Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements

Zebrafish, a popular organism for studying embryonic development and for modeling human diseases, has so far lacked a systematic functional annotation program akin to those in other animal models. To address this, we formed the international DANIO-CODE consortium and created a central repository to store and process zebrafish developmental functional genomic data. Our data coordination center ( https://danio-code.zfin.org ) combines a total of 1,802 sets of unpublished and re-analyzed published genomic data, which we used to improve existing annotations and show its utility in experimental design. We identified over 140,000 cis-regulatory elements throughout development, including classes with distinct features dependent on their activity in time and space. We delineated the distinct distance topology and chromatin features between regulatory elements active during zygotic genome activation and those active during organogenesis. Finally, we matched regulatory elements and epigenomic landscapes between zebrafish and mouse and predicted functional relationships between them beyond sequence similarity, thus extending the utility of zebrafish developmental genomics to mammals.

Myocardial micro-biopsy procedure for molecular characterization with increased precision and reduced trauma

Endomyocardial biopsy is a valuable tool in cardiac diagnostics but is limited by low diagnostic yield and significant complication risks. Meanwhile, recent developments in transcriptomic and proteomic technologies promise a wealth of biological data from minimal tissue samples. To take advantage of the minimal tissue amount needed for molecular analyses, we have developed a sub-millimeter endovascular biopsy device, considerably smaller than current clinical equipment, and devised a low-input RNA-sequencing protocol for analyzing small tissue samples. In in vivo evaluation in swine, 81% of biopsy attempts (n = 157) were successful. High quality RNA-sequencing data was generated from 91% of the sequenced cardiac micro-biopsy samples (n = 32). Gene expression signatures of samples taken with the novel device were comparable with a conventional device. No major complications were detected either during procedures or during 7 days' follow-up, despite acquiring a relatively large number of biopsies (median 30) in each animal. In conclusion, the novel device coupled with RNA-sequencing provides a feasible method to obtain molecular data from the myocardium. The method is less traumatic and has a higher flexibility compared to conventional methods, enabling safer and more targeted sampling from different parts of the myocardium.

P2790Novel endomyocardial micro-biopsy device for higher precision and reduced complication risks

Introduction

Endomyocardial biopsy (EMB) is the gold standard for diagnosis of several cardiac diseases, yet its use is limited by low diagnostic yield and significant complication risks. The size of the current devices allows only limited steering to different parts of the ventricle walls. In transplant monitoring, repeated biopsies with the current devices can cause scarring that makes it increasingly difficult to obtain adequate samples. We hypothesised that several of the shortcomings of EMB can be avoided with a smaller and more steerable device. Further, we hypothesised that the novel sampling procedure could be coupled to a low-input molecular analysis method, such as RNA-sequencing (RNA-seq), to provide molecular characterisation of the tissue without the need of large biopsy samples.

Purpose

To develop an EMB device with significantly smaller dimensions, for future use in diagnostics and research investigations. Specific aims were to test feasibility and safety of the procedure, as well as the quality of the generated molecular data.

Methods

65 “micro biopsy” (micro-EMB) device prototypes were designed and evaluated in-house. The prototypes were evaluated either in an ex-vivo simulator or in acute non-survival pig experiments (n=23). Once the final device design was reached, an in vivo trial was set up using six naive Yorkshire farm pigs. Micro-EMB, conventional EMB, skeletal muscle and blood samples were collected for RNA-seq characterisation and comparison. In half of the animals (n=3), micro-EMB was the only intervention in order to prioritise safety evaluations. The animals were monitored for one week.

Results

The final device design has an outer diameter (OD) of 0.4 mm, compared to a conventional 11 mm device (in the opened position), Fig 1A. The device can be directed to different parts of the myocardium in both ventricles. In the in vivo evaluation in swine, 81% of the biopsy attempts (n=157) were successful. High quality RNA-seq data was generated from 91% of the sequenced heart micro-biopsy samples (n=32). The gene expression signatures of samples taken with the novel device were comparable with samples taken with a conventional device, Fig 1B. No major complications were detected either during periprocedural monitoring or during the follow-up. The tissue mark after micro-biopsy was markedly smaller than after conventional endomyocardial biopsy.

A) Bioptome dimensions. B) RNA-seq data.

Conclusions

Our preliminary data suggest that the novel submillimeter biopsy device, coupled with RNA-seq, provides a feasible method to obtain molecular data from the myocardium. The method is less traumatic and has a higher flexibility compared to conventional methods, enabling safer and more specific sampling from different parts of the myocardium. In the long term, the procedure could open unprecedented diagnostic and research possibilities. Future studies should be directed to establish the capabilities of the novel method in a relevant disease model.

Acknowledgement/Funding

Family Erling Persson Foundation. The Söderberg foundations. KID (Karolinska Institutet). The 4D project. Stockholm county council. Astra Zeneca.