Cellular Location of HNF4α is Linked With Terminal Liver Failure in Humans

Hepatocyte nuclear factor 4 alpha (HNF4α) is a transcription factor that plays a critical role in hepatocyte function, and HNF4α-based reprogramming corrects terminal liver failure in rats with chronic liver disease. In the livers of patients with advanced cirrhosis, HNF4α RNA expression levels decrease as hepatic function deteriorates, and protein expression is found in the cytoplasm. These findings could explain impaired hepatic function in patients with degenerative liver disease. In this study, we analyzed HNF4α localization and the pathways involved in post-translational modification of HNF4α in human hepatocytes from patients with decompensated liver function. RNA-sequencing analysis revealed that AKT-related pathways, specifically phospho-AKT, is down-regulated in cirrhotic hepatocytes from patients with terminal failure, in whom nuclear levels of HNF4α were significantly reduced, and cytoplasmic expression of HNF4α was increased. cMET was also significantly reduced in failing hepatocytes. Moreover, metabolic profiling showed a glycolytic phenotype in failing human hepatocytes. The contribution of cMET and phospho-AKT to nuclear localization of HNF4α was confirmed using Spearman's rank correlation test and pathway analysis, and further correlated with hepatic dysfunction by principal component analysis. HNF4α acetylation, a posttranslational modification important for nuclear retention, was also significantly reduced in failing human hepatocytes when compared with normal controls. Conclusion: These results suggest that the alterations in the cMET-AKT pathway directly correlate with HNF4α localization and level of hepatocyte dysfunction. This study suggests that manipulation of HNF4α and pathways involved in HNF4α posttranslational modification may restore hepatocyte function in patients with terminal liver failure.Fil: Florentino, Rodrigo M.. Univeristy of Pittsburgh. School of Medicine; Estados Unidos. Universidade Federal de Minas Gerais; BrasilFil: Fraunhoffer Navarro, Nicolas Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Centro de Estudios Farmacológicos y Botánicos. Universidad de Buenos Aires. Facultad de Medicina. Centro de Estudios Farmacológicos y Botánicos; ArgentinaFil: Morita, Kazutoyo. University of Pittsburgh at Johnstown; Estados UnidosFil: Takeishi, Kazuki. University of Pittsburgh at Johnstown; Estados UnidosFil: Ostrowska, Alina. University of Pittsburgh at Johnstown; Estados UnidosFil: Achreja, Abhinav. Michigan State University; Estados UnidosFil: Animasahun, Olamide. Michigan State University; Estados UnidosFil: Haep, Nils. University of Pittsburgh at Johnstown; Estados UnidosFil: Arazov, Shohrat. University of Pittsburgh at Johnstown; Estados UnidosFil: Agarwal, Nandini. University of Pittsburgh at Johnstown; Estados UnidosFil: Collin de lHortet, Alexandra. University of Pittsburgh at Johnstown; Estados UnidosFil: Guzman Lepe, Jorge. University of Pittsburgh at Johnstown; Estados UnidosFil: Tafaleng, Edgar N.. University of Pittsburgh at Johnstown; Estados UnidosFil: Mukherjee, Amitava. University of Pittsburgh at Johnstown; Estados UnidosFil: Troy, Kris. University of Pittsburgh at Johnstown; Estados UnidosFil: Banerjee, Swati. University of Pittsburgh at Johnstown; Estados UnidosFil: Paranjpe, Shirish. University of Pittsburgh at Johnstown; Estados UnidosFil: Michalopoulos, George K.. University of Pittsburgh at Johnstown; Estados UnidosFil: Bell, Aaron. University of Pittsburgh at Johnstown; Estados UnidosFil: Nagrath, Deepak. Michigan State University; Estados UnidosFil: Hainer, Sarah J.. University of Pittsburgh at Johnstown; Estados UnidosFil: Fox, Ira J.. University of Pittsburgh at Johnstown; Estados UnidosFil: Soto Gutierrez, Alejandro. University of Pittsburgh at Johnstown; Estados Unido

Effect of Hydrocortisone on Mortality and Organ Support in Patients With Severe COVID-19: The REMAP-CAP COVID-19 Corticosteroid Domain Randomized Clinical Trial.

Importance: Evidence regarding corticosteroid use for severe coronavirus disease 2019 (COVID-19) is limited. Objective: To determine whether hydrocortisone improves outcome for patients with severe COVID-19. Design, Setting, and Participants: An ongoing adaptive platform trial testing multiple interventions within multiple therapeutic domains, for example, antiviral agents, corticosteroids, or immunoglobulin. Between March 9 and June 17, 2020, 614 adult patients with suspected or confirmed COVID-19 were enrolled and randomized within at least 1 domain following admission to an intensive care unit (ICU) for respiratory or cardiovascular organ support at 121 sites in 8 countries. Of these, 403 were randomized to open-label interventions within the corticosteroid domain. The domain was halted after results from another trial were released. Follow-up ended August 12, 2020. Interventions: The corticosteroid domain randomized participants to a fixed 7-day course of intravenous hydrocortisone (50 mg or 100 mg every 6 hours) (n = 143), a shock-dependent course (50 mg every 6 hours when shock was clinically evident) (n = 152), or no hydrocortisone (n = 108). Main Outcomes and Measures: The primary end point was organ support-free days (days alive and free of ICU-based respiratory or cardiovascular support) within 21 days, where patients who died were assigned -1 day. The primary analysis was a bayesian cumulative logistic model that included all patients enrolled with severe COVID-19, adjusting for age, sex, site, region, time, assignment to interventions within other domains, and domain and intervention eligibility. Superiority was defined as the posterior probability of an odds ratio greater than 1 (threshold for trial conclusion of superiority >99%). Results: After excluding 19 participants who withdrew consent, there were 384 patients (mean age, 60 years; 29% female) randomized to the fixed-dose (n = 137), shock-dependent (n = 146), and no (n = 101) hydrocortisone groups; 379 (99%) completed the study and were included in the analysis. The mean age for the 3 groups ranged between 59.5 and 60.4 years; most patients were male (range, 70.6%-71.5%); mean body mass index ranged between 29.7 and 30.9; and patients receiving mechanical ventilation ranged between 50.0% and 63.5%. For the fixed-dose, shock-dependent, and no hydrocortisone groups, respectively, the median organ support-free days were 0 (IQR, -1 to 15), 0 (IQR, -1 to 13), and 0 (-1 to 11) days (composed of 30%, 26%, and 33% mortality rates and 11.5, 9.5, and 6 median organ support-free days among survivors). The median adjusted odds ratio and bayesian probability of superiority were 1.43 (95% credible interval, 0.91-2.27) and 93% for fixed-dose hydrocortisone, respectively, and were 1.22 (95% credible interval, 0.76-1.94) and 80% for shock-dependent hydrocortisone compared with no hydrocortisone. Serious adverse events were reported in 4 (3%), 5 (3%), and 1 (1%) patients in the fixed-dose, shock-dependent, and no hydrocortisone groups, respectively. Conclusions and Relevance: Among patients with severe COVID-19, treatment with a 7-day fixed-dose course of hydrocortisone or shock-dependent dosing of hydrocortisone, compared with no hydrocortisone, resulted in 93% and 80% probabilities of superiority with regard to the odds of improvement in organ support-free days within 21 days. However, the trial was stopped early and no treatment strategy met prespecified criteria for statistical superiority, precluding definitive conclusions. Trial Registration: ClinicalTrials.gov Identifier: NCT02735707

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Morning, midday, or night: Learning time-of-day affects student expereience- but not performance- in upper division genetics course

Research on K-12th grade students shows reduced performance in classes scheduled early in the morning if the student prefers to learn and work later in the day. Not much research has been done on undergraduate learners in the morning, nor research at either level on learning in the late evening-- like the Spring 2022 UC Merced Genetics course where some sections were scheduled to end as late as 9:20 pm. To understand the experiences and effects on performance for students in these courses, we compiled 143 survey responses querying student time-of-day learning preference, including free response questions about student experience at different times of day and with different course modalities (in-person vs remote instruction), from the 167-student Genetics course. We found that although students do have different time-of-day learning preferences, their overall exam grades were not affected by whether these preferences aligned with scheduled class time. However, asking open ended questions about the experiences that come with late evening classes elucidated important health, safety, and equity concerns that would be missed by looking at student performance alone. For example, students shared concerns about not having time to eat before the dining hall closes, being expected to wait on campus for several hours for their scheduled class time, being worried about late-night transportation accessibility, and with fear of being assaulted walking home past sunset. Additionally, students expressed that changing the course modality can offset some of the downsides of learning late at night, and students were significantly more likely to prefer sections in the early morning or late night if the courses were instructed remotely. Taken together, the responses indicate that these quality-of-life concerns might not be visible in their grade performance, but still represent an area in need of consideration and improvement for the sake of student's well-being.Kris Troy, Graduate Student, UC Merce

PathSTORM: a road to early cancer detection

Disruption of chromatin structure could enable early carcinogenesis by facilitating malignant transformation. Using stochastic optical reconstruction microscopy optimized for pathological tissue (PathSTORM), we uncovered a gradual decompaction of higher-order chromatin folding through progressive stages of carcinogenesis. We demonstrated potential detection of pre-cancerous genomic architecture not easily discernible by conventional pathology

Tumor Necrosis Factor alpha Drives Cadherin 11 Expression in Rheumatoid Inflammation

Objective. Cadherin 11 expressed on fibroblast-like synoviocytes (FLS) plays a key role in normal synovial architecture. The purpose of this study was to examine the expression of cadherin 11 in human synovitis. Methods. Cadherin 11 expression in synovial biopsy samples from patients with various types of arthritis and in lung biopsy samples from patients with interstitial pneumonitis (IP) was examined by immunostaining. The regulation of cadherin 11 expression in human FLS was assessed by quantitative reverse transcription-polymerase chain reaction analysis and Western blotting. Therapeutic modulation of synovial cadherin It was assessed before and after effective antiinflammatory therapy. Results. Abundant staining for cadherin 11 was seen in the intimal lining layer and the synovial sublining in inflamed tissues, with discrete staining in noninflammatory osteoarthritic (OA) tissues. The pattern and degree of inummostaining were similar in tissues from patients with rheumatoid arthritis (RA), nonpsoriatic spondylarthritis (SpA), psoriatic arthritis (PsA), and inflammatory OA. Clear staining for cadherin 11 was also observed in lung tissues from RA-associated IP and idiopathic IP patients, but was very limited in normal lung tissue. Cadherin 11 staining correlated strongly with the degree of inflammatory infiltration of the tissue, as well as with the C-reactive protein level and the erythrocyte sedimentation rate in RA patients. In vitro, cadherin 11 expression by FLS was consistently up-regulated by tumor necrosis factor alpha (TNF alpha) at the protein, but not the messenger RNA, level. Cadherin 11 staining in vivo was strongly down-regulated by prednisone treatment in RA patients and by TNF alpha blockade in SpA patients. Conclusion. Cadherin 11 expression is regulated by mediators of inflammation, such as TNF alpha. Since cadherin 11 plays an important role in cartilage destruction in experimental arthritis, down-modulation of cadherin 11 by potent antiinflammatory therapies in humans with arthritis may contribute to halting cartilage damage

Baseline Assessment of Systemic Racism Education in Pharmacy Curricula.

Objective. To determine, by survey, the inclusion of systemic racism (SR) education in US Doctor of Pharmacy curricula and identify barriers and facilitators to addressing this content. Methods. A survey was developed and distributed to curricular representatives at US colleges and schools of pharmacy (COP/SOPs). The survey assessed inclusion of SR education in curricula, faculty involvement in teaching SR content, barriers to adding SR content in curricula, and future curricular plans. Data were analyzed using descriptive statistics for institutional background information, curricular content, and barriers to inclusion. Chi-square test examined relationships between SR inclusion at public versus private programs. Fisher\u27s exact test assessed associations between traditional and accelerated programs. Results. Fifty-eight COP/SOPs provided usable responses. Of the respondents, 84% indicated teaching of SR and its impact on health and healthcare as a low priority. For 24% of respondents, SR was not currently included in their curriculum, while 34% indicated that SR was included in one or more courses or modules but was not a focus. Despite SR being offered in any didactic year, it was rarely included in experiential curricula. Top barriers to inclusion were lack of faculty knowledge and comfort with content and limited curricular space. No significant differences were found between program types. Conclusion. Based on the current level of SR education and barriers to inclusion, faculty need training and resources to teach SR concepts within pharmacy curricula. The inclusion of SR concepts and guidance in APE standards could help to drive meaningful change and promote health equity

Ecological transcriptomics of lake-type and riverine sockeye salmon (Oncorhynchus nerka)

BACKGROUND: There are a growing number of genomes sequenced with tentative functions assigned to a large proportion of the individual genes. Model organisms in laboratory settings form the basis for the assignment of gene function, and the ecological context of gene function is lacking. This work addresses this shortcoming by investigating expressed genes of sockeye salmon (Oncorhynchus nerka) muscle tissue. We compared morphology and gene expression in natural juvenile sockeye populations related to river and lake habitats. Based on previously documented divergent morphology, feeding strategy, and predation in association with these distinct environments, we expect that burst swimming is favored in riverine population and continuous swimming is favored in lake-type population. In turn we predict that morphology and expressed genes promote burst swimming in riverine sockeye and continuous swimming in lake-type sockeye. RESULTS: We found the riverine sockeye population had deep, robust bodies and lake-type had shallow, streamlined bodies. Gene expression patterns were measured using a 16K microarray, discovering 141 genes with significant differential expression. Overall, the identity and function of these genes was consistent with our hypothesis. In addition, Gene Ontology (GO) enrichment analyses with a larger set of differentially expressed genes found the "biosynthesis" category enriched for the riverine population and the "metabolism" category enriched for the lake-type population. CONCLUSIONS: This study provides a framework for understanding sockeye life history from a transcriptomic perspective and a starting point for more extensive, targeted studies determining the ecological context of genes