Pharmacokinetic and pharmacodynamic assessment of oligonucleotide and other DNA or RNA-targeting therapeutics in vivo typically involves bioanalytical procedures carried out at tissue level. After following standardized procedures on animal models of disease, animals are terminally anaesthetized at set time points, tissues are excised, and homogenized, to extract and purify protein, DNA or RNA [1]. Analytes are then processed for the measurement of specific gene/protein expression or, more recently, full proteomic and transcriptomic analysis. Where possible, drug loading can also be assessed (e.g., using mass spectrometry [2], hybridization-based nucleic acid capture assays, or amplification methods such as PCR), provided oligonucleotide drug chemistry is compatible with DNA polymerases. Unfortunately, the 1–2 log knockdown effects of antisense and short interfering RNA (siRNA) therapeutics typically measured in cell culture only translates to 40–60% target RNA reduction at the whole lung tissue level in animals; clinical data can be even more disappointing [3].
In an ideal scenario, therefore, the effect of an oligonucleotide drug on a tissue as complex as the lung should be measured by cell type, and in relation to its degree of transfection. This can be achieved by applying mechanoenzymatic Tissue Disruption and Cell Sorting (TDCS) on in vivo pharmacology experiments. Indeed, industry evidence on what makes for successful drug discovery [5] points to TDCS as a tool that would offer added value to project decision making. By sorting tissue cells by type, measuring drug loading, and on-target effect, one can obtain evidence of target engagement, and an on-target mechanism of action [6] in cells relevant to disease, in vivo, and potentially even in patients. Obtaining such pharmacological evidence is now considered pivotal to drug development efforts [7].
Using TDCS we were therefore able to show that oligonucleotide drugs dosed directly into mouse tracheas loaded at appreciable amounts only in airway/alveolar macrophages but with no statistically significant effect on a target gene, despite statistical power for measuring a 50% change exceeding 94% [2]. Histological and ADME follow-up experiments explained this outcome through the observation of rapid oligonucleotide transcytosis from the airway lumen into circulation, and elimination in urine in as little as 15 min after dosing. Tissues were obtained from animals in accordance with regulations and established guidelines and were reviewed and approved by an Institutional Animal Care and Use Committee or through an Ethical Review Board. Although our results were with modified short interfering RNA (siRNA) and third generation, short locked nucleic acid (LNA) drugs, the findings were in line with historical pharmacokinetic studies by Ionis pharmaceuticals on longer, second generation antisense oligonucleotides [9]. This suggested that more recent clinical measurements were not sensitive enough to measure circulatory and urine oligonucleotide levels in man [3]. Clinical efforts with naked siRNA and antisense oligonucleotides performed by a number of pharmaceutical companies were abandoned shortly afterward.
In this protocol we therefore detail the approach for processing an excised mouse lung to sort precise numbers of specific cell types for appropriate downstream analytics. We describe the steps needed to successfully prepare monocellular suspensions, and detail the approach for sorting three cell preparations, each consisting of 20,000 lung epithelial cells, macrophages, or nonepithelial/nonmacrophage cells from a single lung lobe (Fig. 1). The two-stage sorting protocol first makes use of magnetic bead-based separation, followed by flow cytometric sorting using fluorochrome conjugated antibodies against cell surface markers of interest. This protocol is therefore an extension to a previously published method for in vivo RNA therapeutics pharmacology [1], and focuses exclusively on how to implement TDCS. In our hands, TDCS can be reliably followed up with transcriptomics, proteomics, and mass spectrometry, as well as subculturing (where cell division is naturally accommodated by the cell type of interest). With the emergence of single cell ‘omics, the anticipated parallelization, and cost reduction of these newer bioanalytical approaches, we look forward to TDCS-based in vivo pharmacology delivering highly potent, safe, and targeted airway therapeutics.
The source of DNase I, but more so collagenase, impacts significantly on process success and cell viability at completion of the TDCS process. This particular collagenase is sold as low protease activity which makes it also more appropriate for cell sorting applications. Although we have not tested the protease activity of the particular DNase I enzyme supplied from Sigma, we have not evaluated other enzymes in our workflow for impact on cell viability.
Important! Do not use the M tubes as these homogenize the tissue by vigorous mechanical shearing stress.
For infectious models/microbiome studies ensure that separate sterile spatulas are used per tissue.
The autoMACS Pro instrument was used to standardize multiple separations and help increase throughput but is not an absolute requirement. During method development, individual single use columns were used for some experiments and an acceptable throughput could be achieved in this manner with sufficient operators, although care would need to be taken to standardize technique.
The sorter used by the authors was a BD FACS Aria with 488 nm blue laser and 633 nm red laser. The laser and filter combinations available on any particular cell sorter will dictate the fluorochromes and combinations that can be used during cell sorting. If an instrument does not have a plate collection option, up to four populations can be sorted into tubes for later transfer to appropriate plates. It is worth bearing in mind though that at least one factor in the improved coefficients of variation observed with this method is the accurate deposition of defined cell numbers by the instrument—the equivalent of which is unlikely to be achieved manually.
For highly fibrous tissue (e.g., fibrosis models) it is advised to mince the tissue down into 1 mm3 cubes first using a sterile scalpel and petri dish or an automated tissue chopping station before loading it into the gentleMACS C tube.
If a gentleMACS cell dissociator is not available, then skip steps 3–11 (section/protocol 3.1); instead, process the tissue by mincing as described in the previous note, transfer it into a sterile vial, suspend in 5 ml digestion buffer/lung and incubate for 30 min on an oscillating platform incubator at 37 °C. Then triturate through a 5 ml syringe without a needle ~25 times and subsequently press the suspension through a 100 μm cell strainer using a sterile syringe plunger into a 50 ml cell centrifugation tube; push tissue clumps through the mesh if necessary. Proceed with step 11 (section/protocol 3.1). This method is harsher and less reliable than the gentleMACS procedure in our experience. Do not use normal cell centrifugation tube caps, as these will not allow the mechanic disruption to proceed.
Steps 19 and 20 (section/protocol 3.1) lyse any remaining red blood cells. This protocol is suited to other red blood cell lysis procedures (e.g., to obtain peripheral blood nucleated cells). In our experience, cells will lose minimal viability (2–3%) over the next 48 h if kept at 4 °C and can even be safely shipped between sites within this timeframe if necessary.
CD11b is expressed on murine monocytes and macrophages but also on neutrophils, NK cells, dendritic cells and some subsets of activated lymphocytes. Using CD11b-specific magnetic separation is therefore not a purification, but an enrichment in one fraction and a reduction of autofluorescent cells in the other fraction. Further staining of the CD11b+ fraction allows for further discrimination of cell types of interest.
As only one sample can be processed by the machine at a time it is not recommended to stain all samples simultaneously as there will be a considerable lag time between staining and separation for the last samples processed. Subsequent samples can be stained and washed while previous ones are running through the machine. For this reason, it is useful (though not mandatory) to have two people carrying out this part of the protocol.
It is recommended to retain some of each fraction post magnetic separation to assess for viability and successful enrichment. A 100 μl sample can be stained with 2.5 μl of anti-CD11b antibody, incubated for 30 min and then washed with cell resuspension buffer. For viability, add 2 μl Sytox red, mix gently and proceed to analysis. Dead cells will stain positive in the APC channel and a % viability can be determined by gating on the negative cells.
Ideally, all steps will be completed in one day but it is possible to leave cells overnight at 4 °C at this stage for staining and sorting the following day. Viability was not affected and biomarker data showed that populations sorted on day 1 or day 2 were highly comparable, suggesting that sorting of a lung digest sample up to 24 h after preparation is an acceptable strategy when processing large numbers of mice. In our hands, the maximum throughput of lungs in one day was 12 and each sort (per animal) took approximately 30 min to achieve the required cell numbers.
Compensation controls will be required for most multicolor sorting experiments. With multilaser instruments it may be possible to select fluorochromes that avoid the need for compensation by being sufficiently spectrally separate or by being excited by different lasers. For example, on a four laser instrument, choosing one fluorochrome for each laser line may remove the requirement for compensation. However, this should always be checked initially with the appropriate single color controls. Compensation beads are most suitable in this instance due to the variable autofluorescence of cell populations in digested tissues. Unstained beads should be used for the unstained control, not unstained lung digest sample.
When first developing a panel, use irrelevant specificity isotype control antibodies to rule out nonspecific binding. Once confidence has been established in the antibodies to be used, isotype controls are not necessary for every experiment and Fluorescence Minus One (FMO) controls should be used to set population gates. For example, during method development, tests on ten different antibodies sold as luciferase-specific and compatible with sorting from a variety of suppliers failed to exhibit antigen specificity with this method; in stark contrast, no such issues were experienced with all other markers.
Depending on the cell type of interest and downstream application, a 100 μm nozzle might be more appropriate. The lower pressure and wider sort orifice causes less stress to sorted cells but in our hands resulted in poorer sort efficiency and fewer recovered cells. Viability staining of cells straight after sorting on a 70% nozzle showed the majority of the cells survived the sort and in our system those cells were assessed straight away, meaning that long term survival was not a concern. If downstream applications are to include culturing or functional studies, a 100 μm nozzle would be recommended. A purity sort mode was used in this protocol but each investigator should determine their own requirements of yield versus purity for specific applications. Efficiency on purity sort mode in our hands ranged from 79% to 95%.
The potential combination of cell surface markers and gating strategies for cell types in a digested mouse lung are very large. Since this method was developed there have been extensive studies published looking at full phenotypic characterization of cell types in digested mouse lung—both hematological and structural. The populations identified with the antibodies described here are rather broad and can be added to or altered to more precisely identify numerous cell types depending on the investigator’s specific interests. Staining for cell surface markers can be considerably more challenging in digested tissue than in blood due to the digestion process itself which may result in loss of cell surface epitopes. As an example, with the digestion protocol described herein, the authors had no success with a variety of anti-cytokeratin antibodies which had been described to bind strongly and specifically to epithelial cells which we hypothesize may be due to the loss of those markers during the digestion process itself.
“Fc block” (rat anti-mouse CD16/32) was trialed during development to prevent interaction of leukocyte Fc receptors with the Fc region of fluorescent antibodies but it made no difference compared to no Fc block controls so this was not continued. Other nonspecific binding was avoided by the presence of protein in the stain and sort buffers.
If fluorescence is being used to track delivery of oligonucleotides, the spectral profile of that dye will need to be considered in the panel design for cell sorting. For example, the use of Cy5-labeled oligonucleotides precluded the use of APC as a fluorochrome in this study.