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Introduction: Granular cancer patient treatment data collection, and subsequent mapping to standard regimen definitions, are vital next steps in advancement of observational studies in oncology. However, the identification of regimen details, including dose and schedule, is a prerequisite for both collection and mapping. At the patient level, claims databases are a useful but limited resource. Most cancer registries, such as the National Cancer Institute Surveillance, Epidemiology, and End Results (SEER) program and the Commission on Cancer National Cancer Database, capture only a simplification of actual treatments, such as binary exposure to chemotherapy (yes/no) or a list of individual chemotherapeutic agent names. Moreover, even with optimal patient data collection, a “gold standard” database of expected chemotherapy doses and schedules as part of standard-of-care (SOC) does not currently exist. Methods: We extracted and normalized the semistructured dosing and timing data from HemOnc.org, the largest publicly available website of SOC chemotherapy drugs and regimens. To that end, we undertook two broad and parallel approaches: 1) standardization of prescribing instructions within a given cycle (SIGs) or pertaining to cycle timing (“cycleSIGs”); and 2) parsing of resultant content into structured variables. This effort was carried out iteratively with the goal of creating standard “canonical” forms for intermittent intravenous (IV), continuous IV (CIV), other routes (e.g., oral), and radiation SIGs. All SIGs were bound to regimen and treatment context (e.g., cyclophosphamide dosing differs in R-CHOP versus R-CVP, and number of cycles often differs between adjuvant and metastatic contexts). Results: There are currently 14,569 regimen-context-SIG-cycleSIG quartets in the database (October 2019). Parsing of SIGs into structured variables resulted in 7,792 canonical IV, 675 canonical CIV, 3,762 canonical other, 510 canonical radiation, and 2,249 noncanonical results. Some SIGs are multipart and were broken into steps. For example, “6 mg/m2 IV once on day 1, then 3 mg/m2 IV once on day 8” constitutes two separate steps. There were 948 unique cycleSIGs (e.g., “21-day cycle for 4 cycles”), which were also parsed into components. Discussion: This effort has produced a large dataset of granular drug and cycle SIG information that reflects SOC dosing parameters in hematology/oncology. This dataset can be used to understand discrepancies between real-world outcomes and clinical trial results, e.g., by elucidating the effect of dose reductions and treatment delays on treatment outcomes. The Observational Health Data Sciences and Informatics (OHDSI) oncology workgroup is arranging to add this new information to the portion of the HemOnc vocabulary that is available through the OHDSI terminology management tool. Ongoing efforts also include translating the maximum possible number of noncanonical sigs into canonical forms, which can further enhance simplicity and usability of the dataset. Citation Format: Zachary H. Moldwin, Andrew Malty, Donna R. Rivera, Anastasios Siapos, Christian G. Reich, Michael J. Gurley, Rimma Belenkaya, Dmitry Dymshyts, Jeremy L. Warner. Getting granular: A structured database of doses and schedules in hematology/oncology [abstract]. In: Proceedings of the AACR Special Conference on Advancing Precision Medicine Drug Development: Incorporation of Real-World Data and Other Novel Strategies; Jan 9-12, 2020; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(12_Suppl_1):Abstract nr 27.

Connectivity webs mediate the unique biology of the mammalian brain. Yet, while cell circuit maps are increasingly available, knowledge of their underlying molecular networks remains limited. Here, we applied multi-dimensional biochemical fractionation with mass spectrometry and machine learning to survey endogenous macromolecules across the adult mouse brain. We defined a global "interactome" comprising over one thousand multi-protein complexes. These include hundreds of brain-selective assemblies that have distinct physical and functional attributes, show regional and cell-type specificity, and have links to core neurological processes and disorders. Using reciprocal pull-downs and a transgenic model, we validated a putative 28-member RNA-binding protein complex associated with amyotrophic lateral sclerosis, suggesting a coordinated function in alternative splicing in disease progression. This brain interaction map (BraInMap) resource facilitates mechanistic exploration of the unique molecular machinery driving core cellular processes of the central nervous system. It is publicly available and can be explored here https://www.bu.edu/dbin/cnsb/mousebrain/.

Connectivity webs mediate the unique biology of the mammalian brain. Yet while cell circuit maps are increasingly available, knowledge of the underlying molecular networks remains limited. Here, we applied multi-dimensional biochemical fractionation with precision mass spectrometry and machine learning to survey endogenous macromolecules in adult mouse brain. We defined a global ‘interactome’ of multi-protein complexes, most never reported before. These brain-selective assemblies have distinct physical and functional attributes and show regional- and cell-type specificity. A striking number are also linked to neurological disorders and disease variants with broad pathophysiological relevance. Using reciprocal pulldowns and a transgenic model, we validated a putative 15-member RNA-binding protein complex associated with amyotrophic lateral sclerosis, establishing regulatory functions in alternative splicing and disease progression. This Brain Interaction Map – or BraInMap – resource facilitates mechanistic exploration of the molecular machinery driving core processes and diseases of the central nervous system.

SummaryThe prevalence of autism spectrum disorders (ASDs) is rapidly growing, yet its molecular basis is poorly understood. Here, we sought to gain a systems-level understanding of ASD candidate genes by mapping them onto ubiquitous human protein complexes and characterizing the resulting complexes. These studies revealed the role of histone deacetylases (HDAC1/2) in regulating the expression of ASD orthologs in the embryonic mouse brain. Next, proteome-wide screens for subunits co-complexed with HDAC1 and six other key ASD proteins in human neuronal cells revealed a protein interaction network that displayed preferential expression in fetal brain development, exhibited increased deleterious mutations in ASD cases, and encompassed genes strongly regulated by FMRP and MECP2, mutations that are causal for fragile X and Rett syndromes, respectively. Overall, our study reveals molecular components in ASD, suggests a shared mechanism between the syndromic and idiopathic forms of ASDs, and provides a groundwork for analyzing complex human diseases.

Mitochondrial protein (MP) dysfunction has been linked to neurodegenerative disorders (NDs); however, the discovery of the molecular mechanisms underlying NDs has been impeded by the limited characterization of interactions governing MP function. Here, using mass spectrometry (MS)-based analysis of 210 affinity-purified mitochondrial (mt) fractions isolated from 27 epitope-tagged human ND-linked MPs in HEK293 cells, we report a high-confidence MP network including 1,964 interactions among 772proteins (>90% previously unreported). Nearly three-fourths of these interactions were confirmed in mouse brain and multiple human differentiated neuronal cell lines by primary antibody immunoprecipitation and MS, with many linked to NDs and autism. We show that the SOD1-PRDX5 interaction, critical for mt redox homeostasis, can be perturbed by amyotrophic lateral sclerosis-linked SOD1 allelic variants and establish a functional role for ND-linked factors coupled with IκBɛ in NF-κB activation. Our results identify mechanisms for ND-linked MPs and expand the human mt interaction landscape.

Over the past several years, mitochondrial dysfunction has been linked to an increasing number of human illnesses, making mitochondrial proteins (MPs) an ever more appealing target for therapeutic intervention. With 20% of the mitochondrial proteome (312 of an estimated 1500 MPs) having known interactions with small molecules, MPs appear to be highly targetable. Yet, despite these targeted proteins functioning in a range of biological processes (including induction of apoptosis, calcium homeostasis, and metabolism), very few of the compounds targeting MPs find clinical use. Recent work has greatly expanded the number of proteins known to localize to the mitochondria and has generated a considerable increase in MP 3D structures available in public databases, allowing experimental screening and in silico prediction of mitochondrial drug targets on an unprecedented scale. Here, we summarize the current literature on clinically active drugs that target MPs, with a focus on how existing drug targets are distributed across biochemical pathways and organelle substructures. Also, we examine current strategies for mitochondrial drug discovery, focusing on genetic, proteomic, and chemogenomic assays, and relevant model systems. As cell models and screening techniques improve, MPs appear poised to emerge as relevant targets for a wide range of complex human diseases, an eventuality that can be expedited through systematic analysis of MP function.

Herein, we report a facile route for the synthesis of foam-like porous oxides using carbon spheres and polyvinylpyrrolidone (PVP) as sacrificial templates. The as-prepared porous structures were characterized by XRD, FESEM, TEM and BET methods. These foam-like macroporous oxides are formed through the fusion of oxide nanoparticles around the gas bubbles liberated during the combustion of composites and show good BET surface areas.

Background Acute exposure to prostaglandin E2 (PGE2) activates EP receptors in sensory neurons which triggers the cAMP-dependent protein kinase A (PKA) signaling cascade resulting in enhanced excitability of the neurons. With long-term exposure to PGE2, however, the activation of PKA does not appear to mediate persistent PGE2-induced sensitization. Consequently, we examined whether homologous desensitization of PGE2-mediated PKA activation occurs after long-term exposure of isolated sensory neurons to the eicosanoid. Methods Sensory neuronal cultures were harvested from the dorsal root ganglia of adult male Sprague-Dawley rats. The cultures were pretreated with vehicle or PGE2 and used to examine signaling mechanisms mediating acute versus persistent sensitization by exposure to the eicosanoid using enhanced capsaicin-evoked release of immunoreactive calcitonin gene-related peptide (iCGRP) as an endpoint. Neuronal cultures chronically exposed to vehicle or PGE2 also were used to study the ability of the eicosanoid and other agonists to activate PKA and whether long-term exposure to the prostanoid alters expression of EP receptor subtypes. Results Acute exposure to 1 μM PGE2 augments the capsaicin-evoked release of iCGRP, and this effect is blocked by the PKA inhibitor H-89. After 5 days of exposure to 1 μM PGE2, administration of the eicosanoid still augments evoked release of iCGRP, but the effect is not attenuated by inhibition of PKA or by inhibition of PI3 kinases. The sensitizing actions of PGE2 after acute and long-term exposure were attenuated by EP2, EP3, and EP4 receptor antagonists, but not by an EP1 antagonist. Exposing neuronal cultures to 1 μM PGE2 for 12 h to 5 days blocks the ability of PGE2 to activate PKA. The offset of the desensitization occurs within 24 h of removal of PGE2 from the cultures. Long-term exposure to PGE2 also results in desensitization of the ability of a selective EP4 receptor agonist, L902688 to activate PKA, but does not alter the ability of cholera toxin, forskolin, or a stable analog of prostacyclin to activate PKA. Conclusions Long-term exposure to PGE2 results in homologous desensitization of EP4 receptor activation of PKA, but not to neuronal sensitization suggesting that activation of PKA does not mediate PGE2-induced sensitization after chronic exposure to the eicosanoid.

The purpose of this study was to investigate skin blood flow at rest and the effects of electrical stimulation on skin blood flow during the menstrual cycle and after menopause. Nineteen subjects participated in the study. Nine volunteers with normal menstrual cycles (mean age = 25.6 ± 3.5 years, height = 162.6 ± 5.8 cm, weight = 55.8 ± 7.6 kg, Body Mass Index (BMI) = 21.1 ± 2.9) and 10 postmenopausal volunteers (mean age 59.2 ± 4.7 years). The effect of electrical stimulation on skin blood flow was studied in a thermoneutral room (25 ± 0.5°C) and a warm room (35 ± 0.5°C) for eight subjects. Electrical stimulation was applied on the right thigh for 15 min at an intensity below the threshold of muscle contraction. Skin blood flow measurements were taken using a Laser Doppler Imager. Sweat rate and skin temperature were monitored at the forehead, chest, and each thigh. Tympanic temperature was taken every 5 min. In the thermoneutral environment, there was no significant effect of electrical stimulation on s...

Contrast baths have been used for therapy for over 2,000 years. The basic concept is to alternate warm and cool water baths during a treatment session. It is believed that this will increase circulation better than just placing the limb in a warm water bath. However, there is little supportive evidence for this assertion. Further, for subjects with diabetes, with underlying impairments in their circulation, this may not work at all. Fourteen people with type 2 diabetes were compared to 14 age-matched controls. Skin blood flow of the foot (BF) was measured during 16 minutes of contrast baths at two different intervals: 3 minutes warm and 1 minute cold and 6 minutes warm and 2 minutes cold. In control subjects, warm and cold contrast baths with the ratio 3 minutes warm to 1 minute cold elicited significantly (p0.01) greater BF than placing the limb continuously in warm water or using a 6:2 ratio of warm to cold bath time. In control subjects, there was also a greater plantar than dorsal BF. For subjects with diabetes, there was no statistical difference between BF with contrast baths versus warm whirlpool; but in both cases BF was significantly less than that seen in control subjects under similar circumstances. There was also very little difference between BF on the plantar and dorsal aspects of the foot in the subjects with diabetes. Patients with diabetes do not show a vascular response to contrast bath therapy. The BF response to contrast temperatures may be a good diagnostic test for diabetic vascular impairment.

We examined whether nerve growth factor (NGF), an inflammatory mediator that contributes to chronic hypersensitivity, alters the intracellular signaling that mediates the sensitizing actions of PGE2 from activation of protein kinase A (PKA) to exchange proteins directly activated by cAMP (Epacs). When isolated sensory neurons are grown in the absence of added NGF, but not in cultures grown with 30 ng/ml NGF, inhibiting protein kinase A (PKA) activity blocks the ability of PGE2 to augment capsaicin-evoked release of the neuropeptide CGRP and to increase the number of action potentials (APs) evoked by a ramp of current. Growing sensory neurons in culture in the presence of increasing concentrations of NGF increases the expression of Epac2, but not Epac1. An intradermal injection of complete Freund's adjuvant into the rat hindpaw also increases the expression of Epac2, but not Epac1 in the dorsal root ganglia and spinal cord: an effect blocked by intraplantar administration of NGF antibodies. Treating cultures grown in the presence of 30 ng/ml NGF with Epac1siRNA significantly reduced the expression of Epac1, but not Epac2, and did not block the ability of PGE2 to augment capsaicin-evoked release of CGRP from sensory neurons. Exposing neuronal cultures grown in NGF to Epac2siRNAreduced the expression of Epac2, but not Epac1 and prevented the PGE2-induced augmentation of capsaicin and potassium-evoked CGRP release in sensory neurons and the PGE2-induced increase in the number of APs generated by a ramp of current. In neurons grown with no added NGF, Epac siRNAs did not attenuate PGE2-induced sensitization. These results demonstrate that NGF, through increasing Epac2 expression, alters the signaling cascade that mediates PGE2-induced sensitization of sensory neurons, thus providing a novel mechanism for maintaining PGE2-induced hypersensitivity during inflammation.

Background: Repetitive stress injuries due to prolonged recurrent movement of hands such as using a keyboard could cause inflammation, discomfort of the hand and finger joints, pain, weakness, and stiffness. Paraffin wax has been used to treat many musculoskeletal problems that affect hands and feet because of its good contact to irregular contoured areas. The purpose of this study was to compare the effectiveness of using paraffin wax and exercise, versus exercise alone in treating keyboard users who are at risk of developing hands repetitive stress injury. Method and Procedure: thirty female subjects using keyboard for at least four hours a day complained of hands pain and discomfort were divided into two groups: Paraffin-Exercise Group (PEG) ( n=15) treated with paraffin wax for 15 minutes prior to exercise, five days a week, for two weeks, and Exercise Group (EG) (n=15) treated with exercise regimen only. Hands and fingers strength and pain level were measured at baseline, and one and two weeks post treatment. Result: Visual Analog Scale (VAS) and fingers key-pinch showed significant pain reduction starting 1st week for PEG and 2nd week for EG. Hands grips were significantly improved for both groups after the 2nd week (p