Activity of pemetrexed in pre-clinical chordoma models and humans

Chordomas are rare slow growing tumors, arising from embryonic remnants of notochord with a close predilection for the axial skeleton. Recurrence is common and no effective standard medical therapy exists. Thymidylate synthase (TS), an intracellular enzyme, is a key rate-limiting enzyme of DNA biosynthesis and repair which is primarily active in proliferating and metabolically active cells. Eighty-four percent of chordoma samples had loss of TS expression which may predict response to anti-folates. Pemetrexed suppresses tumor growth by inhibiting enzymes involved in folate metabolism, resulting in decreased availability of thymidine which is necessary for DNA synthesis. Pemetrexed inhibited growth in a preclinical mouse xenograft model of human chordoma. We report three cases of metastatic chordoma that had been heavily treated previously with a variety of standard therapies with poor response. In two cases, pemetrexed was added and objective responses were observed on imaging with one patient on continuous treatment for > 2 years with continued shrinkage. One case demonstrated tumor growth after treatment with pemetrexed. The two cases which had a favorable response had a loss of TS expression, whereas the one case with progressive disease had TS present. These results demonstrate the activity of pemetrexed in recurrent chordoma and warrant a prospective clinical trial which is ongoing (NCT03955042).

Mapping the landscape of genetic dependencies in chordoma

Identifying the spectrum of genes required for cancer cell survival can reveal essential cancer circuitry and therapeutic targets, but such a map remains incomplete for many cancer types. We apply genome-scale CRISPR-Cas9 loss-of-function screens to map the landscape of selectively essential genes in chordoma, a bone cancer with few validated targets. This approach confirms a known chordoma dependency, TBXT (T; brachyury), and identifies a range of additional dependencies, including PTPN11, ADAR, PRKRA, LUC7L2, SRRM2, SLC2A1, SLC7A5, FANCM, and THAP1. CDK6, SOX9, and EGFR, genes previously implicated in chordoma biology, are also recovered. We find genomic and transcriptomic features that predict specific dependencies, including interferon-stimulated gene expression, which correlates with ADAR dependence and is elevated in chordoma. Validating the therapeutic relevance of dependencies, small-molecule inhibitors of SHP2, encoded by PTPN11, have potent preclinical efficacy against chordoma. Our results generate an emerging map of chordoma dependencies to enable biological and therapeutic hypotheses.

Abstract 4865: Mechanisms of EGFR inhibitor sensitivity and resistance in chordoma

Target discovery studies have identified EGFR inhibition as a promising therapeutic strategy in chordoma, motivating ongoing clinical trials. Yet EGFR is not mutated in chordoma, leaving the mechanisms associated with EGFR inhibitor (EGFRi) sensitivity and resistance unclear. In this study, we profiled a panel of over 10 chordoma cell lines to categorize their sensitivity to afatinib, a second-generation EGFRi with potency against the wild-type receptor. Several cell lines, including U-CHCF365, UM-Chor1, MUG-Chor1, and U-CH1, were highly sensitive to afatinib in cell viability assays, with absolute IC50 values below 50 nanomolar. In contrast, other chordoma cell lines, including UM-Chor5C and U-CHCF359B, exhibited limited response to EGFRi at concentrations exceeding 1 micromolar. Among sensitive cell lines, we found that afatinib promoted cell death in some cases (e.g., U-CH1) whereas in others it induced a profound cell cycle arrest. Moreover, in U-CH1 cells, acute afatinib treatment enriched a population of drug-tolerant persister cells with a fusiform morphology, potentially indicative of an epithelial-mesenchymal transition. Ongoing studies are focused on understanding the mechanisms of afatinib-induced cell death, drug tolerance, and acquired resistance, with a view to designing rational combination strategies capable of enhancing the magnitude and duration of therapeutic response. In cell lines with matched xenograft models, in vitro responses to afatinib were consistent in vivo. In a panel of 12 chordoma patient-derived xenograft (PDX) models treated with afatinib or cetuximab, differential sensitivity to EGFRi was recapitulated - with EGFRi promoting complete or negligent tumor growth inhibition in sensitive or resistant models, respectively. Finally, we combined drug sensitivity profiling of chordoma cell lines and PDXs with whole-exome and whole-transcriptome sequencing to identify genomic and transcriptomic features associated with sensitivity and resistance to EGFRi in chordoma. Collectively, our data identify a striking degree of differential sensitivity to EGFRi in chordoma, and begin to shed light on factors associated with primary and acquired resistance. These results provide a framework for guiding patient selection and identifying potential combination therapy regimens to improve EGFRi efficacy and address resistance.

Citation Format: Nindo Punturi, Lee Dolat, Joan Levy, Josh Sommer, Daniel M. Freed. Mechanisms of EGFR inhibitor sensitivity and resistance in chordoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4865.

Emerging target discovery and drug repurposing opportunities in chordoma

The development of effective and personalized treatment options for patients with rare cancers like chordoma is hampered by numerous challenges. Biomarker-guided repurposing of therapies approved in other indications remains the fastest path to redefining the treatment paradigm, but chordoma's low mutation burden limits the impact of genomics in target discovery and precision oncology efforts. As our knowledge of oncogenic mechanisms across various malignancies has matured, it's become increasingly clear that numerous properties of tumors transcend their genomes - leading to new and uncharted frontiers of therapeutic opportunity. In this review, we discuss how the implementation of cutting-edge tools and approaches is opening new windows into chordoma's vulnerabilities. We also note how a convergence of emerging observations in chordoma and other cancers is leading to the identification and evaluation of new therapeutic hypotheses for this rare cancer.

Abstract 2564: CDK9 inhibition via KB-0742 is a potential strategy to treat transcriptionally addicted cancers

Lineage-specific transcriptional networks drive cellular differentiation and development. Disruption of these specific cell programs can result in cancer and create a subset of tumors that are “transcriptionally addicted.” Sarcomas, for example, are characterized by an oncogenic fusion protein consisting of a FET family RNA-binding protein fused to a transcription factor (TF). The oncogenic fusions result in a restructuring of the transcriptome promoting cancer. In chordoma, TBXT (brachyury)—normally involved in notochord differentiation—is aberrantly expressed, resulting in promotion of cancer. As these oncogenic TFs are difficult to target directly, we and others have proposed targeting associated transcriptional regulators to inhibit their activity. Cyclin-dependent kinase 9 (CDK9) interacts with TFs to promote activation of target genes and promotes transcription elongation through phosphorylation of RNA polymerase II. We have developed a potent, selective, and orally bioavailable CDK9 inhibitor, KB-0742. Here we present the preclinical activity of KB-0742 in models of sarcoma and chordoma. We first evaluated KB-0742 activity in sarcoma in a 300-immortalized cell line screen containing 18 soft tissue sarcoma cell lines. The median IC50 of the cell lines in the study was 0.8705 µM. Sarcoma cell lines were enriched for sensitivity to KB-0742 with 61% (11/18) of the lines with an IC50 below the median. The 11 cell lines had a median IC50 of 0.679 µM. We then evaluated the activity of KB-0742 in 5 patient-derived cell line (PDC) models, with all 5 showing a cytotoxic response to treatment as measured by negative GRmax values. Last, a single patient-derived organoid (PDO) model of adult rhabdomyosarcoma was evaluated. KB-0742 treatment resulted in an IC50 of 2.75 µM and a max inhibition rate of 98.61%. For chordoma we examined the activity of KB-0742 in vivo using 2 patient-derived xenograft (PDX) models. In model CF466, we observed a dose-dependent response with increased TGI and greater reductions in RNA polymerase II phosphorylation in tumors treated with KB-0742 at 60 mg/kg as compared to 30 mg/kg. We then evaluated KB-0742 as a single agent and in combination with afatinib in the model CF539. KB-0742 as a single agent showed similar TGI activity as afatinib, whereas the combination showed increased response as compared to the two single-agent arms.

These data show that transcriptionally addicted tumors are sensitive to CDK9 inhibition via KB-0742 treatment, and support the continued development of our compound to potentially treat sarcoma and chordoma. KB-0742 is currently being evaluated in a phase 1/2 clinical trial (NCT04718675) for relapsed or refractory solid tumors or non-Hodgkin lymphoma. Once a recommended phase 2 dose is established, expansion cohorts for patients with sarcoma, chordoma, and other transcriptionally addicted tumors may be opened.

Citation Format: Melinda A. Day, Douglas C. Saffran, Tressa Hood, Nikolaus Obholzer, Akanksha Pandey, Charles Y. Lin, Pavan Kumar, Daniel M. Freed, Jorge DiMartino. CDK9 inhibition via KB-0742 is a potential strategy to treat transcriptionally addicted cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2564.

Abstract LB-287: Combination therapies with CDK4/6 inhibitors to treat KRAS-mutant pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) patients have a dismal five-year survival rate of just eight percent in the advanced metastatic setting. Outcomes with standard chemotherapy regimens are less than ideal; therefore, the development of targeted therapies for the treatment of PDAC is a significant unmet clinical need. The two most frequent genetic events in PDAC (mutational activation of KRAS and loss of the tumor suppressor CDKN2A) converge on activation of the kinases CDK4 and CDK6, which promote G1 cell cycle progression. While clinically relevant agents directly targeting KRAS in PDAC remain elusive, pharmacologic restoration of CDKN2A function by inhibition of CDK4/6 may be an effective anti-KRAS therapeutic strategy. Supporting this hypothesis, we found that CDK4/6 inhibitors (e.g., palbociclib, abemaciclib, lerociclib) elicited single-agent activity in a subset of tested PDAC cell lines. However, using Reverse Phase Protein Array (RPPA), we observed widespread compensatory changes that overcome CDK4/6 inhibition, including increased anti-apoptotic protein expression, PI3K-mTOR and ERK MAPK signaling. Concurrent treatment with the potent and selective ERK1/2 inhibitor (ERKi) SCH772984 reversed resistance and increased sensitivity to palbociclib. This combination caused synergistic reduction in anchorage-dependent cell growth, and increased apoptosis, G1 arrest, and senescence. In an organoid model of pancreatic cancer, cell viability was synergistically reduced and caspase activation enhanced. We have also evaluated the combination of ERKi with palbociclib or the clinical-stage CDK4/6 inhibitor lerociclib (G1T38) in mouse models of PDAC, supporting our initiation of a phase Ib clinical trial of the ERK inhibitor ulixertinib/BVD-523 in combination with palbociclib in advanced metastatic pancreatic cancer (NCT03454035). Next, we sought to identify additional genes that regulate sensitivity to CDK4/6 inhibition. Using a CRISPR/Cas9 loss-of-function screen, we individually silenced expression of 2500 genes from the “druggable genome” in combination with palbociclib in six KRAS-mutant pancreatic and two KRAS-mutant colorectal cancer cell lines. We identified a wide array of genes that enhanced growth suppression in combination, centered around diverse signaling nodes including PI3K-AKT-mTOR signaling, cell cycle regulation and mitosis, SRC family kinase signaling, cell metabolism and biosynthesis, chromosome regulation and maintenance, and DNA damage & repair pathways, suggesting novel small molecule combinations to overcome de novo or acquired CDK4/6 inhibitor resistance in the clinic. We also identified genes whose loss imparts a survival advantage, suggesting possible resistance mechanisms to single-agent CDK4/6 inhibition. In total, these data suggest that CDK4/6 inhibitors alone, or in combination, may benefit PDAC patients clinically.

Citation Format: Craig M. Goodwin, Sehrish Javaid, Andrew M. Waters, Bjoern Papke, Runying Yang, Mariaelena Pierobon, Daniel M. Freed, Patrick J. Roberts, Adrienne D. Cox, Kris C. Wood, Emanuel F. Petricoin, Autumn J. McRee, Channing J. Der. Combination therapies with CDK4/6 inhibitors to treat KRAS-mutant pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-287.

Abstract 4732: CDK4/6 inhibition with lerociclib (G1T38) enhances response to PI3K or ERK inhibitors in high-throughput, ex vivo pancreatic PDX screens

Introduction: In pancreatic ductal adenocarcinoma (PDAC), mutations in KRAS and deletion or promoter methylation of the CDKN2A gene - resulting in deregulation of the p16/CDK4/CDK6/RB axis - each occur in over 90% of cases. Therefore, combination therapy approaches targeting KRAS effectors and CDK4/6 may be a promising treatment strategy in a majority of PDAC patients. Lerociclib (G1T38) is an oral and selective CDK4/6 inhibitor in clinical development as a potential backbone therapy for multiple combination regimens in cancer. Here, we used a powerful and reliable ex vivo drug screening platform, the live tissue sensitivity assay (LTSA), to evaluate the ability of lerociclib to synergize with inhibitors of KRAS effectors across a panel of 24 well-characterized PDAC patient-derived xenografts (PDXs).

Methods: PDX tumors were sectioned into uniform tissue slices at 200 µm thickness and arrayed in 96-well plates. For each PDX model, tumor tissue slices were treated with 0.3 µM, 1 µM, and 3 µM of lerociclib, alone and in combination with identical concentrations of a PI3K (pictilisib), mTOR (AZD2014), MEK (trametinib), ERK (ulixertinib), BRAF (vemurafenib) or EGFR (erlotinib) inhibitor for 72 hours. The viabilities of individual tissue slices were measured with PrestoBlue® reagent. A quantitative drug response analysis approach was implemented in which “responder” PDXs were defined as those exhibiting a statistically significant reduction in area under the dose-response curve (AUC) for the combination treatment compared to the most efficacious single agent. Statistical significance was defined as p < 0.05 using Student’s t-test.

Results: Treatment of 24 PDAC PDXs using the LTSA revealed a range of sensitivities to each inhibitor as a single agent. When KRAS effectors and CDK4/6 were inhibited in tandem, statistically significant (p < 0.05) enhancements of efficacy were observed when lerociclib was added to pictilisib (21% of PDX models tested), ulixertinib (15%), vemurafenib (10%), erlotinib (5%), trametinib (4%), or AZD2014 (4%). These ex vivo data narrowed the focus of follow-up in vivo work; studies of PDX models in mice treated with lerociclib +/- pictilisib or ulixertinib are ongoing to validate these results. Moreover, differential gene expression and mutational analysis for responders versus non-responders identified through the PDAC PDX LTSA platform are underway, to elucidate molecular factors that predict tumor response or enrich for populations that are sensitive to CDK4/6 and PI3K/ERK inhibitors.

Conclusion: The LTSA platform was used to evaluate drug combinations in viable, PDX tumor tissue. We found that lerociclib significantly enhances the response to PI3K or ERK inhibition in a substantial proportion of the tested PDAC PDXs as measured by AUC analysis in the LTSA platform, supporting future clinical evaluation of these combinations.

Citation Format: Bingbing Dai, Daniel M. Freed, Jessica A. Sorrentino, Jithesh Jose Augustine, Tara G. Hughes, Ya'an Kang, Patrick J. Roberts, Jason B. Fleming, Michael P. Kim. CDK4/6 inhibition with lerociclib (G1T38) enhances response to PI3K or ERK inhibitors in high-throughput, ex vivo pancreatic PDX screens [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4732.

Abstract 4415: CDK4/6 inhibition with lerociclib (G1T38) delays acquired resistance to targeted therapies in preclinical models of non-small cell lung cancer

Tyrosine kinase inhibitors (TKIs) targeting oncogenes such as EGFR, ALK, or RET have dramatically improved anti-tumor efficacy in patients with non-small cell lung cancer (NSCLC). Despite the significant clinical benefit offered by these agents, tumor responses to single-agent TKIs nevertheless remain limited in their magnitude and duration. Here we investigate combination therapy approaches with lerociclib (G1T38), a selective, oral, and potential best-in-class inhibitor of cyclin-dependent kinases 4 and 6 (CDK4/6). Consistent with previous studies reporting frequent cell-cycle gene alterations in NSCLC, we show that lerociclib synergizes with TKIs targeting EGFR, ALK, and RET in lung cancer cell lines and enhances the efficacy of osimertinib and crizotinib in PDX models harboring EGFR or ALK mutations, respectively. Moreover, in a well-characterized murine xenograft model of EGFR-mutant NSCLC, seven days of treatment with a clinically-relevant dose of osimertinib (25 mg/kg p.o. QDx7) resulted in 60% complete tumor responses, versus 100% complete tumor responses in the osimertinib plus lerociclib (25 mg/kg osi + 100 mg/kg lero, p.o. QDx7) group. Strikingly, complete tumor responses in the combination group persisted through an additional 35 days (or more) of observation, by which time all tumors in the osimertinib monotherapy group had re-emerged - suggesting a role for lerociclib in extending the duration of antitumor response. Based on this result, we assessed the ability of lerociclib to delay the emergence of resistance by chronically treating NSCLC cell lines with TKI +/- lerociclib. These experiments revealed that combination treatment with lerociclib significantly delayed acquired TKI resistance in multiple NSCLC cell lines. The same result was achieved in vivo in an EGFR-mutant NSCLC xenograft model known to develop resistance to EGFR TKI therapy, wherein combination treatment with lerociclib delayed the outgrowth of osimertinib-resistant tumors. Studies to characterize the mechanism by which lerociclib delays TKI resistance in NSCLC are ongoing. Finally, we addressed whether combination therapy with lerociclib can treat TKI resistance after it develops. In EGFR-mutant NSCLC xenografts harboring MET amplification - one of the more common mechanisms of resistance observed to EGFR TKIs in the clinic - the combination of lerociclib plus osimertinib caused significant tumor growth inhibition (90%) compared to osimertinib monotherapy (34%) after 46 days of continuous daily dosing. Collectively, our results suggest a compelling rationale for utilizing lerociclib as a backbone therapy for multiple combination regimens in NSCLC. A phase 1b/2 clinical trial evaluating lerociclib plus osimertinib in EGFR-mutant NSCLC is ongoing (NCT03455829).

Citation Format: Daniel M. Freed, Claire R. Hall, Jay C. Strum, Patrick J. Roberts. CDK4/6 inhibition with lerociclib (G1T38) delays acquired resistance to targeted therapies in preclinical models of non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4415.

Regulation of Kinase Activity in the Caenorhabditis elegans EGF Receptor, LET-23

In the active HER receptor dimers, kinases play distinct roles; one is the catalytically active kinase and the other is its allosteric activator. This specialization enables signaling by the catalytically inactive HER3, which functions exclusively as an allosteric activator upon heterodimerization with other HER receptors. It is unclear whether the allosteric activation mechanism evolved before HER receptors functionally specialized. We determined the crystal structure of the kinase domain of the only EGF receptor in Caenorhabditis elegans, LET-23. Our structure of a non-human EGFR kinase reveals autoinhibitory features conserved in the human counterpart. Strikingly, mutations within the putative allosteric dimer interface abrogate activity of the isolated LET-23 kinase and of the full-length receptor despite these regions being only partially conserved with human EGFR. Our results indicate that ancestral EGFRs have built-in features that poise them for allosteric activation that could facilitate emergence of the catalytically dead, yet functional, orthologs.

EGFR Ligands Differentially Stabilize Receptor Dimers to Specify Signaling Kinetics

Epidermal growth factor receptor (EGFR) regulates many crucial cellular programs, with seven different activating ligands shaping cell signaling in distinct ways. Using crystallography and other approaches, we show how the EGFR ligands epiregulin (EREG) and epigen (EPGN) stabilize different dimeric conformations of the EGFR extracellular region. As a consequence, EREG or EPGN induce less stable EGFR dimers than EGF-making them partial agonists of EGFR dimerization. Unexpectedly, this weakened dimerization elicits more sustained EGFR signaling than seen with EGF, provoking responses in breast cancer cells associated with differentiation rather than proliferation. Our results reveal how responses to different EGFR ligands are defined by receptor dimerization strength and signaling dynamics. These findings have broad implications for understanding receptor tyrosine kinase (RTK) signaling specificity. Our results also suggest parallels between partial and/or biased agonism in RTKs and G-protein-coupled receptors, as well as new therapeutic opportunities for correcting RTK signaling output.

The Dark Side of Cell Signaling: Positive Roles for Negative Regulators

Cell signaling is dominated by analyzing positive responses to stimuli. Signal activation is balanced by negative regulators that are generally considered to terminate signaling. Rather than exerting only negative effects, however, many such regulators play important roles in enhancing cell-signaling control. Considering responses downstream of selected cell-surface receptors, we discuss how receptor internalization affects signaling specificity and how rapid kinase/phosphatase and GTP/GDP cycles increase responsiveness and allow kinetic proofreading in receptor signaling. We highlight the blurring of distinctions between positive and negative signals, recasting signal termination as the response to a switch-like transition into a new cellular state.

Deletion Mutations Keep Kinase Inhibitors in the Loop

Effective clinical application of conformationally selective kinase inhibitors requires tailoring drug choice to the tumor's activating mutation(s). In this issue of Cancer Cell, Foster et al. (2016) describe how activating deletions in BRAF, EGFR, and HER2 cause primary resistance to common inhibitors, suggesting strategies for improved inhibitor selection.

Ligand regulation of a constitutively dimeric EGF receptor

Ligand-induced receptor dimerization has traditionally been viewed as the key event in transmembrane signalling by epidermal growth factor receptors (EGFRs). Here we show that the Caenorhabditis elegans EGFR orthologue LET-23 is constitutively dimeric, yet responds to its ligand LIN-3 without changing oligomerization state. SAXS and mutational analyses further reveal that the preformed dimer of the LET-23 extracellular region is mediated by its domain II dimerization arm and resembles other EGFR extracellular dimers seen in structural studies. Binding of LIN-3 induces only minor structural rearrangements in the LET-23 dimer to promote signalling. Our results therefore argue that EGFR can be regulated by allosteric changes within an existing receptor dimer--resembling signalling by insulin receptor family members, which share similar extracellular domain compositions but form covalent dimers.

Putting together structures of epidermal growth factor receptors

Numerous crystal structures have been reported for the isolated extracellular region and tyrosine kinase domain of the epidermal growth factor receptor (EGFR) and its relatives, in different states of activation and bound to a variety of inhibitors used in cancer therapy. The next challenge is to put these structures together accurately in functional models of the intact receptor in its membrane environment. The intact EGFR has been studied using electron microscopy, chemical biology methods, biochemically, and computationally. The distinct approaches yield different impressions about the structural modes of communication between extracellular and intracellular regions. They highlight possible differences between ligands, and also underline the need to understand how the receptor interacts with the membrane itself.

Monomeric TonB and the Ton box are required for the formation of a high-affinity transporter-TonB complex

The energy-dependent uptake of trace nutrients by Gram-negative bacteria involves the coupling of an outer membrane transport protein to the transperiplasmic protein TonB. In this study, a soluble construct of Escherichia coli TonB (residues 33-239) was used to determine the affinity of TonB for outer membrane transporters BtuB, FecA, and FhuA. Using fluorescence anisotropy, TonB(33-239) was found to bind with high affinity (tens of nanomolar) to both BtuB and FhuA; however, no high-affinity binding to FecA was observed. In BtuB, the high-affinity binding of TonB(33-239) was eliminated by mutations in the Ton box, which yield transport-defective protein, or by the addition of a Colicin E3 fragment, which stabilizes the Ton box in a folded state. These results indicate that transport requires a high-affinity transporter-TonB interaction that is mediated by the Ton box. Characterization of TonB(33-239) using double electron-electron resonance (DEER) demonstrates that a significant population of TonB(33-239) exists as a dimer; moreover, interspin distances are in approximate agreement with interlocked dimers observed previously by crystallography for shorter TonB fragments. When the TonB(33-239) dimer is bound to the outer membrane transporter, DEER shows that the TonB(33-239) dimer is converted to a monomeric form, suggesting that a dimer-monomer conversion takes place at the outer membrane during the TonB-dependent transport cycle.

Lipid and membrane mimetic environments modulate spin label side chain configuration in the outer membrane protein A

In the present work, the factors that determine EPR line shapes from spin labels at the protein-hydrocarbon interface of a β-barrel membrane protein are examined. The EPR spectra from hydrocarbon facing sites in the outer membrane protein A (OmpA) are highly dependent upon the detergent or lipid into which OmpA is reconstituted. In general, line shapes at these sites are correlated with the solvent accessibility in the supporting amphiphile. A notable exception is CHAPS, which yields rigid limit EPR line shapes for labels at every position along a transmembrane β-strand in OmpA. EPR line shapes from the surface of OmpA are not strongly influenced by steric interference with neighboring side chains, but are modulated by solutes that should interact with hydrophobic surfaces. These results suggest that differences in EPR spectra in different supporting environments are not the result of differences in protein dynamics but are a result of different configurations or rotameric states that are assumed by the label. This conclusion is supported by distance measurements across the OmpA β-barrel, which indicate that labels yielding more motionally restricted line shapes interact more closely with the protein surface. These results have implications for the use of spin-label-derived distance constraints in protein structure determination and demonstrate that spin labels on membrane proteins provide a highly sensitive probe for the environment surrounding a membrane protein.

Molecular origin of electron paramagnetic resonance line shapes on β-barrel membrane proteins: the local solvation environment modulates spin-label configuration

In this work, electron paramagnetic resonance (EPR) spectroscopy and X-ray crystallography were used to examine the origins of EPR line shapes from spin-labels at the protein-lipid interface on the β-barrel membrane protein BtuB. Two atomic-resolution structures were obtained for the methanethiosulfonate spin-label derivatized to cysteines on the membrane-facing surface of BtuB. At one of these sites, position 156, the label side chain resides in a pocket formed by neighboring residues; however, it extends from the protein surface and yields a single-component EPR spectrum in the crystal that results primarily from fast rotation about the fourth and fifth bonds linking the spin-label to the protein backbone. In lipid bilayers, site 156 yields a multicomponent spectrum resulting from different rotameric states of the labeled side chain. Moreover, changes in the lipid environment, such as variations in bilayer thickness, modulate the EPR spectrum by modulating label rotamer populations. At a second site, position 371, the labeled side chain interacts with a pocket on the protein surface, leading to a highly immobilized single-component EPR spectrum that is not sensitive to hydrocarbon thickness. This spectrum is similar to that seen at other sites that are deep in the hydrocarbon, such as position 170. This work indicates that the rotameric states of spin-labels on exposed hydrocarbon sites are sensitive to the environment at the protein-hydrocarbon interface, and that this environment may modulate weak interactions between the labeled side chain and the protein surface. In the case of BtuB, lipid acyl chain packing is not symmetric around the β-barrel, and EPR spectra from labeled hydrocarbon-facing sites in BtuB may reflect this asymmetry. In addition to facilitating the interpretation of EPR spectra of membrane proteins, these results have important implications for the use of long-range distance restraints in protein structure refinement that are obtained from spin-labels.

Conformational exchange in a membrane transport protein is altered in protein crystals

Successful macromolecular crystallography requires solution conditions that may alter the conformational sampling of a macromolecule. Here, site-directed spin labeling is used to examine a conformational equilibrium within BtuB, the Escherichia coli outer membrane transporter for vitamin B(12). Electron paramagnetic resonance (EPR) spectra from a spin label placed within the N-terminal energy coupling motif (Ton box) of BtuB indicate that this segment is in equilibrium between folded and unfolded forms. In bilayers, substrate binding shifts this equilibrium toward the unfolded form; however, EPR spectra from this same spin-labeled mutant indicate that this unfolding transition is blocked in protein crystals. Moreover, crystal structures of this spin-labeled mutant are consistent with the EPR result. When the free energy difference between substates is estimated from the EPR spectra, the crystal environment is found to alter this energy by 3 kcal/mol when compared to the bilayer state. Approximately half of this energy change is due to solutes or osmolytes in the crystallization buffer, and the remainder is contributed by the crystal lattice. These data provide a quantitative measure of how a conformational equilibrium in BtuB is modified in the crystal environment, and suggest that more-compact, less-hydrated substates will be favored in protein crystals.

Coexistence of Alzheimer disease neuropathology with herpes simplex encephalitis

Several unusual features were observed during routine histopathological confirmation of a clinical diagnosis of Alzheimer's disease (AD) in an 85-year-old, right-handed, married male. The patient presented with a 12-year history of slowly progressive cognitive impairment, which increased in severity just prior to death. Detailed postmortem examination of the frontal lobes revealed a significant number of neuritic plaques and neurofibrillary tangles. Multifocal spongiform encephalopathic changes, mononuclear perivascular infiltrates, subcortical demyelination and gliosis were also found. Of particular interest were well-defined neuronal and astrocytic intranuclear inclusion bodies (Cowdry type I and I), suggestive of viral disease. Electron microscopy, immunohistochemical and immunohistofluorescent studies confirmed a Herpes simplex type I encephalitis (HSV-I). These histological results and the clinical history of progression suggest that reactivation of a latent viral infection may have contributed to the rapid progression of dementia prior to death. The present analysis underscores the fact that multiple etiologic factors may act simultaneously to produce dementia. While one such process may be identified or diagnosed (in the present case AD), it is necessary to be open to the possibility that another mechanism may come into play during the time course of that illness. A differential diagnosis may be difficult when the symptoms of the two disease processes are very similar. Such may be the case if there is reactivation of a previously undiagnosed herpes virus infection. With the development of PCR and in situ hybridization diagnosis will be simplified and more definitive.

Lay person-based screening for early detection of Alzheimer's disease: development and validation of an instrument

Symptoms of cognitive impairment reported to telephone interviewers by caregivers of 272 patients were analyzed with respect to research diagnoses of dementia. All patients received neuropsychological evaluation for establishing the research diagnoses. A data mining program that used machine learning algorithms produced an optimized binary decision tree for differentiating patient groups according to all available information. The results of this analysis were used to help four dementia experts create a dementia screening instrument amenable to application and scoring by nonclinical personnel. The validity of the resulting instrument was then evaluated in an independent sample of 103 patients administered neuropsychological testing within the previous 60 days. The psychometric properties of the empirically derived scale and its performance for discriminating control from probable or possible Alzheimer's patients indicate strong potential for use as a dementia screener for the general population.

Traumatic brain injury: influence of blood alcohol level on post-acute cognitive function

Alcohol intoxication frequently contributes to the occurrence of traumatic brain injury. Few studies, however, have examined whether acute pre-injury alcohol intoxication or premorbid history of alcohol abuse exacerbate cognitive impairments that commonly result from traumatic brain injury. This study examined the influence of blood alcohol level at time of hospital admission on cognitive functioning during the post-acute stage of recovery from traumatic brain injury. After controlling for pre-injury history of alcohol abuse, hospital admission blood alcohol level was predictive of poorer delayed verbal memory, greater decrement in verbal memory over time, and poorer visuospatial functioning. Moreover, there were non-significant trends for higher blood alcohol levels to predict poorer performance on measures of immediate verbal memory and perseveration.

An integrated program for dementia evaluation and care management

The growth of the geriatric population and the emergence of managed care dictate new approaches to dementia care. Management of Alzheimer's disease (AD) is a critical issue for health care policy as well as quality of life for patients and caregivers. The Alzheimer's Disease Education Program (ADEP) seeks to improve the quality of care for individuals with AD and to reduce the burden of caregiving experienced by families. Objectives of ADEP include early detection of AD through dementia screening followed by caregiver education and support. This article outlines an effective method of dementia evaluation and management.

The P1 component of the middle latency auditory potential may differentiate a brainstem subgroup of Alzheimer disease

The P1 component of the middle latency auditory evoked potential (MLAEP) was found to be absent in 47.5% of 101 patients with Alzheimer disease (AD). Lack of a P1 component recently has been associated with a more rapid decline in cognitive performance. The blink reflex (BR) was tested in 36 patients with probable AD and 17 elderly control subjects. All subjects also underwent P1 recording. Patients lacking a P1 potential showed a significant increase in latency of the contralateral R2 response of the BR. The P1 component and the R2 response may differentiate a subgroup of AD patients with involvement of the brainstem, especially the reticular formation.

The P1 component of the middle latency auditory evoked potential predicts a practice effect during clinical trials in Alzheimer's disease

Thirty-five patients with probable Alzheimer's disease who were enrolled in an experimental drug trial of linopirdine underwent repeated testing that included recording the middle latency auditory evoked potential (MLAEP), the Mini-Mental State Examination (MMSE), and the Alzheimer's Disease Assessment Scale Cognitive Subscale (ADASCOG). Patients lacking the P1 component of the MLAEP exhibited a significantly greater decline in cognitive function as measured by the ADASCOG over 56 weeks. This decline appeared to be due to a less robust practice effect, which was maximal in all patients at 16 weeks. At the end of 56 weeks the entire group of patients was near baseline with respect to the ADASCOG. This lack of the annualized decline expected from other longitudinal studies may be explained by practice and placebo effects. The MMSE did not exhibit a practice effect and showed the expected decline in scores.

The middle latency auditory evoked potential may be abnormal in dementia

The P1 potential (50 msec) of the middle latency auditory evoked potential was lacking in 12 of 31 (39%) patients with probable Alzheimer's disease and seven of 12 (58%) demented patients with Parkinson's disease. Component P1 was not present in one normal control subject and one nondemented Parkinson's disease patient. Clinical and experimental evidence suggests that abnormalities of P1 in dementia may be due to cholinergic dysfunction.

Boston Naming Test: shortened versions for use in Alzheimer's disease

Four new 15-item versions of the Boston Naming Test (BNT), a 15-item version used by the Consortium To Establish a Registry for Alzheimer's Disease (CERAD), and three 30-item BNT versions were studied in 26 subjects with Alzheimer's disease (AD) and 26 nondemented, neurologically normal controls. The four 15-item versions were statistically equivalent. On each version, controls performed significantly better than AD subjects, and scores on each could be extrapolated to a complete 60-item BNT score. The CERAD version also differentiated between AD and control subjects, but it was not equivalent to our four versions and could not be as easily extrapolated to a 60-item score. Even and Odd 30-item BNT versions were confirmed to be equivalent, and we further validated a 30-item Empirical Version designed to maximally discriminate between AD and normal subjects. Equivalent 15- or 30-item versions of the BNT will be useful in repeated assessments requiring independent forms of a naming task, as well as in situations where administration of the complete BNT is not practical.

The agraphia of Alzheimer's disease

Hypothesizing that agraphia in Alzheimer's disease (AD) reflects disturbances in multiple cognitive domains, we evaluated writing samples from 33 patients meeting strict criteria for probable AD. We found agraphia to be common on a standard narrative writing task. When compared with 41 education- and age-matched normal control subjects, AD patients had significantly lower writing scores, wrote significantly fewer words, mentioned significantly fewer categories of information, and were significantly more likely to make writing errors. On stepwise regression procedures, neuropsychological measures of visuoperceptual impairment and disease severity were the strongest predictors of agraphia, but other analyses indicated that measures of language, praxis, and attention could also contribute significantly to agraphia. On two writing tasks, we failed to confirm the previous contention that agraphia is a marker for familial AD. However, there was a highly significant interaction between family history, oral naming, and writing: patients with nonfamilial AD, but not those with a family history of dementia, showed a strong correlation between naming and writing performance. We conclude that agraphia in AD can be variously determined and that agraphia is not a reliable marker for familial disease.

Rotary Diamond Chart--a new visual field screening device

The Rotary Diamond Chart (RDC) is presented as a new clinical method suitable for screening general optometry patients for visual field defects. A pilot study was conducted using both the rotary diamond chart and a central 76-point threshold-related screening test (Allergan-Humphrey) on 21 consecutive clinical patients. Full-threshold field testing was then completed on those subjects failing either screening test. The RDC detected five of six visual field defects including one very subtle defect which was not detected by the automated screening test. The sensitivity of the RDC visual field screening assessment was 83.33 percent with a specificity of 100 percent. These results suggest that the RDC is an effective clinical visual field screening test. It is easy for the clinician to use and for the patient to understand.

Stroop Color-Word Test performance in patients with Alzheimer's disease

Patients with Alzheimer's disease (AD) (n = 36) and normal older adults (n = 36) were individually administered the Stroop Color-Word Test. Eight of 36 (22%) AD patients exhibited confusion between the colors blue and green, while no control subject had difficulty distinguishing among the colors. In a second experiment, a subset of the original sample (15 AD patients and 8 control subjects) was retested using the Stroop. Only 2 AD patients showed color confusion on both test occasions, while 7 AD patients exhibited color confusion on one occasion. No control subject exhibited confusion between colors the second time. These results indicate that color confusion in AD patients is inconsistent. Due to the high incidence of color confusion in AD patients, the Stroop should be used with caution in patient populations.

Selective attention in Alzheimer's disease: characterizing cognitive subgroups of patients

Picture recognition was studied in 20 patients with AD and in 20 control subjects, using a procedure that matched these groups for initial performance. The groups did not differ significantly in overall forgetting, although 10 patients displayed improved recognition performance 72 hr after learning. These same patients were impaired in a test of attentional focusing, as revealed by post hoc analyses. A predictive experiment involving 20 new patients with AD confirmed the initial findings: a subgroup of patients displayed improved recognition performance 72 hr after learning and impairments in attentional focusing. Neuropsychological tests thus identify a subgroup of patients with impaired selective attention, perhaps related to locus coeruleus neuropathology.

Rate of forgetting in H.M.: 6-month recognition

The picture-recognition performance of H.M. and six control subjects was evaluated 6 months after initial learning, using materials from an earlier study in which H.M. received additional study time in order to equate his yes-no and delayed-match-to-sample (DMS) performance 10 min after learning to that of control subjects. In the study detailed here, 6-month recognition performance was assessed with no intervening exposure to the target items. H.M. performed at chance levels when tested using the standard yes-no recognition procedure. When the yes-no procedure was modified so that distractor stimuli required positive responses, H.M.'s performance was comparable with that of control subjects. In addition, H.M.'s DMS and delayed-nonmatch-to-sample (DNMS) performance were comparable with that of control subjects 6 months after learning. Conclusions regarding H.M.'s 6-month recognition performance are thus dependent on the procedures used to assess memory.

Selective attention in Alzheimer's disease: CSF correlates of behavioral impairments

CSF levels of HVA, 5-HIAA, and free MHPG, the major metabolites of dopamine, serotonin, and norepinephrine respectively, were measured in 22 patients with AD. These 22 patients were also administered tests of picture-recognition and attentional focusing as part of an earlier experiment. A significant association between deficits in attentional focusing and reduced levels of free MHPG in CSF was noted. These results suggest that behavioral measures can identify patients with noradrenergic involvement.

Rate of forgetting in H.M.: 6-month recognition

The picture-recognition performance of H.M. and six control subjects was evaluated 6 months after initial learning, using materials from an earlier study in which H.M. received additional study time in order to equate his yes-no and delayed-match-to-sample (DMS) performance 10 min after learning to that of control subjects. In the study detailed here, 6-month recognition performance was assessed with no intervening exposure to the target items. H.M. performed at chance levels when tested using the standard yes-no recognition procedure. When the yes-no procedure was modified so that distractor stimuli required positive responses, H.M.'s performance was comparable with that of control subjects. In addition, H.M.'s DMS and delayed-nonmatch-to-sample (DNMS) performance were comparable with that of control subjects 6 months after learning. Conclusions regarding H.M.'s 6-month recognition performance are thus dependent on the procedures used to assess memory.

Forgetting in H.M.: a second look

Forgetting was assessed in the amnesic patient H.M. using forced-choice and yes-no picture recognition at four delay intervals: 10 min, 24 hr, 72 hr, and 1 week after learning. In order to make H.M.'s initial recognition performance comparable to that of control subjects who viewed each slide for 1 sec, H.M. viewed each slide for 20 sec. H.M. displayed normal forgetting in forced-choice and yes-no recognition, although he was impaired in yes-no recognition at the 24-hr delay interval. These data contradict Huppert and Piercy's hypothesis that medical temporal-lobe pathology is associated with rapid forgetting.