We would like to thank the Flow cytometry Core Facilities at the University of Ottawa and the Keenan Research Centre for Biomedical Sciences (KRC), St Michaels Hospital Unity Health Toronto for their expertise and guidance in optimization of the flow cytometry/FACS protocol presented in this manuscript. This work was funded by Medicine by Design New Ideas 2018 Fund (MbDNI-2018-01) to JB.

The authors have no conflicts to disclose.

An optimized, validated FAPs isolation protocol for rat muscle is essential for researchers who wish to study injury models that are not feasible in the mouse for biologic or technical reasons. For example, mice are not an optimal animal model in which to study chronic local, or neurodegenerative injuries such as long-term denervation. Biologically, the short lifespan and rapid aging of mice make it difficult to accurately delineate the muscle sequalae due to denervation from the confounding factor of aging. From a techn...

Fibro-adipogenic progenitor cells (FAPs) are a population of resident multipotent progenitor cells in skeletal muscle that play a critical role in muscle homeostasis, repair, and regeneration, and conversely, also mediate pathologic responses to muscle injury. As the name suggests, FAPs were originally identified as a progenitor population with the potential to differentiate into fibroblasts and adipocytes1&#160;and were purported to be the key mediators of fibro-fatty infiltration of skeletal muscle in chronic injury and disease. Further study revealed that FAPs are additionally capable of osteogenesis and chondrogenesis2,3,4. Thus, they are more broadly notated in the literature as mesenchymal or stromal progenitors3,5,6,7,8. In acute skeletal muscle injury, FAPs indirectly aid in regenerative myogenesis by transiently proliferating to provide a favorable environment for activated muscle satellite cells and their downstream myogenic progenitor (MPs) counterparts1,9,10. In parallel with successful regeneration, FAPs undergo apoptosis, returning their numbers to baseline levels1,9,10,11. In contrast, in chronic muscle injury, FAPs override pro-apoptotic signals, which results in their persistence9,10,11&#160;and abnormal muscle repair.
In vivo studies evaluating the cellular and molecular mechanisms by which FAPs mediate muscle responses have utilized murine animal models to date1,7,9,10,11,12,13,14. While genetically engineered mice are powerful tools for&#160;use in these analyses, the small size of the animal limits tissue availability for study in long-term localized injury models where muscle atrophy can be profound, such as traumatic denervation. Furthermore, measurement of muscle strength and physical function requires ex vivo or in situ measurements that necessitate termination of the mouse, or in vivo methods that require surgery and/or a general anaesthetic to permit evaluation of muscle contractile performance15,16,17,18,19,20. In rats, well validated and globally utilized muscle functional analyses, in addition to analyses for more complex motor behaviors such as gait analysis (e.g., Sciatic Function Index, CatWalk analysis) exist and are performed in awake and spontaneously moving animals21,22,23,24. This additionally optimizes the principles of minimal morbidity in animal experimentation, and numbers of research animals used. The rat thereby provides the FAPs investigator the added flexibility of greater injured muscle volume for protein and cellular analyses and the ability to undertake serial assessments of muscle complex static and dynamic functional activity and behaviors, in the alert animal.
FAPs have primarily been identified and isolated from whole muscle samples using flow cytometry and Fluorescence-activated cell sorting (FACS) respectively. These are laser-based assays that are able to identify multiple specific cell populations based on characteristic features such as size, granularity, and a specific combination of cell surface or intracellular markers25. This is highly advantageous in the study of an organ system such as skeletal muscle, as homeostasis and regeneration are&#160;complex, multifactorial processes coordinated by a plethora of cell types. A seminal study identified FAPs, as well as MPs, using flow cytometric methods in mouse skeletal muscle1. They demonstrated that FAPs are mesenchymal in nature, as they lacked surface antigens specific to cells from endothelial (CD31), hematopoietic (CD45), or myogenic (Integrin-&#945;7 [ITGA7]) origins, but expressed the mesenchymal stem cell marker Sca-1 (Stem cell antigen 1)1&#160;and differentiated into fibrogenic and adipogenic cells in culture. Other studies demonstrated successful isolation of mesenchymal progenitors in muscle based on the expression of an alternative stem cell marker, platelet-derived growth factor receptor alpha (PDGFR&#945;)2,7,8&#160;and further analysis revealed these likely to be the same cell population as FAPs3. FAPs are now commonly identified in flow cytometry using either Sca-1 or PDGFR&#945; as a positive selection marker1,9,10,11,12,13,14,26,27,28,29,30,31. The use of PDGFR&#945; is preferential for human tissue&#160;however, as a direct human homologue of murine Sca-1 has yet to be identified32. In addition, other cell surface proteins have been reported as markers of MPs (e.g., VCAM-1), providing a potential alternative to ITGA7 as an indicator of cells of myogenic lineage during FAPs isolation33.
While flow cytometry/FACS is a powerful methodology for studying the role and pathogenic potential of FAPs in skeletal muscle1,9,10,11,13,29, it is limited technically by the specificity and optimization of its required reagents. Since flow cytometric identification and isolation of FAPs has been developed and conducted in mouse animal models1,9,10,11,29, this poses challenges for researchers who wish to study FAPs in other model organisms. Many factors - such as optimal tissue size to be processed, as well as reagent and/or antibody specificity and availability - differ depending on the species used.
In addition to the technical barriers to studying FAPs in a novel animal model, they have largely been studied in an acute, toxic setting - usually via intramuscular chemical injection or cardiotoxin. Evaluation of the long-term dynamics of FAPs is limited primarily to assessment in Duchenne&#39;s muscular dystrophy, using the mdx mouse model9,10,11, and models of combination muscle injury such as massive rotator cuff tear where concurrent tendon transection and denervation is performed on shoulder musculature26,27,28. The response of FAPs to the sole insult of chronic traumatic denervation, a common occurrence in work-place accidents in heavy industry, agriculture, and in birth traumas (brachial plexus injury)34,35,36,37&#160;with significant morbidity, has not been as well characterized, often limited to a short-term time frame11,38.
We describe a method for identifying and isolating FAPs and MPs from healthy as well as severely atrophic and fibrotic skeletal muscle in the rat. First, identification of CD31-/CD45-/Sca-1+/VCAM-1- FAPs and CD31-/CD45-/Sca-1-/VCAM-1+ MPs using a tissue digestion and flow cytometry staining protocol is demonstrated and subsequent validation of our findings is performed through culture and immunocytochemical staining of FACS-isolated cells. Using this method, we also report a novel FAPs time-course in a long-term isolated denervation injury model in the rat.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>5 mL Polypropylene Round-Bottom Tube</td>
			<td>Falcon</td>
			<td>352063</td>
			<td></td>
		</tr>
		<tr>
			<td>5 mL Polystyrene Round-Bottom Tube with Cell-Strainer Cap</td>
			<td>Falcon</td>
			<td>352235</td>
			<td></td>
		</tr>
		<tr>
			<td>10 cm cell culture dishes</td>
			<td>Sarstedt</td>
			<td>83.3902</td>
			<td></td>
		</tr>
		<tr>
			<td>12-well cell culture plate</td>
			<td>ThermoFisher</td>
			<td>130185</td>
			<td></td>
		</tr>
		<tr>
			<td>12 mm glass coverslips, No.2</td>
			<td>VWR</td>
			<td>89015-724</td>
			<td></td>
		</tr>
		<tr>
			<td>10 mL Syringe</td>
			<td>Beckton Dickenson</td>
			<td>302995</td>
			<td></td>
		</tr>
		<tr>
			<td>15 mL centrifuge tubes</td>
			<td>FroggaBio</td>
			<td>91014</td>
			<td></td>
		</tr>
		<tr>
			<td>20 gauge needle</td>
			<td>Beckton Dickenson</td>
			<td>305176</td>
			<td></td>
		</tr>
		<tr>
			<td>25mL Serological pipette</td>
			<td>Sarstedt</td>
			<td>86.1685.001</td>
			<td></td>
		</tr>
		<tr>
			<td>40&#181;m cell strainer</td>
			<td>Fisher Scientific</td>
			<td>22363547</td>
			<td></td>
		</tr>
		<tr>
			<td>50mL centrifuge tubes</td>
			<td>FroggaBio</td>
			<td>TB50</td>
			<td></td>
		</tr>
		<tr>
			<td>AbC Total Antibody Compensation Beads&#160;</td>
			<td>ThermoFisher</td>
			<td>A10497</td>
			<td></td>
		</tr>
		<tr>
			<td>Ammonium Chloride, Reagent Grade</td>
			<td>Bioshop</td>
			<td>AMC303.500</td>
			<td></td>
		</tr>
		<tr>
			<td>APC Conjugation Kit, 50-100&#181;g</td>
			<td>Biotium</td>
			<td>92307</td>
			<td></td>
		</tr>
		<tr>
			<td>Aquatex Aqueous Mounting Medium</td>
			<td>Merck</td>
			<td>108562</td>
			<td></td>
		</tr>
		<tr>
			<td>Biolaminin 411 LN</td>
			<td>Biolamina</td>
			<td>LN411</td>
			<td></td>
		</tr>
		<tr>
			<td>Bovine Serum Albumin (BSA)</td>
			<td>Bioshop</td>
			<td>ALB001</td>
			<td></td>
		</tr>
		<tr>
			<td>Calcium Chloride</td>
			<td>Bioshop</td>
			<td>CCL444.500</td>
			<td></td>
		</tr>
		<tr>
			<td>Collagenase Type II</td>
			<td>Gibco</td>
			<td>17101015</td>
			<td></td>
		</tr>
		<tr>
			<td>CountBright Plus Absolute Counting Beads</td>
			<td>ThermoFisher</td>
			<td>C36995</td>
			<td></td>
		</tr>
		<tr>
			<td>Dexamethasone</td>
			<td>Millipore Sigma</td>
			<td>D4902</td>
			<td></td>
		</tr>
		<tr>
			<td>Dispase</td>
			<td>Gibco</td>
			<td>17105041</td>
			<td></td>
		</tr>
		<tr>
			<td>Dulbecco&#8217;s Modified Eagle Medium (DMEM) (1X)</td>
			<td>Gibco</td>
			<td>11995-065</td>
			<td>(+)4.5 g/L D-Glucose 
			(+)L-Glutamine 
			(+)110 mg/L Sodium Pyruvate
			</td>
		</tr>
		<tr>
			<td>EDTA</td>
			<td>FisherScientific</td>
			<td>S311</td>
			<td></td>
		</tr>
		<tr>
			<td>FACSClean Solution</td>
			<td>Beckton Dickenson</td>
			<td>340345</td>
			<td></td>
		</tr>
		<tr>
			<td>FACSDiva Software</td>
			<td>Beckton Dickenson</td>
			<td>--</td>
			<td></td>
		</tr>
		<tr>
			<td>FACSRinse Solution</td>
			<td>Beckton Dickenson</td>
			<td>340346</td>
			<td></td>
		</tr>
		<tr>
			<td>Fetal Bovine Serum</td>
			<td>Sigma</td>
			<td>F1051</td>
			<td></td>
		</tr>
		<tr>
			<td>Flow Cytometry Sheath Fluid</td>
			<td>Beckton Dickenson</td>
			<td>342003</td>
			<td></td>
		</tr>
		<tr>
			<td>FlowJo Software</td>
			<td>Beckton Dickenson</td>
			<td>--</td>
			<td></td>
		</tr>
		<tr>
			<td>Fluorescent Mounting Medium</td>
			<td>Dako</td>
			<td>S302380-2</td>
			<td></td>
		</tr>
		<tr>
			<td>Goat anti-mouse Alexa Fluor 555 secondary antibody</td>
			<td>Invitrogen</td>
			<td>A21424</td>
			<td></td>
		</tr>
		<tr>
			<td>Goat anti-rabbit Alexa Fluor 488 secondary antibody</td>
			<td>Invitrogen</td>
			<td>A11008</td>
			<td></td>
		</tr>
		<tr>
			<td>Goat anti-rabbit Alexa Fluor 555 secondary antibody</td>
			<td>Invitrogen</td>
			<td>A21429</td>
			<td></td>
		</tr>
		<tr>
			<td>Goat Serum</td>
			<td>Gibco</td>
			<td>16210-064</td>
			<td></td>
		</tr>
		<tr>
			<td>Ham&#39;s F10 Media</td>
			<td>ThermoFisher&#160;</td>
			<td>11550043</td>
			<td>(+) Phenol Red 
			(+) L-Glutamine 
			(-) HEPES</td>
		</tr>
		<tr>
			<td>Hank&#8217;s Balanced Salt Solution (HBSS) (1X)</td>
			<td>Multicell</td>
			<td>311-513-CL</td>
			<td></td>
		</tr>
		<tr>
			<td>Heat Inactivated Horse Serum</td>
			<td>Gibco</td>
			<td>26050-088</td>
			<td></td>
		</tr>
		<tr>
			<td>Hemocytometer</td>
			<td>Reichert</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>HEPES, minimum 99.5% titration</td>
			<td>Sigma</td>
			<td>H3375</td>
			<td></td>
		</tr>
		<tr>
			<td>Horse Serum</td>
			<td>ThermoFisher</td>
			<td>16050130</td>
			<td></td>
		</tr>
		<tr>
			<td>Human Transforming Growth Factor &#946;1 (hTGF-&#946;1)</td>
			<td>Cell Signaling</td>
			<td>8915LF</td>
			<td></td>
		</tr>
		<tr>
			<td>Humulin R</td>
			<td>Lilly</td>
			<td>HI0210</td>
			<td></td>
		</tr>
		<tr>
			<td>IBMX</td>
			<td>Millipore Sigma</td>
			<td>I5879</td>
			<td>Also known as 3-Isobutyl-1-methylxanthine</td>
		</tr>
		<tr>
			<td>Isopropanol</td>
			<td>Sigma</td>
			<td>I9516</td>
			<td>Also known as 2-propanol</td>
		</tr>
		<tr>
			<td>Lewis Rat, Female</td>
			<td>Charles River Kingston</td>
			<td>004 (Strain Code)</td>
			<td>200-250 grams used</td>
		</tr>
		<tr>
			<td>LSRFortessa X-20 Benchtop Cytometer</td>
			<td>Beckton Dickenson</td>
			<td>--</td>
			<td></td>
		</tr>
		<tr>
			<td>Microcentrifuge</td>
			<td>Eppendorf</td>
			<td>EP-5417R</td>
			<td></td>
		</tr>
		<tr>
			<td>MoFlo XDP Cell Sorter</td>
			<td>Beckman Coulter</td>
			<td>--</td>
			<td></td>
		</tr>
		<tr>
			<td>Mouse Anti-CD31::FITC Antibody</td>
			<td>Abcam</td>
			<td>ab33858</td>
			<td>Clone TLD-3A12</td>
		</tr>
		<tr>
			<td>Mouse Anti-CD45::FITC Antibody</td>
			<td>Biolegend</td>
			<td>202205</td>
			<td>Clone OX-1</td>
		</tr>
		<tr>
			<td>Mouse Anti-CD106::PE Antibody</td>
			<td>Biolegend</td>
			<td>200403</td>
			<td>Also known as VCAM-1</td>
		</tr>
		<tr>
			<td>Mouse Anti-MHC Antibody</td>
			<td>Developmental Studies Hybridoma Bank (DSHB)</td>
			<td>N/A</td>
			<td>Also known as MF20</td>
		</tr>
		<tr>
			<td>Mouse Anti-Pax7 Antibody</td>
			<td>Developmental Studies Hybridoma Bank (DSHB)</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Neutral Buffered Formalin, 10 %</td>
			<td>Sigma</td>
			<td>HT501128</td>
			<td></td>
		</tr>
		<tr>
			<td>Oil Red O</td>
			<td>Millipore Sigma</td>
			<td>O0625</td>
			<td></td>
		</tr>
		<tr>
			<td>PE-Cy7 Conjugation Kit</td>
			<td>Abcam</td>
			<td>ab102903</td>
			<td></td>
		</tr>
		<tr>
			<td>Penicillin-Streptomycin</td>
			<td>Sigma&#160;</td>
			<td>P4333</td>
			<td></td>
		</tr>
		<tr>
			<td>Phosphate Buffered Saline, pH 7.4 (1X)</td>
			<td>Gibco</td>
			<td>10010-023</td>
			<td>(-)Calcium Chloride 
			(-)Magnesium Chloride
			</td>
		</tr>
		<tr>
			<td>Potassium Bicarbonate, Reagent Grade</td>
			<td>Bioshop</td>
			<td>PBC401.250</td>
			<td></td>
		</tr>
		<tr>
			<td>Rabbit Anti-Fibroblast Specific Protein 1 (FSP-1) Antibody</td>
			<td>Invitrogen</td>
			<td>MA5-32347</td>
			<td>FSP-1 also known as S100A4</td>
		</tr>
		<tr>
			<td>Rabbit Anti-Integrin-a7 Antibody</td>
			<td>Abcam</td>
			<td>ab203254</td>
			<td></td>
		</tr>
		<tr>
			<td>Rabbit Anti-Laminin Antibody</td>
			<td>Sigma</td>
			<td>L9393</td>
			<td></td>
		</tr>
		<tr>
			<td>Rabbit Anti-Perilipin-1 Antibody</td>
			<td>Abcam</td>
			<td>ab3526</td>
			<td></td>
		</tr>
		<tr>
			<td>Rabbit Anti-Sca-1 Antibody</td>
			<td>Millipore Sigma</td>
			<td>AB4336</td>
			<td></td>
		</tr>
		<tr>
			<td>Rabbit Recombinant Anti-Collagen Type I Antibody</td>
			<td>Abcam</td>
			<td>ab260043</td>
			<td>Also known as Col1a1</td>
		</tr>
		<tr>
			<td>Rabbit Recombinant Anti-PDGFR Alpha Antibody</td>
			<td>Abcam</td>
			<td>ab203491</td>
			<td></td>
		</tr>
		<tr>
			<td>Recombinant Human FGF-basic</td>
			<td>Gibco</td>
			<td>PHG0266</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium Azide</td>
			<td>Sigma</td>
			<td>S2002</td>
			<td></td>
		</tr>
		<tr>
			<td>Triton-X-100</td>
			<td>Fisher Scientific</td>
			<td>BP151</td>
			<td></td>
		</tr>
		<tr>
			<td>Troglitazone</td>
			<td>Millipore Sigma</td>
			<td>T2573</td>
			<td></td>
		</tr>
		<tr>
			<td>Tween-20</td>
			<td>Bioshop</td>
			<td>TWN510</td>
			<td></td>
		</tr>
	</tbody>
</table>

identification, isolation, and characterization of fibro-adipogenic progenitors (faps) and myogenic progenitors (mps) in skeletal muscle in the rat

Fibro-adipogenic Progenitors (FAPs) are resident interstitial cells in skeletal muscle that, together with myogenic progenitors (MPs), play a key role in muscle homeostasis, injury, and repair. Current protocols for FAPs identification and isolation use flow cytometry/fluorescence-activated cell sorting (FACS) and studies evaluating their function in vivo to date have been undertaken exclusively in mice. The larger inherent size of the rat allows for a more comprehensive analysis of FAPs in skeletal muscle injury models, especially in severely atrophic muscle or when investigators require substantial tissue mass to conduct multiple downstream assays. The rat additionally provides a larger selection of muscle functional assays that do not require animal sedation or sacrifice, thus minimizing morbidity and animal use by enabling serial assessments. The flow cytometry/FACS protocols optimized for mice are species specific, notably restricted by the characteristics of commercially available antibodies. They have not been optimized for separating FAPs from rat or highly fibrotic muscle. A flow cytometry/FACS protocol for the identification and isolation of FAPs and MPs from both healthy and denervated rat skeletal muscle was developed, relying on the differential expression of surface markers CD31, CD45, Sca-1, and VCAM-1. As rat-specific, flow cytometry-validated primary antibodies are severely limited, in-house conjugation of the antibody targeting Sca-1 was performed. Using this protocol, successful Sca-1 conjugation was confirmed, and flow cytometric identification of FAPs and MPs was validated by cell culture and immunostaining of FACS-isolated FAPs and MPs. Finally, we report a novel FAPs time-course in a prolonged (14 week) rat denervation model. This method provides the investigators the ability to study FAPs in a novel animal model.

Identifying FAPs and MPs via flow cytometry using a novel antibody panel including Sca-1 and VCAM-1 
The gating strategy for identifying FAPs in rat muscle is based upon flow cytometry protocols in the mouse29, which gate on CD31 (endothelial) and CD45 (hematopoietic) positive cells (termed the lineage [Lin]) and examines the fluorescent profile of FAPs marker Sca-1 and MPs marker ITGA7 from the linage-negative (Lin-) populat...

Watch this Scientific Journal Video about Identification, Isolation, and Characterization of Fibro-Adipogenic Progenitors FAPs and Myogenic Progenitors MPs in Skeletal Muscle in the Rat at JoVE.com

Identification, Isolation, and Characterization of Fibro-Adipogenic Progenitors FAPs and Myogenic Progenitors MPs in Skeletal Muscle in the Rat

This protocol outlines a method to isolate Fibro-adipogenic progenitors (FAPs) and myogenic progenitors (MPs) from rat skeletal muscle. Utilization of the rat in muscle injury models provides increased tissue availability from atrophic muscle for the analysis and a larger repertoire of validated methods to assess muscle strength and gait in free-moving animals.

Identification, Isolation, and Characterization of Fibro-Adipogenic Progenitors (FAPs) and Myogenic Progenitors (MPs) in Skeletal Muscle in the Rat

Fibro-adipogenic Progenitors (FAPs) are resident interstitial cells in skeletal muscle that, together with myogenic progenitors (MPs), play a key role in ...

identification-isolation-characterization-fibro-adipogenic

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JoVE Journal

Biology

5.6K Views.  St Michaels Hospital, Unity Health Toronto. This protocol outlines a method to isolate Fibro-adipogenic progenitors (FAPs) and myogenic progenitors (MPs) from rat skeletal muscle. Utilization of the rat in muscle injury models provides increased tissue availability from atrophic muscle for the analysis and a larger repertoire of validated methods to assess muscle strength and gait in free-moving animals.

Video: Identification, Isolation, and Characterization of Fibro-Adipogenic Progenitors FAPs and Myogenic Progenitors MPs in Skeletal Muscle in the Rat

Adult and Embryonic Skeletal Muscle Microexplant Culture and Isolation of Skeletal Muscle Stem Cells

Cultured embryonic and adult skeletal muscle cells have a number of different uses. The micro-dissected explants technique described in this chapter is a robust and reliable method for isolating relatively large numbers of proliferative skeletal muscle cells from juvenile, adult or embryonic muscles as a source of skeletal muscle stem cells. The authors have used micro-dissected explant cultures to analyse the growth characteristics of skeletal muscle cells in wild-type and dystrophic muscles. Each of the components of tissue growth, namely cell survival, proliferation, senescence and differentiation can be analysed separately using the methods described here. The net effect of all components of growth can be established by means of measuring explant outgrowth rates. The micro-explant method can be used to establish primary cultures from a wide range of different muscle types and ages and, as described here, has been adapted by the authors to enable the isolation of embryonic skeletal muscle precursors.
Uniquely, micro-explant cultures have been used to derive clonal (single cell origin) skeletal muscle stem cell (SMSc) lines which can be expanded and used for in vivo transplantation. In vivo transplanted SMSc behave as functional, tissue-specific, satellite cells which contribute to skeletal muscle fibre regeneration but which are also retained (in the satellite cell niche) as a small pool of undifferentiated stem cells which can be re-isolated into culture using the micro-explant method.

The micro-dissected explants technique is a robust and reliable method for isolating proliferative skeletal muscle cells from juvenile, adult or embryonic muscles as a source of skeletal muscle stem cells. Uniquely, these cells have been clonally derived to produce skeletal muscle stem cell lines used for in vivo transplantation.

Cultured embryonic and adult skeletal muscle cells have a number of different uses. The micro-dissected explants technique described in this chapter is a ...

Purification of Progenitors from Skeletal Muscle

Skeletal muscle contains multiple progenitor populations of distinct embryonic origins and developmental potential. Myogenic progenitors, usually residing in a "satellite cell position" between the myofiber plasma membrane and the laminin-rich basement membrane that ensheaths it, are self-renewing cells that are solely committed to the myogenic lineage1,2. We have recently described a second class of vessel associated progenitors that can generate myofibroblasts and white adipocytes, which responds to damage by efficiently entering proliferation and provides trophic support to myogenic cells during tissue regeneration3,4. One of the most trusted assays to determine the developmental and regenerative potential of a given cell population relies on their isolation and transplantation5-7. To this end we have optimized protocols for their purification by flow cytometry from enzymatically dissociated muscle, which we will outline in this article. The populations obtained using this method will contain either myogenic or fibro/adipogenic colony forming cells: no other cell types are capable of expanding in vitro or surviving in vivo delivery. However, when these populations are used immediately after the sort for molecular analysis (e.g qRT-PCR) one must keep in mind that the freshly sorted subsets may contain other contaminant cells that lack the ability of forming colonies or engrafting recipients.

Method for the enzymatic dissociation, surface labeling and purification by flow cytometry of fibro/adipogenic and myogenic progenitors from murine skeletal muscle.

Skeletal muscle contains multiple progenitor populations of distinct embryonic origins and developmental potential. Myogenic progenitors, usually residing ...

Identification and Analysis of Mouse Erythroid Progenitors using the CD71/TER119 Flow-cytometric Assay

The study of erythropoiesis aims to understand how red cells are formed from earlier hematopoietic and erythroid progenitors. Specifically, the rate of red cell formation is regulated by the hormone erythropoietin (Epo), whose synthesis is triggered by tissue hypoxia. A threat to adequate tissue oxygenation results in a rapid increase in Epo, driving an increase in erythropoietic rate, a process known as the erythropoietic stress response. The resulting increase in the number of circulating red cells improves tissue oxygen delivery. An efficient erythropoietic stress response is therefore critical to the survival and recovery from physiological and pathological conditions such as high altitude, anemia, hemorrhage, chemotherapy or stem cell transplantation. 
The mouse is a key model for the study of erythropoiesis and its stress response. Mouse definitive (adult-type) erythropoiesis takes place in the fetal liver between embryonic days 12.5 and 15.5, in the neonatal spleen, and in adult spleen and bone marrow. Classical methods of identifying erythroid progenitors in tissue rely on the ability of these cells to give rise to red cell colonies when plated in Epo-containing semi-solid media. Their erythroid precursor progeny are identified based on morphological criteria. Neither of these classical methods allow access to large numbers of differentiation-stage-specific erythroid cells for molecular study. Here we present a flow-cytometric method of identifying and studying differentiation-stage-specific erythroid progenitors and precursors, directly in the context of freshly isolated mouse tissue. The assay relies on the cell-surface markers CD71, Ter119, and on the flow-cytometric 'forward-scatter' parameter, which is a function of cell size. The CD71/Ter119 assay can be used to study erythroid progenitors during their response to erythropoietic stress in vivo, for example, in anemic mice or mice housed in low oxygen conditions. It may also be used to study erythroid progenitors directly in the tissues of genetically modified adult mice or embryos, in order to assess the specific role of the modified molecular pathway in erythropoiesis.

A flow-cytometric method for identification and molecular analysis of differentiation-stage-specific murine erythroid progenitors and precursors, directly in freshly &#x2013;harvested mouse bone marrow, spleen or fetal liver. The assay relies on cell-surface markers CD71, Ter119, and cell size.

The study of erythropoiesis aims to understand how red cells are formed from earlier hematopoietic and erythroid progenitors. Specifically, the rate of ...

A Quantitative Assay for Insulin-expressing Colony-forming Progenitors

The field of pancreatic stem and progenitor cell biology has been hampered by a lack of in vitro functional and quantitative assays that allow for the analysis of the single cell. Analyses of single progenitors are of critical importance because they provide definitive ways to unequivocally demonstrate the lineage potential of individual progenitors. Although methods have been devised to generate "pancreatospheres" in suspension culture from single cells, several limitations exist. First, it is time-consuming to perform single cell deposition for a large number of cells, which in turn commands large volumes of culture media and space. Second, numeration of the resulting pancreatospheres is labor-intensive, especially when the frequency of the pancreatosphere-initiating progenitors is low. Third, the pancreatosphere assay is not an efficient method to allow both the proliferation and differentiation of pancreatic progenitors in the same culture well, restricting the usefulness of the assay.
To overcome these limitations, a semi-solid media based colony assay for pancreatic progenitors has been developed and is presented in this report. This method takes advantage of an existing concept from the hematopoietic colony assay, in which methylcellulose is used to provide viscosity to the media, allowing the progenitor cells to stay in three-dimensional space as they undergo proliferation as well as differentiation. To enrich insulin-expressing colony-forming progenitors from a heterogeneous population, we utilized cells that express neurogenin (Ngn) 3, a pancreatic endocrine progenitor cell marker. Murine embryonic stem (ES) cell-derived Ngn3 expressing cells tagged with the enhanced green fluorescent protein reporter were sorted and as many as 25,000 cells per well were plated into low-attachment 24-well culture dishes. Each well contained 500 &mu;L of semi-solid media with the following major components: methylcellulose, Matrigel, nicotinamide, exendin-4, activin &beta;B, and conditioned media collected from murine ES cell-derived pancreatic-like cells. After 8 to 12 days of culture, insulin-expressing colonies with distinctive morphology were formed and could be further analyzed for pancreatic gene expression using quantitative RT-PCR and immunoflourescent staining to determine the lineage composition of each colony.
In summary, our colony assay allows easy detection and quantification of functional progenitors within a heterogeneous population of cells. In addition, the semi-solid media format allows uniform presentation of extracellular matrix components and growth factors to cells, enabling progenitors to proliferate and differentiate in vitro. This colony assay provides unique opportunities for mechanistic studies of pancreatic progenitor cells at the single cell level.

A three-dimensional clonogenic assay that allows pancreatic-like progenitors to differentiate into insulin-expressing colonies is described. This method takes advantage of semi-solid media containing methylcellulose, Matrigel and growth factors, in which single progenitors proliferate and differentiate in vitro, permitting quantification of the number of functional progenitors in a population.

The field of pancreatic stem and progenitor cell biology has been hampered by a lack of in vitro functional and quantitative assays that allow for the ...

Phenotypic Analysis and Isolation of Murine Hematopoietic Stem Cells and Lineage-committed Progenitors

The bone marrow is the principal site where HSCs and more mature blood cells lineage progenitors reside and differentiate in an adult organism. HSCs constitute a minute cell population of pluripotent cells capable of generating all blood cell lineages for a life-time1. The molecular dissection of HSCs homeostasis in the bone marrow has important implications in hematopoiesis, oncology and regenerative medicine. We describe the labeling protocol with fluorescent antibodies and the electronic gating procedure in flow cytometry to score hematopoietic progenitor subsets and HSCs distribution in individual mice (Fig. 1). In addition, we describe a method to extensively enrich hematopoietic progenitors as well as long-term (LT) and short term (ST) reconstituting HSCs from pooled bone marrow cell suspensions by magnetic enrichment of cells expressing c-Kit. The resulting cell preparation can be used to sort selected subsets for in vitro and in vivo functional studies (Fig. 2).
Both trabecular osteoblasts2,3 and sinusoidal endothelium4 constitute functional niches supporting HSCs in the bone marrow. Several mechanisms in the osteoblastic niche, including a subset of N-cadherin+ osteoblasts3 and interaction of the receptor tyrosine kinase Tie2 expressed in HSCs with its ligand angiopoietin-15 concur in determining HSCs quiescence. "Hibernation" in the bone marrow is crucial to protect HSCs from replication and eventual exhaustion upon excessive cycling activity6. Exogenous stimuli acting on cells of the innate immune system such as Toll-like receptor ligands7 and interferon-&alpha;6 can also induce proliferation and differentiation of HSCs into lineage committed progenitors. Recently, a population of dormant mouse HSCs within the lin- c-Kit+ Sca-1+ CD150+ CD48- CD34- population has been described8. Sorting of cells based on CD34 expression from the hematopoietic progenitors-enriched cell suspension as described here allows the isolation of both quiescent self-renewing LT-HSCs and ST-HSCs9. A similar procedure based on depletion of lineage positive cells and sorting of LT-HSC with CD48 and Flk2 antibodies has been previously described10. In the present report we provide a protocol for the phenotypic characterization and ex vivo cell cycle analysis of hematopoietic progenitors, which can be useful for monitoring hematopoiesis in different physiological and pathological conditions. Moreover, we describe a FACS sorting procedure for HSCs, which can be used to define factors and mechanisms regulating their self-renewal, expansion and differentiation in cell biology and signal transduction assays as well as for transplantation.

A method to analyse the distribution of bone marrow hematopoietic progenitors in flow cytometry as well as to efficiently isolate highly purified hematopoietic stem cells (HSCs) is described. The isolation procedure is essentially based on magnetic enrichment of c-Kit+ cells and cell sorting to purify HSCs for cellular and molecular studies.

The bone marrow is the principal site where HSCs and more mature blood cells lineage progenitors reside and differentiate in an adult organism. HSCs ...

Isolation and Primary Culture of Rat Hepatic Cells

Primary hepatocyte culture is a valuable tool that has been extensively used in basic research of liver function, disease, pathophysiology, pharmacology and other related subjects. The method based on two-step collagenase perfusion for isolation of intact hepatocytes was first introduced by Berry and Friend in 1969 1 and, since then, has undergone many modifications. The most commonly used technique was described by Seglenin 1976 2. Essentially, hepatocytes are dissociated from anesthetized adult rats by a non-recirculating collagenase perfusion through the portal vein. The isolated cells are then filtered through a 100 &mu;m pore size mesh nylon filter, and cultured onto plates. After 4-hour culture, the medium is replaced with serum-containing or serum-free medium, e.g. HepatoZYME-SFM, for additional time to culture. These procedures require surgical and sterile culture steps that can be better demonstrated by video than by text. Here, we document the detailed steps for these procedures by both video and written protocol, which allow consistently in the generation of viable hepatocytes in large numbers.

Primary hepatocytes provide a valuable tool to evaluate biochemical, molecular, and metabolic functions in a physiologically relevant experimental system. We describe a reliable protocol for rat in situ liver perfusion, which consistently generates viable hepatocytes up to 1.0 &times; 108 cells per preparation with cell viability between 88 ~ 96%.

Primary hepatocyte culture is a valuable tool that has been extensively used in basic research of liver function, disease, pathophysiology, pharmacology ...

Assessment of Calcium Sparks in Intact Skeletal Muscle Fibers

Maintaining homeostatic Ca2+ signaling is a fundamental physiological process in living cells. Ca2+ sparks are the elementary units of Ca2+ signaling in the striated muscle fibers that appear as highly localized Ca2+ release events mediated by ryanodine receptor (RyR) Ca2+ release channels on the sarcoplasmic reticulum (SR) membrane. Proper assessment of muscle Ca2+ sparks could provide information on the intracellular Ca2+&#160;handling properties of healthy and diseased striated muscles. Although Ca2+ sparks events are commonly seen in resting cardiomyocytes, they are rarely observed in resting skeletal muscle fibers; thus there is a need for methods to generate and analyze sparks in skeletal muscle fibers.
Detailed here is an experimental protocol for measuring Ca2+ sparks in isolated flexor digitorm brevis (FDB) muscle fibers using fluorescent Ca2+ indictors and laser scanning confocal microscopy. In this approach, isolated FDB fibers are exposed to transient hypoosmotic stress followed by a return to isotonic physiological solution. Under these conditions, a robust Ca2+ sparks response is detected adjacent to the sarcolemmal membrane in young healthy FDB muscle fibers. Altered Ca2+ sparks response is detected in dystrophic or aged skeletal muscle fibers. This approach has recently demonstrated that membrane-delimited signaling involving cross-talk between inositol (1,4,5)-triphosphate receptor (IP3R) and RyR contributes to Ca2+ spark activation in skeletal muscle. In summary, our studies using osmotic stress induced Ca2+ sparks showed that this intracellular response reflects a muscle signaling mechanism in physiology and aging/disease states, including mouse models of muscle dystrophy (mdx mice) or amyotrophic lateral sclerosis (ALS model).

Described here is a method to directly measure calcium sparks, the elementary units of Ca2+ release from sarcoplasmic reticulum&#160;in intact skeletal muscle fibers. This method utilizes osmotic-stress-mediated triggering of Ca2+ release from ryanodine receptor in isolated muscle fibers. The dynamics and homeostatic capacity of intracellular Ca2+ signaling can be employed to assess muscle function in health and disease.

Maintaining homeostatic Ca2+ signaling is a fundamental physiological process in living cells. Ca2+ sparks are the elementary units of Ca2+ signaling in ...

Isolation and Characterization of Exosomes from Skeletal Muscle Fibroblasts

Exosomes are small extracellular vesicles released by virtually all cells and secreted in all biological fluids. Many methods have been developed for the isolation of these vesicles, including ultracentrifugation, ultrafiltration, and size exclusion chromatography. However, not all are suitable for large scale exosome purification and characterization. Outlined here is a protocol for establishing cultures of primary fibroblasts isolated from adult mouse skeletal muscles, followed by purification and characterization of exosomes from the culture media of these cells. The method is based on the use of sequential centrifugation steps followed by sucrose density gradients. Purity of the exosomal preparations is then validated by western blot analyses using a battery of canonical markers (i.e., Alix, CD9, and CD81). The protocol describes how to isolate and concentrate bioactive exosomes for electron microscopy, mass spectrometry, and uptake experiments for functional studies. It can easily be scaled up or down and adapted for exosome isolation from different cell types, tissues, and biological fluids.

This protocol illustrates the 1) the isolation and culture of primary fibroblasts from the adult mouse gastrocnemius muscle as well as 2) purification and characterization of exosomes using a differential ultracentrifugation method combined with sucrose density gradients followed by western blot analyses.

Exosomes are small extracellular vesicles released by virtually all cells and secreted in all biological fluids. Many methods have been developed for the ...

Isolation of Mouse Megakaryocyte Progenitors

Bone marrow megakaryocytes are large polyploid cells that ensure the production of blood platelets. They arise from hematopoietic stem cells through megakaryopoiesis. The final stages of this process are complex and classically involve the bipotent Megakaryocyte-Erythrocyte Progenitors (MEP) and the unipotent Megakaryocyte Progenitors (MKp). These populations precede the formation of bona fide megakaryocytes and, as such, their isolation and characterization could allow for the robust and unbiased analysis of megakaryocyte formation. This protocol presents in detail the procedure to collect hematopoietic cells from mouse bone marrow, the enrichment of hematopoietic progenitors through magnetic depletion and finally a cell sorting strategy that yield highly purified MEP and MKp populations. First, bone marrow cells are collected from the femur, the tibia, and also the iliac crest, a bone that contains a high number of hematopoietic progenitors. The use of iliac crest bones drastically increases the total cell number obtained per mouse and thus contributes to a more ethical use of animals. A magnetic lineage depletion was optimized using 450 nm magnetic beads allowing a very efficient cell sorting by flow cytometry. Finally, the protocol presents the labeling and gating strategy for the sorting of the two highly purified megakaryocyte progenitor populations: MEP (Lin-Sca-1-c-Kit+CD16/32-CD150+CD9dim) and MKp (Lin- Sca-1-c-Kit+CD16/32-CD150+CD9bright). This technique is easy to implement and provides enough cellular material to perform i) molecular characterization for a deeper knowledge of their identity and biology, ii) in vitro differentiation assays, that will provide a better understanding of the mechanisms of maturation of megakaryocytes, or iii) in vitro models of interaction with their microenvironment.

This method describes the purification by flow cytometry of MEP and MKp from mice femurs, tibias, and pelvic bones.

Bone marrow megakaryocytes are large polyploid cells that ensure the production of blood platelets. They arise from hematopoietic stem cells through ...

In Silico Identification and Characterization of circRNAs During Host-Pathogen Interactions

Circular RNAs (circRNAs) are a class of non-coding RNAs that are formed via back-splicing. These circRNAs are predominantly studied for their roles as regulators of various biological processes. Notably, emerging evidence demonstrates that host circRNAs can be differentially expressed (DE) upon infection with&#160;pathogens (e.g., influenza and coronaviruses), suggesting a role for circRNAs in regulating host innate immune responses. However, investigations on the role of circRNAs during pathogenic infections are limited by the knowledge and skills required to carry out the necessary bioinformatic analysis to identify DE circRNAs from RNA sequencing (RNA-seq) data. Bioinformatics prediction and identification of circRNAs is crucial before any verification, and functional studies using costly and time-consuming wet-lab techniques. To solve this issue, a step-by-step protocol of in silico prediction and characterization of circRNAs using RNA-seq data is provided in this manuscript. The protocol can be divided into four steps: 1) Prediction and quantification of DE circRNAs via the CIRIquant pipeline; 2) Annotation via circBase and characterization of DE circRNAs; 3) CircRNA-miRNA interaction prediction through Circr pipeline; 4) functional enrichment analysis of circRNA parental genes using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). This pipeline will be useful in driving future in vitro and in vivo research to further unravel the role of circRNAs in host-pathogen interactions.

In Silico Identification and Characterization of circRNAs During Host-Pathogen Interactions

The protocol submitted here explains the complete in silico pipeline needed to predict and functionally characterize circRNAs from RNA-sequencing transcriptome data studying host-pathogen interactions.

Circular RNAs (circRNAs) are a class of non-coding RNAs that are formed via back-splicing. These circRNAs are predominantly studied for their roles as ...