Dual IKZF2 and CK1α degrader targets acute myeloid leukemia cells

Acute myeloid leukemia (AML) is a hematologic malignancy for which several epigenetic regulators have been identified as therapeutic targets. Here we report the development of cereblon-dependent degraders of IKZF2 and casein kinase 1α (CK1α), termed DEG-35 and DEG-77. We utilized a structure-guided approach to develop DEG-35 as a nanomolar degrader of IKZF2, a hematopoietic-specific transcription factor that contributes to myeloid leukemogenesis. DEG-35 possesses additional substrate specificity for the therapeutically relevant target CK1α, which was identified through unbiased proteomics and a PRISM screen assay. Degradation of IKZF2 and CK1α blocks cell growth and induces myeloid differentiation in AML cells through CK1α-p53- and IKZF2-dependent pathways. Target degradation by DEG-35 or a more soluble analog, DEG-77, delays leukemia progression in murine and human AML mouse models. Overall, we provide a strategy for multitargeted degradation of IKZF2 and CK1α to enhance efficacy against AML that may be expanded to additional targets and indications.

Targeted Protein Degradation: Design Considerations for PROTAC Development

Targeted protein degradation has recently gained widespread interest as both a novel therapeutic strategy and a useful tool in biomedical research. Targeted protein degraders are often sub-stoichiometric and do not require strong binding affinity for their targets, enabling access to previously inaccessible targets. Proteolysis-targeting chimeras (PROTACs) are one class of targeted protein degraders that promote degradation by recruiting a target protein to an E3-ligase complex via a heterobifunctional molecule. The modular nature of PROTACs allows for their rational design and systematic optimization. Here we suggest resources and methodologies for developing PROTAC degraders for researchers that may be new to the field. © 2022 Wiley Periodicals LLC.

Intersubband Polariton-Polariton Scattering in a Dispersive Microcavity

The ultrafast scattering dynamics of intersubband polaritons in dispersive cavities embedding GaAs/AlGaAs quantum wells are studied directly within their band structure using a noncollinear pump-probe geometry with phase-stable midinfrared pulses. Selective excitation of the lower polariton at a frequency of ∼25  THz and at a finite in-plane momentum k_{‖} leads to the emergence of a narrowband maximum in the probe reflectivity at k_{‖}=0. A quantum mechanical model identifies the underlying microscopic process as stimulated coherent polariton-polariton scattering. These results mark an important milestone toward quantum control and bosonic lasing in custom-tailored polaritonic systems in the mid and far infrared.

In vitro reconstitution reveals major differences between human and bacterial cytochrome c synthases

Cytochromes c are ubiquitous heme proteins in mitochondria and bacteria, all possessing a CXXCH (CysXxxXxxCysHis) motif with covalently attached heme. We describe the first in vitro reconstitution of cytochrome c biogenesis using purified mitochondrial (HCCS) and bacterial (CcsBA) cytochrome c synthases. We employ apocytochrome c and peptide analogs containing CXXCH as substrates, examining recognition determinants, thioether attachment, and subsequent release and folding of cytochrome c. Peptide analogs reveal very different recognition requirements between HCCS and CcsBA. For HCCS, a minimal 16-mer peptide is required, comprised of CXXCH and adjacent alpha helix 1, yet neither thiol is critical for recognition. For bacterial CcsBA, both thiols and histidine are required, but not alpha helix 1. Heme attached peptide analogs are not released from the HCCS active site; thus, folding is important in the release mechanism. Peptide analogs behave as inhibitors of cytochrome c biogenesis, paving the way for targeted control.

From tiny bacteria to the tallest trees, most life on Earth carries a protein called cytochrome c, which helps to create the energy that powers up cells. Cytochrome c does so thanks to its heme, a molecule that enables the chemical reactions required for the energy-creating process.

Despite both relying on cytochrome c, animals and bacteria differ in the enzyme they use to attach the heme to the cytochrome. Spotting variations in how this ‘cytochrome c synthase’ works would help to find compounds that deactivate the enzyme in bacteria, but not in humans. However, studying cytochrome c synthase in living cells is challenging.

To bypass this issue, Sutherland, Mendez, Babbitt et al. successfully reconstituted cytochrome c synthases from humans and bacteria in test tubes. This allowed them to examine in detail which structures the enzymes recognize to spot where to attach the heme onto their target. The experiments revealed that human and bacterial synthases actually rely on different parts of the cytochrome c to orient themselves. Different short compounds could also block either the human or bacterial enzyme.

Variations between human and bacterial cytochrome c synthase could lead to new antibiotics which deactivate the cytochrome and kill bacteria while sparing patients. The next step is to identify molecules that specifically interfere with cytochrome c synthase in bacteria, and could be tested in clinical trials.

Accurate Patient-Specific Machine Learning Models of Glioblastoma Invasion Using Transfer Learning

BACKGROUND AND PURPOSE

MR imaging-based modeling of tumor cell density can substantially improve targeted treatment of glioblastoma. Unfortunately, interpatient variability limits the predictive ability of many modeling approaches. We present a transfer learning method that generates individualized patient models, grounded in the wealth of population data, while also detecting and adjusting for interpatient variabilities based on each patient's own histologic data.

MATERIALS AND METHODS

We recruited patients with primary glioblastoma undergoing image-guided biopsies and preoperative imaging, including contrast-enhanced MR imaging, dynamic susceptibility contrast MR imaging, and diffusion tensor imaging. We calculated relative cerebral blood volume from DSC-MR imaging and mean diffusivity and fractional anisotropy from DTI. Following image coregistration, we assessed tumor cell density for each biopsy and identified corresponding localized MR imaging measurements. We then explored a range of univariate and multivariate predictive models of tumor cell density based on MR imaging measurements in a generalized one-model-fits-all approach. We then implemented both univariate and multivariate individualized transfer learning predictive models, which harness the available population-level data but allow individual variability in their predictions. Finally, we compared Pearson correlation coefficients and mean absolute error between the individualized transfer learning and generalized one-model-fits-all models.

RESULTS

Tumor cell density significantly correlated with relative CBV (r = 0.33, P < .001), and T1-weighted postcontrast (r = 0.36, P < .001) on univariate analysis after correcting for multiple comparisons. With single-variable modeling (using relative CBV), transfer learning increased predictive performance (r = 0.53, mean absolute error = 15.19%) compared with one-model-fits-all (r = 0.27, mean absolute error = 17.79%). With multivariate modeling, transfer learning further improved performance (r = 0.88, mean absolute error = 5.66%) compared with one-model-fits-all (r = 0.39, mean absolute error = 16.55%).

CONCLUSIONS

Transfer learning significantly improves predictive modeling performance for quantifying tumor cell density in glioblastoma.

Guanine nucleotide exchange factor Dock7 mediates HGF-induced glioblastoma cell invasion via Rac activation

Background:

Glioblastoma multiforme (GBM), a highly invasive primary brain tumour, remains an incurable disease. Rho GTPases and their activators, guanine nucleotide exchange factors (GEFs), have central roles in GBM invasion. Anti-angiogenic therapies may stimulate GBM invasion via HGF/c-Met signalling. We aim to identify mediators of HGF-induced GBM invasion that may represent targets in a combination anti-angiogenic/anti-invasion therapeutic paradigm.

Methods:

Guanine nucleotide exchange factor expression was measured by microarray analysis and western blotting. Specific depletion of proteins was accomplished using siRNA. Cell invasion was determined using matrigel and brain slice assays. Cell proliferation and survival were monitored using sulforhodamine B and colony formation assays. Guanine nucleotide exchange factor and GTPase activities were determined using specific affinity precipitation assays.

Results:

We found that expression of Dock7, a GEF, is elevated in human GBM tissue in comparison with non-neoplastic brain. We showed that Dock7 mediates serum- and HGF-induced glioblastoma cell invasion. We also showed that Dock7 co-immunoprecipitates with c-Met and that this interaction is enhanced upon HGF stimulation in a manner that is dependent on the adaptor protein Gab1. Dock7 and Gab1 also co-immunoprecipitate in an HGF-dependent manner. Furthermore, Gab1 is required for HGF-induced Dock7 and Rac1 activation and glioblastoma cell invasion.

Conclusions:

Dock7 mediates HGF-induced GBM invasion. Targeting Dock7 in GBM may inhibit c-MET-mediated invasion in tumours treated with anti-angiogenic regimens.

Molecular targets of glioma invasion

Glioblastoma multiforme is the most common and lethal primary malignant brain tumor. Although considerable progress has been made in technical proficiencies of surgical and radiation treatment for brain tumor patients, the impact of these advances on clinical outcome has been disappointing, with median survival time not exceeding 15 months. Over the last 30 years, no significant increase in survival of patients suffering from this disease has been achieved. A fundamental source of the management challenge presented in glioma patients is the insidious propensity of tumor invasion into distant brain tissue. Invasive tumor cells escape surgical removal and geographically dodge lethal radiation exposure and chemotherapy. Recent improved understanding of biochemical and molecular determinants of glioma cell invasion provide valuable insight into the underlying biological features of the disease, as well as illuminating possible new therapeutic targets. These findings are moving forward to translational research and clinical trials as novel antiglioma therapies.

A knowledge based approach for representing and reasoning about signaling networks

MOTIVATION

In this paper we propose to use recent developments in knowledge representation languages and reasoning methodologies for representing and reasoning about signaling networks. Our approach is different from most other qualitative systems biology approaches in that it is based on reasoning (or inferencing) rather than simulation. Some of the advantages of our approach are, we can use recent advances in reasoning with incomplete and partial information to deal with gaps in signal network knowledge; and can perform various kinds of reasoning such as planning, hypothetical reasoning and explaining observations.

RESULTS

Using our approach we have developed the system BioSigNet-RR for representation and reasoning about signaling networks. We use a NFkappaB related signaling pathway to illustrate the kinds of reasoning and representation that our system can currently do.

AVAILABILITY

The system is available on the Web at http://www.public.asu.edu/~cbaral/biosignet

Experimental and simulation studies of heat flow and heterocyclic amine mutagen/carcinogen formation in pan-fried meat patties

Heterocylic amine (HA) compounds formed in the cooking of certain foods have been shown to be bacterial mutagens and animal carcinogens, and may be a risk factor for human cancer. To help explain the variation observed in HA formation under different cooking conditions, we have performed heat-flow simulations and experiments on the pan-frying of beef patties. The simulations involve modeling the heat flow within a meat patty using empirically derived thermal transport coefficients for the meat. The predicted temperature profiles are used to integrate the Arrhenius rate equation to estimate the concentration of HAs formed in the meat. We find that our simulations accurately model experimentally determined temperature profiles, cooking times, HA spatial distributions and total HA formation in patties that are flipped once during the pan-frying process. For patties flipped every 60 s, the simulations qualitatively agree with experiment in predicting reduced cooking times and HA formation relative to the singly-flipped patties. However, the simulations overestimate the effect of rapid flipping on cooking times and underestimate the effect of flipping on total HAs formed. These results suggest that the dramatic reductions in HA formation due to rapid flipping may be due to factors other than the heating process or that there is a critical feature of the flipping process that is not captured in our model.

Integrin- and cadherin-mediated induction of the matrix metalloprotease matrilysin in cocultures of malignant oral squamous cell carcinoma cells and dermal fibroblasts

Matrilysin is a matrix metalloprotease (MMP) overexpressed in a number of cancers including skin, head and neck squamous cell carcinomas, and prostate and colon adenocarcinomas. Matrilysin has been shown to play a role in the degradation of the basement membrane that separates epithelium from stroma allowing tumor cells to intravasate into the bloodstream and metastasize. Here, we show that an oral squamous cell carcinoma cell line (SCC-25) expresses low levels of promatrilysin when cultured alone. However, when SCC-25 cells are cocultured with human foreskin fibroblasts (HFF), there is a 40-fold induction of promatrilysin expression. We tested whether this induction of promatrilysin expression was due to the release of paracrine factors, cell-cell interactions, or cell-matrix interactions. Our results indicate induced promatrilysin expression is the result of both cell-cell and cell-matrix interactions. We demonstrate that beta1 integrins as well as cadherins, specifically N-cadherin and E-cadherin, are involved in the induction of promatrilysin expression. Our results are of general interest in relation to the regulation of MMP expression through cell surface receptor regulation. Further investigation may lead to the identification of novel targets for suppression of invasion and metastasis in oral tumors.

Chemical and radiation environmental risk management: differences, commonalities, and challenges

Driven by differing statutory mandates and programmatic separation of regulatory responsibilities between federal, state, and tribal agencies, distinct chemical and radiation risk management strategies have evolved. In the field this separation poses real challenges since many of the major environmental risk management decisions we face today require the evaluation of both types of risks. Over the last decade, federal, state, and tribal agencies have continued to discuss their different approaches and explore areas where their activities could be harmonized. The current framework for managing public exposures to chemical carcinogens has been referred to as a "bottom up approach." Risk between 10(-4) and 10(-6) is established as an upper bound goal. In contrast, a "top down" approach that sets an upper bound dose limit and couples with site specific As Low As Reasonably Achievable Principle (ALARA), is in place to manage individual exposure to radiation. While radiation risk are typically managed on a cumulative basis, exposure to chemicals is generally managed on a chemical-by-chemical, medium-by-medium basis. There are also differences in the nature and size of sites where chemical and radiation contamination is found. Such differences result in divergent management concerns. In spite of these differences, there are several common and practical concerns among radiation and chemical risk managers. They include 1) the issue of cost for site redevelopment and long-term stewardship, 2) public acceptance and involvement, and 3) the need for flexible risk management framework to address the first two issues. This article attempts to synthesize key differences, opportunities for harmonization, and challenges ahead.

An examination of the educational needs for environmental health and protection

The practice of environmental health and protection is at a crossroads. Expanded responsibilities throughout this nation's agencies, prescriptive statutory mandates, and shrunken resources for fundamental public health services have combined to change the infrastructure and the workforce. This article presents the results of the Crossroads Colloquium, a forum of leaders in environmental health, convened to address the educational needs of the workforce. Major recommendations from the Crossroads Colloquium include redefining training by moving from discipline-specific to multidisciplinary training, developing collaborations among agencies, academia, and industry for training and education, and providing opportunities ranging from distance education to graduate degree programs.

N-Cadherin expression in human prostate carcinoma cell lines. An epithelial-mesenchymal transformation mediating adhesion withStromal cells

In human prostate adenocarcinoma, an association between loss of E-cadherin, increased Gleason score, and extracapsular dissemination has been observed. Further characterization of the E-cadherin/catenin phenotype of human prostate carcinoma cell lines showed loss of E-cadherin and expression of N-cadherin in poorly differentiated prostate carcinoma cell lines (PC-3N derived from PC-3, PC-3, and JCA1). We showed that N-cadherin is concentrated at sites of cell-cell contact in PC-3N cellular extensions. N-cadherin was also expressed in prostate stromal fibroblasts both in vitro and in prostate tissue. Co-cultures of prostate stromal fibroblasts and PC-3N cells showed the immunolocalization of N-cadherin in intercellular contacts. In addition, the isoform expression of the cadherin binding protein p120(ctn) differed in relation to the expression of E- versus N-cadherin by the prostate carcinoma cell lines. The p100 isoform was more highly expressed in E-cadherin-positive carcinoma cell lines, whereas p120 was predominantly expressed only in N-cadherin-positive prostate carcinoma cell lines and prostate stromal fibroblasts. The N-cadherin-positive carcinoma cell line, PC-3N, displayed aggressive invasion into the surface of the diaphragm muscle after intraperitoneal injection of SCID mice. The gain of N-cadherin and loss of E-cadherin by invasive prostate carcinoma cell lines suggests a progression from an epithelial to a mesenchymal phenotype, which may allow for their interaction with surrounding stromal fibroblasts and facilitate metastasis.

Chemical factors in the action of phosphoramidic mustard alkylating anticancer drugs: roles for computational chemistry

The nitrogen mustard based DNA alkylating agents were the first effective anticancer agents and remain important drugs against many forms of cancer. More than fifty years of research on the nitrogen mustards has yielded a broad range of therapeutically useful compounds and a detailed knowledge of the biochemical mechanism of these drugs. Nevertheless, there is much ongoing research on the phosphosphoramidic and other nitrogen mustards to increase their potency and reduce their toxic and mutagenic side effects. To understand the existing nitrogen mustards, and to design the next generation of these drugs, more knowledge is needed about the effects of chemical modifications on their activation and selectivity. Because of the existing knowledge of these drugs, atomic-level chemical modeling can play an important role in the understanding of the phosphoramidic mustard compounds; however, it has not proved straight forward to directly relate the activity of these mustards with simple chemical properties such as bond lengths or atomic charges. Instead, quantum chemical simulations will be required to simulate the activation and alkylation reactions of these compounds, which will require the newest generation of quantum chemical and solvent modeling methods. Additionally, molecular dynamics simulations of the adducted DNA can provide data on the factors favoring crosslinking and its structural consequences. This review summarizes the extensive literature on the metabolism, activation, and action of the phosphoramidic mustards, with an emphasis on the roles that chemical modeling has and will play in the development of this important class of drugs.

The environmental Web: a national profile of the state infrastructure for environmental health and protection

The success of our national environmental policies depends upon the capacity of states to implement them. This article presents the findings of an examination of the state level organization of environmental health and protection services. The goals of the project were to conduct a descriptive analysis of the structure, functions, and funding of state environmental health and protection services, and to examine the impact of the major federal environmental statutes on the organization of the state infrastructure. Future environmental progress will depend upon an improved understanding of the relationship between human health and the environment. This will require a commitment to improving the public health training of environmental professionals, and improved cooperation between health and environmental agencies to assure that they do not lose sight of their fundamental mission--the protection of public health.

Development of a Dietary Exposure Potential Model for evaluating dietary exposure to chemical residues in food

The Dietary Exposure Potential Model (DEPM) is a computer-based model developed for estimating dietary exposure to chemical residues in food. The DEPM is based on food consumption data from the 1987-1988 Nationwide Food Consumption Survey (NFCS) administered by the United States Department of Agriculture (USDA) and on residue data from government-sponsored monitoring programs. Foods reported in the NFCS were categorized into exposure core foods (ECFs). A computer program for DOS-based personal computers was developed to link consumption of the ECFs with residue values observed in the foods. The data files utilized by the DEPM were designed in dBASE IV with FoxPro for Windows applications programs for queries and reporting. The program calculates exposure estimates for categories of core foods, such as grain dishes, fruits, or vegetables; for individual core foods, such as wheat and apple combination dishes; and for individual foods, such as apples or carrots. The program, residue summary databases, and core food consumption database permit the analyst to evaluate potential exposure of several population groups to various chemicals via the diet. The DEPM is not intended for risk assessments, but is a suitable tool for identifying data gaps and establishing priorities for research, and for identifying potentially significant foods for human exposure monitoring.

Bioequivalence: individual and population compartmental modeling compared to the noncompartmental approach

PURPOSE

The purpose of this study were to evaluate the use of individual compartmental and population compartmental methods for bioequivalence determination, and to determine their utility as adjuncts to the current methods used for bioequivalence assessment.

METHODS

Data from three bioequivalence studies of chlorthalidone were analyzed with PCNONLIN using individual compartmental modeling and NONMEM for population analyses. These results were compared with results obtained from the traditional noncompartmental or SHAM (slopes, heights, areas, and moments) approach for bioequivalence assessment and the 90% confidence interval procedure.

RESULTS

Individual compartmental modeling and population compartmental modeling techniques performed well on this routine set of bioequivalence data which displayed simple pharmacokinetic properties. A direct assessment of the analysis methods was made by comparing the final estimates and 90% confidence intervals for the test to reference ratios (T/R) of AUC and CMAX. The final estimates and 90% confidence intervals for AUC T/R and CMAX T/R were similar and suggest consistency of results, independent of the method used.

CONCLUSIONS

These results demonstrate the utility of modeling techniques as adjuncts to the traditional noncompartmental approach for bioequivalence determination.

Specific attachment and migration of human astrocytoma cells on human but not murine laminin

Attachment sites and biological functions of laminin isolated from murine EHS sarcoma have been well studied. Recently several variants of laminin including human placental laminin have been shown to be distinct from EHS-laminin. This study was undertaken to determine attachment, proliferation, and migration phenomena of human astrocytoma cell lines to human and murine sarcoma EHS-laminin. Using short-term attachment assays human placental laminin was shown to be the better substrate for cell adhesion. EHS-laminin mediated approximately 30-50% of the effect observed on human laminin. The astrocytoma cells expressed beta 1, beta 3, and beta 4 subunit mRNA as determined by RT-PCR. Anti-beta 1 antibodies blocked adhesion to EHS-laminin, but antibodies against beta 1, beta 4, and alpha v subunits were all ineffective in blocking adhesion to human laminin. A migration assay showed that astrocytoma cells on human laminin dispersed from a central seeding area, while cells on EHS-laminin remained where they were seeded. The pattern of dispersion could not be accounted for by changes in growth rates of astrocytoma cells on the different proteins, since both cell lines grew equally well on the two laminins. We conclude that unique epitopes on human laminin are recognized by novel receptors on human astrocytoma cells which confer a migratory phenotype to the cells.