Patient selection for a developmental therapeutics program using whole genome and Transcriptome analysis.

Introduction Given the high level of uncertainty surrounding the outcomes of early phase clinical trials, whole genome and transcriptome analysis (WGTA) can be used to optimize patient selection and study assignment. In this retrospective analysis, we reviewed the impact of this approach on one such program. Methods Patients with advanced malignancies underwent fresh tumor biopsies as part of our personalized medicine program (NCT02155621). Tumour molecular data were reviewed for potentially clinically actionable findings and patients were referred to the developmental therapeutics program. Outcomes were reviewed in all patients, including those where trial selection was driven by molecular data (matched) and those where there was no clear molecular rationale (unmatched). Results From January 2014 to January 2018, 28 patients underwent WGTA and enrolled in clinical trials, including 2 patients enrolled in two trials. Fifteen patients were matched to a treatment based on a molecular target. Five patients were matched to a trial based upon single-gene DNA changes, all supported by RNA data. Ten cases were matched on the basis of genome-wide data (n = 4) or RNA gene expression only (n = 6). With a median follow-up of 6.7 months, the median time on treatment was 8.2 weeks. Discussion When compared to single-gene DNA-based data alone, WGTA led to a 3-fold increase in treatment matching. In a setting where there is a high level of uncertainty around both the investigational agents and the biomarkers, more data are needed to fully evaluate the impact of routine use of WGTA.

Eye tracking research to answer questions about augmentative and alternative communication assessment and intervention.

Recently, eye tracking technologies (i.e., technologies that automatically track the point of an individual's gaze while that person views or interacts with a visual image) have become available for research purposes. Based on the sampling of the orientation of the individual's eyes, researchers can quantify which locations within the visual image were fixated (viewed), for how long, and how many times. These automated eye tracking research technologies open up a wealth of avenues for investigating how individuals with developmental or acquired communication disabilities may respond to aided augmentative and alternative communication (AAC) systems. In this paper, we introduce basic terminology and explore some of the special challenges of conducting eye tracking research with populations with disabilities who might use AAC, including challenges of inferring attention from the presence of fixation and challenges related to calibration that may result from participant characteristics, behavioral idiosyncracies, and/or the number of calibration points. We also examine how the technology can be applied to ask well-structured experimental questions that have direct clinical relevance, with a focus on the unique contributions that eye tracking research can provide by (a) allowing evaluation of skills in individuals who are difficult to assess via traditional methods, and (b) facilitating access to information on underlying visual cognitive processes that is not accessible via traditional behavioral measures.

A platform for oncogenomic reporting and interpretation.

Manual interpretation of variants remains rate limiting in precision oncology. The increasing scale and complexity of molecular data generated from comprehensive sequencing of cancer samples requires advanced interpretative platforms as precision oncology expands beyond individual patients to entire populations. To address this unmet need, we introduce a Platform for Oncogenomic Reporting and Interpretation (PORI), comprising an analytic framework that facilitates the interpretation and reporting of somatic variants in cancer. PORI integrates reporting and graph knowledge base tools combined with support for manual curation at the reporting stage. PORI represents an open-source platform alternative to commercial reporting solutions suitable for comprehensive genomic data sets in precision oncology. We demonstrate the utility of PORI by matching 9,961 pan-cancer genome atlas tumours to the graph knowledge base, calculating therapeutically informative alterations, and making available reports describing select individual samples.

Elimination of ß-mannose glycan structures in Pichia pastoris.

The methylotrophic yeast, Pichia pastoris, is an important organism used for the production of therapeutic proteins. However, the presence of fungal-like glycans, such as those containing ß-mannose (Man) linkages, can elicit an immune response or bind to Man receptors, thus reducing their efficacy. Recent studies have confirmed that P. pastoris has four genes from the ß-mannosyl transferase (BMT) family and that Bmt2p is responsible for the majority of ß-Man linkages on glycans. While expressing recombinant human erythropoietin (rhEPO) in a developmental glycoengineered strain devoid of BMT2 gene expression, cross-reactivity was observed with an antibody raised against host cell antigens. Treatment of the rhEPO with protein N-glycosidase F eliminated cross-reactivity, indicating that the antigen was associated with the glycan. Thorough analysis of the glycan profile of rhEPO demonstrated the presence of low amounts of α-1,2-mannosidase resistant high-Man glycoforms. In an attempt to eliminate the α-mannosidase resistant glycoforms, we used a systemic approach to genetically knock-out the remaining members of the BMT family culminating in a quadruple bmt2,4,1,3 knock-out strain. Data presented here conclude that the additive elimination of Bmt2p, Bmt3p and Bmt1p activities are required for total abolition of ß-Man-associated glycans and their related antigenicity. Taken together, the elimination of ß-Man containing glycoforms represents an important step forward for the Pichia production platform as a suitable system for the production of therapeutic glycoproteins.

Structural elucidation of an α-1,2-mannosidase resistant oligosaccharide produced in Pichia pastoris.

The N-glycosylation pathway in Pichia pastoris has been humanized by the deletion of genes responsible for fungal-type glycosylation (high mannose) as well as the introduction of heterologous genes capable of forming human-like N-glycosylation. This results in a yeast host that is capable of expressing therapeutic glycoproteins. A thorough investigation was performed to examine whether glycoproteins expressed in glycoengineered P. pastoris strains may contain residual fungal-type high-mannose structures. In a pool of N-linked glycans enzymatically released by protein N-glycosidase from a reporter glycoprotein expressed in a developmental glycoengineered P. pastoris strain, an oligosaccharide with a mass consistent with a Hexose(9)GlcNAc(2) oligosaccharide was identified. When this structure was analyzed by a normal-phase high-performance liquid chromatography (HPLC), its retention time was identical to a Man(9)GlcNAc(2) standard. However, this Hexose(9)GlcNAc(2) oligosaccharide was found to be resistant to α-1,2-mannosidase as well as endomannosidase, which preferentially catabolizes endoplasmic reticulum oligosaccharides containing terminal α-linked glucose. To further characterize this oligosaccharide, we purified the Hexose(9)GlcNAc(2) oligosaccharide by HPLC and analyzed the structure by high-field one-dimensional (1D) and two-dimensional (2D) (1)H NMR (nuclear magnetic resonance) spectroscopy followed by structural elucidation by homonuclear and heteronuclear 1D and 2D (1)H and (13)C NMR spectroscopy. The results of these experiments lead to the identification of an oligosaccharide α-Man-(1 → 2)-ß-Man-(1 → 2)-ß-Man-(1 → 2)-α-Man-(1 → 2) moiety as part of a tri-antennary structure. The difference in enzymatic reactivity can be attributed to multiple ß-linkages on the α-1,3 arm of the Man(9)GlcNAc(2) oligosaccharide.

A combinatorial genetic library approach to target heterologous glycosylation enzymes to the endoplasmic reticulum or the Golgi apparatus of Pichia pastoris.

To humanize the glycosylation pathway in the yeast Pichia pastoris, we developed several combinatorial genetic libraries and used them to properly localize active eukaryotic mannosidases and sugar transferases. Here we report the details of the fusion of up to 66 N-terminal targeting sequences of fungal type II membrane proteins to 33 catalytic domains of heterologous glycosylation enzymes. We show that while it is difficult to predict which leader/catalytic domain will result in the desired activity, analysis of the fusion protein libraries allows for the selection of the leader/catalytic domain combinations that function properly. This combinatorial approach, together with a high-throughput screening protocol, has allowed us to humanize the yeast glycosylation pathway to secrete human glycoprotein with complex N-glycosylation.

Purification process development of a recombinant monoclonal antibody expressed in glycoengineered Pichia pastoris.

A robust and scalable purification process was developed to quickly generate antibody of high purity and sufficient quantity from glycoengineered Pichia pastoris fermentation. Protein A affinity chromatography was used to capture the antibody from fermentation supernatant. A pH gradient elution was applied to the Protein A column to prevent antibody precipitation at low pH. Antibody from Protein A chromatography contained some product related impurities, which were the misassembling of cleaved heavy chain, heavy chain and light chain. It also had some process related impurities, including Protein A residues, endotoxin, host cell DNA and proteins. Cation exchange chromatography with optimal NaCl gradient at pH 4.5-6.0 efficiently removed these product and process related impurities. The antibody from glycoengineered P. pastoris was comparable to its commercial counterpart in heterotetramer folding, physical stability and binding affinity.

High-throughput screening and selection of yeast cell lines expressing monoclonal antibodies.

The methylotrophic yeast Pichia pastoris has recently been engineered to express therapeutic glycoproteins with uniform human N-glycans at high titers. In contrast to the current art where producing therapeutic proteins in mammalian cell lines yields a final product with heterogeneous N-glycans, proteins expressed in glycoengineered P. pastoris can be designed to carry a specific, preselected glycoform. However, significant variability exists in fermentation performance between genotypically similar clones with respect to cell fitness, secreted protein titer, and glycan homogeneity. Here, we describe a novel, multidimensional screening process that combines high and medium throughput tools to identify cell lines producing monoclonal antibodies (mAbs). These cell lines must satisfy multiple selection criteria (high titer, uniform N-glycans and cell robustness) and be compatible with our large-scale production platform process. Using this selection process, we were able to isolate a mAb-expressing strain yielding a titer (after protein A purification) in excess of 1 g/l in 0.5-l bioreactors.

Cell-to-cell communication mediates glioblastoma progression in Drosophila.

Glioblastoma (GB) is the most aggressive and lethal tumour of the central nervous system (CNS). GB cells grow rapidly and display a network of projections, ultra-long tumour microtubes (TMs), that mediate cell to cell communication. GB-TMs infiltrate throughout the brain, enwrap neurons and facilitate the depletion of the signalling molecule wingless (Wg)/WNT from the neighbouring healthy neurons. GB cells establish a positive feedback loop including Wg signalling upregulation that activates cJun N-terminal kinase (JNK) pathway and matrix metalloproteases (MMPs) production, which in turn promote further TMs infiltration, GB progression and neurodegeneration. Thus, cellular and molecular signals other than primary mutations emerge as central players of GB. Using a Drosophila model of GB, we describe the temporal organisation of the main cellular events that occur in GB, including cell-to-cell interactions, neurodegeneration and TM expansion. We define the progressive activation of JNK pathway signalling in GB mediated by the receptor Grindelwald (Grnd) and activated by the ligand Eiger (Egr)/TNFα produced by surrounding healthy brain tissue. We propose that cellular interactions of GB with the healthy brain tissue precede TM expansion and conclude that non-autonomous signals facilitate GB progression. These results contribute to deciphering the complexity and versatility of these incurable tumours.

A quality improvement initiative to implement the eat, sleep, console neonatal opioid withdrawal syndrome care tool in Massachusetts' PNQIN collaborative.

OBJECTIVE: To support hospitals in the Massachusetts PNQIN collaborative with adoption of the ESC Neonatal Opioid Withdrawal Syndrome (NOWS) Care Tool© and assess NOWS hospitalization outcomes. STUDY DESIGN: Statewide QI study where 11 hospitals adopted the ESC NOWS Care Tool©. Outcomes of pharmacotherapy and length of hospital stay (LOS) and were compared in Pre- and Post-ESC implementation cohorts. Statistical Process Control (SPC) charts were used to examine changes over time. RESULTS: The Post-ESC group had lower rates of pharmacotherapy (OR 0.35, 95% CI 0.26, 0.46) with shorter LOS (RR 0.79, 95% CI 0.76, 0.82). The 30-day NOWS readmission rate was 1.2% in the Pre- and 0.4% in the Post-ESC cohort. SPC charts indicate a shift in pharmacotherapy from 54.8 to 35.0% and LOS from 14.2 to 10.9 days Post-ESC. CONCLUSIONS: The ESC NOWS Care Tool was successfully implemented across a state collaborative with improvement in NOWS outcomes without short-term adverse effects.

Alpha band signatures of social synchrony.

Previous research has reported changes in mu rhythm, the central rhythm of the alpha frequency band, in both intentional and spontaneous interpersonal coordination. The current study was designed to extend existing findings on social synchrony to the pendulum swinging task and simultaneously measured time unfolding behavioral synchrony and EEG estimation of mu activity during spontaneous, intentional in-phase and intentional anti-phase interpersonal coordination. As expected, the behavioral measures of synchrony demonstrated the expected pattern of weak synchronization for spontaneous coordination, moderate synchronization for intentional anti-phase coordination, and strong synchronization for in-phase coordination. With respect to the EEG measures, we found evidence for mu enhancement for spontaneous coordination in contrast to mu suppression for intentional coordination (both in phase and anti-phase), with higher levels of synchronization associated with higher levels of mu suppression in the right hemisphere. The implications of the research findings and methodology for understanding the underlying mechanisms contributing to social problems in psychological disorders, leader-follower relationships, and inter-brain dynamics are discussed.

Neural correlates of automatic and controlled auditory processing in schizophrenia.

Individuals with schizophrenia demonstrate impairments in selective attention and sensory processing. The authors assessed differences in brain function between 26 participants with schizophrenia and 17 comparison subjects engaged in automatic (unattended) and controlled (attended) auditory information processing using event-related functional MRI. Lower regional neural activation during automatic auditory processing in the schizophrenia group was not confined to just the temporal lobe, but also extended to prefrontal regions. Controlled auditory processing was associated with a distributed frontotemporal and subcortical dysfunction. Differences in activation between these two modes of auditory information processing were more pronounced in the comparison group than in the patient group.

Behavioral and ERP measures of holistic face processing in a composite task.

Holistic processing of faces is characterized by encoding of the face as a single stimulus. This study employed a composite face task to examine whether holistic processing varies when attention is restricted to the top as compared to the bottom half of the face, and whether evidence of holistic processing would be observed in event-related potentials. Analyses of behavioral data showed that spatial misalignment of the face halves disrupted holistic processing and enhanced detection of repeated attended halves. Effects of misalignment on the N170, VPP and N250 ERP components resembled effects of face inversion. Attention to the top half of the face was associated with faster P1, N170, VPP, and P2 latencies than attending to the bottom, suggesting automatic processing of the eye region. Further, N170 latency effects suggested that structural encoding of the face is facilitated during holistic processing. N250 latency effects reflected task difficulty. Finally, an overall right hemispheric asymmetry was most pronounced when holistic face processing was greatest. Results are discussed in light of recent proposals that holistic face processing is a subtype of configural face processing.

Relationship Between Theory of Mind, Emotion Recognition, and Social Synchrony in Adolescents With and Without Autism.

Difficulty in social communication and interaction is a primary diagnostic feature of ASD. Research has found that adolescents with ASD display various impairments in social behavior such as theory of mind (ToM), emotion recognition, and social synchrony. However, not much is known about the relationships among these dimensions of social behavior. Adolescents with and without ASD participated in the study. ToM ability was measured by viewing social animations of geometric shapes, recognition of facial emotions was measured by viewing pictures of faces, and synchrony ability was measured with a spontaneously arising interpersonal movement task completed with a caregiver and an intentional interpersonal task. Attention and social responsiveness were measured using parent reports. We then examined the relationship between ToM, emotion recognition, clinical measures of attention and social responsiveness, and social synchronization that arises either spontaneously or intentionally. Results indicate that spontaneous synchrony was related to ToM and intentional synchrony was related to clinical measures of attention and social responsiveness. Facial emotion recognition was not related to either ToM or social synchrony. Our findings highlight the importance of biological motion perception and production and attention for more fully understanding the social behavior characteristic of ASD. The findings suggest that the processes underlying difficulties in spontaneous synchrony in ASD are different than the processes underlying difficulties in intentional synchronization.

N-linked glycan characterization of heterologous proteins.

Our laboratory has focused on the re-engineered of the secretory pathway of Pichia pastoris to perform glycosylation reactions that mimic processing of N-glycans in humans and other higher mammals (1,2). A reporter protein with a single N-linked glycosylation site, a His-tagged Kringle 3 domain of human plasminogen (K3), was used to identify combinations of optimal leader/catalytic domain(s) to recreate human N-glycan processing in the Pichia system. In this chapter we describe detailed protocols for high-throughput purification of K3, enzymatic release of N-glycans, matrix-assisted laser desorption ionization time-of-flight and high-performance liquid chromatography analysis of the released N-glycans. The developed protocols can be adapted to the characterization of N-glycans from any purified protein expressed in P. pastoris.

Category selectivity of the N170 and the role of expertise in deaf signers.

Deafness is known to affect processing of visual motion and information in the visual periphery, as well as the neural substrates for these domains. This study was designed to characterize the effects of early deafness and lifelong sign language use on visual category sensitivity of the N170 event-related potential. Images from nine categories of visual forms including upright faces, inverted faces, and hands were presented to twelve typically hearing adults and twelve adult congenitally deaf signers. Classic N170 category sensitivity was observed in both participant groups, whereby faces elicited larger amplitudes than all other visual categories, and inverted faces elicited larger amplitudes and slower latencies than upright faces. In hearing adults, hands elicited a right hemispheric asymmetry while in deaf signers this category elicited a left hemispheric asymmetry. Pilot data from five hearing native signers suggests that this effect is due to lifelong use of American Sign Language rather than auditory deprivation itself.

Imaging frontostriatal function in ultra-high-risk, early, and chronic schizophrenia during executive processing.

CONTEXT: Individuals experiencing prodromal symptoms of schizophrenia (ultra-high-risk group) demonstrate impaired performance on tasks of executive function, attention, and working memory. The neurobiological underpinnings of such executive deficits in ultra-high-risk individuals remains unclear. OBJECTIVE: We assessed frontal and striatal functions during a visual oddball continuous performance task, in ultra-high-risk, early, and chronic schizophrenic patients with the use of functional magnetic resonance imaging. DESIGN: Cross-sectional case-control design. SETTING: Community; outpatient clinic. Patients Fifty-two individuals (control, n = 16; ultra-high risk, n = 10; early, n = 15; chronic, n = 11) from a referred clinical sample and age- and sex-matched control volunteers underwent scanning. MAIN OUTCOME MEASURES: Percentage of active voxels and percentage signal change calculated for the anterior cingulate gyrus (ACG), middle frontal gyrus (MFG), inferior frontal gyrus (IFG), basal ganglia, and thalamus. Performance on the visual oddball task was measured with percentage of hits and d' (a measure based on the hit rate and the false-alarm rate). RESULTS: The ultra-high-risk group showed significantly smaller differential activation between task-relevant and task-irrelevant stimuli in the frontal regions (ACG, IFG, MFG) than the control group. Frontostriatal activation associated with target stimuli in the early and chronic groups was significantly lower than the control group, while the ultra-high-risk group showed a trend toward the early group. CONCLUSIONS: Our findings suggest that prefrontal function begins to decline before the onset of syndromally defined illness and hence may represent a vulnerability marker in assessing the risk of developing psychotic disorders among ultra-high-risk individuals.

Impairments of Social Motor Synchrony Evident in Autism Spectrum Disorder.

Social interactions typically involve movements of the body that become synchronized over time and both intentional and spontaneous interactional synchrony have been found to be an essential part of successful human interaction. However, our understanding of the importance of temporal dimensions of social motor synchrony in social dysfunction is limited. Here, we used a pendulum coordination paradigm to assess dynamic, process-oriented measures of social motor synchrony in adolescents with and without autism spectrum disorder (ASD). Our data indicate that adolescents with ASD demonstrate less synchronization in both spontaneous and intentional interpersonal coordination. Coupled oscillator modeling suggests that ASD participants assembled a synchronization dynamic with a weaker coupling strength, which corresponds to a lower sensitivity and decreased attention to the movements of the other person, but do not demonstrate evidence of a delay in information transmission. The implication of these findings for isolating an ASD-specific social synchronization deficit that could serve as an objective, bio-behavioral marker is discussed.

Brain activity evoked by the perception of human walking: controlling for meaningful coherent motion.

Many functional neuroimaging studies of biological motion have used as stimuli point-light displays of walking figures and compared the resulting activations with those evoked by the same display elements moving in a random or noncoherent manner. Although these studies have established that biological motion activates the superior temporal sulcus (STS), the use of random motion controls has left open the possibility that coordinated and meaningful nonbiological motion might activate these same brain regions and thus call into question their specificity for processing biological motion. Here we used functional magnetic resonance imaging and an anatomical region-of-interest approach to test a hierarchy of three questions regarding activity within the STS. First, by comparing responses in the STS with animations of human and robot walking figures, we determined (1) that the STS is sensitive to biological motion itself, not merely to the superficial characteristics of the stimulus. Then we determined that the STS responds more strongly to biological motion (as conveyed by the walking robot) than to (2) a nonmeaningful but complex nonbiological motion (a disjointed mechanical figure) and (3) a complex and meaningful nonbiological motion (the movements of a grandfather clock). In subsequent whole-brain voxel-based analyses, we confirmed robust STS activity that was strongly right lateralized. In addition, we observed significant deactivations in the STS that differentiated biological and nonbiological motion. These voxel-based analyses also revealed regions of motion-related positive activity in other brain regions, including MT or V5, fusiform gyri, right premotor cortex, and the intraparietal sulci.

Functional magnetic resonance imaging measure of automatic and controlled auditory processing.

Activity within fronto-striato-temporal regions during processing of unattended auditory deviant tones and an auditory target detection task was investigated using event-related functional magnetic resonance imaging. Activation within the middle frontal gyrus, inferior frontal gyrus, anterior cingulate gyrus, superior temporal gyrus, thalamus, and basal ganglia were analyzed for differences in activity patterns between the two stimulus conditions. Unattended deviant tones elicited robust activation in the superior temporal gyrus; by contrast, attended tones evoked stronger superior temporal gyrus activation and greater frontal and striatal activation. The results suggest that attention enhances neural activation evoked by auditory pitch deviance in auditory brain regions, possibly through top-down control from the dorsolateral prefrontal cortex involved in goal-directed selection and response generation.