Integrative Computational Framework, , Links Mutated Driver Genes to Expression Dysregulation Across 19 Cancer Types.

Though somatic mutations play a critical role in driving cancer initiation and progression, the systems-level functional impacts of these mutations-particularly, how they alter expression across the genome and give rise to cancer hallmarks-are not yet well-understood, even for well-studied cancer driver genes. To address this, we designed an integrative machine learning model, Dyscovr, that leverages mutation, gene expression, copy number alteration (CNA), methylation, and clinical data to uncover putative relationships between nonsynonymous mutations in key cancer driver genes and transcriptional changes across the genome. We applied Dyscovr pan-cancer and within 19 individual cancer types, finding both broadly relevant and cancer type-specific links between driver genes and putative targets, including a subset we further identify as exhibiting negative genetic relationships.

Proteo-metabolomics and patient tumor slice experiments point to amino acid centrality for rewired mitochondria in fibrolamellar carcinoma.

Fibrolamellar carcinoma (FLC) is a rare, lethal, early-onset liver cancer with a critical need for new therapeutics. The primary driver in FLC is the fusion oncoprotein, DNAJ-PKAc, which remains challenging to target therapeutically. It is critical, therefore, to expand understanding of the FLC molecular landscape to identify druggable pathways/targets.

Selected Ion Monitoring for Orbitrap-Based Metabolomics.

Orbitrap mass spectrometry in full scan mode enables the simultaneous detection of hundreds of metabolites and their isotope-labeled forms. Yet, sensitivity remains limiting for many metabolites, including low-concentration species, poor ionizers, and low-fractional-abundance isotope-labeled forms in isotope-tracing studies. Here, we explore selected ion monitoring (SIM) as a means of sensitivity enhancement.

Reprogramming neuroblastoma by diet-enhanced polyamine depletion.

Neuroblastoma is a highly lethal childhood tumor derived from differentiation-arrested neural crest cells. Like all cancers, its growth is fueled by metabolites obtained from either circulation or local biosynthesis. Neuroblastomas depend on local polyamine biosynthesis, with the inhibitor difluoromethylornithine showing clinical activity.

Glycine homeostasis requires reverse SHMT flux.

The folate-dependent enzyme serine hydroxymethyltransferase (SHMT) reversibly converts serine into glycine and a tetrahydrofolate-bound one-carbon unit. Such one-carbon unit production plays a critical role in development, the immune system, and cancer. Using rodent models, here we show that the whole-body SHMT flux acts to net consume rather than produce glycine.

Predicting the Electrical, Mechanical, and Geometric Contributions to Soft Electroadhesives through Fracture Mechanics.

Electroadhesion is the modulation of adhesive forces through electrostatic interactions and has potential applications in a number of next-generation technologies. Recent efforts have focused on using electroadhesion in soft robotics, haptics, and biointerfaces that often involve compliant materials and nonplanar geometries. Current models for electroadhesion provide limited insight on other contributions that are known to influence adhesion performance, such as geometry and material properties.

Convergent and complementary selection shaped gains and losses of eusociality in sweat bees.

Sweat bees have repeatedly gained and lost eusociality, a transition from individual to group reproduction. Here we generate chromosome-length genome assemblies for 17 species and identify genomic signatures of evolutionary trade-offs associated with transitions between social and solitary living. Both young genes and regulatory regions show enrichment for these molecular patterns.

Glycine homeostasis requires reverse SHMT flux.

The folate-dependent enzyme serine hydroxymethyltransferase (SHMT) reversibly converts serine into glycine and a tetrahydrofolate-bound one-carbon unit. Such one-carbon unit production plays a critical role in development, the immune system, and cancer. Here we show that the whole-body SHMT flux acts to net consume rather than produce glycine.

Ketogenic diet and chemotherapy combine to disrupt pancreatic cancer metabolism and growth.

Background: Ketogenic diet is a potential means of augmenting cancer therapy. Here, we explore ketone body metabolism and its interplay with chemotherapy in pancreatic cancer.

Methods: Metabolism and therapeutic responses of murine pancreatic cancer were studied using KPC primary tumors and tumor chunk allografts.

Local production of lactate, ribose phosphate, and amino acids within human triple-negative breast cancer.

Background: Upregulated glucose metabolism is a common feature of tumors. Glucose can be broken down by either glycolysis or the oxidative pentose phosphate pathway (oxPPP). The relative usage within tumors of these catabolic pathways remains unclear.

The nucleosome acidic patch and H2A ubiquitination underlie mSWI/SNF recruitment in synovial sarcoma.

Interactions between chromatin-associated proteins and the histone landscape play major roles in dictating genome topology and gene expression. Cancer-specific fusion oncoproteins, which display unique chromatin localization patterns, often lack classical DNA-binding domains, presenting challenges in identifying mechanisms governing their site-specific chromatin targeting and function. Here we identify a minimal region of the human SS18-SSX fusion oncoprotein (the hallmark driver of synovial sarcoma) that mediates a direct interaction between the mSWI/SNF complex and the nucleosome acidic patch.

A Novel SS18-SSX Fusion-specific Antibody for the Diagnosis of Synovial Sarcoma.

Synovial sarcoma (SS), an aggressive soft tissue sarcoma with a predilection for the extremities of young adults, harbors the pathognomonic t(X;18)(p11;q11) translocation, resulting in SS18-SSX rearrangements. SS includes monophasic, biphasic, and poorly differentiated variants, which show considerable histologic overlap with a range of other tumor types, making the diagnosis challenging on limited biopsies. Immunohistochemistry (IHC) is routinely used in the differential diagnosis; however, presently available markers lack specificity.

Toward Stimuli-Responsive Dynamic Thermosets through Continuous Development and Improvements in Covalent Adaptable Networks (CANs).

Covalent adaptable networks (CANs), unlike typical thermosets or other covalently crosslinked networks, possess a unique, often dormant ability to activate one or more forms of stimuli-responsive, dynamic covalent chemistries as a means to transition their behavior from that of a viscoelastic solid to a material with fluid-like plastic flow. Upon application of a stimulus, such as light or other irradiation, temperature, or even a distinct chemical signal, the CAN responds by transforming to a state of temporal plasticity through activation of either reversible addition or reversible bond exchange, either of which allows the material to essentially re-equilibrate to an altered set of conditions that are distinct from those in which the original covalently crosslinked network is formed, often simultaneously enabling a new and distinct shape, function, and characteristics. As such, CANs span the divide between thermosets and thermoplastics, thus offering unprecedented possibilities for innovation in polymer and materials science.

Combining Fixed-Time Insemination and Improved Catheter Design in an Effort to Improve Swine Reproduction Efficiency.

Conventional practice is to breed sows by artificial insemination (AI) at least twice using approximately three billion sperm per insemination upon estrus at standing heat. This research explored the use of combined technologies, including fixed-time insemination (FTAI) and an alternative catheter design that reportedly reduces semen backflow, in order to reduce the number of inseminations and the semen dosage and maintain reproductive efficiency. The FTAI technique used in this study was to inject I.

Enabling Applications of Covalent Adaptable Networks.

The ability to behave in a fluidlike manner fundamentally separates thermoset and thermoplastic polymers. Bridging this divide, covalent adaptable networks (CANs) structurally resemble thermosets with permanent covalent crosslinks but are able to flow in a manner that resembles thermoplastic behavior only when a dynamic chemical reaction is active. As a consequence, the rheological behavior of CANs becomes intrinsically tied to the dynamic reaction kinetics and the stimuli that are used to trigger those, including temperature, light, and chemical stimuli, providing unprecedented control over viscoelastic properties.

Inositol monophosphatase 1 as a novel interacting partner of RAGE in pulmonary hypertension.

Pulmonary arterial hypertension (PAH) is a lethal disease characterized by progressive pulmonary vascular remodeling. The receptor for advanced glycation end products (RAGE) plays an important role in PAH by promoting proliferation of pulmonary vascular cells. RAGE is also known to mediate activation of Akt signaling, although the particular molecular mechanism remains unknown.

A non-canonical SWI/SNF complex is a synthetic lethal target in cancers driven by BAF complex perturbation.

Mammalian SWI/SNF chromatin remodelling complexes exist in three distinct, final-form assemblies: canonical BAF (cBAF), PBAF and a newly characterized non-canonical complex (ncBAF). However, their complex-specific targeting on chromatin, functions and roles in disease remain largely undefined. Here, we comprehensively mapped complex assemblies on chromatin and found that ncBAF complexes uniquely localize to CTCF sites and promoters.

Dynamic and Responsive DNA-like Polymers.

The synthesis of thiolactone monomers that mimic natural nucleosides and engage in robust ring opening polymerizations (ROP) is herein described. As each repeat unit contains a thioester functional group, dynamic rearrangement of the polymer is feasible via thiol-thioester exchange, demonstrated here by depolymerization of the polymers and coalescing of two polymers of different molecular weight or chemical composition. This approach constitutes the first step toward a platform that enables for the routine synthesis of sequence controlled polymers via dynamic template directed synthesis.

A readily programmable, fully reversible shape-switching material.

Liquid crystalline (LC) elastomers (LCEs) enable large-scale reversible shape changes in polymeric materials; however, they require intensive, irreversible programming approaches in order to facilitate controllable actuation. We have implemented photoinduced dynamic covalent chemistry (DCC) that chemically anneals the LCE toward an applied equilibrium only when and where the light-activated DCC is on. By using light as the stimulus that enables programming, the dynamic bond exchange is orthogonal to LC phase behavior, enabling the LCE to be annealed in any LC phase or in the isotropic phase with various manifestations of this capability explored here.

Publisher Correction: Bistable and photoswitchable states of matter.

The original version of this Article contained errors in Fig. 3. In Fig.