Reduction of neuroinflammation and seizures in a mouse model of CLN1 batten disease using the small molecule enzyme mimetic, N-Tert-butyl hydroxylamine

Infantile neuronal ceroid lipofuscinosis (CLN1 Batten Disease) is a devastating pediatric lysosomal storage disease caused by pathogenic variants in the CLN1 gene, which encodes the depalmitoylation enzyme, palmitoyl-protein thioesterase 1 (PPT1). CLN1 patients present with visual deterioration, psychomotor dysfunction, and recurrent seizures until neurodegeneration results in death, typically before fifteen years of age. Histopathological features of CLN1 include aggregation of lysosomal autofluorescent storage material (AFSM), as well as profound gliosis. The current management of CLN1 is relegated to palliative care. Here, we examine the therapeutic potential of a small molecule PPT1 mimetic, N-tert-butyl hydroxylamine (NtBuHA), in a Cln1−/− mouse model. Treatment with NtBuHA reduced AFSM accumulation both in vitro and in vivo. Importantly, NtBuHA treatment in Cln1−/− mice reduced neuroinflammation, mitigated epileptic episodes, and normalized motor function. Live cell imaging of Cln1−/− primary cortical neurons treated with NtBuHA partially rescued aberrant synaptic calcium dynamics, suggesting a potential mechanism contributing to the therapeutic effects of NtBuHA in vivo. Taken together, our findings provide supporting evidence for NtBuHA as a potential treatment for CLN1 Batten Disease

Preclinical and clinical biomarker studies of CT1812:A novel approach to Alzheimer's disease modification

INTRODUCTION: Amyloid beta (Aβ) oligomers are one of the most toxic structural forms of the Aβ protein and are hypothesized to cause synaptotoxicity and memory failure as they build up in Alzheimer’s disease (AD) patients’ brain tissue. We previously demonstrated that antagonists of the sigma-2 receptor complex effectively block Aβ oligomer toxicity. CT1812 is an orally bioavailable, brain penetrant small molecule antagonist of the sigma-2 receptor complex that appears safe and well tolerated in healthy elderly volunteers. We tested CT1812’s effect on Aβ oligomer pathobiology in preclinical AD models and evaluated CT1812’s impact on cerebrospinal fluid (CSF) protein biomarkers in mild to moderate AD patients in a clinical trial (ClinicalTrials.gov NCT02907567). METHODS: Experiments were performed to measure the impact of CT1812 versus vehicle on Aβ oligomer binding to synapses in vitro, to human AD patient post mortem brain tissue ex vivo, and in living APP(Swe)/PS1dE9 transgenic mice in vivo. Additional experiments were performed to measure the impact of CT1812 versus vehicle on Aβ oligomer-induced deficits in membrane trafficking rate, synapse number, and protein expression in mature hippocampal/cortical neurons in vitro. The impact of CT1812 on cognitive function was measured in transgenic Thy1 huAPP(Swe/Lnd+) and wild-type littermates. A multicenter, double-blind, placebo-controlled parallel group trial was performed to evaluate the safety, tolerability, and impact on protein biomarker expression of CT1812 or placebo given once daily for 28 days to AD patients (Mini-Mental State Examination 18–26). CSF protein expression was measured by liquid chromatography with tandem mass spectrometry or enzyme-linked immunosorbent assay in samples drawn prior to dosing (Day 0) and at end of dosing (Day 28) and compared within each patient and between pooled treated versus placebo-treated dosing groups. RESULTS: CT1812 significantly and dose-dependently displaced Aβ oligomers bound to synaptic receptors in three independent preclinical models of AD, facilitated oligomer clearance into the CSF, increased synaptic number and protein expression in neurons, and improved cognitive performance in transgenic mice. CT1812 significantly increased CSF concentrations of Aβ oligomers in AD patient CSF, reduced concentrations of synaptic proteins and phosphorylated tau fragments, and reversed expression of many AD-related proteins dysregulated in CSF. DISCUSSION: These preclinical studies demonstrate the novel disease-modifying mechanism of action of CT1812 against AD and Aβ oligomers. The clinical results are consistent with preclinical data and provide evidence of target engagement and impact on fundamental disease-related signaling pathways in AD patients, supporting further development of CT1812

Large-Scale Discovery and Characterization of Protein Regulatory Motifs in Eukaryotes

The increasing ability to generate large-scale, quantitative proteomic data has brought with it the challenge of analyzing such data to discover the sequence elements that underlie systems-level protein behavior. Here we show that short, linear protein motifs can be efficiently recovered from proteome-scale datasets such as sub-cellular localization, molecular function, half-life, and protein abundance data using an information theoretic approach. Using this approach, we have identified many known protein motifs, such as phosphorylation sites and localization signals, and discovered a large number of candidate elements. We estimate that ∼80% of these are novel predictions in that they do not match a known motif in both sequence and biological context, suggesting that post-translational regulation of protein behavior is still largely unexplored. These predicted motifs, many of which display preferential association with specific biological pathways and non-random positioning in the linear protein sequence, provide focused hypotheses for experimental validation

Company Profile: Caprion Proteomics, Inc.

Caprion Proteomics, Inc. is a leading provider of proteomics biomarker services with over 20 pharmaceutical, biotechnology and diagnostics industry clients in North America, Europe and Japan. An unbiased approach to the identification of biomarker candidates is paired with a rapid tool for biomarker verification and validation in large patient populations. Caprion is now also a strategic partner of Covance, Inc., one of the world’s largest and most experienced providers of drug-development services. </jats:p

Spoke: a 120-kD protein associated with a novel filamentous structure on or near kinetochore microtubules in the mitotic spindle

Abstract. We have characterized an antiserum that recognizes a single 120-kD protein in CHO cells which is soluble and cytoplasmically localized in interphase, but which is associated with a novel filamentous structure localized on or near kinetochore microtubules in mid-mitosis. These filaments, one per sister chromatid, run from near the mitotic spindle pole to within,,00.3 ~,m of each kinetochore. In metaphase, the staining pattern shows considerable substructure at light microscopy resolution, appearing as bright nodes or striations, often with a kinked or helical appearance. This overall localization pattern is retained throughout anaphase, with the filaments shortening as the chromosomes move toward the mitotic spindle poles. Also in anaphase, a separate ring-lik

Abstract 1562: Proteomic changes observed in colon cancer tumors by label-free differential profiling of paired tumor versus normal FFPE samples

Abstract Colorectal cancer (CRC) is the third most common cancer and if caught early enough has a good prognosis. Mass screening of the adult population is advisable to reduce CRC mortality rate as well as reduce the cost of treating advanced CRC cases. A blood-based biomarker panel with the ability to diagnose CRC as well as determine prognosis and predict the response to drug therapy is desired. However, blood biomarker discovery is hampered by problems of complexity and dynamic range of protein abundance. Formalin-fixed and paraffin-embedded (FFPE) tissue is an ideal sample type for cancer biomarker analysis due to its ubiquitous use in cancer diagnosis in the clinic and consequent availability in oncology hospitals and clinics as well as biobanks. Biomarker discovery to date using FFPE have used only very few patient samples, making clinically relevant biomarker discovery difficult due to large patient-to-patient variation. As a part of our Biospecimen Research Network (BRN) program we funded a proteomic biomarker study of a large number of colorectal cancer and adjacent normal tissue samples. The investigators employed two platforms for biomarker discovery: label-free intensity based discovery using high resolution tandem mass spectrometry and targeted quantitation using multiple reaction monitoring. These two techniques allowed them to dig deeper into the proteome and to profile phosphopeptides. Paired tissue from 40 patients was profiled and of the 2875 proteins quantified, 367 proteins changed significantly in patients whose tumor size was greater than 50%. Large changes in secreted proteins were observed and many of these proteins were also observed in blood, offering promise for a potential blood-based biomarker for colorectal cancer. A blood-based biomarker assay for colorectal cancer could ultimately reduce the number of colonoscopies required, reducing cost and discomfort. Citation Format: Lokesh Agrawal, Fiona McAlister, Sushmita Roy, Florian Unger, Kerstin David, Harmut Juhl, Daniel Chelsky, Helen Moore. Proteomic changes observed in colon cancer tumors by label-free differential profiling of paired tumor versus normal FFPE samples. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1562. doi:10.1158/1538-7445.AM2015-1562</jats:p

Metaproteomic and 16S rRNA Gene Sequencing Analysis of the Infant Fecal Microbiome

A metaproteomic analysis was conducted on the fecal microbiome of eight infants to characterize global protein and pathway expression. Although mass spectrometry-based proteomics is now a routine tool, analysis of the microbiome presents specific technical challenges, including the complexity and dynamic range of member taxa, the need for well-annotated metagenomic databases, and high inter-protein sequence redundancy and similarity. In this study, an approach was developed for assessment of biological phenotype and metabolic status, as a functional complement to DNA sequence analysis. Fecal samples were prepared and analysed by tandem mass spectrometry and a homology-based meta-clustering strategy was used to combine peptides from multiple species into representative proteins. In total, 15,250 unique peptides were sequenced and assigned to 2154 metaclusters, which were then assigned to pathways and functional groups. Differences were noted in several pathways, consistent with the dominant genera observed in different subjects. Although this study was not powered to draw conclusions from the comparisons, the results obtained demonstrate the applicability of this approach and provide the methods needed for performing semi-quantitative comparisons of human fecal microbiome composition, physiology and metabolism, as well as a more detailed assessment of microbial composition in comparison to 16S rRNA gene sequencing.</jats:p

A signature for immune response correlates with HCV treatment outcome in Caucasian subjects

AbstractBroad proteomic profiling was performed on serum samples of phase 2 studies (PROVE1, PROVE2, and PROVE3) of the direct-acting antiviral drug telaprevir in combination with peg-interferon and ribavirin in subjects with HCV. Using only profiling data from subjects treated with peg-interferon and ribavirin, a signature composed of pretreatment levels of 13 components was identified that correlated well (R2=0.68) with subjects' underlying immune response as measured by week 4 viral decline and was highly predictive of sustained virologic response in non-African American subjects (AUC=0.99). The signature was validated by predicting in an independent cohort of non-African American subjects treated with telaprevir, peg-interferon and ribavirin (AUC=0.854). Samples from extreme responders were over-represented in these analyses. Proteins identified as differentially-expressed between responders and non-responders to HCV treatment were quantified using multiple reaction monitoring in samples from all Caucasian subjects in the peg-interferon and ribavirin arms of PROVE1 and PROVE2, revealing 15 proteins that were significantly differentially expressed between treatment responders and non-responders. Seven of the proteins are part of focal adhesions or other macromolecular assemblies that form structural links between integrins and the actin cytoskeleton and are involved in antiviral response.Biological significanceHCV is a significant health problem. We describe a novel approach for identifying markers that predicts HCV treatment response different treatment regimens and use this approach to identify a novel HCV treatment response signature. The signature has potential to guide optimization of HCV treatment regimens

Metaproteomic and 16S rRNA Gene Sequencing Analysis of the Infant Fecal Microbiome

A metaproteomic analysis was conducted on the fecal microbiome of eight infants to characterize global protein and pathway expression. Although mass spectrometry-based proteomics is now a routine tool, analysis of the microbiome presents specific technical challenges, including the complexity and dynamic range of member taxa, the need for well-annotated metagenomic databases, and high inter-protein sequence redundancy and similarity. In this study, an approach was developed for assessment of biological phenotype and metabolic status, as a functional complement to DNA sequence analysis. Fecal samples were prepared and analysed by tandem mass spectrometry and a homology-based meta-clustering strategy was used to combine peptides from multiple species into representative proteins. In total, 15,250 unique peptides were sequenced and assigned to 2154 metaclusters, which were then assigned to pathways and functional groups. Differences were noted in several pathways, consistent with the dominant genera observed in different subjects. Although this study was not powered to draw conclusions from the comparisons, the results obtained demonstrate the applicability of this approach and provide the methods needed for performing semi-quantitative comparisons of human fecal microbiome composition, physiology and metabolism, as well as a more detailed assessment of microbial composition in comparison to 16S rRNA gene sequencing.</p