Tumor‐stroma interactions differentially alter drug sensitivity based on the origin of stromal cells

Due to tumor heterogeneity, most believe that effective treatments should be tailored to the features of an individual tumor or tumor subclass. It is still unclear, however, what information should be considered for optimal disease stratification, and most prior work focuses on tumor genomics. Here, we focus on the tumor microenvironment. Using a large‐scale coculture assay optimized to measure drug‐induced cell death, we identify tumor–stroma interactions that modulate drug sensitivity. Our data show that the chemo‐insensitivity typically associated with aggressive subtypes of breast cancer is not observed if these cells are grown in 2D or 3D monoculture, but is manifested when these cells are cocultured with stromal cells, such as fibroblasts. Furthermore, we find that fibroblasts influence drug responses in two distinct and divergent manners, associated with the tissue from which the fibroblasts were harvested. These divergent phenotypes occur regardless of the drug tested and result from modulation of apoptotic priming within tumor cells. Our study highlights unexpected diversity in tumor–stroma interactions, and we reveal new principles that dictate how fibroblasts alter tumor drug responses

Expressed sequence tag analysis of khat (Catha edulis) provides a putative molecular biochemical basis for the biosynthesis of phenylpropylamino alkaloids

Khat (Catha edulis Forsk.) is a flowering perennial shrub cultivated for its neurostimulant properties resulting mainly from the occurrence of (S)-cathinone in young leaves. The biosynthesis of (S)-cathinone and the related phenylpropylamino alkaloids (1S,2S)-cathine and (1R,2S)-norephedrine is not well characterized in plants. We prepared a cDNA library from young khat leaves and sequenced 4,896 random clones, generating an expressed sequence tag (EST) library of 3,293 unigenes. Putative functions were assigned to > 98% of the ESTs, providing a key resource for gene discovery. Candidates potentially involved at various stages of phenylpropylamino alkaloid biosynthesis from L-phenylalanine to (1S,2S)-cathine were identified

Early ultrasound surveillance of newly-created haemodialysis arteriovenous fistula

IntroductionWe assess if ultrasound surveillance of newly-created arteriovenous fistulas (AVFs) can predict nonmaturation sufficiently reliably to justify randomized controlled trial (RCT) evaluation of ultrasound-directed salvage intervention.MethodsConsenting adults underwent blinded fortnightly ultrasound scanning of their AVF after creation, with scan characteristics that predicted AVF nonmaturation identified by logistic regression modeling.ResultsOf 333 AVFs created, 65.8% matured by 10 weeks. Serial scanning revealed that maturation occurred rapidly, whereas consistently lower fistula flow rates and venous diameters were observed in those that did not mature. Wrist and elbow AVF nonmaturation could be optimally modeled from week 4 ultrasound parameters alone, but with only moderate positive predictive values (PPVs) (wrist, 60.6% [95% confidence interval, CI: 43.9–77.3]; elbow, 66.7% [48.9–84.4]). Moreover, 40 (70.2%) of the 57 AVFs that thrombosed by week 10 had already failed by the week 4 scan, thus limiting the potential of salvage procedures initiated by that scan’s findings to alter overall maturation rates. Modeling of the early ultrasound characteristics could also predict primary patency failure at 6 months; however, that model performed poorly at predicting assisted primary failure (those AVFs that failed despite a salvage attempt), partly because patency of at-risk AVFs was maintained by successful salvage performed without recourse to the early scan data.ConclusionEarly ultrasound surveillance may predict fistula maturation, but is likely, at best, to result in only very modest improvements in fistula patency. Power calculations suggest that an impractically large number of participants (>1700) would be required for formal RCT evaluation

Effect of angiotensin-converting enzyme inhibitor and angiotensin receptor blocker initiation on organ support-free days in patients hospitalized with COVID-19

IMPORTANCE Overactivation of the renin-angiotensin system (RAS) may contribute to poor clinical outcomes in patients with COVID-19. Objective To determine whether angiotensin-converting enzyme (ACE) inhibitor or angiotensin receptor blocker (ARB) initiation improves outcomes in patients hospitalized for COVID-19. DESIGN, SETTING, AND PARTICIPANTS In an ongoing, adaptive platform randomized clinical trial, 721 critically ill and 58 non–critically ill hospitalized adults were randomized to receive an RAS inhibitor or control between March 16, 2021, and February 25, 2022, at 69 sites in 7 countries (final follow-up on June 1, 2022). INTERVENTIONS Patients were randomized to receive open-label initiation of an ACE inhibitor (n = 257), ARB (n = 248), ARB in combination with DMX-200 (a chemokine receptor-2 inhibitor; n = 10), or no RAS inhibitor (control; n = 264) for up to 10 days. MAIN OUTCOMES AND MEASURES The primary outcome was organ support–free days, a composite of hospital survival and days alive without cardiovascular or respiratory organ support through 21 days. The primary analysis was a bayesian cumulative logistic model. Odds ratios (ORs) greater than 1 represent improved outcomes. RESULTS On February 25, 2022, enrollment was discontinued due to safety concerns. Among 679 critically ill patients with available primary outcome data, the median age was 56 years and 239 participants (35.2%) were women. Median (IQR) organ support–free days among critically ill patients was 10 (–1 to 16) in the ACE inhibitor group (n = 231), 8 (–1 to 17) in the ARB group (n = 217), and 12 (0 to 17) in the control group (n = 231) (median adjusted odds ratios of 0.77 [95% bayesian credible interval, 0.58-1.06] for improvement for ACE inhibitor and 0.76 [95% credible interval, 0.56-1.05] for ARB compared with control). The posterior probabilities that ACE inhibitors and ARBs worsened organ support–free days compared with control were 94.9% and 95.4%, respectively. Hospital survival occurred in 166 of 231 critically ill participants (71.9%) in the ACE inhibitor group, 152 of 217 (70.0%) in the ARB group, and 182 of 231 (78.8%) in the control group (posterior probabilities that ACE inhibitor and ARB worsened hospital survival compared with control were 95.3% and 98.1%, respectively). CONCLUSIONS AND RELEVANCE In this trial, among critically ill adults with COVID-19, initiation of an ACE inhibitor or ARB did not improve, and likely worsened, clinical outcomes. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT0273570

Cloning and analysis of the ribonucleotide reductase subunit gene promoters from Plasmodium falciparum

Ribonucleotide Reductase (RNR) is an essential enzyme required for DNA replication. During the erythrocytic growth cycle of the malaria parasite Plasmodium falciparum, mRNAs of the two RNR subunit genes, PfR1 and PfR2, are expressed during a specific period in the cell cycle just prior to DNA synthesis. To investigate the transcriptional regulation of R1 and R2, as well as to address larger issues of transcription in P. falciparum , I cloned the upstream regions of each gene, mapped the 5 ′ start of transcription, and performed promoter analysis by transient transfection of synchronized parasites with CAT reporter constructs. Results show that transcription of both genes initiates at multiple sites. R1 and R2 transcription start sites are preceded by a dT-rich T-Box element, but are not always associated with a TATA box. Two introns were discovered in the 5′ UTR of the R2 gene just upstream from the R2 coding region. Promoter deletion analysis of the R2 gene suggests that a consensus AP-1 site is a candidate transcriptional repressor of R2 expression. Results show that the T-Box and/or the recently discovered P. falciparum-specific GTATT element may enhance R2 transcription. One TATA-less R2 start site is shown to be transcriptionally active, suggesting that R2 transcription does not require a TATA box. Elements at the 3′ (proximal) end of the 5′ UTR of both the R1 and R2 genes are necessary for gene expression, but may play a role in translation rather than transcription. In summary, the R2 promoter appears to use a combination of well defined transcription factors and novel elements to regulate transcription

Cloning and analysis of the ribonucleotide reductase subunit gene promoters from Plasmodium falciparum

Ribonucleotide Reductase (RNR) is an essential enzyme required for DNA replication. During the erythrocytic growth cycle of the malaria parasite Plasmodium falciparum, mRNAs of the two RNR subunit genes, PfR1 and PfR2, are expressed during a specific period in the cell cycle just prior to DNA synthesis. To investigate the transcriptional regulation of R1 and R2, as well as to address larger issues of transcription in P. falciparum , I cloned the upstream regions of each gene, mapped the 5 ′ start of transcription, and performed promoter analysis by transient transfection of synchronized parasites with CAT reporter constructs. Results show that transcription of both genes initiates at multiple sites. R1 and R2 transcription start sites are preceded by a dT-rich T-Box element, but are not always associated with a TATA box. Two introns were discovered in the 5′ UTR of the R2 gene just upstream from the R2 coding region. Promoter deletion analysis of the R2 gene suggests that a consensus AP-1 site is a candidate transcriptional repressor of R2 expression. Results show that the T-Box and/or the recently discovered P. falciparum-specific GTATT element may enhance R2 transcription. One TATA-less R2 start site is shown to be transcriptionally active, suggesting that R2 transcription does not require a TATA box. Elements at the 3′ (proximal) end of the 5′ UTR of both the R1 and R2 genes are necessary for gene expression, but may play a role in translation rather than transcription. In summary, the R2 promoter appears to use a combination of well defined transcription factors and novel elements to regulate transcription

Mutant rescue analysis of SRF-6 in Caenorhabditis elegans

Following Ph.D. research performed by Brian Libby in 1998, this project provides additional evidence that the srf-6 gene in C. elegans may be located on a 1.9kb fragment from cosmid F41G3. This evidence was obtained via monoclonal antibody staining of transformed worms grown at 16?C and comparison to the 20?C results presented by Libby's. In order to follow up on these findings, genomic DNA was then harvested from eight srf-6 mutant strains for future sequencing

A Biomolecular Implementation of Logically Reversible Computation With Minimal Energy Dissipation

Energy dissipation associated with logic operations imposes a fundamental physical limit on computation and is generated by the entropic cost of information erasure, which is a consequence of irreversible logic elements. We show how to encode information in DNA and use DNA amplification to implement a logically reversible gate that comprises a complete set of operators capable of universal computation. We also propose a method using this design to connect, or 'wire', these gates together in a biochemical fashion to create a logic network, allowing complex parallel computations to be executed. The architecture of the system permits highly parallel operations and has properties that resemble well known genetic regulatory systems. Logically reversible operations occupy a central role in considerations of the fundamental physical limits of information handling (1). The early work of Landauer (2) showed that energy dissipation occurs during the destruction of information of the previous st..