Single-sample, multi-omic mass spectrometry for investigating mechanisms of drug toxicity.

Poor therapeutic index is a principal cause of drug attrition during development. A case in point is L-asparaginase (ASNase), an enzyme-drug approved for treatment of pediatric acute lymphoblastic leukemia (ALL) but too toxic for adults. To elucidate potentially targetable mechanisms for mitigation of ASNase toxicity, we performed multi-omic profiling of the response to sub-toxic and toxic doses of ASNase in mice.

Mitochondrial defects and metabolic vulnerabilities in Lynch syndrome-associated MSH2-deficient endometrial cancer.

Lynch syndrome (LS), caused by inherited mutations in DNA mismatch repair genes including MSH2, carries a 60% lifetime risk of developing endometrial cancer (EC). Beyond hypermutability, mechanisms driving LS-associated EC remain unclear. We investigated MSH2 loss in EC pathogenesis using a mouse model (PR-Cre Msh2LoxP/LoxP, abbreviated Msh2KO), primary cell lines, human tissues, and human EC cells with isogenic MSH2 knockdown.

Ion suppression correction and normalization for non-targeted metabolomics.

Ion suppression is a major problem in mass spectrometry (MS)-based metabolomics; it can dramatically decrease measurement accuracy, precision, and sensitivity. Here we report a method, the IROA TruQuant Workflow, that uses a stable isotope-labeled internal standard (IROA-IS) library plus companion algorithms to: 1) measure and correct for ion suppression, and 2) perform Dual MSTUS normalization of MS metabolomic data. We evaluate the method across ion chromatography (IC), hydrophilic interaction liquid chromatography (HILIC), and reversed-phase liquid chromatography (RPLC)-MS systems in both positive and negative ionization modes, with clean and unclean ion sources, and across different biological matrices.

Cancer cells avoid ferroptosis induced by immune cells via fatty acid binding proteins.

Background: Cancer creates an immunosuppressive environment that hampers immune responses, allowing tumors to grow and resist therapy. One way the immune system fights back is by inducing ferroptosis, a type of cell death, in tumor cells through CD8  T cells. This involves lipid peroxidation and enzymes like lysophosphatidylcholine acyltransferase 3 (Lpcat3), which makes cells more prone to ferroptosis.

Ultra-Fast Multi-Organ Proteomics Unveils Tissue-Specific Mechanisms of Drug Efficacy and Toxicity.

Rapid and comprehensive analysis of complex proteomes across large sample sets is vital for unlocking the potential of systems biology. We present UFP-MS, an ultra-fast mass spectrometry (MS) proteomics method that integrates narrow-window data-independent acquisition (nDIA) with short-gradient micro-flow chromatography, enabling profiling of >240 samples per day. This optimized MS approach identifies 6,201 and 7,466 human proteins with 1- and 2-min gradients, respectively.

Therapeutic modulation of ROCK overcomes metabolic adaptation of cancer cells to OXPHOS inhibition and drives synergistic anti-tumor activity.

Genomic studies have identified frequent mutations in subunits of the SWI/SNF chromatin remodeling complex including and in non-small cell lung cancer. Previously, we and others have identified that -mutant lung cancers are highly dependent on oxidative phosphorylation (OXPHOS). Despite initial excitements, therapeutics targeting metabolic pathways such as OXPHOS have largely been disappointing due to rapid adaptation of cancer cells to inhibition of single metabolic enzymes or pathways, suggesting novel combination strategies to overcome adaptive responses are urgently needed.

Novel and Advanced Ultrasound Techniques for Thyroid Thermal Ablation.

Thyroid radiofrequency ablation and microwave ablation are widely adopted minimally invasive treatments for diverse thyroid conditions worldwide. Fundamental skills such as the trans-isthmic approach and the moving shot technique are crucial for performing thyroid ablation, and advanced techniques, including hydrodissection and vascular ablation, improve safety and efficacy and reduce complications. Given the learning curve associated with ultrasound-guided therapeutic procedures, operators need training and experience.

stabilization of a less toxic asparaginase variant leads to a durable antitumor response in acute leukemia.

Asparagine is a non-essential amino acid since it can either be taken up via the diet or synthesized by asparagine synthetase. Acute lymphoblastic leukemia (ALL) cells do not express asparagine synthetase or express it only minimally, which makes them completely dependent on extracellular asparagine for their growth and survival. This dependency makes ALL cells vulnerable to treatment with L-asparaginase, an enzyme that hydrolyzes asparagine.

Successful Applications of Food-Assisted and -Simulated Training Model of Thyroid Radiofrequency Ablation.

Background: Radiofrequency ablation (RFA) for benign thyroid nodules is one kind of scarless treatment for symptomatic or cosmetic benign thyroid nodules. However, how to train RFA-naive physicians to become qualified operators for thyroid RFA is an important issue. Our study aimed to introduce a successful training model of thyroid RFA.

Using Deep Convolutional Neural Networks for Enhanced Ultrasonographic Image Diagnosis of Differentiated Thyroid Cancer.

Differentiated thyroid cancer (DTC) from follicular epithelial cells is the most common form of thyroid cancer. Beyond the common papillary thyroid carcinoma (PTC), there are a number of rare but difficult-to-diagnose pathological classifications, such as follicular thyroid carcinoma (FTC). We employed deep convolutional neural networks (CNNs) to facilitate the clinical diagnosis of differentiated thyroid cancers.

Concordant Androgen-Regulated Expression of Divergent Rhox5 Promoters in Sertoli Cells.

Concordant transcriptional regulation can generate multiple gene products that collaborate to achieve a common goal. Here we report a case of concordant transcriptional regulation that instead drives a single protein to be produced in the same cell type from divergent promoters. This gene product-the RHOX5 homeobox transcription factor-is translated from 2 different mRNAs with different 5' untranslated regions (UTRs) transcribed from alternative promoters.

Mechanism of Catalysis by l-Asparaginase.

Two bacterial type II l-asparaginases, from and , have played a critical role for more than 40 years as therapeutic agents against juvenile leukemias and lymphomas. Despite a long history of successful pharmacological applications and the apparent simplicity of the catalytic reaction, controversies still exist regarding major steps of the mechanism. In this report, we provide a detailed description of the reaction catalyzed by type II l-asparaginase (EcAII).

Synthesis of Pyrazinopyrazine-Fused Azaacenes through Direct Condensation Reactions between Quinoxalinediamine and Diketones.

We report the synthesis of a new type of pyrazinopyrazine-fused azaacene molecules by a simple and versatile procedure. 6,9-Dihexyldithieno[3,2-f:2',3'-h]quinoxaline-2,3-diamine was synthesized through the condensation between 2,7-dihexylbenzo[1,2-b:6,5-b']dithiophene-4,5-diamine and bis(2,2,2-trifluoroethyl) oximidate. A series of derivatized molecules with extended two-dimensional aromatic fused-ring structures could be obtained by simple condensation reactions between the quinoxalinediamine intermediate and various diketones.

Opportunistic complexes of E. coli L-asparaginases with citrate anions.

Active sites of enzymes are highly optimized for interactions with specific substrates, thus binding of opportunistic ligands is usually observed only in the absence of native substrates or products. However, during growth of crystals required for structure determination enzymes are often exposed to conditions significantly divergent from the native ones, leading to binding of unexpected ligands to active sites even in the presence of substrates. Failing to recognize this possibility may lead to incorrect interpretation of experimental results and to faulty conclusions.

Glutaminase Activity of L-Asparaginase Contributes to Durable Preclinical Activity against Acute Lymphoblastic Leukemia.

We and others have reported that the anticancer activity of L-asparaginase (ASNase) against asparagine synthetase (ASNS)-positive cell types requires ASNase glutaminase activity, whereas anticancer activity against ASNS-negative cell types does not. Here, we attempted to disentangle the relationship between asparagine metabolism, glutamine metabolism, and downstream pathways that modulate cell viability by testing the hypothesis that ASNase anticancer activity is based on asparagine depletion rather than glutamine depletion per se. We tested ASNase wild-type (ASNase) and its glutaminase-deficient Q59L mutant (ASNase) and found that ASNase glutaminase activity contributed to durable anticancer activity against xenografts of the ASNS-negative Sup-B15 leukemia cell line in NOD/SCID gamma mice, whereas asparaginase activity alone yielded a mere growth delay.

Lead removal from water - dependence on the form of carbon and surface functionalization.

We have investigated lead adsorption on different forms of nanostructured carbon, namely multiwall carbon nanotubes (MWCNT) and reduced graphene oxide (RGO) functionalized with different functional groups (hydroxyl, carboxyl, and amino groups). We found that the same functional group does not result in the same performance trends for different nanostructured carbons. Drastically different behavior was observed for the amino-group functionalization, where a significant improvement is observed for MWCNT, while worse performance compared to non-functionalized material is obtained for RGO.

The Antagonistic Gene Paralogs Upf3a and Upf3b Govern Nonsense-Mediated RNA Decay.

Gene duplication is a major evolutionary force driving adaptation and speciation, as it allows for the acquisition of new functions and can augment or diversify existing functions. Here, we report a gene duplication event that yielded another outcome--the generation of antagonistic functions. One product of this duplication event--UPF3B--is critical for the nonsense-mediated RNA decay (NMD) pathway, while its autosomal counterpart--UPF3A--encodes an enigmatic protein previously shown to have trace NMD activity.

Very-low-bandgap metallopolyynes of platinum with a cyclopentadithiophenone ring for organic solar cells absorbing down to the near-infrared spectral region.

Two solution-processable metallopolyynes of platinum functionalized with the electron-deficient 4H-cyclopenta[2,1-b:3,4-b']dithiophen-4-one spacer and their model molecular complexes were synthesized and developed for the applications of polymer solar cells. These metallated polymers possess extremely low bandgaps of 1.44-1.

Frame-disrupting mutations elicit pre-mRNA accumulation independently of frame disruption.

The T-cell receptor (TCR) and immunoglobulin (Ig) genes are unique among vertebrate genes in that they undergo programmed rearrangement, a process that allows them to generate an enormous array of receptors with different antigen specificities. While crucial for immune function, this rearrangement mechanism is highly error prone, often generating frameshift or nonsense mutations that render the rearranged TCR and Ig genes defective. Such frame-disrupting mutations have been reported to increase the level of TCRbeta and Igmicro pre-mRNA, suggesting the hypothesis that RNA processing is blocked when frame disruption is sensed.

A UPF3-mediated regulatory switch that maintains RNA surveillance.

Nonsense-mediated decay (NMD) is an RNA decay pathway that downregulates aberrant mRNAs and a subset of normal mRNAs. The regulation of NMD is poorly understood. Here we identify a regulatory mechanism acting on two related UPF (up-frameshift) factors crucial for NMD: UPF3A and UPF3B.

Control of HIF-1alpha expression by eIF2 alpha phosphorylation-mediated translational repression.

Hypoxia inducible factor 1alpha (HIF-1alpha) plays a central role in regulating tumor angiogenesis via its effects on vascular endothelial growth factor (VEGF) transcription, and its expression is regulated through proteasome-mediated degradation. Paradoxically, previous studies have shown that proteasome inhibitors (PI) block tumor angiogensis by reducing VEGF expression, but the mechanisms have not been identified. Here, we report that PIs down-regulated HIF-1alpha protein levels and blocked HIF-1alpha transcriptional activity in human prostate cancer cells.

Nonsense codons trigger an RNA partitioning shift.

T-cell receptor-beta (TCRbeta) genes naturally acquire premature termination codons (PTCs) as a result of programmed gene rearrangements. PTC-bearing TCRbeta transcripts are dramatically down-regulated to protect T-cells from the deleterious effects of the truncated proteins that would otherwise be produced. Here we provide evidence that two responses collaborate to elicit this dramatic down-regulation.

Polymer solar cells based on very narrow-bandgap polyplatinynes with photocurrents extended into the near-infrared region.

The synthesis, characterization and photophysics of some solution-processable intensely coloured polyplatinynes functionalized with the thienopyrazine-thiophene hybrid spacer and their model molecular complexes are described. These metallated polymers possess extremely low bandgaps of 1.47-1.