Chronic calcium signaling in IgE+ B cells limits plasma cell differentiation and survival.

In contrast to other antibody isotypes, B cells switched to IgE respond transiently and do not give rise to long-lived plasma cells (PCs) or memory B cells. To better understand IgE-BCR-mediated control of IgE responses, we developed whole-genome CRISPR screening that enabled comparison of IgE+ and IgG1+ B cell requirements for proliferation, survival, and differentiation into PCs. IgE+ PCs exhibited dependency on the PI3K-mTOR axis that increased protein amounts of the transcription factor IRF4. In contrast, loss of components of the calcium-calcineurin-NFAT pathway promoted IgE+ PC differentiation. Mice bearing a B cell-specific deletion of calcineurin B1 exhibited increased production of IgE+ PCs. Mechanistically, sustained elevation of intracellular calcium in IgE+ PCs downstream of the IgE-BCR promoted BCL2L11-dependent apoptosis. Thus, chronic calcium signaling downstream of the IgE-BCR controls the self-limiting character of IgE responses and may be relevant to the accumulation of IgE-producing cells in allergic disease.

Maintenance of the marginal-zone B cell compartment specifically requires the RNA-binding protein ZFP36L1.

RNA-binding proteins of the ZFP36 family are best known for inhibiting the expression of cytokines through binding to AU-rich elements in the 3' untranslated region and promoting mRNA decay. Here we identified an indispensable role for ZFP36L1 as the regulator of a post-transcriptional hub that determined the identity of marginal-zone B cells by promoting their proper localization and survival. ZFP36L1 controlled a gene-expression program related to signaling, cell adhesion and locomotion; it achieved this in part by limiting expression of the transcription factors KLF2 and IRF8, which are known to enforce the follicular B cell phenotype. These mechanisms emphasize the importance of integrating transcriptional and post-transcriptional processes by RNA-binding proteins for maintaining cellular identity among closely related cell types.

Endophilin A2 regulates B-cell endocytosis and is required for germinal center and humoral responses.

Antigen-specific B-cell responses require endosomal trafficking to regulate antigen uptake and presentation to helper T cells, and to control expression and signaling of immune receptors. However, the molecular composition of B-cell endosomal trafficking pathways and their specific roles in B-cell responses have not been systematically investigated. Here, we report high-throughput identification of genes regulating B-cell receptor (BCR)-mediated antigen internalization using genome-wide functional screens. We show that antigen internalization depends both on constitutive, clathrin-mediated endocytosis and on antigen-induced, clathrin-independent endocytosis mediated by endophilin A2. Although endophilin A2-mediated endocytosis is dispensable for antigen presentation, it is selectively required for metabolic support of B-cell proliferation, in part through regulation of iron uptake. Consequently, endophilin A2-deficient mice show defects in GC B-cell responses and production of high-affinity IgG. The requirement for endophilin A2 highlights a unique importance of clathrin-independent intracellular trafficking in GC B-cell clonal expansion and antibody responses.

Evaluating the druggability of TrmD, a potential antibacterial target, through design and microbiological profiling of a series of potent TrmD inhibitors.

The post-transcriptional modifier tRNA-(N1G37) methyltransferase (TrmD) has been proposed to be essential for growth in many Gram-negative and Gram-positive pathogens, however previously reported inhibitors show only weak antibacterial activity. In this work, optimisation of fragment hits resulted in compounds with low nanomolar TrmD inhibition incorporating features designed to enhance bacterial permeability and covering a range of physicochemical space. The resulting lack of significant antibacterial activity suggests that whilst TrmD is highly ligandable, its essentiality and druggability are called into question.

Discovery and structure-activity relationships of a novel oxazolidinone class of bacterial type II topoisomerase inhibitors.

There is an increasingly urgent and unmet medical need for novel antibiotic drugs that tackle infections caused by multidrug-resistant (MDR) pathogens. Novel bacterial type II topoisomerase inhibitors (NBTIs) are of high interest due to limited cross-resistance with fluoroquinolones, however analogues with Gram-negative activity often suffer from hERG channel inhibition. A novel series of bicyclic-oxazolidinone inhibitors of bacterial type II topoisomerase were identified which display potent broad-spectrum anti-bacterial activity, including against MDR strains, along with an encouraging in vitro safety profile. In vivo proof of concept was achieved in a A. baumannii mouse thigh infection model.

Effects of the COVID-19 Crisis on Resident Well-Being in a Community Teaching Hospital.

OBJECTIVES: The coronavirus disease 2019 (COVID-19) pandemic has been an unexpected crisis that continues to challenge the medical community at large. Healthcare environments have been forced to change dramatically, including for medical residents, who are vital members of the innovative emergency response teams. Articles have previously been published on the effects of crises on the well-being of healthcare practitioners; however, there is a paucity of literature targeting medical residents' experiences and general wellness during devastating events. The objective of our study aimed at understanding the emotional impact of the COVID-19 pandemic on residents' stress, academics, and support systems. METHODS: An anonymous, voluntary Likert scale questionnaire was sent via SurveyMonkey to Internal Medicine and Family Medicine residents in July 2020. Questions focused on residents' mood; stress levels; sense of support; and academics before, during, and immediately after the first surge of COVID-19 at our hospital between March 13 and June 15, 2020. RESULTS: Residents felt sad, stressed, and overworked during the first wave, as opposed to feelings of neutrality and happiness before and immediately after. Levels of concern for personal and loved ones' safety were significantly increased during and after our first wave. The impact on educational training was rated as neutral. Residents noted that institutional support could be improved by the provision of wellness activities and sponsored social events. CONCLUSIONS: This study provides insight on resident well-being during the initial months of the pandemic and identifies areas that could be improved. Our results demonstrated that the pandemic affected many aspects of residents' well-being and education, and the lessons learned can help guide healthcare institutions when implementing wellness activities for trainees during subsequent crises.

Restoring carbapenem efficacy: a novel carbapenem companion targeting metallo-ß-lactamases in carbapenem-resistant Enterobacterales.

BACKGROUND: The dissemination of MBLs compromises effective use of many ß-lactams in the treatment of patients with life-threatening bacterial infections. Predicted global increases in the prevalence of MBL-producing carbapenem-resistant Enterobacterales (CRE) are being realized, yielding infections that are untreatable with existing therapies including newly approved ß-lactam/ß-lactamase inhibitor combinations. Developing MBL inhibitors (MBLIs) now is essential to address the growing threat that MBL-producing CRE pose to patients. METHODS: A novel MBLI series was assessed by susceptibility testing and time-kill assays. Target activity and selectivity was evaluated using bacterial NDM, VIM and IMP enzyme assays and human matrix metallopeptidase enzyme assays, respectively, and cytotoxicity was assessed in HepG2 cells. In vivo efficacy of meropenem/MBLI combinations was evaluated in a mouse thigh infection model using an NDM-1-producing Escherichia coli strain. RESULTS: Combination of MBLIs with carbapenems reduced MICs for NDM/IMP/VIM-producing Enterobacterales by up to 128-fold compared with the carbapenems alone. Supplementation of meropenem with the promising compound 272 reduced the MIC90 from 128 to 0.25 mg/L in a panel of MBL-producing CRE clinical isolates (n = 115). Compound 272 restored the bactericidal activity of meropenem and was non-cytotoxic, potentiating the antimicrobial action of meropenem through specific inhibition of NDM, IMP and VIM. In vivo efficacy was achieved in a mouse thigh infection model with meropenem/272 dosed subcutaneously. CONCLUSIONS: We have developed a series of rationally designed MBLIs that restore activity of carbapenems against NDM/IMP/VIM-producing Enterobacterales. This series warrants further development towards a novel combination therapy that combats antibiotic-resistant organisms, which pose a critical threat to human health.

Investigating the potential of clinical and biochemical markers to differentiate between functional hypothalamic amenorrhoea and polycystic ovarian syndrome: A retrospective observational study.

OBJECTIVES: Functional hypothalamic amenorrhoea (FHA) is a common cause of amenorrhoea, but diagnosis can be challenging. The aim of this study was to investigate the clinical and biochemical features of FHA, compared to that of polycystic ovarian syndrome (PCOS) and assess the diagnostic performance of the different parameters for differentiating the two conditions. DESIGN AND PATIENTS: This was a retrospective observational study. We analysed clinical and biochemical parameters of women diagnosed with FHA and PCOS following specialist assessment at the reproductive endocrine gynaecology clinic, St Mary's Hospital. RESULTS: Compared with PCOS, women with FHA had significantly lower body mass index (BMI; 20.1 ± 2.9 vs. 31.1 ± 7.8 kg/m2 ; p< .0001) and a thinner endometrium (3.75 ± 2.23 vs. 6.82 ± 3.32 mm; p< .0001). Women with FHA had significantly lower luteinising hormone (LH; 3.46 ± 7.31 vs. 8.79 ± 4.98 IU/L; p< .0001), and lower LH to follicle-stimulating hormone (FSH) ratio, estradiol, thyroid-stimulating hormone, free thyroxine and prolactin levels; there was no significant difference in FSH levels. BMI had the greatest predictive performance for FHA (area under the curve [AUC]: 0.93; p< .001), followed by estradiol (AUC: 0.89; p< .001), LH (AUC: 0.88; p< .001) and LH:FSH ratio (AUC: 0.86; p< .001). CONCLUSIONS: Our data provides quantification for diagnostic accuracy of clinical parameters to differentiate FHA from PCOS, namely low BMI, estradiol, LH and LH:FSH ratio. These data could help clinicians more reliably diagnose FHA in women with secondary amenorrhoea.

Enhancing HIV Pre-exposure Prophylaxis Practices via an Educational Intervention.

BACKGROUND: Pre-exposure prophylaxis (PrEP) for HIV involves using antiretroviral drugs to prevent individuals at high risk from acquiring HIV infection. Most practicing primary care providers believe PrEP to be safe and effective, but less than half have prescribed or referred for PrEP. Attitudes and prescribing patterns among house officers have not been well described previously. STUDY QUESTION: Can an educational intervention enhance HIV PrEP practices among internal medicine house officers? STUDY DESIGN: This study relied on a pretest/posttest design. All categorical trainees at a medium-sized internal medicine program were offered a baseline survey to assess their knowledge on PrEP. This was followed by a PrEP-focused educational intervention and a postintervention survey. MEASURES AND OUTCOMES: Likert scales captured perceptions regarding safety, effectiveness, barriers, factors that would promote PrEP use, potential side effects, impact on risk-taking behavior, and provider comfort level in assessing behavioral risks and in PrEP prescribing. Data were analyzed using descriptive statistics, Wilcoxon signed rank test, and the Kruskal-Wallis test. Significance was accepted for P < 0.05. RESULTS: Forty-eight (100%) trainees participated in the educational session, 45 (94%) in a preintervention survey, and 36 (75%) in a postintervention survey. Before PrEP training, 22% of respondents were unaware of PrEP, 78% believed PrEP was effective, 66% believed PrEP was safe, 62% had fair or poor awareness of side effects; 18% of residents had referred for or prescribed PrEP, and 31% believed they were likely to prescribe PrEP in the next 6 months. After the intervention, 94% of trainees believed PrEP was effective (P < 0.001), 92% believed PrEP was safe (P < 0.001), and two-thirds believed they were likely to prescribe PrEP in the next 6 months. CONCLUSIONS: Brief, focused training on HIV prevention promotes awareness, acceptance, and likelihood of prescribing PrEP by internal medicine trainees.

Novel Bacterial Topoisomerase Inhibitors with Potent Broad-Spectrum Activity against Drug-Resistant Bacteria.

The novel bacterial topoisomerase inhibitor class is an investigational type of antibacterial inhibitor of DNA gyrase and topoisomerase IV that does not have cross-resistance with the quinolones. Here, we report the evaluation of the in vitro properties of a new series of this type of small molecule. Exemplar compounds selectively and potently inhibited the catalytic activities of Escherichia coli DNA gyrase and topoisomerase IV but did not block the DNA breakage-reunion step. Compounds showed broad-spectrum inhibitory activity against a wide range of Gram-positive and Gram-negative pathogens, including biodefence microorganisms and Mycobacterium tuberculosis No cross-resistance with fluoroquinolone-resistant Staphylococcus aureus and E. coli isolates was observed. Measured MIC90 values were 4 and 8 µg/ml against a panel of contemporary multidrug-resistant isolates of Acinetobacter baumannii and E. coli, respectively. In addition, representative compounds exhibited greater antibacterial potency than the quinolones against obligate anaerobic species. Spontaneous mutation rates were low, with frequencies of resistance typically <10-8 against E. coli and A. baumannii at concentrations equivalent to 4-fold the MIC. Compound-resistant E. coli mutants that were isolated following serial passage were characterized by whole-genome sequencing and carried a single Arg38Leu amino acid substitution in the GyrA subunit of DNA gyrase. Preliminary in vitro safety data indicate that the series shows a promising therapeutic index and potential for low human ether-a-go-go-related gene (hERG) inhibition (50% inhibitory concentration [IC50], >100 µM). In summary, the compounds' distinct mechanism of action relative to the fluoroquinolones, whole-cell potency, low potential for resistance development, and favorable in vitro safety profile warrant their continued investigation as potential broad-spectrum antibacterial agents.

Amniotic fluid transcriptomics reflects novel disease mechanisms in fetuses with myelomeningocele.

BACKGROUND: Cell-free RNA in amniotic fluid supernatant reflects developmental changes in gene expression in the living fetus, which includes genes that are specific to the central nervous system. Although it has been previously shown that central nervous system-specific transcripts are present in amniotic fluid supernatant, it is not known whether changes in the amniotic fluid supernatant transcriptome reflect the specific pathophysiologic condition of fetal central nervous system disorders. In myelomeningocele, there is open communication between the central nervous system and amniotic fluid. OBJECTIVES: The purpose of this study was to identify molecular pathophysiologic changes and novel disease mechanisms that are specific to myelomeningocele by the analysis of amniotic fluid supernatant cell-free RNA in fetuses with open myelomeningocele. STUDY DESIGN: Amniotic fluid supernatant was collected from 10 pregnant women at the time of the open myelomeningocele repair in the second trimester (24.5±1.0 weeks); 10 archived amniotic fluid supernatant from sex and gestational age-matched euploid fetuses without myelomeningocele were used as controls (20.9±0.9 weeks). Differentially regulated gene expression patterns were analyzed with the use of human genome expression arrays. RESULTS: Fetuses with myelomeningocele had 284 differentially regulated genes (176 up- and 108 down-regulated) in amniotic fluid supernatant. Known genes that were associated with myelomeningocele (PRICKLE2, GLI3, RAB23, HES1, FOLR1) and novel dysregulated genes were identified in association with neurodevelopment and neuronal regeneration (up-regulated, GAP43 and ZEB1) or axonal growth and guidance (down-regulated, ACAP1). Pathway analysis demonstrated a significant contribution of inflammation to disease and a broad influence of Wnt signaling pathways (Wnt1, Wnt5A, ITPR1). CONCLUSION: Transcriptomic analyses of living fetuses with myelomeningocele with the use of amniotic fluid supernatant cell-free RNA demonstrated differential regulation of specific genes and molecular pathways relevant to this central nervous system disorder, which resulted in a new understanding of pathophysiologic changes. The data also suggested the importance of pathways that involve secondary disease, such as inflammation, in myelomeningocele. These newly identified pathways may lead to hypotheses that can test novel therapeutic targets as adjuncts to fetal surgical repair.

The Role of p110δ in the Development and Activation of B Lymphocytes.

The phosphatidylinositol-3-kinase (PI3K) pathway has an essential role in signal transduction, where it is required for a number of different cellular processes including proliferation, differentiation, development, migration and growth. In the immune system, PI3K regulates inflammation by controlling the activation and recruitment of leukocytes. The generation of conditional knockout mice has allowed the study of PI3K isoforms specifically in B and T lymphocytes, and demonstrates the importance of intact signalling in their development and function. PI3K signalling must be tightly regulated in lymphocytes as excessive PI3K can lead to autoimmunity, immunodeficiency or cancer, whilst diminished signalling can result in developmental defects and immunodeficiency. Recent advances in the understanding of PI3K signalling have hastened the application of isoform-specific PI3K inhibitors, which are currently undergoing clinical trials. This review will focus on the p110δ catalytic subunit of the class 1A family of PI3K, and its role in the development and activation of B lymphocytes through various downstream effectors.

Regulation of BCR-mediated Ca2+ mobilization by MIZ1-TMBIM4 safeguards IgG1+ GC B cell-positive selection.

The transition from immunoglobulin M (IgM) to affinity-matured IgG antibodies is vital for effective humoral immunity. This is facilitated by germinal centers (GCs) through affinity maturation and preferential maintenance of IgG+ B cells over IgM+ B cells. However, it is not known whether the positive selection of the different Ig isotypes within GCs is dependent on specific transcriptional mechanisms. Here, we explored IgG1+ GC B cell transcription factor dependency using a CRISPR-Cas9 screen and conditional mouse genetics. We found that MIZ1 was specifically required for IgG1+ GC B cell survival during positive selection, whereas IgM+ GC B cells were largely independent. Mechanistically, MIZ1 induced TMBIM4, an ancestral anti-apoptotic protein that regulated inositol trisphosphate receptor (IP3R)-mediated calcium (Ca2+) mobilization downstream of B cell receptor (BCR) signaling in IgG1+ B cells. The MIZ1-TMBIM4 axis prevented mitochondrial dysfunction-induced IgG1+ GC cell death caused by excessive Ca2+ accumulation. This study uncovers a unique Ig isotype-specific dependency on a hitherto unidentified mechanism in GC-positive selection.

Cognitive behavioural therapy for psychosis and anxiety.

This article discusses the effectiveness of a cognitive behavioural therapy (CBT) group for clients with a first episode of psychosis, who were also experiencing comorbid symptoms of anxiety. Clients of 18-35 years of age who reported anxiety symptoms, either as a direct or indirect result of psychotic symptoms, were invited to attend a 12-week CBT-based group. The effectiveness of the intervention was evaluated at screening and 3-month follow-up with the Depression, Anxiety and Stress Scale (DASS-21) (Lovibond and Lovibond, 2004). The results showed a statistically significant improvement in symptoms (depression, p=0.06; anxiety, p=0.05; stress, p=.014), sustainable at 3-month follow-up. The authors concluded that a CBT group for people with a first episode of psychosis that focuses on the management of anxiety can be an effective and viable means of reducing levels of anxiety and associated stress and depression. This model is recommended for use by community mental health teams.

The global costs of extreme weather that are attributable to climate change.

Extreme weather events lead to significant adverse societal costs. Extreme Event Attribution (EEA), a methodology that examines how anthropogenic greenhouse gas emissions had changed the occurrence of specific extreme weather events, allows us to quantify the climate change-induced component of these costs. We collect data from all available EEA studies, combine these with data on the socio-economic costs of these events and extrapolate for missing data to arrive at an estimate of the global costs of extreme weather attributable to climate change in the last twenty years. We find that US[Formula: see text] 143 billion per year of the costs of extreme events is attributable to climatic change. The majority (63%), of this is due to human loss of life. Our results suggest that the frequently cited estimates of the economic costs of climate change arrived at by using Integrated Assessment Models may be substantially underestimated.

Home Oxygen and Monitoring for COVID-19 Patients: A Multidisciplinary Team Approach.

Introduction: During the initial COVID-19 pandemic peak, Stamford Hospital implemented a home oxygen program (HOP) to create a comprehensive, multi-disciplinary outpatient initiative without sacrificing a safe discharge. Primary care physicians monitored program participants, whose only indication for remaining admitted was an oxygen requirement. We retrospectively examined participant co-morbidities and outcomes, including death and readmission rates to evaluate HOP safety. Methods: A retrospective analysis of program participants discharged between April 2020-Janurary 2021 was performed. Variables included demographics, oxygen requirement, days enrolled in the HOP, and major comorbidities such as cardiovascular disease (CVD), diabetes (DM), hypertension (HTN), obesity, chronic kidney disease, malignancies and underlying chronic obstructive pulmonary disease (COPD). Results: Among the 138 HOP participants, ages ranged from 23 to 96 (Mean 65.5), with 47.1% female and 52.9% male. The most represented ethnicity included White (48.6%), Hispanic (29.7%), and Black (15.2%). Patients' average time in the HOP was 19 days, requiring an average of 1.7 L/min of home oxygen. Thirteen patients (9.4%) were readmitted to the hospital with 2.9% secondary to worsening COVID-19 hypoxia, but no deaths occurred at home. A significant relationship was found between age and highest home oxygen need. Patients with COPD, HTN, and DM had significantly higher oxygen requirements (P-value <0.05). Conclusion: Increasing age, underlying COPD, HTN, and DM were associated with higher oxygen requirements in participants. Given limited availability of hospital beds, and no occurrences of death at home, Stamford Hospital HOP safely helped provide care for sicker patients and enhanced resource allocation.

Developing Message Strategies to Engage Racial and Ethnic Minority Groups in Digital Oral Self-Care Interventions: Participatory Co-Design Approach.

BACKGROUND: The prevention of oral health diseases is a key public health issue and a major challenge for racial and ethnic minority groups, who often face barriers in accessing dental care. Daily toothbrushing is an important self-care behavior necessary for sustaining good oral health, yet engagement in regular brushing remains a challenge. Identifying strategies to promote engagement in regular oral self-care behaviors among populations at risk of poor oral health is critical. OBJECTIVE: The formative research described here focused on creating messages for a digital oral self-care intervention targeting a racially and ethnically diverse population. Theoretically grounded strategies (reciprocity, reciprocity-by-proxy, and curiosity) were used to promote engagement in 3 aspects: oral self-care behaviors, an oral care smartphone app, and digital messages. A web-based participatory co-design approach was used to develop messages that are resource efficient, appealing, and novel; this approach involved dental experts, individuals from the general population, and individuals from the target population-dental patients from predominantly low-income racial and ethnic minority groups. Given that many individuals from racially and ethnically diverse populations face anonymity and confidentiality concerns when participating in research, we used an approach to message development that aimed to mitigate these concerns. METHODS: Messages were initially developed with feedback from dental experts and Amazon Mechanical Turk workers. Dental patients were then recruited for 2 facilitator-mediated group webinar sessions held over Zoom (Zoom Video Communications; session 1: n=13; session 2: n=7), in which they provided both quantitative ratings and qualitative feedback on the messages. Participants interacted with the facilitator through Zoom polls and a chat window that was anonymous to other participants. Participants did not directly interact with each other, and the facilitator mediated sessions by verbally asking for message feedback and sharing key suggestions with the group for additional feedback. This approach plausibly enhanced participant anonymity and confidentiality during the sessions. RESULTS: Participants rated messages highly in terms of liking (overall rating: mean 2.63, SD 0.58; reciprocity: mean 2.65, SD 0.52; reciprocity-by-proxy: mean 2.58, SD 0.53; curiosity involving interactive oral health questions and answers: mean 2.45, SD 0.69; curiosity involving tailored brushing feedback: mean 2.77, SD 0.48) on a scale ranging from 1 (do not like it) to 3 (like it). Qualitative feedback indicated that the participants preferred messages that were straightforward, enthusiastic, conversational, relatable, and authentic. CONCLUSIONS: This formative research has the potential to guide the design of messages for future digital health behavioral interventions targeting individuals from diverse racial and ethnic populations. Insights emphasize the importance of identifying key stimuli and tasks that require engagement, gathering multiple perspectives during message development, and using new approaches for collecting both quantitative and qualitative data while mitigating anonymity and confidentiality concerns.

Economic and humanistic burden of HPV-related disease in Indonesia: A qualitative analysis.

The burden of human papillomavirus (HPV) and HPV-related cancers and genital warts is increasing in developing countries, including Indonesia. The objective of this study was to qualitatively explore the humanistic and economic burden of these HPV-related diseases in patients in Indonesia. In 2021, in-depth interviews and focus groups were conducted with patients (N = 18) with HPV-related diseases and healthcare professionals (HCPs; N = 10) specialised in treating these patients. Interviews explored the physical, mental, social, and economic burden of HPV-related diseases. Patients emphasised the psychological and social burden of HPV-related diseases, which negatively impacted their mental state and close relationships. Treatment for HPV-related diseases was also associated with a substantial cost, which health insurance only partially alleviated. HCPs understood the physical negative impact of HPV-related diseases, but some understated patients' social, psychological, and financial burden. This research underscores the substantial economic and humanistic burden of HPV-related diseases that could be prevented by vaccination. In addition, it highlights the need for novel interventions to reduce negative psychosocial consequences of HPV-related diseases in Indonesia. Increased HCP education of the broader humanistic impacts of HPV-related diseases may improve patient support and increase awareness for preventive strategy.

Cell-specific imputation of drug connectivity mapping with incomplete data.

Drug repositioning allows expedited discovery of new applications for existing compounds, but re-screening vast compound libraries is often prohibitively expensive. "Connectivity mapping" is a process that links drugs to diseases by identifying compounds whose impact on expression in a collection of cells reverses the disease's impact on expression in disease-relevant tissues. The LINCS project has expanded the universe of compounds and cells for which data are available, but even with this effort, many clinically useful combinations are missing. To evaluate the possibility of repurposing drugs despite missing data, we compared collaborative filtering using either neighborhood-based or SVD imputation methods to two naive approaches via cross-validation. Methods were evaluated for their ability to predict drug connectivity despite missing data. Predictions improved when cell type was taken into account. Neighborhood collaborative filtering was the most successful method, with the best improvements in non-immortalized primary cells. We also explored which classes of compounds are most and least reliant on cell type for accurate imputation. We conclude that even for cells in which drug responses have not been fully characterized, it is possible to identify unassayed drugs that reverse in those cells the expression signatures observed in disease.

Multiomics analysis couples mRNA turnover and translational control of glutamine metabolism to the differentiation of the activated CD4+ T cell.

The ZFP36 family of RNA-binding proteins acts post-transcriptionally to repress translation and promote RNA decay. Studies of genes and pathways regulated by the ZFP36 family in CD4+ T cells have focussed largely on cytokines, but their impact on metabolic reprogramming and differentiation is unclear. Using CD4+ T cells lacking Zfp36 and Zfp36l1, we combined the quantification of mRNA transcription, stability, abundance and translation with crosslinking immunoprecipitation and metabolic profiling to determine how they regulate T cell metabolism and differentiation. Our results suggest that ZFP36 and ZFP36L1 act directly to limit the expression of genes driving anabolic processes by two distinct routes: by targeting transcription factors and by targeting transcripts encoding rate-limiting enzymes. These enzymes span numerous metabolic pathways including glycolysis, one-carbon metabolism and glutaminolysis. Direct binding and repression of transcripts encoding glutamine transporter SLC38A2 correlated with increased cellular glutamine content in ZFP36/ZFP36L1-deficient T cells. Increased conversion of glutamine to α-ketoglutarate in these cells was consistent with direct binding of ZFP36/ZFP36L1 to Gls (encoding glutaminase) and Glud1 (encoding glutamate dehydrogenase). We propose that ZFP36 and ZFP36L1 as well as glutamine and α-ketoglutarate are limiting factors for the acquisition of the cytotoxic CD4+ T cell fate. Our data implicate ZFP36 and ZFP36L1 in limiting glutamine anaplerosis and differentiation of activated CD4+ T cells, likely mediated by direct binding to transcripts of critical genes that drive these processes.