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),&lt;br/&gt; AmCyan (502LP; 530/30), SSC (488/10), FITC (502LP; 530/30), PerCP-Cy5.5 (655LP; 695/40),&lt;br/&gt; 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&#039;,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&amp;amp;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',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 &lt;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="AID enzyme role in SHM and CSR process diagram, showing IgM/IgE switching in immunoglobulin DNA." class="xfigimg" src="/files/ftp_upload/61551/61551fig01.jpg" data-altupdatedat="1747911167000" data-alt="Figure 1"> 
Figure 1: Schematic of the IgH gene locus and the regions targeted by AID during CSR and SHM. The red bar indicates the 580 bp JH4 intron that is 3’ of VDJH4 rearrangements and is analyzed in this protocol. In CSR, AID-dependent deamination of intronic switch regions (Sμ and Sε) 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="Harvesting PP, GCBC sorting diagram; DNA extraction, PCR, ligation, transformation, sequencing." class="xfigimg" src="/files/ftp_upload/61551/61551fig02.jpg" data-altupdatedat="1747911167000" data-alt="Figure 2"> 
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="Peyer's Patches cell number, germinal center B cells graphs, and flow cytometry analysis setup." class="xfigimg" src="/files/ftp_upload/61551/61551fig03.jpg" data-altupdatedat="1747911167000" data-alt="Figure 3"> 
Figure 3: Characterization of PP GCBCs. (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&lt;0.05 using student’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="DNA sequencing results; comparison of high and low quality sequences; chromatogram analysis." class="xfigimg" src="/files/ftp_upload/61551/61551fig04.jpg" data-altupdatedat="1747911167000" data-alt="Figure 4"> 
Figure 4: Analysis of JH4 Sanger sequence data. (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.  <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="DNA mutation analysis; AID knockout vs WT; transition-transversion matrix and pie charts comparison." class="xfigimg" src="/files/ftp_upload/61551/61551fig05.jpg" data-altupdatedat="1747911167000" data-alt="Figure 5"> 
Figure 5: Analysis of mutations in the JH4 intron in WT and AID-/- GCBCs. (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 μL</td>
		</tr>
		<tr>
			<td>Antibody or Dye</td>
			<td>Fluorophore</td>
			<td>Dilution</td>
			<td>μL</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 μL for flow cytometry.
   
<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 μL</td>
		</tr>
		<tr>
			<td>Antibody or Dye</td>
			<td>Fluorophore</td>
			<td>Dilution</td>
			<td>μL</td>
		</tr>
		<tr>
			<td>B220</td>
			<td>PE</td>
			<td>1000</td>
			<td>0.5</td>
		</tr>
		<tr>
			<td>B220</td>
			<td>APC-eFluor780 </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.
   
<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 μL</td>
			<td>1</td>
			<td>95 °C</td>
			<td>3 min</td>
		</tr>
		<tr>
			<td>10 mM dNTP</td>
			<td>2 μL</td>
			<td>2</td>
			<td>94 °C</td>
			<td>30 sec</td>
		</tr>
		<tr>
			<td>10 μM J558FR3Fw</td>
			<td>1 μL</td>
			<td>3</td>
			<td>55 °C</td>
			<td>30 sec</td>
		</tr>
		<tr>
			<td>10 μM VHJ558.2</td>
			<td>1 μL</td>
			<td>4</td>
			<td>72 °C</td>
			<td>1:30 min</td>
		</tr>
		<tr>
			<td>High Fidelity DNA polymerase</td>
			<td>0.25 μL</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 μL</td>
			<td>5</td>
			<td>72 °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 μL of this dilution for the second PCR.
   
<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 μL</td>
			<td>1</td>
			<td>94 °C</td>
			<td>3 min</td>
		</tr>
		<tr>
			<td>10 mM dNTP</td>
			<td>2 μL</td>
			<td>2</td>
			<td>94 °C</td>
			<td>30 sec</td>
		</tr>
		<tr>
			<td>10 μM VHJ558.3</td>
			<td>1 μL</td>
			<td>3</td>
			<td>55 °C</td>
			<td>30 sec</td>
		</tr>
		<tr>
			<td>10 μM VHJ558.4</td>
			<td>1 μL</td>
			<td>4</td>
			<td>72 °C</td>
			<td>30 sec</td>
		</tr>
		<tr>
			<td>High Fidelity DNA polymerase</td>
			<td>0.25 μL</td>
			<td colspan="3" rowspan="2">Cycle 2-4 21x</td>
		</tr>
		<tr>
			<td>Diluted PCR#1</td>
			<td>1 μL</td>
		</tr>
		<tr>
			<td>H2O</td>
			<td>to 20 μL</td>
			<td>5</td>
			<td>72 °C</td>
			<td>5 min</td>
		</tr>
	</tbody>
</table>
Table 4: PCR components and thermocycler conditions for the second PCR.
   
<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 μL</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 μL</td>
		</tr>
		<tr>
			<td>T4 DNA Ligase</td>
			<td>1 μL</td>
		</tr>
		<tr>
			<td>H2O</td>
			<td>to 20 μL</td>
		</tr>
		<tr>
			<td colspan="2">Incubate at room temp for 5 min or overnight at 16ºC</td>
		</tr>
	</tbody>
</table>
Table 5: Ligation reaction. Components for the ligation of the purified JH4 intron PCR product into the plasmid.
   
<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 ˚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˚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.
   
<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’-GCCTGACATCTGAGGACTCTGC-3’</td>
		</tr>
		<tr>
			<td>VHJ558.2</td>
			<td colspan="2">5’-CTGGACTTTCGGTTTGGTG-3’</td>
		</tr>
		<tr>
			<td>VHJ558.3</td>
			<td colspan="2">5’-GGTCAAGGAACCTCAGTCA-3’</td>
		</tr>
		<tr>
			<td>VHJ558.4</td>
			<td colspan="2">5’-TCTCTAGACAGCAACTAC-3’</td>
		</tr>
	</tbody>
</table>
Table 7: Oligonucleotides used in the assay.
   
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. ɸ 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

Research

JoVE Journal

Immunology and Infection

6.7K 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

Induction and Assessment of Class Switch Recombination in Purified Murine B Cells

Humoral immunity is the branch of the immune system maintained by B cells and mediated through the secretion of antibodies. Upon B cell activation, the immunoglobulin locus undergoes a series of genetic modifications to alter the binding capacity and effector function of secreted antibodies. This process is highlighted by a genomic recombination event known as class switch recombination (CSR) in which the default IgM antibody isotype is substituted for one of IgG, IgA, or IgE. Each isotype possesses distinct effector functions thereby making CSR crucial to the maintenance of immunity. Diversification of the immunoglobulin locus is mediated by the enzyme activation-induced cytidine deaminase (AID). A schematic video describing this process in detail is available online (http://video.med.utoronto.ca/videoprojects/immunology/aam.html). AID's activity and the CSR pathway are commonly studied in the assessment of B cell function and humoral immunity in mice. The protocol outlined in this report presents a method of B cell isolation from murine spleens and subsequent stimulation with bacterial lipopolysaccharide (LPS) to induce class switching to IgG3 (for other antibody isotypes see Table 1). In addition, the fluorescent cell staining dye Carboxyfluorescein succinimidyl ester (CFSE) is used to monitor cell division of stimulated cells, a process crucial to isotype switching 1, 2. The regulation of AID and the mechanism by which CSR occurs are still unclear and thus in vitro class switch assays provide a reliable method for testing these processes in various mouse models. These assays have been previously used in the context of gene deficiency using knockout mice 3. Furthermore, in vitro switching of B cells can be preceded by viral transduction to modulate gene expression by RNA knockdown or transgene expression 4-6. The data from these types of experiments have impacted our understanding of AID activity, resolution of the CSR reaction, and antibody-mediated immunity in the mouse.

Following antigen exposure, subpopulations of activated B cells undergo a process known as class switch recombination (CSR) to produce antibody isotypes with distinct effector functions. The protocol outlined in this report explains how CSR can be induced and analyzed in vitro for the purposes of studying B cell function.

Humoral immunity is the branch of the immune system maintained by B cells and mediated through the secretion of antibodies. Upon B cell activation, the ...

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 ...

Unraveling Key Players of Humoral Immunity: Advanced and Optimized Lymphocyte Isolation Protocol from Murine Peyer's Patches

In the gut mucosa, immune cells constitute a unique immunological entity, which promotes immune tolerance while concurrently conferring immune defense against pathogens. It is well established that Peyer&#39;s patches (PPs) have an essential role in the mucosal immune network by hosting several effector T and B cell subsets. A certain fraction of these effector cells, follicular T helper (TFH) and germinal center (GC) B cells are professionalized in the regulation of humoral immunity. Hence, the characterization of these cell subsets within PPs in terms of their differentiation program and functional properties can provide important information about mucosal immunity. To this end, an easily applicable, efficient and reproducible method of lymphocyte isolation from PPs would be valuable to researchers. In this study, we aimed to generate an effective method to isolate lymphocytes from mouse PPs with high cell yield. Our approach revealed that initial tissue processing such as the use of digestive reagents and tissue agitation, as well as cell staining conditions and selection of antibody panels, have great influence on the quality and identity of the isolated lymphocytes and on experimental outcomes.
Here, we describe a protocol enabling researchers to efficiently isolate lymphocyte populations from PPs allowing reproducible flow cytometry-based assessment of T and B cell subsets primarily focusing on&#160;TFH and GC B cell subsets.

In this study, we present a novel and effective protocol for the isolation of lymphocytes from Peyer&#39;s Patches (PPs), which can be subsequently used for in vivo and in vitro functional assays as well as flow cytometric studies of follicular T helper and germinal center B cells.

In the gut mucosa, immune cells constitute a unique immunological entity, which promotes immune tolerance while concurrently conferring immune defense ...

Cancer Research

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.

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 ...

Highly Resolved Intravital Striped-illumination Microscopy of Germinal Centers

Monitoring cellular communication by intravital deep-tissue multi-photon microscopy is the key for understanding the fate of immune cells within thick tissue samples and organs in health and disease. By controlling the scanning pattern in multi-photon microscopy and applying appropriate numerical algorithms, we developed a striped-illumination approach, which enabled us to achieve 3-fold better axial resolution and improved signal-to-noise ratio, i.e. contrast, in more than 100 &#181;m tissue depth within highly scattering tissue of lymphoid organs as compared to standard multi-photon microscopy. The acquisition speed as well as photobleaching and photodamage effects were similar to standard photo-multiplier-based technique, whereas the imaging depth was slightly lower due to the use of field detectors. By using the striped-illumination approach, we are able to observe the dynamics of immune complex deposits on secondary follicular dendritic cells &#8211; on the level of a few protein molecules in germinal centers.

High-resolution intravital imaging with enhanced contrast up to 120 &#181;m depth in lymph nodes of adult mice is achieved by spatially modulating the excitation pattern of a multi-focal two-photon microscope. In 100 &#181;m depth we measured resolutions of 487 nm (lateral) and 551 nm (axial), thus circumventing scattering and diffraction limits.

Monitoring cellular communication by intravital deep-tissue multi-photon microscopy is the key for understanding the fate of immune cells within thick ...

VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma

Understanding tumor clonality is critical to understanding the mechanisms involved in tumorigenesis and disease progression. In addition, understanding the clonal composition changes that occur within a tumor in response to certain micro-environment or treatments may lead to the design of more sophisticated and effective approaches to eradicate tumor cells. However, tracking tumor clonal sub-populations has been challenging due to the lack of distinguishable markers. To address this problem, a VDJ-seq protocol was created to trace the clonal evolution patterns of diffuse large B cell lymphoma (DLBCL) relapse by exploiting VDJ recombination and somatic hypermutation (SHM), two unique features of B cell lymphomas.
In this protocol, Next-Generation sequencing (NGS) libraries with indexing potential were constructed from amplified rearranged immunoglobulin heavy chain (IgH) VDJ region from pairs of primary diagnosis and relapse DLBCL samples. On average more than half million VDJ sequences per sample were obtained after sequencing, which contain both VDJ rearrangement and SHM information. In addition, customized bioinformatics pipelines were developed to fully utilize sequence information for the characterization of IgH-VDJ repertoire within these samples. Furthermore, the pipeline allows the reconstruction and comparison of the clonal architecture of individual tumors, which enables the examination of the clonal heterogeneity within the diagnosis tumors and deduction of clonal evolution patterns between diagnosis and relapse tumor pairs. When applying this analysis to several diagnosis-relapse pairs, we uncovered key evidence that multiple distinctive tumor evolutionary patterns could lead to DLBCL relapse. Additionally, this approach can be expanded into other clinical aspects, such as identification of minimal residual disease, monitoring relapse progress and treatment response, and investigation of immune repertoires in non-lymphoma contexts.

This protocol describes an approach to interrogate the recombined immunoglobulin heavy chain VDJ regions of lymphomas by deep-sequencing and retrieve VDJ rearrangement and somatic hypermutation status to delineate clonal architecture of individual tumor. Comparing clonal architecture between paired diagnosis and relapse samples reveals lymphoma relapse clonal evolution modes.

Understanding tumor clonality is critical to understanding the mechanisms involved in tumorigenesis and disease progression. In addition, understanding ...

Medicine

Characterization of Thymus-dependent and Thymus-independent Immunoglobulin Isotype Responses in Mice Using Enzyme-linked Immunosorbent Assay

Antibodies, also termed as immunoglobulins (Ig), secreted by differentiated B lymphocytes, plasmablasts/plasma cells, in humoral immunity provide a formidable defense against invading pathogens via diverse mechanisms. One major goal of vaccination is to induce protective antigen-specific antibodies to prevent life-threatening infections. Both thymus-dependent (TD) and thymus-independent (TI) antigens can elicit robust antigen-specific IgM responses and can also induce the production of isotype-switched antibodies (IgG, IgA and IgE) as well as the generation of memory B cells with the help provided by antigen presenting cells (APCs). Here, we describe a protocol to characterize TD and TI Ig isotype responses in mice using enzyme-linked immunosorbent assay (ELISA). In this protocol, TD and TI Ig responses are elicited in mice by intraperitoneal (i.p.) immunization with hapten-conjugated model antigens TNP-KLH (in alum) and TNP-polysaccharide (in PBS), respectively. To induce TD memory response, a booster immunization of TNP-KLH in alum is given at 3 weeks after the first immunization with the same antigen/adjuvant. Mouse sera are harvested at different time points before and after immunization. Total serum Ig levels and TNP-specific antibodies are subsequently quantified using Ig isotype-specific Sandwich and indirect ELISA, respectively. In order to correctly quantify the serum concentration of each Ig isotype, the samples need to be appropriately diluted to fit within the linear range of the standard curves. Using this protocol, we have consistently obtained reliable results with high specificity and sensitivity. When used in combination with other complementary methods such as flow cytometry, in vitro culture of splenic B cells and immunohistochemical staining (IHC), this protocol will allow researchers to gain a comprehensive understanding of antibody responses in a given experimental setting.

In this paper, we describe a protocol to characterize T-dependent and T-independent immunoglobulin (Ig) isotype responses in mice using ELISA. This method used alone or in combination with flow cytometry will allow researchers to identify differences in B cell-mediated Ig isotype responses in mice following T-dependent and T-independent antigen immunization.

Antibodies, also termed as immunoglobulins (Ig), secreted by differentiated B lymphocytes, plasmablasts/plasma cells, in humoral immunity provide a ...

Identification of Mouse and Human Antibody Repertoires by Next-Generation Sequencing

The immense adaptability of antigen recognition by antibodies is the basis of the acquired immune system. Despite our understanding of the molecular mechanisms underlying the production of the vast repertoire of antibodies by the acquired immune systems, it has not yet been possible to arrive at a global view of a complete antibody repertoire. In particular, B cell repertoires have been regarded as a black box because of their astronomical number of antibody clones. However, next-generation sequencing technologies are enabling breakthroughs to increase our understanding of the B cell repertoire. In this report, we describe a simple and efficient method to visualize and analyze whole individual mouse and human antibody repertoires. From the immune organs, representatively from spleen in mice and peripheral blood mononuclear cells in humans, total RNA was prepared, reverse transcribed, and amplified using the 5&#39;-RACE method. Using a universal forward primer and antisense primers for the antibody class-specific constant domains, antibody mRNAs were uniformly amplified in proportions reflecting their frequencies in the antibody populations. The amplicons were sequenced by next-generation sequencing (NGS), yielding more than 105 antibody sequences per immunological sample. We describe the protocols for antibody sequence analyses including V(D)J-gene-segment annotation, a bird&#39;s-eye view of the antibody repertoire, and our computational methods.

Here, we describe protocols for the analysis and visualization of the structure and constitution of whole antibody repertoires. This involves the acquisition of vast sequences of antibody RNA using next-generation sequencing.

The immense adaptability of antigen recognition by antibodies is the basis of the acquired immune system. Despite our understanding of the molecular ...

Interrogating Individual Autoreactive Germinal Centers by Photoactivation in a Mixed Chimeric Model of Autoimmunity

Autoimmune diseases present a significant health burden. Fundamental questions regarding the development and progression of autoimmune disease remain unanswered. One requirement for advancements in our understanding of the underlying disease mechanisms and cellular dynamics is the precise coupling of the microanatomical location of cell subsets with downstream molecular or functional analyses; a goal that has traditionally been difficult to achieve. The development of stable photoactivatable biological fluorophores and their integration into reporter strains has recently enabled precise microanatomical labeling and tracking of cellular subsets in murine models. Here, we describe how the ability to analyze autoreactive lymphocytes from single germinal centers may help to provide novel insights into autoimmunity, using the combination of a novel chimeric model of autoimmunity with a photoactivatable reporter as an example. We demonstrate a procedure for generating mixed chimeras with spontaneous autoreactive germinal centers populated by lymphocytes carrying a photoactivatable green fluorescent protein reporter. Using in vivo labeling strategies, single germinal centers can be visualized in explanted lymphoid tissues and their cellular constituents photoactivated by two-photon microscopy. Photoactivated lymphocytes from single germinal centers can then be analyzed or sorted flow cytometrically, as single cells or in bulk, and may be subjected to additional downstream molecular and functional analyses. This approach may directly be applied to provide renewed insights in the field of autoimmunity, but the procedure for generating bone marrow chimeras and the photoactivation procedure may additionally find broad application in studies of infectious diseases and tumor metastases.

This protocol describes the generation of mixed murine bone marrow chimeras with spontaneous autoimmune germinal centers, in which autoreactive lymphocytes carry a photoactivatable green fluorescent protein (PA-GFP) reporter. This provides the ability to link cellular location in tissues with downstream molecular and functional analyses.

Autoimmune diseases present a significant health burden. Fundamental questions regarding the development and progression of autoimmune disease remain ...

Flow Cytometric Characterization of Murine B Cell Development

Extensive studies have characterized the development and differentiation of murine B cells in secondary lymphoid organs. Antibodies secreted by B cells have been isolated and developed into well-established therapeutics. Validation of murine B cell development, in the context of autoimmune prone mice, or in mice with modified immune systems, is a crucial component of developing or testing therapeutic agents in mice and is an appropriate use of flow cytometry. Well established B cell flow cytometric parameters can be used to evaluate B cell development in the murine peritoneum, bone marrow, and spleen, but a number of best practices must be adhered to. In addition, flow cytometric analysis of B cell compartments should also complement additional readouts of B cell development. Data generated using this technique can further our understanding of wild type, autoimmune prone mouse models as well as humanized mice that can be used to generate antibody or antibody-like molecules as therapeutics.

We describe herein a simple analysis of the heterogeneity of the murine immune B cell compartment in the peritoneum, spleen, and bone marrow tissues by flow cytometry. The protocol can be adapted and extended to other mouse tissues.

Extensive studies have characterized the development and differentiation of murine B cells in secondary lymphoid organs. Antibodies secreted by B cells ...