A community-based approach to image analysis of cells, tissues and tumors

Emerging multiplexed imaging platforms provide an unprecedented view of an increasing number of molecular markers at subcellular resolution and the dynamic evolution of tumor cellular composition. As such, they are capable of elucidating cell-to-cell interactions within the tumor microenvironment that impact clinical outcome and therapeutic response. However, the rapid development of these platforms has far outpaced the computational methods for processing and analyzing the data they generate. While being technologically disparate, all imaging assays share many computational requirements for post-collection data processing. As such, our Image Analysis Working Group (IAWG), composed of researchers in the Cancer Systems Biology Consortium (CSBC) and the Physical Sciences - Oncology Network (PS-ON), convened a workshop on "Computational Challenges Shared by Diverse Imaging Platforms" to characterize these common issues and a follow-up hackathon to implement solutions for a selected subset of them. Here, we delineate these areas that reflect major axes of research within the field, including image registration, segmentation of cells and subcellular structures, and identification of cell types from their morphology. We further describe the logistical organization of these events, believing our lessons learned can aid others in uniting the imaging community around self-identified topics of mutual interest, in designing and implementing operational procedures to address those topics and in mitigating issues inherent in image analysis (e.g., sharing exemplar images of large datasets and disseminating baseline solutions to hackathon challenges through open-source code repositories)

P.025 Efficacy and safety results of the avalglucosidase alfa phase 3 COMET trial in participants with late-onset Pompe disease (LOPD)

Background: Phase 3 COMET trial (NCT02782741) compares avalglucosidase alfa (n=51) with alglucosidase alfa (n=49) in treatment-naïve LOPD. Methods: Primary objective: determine avalglucosidase alfa effect on respiratory muscle function. Secondary/other objectives include: avalglucosidase alfa effect on functional endurance, inspiratory/expiratory muscle strength, lower/upper extremity muscle strength, motor function, health-related quality of life, safety. Results: At Week 49, change (LSmean±SE) from baseline in upright forced vital capacity %predicted was greater with avalglucosidase alfa (2.89%±0.88%) versus alglucosidase alfa (0.46%±0.93%)(absolute difference+2.43%). The primary objective, achieving statistical non-inferiority (p=0.0074), was met. Superiority testing was borderline significant (p=0.0626). Week 49 change from baseline in 6-minute walk test was 30.01-meters greater for avalglucosidase alfa (32.21±9.93m) versus alglucosidase alfa (2.19±10.40m). Positive results for avalglucosidase alfa were seen for all secondary/other efficacy endpoints. Treatment-emergent adverse events (AEs) occurred in 86.3% of avalglucosidase alfa-treated and 91.8% of alglucosidase alfa-treated participants. Five participants withdrew, 4 for AEs, all on alglucosidase alfa. Serious AEs occurred in 8 avalglucosidase alfa-treated and 12 alglucosidase alfa-treated participants. IgG antidrug antibody responses were similar in both. High titers and neutralizing antibodies were more common for alglucosidase alfa. Conclusions: Results demonstrate improvements in clinically meaningful outcome measures and a more favorable safety profile with avalglucosidase alfa versus alglucosidase alfa. Funding: Sanofi Genzym

Xrp1 genetically interacts with the ALS-associated FUS orthologue caz and mediates its toxicity

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Microscopy-based chromosome conformation capture enables simultaneous visualization of genome organization and transcription in intact organisms

Eukaryotic chromosomes are organized in multiple scales, from nucleosomes to chromosome territories. Recently, genome-wide methods identified an intermediate level of chromosome organization, topologically associating domains (TADs), that play key roles in transcriptional regulation. However, these methods cannot directly examine the interplay between transcriptional activation and chromosome architecture while maintaining spatial information. Here we present a multiplexed, sequential imaging approach (Hi-M) that permits simultaneous detection of chromosome organization and transcription in single nuclei. This allowed us to unveil the changes in 3D chromatin organization occurring upon transcriptional activation and homologous chromosome unpairing during awakening of the zygotic genome in intact Drosophila embryos. Excitingly, the ability of Hi-M to explore the multi-scale chromosome architecture with spatial resolution at different stages of development or during the cell cycle will be key to understanding the mechanisms and consequences of the 4D organization of the genome. Cardozo Gizzi et al. developed Hi-M, a multiplexed imaging-based approach to detect 3D chromatin folding in single cells within intact Drosophila embryos. The ability of Hi-M to detect the spatial organization of cells enabled measurement of changes in TAD organization during early embryogenesis and upon transcriptional activation.Fil: Cardozo Gizzi, Andres Mauricio. Instituto Universitario de Ciencias Biomédicas de Córdoba; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Université Montpellier II; FranciaFil: Cattoni, Diego Ignacio. Université Montpellier II; Francia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Química y Físico-Química Biológicas "Prof. Alejandro C. Paladini". Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Química y Físico-Química Biológicas; ArgentinaFil: Fiche, Jean-Bernard. Centre de Biochimie Structurale; FranciaFil: Espínola, Sergio Martín. Centre de Biochimie Structurale; FranciaFil: Gurgo, Julián Roberto. Centre de Biochimie Structurale; FranciaFil: Messina, Olivier. Centre de Biochimie Structurale; FranciaFil: Houbron, Christophe. Centre de Biochimie Structurale; FranciaFil: Ogiyama, Yuki. Institute Of Human Genetics; FranciaFil: Papadopoulos, Giorgio L.. Institute Of Human Genetics; FranciaFil: Cavalli, Giacomo. Institut de Génétique Humaine, Cnrs Umr 9002; Francia. Institute Of Human Genetics; FranciaFil: Lagha, Mounia. Institut de Génétique Moléculaire de Montpellier; FranciaFil: Nollmann, Marcelo. Centre de Biochimie Structurale; Franci