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This report describes a new and convenient method for the preparation of 5beta-cholestane-3alpha,7alpha,24-triol (24R and 24S) and 5beta-cholestane-3alpha,7alpha,26-triol (25R and 25S) starting from 5beta-cholestane-3alpha,7alpha,25-triol. Dehydration of the latter with acetic anhydride and glacial acetic acid yielded a mixture of 5beta-cholest-24ene-3alpha,7alpha-diol and the corresponding delta25 compound. Hydroboration and oxidation of the delta24 unsaturated bile alcohol resulted in the formation of 5beta-cholestane-3alpha,7alpha,24-triol. 5beta-Cholestane-3alpha,7alpha,26-triol and 5beta-cholestane-3alpha,7alpha-diol were obtained from the delta25 bile alcohol. In each case the bile alcohols epimeric at C-24 and C-25 were resolved by analytical and preparative thin-layer chromatography and characterized by gas-liquid chromatography, infrared-, proton magnetic resonance-, and mass spectrometry. Tentative assignment of the 24R, 24S and 25R, 25S configurations was made on the basis of molecular rotation differences. These epimeric bile alcohols will be useful for biological studies of chenodeoxycholic acid biosynthesis.
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INTRODUCTION: R-loops, RNA-DNA hybrid structures with a displaced single-stranded DNA loop, are key regulators of transcriptional control, chromatin architecture, and genome stability and have emerging roles in inflammatory signaling. However, the relationship between R-loop abundance and strongly modulated inflammatory effector genes in metabolic inflammation and influenza virus infection remains underexplored. METHODS: We performed a locus-centric integrative analysis combining robust differentially expressed genes (DEGs) from multiple inflammatory and infection-related murine and human transcriptomic disease models with experimentally validated multi-cell R-loop annotations from the reference atlas RLoopBase. Our correlation framework evaluated the directional relationship between R-loop abundance and inflammatory gene expression rather than assuming disease-sample-matched R-loop measurements. We further analyzed R-loop regulatory proteins, NRF2-associated R-loop regulators, and overlaps between R-loop regulators and CRISPRi-identified mitochondrial and cellular reactive oxygen species (ROS) regulators. RESULTS: In angiotensin II-infused apolipoprotein E-deficient (ApoE-/-) mice, a model of abdominal aortic aneurysm (AAA), genomic regions encoding the top significantly upregulated genes exhibited significantly fewer R-loops than those encoding downregulated genes at days 14 and 28. Similarly, in atherosclerotic ApoE-/- mice fed a high-fat diet for 32 and 78 weeks, upregulated genes were associated with fewer R-loops than downregulated genes. Reduced R-loop abundance was also observed in genomic regions encoding the top significantly upregulated genes in liver tissues from patients with non-alcoholic steatohepatitis (NASH), as well as in monosodium urate (MSU)-stimulated lymphatic endothelial cells (LECs) and influenza virus-infected human umbilical vein endothelial cells (HUVECs). R-loop regulatory proteins upregulated during metabolic inflammation were enriched in immune and inflammatory pathways. NRF2 was identified as a regulator of 27 R-loop regulatory proteins, including 10 positively and 17 negatively regulated proteins. Furthermore, 54 R-loop regulatory proteins overlapped with CRISPRi-identified mitochondrial and cellular ROS regulators, suggesting potential reciprocal regulation between R-loop homeostasis and ROS signaling. Disease-associated changes in pro-ROS and anti-ROS R-loop regulatory proteins further linked R-loop regulation to inflammatory and oxidative stress pathways. DISCUSSION: These findings identify reduced R-loop abundance at genomic regions encoding strongly upregulated inflammatory genes as a shared feature across multiple models of metabolic inflammation and influenza virus infection. The results further suggest that immune-associated R-loop regulatory proteins and the NRF2-ROS axis may contribute to R-loop remodeling during inflammatory disease. This integrative framework provides new insight into the potential role of R-loops and ROS-sensitive R-loop regulators in inflammatory and metabolic diseases and identifies candidate pathways for future mechanistic investigation and therapeutic targeting.
BACKGROUND: High-grade B-cell lymphoma with rearrangements of MYC and BCL2 and/or BCL6, known as double-hit lymphoma, is a highly aggressive malignancy with poor outcomes after standard chemoimmunotherapy. We aimed to study whether the addition of the BCL2-inhibitor venetoclax to chemoimmunotherapy in patients with double-hit lymphoma resulted in superior efficacy compared with chemotherapy alone. METHODS: ALLIANCE A051701 is an open-label, randomised, controlled, phase 2-3 trial in separate cohorts of patients with double-hit lymphoma and patients with double-expressor lymphoma. In this analysis, we report phase 2 results from the double-hit lymphoma cohort. Patients aged 18-80 years with newly diagnosed double-hit lymphoma and Eastern Cooperative Oncology Group (ECOG) performance status 0-2 were recruited from 41 hospitals and outpatient clinics in the USA. Patients were randomly assigned (1:1) to receive DA-EPOCH-R (dose-adjusted etoposide, prednisone, vincristine, cyclophosphamide, doxorubicin, and rituximab) either alone (DA-EPOCH-R group) or with venetoclax (DA-EPOCH-R plus venetoclax group) using permuted block randomisation schedule. All patients and investigators were aware of group assignment. DA-EPOCH-R was administered on a 21-day schedule for up to six total cycles. Venetoclax was given as 600 mg by mouth daily on days 4-8 of cycle 1 and on days 1-5 of cycles 2-6. The primary endpoint was progression-free survival in the modified intent-to-treat population inclusive of all eligible patients with centrally confirmed double-hit lymphoma. The safety analysis population consisted of all evaluable patients who received at least one dose of protocol treatment. This trial is registered with ClinicalTrials.gov (NCT03984448) and is closed to enrolment. FINDINGS: 36 patients were randomly assigned to the DA-EPOCH-R group and 37 to the DA-EPOCH-R plus venetoclax group between Oct 22, 2019, and Sept 18, 2020. Median age was 65 years (IQR 56-73) and baseline demographic factors were well balanced between groups, with 30 (45%) female and 36 (55%) male patients. Most patients (59 [89%]) were white, two (3%) were Asian, one (2%) was Black or African American, and four (6%) had unknown or unreported ethnicity. The majority of patients had MYC-BCL2 double-hit lymphoma (59 [89%] patients), advanced stage disease (57 [86%] patients), and high-intermediate/high-risk IPI score (42 [64%] patients). Median follow-up was 34·7 months (IQR 30·1-36·8). Median progression-free survival was 28·4 months (95% CI 5·2-not estimable) in the DA-EPOCH-R group (n=30) and 7·7 months (95% CI 4·7-NE) in the DA-EPOCH-R plus venetoclax group (n=36; hazard ratio [HR] 1·13, 95% CI 0·53-2·37; p=0·75). Deaths on treatment occurred in one (3%) patient in the DA-EPOCH-R group (due to dyspnoea; possibly related to treatment) and six (17%) patients in the DA-EPOCH-R plus venetoclax group (four due to sepsis [three at least possible related and one unrelated], two due to cardiac arrest [at least possibly related]), prompting early closure of the double-hit lymphoma cohort. The most common grade 3-4 non-haematological adverse event was febrile neutropenia, occurring in 15 (43%) of 35 patients in the DA-EPOCH-R plus venetoclax group and 11 (37%) of 30 patients in the DA-EPOCH-R group. The median overall survival has not been reached in either group. The 24-month overall survival estimates were 72% (95% CI 52-85) in the DA-EPOCH-R group compared with 52% (95% CI 33-68) in the DA-EPOCH-R plus venetoclax group (HR 2·49, 95% CI 1·03-6·04; p=0·038). INTERPRETATION: The addition of venetoclax to DA-EPOCH-R resulted in excess mortality, prompting early study closure. Robust accrual shows that prospective multicentre trials are feasible in double-hit lymphoma, and the outcomes in the DA-EPOCH-R group serve as a benchmark for future studies. FUNDING: National Cancer Institute of the National Institutes of Health.
R-loops are three-stranded nucleic acid structures consisting of an RNA/DNA hybrid and a displaced strand of DNA. These structures have been implicated in a variety of regulatory cellular processes. Their untimed or excess accumulation, however, can cause genomic instability and induce DNA damage. Most R-loops form co-transcriptionally when the nascent transcript reanneals to unwound DNA duplex. Changes in transcription rates have the potential to impact R-loop formation, and compounds that modulate R-loop formation would be useful molecular tools and therapeutic leads. Cleavage and Polyadenylation Specific Factor 3 (CPSF3) recognizes the pre-mRNA 3' cleavage site, cleaves the transcript prior to polyadenylation, and has been linked to R-loop formation. Inhibition of CPSF3 has been found to induce transcriptional readthrough and cell proliferation defects. A previous report suggested that inhibition of CPSF3 with a small molecule causes a global increase in R-loop formation. Here, we test the impact of YT-II-100, a novel inhibitor of CPSF3. We find that addition of YT-II-100 increases global R-loop formation but does not change R-loop formation at specific genes that are normally used as positive controls for R-loop formation. We performed parallel assays using a previously reported compound, JTE-607, and observed similar results. Our data emphasize the need for cautious interpretation of experiments using JTE-607 and YT-II-100. There may be different mechanisms of R-loop formation depending on gene loci, where the control of R-loop formation by agonists at certain genes may differ from the trends observed for impacts on global R-loop formation.
The minimal nutritional requirements of Escherichia coli have been quantitatively determined in batch culture for cells with (R+) and without (R-) the R plasmid RP1. In these conditions R+ cells have a greater requirement than R- for several nutrients, particularly Mg2+, K+, Fe2+ and PO43-. The maximum growth rate in a simple salts medium was the same for R+ and R- cells. At low concentrations of phosphate, the specific growth rate of R+ cells differed from that found for R- cells. The R plasmid was stable in simple salts medium, irrespective of the nutrient ultimately depleted by growth, but, on storage, R+ cells survived for a shorter time than R- cells.
INTRODUCTION: Diabetic kidney disease (DKD) is fundamentally a podocytopathy in which sterile inflammation plays a central pathogenic role, yet the upstream triggers that initiate inflammatory cascades in podocytes remain elusive. R-loops are critical regulators of genomic stability, and their pathological accumulation triggers DNA damage and innate immune activation. Whether R-loop dysregulation contributes to podocyte-driven inflammation in DKD is unknown. METHODS: We integrated single-cell transcriptomic profiling, dual machine learning algorithms, and functional experiments to dissect the R-loop regulatory network in the diabetic kidney. RESULTS: Integrated analysis of human diabetic kidney single-cell RNA-seq data revealed a globally compromised R-loop regulatory network selectively within podocytes. Intersection of podocyte-specific transcriptomic shifts with validated R-loop regulators identified 93 candidate genes, from which dual machine learning algorithms pinpointed SSB (Sjögren syndrome antigen B) as the principal podocyte-selective R-loop resolver and a superior diagnostic biomarker (AUC = 0.983). SSB expression was selectively downregulated in diabetic podocytes and showed the strongest positive correlation with the R-loop resolution module. Mechanistically, SSB loss impaired RNA splicing and stability pathways, leading to aberrant R-loop accumulation that activated the cGAS-dependent inflammatory signaling in podocytes. In two murine DKD models and high glucose-challenged podocytes, SSB was markedly reduced. Remarkably, SSB knockdown in podocytes alone sufficed to trigger R-loop accumulation and pro-inflammatory cytokine expression, whereas both RNase H1-mediated R-loop removal and cGAS co-depletion blunted this response. DISCUSSION: These findings suggest that an SSB-governed R-loop -cGAS -inflammatory signaling axis may link genomic instability to podocyte inflammation and contribute to DKD progression, nominating R-loop homeostasis as a previously unrecognized potential therapeutic target.
NMRI mice were immunized with acetone-killed bacteria of 6 salmonella R mutants, 5 homologous and 6 heterologous Salmonella S forms and 3 E. coli R mutants. The animals were then challenged with graded amounts of live S. typhimurium. The results show that the protection obtained was dependent on the number of immunizing injections and on the time interval between them. Thus in the case of Salmonella R-mutants two immunizations increased the LD50 of challenge by an index of two (log 10) compaired to one immunization. A third immunization led to only a small further increase, the protection however, was longer lasting. A 3 fold immunization with two Salmonella typhimurium mutants, one SR- and one Ra form, led to a protection comparable to that obtained with S form bacteria. In contrast to the R-mutants, with Salmonella typhimurium S form a high degree of long-lasting protection was achieved already after a single immunization, and was not increased significantly by repeated injections. In animals immunized with Salmonella typhimurium S form the difference between non-lethal and 100% lethal challenge dose varied by a factor of 10 (one injection dose). In contrast, in animals immunized with Salmonella R mutants the above differences were more gradual extending over 3, 4 or more infection doses. This was also true for animals immunized with lower doses of S. typhimurium S form and for the non-immunized control animals. For comparison the protective effect of heterologous Salmonella S forms and of E. coli R-mutants was studied. These were found to be less effective in affording protection to Salmonella typhimurium than the above Salmonella R forms. The various strains used for immunization may be placed in the following sequence in order of decreasing protection: Salmonella typhimurium S form, Salmonella R-mutants, heterologous Salmonella S forms, E. coli R mutants. In a parallel investigation the antibody inducing properties of Salmonella R mutants and heterologous Salmonella S forms were studied. In all cases homologous hemaglutinating antibodies to all the strains used for immunization were detectable. In immunization with Salmonella R mutants in addition to homologous titres, agglutinating antibodies to Salmonella typhimurium S form were also produced in significant amounts. There was, however, no correlation between the time of appearance of protection and that of appearance of antibodies nor between the hight of antibody titres and degree of protection. The detection of agglutinins to the infecting microorganisms represents therefore no valid criterium for the effectiveness of R mutants and heterologous Salmonella S forms as protective vaccines. From the present results it is concluded that in addition to the O antigen one or more further cell components exist which are involved in rendering animals immune to Salmonella typhimurium and probably also to other Salmonella S form bacteria.
Strains of Escherichia coli carrying R-factor R71(a), which codes for a streptomycin-spectinomycin adenylyltransferase, have elevated levels of resistance to dihydrostreptomycin (DHS) compared with isogenic R(-) bacteria. DHS accumulated by whole cells and spheroplasts of R(+) bacteria is lower than that observed for R(-) strains, a result of the absence of the second and more rapid of the two energy-dependent phases of DHS uptake seen in susceptible E. coli. A mutant of R(+)E. coli with reduced DHS resistance has been shown to have reduced levels of streptomycin-spectinomycin adenylyltransferase activity as well as enhanced drug accumulation. Actively accumulated DHS was recovered from R(+) cells as the adenylylated derivative. Neither was inactivated antibiotic detected in culture filtrates, nor was actively accumulated drug lost from R(+) cells under normal conditions. The cellular distribution of actively accumulated DHS in R(+) and R(-) cells was found to be the same. Membranes isolated from these cells retained only a small fraction ( approximately 1%) of the total cell-associated drug. The R(+) derivative of a mutant with defective energy transduction (E. coli NR-70) and reduced ability to transport aminoglycosides has a significantly higher minimal inhibitory concentration of DHS than its R(+) parent (strain 7). Streptomycin-spectinomycin adenylyltransferase activity, from comparisons of K(m) values and total activities of enzyme, was the same in both strains. The enzyme has been localized to the exterior surface of the bacterial inner membrane, although isolated membranes lacked detectable enzyme activity. The preceding observations are consistent with the proposal that the level of R71(a)-mediated DHS resistance is the outcome of competition between the rate of adenylylation and the rate of the first energy-dependent phase of DHS transport. When the rate of adenylylation exceeds the first energy-dependent phase, adenylylated DHS is accumulated, apparently in a manner identical to the accumulation of DHS. Unlike DHS, adenylylated DHS does not interact with ribosomes, and, consequently, there is a failure to initiate ribosomally dependent sequelae such as the second energy-dependent phase of accumulation, inhibition of protein synthesis, and/or misreading of mRNA.
Refractile bodies (R-bodies) of gram-negative bacteria are large proteinaceous assemblies, rolled up in the form of an Archimedean spiral. They exhibit rapid rod-like reversible extension in the micrometer range when cued by chemical environmental triggers and have potential for synthetic biology and biochip applications. Initially described for the Paramecium endosymbionts Caedibacter taeniospiralis and Caedimonas varicaedens, R-bodies have since been discovered in many classes of Pseudomonadota, both in endosymbionts and in non-endosymbionts. However, despite the fact that the genetics and morphologies, as well as the unrolling kinetics of R-bodies from different species, show considerable diversity, no recent study has integrated these aspects into a single framework. The latter would be advantageous for the creation of an R-body biotechnology toolbox, where different properties determine the application area. Here, we have examined the R-bodies from six different Pseudomonadota, comprising both phylogenetically diverse endosymbionts and non-endosymbionts. Comparison of the morphologies of the rolled-up and unrolled forms, obtained using electron microscopy and high-quality images, to their corresponding genetic data indicates that extensive lateral gene transfer has occurred, which confounds a common framework based on these data. However, we have also studied the R-body extension and retraction kinetics using high frame-rate light microscopic video recordings, where we show for the first time that R-bodies can be classified into two classes, showing "fast burst" or "slow" acid-induced extension kinetics, respectively. We propose that this criterion may, in fact, be the most useful for the choice of an R-body tool for biotechnological purposes.IMPORTANCER-bodies are unique proteinaceous macromolecular structures capable of massive reversible extension in response to external environmental triggers without the input of chemical energy. They comprise only a few small polypeptides, which makes them potentially highly amenable to tuning via genetic engineering, as well as being exceptionally stable. These properties would be highly desirable in biotechnology and synthetic biology, as well as in biochip applications, where a controlled mechanical extensor might play an integral part in a nanoscale molecular machine. So far, only R-bodies from a single species, Caedibacter taeniospiralis, have been characterized extensively. However, in recent years, genomic information has revealed that a panoply of R-bodies are widely distributed among gram-negative phyla, although studies have generally not included morphological data. This study brings these two areas together to provide a holistic overview of the field and also reveals new insights into key dynamic aspects of R-body extension.
We have examined the association of an F' plasmid and an R plasmid in Proteus mirabilis with a rapidly sedimenting material that is generated by sodium dodecyl sulfate lysis and low speed centrifugation. Virtually all of the chromosomal deoxyribonucleic acid (DNA) and the F' plasmid DNA are associated with the rapidly sedimenting material after gentle lysis and centrifugation. A portion of R plasmid NR1 DNA (usually 5 to 25%) is not bound to the rapidly sedimenting material and is recovered in the supernatant fraction. This difference in binding is not related to the size of the plasmid DNA, since F' plasmids and R plasmids of different molecular weights showed the same behavior. R plasmid DNA labeled by a brief pulse of [(3)H]thymine is recovered in the supernatant fraction to a lower extent than the total R plasmid DNA. It would appear that R plasmid replication takes place in association with the rapidly sedimenting material. With prolongation of the [(3)H]thymine pulse, the [(3)H]thymine-labeled R plasmid DNA is recovered in the supernatant fraction with the same probability as the total R plasmid DNA. This finding indicates that a change in R plasmid attachment to the rapidly sedimenting material occurs some time after its replication. The differences observed in the replication of F' plasmids and R plasmids in P. mirabilis may be related to their different modes of association with the rapidly sedimenting material.
The drug-resistance plasmid, NR1, is a 37-micron circular DNA molecule that contains two components: the resistance transfer factor (29 micron) carrying the transfer genes and the genes for tetracycline resistance, and the r-determinant (8 micron) carrying the genes for resistance to several other antibiotics including chloramphenicol (Cm). In Proteus mirabilis, these two components are capable of independent replication, or they may replicate as a composite molecule. When cells of P. mirabilis containing NR1 are cultured in medium containing Cm at 250 microgram/ml a growth lag of 20-35 hr ensues. During this lag, Cm induces the selective amplification of the r-determinant, including the gene for resistance to Cm. The amplification results from the excision of the r-determinant from the R plasmid, the independent replication of the r-determinant to give polymeric as well as monomeric r-determinants, and the eventual reintegration of multiple tandem copies of the r-determinant with the resistance transfer factor to form a new R plasmid with multiple copies of the r-determinant. This mechanism represents a new level of control of gene expression in bacterial systems--namely, the induction of selective gene amplification.
Hydroxyurea (HU) and cytosine arabinoside (Ara-C) eliminate R factor R46 from Escherichia coli strain J5-3. The highest frequency of elimination for both drugs occurred at concentrations and times that produced the lowest survivor levels. 5% of cells were antibiotic-sensitive after 5 h incubation in 5 mg/ml Ara-C, whilst 6 and 7% of the survivors had lost the R factor after 8 and 24 h incubation, respectively in 20 mg/ml HU. The number of survivors began to increase after 5 h incubation in Ara-C, probably due to the inactivation of the drug in the phosphate-buffered medium. All four antibiotic resistances (ampicillin, streptomycin, sulphonamide and tetracycline) mediated by R46 were lost simultaneously and elimination of the whole plasmid was confirmed by conjugation experiments in which the 'cured' cells was shown to be as efficient recipients of R46 as the control R- strain in crosses with E. coli strain J6-2 (R46). No covalently closed circular plasmid DNA was demonstrable in cured cell lines. R+ and R- strains had similar sensitivities to HU but J5-3 R+ was much more sensitive to Ara-C than the isogenic R- strain. It may be concluded that HU eliminates R46 actively whereas although Ara-C may produce some active elimination it acts mainly by selection of R- cells present in the culture.
A terminal r wave in Lead V1 lower than 0.6 mV. was studied in the ECGs of four groups: (1) 104 healthy children, (2) 207 healthy young adults, (3) 171 patients with no autopsy evidence of a cardiopulmonary disease, and (4) 1,078 autopsy patients with a cardiopulmonary disease. Cases with a complete right bundle branch block were excluded. A terminal r wave occurred in 2.9 per cent healthy children, 1.4 per cent of healthy young adults, 0.6 per cent of patients without and in 5.9 per cent of patients with autopsy evidence of a cardiopulmonary disease. The occurrence of a terminal r wave was most common in pulmonary patients (10 per cent). But it was also found in patients with an anterior or a posterior myocardial infarction and in some cases of left ventricular hypertrophy. In the autopsy series RVH occurred in 57 per cent of patients with a Qr pattern, in 30 per cent of patients with a terminal r wave higher than the initial one, and in none of the patients with a terminal r wave lower than the initial one. It is concluded that the height of the terminal r wave has clinical significance. A terminal r wave higher than the initial one in Lead V1 is associated with a cardiopulmonary disease in subjects over 30 years of age, while an r wave lower than the initial one seems to be an innocent finding.
Coronary angiograms and treadmill stress tests were reviewed in 89 patients. Changes in R wave amplitude were measured in the control and immediate postexercise periods. Of 45 patients with normal coronary arteries, 41 (91 percent) had a decrease in R wave amplitude (P less than 0.01); 3 (7 percent) had an increase in amplitude, including 2 with abnormal left ventriculograms. The remaining patient (2 percent) had abnormal wall motion but no change in R wave amplitude. Among the 44 patients with significant coronary artery disease (70 percent or greater luminal narrowing in one or more vessels), R wave amplitude increased after exercise in 26 (59 percent) with more severe coronary artery disease. R wave amplitude decreased in 18 patients (41 percent) with normal or minimally abnormal resting ventriculograms and less severe coronary artery disease (P less than 0.01). Changes in R wave amplitude reflect ventricular function, an increase in R wave amplitude reflecting more severe dysfunction and severe coronary narrowing. A decreased R wave amplitude indicates normal or minimal dysfunction and is strongly associated with normal coronary angiograms.