Generation of iPSCs from a Patient with the M694V Mutation in the MEFV Gene Associated with Familial Mediterranean Fever and Their Differentiation into Macrophages

Familial Mediterranean fever (FMF) is a systemic autoinflammatory disorder caused by inherited mutations in the MEFV (Mediterranean FeVer) gene, located on chromosome 16 (16p13.3) and encoding the pyrin protein. Despite the existing data on MEFV mutations, the exact mechanism of their effect on the development of the pathological processes leading to the spontaneous and recurrent autoinflammatory attacks observed in FMF, remains unclear. Induced pluripotent stem cells (iPSCs) are considered an important tool to study the molecular genetic mechanisms of various diseases due to their ability to differentiate into any cell type, including macrophages, which contribute to the development of FMF. In this study, we developed iPSCs from an Armenian patient with FMF carrying the M694V, p.(Met694Val) (c.2080A>G, rs61752717) pathogenic mutation in exon 10 of the MEFV gene. As a result of direct differentiation, macrophages expressing CD14 and CD45 surface markers were obtained. We found that the morphology of macrophages derived from iPSCs of a patient with the MEFV mutation significantly differed from that of macrophages derived from iPSCs of a healthy donor carrying the wild-type MEFV gene.


Introduction
Familial Mediterranean fever (FMF) is a systemic autoinflammatory disorder characterized by recurrent episodes of fever and polyserositis (e.g., peritonitis, pleuritis, synovitis) symptoms.The FMF carrier frequencies are high in several eastern Mediterranean populations, ranging from 37-39% in Armenians and Iraqi Jews, to 20% in Turks, North African and Ashkenazi Jews, and Arabs, which leads to a significant economic burden [1,2].The disease is mainly caused by recessively inherited mutations in MEFV, which encodes pyrin protein, which plays an important role in inflammatory processes [3].There are two "mutation hot-spots" located in the 2nd (E148Q) and 10th (M694V, M694I, M680I, and V726A) exons.These mutations account for over 90% of all FMF cases [4].Mutated pyrin causes an exaggerated inflammatory response by uncontrolled interleukin-1 (IL-1) secretion [5].Besides the advances in molecular genetics of FMF, the molecular mechanisms underlying the disease are not fully understood.These questions have been studied using a battery of experimental and in silico methods.Thus, molecular dynamic simulations gain insight into the role of mutations on pyrin structure, function, and interactions [6,7].Another study of polymorphonuclear neutrophils of FMF patients suggests increased sensitivity of mutated pyrin inflammasome towards cytoskeletal modifications in the absence of pathogens [8].A recent study using different cell types (synovial fibroblasts, monocytes, macrophages) showed that inflammation-related functional assays have an anti-inflammatory effect of miR-197-3p [9].Various cell-line-based models have been developed for a more comprehensive understanding of the etiology and pathogenesis of FMF [10].Furthermore, gene editing with CRISPR/Cas9 is used to understand the effect of the MEFV E583A mutation on IL-1β secretion [11].However, immortalized cell lines are limited in mimicking the disease of interest since they do not account for patient genetic variability [12], may accumulate mutations and lack genetic and cellular diversity, and mainly represent cancer-derived cells [13].Conversely, patient primary cells have limited potential for cultivation and maintenance, posing limitations for experiments.
Induced pluripotent stem cells (iPSCs) are considered a unique tool for studying the molecular genetic mechanisms of this disease, disease modeling, and potential drug screening [14][15][16].The main advantage of iPSCs is the almost unlimited ability of cultivation and differentiation serving as a proper source of pluripotent stem cells and any type of cells in the living organism.IPSCs were successfully used for the studying of autoinflammatory [17,18], neurodegenerative [17][18][19][20][21][22][23][24], and other diseases.There have been few attempts to create iPSCs for FMF patients, for example, a fibroblast-derived cell line of a Turkish patient with a homozygous missense mutation (p.Met694Val) in the MEFV gene [25].
In this study, we generated iPSCs from an Armenian FMF patient carrying a homozygous c.2080A>G (M694V) mutation in the MEFV gene.Molecular genetic characterization proved their stemness characteristics.We further differentiated these cells into macrophagelike cells.Morphological analysis revealed significant differences between the obtained macrophages with mutated MEFV gene and macrophages derived from iPSCs with wildtype MEFV [26].

Generation and Characteristics of iPSCs, Associated with the MEFV Gene Mutation
A 20-year-old patient was admitted to the Rheumatology Department of Mikaelyan Institute of Surgery with symptoms relevant to the mixed thoracoabdominal form of FMF, including pain in joints, arthritis, erysipeloid erythema, and fever.Genetic analysis of the patient revealed a pathogenic homozygous missense mutation c.2080A>G (p.M694V, rs61752717) in exon 10 of the MEFV gene.We isolated peripheral blood mononuclear cells (PBMCs) in a Ficoll gradient and reprogrammed them using episomal vectors OCT4, KLF4, L-MYC, SOX2, LIN28, and Trp53 [27].As a result, 10 independent cell lines were obtained, one of which was characterized in detail.All obtained cell lines have a large nuclearcytoplasmic ratio, grow in densely packed iPSC-like single-layer colonies (Figure 1A), and express the early stem cell marker endogenous alkaline phosphatase (Figure 1B).Cultivation of the obtained cells was carried out on a mitotically inactivated mouse embryonic fibroblast (MEF) substrate.(B) Histochemical detection of alkaline phosphatase (AP).(C) Immunofluorescent staining for pluripotency markers OCT4 (red signal), NANOG (green signal), SSEA-4 (green signal), TRA-1-60 (red signal).(D) Quantitative analysis of the expression of pluripotency markers (OCT4, NANOG, SOX2) using RT-qPCR.Error bars indicate the standard deviation, p-value < 0.05, n = 3. Student's t-test was used to assess statistical significance.(E) Karyotype analysis confirmed the presence of normal (46,XY) chromosome set.(F) Morphology of embryoid bodies on the 18th day of differentiation.(G) Immunofluorescent staining for differentiation markers: αSMA (red signal) and CD29 (green signal) (mesoderm); TUBB3/TUJ1 (red signal) and MAP2 (green signal) (ectoderm); AFP (red signal) and CK18 (green signal) (endoderm).Nuclei were stained with DAPI (blue signal).(H) Chromatograms of MEFV gene regions of PBMCs of a patient with FMF, and iPSCs with wildtype MEFV [26].The position of the detected polymorphism indicated with red box.The detected polymorphism is marked with arrow.(I) PCR test for mycoplasma and episomes of the iPSC line (RAUi002-A).Scale bars for (A-C) and (G)-100 µm.Scale bar for (F)-500 µm.
One cell line was selected for detailed characterization and was registered in the Human Pluripotent Stem Cell Registry (hPSCreg, https://hpscreg.eu,accessed on 14 March 2024) under the name RAUi002-A.We carried out quantitative (RT-qPCR) and qualitative (immunofluorescence) analyses of this line for markers of pluripotent cells.Both analyses confirmed the expression of the transcription factors OCT4, SOX2, and NANOG (Figure 1C,D), as well as the expression of surface marker SSEA-4 (Figure 1C).Cytogenetic analysis (G-banding) of the obtained cells showed the presence of a normal karyotype (46,XY) (Figure 1E).
One of the main pluripotency tests is the ability of cells to give rise to all three germ layers (ectoderm, mesoderm, and endoderm).We performed spontaneous differentiation in embryoid bodies (Figure 1F) and used an immunofluorescence analysis of differentiated cells to show the expression of mesoderm markers (α-smooth muscle actin (αSMA) and the surface marker CD29), ectoderm (tubulin β 3 (TUBB3/TUJ1) and mature neural cell markers methionine aminopeptidase 2 (MAP2)), endoderm (alpha-fetoprotein (AFP), and cytokeratin 18 (CK18)) (Figure 1G).These results demonstrated that RAUi002-A cells are pluripotent and can be qualified as iPSCs.
To confirm the presence of a pathogenic mutation in the resulting iPSC line, we performed Sanger sequencing of DNA isolated from the patient's PBMCs and RAUi002-A iPSCs and compared it to the DNA from a conditionally healthy patient.Sequencing confirmed the substitution at position 2080 A to G in exon 10 of the MEFV gene in both samples compared to the control DNA (Figure 1H, location of substitution indicated by arrow).In addition, to confirm the origin of the iPSCs derived from the patient's PBMCs, we performed STR analysis of the patient's PBMC and the RAUi002-A cells.The results showed a complete match of 25 loci from both samples (data available on request from the authors).RAUi002-A iPSCs were also analyzed for the presence/absence of residual episomes and culture contamination with mycoplasma.Both PCR analyses showed their complete absence (Figure 1I).
Taken together, these results suggest that we obtained viable iPSCs from an FMF patient that can serve as a tool to study the contribution of the p.M694V mutation in the MEFV gene to the pathogenesis of FMF disease.
The characteristic summary of the RAUi002-A iPSC line is shown in Table 1.

Generation and Characteristics of Macrophages from RAUi002-A iPSCs
Subsequently, the RAUi002-A iPSC line was differentiated into macrophages to acquire a cell type relevant to further studies on the pathogenesis of FMF.The previously obtained iPSC line K7-4Lf/ICGi022-A was used as a control cell line in the experiments [26].Differentiation of iPSCs into macrophages was achieved by adding the cytokines interleukin-3 (IL-3) and macrophage colony-stimulating factor (M-CSF) to the differentiating embryoid bodies (Figure 2A,B).This process led differentiation along the myeloid pathway, resulting in a homogeneous population of monocytes.Consequently, starting from the 14th day of differentiation and proceeded for over 3 weeks, monocytes were generated in the culture medium.These monocytes adhered to the plastic and, in the presence of M-CSF, terminally differentiated into cells resembling macrophages.Immunofluorescence of CD14 and CD45 mature macrophage-specific markers confirmed the identity of differentiated cells (Figure 2).The presence of the MEFV mutation in RAUi002-A iPSCs derivatives was again confirmed by Sanger sequencing (Figure 2E).IPSC-derived macrophages from a healthy donor were found to have a classic cloaked, spreading morphology (Figure 2C), whereas macrophages with the pathogenic p.M694V mutation in the MEFV gene had an elongated morphology with many rounded cells (Figure 2D, middle photo, white arrows).Similarly, we calculated the average areas of CD14-positive macrophages.The macrophages derived from FMF patient's iPSCs had a significantly smaller area than those derived from healthy donor's iPSCs (Figure 2F).

Discussion
In this study, we used the technology of reprogramming PBMCs into a pluripotent state to obtain patient-specific iPSCs from a patient with FMF associated with the pathogenic mutation p.M694V (according to the databases Infevers, OMIM, ClinVar, Ensembl, etc.) in the MEFV gene.Among the broad clinical and genetic heterogeneity of FMF, one of the most prevalent mutations substantially contributing to disease development is Met694Val (M694V).Previous studies indicated that disease severity is associated with gain-of-function mutations and, in particular, the presence of M694V homozygosity [28].

Discussion
In this study, we used the technology of reprogramming PBMCs into a pluripotent state to obtain patient-specific iPSCs from a patient with FMF associated with the pathogenic mutation p.M694V (according to the databases Infevers, OMIM, ClinVar, Ensembl, etc.) in the MEFV gene.Among the broad clinical and genetic heterogeneity of FMF, one of the most prevalent mutations substantially contributing to disease development is Met694Val (M694V).Previous studies indicated that disease severity is associated with gain-of-function mutations and, in particular, the presence of M694V homozygosity [28].Also, it has been shown that M694V/M694V and M694V/V726A genotypes have a severe clinical course in Arab patients with FMF compared to patients with M694I/M694I genotype [29].Moreover, it has been detected that FMF patients homozygous for M694V exhibit joint and skin-related issues, a higher rate of secondary amyloidosis, and higher colchicine dose requirements [29][30][31].FMF patients with M694V mutation have been characterized by increased interleukin-18 (IL-18), S100A12, and caspase-1 blood levels [28].In Turkish FMF patients, the M694V/M694V genotype has been associated with an earlier age of onset and higher frequency of arthritis and arthralgia compared with the other genotypes [30].
The cell line obtained in our study meets all the requirements of pluripotent cells, has a stem cell-like morphology, a normal karyotype, and can produce derivatives of three germ layers.These cells demonstrated their ability to differentiate into macrophages, which are one of the key cells involved in the disease pathogenesis [32].
Research related to the establishment of patient-derived iPSCs is expected to be a promising avenue for elucidating the pathogenesis of the disease, disease therapy, and drug discovery [33].They became attractive tools for studying neurodegeneration [21][22][23][24]34], cardiac dysfunction [35][36][37], and genetic disorders, such as Duchenne's muscular dystrophy [38].Recently, these approaches have been actively used for modeling immune-related diseases, such as systemic lupus erythematosus, systemic sclerosis, rheumatoid arthritis, and hereditary autoinflammatory syndromes (for review, see [39]).It has been shown that various cell types differentiated from patient-derived iPSCs can be further used for research into the pathogenesis of these diseases.
To our knowledge, a few attempts have been made to generate iPSCs from FMF patients [14,25].Fidan et al. (2015) reported a cell line derived from fibroblasts of an FMF patient carrying a homozygous p.Met694Val mutation in the MEFV gene [25].In our study, we successfully reprogrammed the PBMCs of the FMF patient with a homozygous MEFV gene mutation (M694V).This method is less invasive for the patients.Furthermore, we differentiated stem cells into macrophages and analyzed the morphological differences between macrophages harboring mutated MEFV compared to those with wild-type MEFV.The morphology of macrophage-like cells derived from control iPSCs significantly differed from that of cells derived from iPSCs with a mutation in the MEFV gene.Control macrophage-like cells had a flattened morphology, whereas patient-derived cells had an elongated morphology with a large number of rounded, dying cells.We noted that under the same culture conditions, macrophages with a mutation in the MEFV gene are less viable, most probably due to a pathogenic mutation.These results are in concordance with the previous observations about the structural and functional features of primary immune cells of FMF patients.Thus, studies indicated characteristics of aged/activated cells (small cell size and granularity, up-regulated CXCR4) for polymorphic neutrophils from the patients in acute flares, while in remission, mixed morphology (normal cell size and granularity, up-regulated CD11b, CD49d, CXCR4, and CD62L) has been described [8].
One of the advantages of iPSC-derived macrophages is the preservation of the initial phenotype of the cells.Previous research showed that iPSC-derived cells at different stages of differentiation demonstrate a complete switch of iPSCs to cells expressing a monocyte, macrophage, or dendritic cell-specific gene profile.Moreover, iPSC-derived LPS-induced macrophages demonstrate the expression of classic macrophage pro-inflammatory response markers [40].In addition, the ability of iPSCs to proliferate indefinitely and differentiate into various cells opens multiple avenues for studying FMF pathogenesis, screening drug candidates, and developing gene-based therapies.Using patient-specific iPSCs from FMF patients and the CRISPR/Cas9 genome editing system, it will be possible to generate modified isogenic iPSC lines with the corrected mutation, as well as introduce the mutation into control "healthy" iPSCs in the future.Thus, it will be possible to study, on isogenic lines, the contribution of this mutation to changes not only in the morphology, but also in the functional characteristics of macrophages.Such cell platforms will be valuable for understanding the effects of the mutations on pyrin inflammasome dysfunction in FMF.

Ethics Statement
The study was approved by the Ethics Committee of the Institute of Molecular Biology NAS RA (IRB 00004079, Protocol N3 from 23.08.2021).A patient provided informed consent about using the blood sample for planned analysis.An ICGi022-A iPSC cell line obtained from a healthy donor [26] was used as a control in the experiments of macrophage differentiation and analysis of the morphological features of mutant and wild-type MEFVcarrying cells.

In Vitro Spontaneous Differentiation of the RAUi002-A into Three Germ Layers
The differentiation capacity of the iPSCs was estimated by spontaneous differentiation in embryoid bodies, as described earlier [41].

Immunofluorescent Staining of the RAUi002-A iPSC Line
For immunofluorescence staining, cells growing on chambered coverglass 8-well plates (Thermo Fisher Scientific, Waltham, MA, USA) were fixed with 4% PFA (Sigma-Aldrich, Darmstadt, Germany), permeabilized with 0.5% Triton-X (Thermo Fisher Scientific, Waltham, MA, USA) in PBS for 30 min, and incubated in blocking buffer containing 1% BSA (Sigma-Aldrich, Darmstadt, Germany) in PBS at room temperature.Primary antibodies were diluted in a blocking buffer, in accordance with Table 2. Cell preparations were incubated with primary antibodies overnight at +4 • C. Preparations were washed with PBS twice for 15 min, and secondary antibodies were added for 1.5 h at room temperature.After incubation, cell preparations were washed twice with PBS and stained with DAPI.Manufacturers, catalog numbers and dilutions of all used antibodies are listed in Table 2.The preparations were analyzed using a Nikon Eclipse Ti-E (Nikon, Tokyo, Japan) microscope and NIS Elements Advanced Research version 4.30 software.For RNA isolation, 2 × 10 6 cells were lysed in 1 mL TRIzol reagent (Ambion by Life technologies, Carlsbad, CA, USA), and processed according to the manufacturer's protocols.
The cDNA was synthesized by reverse transcription of 1 µg RNA using M-MuLV reverse transcriptase (Biolabmix, Novosibirsk, Russia).
Quantitative PCR (qPCR) was performed on a LightCycler 480 II system (Roche, Basel, Switzerland) using BioMaster HS-qPCR SYBR Blue 2x (Biolabmix, Novosibirsk, Russia) with the following program: 95 • C, 5 min; 40 cycles: 95 • C, 10 s; 60 • C, 1 min.The primers used are listed in Table 2.The qPCR reactions for each sample were run in triplicate.CT values of the samples for NANOG, OCT4, and SOX2 expression were normalized to actin beta (ACTB).Statistical analysis was performed using Student's t-test.

Karyotyping of the RAUi002-A iPSC Line
Karyotype analysis was performed as described earlier [22].For chromosome banding, samples were stained with DAPI (4,6-diamino-2-phenylindole) solution (200 ng/mL, in 2xSSC) for 5 min, then rinsed in 2xSSC buffer and water.Air-dried slides were covered with 7-10 µL antifade (Vector, Newark, CA, USA) under a coverslip.Analysis of preparations was performed using an Axioplan 2 microscope (Zeiss, Oberkochen, Germany) equipped with a CV-M300 CCD camera (JAI Corp., Yokohama, Japan) at the Center for Collective Use of Microscopic Analysis of Biological Objects at the Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences.ISIS 5.0 software (MetaSystems Group, Inc., Medford, MA, USA) was used for metaphase processing and chromosome folding.

Genotyping of the RAUi002-A iPSC Line
Sanger sequencing was used to confirm the mutation in the MEFV gene in the RAUi002-A iPSC line.To verify the absence of MEFV mutations, Sanger sequencing was also performed for the line K7-4Lf/ICGi022-A used as a control sample.The list of primers used is shown in Table 2. Genome DNA was isolated using QuickExtract™ DNA Extraction Solution (Lucigen, Madison, WI, USA).PCR reactions were run on a T100 thermal cycler (Bio-Rad) using BioMaster HS-Taq PCR-Color (2×) (Biolabmix, Novosibirsk, Russia) with the program: 95 STR profiling was performed using COrDIS Expert 26 (Moscow, Russia) by Genoanalytica (https://www.genoanalytica.ru,accessed on 14 March 2024).

Detection of Mycoplasma and Reprogramming Vectors in the RAUi002-A iPSC Line
The presence of episomal reprogramming vectors and mycoplasma contamination were assessed by PCR (95 • C, 5 min; 35 cycles: 95 • C, 15 s; 62 • C, 15 s; 72 • C, 20 s) using the primers listed in Table 2 [27,42].As a positive control for episomes (Episom+, Figure 1I), mononuclear cells harvested on the 6th day after transfection were used.As a positive control of mycoplasma contamination (Mico+), we used DNA fragments of Mycoplasma spp.from the Myco-Visor Mycoplasma Detection Kit (Biolabmix, Novosibirsk, Russia).

Differentiation of the RAUi002-A iPSC Line into Macrophages
The differentiation of iPSCs into macrophages was performed according to a previously published protocol [43,44] with modifications.IPSCs were placed on a Petri dish (D60 mm) coated with mitotically inactivated MEFs.Dense iPSC colonies were detached with 0.15% collagenase type IV (Thermo Fisher Scientific, Waltham, MA, USA), washed with medium, and transferred to a Petri dish (D60 mm) coated with 1% agarose (Sigma-Aldrich, Darmstadt, Germany) in iPSC medium without the addition of bFGF.On the 4th day of culture, the formed embryoid bodies were transferred to 3 wells of a 6-well plate coated with 0.1% gelatin (Sigma-Aldrich, Darmstadt, Germany) for spreading and differentiation into monocyte-like cells in RPMI medium supplemented with 10% fetal bovine serum, 2 mM GlutaMax, 100 U/mL penicillin-streptomycin, 0.1 mM MEM NEAA, 1 mM sodium pyruvate (all Thermo Fisher Scientific, Waltham, MA, USA), 0.1 mM 2-mercaptoethanol (2-mce, Sigma-Aldrich, Darmstadt, Germany), 25 ng/mL IL-3 and 100 ng/mL M-CSF (both SCI Store, Moscow, Russia).During the 14-19 days of culture, the cell suspension was collected from embryoid bodies containing monocyte-like cells, centrifuged at 300× g for 5 min, and seeded onto chambered coverglass 8-well plates pretreated with 0.1% gelatin for immunofluorescence staining.

Calculation of Macrophage Area and Statistical Analysis
Macrophage area was calculated using ImageJ version 1.53c (NIH, Bethesda, MD, USA) software.Fifty cells positively stained for CD14 marker were analyzed for each healthy and FMF patient iPSCs-derived macrophages.The Mann-Whitney U test was performed to assess the statistical significance of the obtained results.

Figure 1 .
Figure 1.Characteristics of the iPSC cell line RAUi002-A.(A) Morphology of iPSC colonies.

Figure 2 .
Figure 2. Differentiation of iPSCs into macrophages and characteristics of the resulting cells.(A) Morphology of embryoid bodies on the 4th day of differentiation of RAUi002-A iPSC line.(B) Morphology of spread out embryoid bodies on the 5th day after plating of the RAUi002-A line.(C) Immunofluorescence of CD14 on macrophages derived from control iPSCs line ICGi022-A.(D) Immunofluorescent of CD14 and CD45 on macrophages derived from RAUi002-A iPSC line.White arrows indicate rounded cells.Nuclei were stained with DAPI (blue signal).All scale bars: 100 µm.(E) Sanger sequencing confirmed the presence of c.2080A>G (M694V) mutation in macrophages derived from RAUi002-A iPSCs.The position of the detected polymorphism indicated with red box.The detected polymorphism is marked with arrow.(F) Comparison of average area of macrophages derived from FMF patient's iPSCs and a healthy donor.n = 50, Mann-Whitney U test was used to assess statistical significance.p-value < 0.00001.

2 .
Differentiation of iPSCs into macrophages and characteristics of the resulting cells.(A) Morphology of embryoid bodies on the 4th day of differentiation of RAUi002-A iPSC line.(B) Morphology of spread out embryoid bodies on the 5th day after plating of the RAUi002-A line.(C) Immunofluorescence of CD14 on macrophages derived from control iPSCs line ICGi022-A.(D) Immunofluorescent of CD14 and CD45 on macrophages derived from RAUi002-A iPSC line.White arrows indicate rounded cells.Nuclei were stained with DAPI (blue signal).All scale bars: 100 µm.(E) Sanger sequencing confirmed the presence of c.2080A>G (M694V) mutation in macrophages derived from RAUi002-A iPSCs.The position of the detected polymorphism indicated with red box.The detected polymorphism is marked with arrow.(F) Comparison of average area of macrophages derived from FMF patient's iPSCs and a healthy donor.n = 50, Mann-Whitney U test was used to assess statistical significance.p-value < 0.00001.

Table 1 .
Characteristics and validation of the new line iPSCs RAUi002-A.