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Abstract Background Selenoproteins contain selenocysteine (Sec), commonly considered the 21st genetically encoded amino acid. Many selenoproteins, such as the glutathione peroxidases and thioredoxin reductases, protect cells against oxidative stress by functioning as antioxidants and/or through their roles in the maintenance of intracellular redox balance. Since oxidative stress has been implicated in the pathogenesis of diabetic nephropathy, we hypothesized that selenoproteins protect against this complication of diabetes. Methods C57BL/6 mice that have a podocyte-specific inability to incorporate Sec into proteins (denoted in this paper as PodoTrsp-/-) and control mice were made diabetic by intraperitoneal injection of streptozotocin, or were injected with vehicle. Blood glucose, body weight, microalbuminuria, glomerular mesangial matrix expansion, and immunohistochemical markers of oxidative stress were assessed. Results After 3 and 6 months of diabetes, control and PodoTrsp-/- mice had similar levels of blood glucose. There were no differences in urinary albumin/creatinine ratios. Periodic acid-Schiff staining to examine mesangial matrix expansion also demonstrated no difference between control and PodoTrsp-/- mice after 6 months of diabetes, and there were no differences in immunohistochemical stainings for nitrotyrosine or NAD(P)H dehydrogenase, quinone 1. Conclusion Loss of podocyte selenoproteins in streptozotocin diabetic C57BL/6 mice does not lead to increased oxidative stress as assessed by nitrotyrosine and NAD(P)H dehydrogenase, quinone 1 immunostaining, nor does it lead to worsening nephropathy.

Natural biopolymers have a rich history, with many uses across the fields of healthcare and medicine, including formulations for wound dressings, surgical implants, tissue culture substrates, and drug delivery vehicles. Yet, synthetic-based materials have been more successful in translation due to precise control and regulation achievable during manufacturing. However, there is a renewed interest in natural biopolymers, which offer a diverse landscape of architecture, sustainable sourcing, functional groups, and properties that synthetic counterparts cannot fully replicate as processing and sourcing of these materials has improved. Proteins and polysaccharides derived from various sources (crustaceans, plants, insects, etc.) are highlighted in this review. We discuss the common types of polysaccharide and protein biopolymers used in healthcare and medicine, highlighting methods and strategies to alter structures and intra- and interchain interactions to engineer specific functions, products, or materials. We focus on biopolymers obtained from natural, nonmammalian sources, including silk fibroins, alginates, chitosans, chitins, mucins, keratins, and resilins, while discussing strategies to improve upon their innate properties and sourcing standardization to expand their clinical uses and relevance. Emphasis will be placed on methods that preserve the structural integrity and native biological functions of the biopolymers and their makers. We will conclude by discussing the untapped potential of new technologies to manipulate native biopolymers while controlling their secondary and tertiary structures, offering a perspective on advancing biopolymer utility in novel applications within biomedical engineering, advanced manufacturing, and tissue engineering.

Phage therapeutics offer a potentially powerful approach for combating multidrug-resistant bacterial infections. However, to be effective, phage therapy must overcome existing and developing phage resistance. While phage cocktails can reduce this risk by targeting multiple receptors in a single therapeutic, bacteria have mechanisms of resistance beyond receptor modification. A rapidly growing body of knowledge describes a broad and varied arsenal of antiphage systems encoded by bacteria to counter phage infection. We sought to understand the types and frequencies of antiphage systems present in a highly diverse panel of Pseudomonas aeruginosa clinical isolates utilized to characterize novel antibacterials. Using the web-server tool PADLOC (prokaryotic antiviral defense locator), putative antiphage systems were identified in these P. aeruginosa clinical isolates based on sequence homology to a validated and curated catalog of known defense systems. Coupling this host bacterium sequence analysis with host range data for 70 phages, we observed a correlation between existing phage resistance and the presence of higher numbers of antiphage systems in bacterial genomes. We were also able to identify antiphage systems that were more prevalent in highly phage-resistant P. aeruginosa strains, suggesting their importance in conferring resistance.

We describe the genome of a lytic phage EKq1 isolated on Klebsiella quasipneumoniae , with activity against Klebsiella pneumoniae . EKq1 is an unclassified representative of the class Caudoviricetes, similar to Klebsiella phages VLCpiS8c, phiKp_7-2, and vB_KleS-HSE3. The 48,244-bp genome has a GC content of 56.43% and 63 predicted protein-coding genes., Competing Interests: The authors declare no conflict of interest.

Background: The feasibility of oral dark contrast media is under exploration in abdominal computed tomography (CT) applications. One of the experimental contrast media in this class is dark borosilicate contrast media (DBCM), which has a CT attenuation lower than that of intra-abdominal fat., Purpose: To evaluate the performances of DBCM using single- and multi-energy CT imaging on a clinical photon-counting-detector CT (PCD-CT)., Methods: Five vials, three with iodinated contrast agent (5, 10, and 20 mg/mL; Omnipaque 350) and two with DBCM (6% and 12%; Nextrast, Inc.), and one solid-water rod (neutral contrast agent) were inserted into two multi-energy CT phantoms, and scanned on a clinical PCD-CT system (NAEOTOM Alpha) at 90, 120, 140, Sn100, and Sn140 kV (Sn: tin filter) in multi-energy mode. CARE keV IQ level was 180 (CTDIvol: 3.0 and 12.0 mGy for the small and large phantoms, respectively). Low-energy threshold images were reconstructed with a quantitative kernel (Qr40, iterative reconstruction strength 2) and slice thickness/increment of 2.0/2.0 mm. Virtual monoenergetic images (VMIs) were reconstructed from 40 to 140 keV at 10 keV increments. On all images, average CT numbers for each vial/rod were measured using circular region-of-interests and averaged over eight slices. The contrast-to-noise ratio (CNR) of iodine (5 mg/mL) against DBCM was calculated and plotted against tube potential and VMI energy level, and compared to the CNR of iodine against water. Similar analyses were performed on iodine maps and VNC images derived from the multi-energy scan at 120 kV., Results: With increasing kV or VMI keV, the negative HU of DBCM decreased only slightly, whereas the positive HU of iodine decreased across all contrast concentrations and phantom sizes. CT numbers for DBCM decreased from -178.5 ± 9.6 to -194.4 ± 6.3 HU (small phantom) and from -181.7 ± 15.7 to -192.1 ± 11.9 HU (large phantom) for DBCM-12% from 90 to Sn140 kV; on VMIs, the CT numbers for DBCM decreased minimally from -147.1 ± 15.7 to -185.1 ± 9.2 HU (small phantom) and -158.8 ± 28.6 to -188.9 ± 14.7 HU (large phantom) from 40 to 70 keV, but remained stable from 80 to 140 keV. The highest iodine CNR against DBCM in low-energy threshold images was seen at 90 or Sn140 kV for the small phantom, whereas all CNR values from low-energy threshold images for the large phantom were comparable. The CNR values of iodine against DBCM computed on VMIs were highest at 40 or 70 keV depending on iodine and DBCM concentrations. The CNR values of iodine against DBCM were consistently higher than iodine to water (up to 460% higher dependent on energy level). Further, the CNR of iodine compared to DBCM is less affected by VMI energy level than the identical comparison between iodine and water: CNR values at 140 keV were reduced by 46.6% (small phantom) or 42.6% (large phantom) compared to 40 keV; CNR values for iodine compared to water were reduced by 86.3% and 83.8% for similar phantom sizes, respectively. Compared to 70 keV VMI, the iodine CNR against DBCM was 13%-79% lower on iodine maps and VNC., Conclusions: When evaluated at different tube potentials and VMI energy levels using a clinical PCD-CT system, DBCM showed consistently higher CNR compared to iodine versus water (a neutral contrast)., (© 2023 American Association of Physicists in Medicine.)

We describe the genome of a lytic phage, ESa2, isolated from environmental water and specific for Staphylococcus aureus. ESa2 belongs to the family Herelleviridae and genus Kayvirus . Its genome consists of 141,828 bp, with 30.25% GC content, 253 predicted protein-coding sequences, 3 tRNAs, and 10,130-bp-long terminal repeats., Competing Interests: The authors declare no conflict of interest.

Objective: To evaluate the diagnostic quality of photon-counting detector (PCD) computed tomography (CT) in patients undergoing lung cancer screening compared with conventional energy-integrating detector (EID) CT in a prospective multireader study., Materials: Patients undergoing lung cancer screening with conventional EID-CT were prospectively enrolled and scanned on a PCD-CT system using similar automatic exposure control settings and reconstruction kernels. Three thoracic radiologists blinded to CT system compared PCD-CT and EID-CT images and scored examinations using a 5-point Likert comparison score (-2 [left image is worse] to +2 [left image is better]) for artifacts, sharpness, image noise, diagnostic image quality, emphysema visualization, and lung nodule evaluation focusing on the border. Post hoc correction of Likert scores was performed such that they reflected PCD-CT performance in comparison to EID-CT. A nonreader radiologist measured objective image noise., Results: Thirty-three patients (mean, 66.9 ± 5.6 years; 11 female; body mass index; 30.1 ± 5.1 kg/m 2 ) were enrolled. Mean volume CT dose index for PCD-CT was lower (0.61 ± 0.21 vs 0.73 ± 0.22; P < 0.001). Pooled reader results showed significant differences between imaging modalities for all comparative rankings ( P < 0.001), with PCD-CT favored for sharpness, image noise, image quality, and emphysema visualization and lung nodule border, but not artifacts. Photon-counting detector CT had significantly lower image noise (74.4 ± 10.5 HU vs 80.1 ± 8.6 HU; P = 0.048)., Conclusions: Photon-counting detector CT with similar acquisition and reconstruction settings demonstrated improved image quality and less noise despite lower radiation dose, with improved ability to depict pulmonary emphysema and lung nodule borders compared with EID-CT at low-dose lung cancer CT screening., Competing Interests: Disclosure of Conflicts of Interest: C.H.Mc.C. received a research grant to institution, Siemens Healthcare GmbH. J.G.F. received a research grant to institution, Siemens Healthcare GmbH. The remaining authors none were declared., (Copyright © 2022 Wolters Kluwer Health, Inc. All rights reserved.)

The addition of poly(ethylene glycol) (PEG) to biomolecules and biomaterials is a well-established approach to modify their properties for therapeutic applications. For biomaterials, the approach is typically to blend or electrospray the synthetic polymer with the biomaterial. Effective surface modification approaches such as surface-initiated polymer brushes are challenging since the harsh solvents required for brush synthesis may destroy the biomaterial. Herein, we describe the PEGylation of collagen fibers by surface-initiated PEG brushes using a living anionic grafting-from mechanism. This brush synthesis is done in the absence of solvents to minimize the degradation of the native collagen structure. We quantify the effect the brush synthesis has on the native structure of the collagen fiber using differential scanning calorimetry (DSC) and find that even at long reaction times a significant fraction of the native structure remains. Dynamic mechanical analysis indicates the collagen undergoes only modest structural degradation, while adhesion studies find a significant improvement of antifouling properties. Further, our approach opens the way for further chemistry, as the growing polymer chain is a potassium alkoxy group that can be functionalized by termination or by subsequent reaction by a wide variety of molecules.

Introduction: Despite the prevalence of hypospadias surgery and the common use of postoperative urethral stents, there has been no evaluation of the material properties of common stents. Our study sets out to close this gap with a literature review of recent publications comparing outcomes after hypospadias surgery for different urethral stent types and an evaluation of the material properties of four common urethral stents., Study Design: A review of the English language literature from 2011 to 2021 was performed. Thermal analysis and mechanical analysis of the Zaontz Urethral Stent, the Firlit-Kluge Urethral Stent, the Koyle Diaper Stent, and the Bard Premature Infant Feeding Tube was also undertaken., Results: Out of 165 papers, four met inclusion criteria. There was limited research on this topic, and no significant evidence that different stent materials impacted surgical complication rates. One study found improved comfort with the Zaontz stent, and another found a reduction emergency room visits with the Koyle stent. Using a foley balloon was associated with increased fistula rates, though this was likely due to the balloon design and not the material. Analysis of stents shows that all four are rubbery polymers at body temperature (Summary Table). The Zaontz and Koyle stents are thermoplastic elastomers with strong melting transitions above body temperature, but the Firlit-Kluge stent is amorphous at 37 °C and is likely covalently cross-linked to generate the network. The Bard feeding tube was the stiffest, with a Young's Modulus of 14.0 ± 0.78 (compared to 4.12 ± 0.56 for Zaontz, 4.92 ± 0.63 for Firlit-Kluge, and 4.09 ± 0.49 for Koyle). The Bard Feeding Tube is also the least extensible, fracturing at just over 300% strain compared to the other stents that can be stretched to greater than 2000% strain before fracture. Cyclic deformation studies demonstrate that the Zaontz, Firlit-Kluge, and Koyle stents are able to stretch and recover their shape more completely, a finding determined by the lower amount of plastic deformation those stents display compared to the Bard Feeding Tube., Discussion: While there is little information associating urethral stent type with outcomes after hypospadias surgery, material properties may account for findings of prior studies. Stiffer stents may contribute to decreased postoperative comfort, while a stent that is too soft and extensible may have issues with dislodgement, kinking and breaking., Conclusion: This study provides the foundation for future work optimizing urethral stents, designing support for regenerative medicine applications, and improving hypospadias outcomes., Competing Interests: Conflicts of interest All authors confirm that they have no financial or personal relationships with other people or organizations that could inappropriately influence (bias) their work., (Copyright © 2022 Journal of Pediatric Urology Company. Published by Elsevier Ltd. All rights reserved.)

Formation of membrane-less organelles by self-assembly of disordered proteins can be triggered by external stimuli such as pH, salt, or temperature. These organelles, called biomolecular condensates, have traditionally been classified as liquids, gels, or solids with limited subclasses. Here, the authors show that a thermal trigger can lead to formation of at least two distinct liquid condensed phases of the fused in sarcoma low complexity (FUS LC) domain. Forming FUS LC condensates directly at low temperature leads to formation of metastable, kinetically trapped condensates that show arrested coalescence, escape from which to untrapped condensates can be achieved via thermal annealing. Using experimental and computational approaches, the authors find that molecular structure of interfacial FUS LC in kinetically trapped condensates is distinct (more β-sheet like) compared to untrapped FUS LC condensates. Moreover, molecular motion within kinetically trapped condensates is substantially slower compared to that in untrapped condensates thereby demonstrating two unique liquid FUS condensates. Controlling condensate thermodynamic state, stability, and structure with a simple thermal switch may contribute to pathological protein aggregate stability and provides a facile method to trigger condensate mixing for biotechnology applications., (© 2021 The Authors. Advanced Science published by Wiley-VCH GmbH.)

Alkylation of DNA and RNA is a potentially toxic lesion that can result in mutations and even cell death. In response to alkylation damage, K63-linked polyubiquitin chains are assembled that localize the Alpha-ketoglutarate-dependent dioxygenase alkB homolog 3-Activating Signal Cointegrator 1 Complex Subunit (ASCC) repair complex to damage sites in the nucleus. The protein ASCC2, a subunit of the ASCC complex, selectively binds K63-linked polyubiquitin chains via its coupling of ubiquitin conjugation to ER degradation (CUE) domain. The basis for polyubiquitin-binding specificity was unclear, because CUE domains in other proteins typically bind a single ubiquitin and do not discriminate among different polyubiquitin linkage types. We report here that the ASCC2 CUE domain selectively binds K63-linked diubiquitin by contacting both the distal and proximal ubiquitin. The ASCC2 CUE domain binds the distal ubiquitin in a manner similar to that reported for other CUE domains bound to a single ubiquitin, whereas the contacts with the proximal ubiquitin are unique to ASCC2. Residues in the N-terminal portion of the ASCC2 α1 helix contribute to the binding interaction with the proximal ubiquitin of K63-linked diubiquitin. Mutation of residues within the N-terminal portion of the ASCC2 α1 helix decreases ASCC2 recruitment in response to DNA alkylation, supporting the functional significance of these interactions during the alkylation damage response. Our study reveals the versatility of CUE domains in ubiquitin recognition., Competing Interests: Conflict of interest The authors declare that they have no conflicts of interest with the contents of this article., (Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.)

Ubiquitylation is a posttranslational modification that utilizes protein-protein binding interactions to regulate cellular processes. In ubiquitin signaling, a vast array of mono- and polyubiquitin modifications to substrate proteins are recognized by a diverse group of ubiquitin-binding proteins. Identifying ubiquitin-binding proteins and characterizing their binding properties is necessary for understanding the structural basis of ubiquitin signaling. This chapter provides a means of studying ubiquitin-binding interactions in vitro by describing how to generate monoubiquitin and K63-linked polyubiquitin chains and perform pull-down assays with ubiquitin-binding proteins, which is of particular relevance for DNA damage and other signaling pathways., (© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

In a phase 1b study of acalabrutinib (a covalent Bruton tyrosine kinase (BTK) inhibitor) in combination with vistusertib (a dual mTORC1/2 inhibitor) in patients with relapsed/refractory diffuse large B-cell lymphoma (DLBCL), multiple ascending doses of the combination as intermittent or continuous schedules of vistusertib were evaluated. The overall response rate was 12% (3/25). The pharmacodynamic (PD) profile for acalabrutinib showed that BTK occupancy in all patients was >95%. In contrast, PD analysis for vistusertib showed variable inhibition of phosphorylated 4EBP1 (p4EBP1) without modulation of AKT phosphorylation (pAKT). The pharmacokinetic (PK)/PD relationship of vistusertib was direct for TORC1 inhibition (p4EBP1) but did not correlate with TORC2 inhibition (pAKT). Cell-of-origin subtyping or next-generation sequencing did not identify a subset of DLBCL patients with clinical benefit; however, circulating tumor DNA dynamics correlated with radiographic response. These data suggest that vistusertib does not modulate targets sufficiently to add to the clinical activity of acalabrutinib monotherapy. Clinicaltrials.gov identifier: NCT03205046.

Bombyx mori silk fibroin is a fibrous protein whose tunable properties and biocompatibility have resulted in its utility in a wide-variety of applications, including as drug delivery vehicles, wound dressings, and tissue engineering scaffolds. Control of protein and cell attachment is vital to the performance of biomaterials, but silk fibroin is mostly hydrophobic and interacts nonspecifically with cells and proteins. Silk functionalised with hydrophilic polymers reduces attachment, but the low number of reactive sites makes achieving a uniform conjugation a persistent challenge. This work presents a new approach to grow brush-like polymers from the surface of degradable silk films, where the films were enriched with hydroxyl groups, functionalised with an initiator, and finally reacted with acrylate monomers using atom transfer radical polymerisation. Two different routes to hydroxyl enrichment were investigated, one involving reaction with ethylene oxide (EO) and the other using a two-step photo-catalysed oxidation reaction. Both routes increased surface hydrophilicity, and hydrophilic monomers containing either uncharged (poly(ethylene glycol), PEG) pendant groups or zwitterionic pendant groups were polymerised from the surfaces. The initial processing of the films to induce beta sheet structures was found to impact the success of the polymerizations. Compared to the EO modified or unmodified silk surfaces, the oxidation reaction resulted in more polymer conjugation and the surfaces appear more uniform. Mesenchymal stem cell and protein attachment were the lowest on polymers grown from oxidised surfaces. PEG-containing brush-like polymers displayed lower protein attachment than surfaces conjugated with PEG using a previously reported "grafting to" method, but polymers containing zwitterionic side chains displayed both the lowest contact angles and the lowest cell and protein attachment. This finding may arise from the interactions of the zwitterionic pendant groups through their permanent dipoles and is an important finding because PEG is susceptible to oxidative damage that can reduce efficacy over time. These modified silk materials with lower cell and protein attachments are envisioned to find utility when enhanced diffusion around surfaces is required, such as in drug delivery implants.

A reactive silk fibroin ink formulation designed for extrusion three-dimensional (3D) printing of protein-based hydrogels at room temperature is reported. This work is motivated by the need to produce protein hydrogels that can be printed into complex shapes with long-term stability using extrusion 3D printing at ambient temperature without the need for the addition of nanocomposites, synthetic polymers, or sacrifical templates. Silk fibroin from the Bombyx mori silkworm was purified and synthesized into reactive inks by enzyme-catalyzed dityrosine bond formation. Rheological and printing studies showed that tailoring the peroxide concentration in the reactive ink enables the silk to be extruded as a filament and printed into hydrogel constructs, supporting successive printed layers without flow of the construct or loss of desired geometry. To enable success of longer-term in vitro studies, 3D printed silk hydrogels were found to display excellent shape retention over time, as evidenced by no change in construct dimensions or topography when maintained for nine weeks in culture medium. Caco-2 (an intestinal epithelial cell line) attachment, proliferation, and tight junction formation on the printed constructs was not found to be affected by the geometry of the constructs tested. Intestinal myofibroblasts encapsulated within reactive silk inks were found to survive shearing during printing and proliferate within the hydrogel constructs. The work here thus provides a suitable route for extrusion 3D printing of protein hydrogel constructs that maintain their shape during printing and culture, and is expected to enable longer-term cellular studies of hydrogel constructs that require complex geometries and/or varying spatial distributions of cells on demand via digital printing.

Preclinical models of breast cancer have established mechanistic links between psychological stress and cancer progression. However, epidemiological evidence linking stress and cancer is equivocal. We tested the impact of stress exposure in female mice expressing the mouse mammary tumor virus polyoma middle-T antigen (MMTV-PyMT), a spontaneous model of mammary adenocarcinoma that mimics metastatic hormone receptor-positive human breast cancer development. MMTV-PyMT mice were socially isolated at 6 to 7 weeks of age during premalignant hyperplasia. To increase the potency of the stressor, singly housed mice were exposed to acute restraint stress (2 hours per day for 3 consecutive days) at 8 to 9 weeks of age during early carcinoma. Exposure to this dual stressor activated both major stress pathways, the sympathetic nervous system and hypothalamic-pituitary-adrenal axis throughout malignant transformation. Stressor exposure reduced mammary tumor burden in association with increased tumor cleaved caspase-3 expression, indicative of increased cell apoptosis. Stress exposure transiently increased tumor vascular endothelial growth factor and reduced tumor interleukin-6, but no other significant alterations in immune/inflammation-associated chemokines and cytokines or changes in myeloid cell populations were detected in tumors. No stress-induced change in second-harmonic generation-emitting collagen, indicative of a switch to a metastasis-promoting tumor extracellular matrix, was detected. Systemic indicators of slowed tumor progression included reduced myeloid-derived suppressor cell (MDSC) frequency in lung and spleen, and decreased transforming growth factor β (TGF-β) content in circulating exosomes, nanometer-sized particles associated with tumor progression. Chronic β-adrenergic receptor (β-AR) blockade with nadolol abrogated stress-induced alterations in tumor burden and cleaved caspase-3 expression, lung MDSC frequency, and exosomal TGF-β content. Despite the evidence for reduced tumor growth, metastatic lesions in the lung were not altered by stress exposure. Unexpectedly, β-blockade in nonstressed mice increased lung metastatic lesions and splenic MDSC frequency, suggesting that in MMTV-PyMT mice, β-AR activation also inhibits tumor progression in the absence of stress exposure. Together, these results suggest stress exposure can act through β-AR signaling to slow primary tumor growth in MMTV-PyMT mice., Competing Interests: Declaration of conflicting interests:The author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article., (© The Author(s) 2020.)

Hydrogels are frequently utilized as three-dimensional matrices for the culture and regeneration of soft tissues, but one challenge with the existing hydrogels is that, though the natural extracellular matrix of tissues may be ordered, there are few biocompatible ways to incorporate anisotropy within hydrogels. Liquid crystalline (LC) polymers are well suited for this because of their combination of molecular ordering and polymer elasticity; however, the hydrophobic nature of LC monomers has hindered their polymerization into hydrogels under cytocompatible conditions. This work reports on the generation of main-chain LC hydrogels in aqueous media and the ability of LC phases to affect mesenchymal stem cell behavior. The synthesis results in high gel fraction materials, and calorimetry, thermomechanical analysis, and X-ray scattering show that the networks organize into LC phases in the dry and hydrogel states. Human mesenchymal stem cells (hMSCs) cultured within the hydrogels show excellent viability, and hMSC proliferation proceeds at a faster rate in LC hydrogels compared to non-LC hydrogels. TThe result is a new synthetic approach for calamitic liquid crystalline hydrogels, which support the encapsulation and culture of human stem cells and are expected to enable applications as anisotropic and responsive substrates for tissue engineering and regenerative medicine.

Silk fibroin is a semicrystalline protein used as a renewable polymer source and as a biomaterial platform, but existing methods to synthetically modify fibroin suffer from low efficiencies that can limit the protein's utility. This work reports on a mild synthesis that results in a 2-fold increase in carboxylation through the disruption of noncovalent interactions during the reaction. Importantly, silk fibroin maintains its ability to form β-sheets that are critical for tailoring mechanical and degradation properties, as well as for rendering solid constructs (e.g., films and scaffolds) insoluble in water. Increasing carboxyl functionalization affords control over protein charge, which permits tailoring the loading and release of small molecules using electrostatic interactions. Disruption of noncovalent interactions during aqueous carbodiimide coupling also significantly enhances conjugation efficiency of molecules containing primary amine groups, thus enabling high degrees of functionalization with biological molecules, such as proteins and peptides, for biomaterial applications.

Alterations in fibroblast growth factor receptor (FGFR) genes have been identified as potential driver oncogenes. Pharmacological targeting of FGFRs may therefore provide therapeutic benefit to selected cancer patients, and proof-of-concept has been established in early clinical trials of FGFR inhibitors. Here, we present the molecular structure and preclinical characterization of INCB054828 (pemigatinib), a novel, selective inhibitor of FGFR 1, 2, and 3, currently in phase 2 clinical trials. INCB054828 pharmacokinetics and pharmacodynamics were investigated using cell lines and tumor models, and the antitumor effect of oral INCB054828 was investigated using xenograft tumor models with genetic alterations in FGFR1, 2, or 3. Enzymatic assays with recombinant human FGFR kinases showed potent inhibition of FGFR1, 2, and 3 by INCB054828 (half maximal inhibitory concentration [IC50] 0.4, 0.5, and 1.0 nM, respectively) with weaker activity against FGFR4 (IC50 30 nM). INCB054828 selectively inhibited growth of tumor cell lines with activation of FGFR signaling compared with cell lines lacking FGFR aberrations. The preclinical pharmacokinetic profile suggests target inhibition is achievable by INCB054828 in vivo with low oral doses. INCB054828 suppressed the growth of xenografted tumor models with FGFR1, 2, or 3 alterations as monotherapy, and the combination of INCB054828 with cisplatin provided significant benefit over either single agent, with an acceptable tolerability. The preclinical data presented for INCB054828, together with preliminary clinical observations, support continued investigation in patients with FGFR alterations, such as fusions and activating mutations., Competing Interests: Holly Koblish, Liangxing Wu, Kevin Bowman, Sharon Diamond, Darlise DiMatteo, Yue Zhang, Michael Hansbury, Mark Rupar, Xiaoming Wen, Paul Collier, Patricia Feldman, Ronald Klabe, Krista A. Burke, Maxim Soloviev, Christine Gardiner, Xin He, Alla Volgina, Maryanne Covington, Richard Wynn, Timothy C. Burn, Swamy Yeleswaram, Wenqing Yao are employees of Incyte Corporationand own Incyte stock. Phillip C. C. Liu, Bruce Ruggeri, Peggy Scherle, Reid Huber, and Gregory Hollis were employees of Incyte employees Corporation at the time of this work and own Incyte stock.Our commercial affiliation does not alter our adherence to PLOS ONE policies on sharing data and materials.

Background: Advanced prostate cancer etiology is poorly understood. Few studies have examined associations of anthropometric factors (e.g. early adulthood obesity) with advanced prostate cancer risk., Patients and Methods: We carried out pooled analyses to examine associations between body fatness, height, and prostate cancer risk. Among 830 772 men, 51 734 incident prostate cancer cases were identified, including 4762 advanced (T4/N1/M1 or prostate cancer deaths) cases, 2915 advanced restricted (same as advanced, but excluding localized cancers that resulted in death) cases, 9489 high-grade cases, and 3027 prostate cancer deaths. Cox proportional hazards models were used to calculate study-specific hazard ratios (HR) and 95% confidence intervals (CI); results were pooled using random effects models., Results: No statistically significant associations were observed for body mass index (BMI) in early adulthood for advanced, advanced restricted, and high-grade prostate cancer, and prostate cancer mortality. Positive associations were shown for BMI at baseline with advanced prostate cancer (HR = 1.30, 95% CI = 0.95-1.78) and prostate cancer mortality (HR = 1.52, 95% CI = 1.12-2.07) comparing BMI ≥35.0 kg/m 2 with 21-22.9 kg/m 2 . When considering early adulthood and baseline BMI together, a 27% higher prostate cancer mortality risk (95% CI = 9% to 49%) was observed for men with BMI <25.0 kg/m 2 in early adulthood and BMI ≥30.0 kg/m 2 at baseline compared with BMI <25.0 kg/m 2 in early adulthood and BMI <30.0 kg/m 2 at baseline. Baseline waist circumference, comparing ≥110 cm with <90 cm, and waist-to-hip ratio, comparing ≥1.00 with <0.90, were associated with significant 14%-16% increases in high-grade prostate cancer risk and suggestive or significant 20%-39% increases in prostate cancer mortality risk. Height was associated with suggestive or significant 33%-56% risks of advanced or advanced restricted prostate cancer and prostate cancer mortality, comparing ≥1.90 m with <1.65 m., Conclusion: Our findings suggest that height and total and central adiposity in mid-to-later adulthood, but not early adulthood adiposity, are associated with risk of advanced forms of prostate cancer. Thus, maintenance of healthy weight may help prevent advanced prostate cancer., (Copyright © 2019 European Society for Medical Oncology. All rights reserved.)

Compared to conventional wound closure methods like sutures and staples, polymer-based tissue adhesives afford some distinct advantages, such as greater ease of deployment in spatially constrained surgical sites. One way to achieve aqueous adhesion is by introducing catechol functional groups that form coordinate and covalent bonds with a variety of substrates. This approach, inspired by marine organisms, has been applied to biopolymers and synthetic polymers, but one key challenge is that compositions that are soluble in water are often susceptible to high swelling ratios that can result in undesired compression of neighboring tissues. This work sought to synthesize aqueous adhesive gels that are capable of two modes of association: (1) adhesion and covalent cross-linking reactions arising from catechol oxidation and (2) noncovalent cross-linking arising from self-assembly of polymer backbones within the gelled adhesive. The network's self-assembly after gelation was envisioned to afford control over swelling and reinforce its strength. Bombyx mori silk fibroin was selected as the backbone of the adhesive network because it can be processed into an aqueous solution yet later be rendered insoluble in water through the assembly of its hydrophobic protein core. Distinct from a previous approach to functionalize silk directly with catechol groups, this work investigated in situ generation of catechol on silk fibroin by enzymatically modifying phenolic side chains, where it was found that this enzymatic approach led to conjugates with higher degrees of catechol functionalization and aqueous solubility. Silk fibroin was functionalized with tyramine to enrich the protein's phenolic side chains, which were subsequently oxidized into catechol groups using mushroom tyrosinase (MT). The gelation of the silk conjugates with MT was monitored by rheology, and the gels exhibited low water uptake. Phenolic enrichment increased the rate of chemical cross-linking leading to gelation but did not interrupt assembly of silk's secondary structures. Adhesion of the tyramine-silk conjugates to porcine intestine was found to be superior to fibrin sealant, and induction of β sheet secondary structures was found to further enhance adhesive strength through a second mode of cross-linking. Neither the chemical functionalization nor phenol oxidation affected the ability of intestinal epithelial cells (Caco-2) to attach and proliferate. Phenolic functionalization and oxidative cross-linking of silk fibroin was found to afford a new route to water-soluble, catechol-functionalized polymers, which were found to display excellent adhesion to mucosal tissue and whose secondary structure provides an additional mode to control strength and swelling of adhesive gels.

Liquid crystalline polymer networks (LCNs) couple polymer chain organization to molecular ordering, the switching of which has been shown to impart stimuli-responsive properties, including actuation and one-way shape memory, to the networks. While LCNs have long been proposed as artificial muscles, recent reports have also suggested potential as dynamic biomaterial substrates. In contrast to many existing LCNs synthesized using hydrophobic spacers, this work investigates networks synthesized using more hydrophilic spacers to promote interaction with water. A challenge with such materials is liquid crystalline phases could be disrupted in hydrated networks. This work thus investigates the impact of polyether spacers and mesogen composition on the phase behavior of LCNs. Main-chain LCNs were synthesized using alkyne-azide cycloaddition ("click" chemistry), where two different mesogens (5yH and 5yMe) and a non-LC monomer (5yTe) were coupled with one of two different polyether spacers, poly(ethylene glycol) and poly(propylene glycol), and a crosslinker. The chemistry led to high gel fraction materials, the workup of which resulted in networks that displayed no difference in cellular toxicity due to leachable components compared to tissue culture plastic control. Calorimetric analysis, dynamic mechanical analysis, and X-ray scattering revealed the LC microstructure and temperature-responsive properties of the networks. The use of low molecular weight polyether spacers was found to prevent their crystallization within the LC network, and adjusting mesogen composition to enhance its LC phase stability allowed the use of spacers with larger molecular weights and pendant groups. Hydrated networks were found to rearrange their structure compared to dry networks, while maintaining their LC phases. Like other crosslinked LC materials, the networks display shape changes (actuation) that are tied to changes in LC ordering. The result is a new synthetic approach for polydomain networks that form stable LC phases that are tailorable using polyether spacers and may enable future application as hydrated, stimuli-responsive materials.

We reviewed 62 new cases and 18 published reports of Dracunculus infections in domestic dogs and cats to describe the epidemiology of this parasite in dogs and cats in North America. We collected host and parasite data when available, including age, sex, and breed of dog, nematode location in the host, and any clinical signs at presentation and/or description of the apparent lesion. For dogs, infections were noted in six of the AKC breed groups, but none was reported from the toy group or the miscellaneous breed class. Age of infected dogs ranged from 7 months to 19 years (median 4 years; average 5.3 years), and infection rates were similar in male and female dogs. Most nematodes were associated with the distal extremities, but worms were also found in the chest/thorax, abdomen, head, and flank. Although most infected dogs had a single worm, three dogs had two or more worms that were collected from multiple lesions. Three new cat cases, with similar lesions, presentations and seasonality, were detected in Alabama, North Carolina and Texas. Cases were reported from a wide geographic range throughout eastern North America, during every month of the year, but 72% of infections were diagnosed in the late winter to early spring (December to May). All collected worms were larvigerous females which cannot be identified to species based on morphologic characters. Thus, we attempted to amplify and sequence a portion of the cytochrome c oxidase subunit I (COI) gene for specific identification. Although 13 worms from 12 cases were available, sequences were obtained for only eight worms from seven cases. These eight worms were D. insignis, a common parasite of raccoons (Procyon lotor) and other primarily carnivorous mammals. Female worms are the most likely to be detected in dogs and cats because male worms do not emerge, parasites should be preserved in ethanol for molecular identification. Although this study used convenience sampling of available data, we found that the parasite is widespread throughout the eastern US and Canada and that Dracunculus infections in dogs are more common than is revealed in published literature. However, more research is needed to understand the epidemiology, including transmission route(s), prevalence, and distribution of this parasite., (Copyright © 2018 Elsevier B.V. All rights reserved.)

Although the repertoire of somatic genetic alterations of primary breast cancers has been extensively catalogued, the genetic differences between primary and metastatic tumors have been less studied. In this study, we compared somatic mutations and gene copy number alterations of primary breast cancers and their matched metastases from patients with estrogen receptor (ER)-negative disease. DNA samples obtained from formalin-fixed paraffin-embedded ER-negative/HER2-positive ( n = 9) and ER-, progesterone receptor (PR-), HER2-negative ( n = 8) primary breast cancers and from paired brain or skin metastases and normal tissue were subjected to a hybridization capture-based massively parallel sequencing assay, targeting 341 key cancer genes. A large subset of nonsynonymous somatic mutations (45%) and gene copy number alterations (55%) was shared between the primary tumors and paired metastases. However, mutations restricted to either a given primary tumor or its metastasis, the acquisition of loss of heterozygosity of the wild-type allele, and clonal shifts of genes affected by somatic mutations, such as TP53 and RB1 , were observed in the progression from primary tumors to metastases. No metastasis location-specific alterations were identified, but synchronous metastases showed higher concordance with the paired primary tumor than metachronous metastases. Novel potentially targetable alterations were found in the metastases relative to their matched primary tumors. These data indicate that repertoires of somatic genetic alterations in ER-negative metastatic breast cancers may differ from those of their primary tumors, even by the presence of driver and targetable somatic genetic alterations. Significance: Somatic genetic alterations in ER-negative breast cancer metastases may be distinct from those of their primary tumors, suggesting that for treatment-decision making, genetic analyses of DNA obtained from the metastatic lesion rather than from the primary tumor should be considered. Cancer Res; 78(12); 3112-21. ©2018 AACR ., (©2018 American Association for Cancer Research.)

This study explores how one social-structural variable, control over Sunni-Arab communities during the Iraq civil war, affected the types of violence used by insurgent/non-government actors that killed and injured civilians in these communities from January 2004 to December 2009. The study classifies three levels of control: (1) incumbent (government-supported) control, (2) insurgent control and (3) actively contested control. It uses Iraq Body Count (IBC) fatality data to characterize two general types of violence (selective and indiscriminate) evident during the Iraq conflict. It demonstrates that the type of violence committed by non-government actors was significantly (P > .01) different as related to the level of control insurgents had over territory. Primarily, insurgents/non-governmental actors used more selective forms of violence when insurgents controlled territory and more indiscriminate violence when incumbent (government-supported) forces controlled territory. Also, acts of indiscriminate violence cause considerably more injuries and death per act as compared to selective violence. Importantly, if control over territory has broadly generalizable effects on the types of violence that civilian's experience during civil war, than understanding this relationship could be useful when determining the types of medical assistance, medical supplies and training most needed in combat zones.

Adenomyoepithelioma of the breast is a rare tumor characterized by epithelial-myoepithelial differentiation, whose genetic underpinning is largely unknown. Here we show through whole-exome and targeted massively parallel sequencing analysis that whilst estrogen receptor (ER)-positive adenomyoepitheliomas display PIK3CA or AKT1 activating mutations, ER-negative adenomyoepitheliomas harbor highly recurrent codon Q61 HRAS hotspot mutations, which co-occur with PIK3CA or PIK3R1 mutations. In two- and three-dimensional cell culture models, forced expression of HRAS Q61R in non-malignant ER-negative breast epithelial cells with or without a PIK3CA H1047R somatic knock-in results in transformation and the acquisition of the cardinal features of adenomyoepitheliomas, including the expression of myoepithelial markers, a reduction in E-cadherin expression, and an increase in AKT signaling. Our results demonstrate that adenomyoepitheliomas are genetically heterogeneous, and qualify mutations in HRAS, a gene whose mutations are vanishingly rare in common-type breast cancers, as likely drivers of ER-negative adenomyoepitheliomas.

Many cancer-causing chromosomal translocations result in transactivating protein products encoding FET family (FUS, EWSR1, TAF15) low-complexity (LC) domains fused to a DNA binding domain from one of several transcription factors. Recent work demonstrates that higher-order assemblies of FET LC domains bind the carboxy-terminal domain of the large subunit of RNA polymerase II (RNA pol II CTD), suggesting FET oncoproteins may mediate aberrant transcriptional activation by recruiting RNA polymerase II to promoters of target genes. Here we use nuclear magnetic resonance (NMR) spectroscopy and hydrogel fluorescence microscopy localization and fluorescence recovery after photobleaching to visualize atomic details of a model of this process, interactions of RNA pol II CTD with high-molecular weight TAF15 LC assemblies. We report NMR resonance assignments of the intact degenerate repeat half of human RNA pol II CTD alone and verify its predominant intrinsic disorder by molecular simulation. By measuring NMR spin relaxation and dark-state exchange saturation transfer, we characterize the interaction of RNA pol II CTD with amyloid-like hydrogel fibrils of TAF15 and hnRNP A2 LC domains and observe that heptads far from the acidic C-terminal tail of RNA pol II CTD bind TAF15 fibrils most avidly. Mutation of CTD lysines in heptad position 7 to consensus serines reduced the overall level of TAF15 fibril binding, suggesting that electrostatic interactions contribute to complex formation. Conversely, mutations of position 7 asparagine residues and truncation of the acidic tail had little effect. Thus, weak, multivalent interactions between TAF15 fibrils and heptads throughout RNA pol II CTD collectively mediate complex formation.

Liquid-liquid phase separation (LLPS) is believed to underlie formation of biomolecular condensates, cellular compartments that concentrate macromolecules without surrounding membranes. Physical mechanisms that control condensate formation/dissolution are poorly understood. The RNA-binding protein fused in sarcoma (FUS) undergoes LLPS in vitro and associates with condensates in cells. We show that the importin karyopherin-β2/transportin-1 inhibits LLPS of FUS. This activity depends on tight binding of karyopherin-β2 to the C-terminal proline-tyrosine nuclear localization signal (PY-NLS) of FUS. Nuclear magnetic resonance (NMR) analyses reveal weak interactions of karyopherin-β2 with sequence elements and structural domains distributed throughout the entirety of FUS. Biochemical analyses demonstrate that most of these same regions also contribute to LLPS of FUS. The data lead to a model where high-affinity binding of karyopherin-β2 to the FUS PY-NLS tethers the proteins together, allowing multiple, distributed weak intermolecular contacts to disrupt FUS self-association, blocking LLPS. Karyopherin-β2 may act analogously to control condensates in diverse cellular contexts., (Copyright © 2018 Elsevier Inc. All rights reserved.)

hnRNPA2, a component of RNA-processing membraneless organelles, forms inclusions when mutated in a syndrome characterized by the degeneration of neurons (bearing features of amyotrophic lateral sclerosis [ALS] and frontotemporal dementia), muscle, and bone. Here we provide a unified structural view of hnRNPA2 self-assembly, aggregation, and interaction and the distinct effects of small chemical changes-disease mutations and arginine methylation-on these assemblies. The hnRNPA2 low-complexity (LC) domain is compact and intrinsically disordered as a monomer, retaining predominant disorder in a liquid-liquid phase-separated form. Disease mutations D290V and P298L induce aggregation by enhancing and extending, respectively, the aggregation-prone region. Co-aggregating in disease inclusions, hnRNPA2 LC directly interacts with and induces phase separation of TDP-43. Conversely, arginine methylation reduces hnRNPA2 phase separation, disrupting arginine-mediated contacts. These results highlight the mechanistic role of specific LC domain interactions and modifications conserved across many hnRNP family members but altered by aggregation-causing pathological mutations., (Copyright © 2018 Elsevier Inc. All rights reserved.)

Purpose: Aberrant activation of the PI3K pathway has been implicated in resistance to HER2-targeted therapy, but results of clinical trials are confounded by the co-administration of chemotherapy. We investigated the effect of perturbations of this pathway in breast cancers from patients treated with neoadjuvant anti-HER2-targeted therapy without chemotherapy., Patients and Methods: Baseline tumor samples from patients with HER2-positive breast cancer enrolled in TBCRC006 (NCT00548184), a 12-week neoadjuvant clinical trial with lapatinib plus trastuzumab [plus endocrine therapy for estrogen receptor (ER)-positive tumors], were assessed for PTEN status by immunohistochemistry and PIK3CA mutations by sequencing. Results were correlated with pathologic complete response (pCR)., Results: Of 64 evaluable patients, PTEN immunohistochemistry and PIK3CA mutation analysis were performed for 59 and 46 patients, respectively. PTEN status (dichotomized by H-score median) was correlated with pCR (32% in high PTEN vs. 9% in low PTEN, p = 0.04). PIK3CA mutations were identified in 14/46 tumors at baseline (30%) and did not correlate with ER or PTEN status. One patient whose tumor harbored a PIK3CA mutation achieved pCR (p = 0.14). When considered together (43 cases), 1/25 cases (4%) with a PIK3CA mutation and/or low PTEN expression levels had a pCR compared to 7/18 cases (39%) with wild-type PI3KCA and high PTEN expression levels (p = 0.006)., Conclusion: PI3K pathway activation is associated with resistance to lapatinib and trastuzumab in breast cancers, without chemotherapy. Further studies are warranted to investigate how to use these biomarkers to identify upfront patients who may respond to anti-HER2 alone, without chemotherapy.

A cancer in the contralateral breast in a woman with a previous or synchronous breast cancer is typically considered to be an independent primary tumor. Emerging evidence suggests that in a small subset of these cases the second tumor represents a metastasis. We sought to investigate the issue using massively parallel sequencing targeting 254 genes recurrently mutated in breast cancer. We examined the tumor archives at Memorial Sloan Kettering Cancer Center for the period 1995-2006 to identify cases of contralateral breast cancer where surgery for both tumors was performed at the Center. We report results from 49 patients successfully analyzed by a targeted massively parallel sequencing assay. Somatic mutations and copy number alterations were defined by state-of-the-art algorithms. Clonal relatedness was evaluated by statistical tests specifically designed for this purpose. We found evidence that the tumors in contralateral breasts were clonally related in three cases (6%) on the basis of matching mutations at codons where somatic mutations are rare. Clinical data and the presence of similar patterns of gene copy number alterations were consistent with metastasis for all three cases. In three additional cases, there was a solitary matching mutation at a common PIK3CA locus. The results suggest that a subset of contralateral breast cancers represent metastases rather than independent primary tumors. Massively parallel sequencing analysis can provide important evidence to clarify the diagnosis. However, given the inter-tumor mutational heterogeneity in breast cancer, sufficiently large gene panels need to be employed to define clonality convincingly in all cases., (© 2017 UICC.)

Metaplastic breast cancer (MBC) is a rare special histologic type of triple-negative breast cancer, characterized by the presence of neoplastic cells showing differentiation towards squamous epithelium and/or mesenchymal elements. Here we sought to define whether histologically distinct subgroups of MBCs would be underpinned by distinct genomic and/or transcriptomic alterations. Microarray-based copy number profiling identified limited but significant differences between the distinct MBC subtypes studied here, despite the limited sample size ( n  = 17). In particular, we found that, compared to MBCs with chondroid or squamous cell metaplasia, MBCs with spindle cell differentiation less frequently harbored gain of 7q11.22-23 encompassing CLDN3 and CLDN4 , consistent with their lower expression of claudins and their association with the claudin-low molecular classification. Microarray-based and RNA-sequencing-based gene expression profiling revealed that MBCs with spindle cell differentiation differ from MBCs with chondroid or squamous cell metaplasia on the expression of epithelial-to-mesenchymal transition-related genes, including down-regulation of CDH1 and EPCAM . In addition, RNA-sequencing revealed that the histologic patterns observed in MBCs are unlikely to be underpinned by a highly recurrent expressed fusion gene or a pathognomonic expressed mutation in cancer genes. Loss of PTEN expression or mutations affecting PIK3CA or TSC2 observed in 8/17 MBCs support the contention that PI3K pathway activation plays a role in the development of MBCs. Our data demonstrate that despite harboring largely similar patterns of gene copy number alterations, MBCs with spindle cell, chondroid and squamous differentiation are distinct at the transcriptomic level but are unlikely to be defined by specific pathognomonic genetic alterations.

Neuronal inclusions of aggregated RNA-binding protein fused in sarcoma (FUS) are hallmarks of ALS and frontotemporal dementia subtypes. Intriguingly, FUS's nearly uncharged, aggregation-prone, yeast prion-like, low sequence-complexity domain (LC) is known to be targeted for phosphorylation. Here we map in vitro and in-cell phosphorylation sites across FUS LC We show that both phosphorylation and phosphomimetic variants reduce its aggregation-prone/prion-like character, disrupting FUS phase separation in the presence of RNA or salt and reducing FUS propensity to aggregate. Nuclear magnetic resonance spectroscopy demonstrates the intrinsically disordered structure of FUS LC is preserved after phosphorylation; however, transient domain collapse and self-interaction are reduced by phosphomimetics. Moreover, we show that phosphomimetic FUS reduces aggregation in human and yeast cell models, and can ameliorate FUS-associated cytotoxicity. Hence, post-translational modification may be a mechanism by which cells control physiological assembly and prevent pathological protein aggregation, suggesting a potential treatment pathway amenable to pharmacologic modulation., (© 2017 The Authors. Published under the terms of the CC BY NC ND 4.0 license.)

Breast fibroepithelial lesions (fibroadenomas and phyllodes tumors) are underpinned by recurrent MED12 exon 2 mutations, which are more common in fibroadenomas and benign phyllodes tumors. TERT promoter hotspot mutations have been documented in phyllodes tumors, and found to be more frequent in borderline and malignant lesions. Several lines of evidence suggest that a subset of phyllodes tumors might arise from fibroadenomas. Here we sought to investigate the genetic differences between phyllodes tumors with fibroadenoma-like areas vs. those without. We retrieved data for 16 borderline/ malignant phyllodes tumors, including seven phyllodes tumors with fibroadenoma-like areas and nine phyllodes tumors without fibroadenoma-like areas, which had been previously subjected to targeted capture massively parallel sequencing. Whilst MED12 exon 2 mutations were significantly more frequent in tumors with fibroadenoma-like areas (71 vs. 11%), an enrichment in genetic alterations targeting bona fide cancer genes was found in those without fibroadenoma-like areas, in particular in EGFR mutations and amplifications (78 vs. 14%). No significant difference in the frequency of TERT genetic alterations was observed (71% in cases with fibroadenoma-like areas vs 56% in those without fibroadenoma-like areas). Our data suggest that the development of phyllodes tumors might follow two different evolutionary pathways: a MED12 -mutant pathway that involves the progression from a fibroadenoma to a malignant phyllodes tumor; and a MED12 -wild-type pathway, where malignant phyllodes tumors arise de novo through the acquisition of genetic alterations targeting cancer genes. Additional studies are warranted to confirm our observations and define whether the outcome differs between both pathways.

Clear cell carcinoma of the endometrium is a rare type of endometrial cancer that is generally associated with an aggressive clinical behaviour. Here, we sought to define the repertoire of somatic genetic alterations in endometrial clear cell carcinomas (ECCs), and whether ECCs could be classified into the molecular subtypes described for endometrial endometrioid and serous carcinomas. We performed a rigorous histopathological review, immunohistochemical analysis and massively parallel sequencing targeting 300 cancer-related genes of 32 pure ECCs. Eleven (34%), seven (22%) and six (19%) ECCs showed abnormal expression patterns for p53, ARID1A, and at least one DNA mismatch repair (MMR) protein, respectively. Targeted sequencing data were obtained from 30 of the 32 ECCs included in this study, and these revealed that two ECCs (7%) were ultramutated and harboured mutations affecting the exonuclease domain of POLE. In POLE wild-type ECCs, TP53 (46%), PIK3CA (36%), PPP2R1A (36%), FBXW7 (25%), ARID1A (21%), PIK3R1 (18%) and SPOP (18%) were the genes most commonly affected by mutations; 18% and 11% harboured CCNE1 and ERBB2 amplifications, respectively, and 11% showed DAXX homozygous deletions. ECCs less frequently harboured mutations affecting CTNNB1 and PTEN but more frequently harboured PPP2R1A and TP53 mutations than non-POLE endometrioid carcinomas from The Cancer Genome Atlas (TCGA). Compared to endometrial serous carcinomas (TCGA), ECCs less frequently harboured TP53 mutations. When a surrogate model for the molecular-based TCGA classification was used, all molecular subtypes previously identified in endometrial endometrioid and serous carcinomas were present in the ECCs studied, including POLE, MMR-deficient, copy-number high (serous-like)/p53 abnormal, and copy-number low (endometrioid)/p53 wild-type, which were significantly associated with disease-free survival in univariate analysis. These findings demonstrate that ECCs constitute a histologically and genetically heterogeneous group of tumours with varying outcomes. Furthermore, our data suggest that the classification of ECCs as being generally 'high-grade' or 'type II' tumours may not be warranted. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd., (Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.)

Aims: Breast myxoid fibroadenomas (MFAs) are characterized by a distinctive hypocellular myxoid stroma, and occur sporadically or in the context of Carney complex, an inheritable condition caused by PRKAR1A-inactivating germline mutations. Conventional fibroadenomas (FAs) are underpinned by recurrent MED12 mutations in the stromal components of the lesions. The aim of this study was to investigate the genomic landscape of MFAs and compare it with that of conventional FAs., Methods and Results: Eleven MFAs from patients without clinical and/or genetic evidence of Carney complex were retrieved. DNA samples of tumour and matching normal tissue were subjected to massively parallel sequencing using the Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT) assay, an assay targeting 410 cancer genes. Genetic alterations detected by MSK-IMPACT were tested in samples in which the stromal and epithelial components were separately laser capture-microdissected. Sequencing revealed no germline PRKAR1A mutations and non-synonymous mutations in six MFAs. Interestingly, in three of the MFAs in which the stromal and epithelial components were separately microdissected, the mutations were found to be restricted to the epithelial rather than the stromal component. The sole exception was a lesion harbouring a somatic truncating PRKAR1A mutation. Upon histological re-review, this case was reclassified as a breast myxoma, consistent with the spectrum of tumous observed in Carney complex patients. In this case, the PRKAR1A somatic mutation was restricted to the stromal component., Conclusion: MFAs lack MED12 mutations, and their stromal components seem not to harbour mutations in the 410 cancer genes tested. Whole-exome and/or whole-genome analyses of MFAs are required to elucidate their genetic drivers., (© 2017 John Wiley & Sons Ltd.)

Aims: Low-grade ovarian endometrioid carcinomas may be associated with high-grade components. Whether the latter are clonally related to and originate from the low-grade endometrioid carcinoma remains unclear. The aim of this study was to use massively parallel sequencing to characterize the genomic landscape and clonal relatedness of an ovarian endometrioid carcinoma containing low-grade and high-grade components., Methods and Results: DNA samples extracted from each tumour component (low-grade endometrioid, high-grade anaplastic and high-grade squamous) and matched normal tissue were subjected to targeted massively parallel sequencing with the 410-gene Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT) sequencing assay. Somatic single nucleotide variants, small insertions and deletions, and copy number alterations were detected with state-of-the-art bioinformatics algorithms, and validated with orthogonal methods. The endometrioid carcinoma and the associated high-grade components shared copy number alterations and four clonal mutations, including SMARCA4 mutations, which resulted in loss of BRG1 protein expression. Subclonal mutations and mutations restricted to single components were also identified, such as distinct TP53 mutations restricted to each histological component., Conclusions: Histologically distinct components of ovarian endometrioid carcinomas may show intratumour genetic heterogeneity but be clonally related, harbouring a complex clonal composition. In the present case, SMARCA4 mutations were probably early events, whereas TP53 somatic mutations were acquired later in evolution., (© 2017 John Wiley & Sons Ltd.)

Purpose: Resistance to anti-HER2 therapies in HER2 + breast cancer can occur through activation of alternative survival pathways or reactivation of the HER signaling network. Here we employed BT474 parental and treatment-resistant cell line models to investigate a mechanism by which HER2 + breast cancer can reactivate the HER network under potent HER2-targeted therapies. Experimental Design: Resistant derivatives to lapatinib (L), trastuzumab (T), or the combination (LR/TR/LTR) were developed independently from two independent estrogen receptor ER + /HER2 + BT474 cell lines (AZ/ATCC). Two derivatives resistant to the lapatinib-containing regimens (BT474/AZ-LR and BT474/ATCC-LTR lines) that showed HER2 reactivation at the time of resistance were subjected to massive parallel sequencing and compared with parental lines. Ectopic expression and mutant-specific siRNA interference were applied to analyze the mutation functionally. In vitro and in vivo experiments were performed to test alternative therapies for mutant HER2 inhibition. Results: Genomic analyses revealed that the HER2 L755S mutation was the only common somatic mutation gained in the BT474/AZ-LR and BT474/ATCC-LTR lines. Ectopic expression of HER2 L755S induced acquired lapatinib resistance in the BT474/AZ, SK-BR-3, and AU565 parental cell lines. HER2 L755S-specific siRNA knockdown reversed the resistance in BT474/AZ-LR and BT474/ATCC-LTR lines. The HER1/2-irreversible inhibitors afatinib and neratinib substantially inhibited both resistant cell growth and the HER2 and downstream AKT/MAPK signaling driven by HER2 L755S in vitro and in vivo Conclusions: HER2 reactivation through acquisition of the HER2 L755S mutation was identified as a mechanism of acquired resistance to lapatinib-containing HER2-targeted therapy in preclinical HER2-amplified breast cancer models, which can be overcome by irreversible HER1/2 inhibitors. Clin Cancer Res; 23(17); 5123-34. ©2017 AACR ., (©2017 American Association for Cancer Research.)