We thank Tasuku Honjo for the AID-/- mice. This work was supported by The National Institute on Minority Health and Health Disparities (5G12MD007603), The National Cancer Institute (2U54CA132378), and The National Institute of General Medical Sciences (1SC1GM132035-01).

All mutant mice were maintained on a C57BL/6 background. Age-matched (2-5 months old) male and female mice were used for all experiments. Husbandry of and experiments with mice were conducted according to protocols approved by The City College of New York Institutional Animal Care and Use Committee.
1. Dissection of Peyer&#8217;s patches
<ol>
	<li>Euthanize the mouse with 100% CO2 at 3 L/min for 5 min followed by cervical dislocation to confirm death. Sterilize dissection tools (scissors, forceps, fine forceps) and gloved hands with 70% ethanol.</li>
	<li>Lay the mouse on the dissection pad with the abdomen exposed. Generously spray the body of the mouse with 70% ethanol prior to making any incisions to sterilize the dissection area.</li>
	<li>Make an incision into the skin across the abdomen and remove the skin from the abdomen by pulling simultaneously on both sides of the incision towards the head and tail using forceps (or sterilized, gloved hands).</li>
	<li>Pin down the fore and hind limbs of the mouse.</li>
	<li>Cut the peritoneal cavity with scissors to expose the internal organs.</li>
	<li>Locate the small intestine between the stomach and caecum (&#8220;J&#8221; shaped structure near the colon). Remove the small intestine by cutting below the stomach and above the caecum.</li>
	<li>Remove any connective tissue and fat linking the folds of the small intestine together. 
	NOTE: Fat will have a distinctive white color, unlike the pink color of the small intestine.</li>
	<li>Examine the external surface of the small intestine for the Peyer&#8217;s patches (PPs), which are small (~1 mm), oval-shaped structures that appear white below a thin layer of translucent epithelial cells.</li>
	<li>Carefully excise all visible PP with scissors. 
	NOTE: One C57BL/6 wild-type (WT) mouse can yield 4-8 PPs, whereas an AID-/- mouse will have 6-10 PPs.</li>
	<li>Collect the PPs into a 1.5 mL microcentrifuge tube containing 1 mL of FACS buffer on ice. 
	NOTE: The PP should sink, whereas fat will float to the surface and can be removed.</li>
</ol>
2. Cell isolation for FACS
<ol>
	<li>Place a 40 &#956;m filter in a 6-well dish with 1 mL of cold (4 &#176;C) FACS buffer.</li>
	<li>Pour the PPs from the 1.5 mL tube onto the filter.</li>
	<li>Wash PPs with 1 mL of cold FACS buffer, making sure that they are always in liquid and on ice.</li>
	<li>Use the flat end of the plunger from a 1 mL syringe as a pestle to crush the PPs on the filter until only connective tissue remains on the filter.</li>
	<li>Wash the filter and plunger with 1 mL of cold FACS buffer to release the cells into the 6 well dish.</li>
	<li>Collect the ~4 mL of cells in cold FACS buffer and filter them through a 40 &#956;m strainer cap FACS tube.</li>
	<li>Wash the strainer cap with 1 mL of cold FACS buffer.</li>
	<li>Pellet the cells at 600 x g at 4 &#176;C for 5 min in a swinging bucket centrifuge.</li>
	<li>Decant the supernatant.</li>
	<li>Resuspend the cells in 0.4 mL of cold FACS buffer.</li>
	<li>Remove 10 &#956;L for cell counting to verify yield (expect ~5 x 106 cells/mouse, see Figure 3A)</li>
	<li>Filter the remaining cells through a 40 &#956;m strainer cap into a FACS tube and proceed to staining for FACS.</li>
</ol>
3. Staining GCBCs for FACS
<ol>
	<li>Add 1 &#956;L Fc block (unlabeled anti-mouse CD16/CD32) to the 400 &#956;L cell suspension and place the cells on ice for 15 min.</li>
	<li>Add 2 mL of cold FACS buffer to wash the cells.
	<ol>
		<li>Pellet cells at 600 x g at 4 &#176;C for 5 min and discard the supernatant.</li>
	</ol>
	</li>
	<li>Resuspend the cells in 80 &#956;L of cold FACS buffer.</li>
	<li>Remove 10 &#956;L of cells from the WT PP for each staining control (4 in total, including 3 single stain controls and 1 unstained control). Leave 40 &#956;L of the WT PP for the next step. Alternatively, use compensation beads for the staining controls.</li>
	<li>Stain each of the experimental samples (e.g., WT and AID-/-) in 500 &#956;L of cold FACS buffer with 2.5 &#956;L of peanut agglutinin (PNA)-biotin for 15 min on ice.</li>
	<li>Add 2 mL of cold FACS buffer to wash the cells.
	<ol>
		<li>Pellet cells at 600 x g at 4 &#176;C for 5 min and discard the supernatant.</li>
	</ol>
	</li>
	<li>Stain each experimental sample with 500 &#956;L of the cocktail in the dark, on ice, for 15 min (Table 1). Ensure the cells are fully resuspended in the staining cocktail.</li>
	<li>Prepare single stain controls for the compensation matrix.
	<ol>
		<li>Stain the cells in 500 &#956;L of cold FACS buffer using the dilutions specified in Table 2.</li>
		<li>Incubate the staining controls in the dark, on ice, for 15 min.</li>
	</ol>
	</li>
	<li>Add 2 mL cold FACS buffer to all the tubes in steps 3.7 and 3.8, pellet the cells, and discard the supernatant to wash off unbound antibodies or DAPI.</li>
	<li>Resuspend the cells in 500 &#956;L of cold FACS buffer and place on ice.</li>
	<li>Using a cell sorter, collect B220+PNAHI from each stained experimental sample. Figure 3B shows the typical percentages of B220+ PNAHI obtained from WT and AID-/- PPs. Figure 3C displays the FACS gating strategy.</li>
</ol>
4. DNA extraction from GCBCs
<ol>
	<li>Pellet sorted cells at 600 x g at 4 &#176;C for 5 min and discard the supernatant.</li>
	<li>Resuspend the cells in 1 mL of cold FACS buffer and transfer the cells into a 1.5 mL microcentrifuge tube.
	<ol>
		<li>Pellet the cells at 600 x g at 4 &#176;C for 5 min and discard the supernatant.</li>
	</ol>
	</li>
	<li>Resuspend the cells in 500 &#956;L of DNA extraction buffer and 5 &#956;L of 20 mg/mL Proteinase K.</li>
	<li>Incubate at 56 &#176;C overnight.</li>
	<li>Precipitate DNA with 500 &#956;L isopropanol and 1 &#956;L of 20 mg/mL glycogen. Mix the tube thoroughly by inverting 5-6x.</li>
	<li>Incubate at room temperature for 10 min.</li>
	<li>Centrifuge in a microcentrifuge for 15 min at 25 &#176;C at 21,000 x g.
	<ol>
		<li>Discard the supernatant and retain the pellet, which contains the precipitated DNA and glycogen.</li>
	</ol>
	</li>
	<li>Wash the DNA pellet with 1 mL of 70% ethanol.
	<ol>
		<li>Pellet the DNA in a microcentrifuge for 10 min at 25 &#176;C at 21,000 x g.</li>
		<li>Remove the 70% ethanol and air-dry the DNA pellet for 5-10 min. 
		NOTE: Avoid over-drying as the DNA may not rehydrate completely.</li>
	</ol>
	</li>
	<li>Resuspend the DNA in 30 &#956;L TE buffer and incubate overnight at 56 &#176;C.</li>
</ol>
5. JH4 intron sequence amplification and analysis
<ol>
	<li>Quantify DNA by measuring the absorbance at a wavelength of 260 nm (A260). 
	NOTE: The typical concentration of DNA recovered from sorted B220+PNAHI GCBCs of a C57BL/6 mouse is 20-40 ng/&#956;L.</li>
	<li>Perform the nested PCR for the JH4 intron (Table 3, Table 4). Normalize the total amount of genomic DNA used in the first PCR to the least concentrated sample. (e.g., if the least concentrated sample is 5 ng/&#956;L, use 58.75 ng of DNA for all the samples in the maximum volume of water (11.75 &#956;L) in PCR #1).</li>
	<li>Resolve the PCR product on a 1.5% agarose gel at 200 V for 20 min. The expected amplicon size is 580 bp.</li>
	<li>Excise the amplicon from the gel and extract the DNA using a gel extraction kit according to manufacturer&#8217;s instructions (see Supplementary Figure 1).
	<ol>
		<li>Elute the DNA with 30 &#956;L of water and quantify the amount of DNA by measuring the A260. 
		NOTE: The typical concentration of the purified PCR product is 3-10 ng/&#956;L.</li>
	</ol>
	</li>
	<li>Ligate the purified PCR product into a plasmid with blunt ends. Standardize the total amount of PCR product used in every ligation reaction (Table 5).
	<ol>
		<li>Incubate the ligation reaction at room temperature for 5 min or overnight at 16 &#176;C.</li>
	</ol>
	</li>
	<li>Transform electrocompetent bacterial cells with 2 &#956;L of the ligation reaction.
	<ol>
		<li>Electroporate at 1.65 kV.</li>
		<li>Rescue in 600 &#956;L of SOC media for 1 h at 37 &#176;C in a shaking incubator at 225 rpm.</li>
		<li>Plate 100 &#956;L of transformed bacteria onto LB supplemented with ampicillin (100 &#956;g/mL) agar plates and incubate overnight at 37 &#176;C.</li>
	</ol>
	</li>
	<li>Submit the plate of bacterial colonies for Sanger sequencing using the T7 forward primer. Alternatively, grow overnight cultures of each bacterial colony and perform a plasmid purification.
	<ol>
		<li>If necessary, repeat the PCR, ligation, and/or transformation to optimize the yield of bacterial colonies 
		NOTE: A minimum of 30 colonies should be picked from each plate.</li>
	</ol>
	</li>
	<li>Standardize the sequence data in the .txt files
	<ol>
		<li>Delete the plasmid sequence.</li>
		<li>Ensure every sequence is oriented 5&#8217; to 3&#8217; according to the JH4 intron reference sequence (NG_005838). Generate the reverse complement of any sequence, as necessary.</li>
	</ol>
	</li>
	<li>Align the sequences obtained for each PCR against the JH4 intron reference sequence (NG_005838) using a Clustal Omega software (Figure 4A).
	<ol>
		<li>Identify differences from the reference sequence as mutations</li>
		<li>Verify that all mutations are true point mutations by examining the electropherogram of the Sanger sequencing. Repeat sequencing if necessary. (Figure 4B,C).</li>
	</ol>
	</li>
	<li>Tabulate and quantify unique mutations in the JH4 intron for each genotype (Figure 5).
	<ol>
		<li>Count sequences with identical mutations only once 
		NOTE: It is not possible to determine if the identical sequences were generated during the PCR or identical SHM events in different B cells.</li>
		<li>Count every instance of WT germline JH4 intron sequences (i.e., those with no mutations) as a unique sequence.</li>
	</ol>
	</li>
</ol>

The authors have nothing to disclose.

Characterizing SHM within the IgH and IgL V coding sequences of a heterogenous B cell population presents a challenge, given that each B cell uniquely reorganizes V coding segments during V(D)J recombination34. In this paper, we describe a method to identify mutations in the JH4 intron of GCBCs. The JH4 intron, which is located 3&#8217; of the last J coding segment in the IgH locus, is used as a surrogate for SHM of V regions (Figure 1)31,33,34,35. To catalog these JH4 intron mutations and assess how specific genes affect the production or pattern of mutations, PP GCBCs are specifically analyzed. These cells accumulate JH4 intron mutations as a result of chronic stimulation by intestinal microbiota53. Furthermore, the B220+PNAHI GCBCs from the PPs of unimmunized mice have a mutation spectra that compares to splenic GCBCs from immunized animals54,55. However, mutations in the JH4 intron cannot be correlated to Ig affinity maturation because these mutations are non-coding.
To determine whether SHM alters Ig affinity, mice should be immunized intraperitoneally with an antigen, such as NP (4-hydroxy-3-nitrophenylacetyl) conjugated to CGG (chicken gamma globulin) or KLH (keyhole limpet hemocyanin)56. Subsequently, mRNA can be purified from splenic B220+PNAHI GCBCs to examine SHM within VH186.2, the V coding exon that most frequently recognizes NP and is mutated following NP-CGG or NP-KLH immunization31,57,58,59,60. Mutation of tryptophan-33 to a leucine in VH186.2 has been characterized to increase Ig affinity up to 10-fold59,60 and is, therefore, one indicator that SHM and clonal selection has generated high affinity Ig. Measuring NP7- and NP20-specific serum Ig titers by ELISA and calculating the Ig-specific NP7/NP20 ratio during the course of the immunization also documents Ig affinity maturation resulting from SHM of V regions17,21,36. Both these assays can be used to correlate SHM within the VH186.2 coding sequences with changes in NP-specific Ig affinity maturation.
Whether immunized or unimmunized animals are used to analyze SHM of VH186.2 or the JH4 intron, GCBCs must be accurately identified. We present a FACS based approach to isolate B220+PNAHI GCBCs. Alternatively, Fas and non-sulfated &#945;2-6-sialyl-LacNAc antigen, which is recognized by the GL7 antibody61,62,63,64, can also be used to isolate GCBCs, which are identified as B220+Fas+GL7+65 or CD19+Fas+GL7+37. GL7 expression closely mirrors PNA in activated GCBCs of the lymph nodes64,65,66. In addition to using antibody markers specific for GCBCs, staining cocktails should maximize the excitation of a fluorophore and detection of a biomarker while minimizing spectral overlap of fluorescence emission. Antigens expressed at low levels should be detected with an antibody that is conjugated to a fluorophore with a robust emission fluorescence67. The recommended staining protocol was optimized for analysis on a cell sorter equipped with four lasers (405nm, 488nm, 561nm, 633nm) and 12 filters; however, filter configurations and laser availability vary between cytometers. To amend the protocol according to reagent and equipment availability, the reader is referred to additional resources, online spectrum viewers and published literature67,68,69,70,71,72,73. The multi-color staining protocol described herein requires compensation of spectral overlap to ensure that the sorted cell populations are GCBCs rather than inaccurate detection of fluorescence emission. B220 serves as a useful staining control for the described FACS (Table 1B) because PPs will have distinctive B220 negative and positive populations (Figure 3C), which allows for appropriate compensation of spectral overlap. The gating strategy presented in Figure 3C should be used as a guideline. The flow cytometry plots may vary depending on the staining conditions and cytometer settings. Nevertheless, 4-10% of the live cells should be B220+PNAHI 35, 52.
All mutations within the JH4 intron of PP GCBCs must be validated to ensure that the observed mutations are truly reflective of SHM and not an artefact of PCR or sequencing. AID-/- B cells can serve as a useful negative control when examining the SHM phenotype in other mutant mouse models because these cells cannot complete SHM17,19. The JH4 intron mutation rate in the of AID-/- GCBCs (1.66x10-5 mutations/bp)20,21,36,37,38,50,74 is comparable to the error rate of the high fidelity polymerase (5.3x10-7 sub/base/doubling)51,52 that is used to amplify the DNA in the nested PCR. If AID-/- mice are not available, compare the observed mutation pattern and frequency to the published literature. Ig V regions accumulate 10-3-10-4 mutations per base pair division, which is approximately 106-fold higher than the mutation rate of other gene loci73,75. Results may vary with the age of the animal76. Alternatively, B220+PNALO cells, which marks non-GCBCs, may be used as a negative control in the absence of AID-/- mice52. If the mutation frequency in WT GCBCs is lower than expected, the WT germline JH4 intronic sequence may be disproportionately represented. In this case, ensure that GCBCs were stained and sorted appropriately and PCRs are free from WT germline JH4 intron contamination. Additionally, raw sequencing data in electropherograms should be analyzed thoroughly to ensure that mutations in the sequence text data are not artefacts of sequencing errors. For example, poor Sanger sequencing results may reduce the reliability of the sequence data (Figure 4). This quality control of the Sanger sequence data will increase the accuracy and reproducibility of the JH4 intron mutation analysis.

B cells, members of the adaptive immune system, recognize and eliminate antigens by producing antibodies, also known as immunoglobulins (Ig). Each Ig is composed of two heavy (IgH) and two light (IgL) chain polypeptides, which are held together by disulfide bonds to form the characteristic &#8220;Y&#8221; shape structure of the Ig1. The N-termini of IgH and IgL comprise the variable (V) region of each polypeptide and together they form the antigen binding site of the Ig, whereas the constant region of IgH imparts the effector function of the Ig. Developing B cells in the bone marrow rearrange the V coding exons of IgH and IgL in a process known as V(D)J recombination2,3,4. Transcription of the recombined V exons, coupled with the respective constant region exons, forms the mRNA that is translated into the Ig.
Mature B cells expressing a membrane bound Ig, also known as a B cell receptor (BCR), circulate to secondary lymphoid organs, such as the spleen, lymph node, or Peyer&#8217;s patches, where they survey the environment for antigens and interact with other cells of the immune system1. Within the germinal centers (GC) of secondary lymphoid organs, B cells that recognize antigen through the BCR become activated. Aided by follicular dendritic cells and follicular helper T cells, activated B cells can then proliferate and differentiate into plasma and memory cells, which are important effectors of a robust immune response5,6,7,8,9. Additionally, these activated B cells can undergo secondary Ig gene diversification processes - class switch recombination (CSR) and somatic hypermutation (SHM). During CSR, B cells exchange the default &#956; constant region of the IgH polypeptide with another constant region (&#947;, &#945;, &#949;) through a DNA deletional-recombination reaction (Figure 1). This allows for the expression of a different constant exon and translation of a new Ig. The B cell will switch from expressing IgM to another isotype (IgG, IgA, IgE). CSR changes the effector function of the Ig without altering its antigen specificity10,11,12. However, during SHM, B cells mutate the V coding regions of IgH and IgL to enable the production and selection of higher affinity Igs, which can more effectively eliminate an antigen13,14,15 (Figure 1). Importantly, both CSR and SHM depend on the function of one enzyme: activation-induced cytidine deaminase (AID)16,17,18. Humans and mice deficient in AID cannot complete CSR or SHM and present with elevated IgM serum titers or Hyper-IgM17,19.
In CSR, AID deaminates deoxycytidines (C) in the repetitive switch regions that precede each constant coding exons, converting them into deoxyuridines (U)20,21, which creates mismatched base pairing between deoxyuridines and deoxyguanosines (U:G). These U:G mismatches are converted into the double-stranded DNA breaks, which are required for DNA recombination, by either the base excision repair (BER) or mismatch repair (MMR) pathway22,23,24,25,26,27,28,29. In SHM, AID deaminates C within the V coding exons. Replication across the U:G mismatch generates C:G to T:A transition mutations, whereas removal of the uracil base by the BER protein, uracil DNA glycosylase (UNG), prior to DNA replication produces both transition and transversion mutations16. Null mutations in UNG significantly increase C:G to T:A transition mutations21,22. Similar to CSR, SHM requires the complementary roles of MMR and BER. During SHM, MMR generates mutations at A:T base pairs. Inactivating mutations in MutS homology 2 (MSH2) or DNA polymerase &#951; (Pol&#951;) significantly reduces mutations at A:T bases and compound mutations in MSH2 and Pol&#951; virtually abolishes mutations at A:T bases21,30,31. Consistent with the critical role for BER and MMR in converting AID-generated U into transition or transversion mutations, mice deficient for both MSH2 and UNG (MSH2-/-UNG-/-) display only C:G to T:A transition mutations resulting from replication across the U:G mismatch21.
The analysis of SHM in V coding regions remains complicated because developing B cells can recombine any of the V(D)J coding exons in the IgH and IgL loci1,2,4. Accurate analysis of these uniquely recombined and somatically mutated V regions requires the identification and isolation of clones of B cells or the Ig mRNA11,13. The JH4 intron, which is 3&#8217; of the last J coding exon in the IgH locus, harbors somatic mutations due to the spreading of mutations 3&#8217; of the V promoter32,33,34 and therefore is frequently used as a surrogate marker for SHM in V regions31,35 (Figure 1). To experimentally elucidate how specific genes or genetic mutations alter SHM patterns or rates, the JH4 intron can be sequenced from Peyer&#8217;s patches (PP) germinal center B cells (GCBCs), which undergo high rates of SHM36,37,38. GCBCs can be readily identified and isolated with fluorescently conjugated antibodies against cell surface markers (B220+PNAHI)17,39.
A detailed protocol is presented to characterize JH4 intron mutations in PP GCBCs from mice using a combination of FACS (fluorescence activated cell sorting), PCR, and Sanger sequencing (Figure 2).

<table>
	<tbody>
		<tr>
			<td>0.2 ml PCR 8-tube FLEX-FREE strip, attached clear flat caps, mixed</td>
			<td>USA Scientific</td>
			<td>1402-4708</td>
			<td></td>
		</tr>
		<tr>
			<td>Ampicillin sodium salt</td>
			<td>Fisher</td>
			<td>BP1760-5</td>
			<td></td>
		</tr>
		<tr>
			<td>APC-eFluor780 anti-CD45R/B220</td>
			<td>eBioscience</td>
			<td>47-0452-80</td>
			<td>clone RA3-6B2</td>
		</tr>
		<tr>
			<td>BD FACSAria II</td>
			<td>BD</td>
			<td>643186</td>
			<td>four lasers (405nm, 488nm, 561nm, 633nm) and 12 filters (PacBlue (450/50), 
			AmCyan (502LP; 530/30), SSC (488/10), FITC (502LP; 530/30), PerCP-Cy5.5 (655LP; 695/40), 
			PE (585/15), PE-Texas Red (600LP; 610/20), PE-Cy5 (630LP; 670/14), PE-Cy7 (735LP; 780/60), APC (660/20), Alexa700 (710LP; 730/45), APC-Cy7 (755LP; 780/60))</td>
		</tr>
		<tr>
			<td>BD slip tip 1mL syringe</td>
			<td>Fisher</td>
			<td>14-823-434</td>
			<td>sterile</td>
		</tr>
		<tr>
			<td>Biotinylated peanut agglutinin (PNA)</td>
			<td>Vector Labs</td>
			<td>B-1075-5</td>
			<td></td>
		</tr>
		<tr>
			<td>C57BL/6J mice</td>
			<td>Jackson Laboratories</td>
			<td>664</td>
			<td></td>
		</tr>
		<tr>
			<td>Corning Falcon test tube with cell strainer snap cap</td>
			<td>Fisher</td>
			<td>08-771-23</td>
			<td></td>
		</tr>
		<tr>
			<td>DAPI (4&#39;,6-Diamidino-2-Phenylindole, dihydrochloride)</td>
			<td>Fisher</td>
			<td>D1306</td>
			<td>0.5 mg/ml</td>
		</tr>
		<tr>
			<td>dNTP</td>
			<td>NEB</td>
			<td>N0447L</td>
			<td>10 mM</td>
		</tr>
		<tr>
			<td>ElectroMAX DH10B competent cells</td>
			<td>Fisher</td>
			<td>18-290-015</td>
			<td></td>
		</tr>
		<tr>
			<td>Falcon cell strainer 40mm</td>
			<td>Fisher</td>
			<td>08-771-1</td>
			<td></td>
		</tr>
		<tr>
			<td>Falcon round-bottom polystyrene tubes (FACS tubes)</td>
			<td>Fisher</td>
			<td>14-959-5</td>
			<td></td>
		</tr>
		<tr>
			<td>Falcon round-bottom polystyrene tubes (capped)</td>
			<td>Fisher</td>
			<td>149591A</td>
			<td></td>
		</tr>
		<tr>
			<td>Fetal bovine serum</td>
			<td>R&#38;D Systems (Atlanta Biologicals)</td>
			<td>S11150</td>
			<td></td>
		</tr>
		<tr>
			<td>Gibco phosphate buffered saline PBS pH 7.4</td>
			<td>Fisher</td>
			<td>10-010-049</td>
			<td></td>
		</tr>
		<tr>
			<td>Glycogen</td>
			<td>Sigma</td>
			<td>10901393001</td>
			<td></td>
		</tr>
		<tr>
			<td>Lasergene Molecular Biology (MegAlign Pro)</td>
			<td>DNA Star</td>
			<td></td>
			<td>version 15</td>
		</tr>
		<tr>
			<td>PE anti-CD45R/B220</td>
			<td>BD</td>
			<td>553090</td>
			<td>clone RA3-6B2</td>
		</tr>
		<tr>
			<td>Proteinase K</td>
			<td>Fisher</td>
			<td>BP1700-100</td>
			<td></td>
		</tr>
		<tr>
			<td>Q5 High-Fidelity DNA Polymerase</td>
			<td>NEB</td>
			<td>M0491L</td>
			<td></td>
		</tr>
		<tr>
			<td>QIAquick Gel Extraction Kit</td>
			<td>Qiagen</td>
			<td>28706</td>
			<td></td>
		</tr>
		<tr>
			<td>Seal-Rite 1.5mL microcentrifuge tubes</td>
			<td>USA Scientific</td>
			<td>1615-5500</td>
			<td></td>
		</tr>
		<tr>
			<td>Streptavidin APC-eFluor 780 Conjugate</td>
			<td>eBioscience</td>
			<td>47-4317-82</td>
			<td></td>
		</tr>
		<tr>
			<td>T4 DNA ligase</td>
			<td>NEB</td>
			<td>M020L</td>
			<td></td>
		</tr>
		<tr>
			<td>Thermo Scientific CloneJET PCR Cloning Kit</td>
			<td>ThermoFisher</td>
			<td>FERK1231</td>
			<td></td>
		</tr>
		<tr>
			<td>Tissue culture plate 6 well</td>
			<td>Fisher</td>
			<td>08-772-1B</td>
			<td>sterile</td>
		</tr>
		<tr>
			<td>Unlabeled anti-mouse CD16/CD32 (Fc block), BD</td>
			<td>Fisher</td>
			<td>BDB553142</td>
			<td>Clone 2.4G2</td>
		</tr>
	</tbody>
</table>

analysis of somatic hypermutation in the jh4 intron of germinal center b cells from mouse peyer's patches

Within the germinal centers of lymphoid organs, mature B cells alter their expressed immunoglobulin (Ig) by introducing untemplated mutations into the variable coding exons of the Ig heavy and light chain gene loci. This process of somatic hypermutation (SHM) requires the enzyme activation-induced cytidine deaminase (AID), which converts deoxycytidines (C), into deoxyuridines (U). Processing the AID-generated U:G mismatches into mutations by the base excision and mismatch repair pathways introduces new Ig coding sequences that may produce a higher affinity Ig. Mutations in AID or DNA repair genes can block or significantly alter the types of mutations observed in the Ig loci. We describe a protocol to quantify JH4 intron mutations that uses fluorescence activated cell sorting (FACS), PCR, and Sanger sequencing. Although this assay does not directly measure Ig affinity maturation, it is indicative of mutations in Ig variable coding sequences. Additionally, these methods utilize common molecular biology techniques which&#160;analyze&#160;mutations in Ig sequences of multiple B cell clones. Thus, this assay is an invaluable tool in the study of SHM and Ig diversification.

Flow cytometry 
Mature B cells circulate to germinal centers where they undergo affinity maturation, clonal expansion, and differentiation into plasma or memory cells40,41,42,43,44. These GCBCs can be identified by numerous cell surface markers, including high expression of the CD45R/B220 receptor and binding of peanut agglutinin (PNA)45,46. To isolate activated GCBCs, PP cells were stained with anti-B220 antibodies conjugated to phycoerythrin (PE) and biotinylated-PNA, followed by streptavidin conjugated to APC-eFluor780. Dead cells were eliminated using the fluorescent 4&#39;,6-Diamidino-2-Phenylindole (DAPI) dye, which stains the nucleic acid of dying or dead cells47,48. The stained cells were subsequently analyzed and sorted via flow cytometry. The PPs consisted of ~80% B220+ cells49,50. WT PPs contain on an average 4 x 106 cells per mouse (Figure 3A). Approximately 8% of the WT PP cells were B220+PNAHI, which is half the number observed in AID-/ - (Figure 3B). Thus, 0.3-0.6 x 106 B220+PNAHI GCBCs were obtained after sorting, which were sufficient to analyze mutations in the JH4 intron.
JH4 Sequence Analysis 
The JH4 intron was amplified by a nested PCR using common VHJ558 family primers (J558FR3Fw and VHJ558.2) followed by JH4 intron spanning primers VHJ558.3 and VHJ558.435,37. Of the 105 unique sequences obtained from WT GCBCs, a total of 226 mutations were found (Figure 5A). Analysis of the GCBC mutation spectrum in the WT mice showed a range of transitions and transversions at a rate of 4 x 10-3 mutations/bp, which was calculated by dividing the total number of mutated bases by the total number of bases that were sequenced32,36,37,38. Additionally, each JH4 PCR product from WT GCBCs contained 1-25 mutations (Figure 5B), where multiple mutations were frequently found on one sequence33,36. Only two mutations were identified in 113 AID-/- sequences (Figure 5A). AID-/- B cells exhibited 1.66 x 10-5 mutations/bp, which was significantly lower than WT B cells (p &#60;0.05)36 and compares to the error rate of the high fidelity polymerase (5.3 x 10-7 sub/base/doubling)51,52. Thus, AID-/- B cells served as a useful negative control for this assay.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/61551/61551fig01.jpg" /> 
Figure 1: Schematic of the IgH gene locus and the regions targeted by AID during CSR and SHM.&#160;The red bar indicates the 580 bp JH4 intron that is 3&#8217; of VDJH4 rearrangements and is analyzed in this protocol. In CSR, AID-dependent deamination of intronic switch regions (S&#956; and S&#949;) promotes DSB formation that allows for deletional-recombination and the expression of a new antibody isotype (IgM to IgE). During SHM, V regions (grey boxes) accumulate mutations (blue lines) that may lead to higher affinity Ig. <a href="https://www.jove.com/files/ftp_upload/61551/61551fig01large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/61551/61551fig02.jpg" /> 
Figure 2: Workflow to analyze SHM of the JH4 intron in GCBCs isolated from PPs. <a href="https://www.jove.com/files/ftp_upload/61551/61551fig02large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 3" class="xfigimg" src="/files/ftp_upload/61551/61551fig03.jpg" /> 
Figure 3: Characterization of PP GCBCs.&#160;(A) Total number of PP cells from WT and AID-/- mice (n = 4 per genotype). Error bars represent standard deviation from the mean. (B) Percentage of B220+PNAHI GCBCs obtained from PPs of WT and AID-/- mice (n = 4 per genotype)36. Error bars represent standard deviation from the mean, *p&#60;0.05 using student&#8217;s t-test. (C) Representative FACS plots to sort B220+PNAHI GCBCs from PPs. <a href="https://www.jove.com/files/ftp_upload/61551/61551fig03large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 4" class="xfigimg" src="/files/ftp_upload/61551/61551fig04.jpg" /> 
Figure 4: Analysis of JH4 Sanger sequence data.&#160;(A) Sample sequence alignments of Sanger sequence data of the JH4 PCR product from WT (top) and AID-/- (bottom) GCBCs to the reference genomic sequence (NG_005838), which is the sequence immediately below the numbered tick marks. Alignments were generated using Clustal Omega. (B) Electropherogram of high-quality Sanger sequence data, which displayed distinct peaks for each base. (C) Electropherogram of low-quality sequence data, which showed ambiguous peaks and unspecified bases (N). The nucleotide shown in red must be manually annotated in the sequence text file.&#160;&#160;<a href="https://www.jove.com/files/ftp_upload/61551/61551fig04large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 5" class="xfigimg" src="/files/ftp_upload/61551/61551fig05.jpg" /> 
Figure 5: Analysis of mutations in the JH4 intron in WT and AID-/- GCBCs.&#160;(A) The total number of transition (red) and transversion (blue) mutations at A, C, G, and T bases for each genotype is summarized in the tables. The total number of sequences analyzed is indicated below the table. (B) The number of mutations per PCR amplicon for each genotype is depicted in the pie charts. This figure has been modified from Choi et al.36 Copyright 2020. The American Association of Immunologists, Inc. <a href="https://www.jove.com/files/ftp_upload/61551/61551fig05large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always" style="margin-bottom:0px;">
	<tbody>
		<tr>
			<td colspan="2">Staining Cocktail for GCBCs</td>
			<td colspan="2">Volume: 500 &#956;L</td>
		</tr>
		<tr>
			<td>Antibody or Dye</td>
			<td>Fluorophore</td>
			<td>Dilution</td>
			<td>&#956;L</td>
		</tr>
		<tr>
			<td>B220</td>
			<td>PE</td>
			<td>1000</td>
			<td>0.5</td>
		</tr>
		<tr>
			<td>Streptavidin</td>
			<td>APC-eFluor780</td>
			<td>500</td>
			<td>1</td>
		</tr>
		<tr>
			<td>DAPI</td>
			<td>N/A</td>
			<td>500</td>
			<td>1</td>
		</tr>
	</tbody>
</table>
Table 1: Staining cocktails for GCBCs. Cocktail of the indicated antibodies or dye (indicated in italics) at the specified dilutions were used to stain PP cells in 500 &#956;L for flow cytometry.
&#160; &#160;
<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always" style="margin-bottom:0px;">
	<tbody>
		<tr>
			<td colspan="2">Single Stains for Compensation</td>
			<td colspan="2">Volume: 500 &#956;L</td>
		</tr>
		<tr>
			<td>Antibody or Dye</td>
			<td>Fluorophore</td>
			<td>Dilution</td>
			<td>&#956;L</td>
		</tr>
		<tr>
			<td>B220</td>
			<td>PE</td>
			<td>1000</td>
			<td>0.5</td>
		</tr>
		<tr>
			<td>B220</td>
			<td>APC-eFluor780&#160;</td>
			<td>750</td>
			<td>0.67</td>
		</tr>
		<tr>
			<td>DAPI</td>
			<td>N/A</td>
			<td>500</td>
			<td>1</td>
		</tr>
	</tbody>
</table>
Table 2: Single stain controls for compensation. B220 antibodies conjugated to the indicated fluorophores were used for single stain controls to compensate for spectral overlap.
&#160; &#160;
<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always" style="margin-bottom:0px;">
	<tbody>
		<tr>
			<td colspan="5">PCR #1</td>
		</tr>
		<tr>
			<td>Reagent</td>
			<td>Volume</td>
			<td colspan="3">Thermocycler Conditions</td>
		</tr>
		<tr>
			<td>5x Buffer</td>
			<td>4 &#956;L</td>
			<td>1</td>
			<td>95 &#176;C</td>
			<td>3 min</td>
		</tr>
		<tr>
			<td>10 mM dNTP</td>
			<td>2 &#956;L</td>
			<td>2</td>
			<td>94 &#176;C</td>
			<td>30 sec</td>
		</tr>
		<tr>
			<td>10 &#956;M J558FR3Fw</td>
			<td>1 &#956;L</td>
			<td>3</td>
			<td>55 &#176;C</td>
			<td>30 sec</td>
		</tr>
		<tr>
			<td>10 &#956;M VHJ558.2</td>
			<td>1 &#956;L</td>
			<td>4</td>
			<td>72 &#176;C</td>
			<td>1:30 min</td>
		</tr>
		<tr>
			<td>High Fidelity DNA polymerase</td>
			<td>0.25 &#956;L</td>
			<td colspan="3" rowspan="2">Cycle 2-4 9x</td>
		</tr>
		<tr>
			<td>DNA</td>
			<td>x (standardize to least concentrated sample)</td>
		</tr>
		<tr>
			<td>H2O</td>
			<td>to 20 &#956;L</td>
			<td>5</td>
			<td>72 &#176;C</td>
			<td>5 min</td>
		</tr>
		<tr>
			<td colspan="5">Dilute PCR product 1:5 in H2O before proceeding to PCR #2</td>
		</tr>
	</tbody>
</table>
Table 3: Nested PCR of the JH4 intron. PCR components and thermocycler conditions for the first amplification reaction. Dilute the first PCR product 1:5 with water and use 1 &#956;L of this dilution for the second PCR.
&#160; &#160;
<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always" style="margin-bottom:0px;">
	<tbody>
		<tr>
			<td colspan="5">PCR #2</td>
		</tr>
		<tr>
			<td>Reagent</td>
			<td>Volume</td>
			<td colspan="3">Thermocycler Conditions #2</td>
		</tr>
		<tr>
			<td>5x Buffer</td>
			<td>4 &#956;L</td>
			<td>1</td>
			<td>94 &#176;C</td>
			<td>3 min</td>
		</tr>
		<tr>
			<td>10 mM dNTP</td>
			<td>2 &#956;L</td>
			<td>2</td>
			<td>94 &#176;C</td>
			<td>30 sec</td>
		</tr>
		<tr>
			<td>10 &#956;M VHJ558.3</td>
			<td>1 &#956;L</td>
			<td>3</td>
			<td>55 &#176;C</td>
			<td>30 sec</td>
		</tr>
		<tr>
			<td>10 &#956;M VHJ558.4</td>
			<td>1 &#956;L</td>
			<td>4</td>
			<td>72 &#176;C</td>
			<td>30 sec</td>
		</tr>
		<tr>
			<td>High Fidelity DNA polymerase</td>
			<td>0.25 &#956;L</td>
			<td colspan="3" rowspan="2">Cycle 2-4 21x</td>
		</tr>
		<tr>
			<td>Diluted PCR#1</td>
			<td>1 &#956;L</td>
		</tr>
		<tr>
			<td>H2O</td>
			<td>to 20 &#956;L</td>
			<td>5</td>
			<td>72 &#176;C</td>
			<td>5 min</td>
		</tr>
	</tbody>
</table>
Table 4: PCR components and thermocycler conditions for the second PCR.
&#160; &#160;
<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always" style="margin-bottom:0px;">
	<tbody>
		<tr>
			<td>Reagent</td>
			<td>Volume</td>
		</tr>
		<tr>
			<td>2x Buffer</td>
			<td>10 &#956;L</td>
		</tr>
		<tr>
			<td>Purified PCR</td>
			<td>x (standardize to least concentrated sample)</td>
		</tr>
		<tr>
			<td>Plasmid with blunt ends</td>
			<td>1 &#956;L</td>
		</tr>
		<tr>
			<td>T4 DNA Ligase</td>
			<td>1 &#956;L</td>
		</tr>
		<tr>
			<td>H2O</td>
			<td>to 20 &#956;L</td>
		</tr>
		<tr>
			<td colspan="2">Incubate at room temp for 5 min or overnight at 16&#186;C</td>
		</tr>
	</tbody>
</table>
Table 5: Ligation reaction. Components for the ligation of the purified JH4 intron PCR product into the plasmid.
&#160; &#160;
<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always" style="margin-bottom:0px;">
	<tbody>
		<tr>
			<td>FACS Buffer</td>
		</tr>
		<tr>
			<td>Heat inactivate FBS at 56 &#730;C for one hour prior to use. Supplement PBS, pH 7.4 (Gibco, #10010049) with 2.5% (v/v) of heat-inactivated FBS. Store at 4&#730;C.</td>
		</tr>
		<tr>
			<td>DNA Extraction Buffer (100 mM Tris pH 8.0, 0.1 M EDTA, 0.5% (w/v) SDS)</td>
		</tr>
		<tr>
			<td>Add 50 mL of 1 M Tris pH 8.0, 100mL of 0.5 M EDTA, and 12.5 mL of 20% SDS. Add distilled water to 500 mL. Store at room temperature.</td>
		</tr>
		<tr>
			<td>TE Buffer (10 mM Tris pH 8.0, 1 mM EDTA)</td>
		</tr>
		<tr>
			<td>Add 2.5 mL of 1 M Tris pH 8.0, and 500 mL of 0.5 M EDTA. Add distilled water to 250 mL. Store at room temperature.</td>
		</tr>
	</tbody>
</table>
Table 6: Buffer recipes.
&#160; &#160;
<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always" style="margin-bottom:0px;">
	<tbody>
		<tr>
			<td colspan="3">Oligonucleotides List</td>
		</tr>
		<tr>
			<td>J558FR3Fw</td>
			<td colspan="2">5&#8217;-GCCTGACATCTGAGGACTCTGC-3&#8217;</td>
		</tr>
		<tr>
			<td>VHJ558.2</td>
			<td colspan="2">5&#8217;-CTGGACTTTCGGTTTGGTG-3&#8217;</td>
		</tr>
		<tr>
			<td>VHJ558.3</td>
			<td colspan="2">5&#8217;-GGTCAAGGAACCTCAGTCA-3&#8217;</td>
		</tr>
		<tr>
			<td>VHJ558.4</td>
			<td colspan="2">5&#8217;-TCTCTAGACAGCAACTAC-3&#8217;</td>
		</tr>
	</tbody>
</table>
Table 7: Oligonucleotides used in the assay.
&#160; &#160;
Supplementary Figure 1: Representative agarose gel image after completion of step 5.4. The JH4 intron nested PCR product was resolved on a 1.5% agarose gel and the 580 bp amplicon was excised. WT PP indicates that WT PP GCBC genomic DNA was used as a template for the first PCR and AID PP indicates that AID-/- PP GCBC genomic DNA was used as a template for the first PCR. &#632; indicates the no template PCR control and - indicates nothing was loaded into the well of the agarose gel. The last lane shows a 100 bp DNA ladder. <a href="https://cloudflare.jove.com/files/ftp_upload/61551/61551supfig01.jpg" target="_blank">Please click here to download this figure.</a>

Watch this Scientific Journal Video about Analysis of Somatic Hypermutation in the JH4 intron of Germinal Center B cells from Mouse Peyer's Patches at JoVE.com

Analysis of Somatic Hypermutation in the JH4 intron of Germinal Center B cells from Mouse Peyer's Patches

Presented here is an assay to quantify somatic hypermutation within the immunoglobulin heavy chain gene locus using germinal center B cells from mouse Peyer&#8217;s patches.

Within the germinal centers of lymphoid organs, mature B cells alter their expressed immunoglobulin (Ig) by introducing untemplated mutations into the ...

analysis-somatic-hypermutation-jh4-intron-germinal-center-b-cells

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JoVE Journal

Immunology and Infection

6.5K Views.  The City College of New York and The Graduate Center of The City University of New York. Presented here is an assay to quantify somatic hypermutation within the immunoglobulin heavy chain gene locus using germinal center B cells from mouse Peyer’s patches.

Video: Analysis of Somatic Hypermutation in the JH4 intron of Germinal Center B cells from Mouse Peyer's Patches

Assessing Somatic Hypermutation in Ramos B Cells after Overexpression or Knockdown of Specific Genes

B cells start their life with low affinity antibodies generated by V(D)J recombination. However, upon detecting a pathogen, the variable (V) region of an immunoglobulin (Ig) gene is mutated approximately 100,000-fold more than the rest of the genome through somatic hypermutation (SHM), resulting in high affinity antibodies1,2. In addition, class switch recombination (CSR) produces antibodies with different effector functions depending on the kind of immune response that is needed for a particular pathogen. Both CSR and SHM are initiated by activation-induced cytidine deaminase (AID), which deaminates cytosine residues in DNA to produce uracils. These uracils are processed by error-prone forms of repair pathways, eventually leading to mutations and recombination1-3.
Our current understanding of the molecular details of SHM and CSR come from a combination of studies in mice, primary cells, cell lines, and cell-free experiments. Mouse models remain the gold standard with genetic knockouts showing critical roles for many repair factors (e.g. Ung, Msh2, Msh6, Exo1, and polymerase &eta;)4-10. However, not all genes are amenable for knockout studies. For example, knockouts of several double-strand break repair proteins are embryonically lethal or impair B-cell development11-14. Moreover, sometimes the specific function of a protein in SHM or CSR may be masked by more global defects caused by the knockout. In addition, since experiments in mice can be lengthy, altering expression of individual genes in cell lines has become an increasingly popular first step to identifying and characterizing candidate genes15-18.
Ramos &#x2013; a Burkitt lymphoma cell line that constitutively undergoes SHM &#x2013; has been a popular cell-line model to study SHM18-24. One advantage of Ramos cells is that they have a built-in convenient semi-quantitative measure of SHM. Wild type cells express IgM and, as they pick up mutations, some of the mutations knock out IgM expression. Therefore, assaying IgM loss by fluorescence-activated cell scanning (FACS) provides a quick read-out for the level of SHM. A more quantitative measurement of SHM can be obtained by directly sequencing the antibody genes. 
Since Ramos cells are difficult to transfect, we produce stable derivatives that have increased or lowered expression of an individual gene by infecting cells with retroviral or lentiviral constructs that contain either an overexpression cassette or a short hairpin RNA (shRNA), respectively. Here, we describe how we infect Ramos cells and then use these cells to investigate the role of specific genes on SHM (Figure 1).

We describe how to perform retroviral or lentiviral infections of overexpression or shRNA-containing constructs in the human Ramos B-cell line and how to measure somatic hypermutation in these cells.

B cells start their life with low affinity antibodies generated by V(D)J recombination.  However, upon detecting a pathogen, the variable (V) region of an ...

Isolating And Immunostaining Lymphocytes and Dendritic Cells from Murine Peyer's Patches

Peyer's patches (PPs) are integral components of the gut-associated lymphoid tissues (GALT) and play a central role in intestinal immunosurveillance and homeostasis. Particulate antigens and microbes in the intestinal lumen are continuously sampled by PP M cells in the follicle-associated epithelium (FAE) and transported to an underlying network of dendritic cells (DCs), macrophages, and lymphocytes. In this article, we describe protocols in which murine PPs are (i) dissociated into single cell suspensions and subjected to flow cytometry and (ii) prepared for cryosectioning and immunostaining. For flow cytometry, PPs are mechanically dissociated and then filtered through 70 &mu;m membranes to generate single cell suspensions free of epithelial cells and large debris. Starting with 20-25 PPs (from four mice), this quick and reproducible method yields a population of &gt;2.5 x 106 cells with &gt;90% cell viability. For cryosectioning, freshly isolated PPs are immersed in Optimal Cutting Temperature (OCT) medium, snap-frozen in liquid nitrogen, and then sectioned using a cryomicrotome. Tissue sections (5-12 &mu;m) are air-dried, fixed with acetone or methanol, and then subjected to immunolabeling.

Isolating And Immunostaining Lymphocytes and Dendritic Cells from Murine Peyer&#039;s Patches

There is an increasing interest in understanding the immunological functions of specific subpopulations of cells in Peyer's patches (PPs), the primary inductive sites of gut-associated lymphoid tissues. Here we outline parallel protocols for preparing PP single cell preparations for flow cytometric analysis and PP cryosections for immunostaining.

Peyer's  patches (PPs) are integral components of the gut-associated lymphoid tissues  (GALT) and play a central role in intestinal immunosurveillance and ...

Assessing the Development of Murine Plasmacytoid Dendritic Cells in Peyer's Patches Using Adoptive Transfer of Hematopoietic Progenitors

This protocol details a method to analyze the ability of purified hematopoietic progenitors to generate plasmacytoid dendritic cells (pDC) in intestinal Peyer&#39;s patch (PP). Common dendritic cell progenitors (CDPs, lin- c-kitlo CD115+ Flt3+) were purified from the bone marrow of C57BL6 mice by FACS and transferred to recipient mice that lack a significant pDC population in PP; in this case, Ifnar-/- mice were used as the transfer recipients. In some mice, overexpression of the dendritic cell growth factor Flt3 ligand (Flt3L) was enforced prior to adoptive transfer of CDPs, using hydrodynamic gene transfer (HGT) of Flt3L-encoding plasmid. Flt3L overexpression expands DC populations originating from transferred (or endogenous) hematopoietic progenitors. At 7-10 days after progenitor transfer, pDCs that arise from the adoptively transferred progenitors were distinguished from recipient cells on the basis of CD45 marker expression, with pDCs from transferred CDPs being CD45.1+ and recipients being CD45.2+. The ability of transferred CDPs to contribute to the pDC population in PP and to respond to Flt3L was evaluated by flow cytometry of PP single cell suspensions from recipient mice. This method may be used to test whether other progenitor populations are capable of generating PP pDCs. In addition, this approach could be used to examine the role of factors that are predicted to affect pDC development in PP, by transferring progenitor subsets with an appropriate knockdown, knockout or overexpression of the putative developmental factor and/or by manipulating circulating cytokines via HGT. This method may also allow analysis of how PP pDCs affect the frequency or function of other immune subsets in PPs. A unique feature of this method is the use of Ifnar-/- mice, which show severely depleted PP pDCs relative to wild type animals, thus allowing reconstitution of PP pDCs in the absence of confounding effects from lethal irradiation.

Assessing the Development of Murine Plasmacytoid Dendritic Cells in Peyer&#039;s Patches Using Adoptive Transfer of Hematopoietic Progenitors

This protocol describes experimental procedures to assess the differentiation of plasmacytoid dendritic cells in Peyer&#8217;s patch from common dendritic cell progenitors, using techniques involving FACS-mediated cell isolation, hydrodynamic gene transfer, and flow analysis of immune subsets in Peyer&#8217;s patch.

This protocol details a method to analyze the ability of purified hematopoietic progenitors to generate plasmacytoid dendritic cells (pDC) in intestinal ...

Rapid Analysis of Chromosome Aberrations in Mouse B Lymphocytes by PNA-FISH

Defective DNA repair leads to increased genomic instability, which is the root cause of mutations that lead to tumorigenesis. Analysis of the frequency and type of chromosome aberrations in different cell types allows defects in DNA repair pathways to be elucidated. Understanding mammalian DNA repair biology has been greatly helped by the production of mice with knockouts in specific genes. The goal of this protocol is to quantify genomic instability in mouse B lymphocytes. Labeling of the telomeres using PNA-FISH probes (peptide nucleic acid - fluorescent in situ hybridization) facilitates the rapid analysis of genomic instability in metaphase chromosome spreads. B cells have specific advantages relative to fibroblasts, because they have normal ploidy and a higher mitotic index. Short-term culture of B cells therefore enables precise measurement of genomic instability in a primary cell population which is likely to have fewer secondary genetic mutations than what is typically found in transformed fibroblasts or patient cell lines.

DNA repair pathways are essential for maintenance of genomic integrity and preventing mutation and cancer. The goal of this protocol is to quantify genomic instability by direct observation of chromosome aberrations in metaphase spreads from mouse B cells using fluorescent in situ hybridization (FISH) for telomeric DNA repeats.

Defective DNA repair leads to increased genomic instability, which is the root cause of mutations that lead to tumorigenesis. Analysis of the frequency ...

Derivation of T Cells In Vitro from Mouse Embryonic Stem Cells

The OP9/OP9-DL1 co-culture system has become a well-established method for deriving differentiated blood cell types from embryonic and hematopoietic progenitors of both mouse and human origin. It is now used to address a growing variety of complex genetic, cellular and molecular questions related to hematopoiesis, and is at the cutting edge of efforts to translate these basic findings to therapeutic applications. The procedures are straightforward and routinely yield robust results. However, achieving successful hematopoietic differentiation in vitro requires special attention to the details of reagent and cell culture maintenance. Furthermore, the protocol features technique sensitive steps that, while not difficult, take care and practice to master. Here we focus on the procedures for differentiation of T lymphocytes from mouse embryonic stem cells (mESC). We provide a detailed protocol with discussions of the critical steps and parameters that enable reproducibly robust cellular differentiation in vitro. It is in the interest of the field to consider wider adoption of this technology, as it has the potential to reduce animal use, lower the cost and shorten the timelines of both basic and translational experimentation.

Derivation of T Cells In Vitro from Mouse Embryonic Stem Cells

Mouse embryonic stem cells can be differentiated to T cells in vitro using the OP9-DL1 co-culture system. Success in this procedure requires careful attention to reagent/cell maintenance, and key technique sensitive steps. Here we discuss these critical parameters and provide a detailed protocol to encourage adoption of this technology.

The OP9/OP9-DL1 co-culture system has become a well-established method for deriving differentiated blood cell types from embryonic and hematopoietic ...

Detection of True IgE-expressing Mouse B Lineage Cells

B lymphocyte immunoglobulin heavy chain (IgH) class switch recombination (CSR) is a process wherein initially expressed IgM switches to other IgH isotypes, such as IgA, IgE and IgG. Measurement of IgH CSR in vitro is a key method for the study of a number of biologic processes ranging from DNA recombination and repair to aspects of molecular and cellular immunology. In vitro CSR assay involves the flow cytometric measurement surface Ig expression on activated B cells. While measurement of IgA and IgG subclasses is straightforward, measurement of IgE by this method is problematic due to soluble IgE binding to Fc&#949;RII/CD23 expressed on the surface of activated B cells. Here we describe a unique procedure for accurate measurement of IgE-producing mouse B cells that have undergone CSR in culture. The method is based on trypsin-mediated cleavage of IgE-CD23 complexes on cell surfaces, allowing for detection of IgE-producing B lineage cells by cytoplasmic staining. This procedure offers a convenient solution for flow cytometric analysis of CSR to IgE.

In vitro analysis of class switch recombination in mice is challenging due to cytophilic IgE molecules bound to Fc receptors on the surface of B cells. We describe a method for IgE detection using trypsin-mediated cleavage of surface-bound IgE prior to fixation and permeabilization for cytoplasmic fluorescence staining.

B lymphocyte immunoglobulin heavy chain (IgH) class switch recombination (CSR) is a process wherein initially expressed IgM switches to other IgH ...

Isolation and Flow Cytometric Analysis of Immune Cells from the Ischemic Mouse Brain

Ischemic stroke initiates a robust inflammatory response that starts in the intravascular compartment and involves rapid activation of brain resident cells. A key mechanism of this inflammatory response is the migration of circulating immune cells to the ischemic brain facilitated by chemokine release and increased endothelial adhesion molecule expression. Brain-invading leukocytes are well-known contributing to early-stage secondary ischemic injury, but their significance for the termination of inflammation and later brain repair has only recently been noticed.
Here, a simple protocol for the efficient isolation of immune cells from the ischemic mouse brain is provided. After transcardial perfusion, brain hemispheres are dissected and mechanically dissociated. Enzymatic digestion with Liberase&#160;is followed by density gradient (such as Percoll) centrifugation to remove myelin and cell debris. One major advantage of this protocol is the single-layer density gradient procedure which does not require time-consuming preparation of gradients and can be reliably performed. The approach yields highly reproducible cell counts per brain hemisphere and allows for measuring several flow cytometry panels in one biological replicate. Phenotypic characterization and quantification of brain-invading leukocytes after experimental stroke may contribute to a better understanding of their multifaceted roles in ischemic injury and repair.

Inflammation plays a central role in the pathogenesis of ischemic stroke. Increasing evidence suggests that it acts as a double-edged sword which exacerbates early brain injury, but also contributes to later repair. This protocol describes the isolation of immune cells from the ischemic brain and their subsequent flow cytometric phenotyping.

Ischemic stroke initiates a robust inflammatory response that starts in the intravascular compartment and involves rapid activation of brain resident ...

Detection and Enrichment of Rare Antigen-specific B Cells for Analysis of Phenotype and Function

B cells reactive with a specific antigen usually occur at a frequency of &lt;0.05% of lymphocytes. For decades researchers have sought methods to isolate and enrich these rare cells for studies of their phenotype and biology. Approaches are inevitably based on the principle that B cells recognize native antigen by virtue of cell surface receptors that are representative in specificity of antibodies that will eventually be secreted by their differentiated daughters. Perhaps the most obvious approach to the problem involves use of fluorochrome-conjugated antigens in conjunction with fluorescence-activated cell sorting (FACS). However, the utility of these methods is limited by cell frequency and the achievable rate of analysis and isolation by electronic sorting. A novel method to enrich rare antigen-specific B cells using magnetic nanoparticles that results in high yield enrichment of antigen-reactive B cells from large starting cell populations is described. This method enables improved monitoring of the phenotype and biology of antigen reactive cells before and following in vivo antigen encounter, such as after immunization or during development of autoimmunity.

A simple yet effective method that employs magnetic nanoparticles to detect and enrich antigen-reactive B cells for functional and phenotypic analysis is described.

B cells reactive with a specific antigen usually occur at a frequency of &lt;0.05% of lymphocytes. For decades researchers have sought methods to isolate ...

Analysis of Shear Flow-induced Migration of Murine Marginal Zone B Cells In Vitro

Marginal zone B cells (MZBs) are a population of B cells that reside in the mouse splenic marginal zones that envelop follicles. To reach the follicles, MZBs must migrate up the shear force of blood flow. We present here a method for analyzing this flow-induced MZB migration in vitro. First, MZBs are isolated from the mouse spleen. Second, MZBs are settled on integrin ligands in flow chamber slides, exposed to shear flow, and imaged under a microscope while migrating. Third, images of the migrating MZBs are processed using the MTrack2 automatic cell tracking plugin for ImageJ, and the resulting cell tracks are quantified using the Ibidi chemotaxis tool. The migration data reveal how fast the cells move, how often they change direction, whether the shear flow vector affects their migration direction, and which integrin ligands are involved. Although we use MZBs, the method can easily be adapted for analyzing migration of any leukocyte that responds to the force of shear flow.

Marginal zone B cells (MZBs) respond to the force of shear flow by re-orienting their migration path up the flow. This protocol shows how to record and analyze the migration using a fluidics unit, pump, microscope imaging system, and free software.

Marginal zone B cells (MZBs) are a population of B cells that reside in the mouse splenic marginal zones that envelop follicles. To reach the follicles, ...

Evaluation of T Follicular Helper Cells and Germinal Center Response During Influenza A Virus Infection in Mice

T Follicular Helper (Tfh) cells are an independent CD4+&#160;T cell subset specialized in providing help for germinal center (GC) development and generation of high-affinity antibodies. In influenza virus infection, robust Tfh and GC B cell responses are induced to facilitate effective virus eradication, which confers a qualified mouse model for Tfh-associated study. In this paper, we described protocols in detection of basic Tfh-associated immune response during influenza virus infection in mice. These protocols include: intranasal inoculation of influenza virus; flow cytometry staining and analysis of polyclonal and antigen-specific Tfh cells, GC B cells and plasma cells; immunofluorescence detection of GCs; enzyme-linked immunosorbent assay (ELISA) of influenza virus-specific antibody in serum. These assays basically quantify the differentiation and function of Tfh cells in influenza virus infection, thus providing help for studies in elucidating differentiation mechanism and manipulation strategy.

This paper describes protocols of evaluating Tfh and GC B response in mouse model of influenza virus infection.