Large-scale RNA-seq mining reveals ciclopirox triggers TDP-43 cryptic exons.

Nuclear clearance and cytoplasmic aggregation of TDP-43 in neurons, initially identified in ALS-FTD, are hallmark pathological features observed across a spectrum of neurodegenerative diseases. We previously found that TDP-43 loss-of-function leads to the transcriptome-wide inclusion of deleterious cryptic exons in brains and biofluids post-mortem as well as during the presymptomatic stage of ALS-FTD, but upstream mechanisms that lead to TDP-43 dysregulation remain unclear. Here, we developed a web-based resource (SnapMine) to determine the levels of TDP-43 cryptic exon inclusion across hundreds of thousands of publicly available RNA sequencing datasets. We established cryptic exon inclusion across a variety of human cells and tissues to provide ground truth references for future studies on TDP-43 dysregulation. We then explored studies that were entirely unrelated to TDP-43 or neurodegeneration and found that ciclopirox olamine (CPX), an FDA-approved antifungal, can trigger the inclusion of TDP-43-associated cryptic exons in a variety of mouse and human primary cells. CPX induction of cryptic exon occurs via heavy metal toxicity and oxidative stress, suggesting that similar vulnerabilities could play a role in neurodegeneration. Our work demonstrates how diverse datasets can be linked through common biological features and underscores that public archives of sequencing data represent a vastly underutilized resource with tremendous potential for uncovering novel insights into complex biological mechanisms and diseases.

Age-dependent loss of HAPLN1 erodes vascular integrity via indirect upregulation of endothelial ICAM1 in melanoma.

Melanoma, the most lethal form of skin cancer, often has worse outcomes in older patients. We previously demonstrated that an age-related decrease in the secreted extracellular matrix (ECM) protein HAPLN1 has a role in slowing melanoma progression. Here we show that HAPLN1 in the dermal ECM is sufficient to maintain the integrity of melanoma-associated blood vessels, as indicated by increased collagen and VE-cadherin expression. Specifically, we show that HAPLN1 in the ECM increases hyaluronic acid and decreases endothelial cell expression of ICAM1. ICAM1 phosphorylates and internalizes VE-cadherin, a critical determinant of vascular integrity, resulting in permeable blood vessels. We found that blocking ICAM1 reduces tumor size and metastasis in older mice. These results suggest that HAPLN1 alters endothelial ICAM1expression in an indirect, matrix-dependent manner. Targeting ICAM1 could be a potential treatment strategy for older patients with melanoma, emphasizing the role of aging in tumorigenesis.

Novel Location-Based Survey Using Cognitive Interviews to Assess Geographic Networks and Hotspots of Sex and Drug Use: Implementation and Validation Study.

BACKGROUND: The Ending the HIV Epidemic initiative in the United States relies on HIV hotspots to identify where to geographically target new resources, expertise, and technology. However, interventions targeted at places with high HIV transmission and infection risk, not just places with high HIV incidence, may be more effective at reducing HIV incidence and achieving health equity. OBJECTIVE: We described the implementation and validation of a web-based activity space survey on HIV risk behaviors. The survey was intended to collect geographic information that will be used to map risk behavior hotspots as well as the geography of sexual networks in Los Angeles County. METHODS: The survey design team developed a series of geospatial questions that follow a 3-level structure that becomes more geographically precise as participants move through the levels. The survey was validated through 9 cognitive interviews and iteratively updated based on participant feedback until the saturation of topics and technical issues was reached. RESULTS: In total, 4 themes were identified through the cognitive interviews: functionality of geospatial questions, representation and accessibility, privacy, and length and understanding of the survey. The ease of use for the geospatial questions was critical as many participants were not familiar with mapping software. The inclusion of well-known places, landmarks, and road networks was critical for ease of use. The addition of a Google Maps interface, which was familiar to many participants, aided in collecting accurate and precise location information. The geospatial questions increased the length of the survey and warranted the inclusion of features to simplify it and speed it up. Using nicknames to refer to previously entered geographic locations limited the number of geospatial questions that appeared in the survey and reduced the time taken to complete it. The long-standing relationship between participants and the research team improved comfort to disclose sensitive geographic information related to drug use and sex. Participants in the cognitive interviews highlighted how trust and inclusive and validating language in the survey alleviated concerns related to privacy and representation. CONCLUSIONS: This study provides promising results regarding the feasibility of using a web-based mapping survey to collect sensitive location information relevant to ending the HIV epidemic. Data collection at several geographic levels will allow for insights into spatial recall of behaviors as well as future sensitivity analysis of the spatial scale of hotspots and network characteristics. This design also promotes the privacy and comfort of participants who provide location information for sensitive topics. Key considerations for implementing this type of survey include trust from participants, community partners, or research teams to overcome concerns related to privacy and comfort. The implementation of similar surveys should consider local characteristics and knowledge when crafting the geospatial components.

HIV incidence and risk factors among transgender women and cisgender men who have sex with men in two cities of China: a prospective cohort study.

BACKGROUND: HIV epidemic among men who have sex with men (MSM) remains a major public health concern in China. Despite a growing body of research on transgender women worldwide, little is known about Chinese transgender women within MSM. We sought to estimate HIV incidence and distinguish risk factors of HIV acquisition among them from that among cisgener (non-transgender) MSM (cis-MSM). METHODS: We conducted an open cohort study among Chinese MSM, including those who were identified as transgender in Shanghai and Tianjin. Participants were initially recruited by local community-based organizations from January to June, 2016, and were followed up approximately every 6 months until June 2018. At each visit, a structured questionnaire was used to gather information on demographics, sexual risk behaviors, and HIV status. HIV incidence was calculated as the number of seroconversions divided by total number of person-years of follow-up among HIV-negatives at baseline. Risk factors of HIV acquisition were assessed by univariate and multivariate Cox regression models with time-dependent variables. RESULTS: A total of 1056 participants contributed 1260.53 person-years (PYs) of follow-up, 33 HIV seroconversions occurred during the follow-up period, yielding an estimated HIV incidence of 2.62 (95% CI 1.80-3.68) per 100 PYs. HIV incidence among transgender women was 4.42 per 100 PYs, which was significantly higher than that of 1.35 per 100 PYs among cis-MSM, demonstrating a threefold higher odds of HIV infection than cis-MSM. For transgender women, those lived locally ≤ 2 years (adjusted hazard ratio [aHR] = 1.76, 95% CI 1.13-2.76) and unprotected anal sex last time (aHR = 4.22, 95% CI 1.82-9.79) were more likely to acquire HIV. For cis-MSM, factors associated with HIV acquisition were frequency of anal sex ≥ 3 times in past one month (aHR = 4.19, 95% CI 1.06-16.47) and unprotected anal sex last time (aHR = 5.33, 95% CI 1.52-18.73). CONCLUSIONS: Compared to cis-MSM, transgender women were at higher risk of HIV acquisition, highlighting an urgent need of tailored prevention. Future HIV program should consider to include them to ensure that this population in China are not left behind.

Using Social Media To Increase HIV Testing Among Men Who Have Sex with Men - Beijing, China, 2013-2017.

The prevalence of human immunodeficiency virus (HIV) infection in China is low overall (0.06%) (1); however, it is substantially higher (8.0%) among men who have sex with men (MSM) (2), and the stigmatization of same-sex behaviors in China presents challenges for HIV prevention and treatment efforts. In 2015, Blued, a Beijing-based media company that operates an online dating application popular among Chinese MSM, launched an ongoing HIV testing campaign that combined its push-notification† platform and geolocation capabilities to encourage HIV testing among MSM in Beijing. To assess trends in use of HIV testing services, Blued and CDC's China HIV program examined testing at six Blued-operated Beijing HIV testing centers from 2 years before the campaign launch in 2015 through December 31, 2017. A sharp increase in HIV testing followed the launch of Blued's online campaign, indicating that leveraging social media platforms and their geolocation-based text messaging functionality might be useful in increasing HIV testing among MSM, particularly those aged ≤35 years.

Comparing Outcomes of HIV-Infected Chinese Adults on Antiretroviral Therapy by CD4 Count at Treatment Initiation: A Nationwide Retrospective Observational Cohort Study, 2012-2014.

The chief concerns for antiretroviral therapy (ART) programs considering removal of CD4+ cell count thresholds for treatment are the increased incidence of ART-related adverse events. A nationwide observational cohort study was conducted among patients who initiated ART in 2012. We divided the eligible patients into three groups: an early ART group with a baseline CD4+ cell count of 500 cells/µL or greater, a standard ART group with a baseline CD4+ cell count between 350 and 499 cells/µL, and a late ART group with a baseline CD4+ cell count between 200 and 349 cells/µL. These patients were followed up to December 31, 2014 and observed for three outcomes: virological failure, treatment nonretention, or time to death. Patients who met the eligibility criteria numbered at 26,752. Out of all study participants, 20,827 participants were in late ART group, 4336 were in standard ART group, and 1589 were in early ART group. Patients in late ART group were more likely to become virally suppressed 12 and 24 months after treatment initiation than patients in early ART group [adjusted odds ratio (aOR) 0.81; 95% CI, 0.69-0.95 and aOR, 0.78; 95% CI, 0.65-0.94]. Treatment nonretention was also less likely to occur among patients in late ART group than early ART group 12 months after treatment initiation (aOR, 0.85; 95% CI, 0.75-0.96). Compared with early ART group, neither standard ART group nor late ART group had a statistically significant difference in the time-to-death analysis. Late ART initiates were more likely to be virally suppressed and retained on treatment than early ART initiates. The importance of treatment retention and adherence should be emphasized for high CD4+ patients newly initiated to ART therapy through education and counseling programs.

Content-specific auditing of a large scale anatomy ontology.

Biomedical ontologies are envisioned to be usable in a range of research and clinical applications. The requirements for such uses include formal consistency, adequacy of coverage, and possibly other domain specific constraints. In this report we describe a case study that illustrates how application specific requirements may be used to identify modeling problems as well as data entry errors in ontology building and evolution. We have begun a project to use the UW Foundational Model of Anatomy (FMA) in a clinical application in radiation therapy planning. This application focuses mainly (but not exclusively) on the representation of the lymphatic system in the FMA, in order to predict the spread of tumor cells to regional metastatic sites. This application requires that the downstream relations associated with lymphatic system components must only be to other lymphatic chains or vessels, must be at the appropriate level of granularity, and that every path through the lymphatic system must terminate at one of the two well known trunks of the lymphatic system. It is possible through a programmable query interface to the FMA to write small programs that systematically audit the FMA for compliance with these constraints. We report on the design of some of these programs, and the results we obtained by applying them to the lymphatic system. The algorithms and approach are generalizable to other network organ systems in the FMA such as arteries and veins. In addition to illustrating exact constraint checking methods, this work illustrates how the details of an application may reflect back a requirement to revise the design of the ontology itself.