Pathogenesis, Clinical Features, and Diagnosis.

Extramammary Paget disease (EMPD) is a rare skin cancer of apocrine-rich skin that mimics common inflammatory and infectious dermatoses, leading to delays in diagnosis and increased patient morbidity. Better clinical recognition of this entity, multidisciplinary patient assessment, and deeper understanding of the underlying pathophysiology are essential to improve patient care and disease outcomes. It is important to distinguish primary intraepithelial/micro-invasive EMPD from invasive EMPD or cases with adenocarcinoma arising within EMPD. This 2-part continuing medical education series provides a complete picture of EMPD. Part 1 of this continuing medical education series reviews the epidemiology, oncogenesis, clinical and histopathologic presentation, workup, and prognosis of this rare cancer.

Jet-injection assisted photodynamic therapy for superficial and nodular basal cell carcinoma: A pilot study.

BACKGROUND: Photodynamic therapy (PDT) with topical δ-Aminolevulinic acid (ALA) has efficacy in treating basal cell carcinoma (BCC) but is limited by incomplete penetration of ALA into the deeper dermis. This prospective open-label pilot trial investigated the safety and efficacy of photosensitizer jet injection for PDT (JI-PDT) for BCC treatment. It was performed with 15 patients (n = 15) with histologically confirmed, untreated, low-risk nodular BCCs at a single institution. METHODS: For the intervention, JI-PDT patients (n = 11) received two sessions of jet-injected ALA with PDT separated by four to 6 weeks. To further understand treatment technique, another group of patients (n = 4) received jet-injected ALA followed by tumor excision and fluorescence microscopy (JI-E). Treatment tolerability was assessed by local skin responses (LSR) score at five distinct time intervals. Fluorescence microscopy assessed protoporphyrin IX penetration depth and biodistribution within the tumor. At the primary endpoint, tumor clearance was evaluated via visual inspection, dermoscopy and reflectance confocal microscopy. Postinjection and postillumination pain levels, and patient satisfaction, were scored on a 0-10 scale. RESULTS: Fifteen participants with mean age of 58.3, who were 15/15 White, non-Hispanic enrolled. The median composite LSR score immediately after JI-PDT was 5 (interquartile range [IQR] = 3) which decreased to 0.5 (IQR = 1) at primary endpoint (p < 0.01). Immunofluorescence of excised BCC tumors with jet-injected ALA showed photosensitizer penetration into papillary and reticular dermis. Of the 13 JI-PDT tumors, 11 had tumor clearance confirmed, 1 recurred, and 1 was lost to follow-up. 1/11 patients experienced a serious adverse event of cellulitis. 70% of patients had local scarring at 3 months. Patients reported an average pain level of 5.6 (standard deviation [SD] = 2.3) during jet injection and 3.7 (SD = 1.8) during light illumination. CONCLUSIONS: Jet injection of ALA for PDT treatment of nodular low-risk BCC is tolerable and feasible and may represent a novel modality to improve PDT.

Artificial Intelligence in Dermatology: A Systematic Review of Its Applications in Melanoma and Keratinocyte Carcinoma Diagnosis.

BACKGROUND: Limited access to dermatologic care may pose an obstacle to the early detection and intervention of cutaneous malignancies. The role of artificial intelligence (AI) in skin cancer diagnosis may alleviate potential care gaps. OBJECTIVE: The aim of this systematic review was to offer an in-depth exploration of published AI algorithms trained on dermoscopic and macroscopic clinical images for the diagnosis of melanoma, basal cell carcinoma, and cutaneous squamous cell carcinoma (cSCC). METHODS: Adhering to the Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines, a systematic review was conducted on peer-reviewed articles published between January 1, 2000, and January 26, 2023. RESULTS AND DISCUSSION: Among the 232 studies in this review, the overall accuracy, sensitivity, and specificity of AI for tumor detection averaged 90%, 87%, and 91%, respectively. Model performance improved with time. Despite seemingly impressive performance, the paucity of external validation and limited representation of cSCC and skin of color in the data sets limits the generalizability of the current models. In addition, dermatologists coauthored only 12.9% of all studies included in the review. Moving forward, it is imperative to prioritize robustness in data reporting, inclusivity in data collection, and interdisciplinary collaboration to ensure the development of equitable and effective AI tools.

Current Landscape of Hyaluronic Acid Filler Use in the United States.

BACKGROUND: Hyaluronic acid (HA) fillers are among the most used fillers for soft-tissue augmentation. There are now many FDA-approved HA products, and the successful use of injectable HA fillers requires an understanding of the available options.  Objective: The purpose of this manuscript is to provide a comprehensive list of HA fillers and their indications. An overview of their biochemical properties and formulations will aid dermatologists in appropriate use. METHODS: A comprehensive search of all the FDA-approved dermal fillers was conducted via the FDA "pre-market approval" (PMA) site. Additional details regarding filler properties were obtained using the respective agent's package inserts.  Results: A total of 28 HA dermal fillers were identified and key pharmaceutical properties were discussed. These findings will help the physician match the appropriate HA filler with the area that is to be treated.  Conclusion: Understanding the available fillers and their properties can help physicians select the appropriate fillers for more predictable and sustainable results.  J Drugs Dermatol. 2024;23(1):1247-1252.    doi:10.36849/JDD.7858.

Discovery and Synthesis of a Naturally Derived Protein Kinase Inhibitor that Selectively Inhibits Distinct Classes of Serine/Threonine Kinases.

The DNAJB1-PRKACA oncogenic gene fusion results in an active kinase enzyme, J-PKAcα, that has been identified as an attractive antitumor target for fibrolamellar hepatocellular carcinoma (FLHCC). A high-throughput assay was used to identify inhibitors of J-PKAcα catalytic activity by screening the NCI Program for Natural Product Discovery (NPNPD) prefractionated natural product library. Purification of the active agent from a single fraction of an Aplidium sp. marine tunicate led to the discovery of two unprecedented alkaloids, aplithianines A (1) and B (2). Aplithianine A (1) showed potent inhibition against J-PKAcα with an IC50 of ∼1 µM in the primary screening assay. In kinome screening, 1 inhibited wild-type PKA with an IC50 of 84 nM. Further mechanistic studies including cocrystallization and X-ray diffraction experiments revealed that 1 inhibited PKAcα catalytic activity by competitively binding to the ATP pocket. Human kinome profiling of 1 against a panel of 370 kinases revealed potent inhibition of select serine/threonine kinases in the CLK and PKG families with IC50 values in the range ∼11-90 nM. An efficient, four-step total synthesis of 1 has been accomplished, enabling further evaluation of aplithianines as biologically relevant kinase inhibitors.

Exposure to polylactic acid induces oxidative stress and reduces the ceramide levels in larvae of greater wax moth (Galleria mellonella).

Plastic biodegradation by insects has made significant progress, opening up new avenues for the treatment of plastic waste. Wax moth larvae, for example, have attracted the attention of the scientific community because they are known to chew, ingest, and biodegrade natural polymer bee waxes. Despite this, we know very little about how these insects perform on manufactured plastics or how manufactured plastics affect insect metabolism. As a result, we studied the metabolism of greater wax moths (Galleria mellonella) fed on molasses-supplemented polylactic acid plastic (PLA) blocks. An analysis of the central carbon metabolism (CCM) metabolites was performed using liquid chromatography triple quadrupole mass spectrometry (LC-QQQ-MS), while an analysis of untargeted metabolites and lipids was conducted using liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QToF-MS). In total, 169 targeted CCM metabolites, 222 untargeted polar metabolites, and 196 untargeted nonpolar lipids were identified within the insect samples. In contrast, compared to control larvae, PLA-fed larvae displayed significantly different levels of 97 CCM metabolites, 75 polar metabolites, and 57 lipids. Purine and pyrimidine metabolisms were affected by PLA feeding, as well as amino acid metabolism, carbohydrates, cofactors, vitamins, and related metabolisms. Additionally, PLA exposure disrupted insect energy metabolism and oxidative stress, among other metabolic disturbances. The larvae fed PLA have lower levels of several lipids, suggesting a reduction in lipid reserves, and ceramide levels are likely to have changed due to apoptosis and inflammation. The study indicates that G. mellonella larvae could ingest PLA but this process causes some metabolic stress for the host. Future studies of the molecular pathways of this biodegradation process might help to provide strategies for stress reduction that would speed up insect digestion of plastic.

Postoperative micronutrient changes in bariatric surgery patients compliant with nutritional supplementation.

BACKGROUND: Bariatric surgery is commonly used in patients with body mass indexes over 35 kg/m and obesity-related comorbidities. Despite the significant clinical benefits of bariatric surgery, nutritional deficiencies post-surgery remain a challenge for both patient and healthcare provider [Toninello et al. in Nutrients 13:1565, 2021, Gasmi et al. in Eur J Nutr 61:55-67, 2022]. Nutritional supplementation is a way of reducing the likelihood of postoperative deficiencies; however, prior studies have shown varying degrees of mostly poor to moderate patient adherence [Spetz et al. in Obes Res Clin Pract 16:407-412, 2022, Mahawar et al. in Obes Surg 29:1551-1556, 2019, Santonicola et al. in J Am Nutr Assoc 41:11-19, 2022, Sherf Dagan et al. in Obes Surg 27:2258-2271, 2017]. Our present study aims to provide insights into the micronutrient biochemical profile in patients previously found to be compliant with supplementation following roux-en-y gastric bypass (RYGB) and vertical sleeve gastrectomy (VSG). METHODS: An 11-point outpatient survey was administered to consecutive patients ≥ 18 years who had undergone either RYGB or VSG to determine adherence with nutritional supplementation. Medical records were retrospectively reviewed to determine preoperative and postoperative lab values, including vitamins A, B1, B12, and D, thyroid stimulating hormone (TSH), iron binding capacity, transferrin, ferritin, folate, iron, albumin, hemoglobin A1C, zinc, glomerular filtration rate (GFR, and liver function values. Values were classified as "abnormal" or "normal." Preoperative and postoperative values were compared for differences. Postoperative values were also compared between RYGB and VSG. RESULTS: There were no significant differences between preoperative and postoperative values for any nutritional marker aside from vitamin B12. A total of 51/60 patients (85.0%) had normal preoperative B12 measurements, compared with 40/65 (61.5%) patients postoperatively (P = 0.03). Notably, of 25 "abnormal" postoperative measurements, 20 (80%) were elevated values. There were no differences in postoperative deficiencies between RYGB and VSG. CONCLUSIONS: Patients in our sample did not have worsened micronutrient deficiencies following bariatric surgery, and there were no differences in micronutrient deficiencies between surgical technique.

Patient perspectives on post-bariatric surgery nutritional supplementation.

BACKGROUND: Bariatric procedures increase patient risk of long-term metabolic complications primarily due to nutrient deficiencies. The mainstay of prevention includes routine vitamin and mineral supplementation; however, patient-reported barriers to daily compliance are poorly understood. METHODS: Post-bariatric surgery patients electively participated in an 11-point outpatient survey at a single academic institution. Surgical procedures included either laparoscopic sleeve gastrectomy (SG) or gastric bypass (GB). At the time of survey, patients ranged from 1-month to 15 years from surgery. Survey items consisted of dichotomous (yes/no), multiple choice, and open-ended free response questions. Descriptive statistics were evaluated. RESULTS: Two hundred and fourteen responses were collected, 116 (54%) underwent SG and 98 (46%) underwent GB. Of these, 49% of samples were during short-term postoperative follow-up visits (0-3 months), 34% intermediate follow-up (4-12 months), and 17% long-term follow-up (> 1 year). A total of 98% of patients reported that insurance did not cover their supplement cost. Most patients reported current vitamin use (95%), with 87% reporting daily compliance. Daily compliance was observed in 94%, 79%, and 73% of SG patients at short-, intermediate-, and long-term follow-up visits, respectively. While GB patients reported daily compliance in 84%, 100%, and 92% of short, intermediate, and long-term responses. Of those who were unable to take vitamins daily, non-compliance was attributed most to forgetting (54%), and less often to side effects (11%), or taste (11%). Patient-reported strategies for remembering to take vitamins included tying into daily routine (55%), use of a pill box (7%), and alarm reminders (7%). CONCLUSIONS: Daily compliance with post-bariatric surgery vitamin supplementation does not appear to vary based on postoperative time-period or surgical procedure. While a minority of patients struggle with daily compliance, factors associated with non-compliance include patient forgetting, side effects, and taste. Widespread utilization of patient-reported daily reminder strategies may lead to improved overall compliance and reduce incidence of nutritional deficiencies.

Laser therapy as a treatment for chronic radiation fibrosis.

BACKGROUND: Chronic radiation fibrosis (CRF) is a long-term sequala of radiation therapy that has a significant impact on patient quality of life. There is no standard of care or single therapeutic modality that has been found to be consistently effective. OBJECTIVE: To describe our experience using fractional 10,600 nm carbon dioxide (CO2 ) laser therapy and vascular laser therapy in a series of patients with CRF. METHODS: Patients presenting to the dermatology service for CRF were evaluated for laser therapy eligibility. Patients were eligible if they had a clinical diagnosis of CRF confirmed by physical examination. RESULTS: We identified five patients with CRF treated with fractional ablative CO2 laser and vascular laser. Patients were a median age of 57 years old, and the amount of time between the initiation of radiotherapy and laser treatment ranged between 3 months and 40 years. The satisfactory response was achieved in all cases. LIMITATIONS: Lack of standardized laser protocol, small sample size, lack of a control group, different anatomical locations CONCLUSION: Fractional ablative and vascular laser therapy may serve as an additional treatment for CRF, leading to functional improvements.

A Randomized Control Trial Comparing the Efficacy of Platelet-Rich Plasma and 5% Topical Minoxidil for the Treatment of Androgenetic Alopecia.

Androgenetic alopecia (AGA) is the most common cause of hair loss in men and has limited treatment options. Minoxidil is a common therapeutic option for AGA patients because of its availability. Platelet-rich plasma (PRP) therapy is a newer option in AGA management with promising results that may be suitable for some patients. Despite a great prevalence of AGA outside the United States and Europe, there remains limited studies on the efficacy of PRP for AGA treatment. Our study's objective was to compare the efficacy of PRP and minoxidil therapy for the treatment of AGA in a Pakistani population. 72 patients were included in this randomized control trial and were either treated with PRP or topical minoxidil. After 12 weeks of treatment, the hair pull test was performed and extracted hair was counted. We report a 91.7% negative hair pull rate in the PRP treatment group which was significantly greater than the 69.4% negative hair pull rate in the minoxidil-treated group. Our study suggests that PRP therapy demonstrates a higher efficacy compared to minoxidil for treating AGA, especially in our patient demographic. These results have the opportunity to improve patient compliance and overall satisfaction while offering an improved option in patients unsatisfied with topical minoxidil.  Citation: Shah R, Asim M, Ouellette S, et al. A randomized control trial comparing the efficacy of platelet-rich plasma and 5% topical minoxidil for the treatment of androgenetic alopecia. J Drugs Dermatol. 2023;22(9):905-909. doi:10.36849/JDD.7031.

Topical Application of 0.5% Timolol Maleate Hydrogel for the Treatment of Superficial Infantile Hemangiomas.

BACKGROUND: Oral propranolol is considered the first line therapy in the treatment of infantile hemangiomas (IHs). However, there are considerable side effects due to its ability to penetrate the blood brain barrier. Alternatively, topical timolol, a non-selective beta blocker, has resulted in fewer side effects and is 4–10 times more potent in comparison to oral propranolol. This study evaluates the efficacy of 0.5% timolol maleate hydrogel for the treatment of IH. METHODS: This study was conducted via a quasi-experimental design from October 30, 2020 – April 29, 2021, at the Department of Dermatology Benazir Bhutto Hospital, Rawalpindi. 145 infants between 1–12 months in age diagnosed with superficial cutaneous hemangiomas were included in the study with a male to female ratio of 2.4:1. A thin layer of timolol maleate 0.5% hydrogel was applied to the entire surface of the patient’s IH three times daily. Digital photographs and measurements of the hemangiomas were taken at one-month intervals for a maximum of 6 months. RESULTS: The age range in this study was from 1–12 months with a mean age of 6.10 ± 2.52 months. The majority of the patients 89 (61.4%) were between 1–6 months of age. Of the 145 patients, 89 (61.4%) showed an excellent response, 44 (30.3%) showed a good response, and 12 (8.3%) showed no response to the topical 0.5% timolol maleate hydrogel treatment. CONCLUSION: The use of topical 0.5% timolol maleate hydrogel is a promising therapeutic option for the treatment of superficial IHs. Anwar F, Mahmood E, Sharif S, et al. Topical application of 0.5% timolol maleate hydrogel for the treatment of superficial infantile hemangiomas. J Drugs Dermatol. 2023;22(6):594-598. doi:10.36849/JDD.7054.

Comparing the Efficacy for Pulse Versus Continuous Dose Terbinafine Therapy in Patients With Onychomycosis.

Recently, treatment outcomes in patients with toenail onychomycosis have improved considerably due to more effective oral antifungal medications such as terbinafine and itraconazole. These medications can either be used continuously for several weeks at a lower dose or intermittently (pulsed) at a higher dose. Previous literature comparing pulse and continuous therapy has generated mixed results.  Our study aims to compare the efficacy, in terms of clinical cure rate, of continuous vs pulse dose terbinafine regimens for toenail onychomycosis. Sixty patients with onychomycosis of Fitzpatrick skin types IV to VI, between 15 and 65 years of age, were divided into a continuous treatment group receiving 250 mg terbinafine once daily for 12 weeks and a pulse treatment group receiving 250 mg twice daily terbinafine for 1 week repeated every 4 weeks for 12 weeks. Each patient was followed up at weeks 4, 8, and 12.  Efficacy of the continuous treatment group was significantly greater at 76.67% compared with 26.67% in the pulse treatment group. Thus, we conclude that the clinical cure rate of a continuous dose regimen of terbinafine is a superior treatment option for toenail onychomycosis. However, we also suggest further studies including combinations of multiple agents and hybrid regimen models for the optimal onychomycosis treatment.   J Drugs Dermatol. 2023;22(10):     doi:10.36849/JDD.7323R1.

Gut Microbial Perturbation and Host Response Induce Redox Pathway Upregulation along the Gut-Liver Axis during Giardiasis in C57BL/6J Mouse Model.

Apicomplexan infections, such as giardiasis and cryptosporidiosis, negatively impact a considerable proportion of human and commercial livestock populations. Despite this, the molecular mechanisms of disease, particularly the effect on the body beyond the gastrointestinal tract, are still poorly understood. To highlight host-parasite-microbiome biochemical interactions, we utilised integrated metabolomics-16S rRNA genomics and metabolomics-proteomics approaches in a C57BL/6J mouse model of giardiasis and compared these to Cryptosporidium and uropathogenic Escherichia coli (UPEC) infections. Comprehensive samples (faeces, blood, liver, and luminal contents from duodenum, jejunum, ileum, caecum and colon) were collected 10 days post infection and subjected to proteome and metabolome analysis by liquid and gas chromatography-mass spectrometry, respectively. Microbial populations in faeces and luminal washes were examined using 16S rRNA metagenomics. Proteome-metabolome analyses indicated that 12 and 16 key pathways were significantly altered in the gut and liver, respectively, during giardiasis with respect to other infections. Energy pathways including glycolysis and supporting pathways of glyoxylate and dicarboxylate metabolism, and the redox pathway of glutathione metabolism, were upregulated in small intestinal luminal contents and the liver during giardiasis. Metabolomics-16S rRNA genetics integration indicated that populations of three bacterial families-Autopobiaceae (Up), Desulfovibrionaceae (Up), and Akkermanasiaceae (Down)-were most significantly affected across the gut during giardiasis, causing upregulated glycolysis and short-chained fatty acid (SCFA) metabolism. In particular, the perturbed Akkermanasiaceae population seemed to cause oxidative stress responses along the gut-liver axis. Overall, the systems biology approach applied in this study highlighted that the effects of host-parasite-microbiome biochemical interactions extended beyond the gut ecosystem to the gut-liver axis. These findings form the first steps in a comprehensive comparison to ascertain the major molecular and biochemical contributors of host-parasite interactions and contribute towards the development of biomarker discovery and precision health solutions for apicomplexan infections.

Sequence deeper without sequencing more: Bayesian resolution of ambiguously mapped reads.

Next-generation sequencing (NGS) has transformed molecular biology and contributed to many seminal insights into genomic regulation and function. Apart from whole-genome sequencing, an NGS workflow involves alignment of the sequencing reads to the genome of study, after which the resulting alignments can be used for downstream analyses. However, alignment is complicated by the repetitive sequences; many reads align to more than one genomic locus, with 15-30% of the genome not being uniquely mappable by short-read NGS. This problem is typically addressed by discarding reads that do not uniquely map to the genome, but this practice can lead to systematic distortion of the data. Previous studies that developed methods for handling ambiguously mapped reads were often of limited applicability or were computationally intensive, hindering their broader usage. In this work, we present SmartMap: an algorithm that augments industry-standard aligners to enable usage of ambiguously mapped reads by assigning weights to each alignment with Bayesian analysis of the read distribution and alignment quality. SmartMap is computationally efficient, utilizing far fewer weighting iterations than previously thought necessary to process alignments and, as such, analyzing more than a billion alignments of NGS reads in approximately one hour on a desktop PC. By applying SmartMap to peak-type NGS data, including MNase-seq, ChIP-seq, and ATAC-seq in three organisms, we can increase read depth by up to 53% and increase the mapped proportion of the genome by up to 18% compared to analyses utilizing only uniquely mapped reads. We further show that SmartMap enables the analysis of more than 140,000 repetitive elements that could not be analyzed by traditional ChIP-seq workflows, and we utilize this method to gain insight into the epigenetic regulation of different classes of repetitive elements. These data emphasize both the dangers of discarding ambiguously mapped reads and their power for driving biological discovery.

Pre-COVID-19 National Mortality Trends in Open and Video-Assisted Lobectomy for Non-Small Cell Lung Cancer.

INTRODUCTION: In the current era of episode-based hospital reimbursements, it is important to determine the impact of hospital size on contemporary national trends in surgical technique and outcomes of lobectomy. METHODS: Patients aged >18 y undergoing open and video-assisted thoracoscopic surgery (VATS) lobectomy from 2008 to 2014 were identified using insurance claims data from the National Inpatient Sample. The impact of hospital size on surgical approach and outcomes for both open and VATS lobectomy were analyzed. RESULTS: Over the 7-y period, 202,668 lobectomies were performed nationally, including 71,638 VATS and 131,030 open. Although the overall number of lobectomies decreased (30,058 in 2008 versus 27,340 in 2014, P < 0.01), the proportion of VATS lobectomies increased (24.0% versus 46.9%), and open lobectomies decreased (76.0% versus 53.0%, all P < 0.01). When stratified by hospital size, small hospitals had a significant increase in the proportion of open lobectomies (6.4%-12.2%; P = 0.01) and trend toward increased number of VATS lobectomies (2.7%-12.2%). Annual mortality rates for VATS (range: 1.0%-1.9%) and open (range: 1.9%-2.4%) lobectomy did not significantly differ over time (all P > 0.05) but did decrease among small hospitals (4.1%-1.3% and 5.1%-1.1% for VATS and open, respectively; both P < 0.05). After adjusting for confounders, hospital bed size was not a predictor of in-hospital mortality. CONCLUSIONS: Utilization of VATS lobectomies has increased over time, more so among small hospitals. Mortality rates for open lobectomy remain consistently higher than VATS lobectomy (range 0.4%-1.4%) but did not significantly differ over time. This data can help benchmark hospital performance in the future.

Lichen planus pemphigoides: A unique form of bullous and lichenoid eruptions secondary to nivolumab.

The widespread use of PD-1 inhibitors to treat various solid tumors has brought certain challenges for the clinician, including immune-related adverse events (irAEs). Cutaneous toxicities are among the most observed irAEs. Bullous and lichenoid dermatoses following PD-1 inhibitor therapy have been described. Here we report a novel case of lichen planus pemphigoides, featuring characteristics of both bullous pemphigoid and lichen planus, in a patient treated with nivolumab for renal cell carcinoma. We subsequently review all three cutaneous conditions which may arise in the context of PD-1 inhibitor therapy.