Growth factor-induced activation of MSK2 leads to phosphorylation of H3K9me2S10 and corresponding changes in gene expression

Extracellular signals are transmitted through kinase cascades to modulate gene expression, but it remains unclear how epigenetic changes regulate this response. Here, we provide evidence that growth factor-stimulated changes in the transcript levels of many responsive genes are accompanied by increases in histone phosphorylation levels, specifically at histone H3 serine-10 when the adjacent lysine-9 is dimethylated (H3K9me2S10). Imaging and proteomic approaches show that epidermal growth factor (EGF) stimulation results in H3K9me2S10 phosphorylation, which occurs in genomic regions enriched for regulatory enhancers of EGF-responsive genes. We also demonstrate that the EGF-induced increase in H3K9me2S10ph is dependent on the nuclear kinase MSK2, and this subset of EGF-induced genes is dependent on MSK2 for transcription. Together, our work indicates that growth factor-induced changes in chromatin state can mediate the activation of downstream genes.

Profound phenotypic and epigenetic heterogeneity of the HIV-1-infected CD4+ T cell reservoir

Understanding the complexity of the long-lived HIV reservoir during antiretroviral therapy (ART) remains a considerable impediment in research towards a cure for HIV. To address this, we developed a single-cell strategy to precisely define the unperturbed peripheral blood HIV-infected memory CD4+ T cell reservoir from ART-treated people living with HIV (ART-PLWH) via the presence of integrated accessible proviral DNA in concert with epigenetic and cell surface protein profiling. We identified profound reservoir heterogeneity within and between ART-PLWH, characterized by new and known surface markers within total and individual memory CD4+ T cell subsets. We further uncovered new epigenetic profiles and transcription factor motifs enriched in HIV-infected cells that suggest infected cells with accessible provirus, irrespective of reservoir distribution, are poised for reactivation during ART treatment. Together, our findings reveal the extensive inter- and intrapersonal cellular heterogeneity of the HIV reservoir, and establish an initial multiomic atlas to develop targeted reservoir elimination strategies.

Spectrum of Activity of Raltegravir and Dolutegravir Against Novel Treatment-Associated Mutations in HIV-2 Integrase: A Phenotypic Analysis Using an Expanded Panel of Site-Directed Mutants

BACKGROUND

Integrase inhibitors (INIs) are a key component of antiretroviral therapy for human immunodeficiency virus-1 (HIV-1) and HIV-2 infection. Although INI resistance pathways are well-defined for HIV-1, mutations that emerge in HIV-2 in response to INIs are incompletely characterized.

METHODS

We performed systematic searches of GenBank and HIV-2 drug resistance literature to identify treatment-associated mutations for phenotypic evaluation. We then constructed a library of 95 mutants of HIV-2ROD9 that contained single or multiple amino acid changes in the integrase protein. Each variant was tested for susceptibility to raltegravir and dolutegravir using a single-cycle indicator cell assay.

RESULTS

We observed extensive cross-resistance between raltegravir and dolutegravir in HIV-2ROD9. HIV-2-specific integrase mutations Q91R, E92A, A153G, and H157Q/S, which have not been previously characterized, significantly increased the half maximum effective concentration (EC50) for raltegravir when introduced into 1 or more mutational backgrounds; mutations E92A/Q, T97A, and G140A/S conferred similar enhancements of dolutegravir resistance. HIV-2ROD9 variants encoding G118R alone, or insertions of residues SREGK or SREGR at position 231, were resistant to both INIs.

CONCLUSIONS

Our analysis demonstrates the contributions of novel INI-associated mutations to raltegravir and dolutegravir resistance in HIV-2. These findings should help to improve algorithms for genotypic drug resistance testing in HIV-2-infected individuals.

Assessment of HIV-1 integration in tissues and subsets across infection stages

The integration of HIV DNA into the host genome contributes to lifelong infection in most individuals. Few studies have examined integration in lymphoid tissue, where HIV predominantly persists before and after antiretroviral treatment (ART). Of particular interest is whether integration site distributions differ between infection stages with paired blood and tissue comparisons. Here, we profiled HIV integration site distributions in sorted memory, tissue-resident, and/or follicular helper CD4+ T cell subsets from paired blood and lymphoid tissue samples from acute, chronic, and ART-treated individuals. We observed minor differences in the frequency of nonintronic and nondistal intergenic sites, varying with tissue and residency phenotypes during ART. Genomic and epigenetic annotations were generally similar. Clonal expansion of cells marked by identical integration sites was detected, with increased detection in chronic and ART-treated individuals. However, overlap between or within CD4+ T cell subsets or tissue compartments was only observed in 8 unique sites of the 3540 sites studied. Together, these findings suggest that shared integration sites between blood and tissue may, depending on the tissue site, be the exception rather than the rule and indicate that additional studies are necessary to fully understand the heterogeneity of tissue-sequestered HIV reservoirs.

Elite control of HIV is associated with distinct functional and transcriptional signatures in lymphoid tissue CD8+ T cells

The functional properties of circulating CD8⁺ T cells have been associated with immune control of HIV. However, viral replication occurs predominantly in secondary lymphoid tissues, such as lymph nodes (LNs). We used an integrated single-cell approach to characterize effective HIV-specific CD8⁺ T cell responses in the LNs of elite controllers (ECs), defined as individuals who suppress viral replication in the absence of antiretroviral therapy (ART). Higher frequencies of total memory and follicle-homing HIV-specific CD8⁺ T cells were detected in the LNs of ECs compared with the LNs of chronic progressors (CPs) who were not receiving ART. Moreover, HIV-specific CD8⁺ T cells potently suppressed viral replication without demonstrable cytolytic activity in the LNs of ECs, which harbored substantially lower amounts of CD4⁺ T cell-associated HIV DNA and RNA compared with the LNs of CPs. Single-cell RNA sequencing analyses further revealed a distinct transcriptional signature among HIV-specific CD8⁺ T cells from the LNs of ECs, typified by the down-regulation of inhibitory receptors and cytolytic molecules and the up-regulation of multiple cytokines, predicted secreted factors, and components of the protein translation machinery. Collectively, these results provide a mechanistic framework to expedite the identification of novel antiviral factors, highlighting a potential role for the localized deployment of noncytolytic functions as a determinant of immune efficacy against HIV.

TOX is expressed by exhausted and polyfunctional human effector memory CD8+ T cells

CD8⁺ T cell exhaustion is a hallmark of many cancers and chronic infections. In mice, T cell factor 1 (TCF-1) maintains exhausted CD8⁺ T cell responses, whereas thymocyte selection-associated HMG box (TOX) is required for the epigenetic remodeling and survival of exhausted CD8⁺ T cells. However, it has remained unclear to what extent these transcription factors play analogous roles in humans. In this study, we mapped the expression of TOX and TCF-1 as a function of differentiation and specificity in the human CD8⁺ T cell landscape. Here, we demonstrate that circulating TOX⁺ CD8⁺ T cells exist in most humans, but that TOX is not exclusively associated with exhaustion. Effector memory CD8⁺ T cells generally expressed TOX, whereas naive and early-differentiated memory CD8⁺ T cells generally expressed TCF-1. Cytolytic gene and protein expression signatures were also defined by the expression of TOX. In the context of a relentless immune challenge, exhausted HIV-specific CD8⁺ T cells commonly expressed TOX, often in clusters with various activation markers and inhibitory receptors, and expressed less TCF-1. However, polyfunctional memory CD8⁺ T cells specific for cytomegalovirus (CMV) or Epstein-Barr virus (EBV) also expressed TOX, either with or without TCF-1. A similar phenotype was observed among HIV-specific CD8⁺ T cells from individuals who maintained exceptional immune control of viral replication. Collectively, these data demonstrate that TOX is expressed by most circulating effector memory CD8⁺ T cell subsets and not exclusively linked to exhaustion.

Comparison of the Antiviral Activity of Bictegravir against HIV-1 and HIV-2 Isolates and Integrase Inhibitor-Resistant HIV-2 Mutants

We compared the activity of the integrase inhibitor bictegravir against HIV-1 and HIV-2 using a culture-based, single-cycle assay. Values of 50% effective concentrations ranged from 1.2 to 2.5 nM for 9 HIV-1 isolates and 1.4 to 5.6 nM for 15 HIV-2 isolates. HIV-2 integrase mutants G140S/Q148R and G140S/Q148H were 34- and 110-fold resistant to bictegravir, respectively; other resistance-associated mutations conferred ≤5-fold changes in bictegravir susceptibility. Our findings indicate that bictegravir-based antiretroviral therapy should be evaluated in HIV-2-infected individuals.

Rattlesnake venom-induced thrombocytopenia response to Antivenin (Crotalidae) Polyvalent: a case series

OBJECTIVE

To test the hypothesis that rattlesnake venom-induced thrombocytopenia would improve following Antivenin (Crotalidae) Polyvalent administration, and that the degree of platelet increase would correlate with the dosage of antivenom.

METHODS

The authors conducted a retrospective review of all patients admitted for rattlesnake envenomation at two southern California hospitals between 1980 and 1998. Patients were included if platelet count was less than 150 x 10(9)/L following a rattlesnake bite. Patients were excluded if they received platelet transfusion. The relationship between Antivenin (Crotalidae) Polyvalent administration and venom-induced thrombocytopenia was evaluated by linear regression and paired t-test.

RESULTS

The authors identified 103 cases of rattlesnake envenomation. Seventeen cases met inclusion criteria for thrombocytopenia. Two patients were excluded because they received platelet transfusions. One additional patient was excluded from paired t-test only because no antivenom was given. Thrombocytopenia usually improved between presentation and discharge (mean difference, 44 x 10(9)/L), although complete resolution was often not achieved. A statistically significant partial improvement in platelet counts immediately after antivenom administration was observed in a subset of patients with severe thrombocytopenia (platelet count <100 x 10(9)/L) (mean difference, 64 x 10(9)/L). Using regression analysis, the authors did not detect a linear relationship between the amount of Antivenin (Crotalidae) Polyvalent administered and the degree of improvement.

CONCLUSIONS

Although rattlesnake venom-induced thrombocytopenia usually improves immediately after Antivenin (Crotalidae) Polyvalent administration and by the time of discharge, the degree of improvement is frequently incomplete and of uncertain clinical significance in the absence of life-threatening bleeding. The authors found no correlation between the degree of improvement and the dosage of Antivenin (Crotalidae) Polyvalent.

Measles virus-specific cellular immunity in patients with vaccine failure

The cytotoxic T-lymphocyte (CTL) response to measles virus (MV) was studied in blood samples from 13 acute- and early convalescent-phase patients with measles infection despite previous vaccination with the live-MV vaccine. MV CTL responses were also measured in six healthy peer controls who had live-MV vaccination during childhood and in five healthy adults who had a remote history of natural measles. All patients recovered from illness without complication. Acute MV infection was diagnosed on the basis of the Centers for Disease Control criteria and by measuring MV-specific immunoglobulin G (IgG) and IgM antibodies. Elevated IgG titers occurred in 80% of the patients at 1 to 2 weeks and in 100% at 4 weeks postinfection. IgM antibodies were detectable in all patient tested and were elevated in 60% of the patients at 1 to 2 weeks postinfection. The MV-specific CTL response was enhanced in 10 of the 13 patients tested, with a mean maximal lysis of 48.5% +/- 13.3%, compared with that of healthy peer controls who had had live-MV vaccinations during childhood (mean lysis, 14.6% +/- 12.9%; n = 6) and healthy adults with a remote history of natural measles (mean, 30.8% +/- 12.2%; n = 5). Three patients had low MV CTL levels at two time points following measles, with a mean lysis of 12% +/- 1.7%. It is concluded that while there is no evidence for a deficiency in the generation of cellular immunity to MV in the majority of patients with MV vaccine failure, a small number of individuals may fail to develop an enhanced T-cell response following infection.

Early diagnosis of acute myocardial infarction by rapid analysis of creatine kinase isoenzyme-3 (CK-MM) sub-types

We compared the clinical sensitivity, specificity, and diagnostic efficiency of measuring creatine kinase-3 (MM) isoenzyme sub-types (CK, EC 2.7.3.2) with the measurement of CK-2 (MB) isoenzymes for the diagnosis of acute myocardial infarction. Serial blood collections at 3-h intervals from 35 patients with acute myocardial infarction were examined. In attempts to reperfuse their coronary arteries, some of these patients were treated with pharmacological thrombolysis (streptokinase, tissue plasminogen activator), with or without coronary angioplasty. The infarction patients were divided into two groups: patients who were successfully treated with thrombolytic agents (i.e., they achieved coronary reperfusion), and patients who were treated unsuccessfully or who were not treated acutely. We also examined blood from 34 non-infarction patients. We measured CK-3 sub-types by both anion-exchange liquid chromatography and a modified high-voltage electrophoresis method, and CK-2 by immunoprecipitation. Our results show that during the first few critical 3 to 9 h after onset of chest pain, measurement of CK-3 sub-types has the highest diagnostic efficiency; in contrast, CK-2 has the highest efficiency during the 10- to 21-h time intervals. Thus early diagnosis of acute myocardial infarction can be based on rapid assays of CK-3 sub-types.

Early diagnosis of acute myocardial infarction by rapid analysis of creatine kinase isoenzyme-3 (CK-MM) sub-types

We compared the clinical sensitivity, specificity, and diagnostic efficiency of measuring creatine kinase-3 (MM) isoenzyme sub-types (CK, EC 2.7.3.2) with the measurement of CK-2 (MB) isoenzymes for the diagnosis of acute myocardial infarction. Serial blood collections at 3-h intervals from 35 patients with acute myocardial infarction were examined. In attempts to reperfuse their coronary arteries, some of these patients were treated with pharmacological thrombolysis (streptokinase, tissue plasminogen activator), with or without coronary angioplasty. The infarction patients were divided into two groups: patients who were successfully treated with thrombolytic agents (i.e., they achieved coronary reperfusion), and patients who were treated unsuccessfully or who were not treated acutely. We also examined blood from 34 non-infarction patients. We measured CK-3 sub-types by both anion-exchange liquid chromatography and a modified high-voltage electrophoresis method, and CK-2 by immunoprecipitation. Our results show that during the first few critical 3 to 9 h after onset of chest pain, measurement of CK-3 sub-types has the highest diagnostic efficiency; in contrast, CK-2 has the highest efficiency during the 10- to 21-h time intervals. Thus early diagnosis of acute myocardial infarction can be based on rapid assays of CK-3 sub-types.