Name: lineage tracing of inducible fluorescently-labeled stem cells in the adult mouse brain
Uploaded: 2022-05-20T14:00:00
Description: Watch this Scientific Journal Video about Lineage Tracing of Inducible Fluorescently-Labeled Stem Cells in the Adult Mouse Brain at JoVE.com

The authors wish to thank Dr. Diana Carlone (Boston Children&#39;s Hospital, Harvard Medical School) and Dr. Matthew Lynes (Joslin Diabetes Center; Maine Medical Center Research Institute) for guidance utilizing mTert-rtTA animals.

All methods described here have been approved by the Institutional Animal Care and Use Committee (IACUC) of The Ohio State University.
1. Creation of a lineage tracing Tet-On mouse line, breeding strategies, and genotyping for experimental cohort mice
NOTE: Here, we outline creation of a Tet-On mouse system with Rosa-mTmG as the fluorescent reporter gene that undergoes Cre recombination, however various other Cre-recombination-driven reporter lines ca...

A method for the creation, utilization, and analysis of a triple transgenic lineage tracing mouse line marking stem cells within the adult mouse brain in vivo is described. When combined with immunostaining or brain clearing, the identification and characterization of traced fluorescent cells across the brain can be accomplished. This technique offers the ability to understand the plastic/regenerative/remodeling potential of labeled stem cells as they activate, migrate, differentiate, or proliferate. While previ...

Value of a lineage tracing mouse line 
Analysis of stem cells in vivo can be difficult since many assays that examine such cells only focus on characterizing these cells at the time of death of the animal, which represents a terminal snapshot in time. To better understand the processes of proliferation, differentiation, and migration of progenitor, intermediate/transition cell types, and mature cells over time, a longitudinal analysis approach is required. This can be achieved with lineage tracing studies whereby stem/progenitor cells are marked indelibly and can be followed for any length of time afterwards1.
In the adult mammalian brain, the process of neurogenesis by which adult-born neurons are created from stem and progenitor cells was first analyzed via label retention with thymidine-H3&#160;2,3,4 or 5-bromo-2&#39;-deoxyuridine (BrdU)5,6,7,8. In these studies, proliferative cells were marked with the thymine analog, which was incorporated into the cells&#39; DNA during replication and cell division/proliferation. The marked cell, as well as their progeny, therefore contained this analog, which were then identified post-mortem. However, while thymidine-H3 and BrdU allowed for the marking of proliferative cells and their progeny in brain regions where stem cells were poorly understood, these studies were hindered by the downsides of these tools. Thymidine-H3 induces cell-cycle arrest, apoptosis, and dose-dependent DNA synthesis inhibition9, while BrdU marks cells at varying levels depending on the route of administration10 and is taken up by cells during repair or apoptosis, as well as during cell division11. More efficient labeling methods have been utilized recently, such as labeling with 5-ethynyl-2&#39;-deoxyuridine (EdU), but many of the same issues as BrdU still remain12. These approaches are also limiting in that they mark any proliferative cell, not just stem cells, and thus interpretation of results can be confounded. In the neurogenic lineage, all stem and progenitor cells retain mitotic capacity, and only terminal/mature neurons are not proliferative. For astrocytes and microglia, but not oligodendrocytes, proliferation is maintained indefinitely13,14,15.
Transgenic mice used to lineage trace only cells that express a protein of interest, such as one confirmed to identify adult stem cells as we use here, have therefore become more common when investigating stem cells and their progeny. While difficult to generate through mouse transgenic approaches, lineage-tracing mouse lines allow for the tracing of specifically marked cells in the brain, and do not rely on proliferation alone. In the Tet-On transgenic mouse system, administration of tetracycline or doxycycline (a tetracycline derivative) induces Cre-recombinase expression in cells that have been engineered with a reverse tetracycline transactivator (rtTA), which is transcribed by a promoter of interest. The Tet-inducible Cre-driven recombination will then activate the expression of an indelible fluorescent or luminescent protein in the cells of interest, depending on the Rosa-reporter mouse employed. These indelibly marked cells continue to express this reporter after division, differentiation, or migration, allowing the tracking of these cells and their progeny over time or after different interventions16. Advantages of transgenic lineage-tracing approaches include: 1) specificity of tracing to a particular cell lineage or progenitor/stem cell marked by the rtTA, 2) indelible expression of the fluorescent or luminescent protein despite cell turnover or differentiation, 3) low toxicity, 4) conditional activation during any point in the animal&#39;s life cycle, and 5) ease of use with common assays, including immunostaining/immunofluorescence16.
Other methods of temporally inducible reporter tools in mice include the use of Cre-ERT2 mice, which can be paired with ROSA-GFP, ROSA-mTmG, or other fluorescent reporter transgenes. In these animals, a cell-specific regulatory element, such as a promoter or enhancer region of interest, drives the production of Cre recombinase, which can only be activated via the administration of tamoxifen. While Cre-ERT2 mouse lines allow for the induction of Cre in specific cell lines, there is a wealth of knowledge detailing the effects of tamoxifen on adult neurogenesis17,18. Additionally, there exists many ROSA-driven fluorescent reporter genes that can be utilized instead of GFP or mTmG, including YFP or CFP, which would allow for alternate fluorescent labeling in other fluorescent wavelengths. These fluorescent reporter genes can be used with Tet-On or Cre-ERT2 systems.
Telomerase reverse transcriptase (TERT) is the rate-limiting component of the holoenzyme telomerase, which works to extend telomeres after they are shortened during cell division19,20. TERT has been identified as a marker of adult tissue stem cells in the intestine21,22, bone marrow21, liver23, adipose24, endometrium25,26, and bone1. Whether TERT expression in these adult stem cells is solely for telomerase-extending activity or to perform non-canonical TERT roles27 is still unknown. TERT-expressing quiescent adult stem cells (qASCs) have been identified and traced throughout the body with transgenic lineage tracing mice to study the multipotency and self-renewal ability of these stem cells, as well as their potential to activate, proliferate, differentiate, and migrate1,22,23,28. The creation of the Tert-rtTA transgene has been performed previously1. In this paper, we will describe the use of a lineage tracing TERT mouse line to study TERT + qASCs which we have identified as a novel ASC population in the adult mouse brain.
Generation of a transgenic lineage tracing mouse line 
To generate a lineage-tracing mouse line using the Tet-On system, three transgenes must be combined within a single animal through mouse mating. The first is a rtTA, expressed under the control of the promoter of the gene of interest (ours is TERT-rtTA). In a cell that expresses this gene of interest, the rtTA will therefore be expressed. The second is an oTet-Cre gene, which contains a tetracycline response element (TRE) that will allow for the transcription of Cre recombinase in the presence of both a rtTA fusion transcript and tetracycline or doxycycline. Tetracycline or doxycycline can be administered to an animal via drinking water or chow29. Finally, there must be a gene that will be activated by Cre recombinase cleavage. In this manuscript, the labeling gene we will describe is the Rosa26-mTmG gene, which until Cre recombination will ubiquitously transcribe mTomato (membrane red fluorescence in all cells). However, if a cell expresses the rtTA transcript and contains tetracycline or doxycycline, Cre recombination of a set of lox P sites between the mTomato and mGFP sites will change the R26 site and cause the cell to produce membrane EGFP (mGFP, or membrane green fluorescence) instead of membrane tomato. The indelible nature of this mGFP signal will allow for in vivo labeling and tracing of cells as they proliferate, migrate, and differentiate. Following the trace, cells can be analyzed for expression of GFP via immunofluorescence in standard cryosections or thicker optically cleared brains.
In this paper, we will describe the use of the specific mouse line, mTert-rtTA::oTet-Cre::Rosa-mTmG. To create this triple transgenic mouse line, we first mated oTet-Cre animals (The Jackson Lab strain #006234) to Rosa-mTmG animals (The Jackson Lab strain #007676) to create oTet-Cre::Rosa-mTmG double transgenic mice. These animals were genotyped with primers and PCR templates indicated in Supplementary Tables 1 and 2. mTert-rtTA mice (created by David Breault1) were mated to oTet-Cre::Rosa-mTmG animals to create mTert-rtTA::oTet-Cre::Rosa-mTmG mice (Figure 1A)1,30. The mechanism of action of the mTert-rtTA::oTet-Cre::Rosa-mTmG mouse line is illustrated in Figure 1B.
Doxycycline induction and pulse-chase design 
When planning experiments, it is important to consider several factors that will affect the outcome of lineage tracing experiments, including the age of the animal at doxycycline induction, the length of doxycycline administration (the &#34;pulse&#34; period), the length of time after doxycycline removal before tissue collection (the &#34;chase&#34; period), and the timing of any interventions during these processes. These study design considerations are essential for understanding the labeled cells and their progeny at the conclusion of the experiment. The first step in the process is to identify the age of interest of the animal and the length of the doxycycline administration. Longer pulse periods will allow for the potential for more cells to express the rtTA-linked promoter to be expressed and more cells of interest to be indelibly marked. A cell type that exhibits transient expression of the gene of interest may require a longer pulse period than cells that continuously express the gene of interest. However, if the goal of the study is to understand short-term effects of the cell of interest or an acute intervention, the pulse period cannot be too long, as once a cell is marked, it will be traced through any number of changes during the remainder of the pulse period. In some of our studies, a 2 day pulse with no chase period was used to more closely mimic a direct-reporter for TERT. This is because the minimum length of time for recombination of the Rosa-mTmG gene is 2 days31.
The next essential period in a pulse-chase experiment is the length between removal of doxycycline and perfusion of the animal, also known as the &#39;chase&#39;. The half-life of doxycycline in mice is approximately 170 minutes regardless of administration route, allowing for the conclusion that doxycycline induction is likely no longer occurring several hours after removal32. However, it is important to note that doxycycline metabolism is slower in aged mice, which may lead to longer effective &#39;pulse&#39; periods than young animals33.
During the chase period, labeled cells will continue to be labeled, even after proliferation, differentiation, or migration. The progeny of these cells will also be labeled. The goal of the study will shape the length of the pulse-chase paradigm. If the goal of the study is to understand the regeneration of a tissue over a long period of time with the cells of interest, a long chase period may be required. Finally, the timing of any interventions or treatments must be decided. Administration during the pulse period will affect the cells expressing the gene of interest as well as any progeny created during this time, whereas administration during the chase period may affect mostly progeny of the cells of interest, although this will depend on how quickly the labeled cells divide or differentiate. Examples of pulse-chase experimental designs we have utilized are outlined in Figure 2A.
It is also important to be aware of the possibility of background GFP signal due to leaky expression. Leaky expression occurs as a result of inherent binding potential between rtTA and the Otet sequences in the absence of doxycycline, and residual activity of the Otet transgene in the absence of rtTA (reviewed in34). Leaky expression represents one weakness of the Tet systems, and although the leak is often an acceptable downside to the system, situations where the leaky expression can lead to toxicity and mortality, such as with diptheria toxin (DTA) in Otet-DTA animals can limit the use of these systems35.
Brain processing, sectioning, and immunofluorescence of thin sections for microscopy 
To analyze the brains of mice after a lineage tracing experiment, mice must first be perfused via transcardial perfusion to remove blood and CSF that can lead to high autofluorescence in the brain. There are two commonly used fixatives that the animal may be perfused with: Histochoice Tissue Fixative, a glyoxal fixative (GF), or 4% paraformaldehyde (PFA). Glyoxal fixatives allow for a relatively gentle fixation process with less cross-linking than PFA. This reduces tissue stiffness, reduces the need for antigen retrieval, and allows for less concentrated antibody solutions during immunostaining. However, if they contain methanol this may serve to increase autofluorescence36. On the other hand, PFA will often allow for a more robust fixation, and while antigen retrieval will be required during immunostaining, there are antibodies that will only work with PFA-fixed tissues, and perfusion with 4% PFA is required for the optical clearing technique described later.
Following perfusion is a post-fixation step, in which brains are immersed in the same type of fixative utilized during the perfusion overnight. This allows for any brain regions that may not have been fully fixed during the perfusion to continue to fix. Next, brains will be incubated in sucrose in phosphate buffered saline (PBS) to remove as much water as possible before the freezing step to prevent ice formation within the tissue (&#34;cryo-preservation&#34;). Brains may then be cut into any number of sagittal, coronal, or transverse tissue sections for processing. For both precision and reproducibility, calibrated brain blocks need to be used in a way that ensures consistent bregma cuts between animals. The most important factor that can affect how brains are sectioned is the brain region(s) of interest. For example, while a sagittal cut may allow for more brain regions to be analyzed in one tissue section, this cut will not allow analysis of neuro/gliogenic regions of the ventricular-subventricular zone (V-SVZ) as the lateral and medial sides of the lateral ventricle will be impossible to discern in that dimension and are better observed in the coronal plane. This can be an important distinction to make in adult neurogenesis studies, as the lateral side of the lateral ventricle contains the neurogenic V-SVZ, while the medial wall of the lateral ventricle is a more gliogenic niche37.
After tissues have been divided into coronal, sagittal, or transverse sections, they will be frozen into blocks using Optimal Cooling Temperature (OCT) embedding solution. Here, brains are frozen within this embedding material, with the use of a mixture of dry ice and ethanol. If thin section analysis is required, blocks will be sliced on a cryostat, and depending on the downstream analysis required can be adhered to positively charged glass slides as thin sections (&#60;20 &#181;m). Glass slides that are not charged can also be used, but the use of uncharged slides may result in tissues becoming unstuck from the slides38. If medium-thickness free-floating tissue sections (&#62;20 &#181;m) are required, tissues will be collected as free-floating sections. If thick sections (0.5-4 mm) are required, slicing non-frozen brain sections with a vibratome is required. It is important to note the storage differences between sections on slides, which require freezing at -20 to -80 &#176;C and free-floating sections, which will be stored at 4 &#176;C.
Brain clearing and whole mount immunofluorescent confocal microscopy 
If a broader, yet less detailed analysis of the lineage-traced cells in the mouse brain is desired, a comprehensive analysis of thicker segments of brain tissue is possible with iDISCO brain clearing39 followed by immunostaining and tiled z-stack confocal microscopy or light-sheet microscopy. Here, large sections of mouse brain will be optically cleared (a process of delipidation39), which better allows for fluorescent signal imaging across a 1 mm tissue section. The downsides of this process are high autofluorescence and a diminished ability to obtain high resolution images of cell morphology and detailed co-staining analysis due to the increased working distances required when compared to more traditional methods (thin cryosections or free-floating sections). For this reason, we recommend brain clearing to analyze the large-scale lineage tracing results throughout multiple brain areas, instead of attempting to characterize or analyze individual cells.

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			<td>Agilent</td>
			<td>S2367</td>
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			<td>anti-GFP antibody</td>
			<td>Invitrogen</td>
			<td>A2311</td>
			<td>Use at 1:500-1:000</td>
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			<td>Acetone</td>
			<td>Fisher Scientific</td>
			<td>A18-4</td>
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			<td>B6.Cg-Tg(tet0-cre)1Jaw/J</td>
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			<td>B6.129(Cg)-Gt(ROSA)26Sortm4(ACTB-tdTomato,-EGFP)Luo/J</td>
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			<td>Coronal brain block</td>
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			<td>Sigma-Aldrich</td>
			<td>H3393</td>
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			<td>Histochoice Molecular Biology Tissue Fixative</td>
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			<td>516813</td>
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			<td>Ketamine</td>
			<td>Westward</td>
			<td>0143-95095-10</td>
			<td>This product requires a DEA license for storage and use.</td>
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			<td>A452-4</td>
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			<td>Microscope Slides</td>
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			<td>Teknova</td>
			<td>P0496</td>
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			<td>Sigma-Aldrich</td>
			<td>S7903</td>
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			<td>Sudan (Typogen) Black</td>
			<td>Millipore Sigma</td>
			<td>199664</td>
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			<td>Tetrahydrofuran</td>
			<td>Sigma-Aldrich</td>
			<td>186562</td>
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lineage tracing of inducible fluorescently-labeled stem cells in the adult mouse brain

A telomerase reverse transcriptase (Tert) lineage-tracing mouse line was developed to investigate the behavior and fate of adult tissue stem cells, by crossing the &#39;Tet-On&#39; system oTet-Cre mouse with a novel reverse tetracycline transactivator (rtTA) transgene linked to the Tert promoter, which we have demonstrated marks a novel population of adult brain stem cells. Here, administration of the tetracycline derivative doxycycline to mTert-rtTA::oTet-Cre mice will indelibly mark a population of cells that express a 4.4 kb fragment of the promoter region of the gene Tert. When combined the Rosa-mTmG reporter, mTert-rtTA::oTet-Cre::Rosa-mTmG mice will express membrane tdTomato (mTomato) until doxycycline treatment induces the replacement of mTomato expression with membrane EGFP (mGFP) in cells that also express Tert. Therefore, when these triple-transgenic lineage tracing mice receive doxycycline (the &#34;pulse&#34; period during which TERT expressing cells are marked), these cells will become indelibly marked mGFP+ cells, which can be tracked for any desirable amount of time after doxycycline removal (the &#34;chase&#34; period), even if Tert expression is subsequently lost. Brains are then perfusion-fixed and processed for immunofluorescence and other downstream applications in order to interpret changes to stem cell activation, proliferation, lineage commitment, migration to various brain niches, and differentiation to mature cell types. Using this system, any rtTA mouse can be mated to oTet-Cre and a Rosa reporter to conduct doxycycline-inducible &#34;pulse-chase&#34; lineage&#160;tracing experiments using markers of stem cells.

While the fluorescent signal resulting from a Tet-On system with a fluorescent reporter will vary depending on the promoter of interest and fluorophore(s) used, we will describe how findings were analyzed with mTert-rtTA::oTet-Cre::Rosa-mTmG animals. Analysis of adult brains after a pulse-chase resulted in membrane GFP-expressing cells throughout various anatomical niches. The difference in fluorescent intensity between various cell types must be noted. One variable regarding fluorescent intensity is the size of the cell...

Watch this Scientific Journal Video about Lineage Tracing of Inducible Fluorescently-Labeled Stem Cells in the Adult Mouse Brain at JoVE.com

Lineage Tracing of Inducible Fluorescently-Labeled Stem Cells in the Adult Mouse Brain

The ability to permanently mark stem cells and their progeny with a fluorophore using an inducible transgenic lineage tracing mouse line allows for spatial and temporal analysis of activation, proliferation, migration, and/or differentiation in vivo. Lineage tracing can reveal novel information about lineage commitment, response to intervention(s), and multipotency.

A telomerase reverse transcriptase (Tert) lineage-tracing mouse line was developed to investigate the behavior and fate of adult tissue stem cells, by ...

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