# CRISPR and Beyond: Genome-Editing Strategies in Retinal Stem Cell Research

**Authors:** Małgorzata Woronkowicz, Maya Natasha Thomas, Sarah Jacqueline Saram, Amanda-Jayne F. Carr, Ana Alonso-Carriazo Fernandez, Zaynab Butt, Piotr Skopiński, Conor M. Ramsden

PMC · DOI: 10.3390/cells15060489 · Cells · 2026-03-10

## TL;DR

This review discusses how genome editing, especially CRISPR-Cas9, is used with stem cells to study and treat retinal diseases.

## Contribution

The paper provides a comprehensive overview of genome-editing techniques in retinal stem cell research, emphasizing recent advancements like base and prime editing.

## Key findings

- CRISPR-Cas9 in iPSCs and ESCs is a powerful tool for modeling retinal diseases.
- Base and prime editing offer improved precision for correcting genetic mutations in retinal cells.
- Refining genome-editing techniques is crucial for developing effective retinal disease therapies.

## Abstract

Genome editing has emerged as a transformative approach for understanding and treating retinal degenerative diseases. Combining this technology with pluripotent stem cells provides an ideal platform for modeling human development and disease, and investigating emerging therapeutic strategies ultimately aimed towards in vivo correction. This approach enables both functional studies to understand retinal degeneration and the early development of targeted therapies for inherited disease. This review offers a comprehensive overview of genome-editing techniques and the ability to create new clinically relevant models to understand human disease in retinal research, focusing on the use of the CRISPR-Cas9 system in induced pluripotent stem cells (iPSCs) and embryonic stem cells (ESCs), as well as highlighting recent advancements in base and prime editing. Gene editing in various retinal diseases is discussed in context of studies focusing on disease modeling or developing therapeutic strategies. Continued refinement of these techniques will be essential for advancing translational applications in retinal disease treatment.

## Full-text entities

- **Genes:** Sox2 (SRY (sex determining region Y)-box 2) [NCBI Gene 20674] {aka Sox-2, lcc, ysb}, ANO2 (anoctamin 2) [NCBI Gene 57101] {aka C12orf3, TMEM16B}, HLA-A (major histocompatibility complex, class I, A) [NCBI Gene 3105] {aka HLAA}, MITF (melanocyte inducing transcription factor) [NCBI Gene 4286] {aka CMM8, COMMAD, MI, MITF-A, WS2, WS2A}, RHO (rhodopsin) [NCBI Gene 6010] {aka CSNBAD1, OPN2, RP4}, GPR143 (G protein-coupled receptor 143) [NCBI Gene 4935] {aka NYS6, OA1}, PLIN2 (perilipin 2) [NCBI Gene 123] {aka ADFP, ADRP}, AGFG1 (ArfGAP with FG repeats 1) [NCBI Gene 3267] {aka HRB, RAB, RIP}, PDE6B (phosphodiesterase 6B) [NCBI Gene 5158] {aka CSNB3, CSNBAD2, GMP-PDEbeta, PDEB, RP40, rd1}, CEP290 (centrosomal protein 290) [NCBI Gene 80184] {aka 3H11Ag, BBS14, CT87, JBTS5, LCA10, MKS4}, TP53 (tumor protein p53) [NCBI Gene 7157] {aka BCC7, BMFS5, LFS1, P53, TRP53}, TJP1 (tight junction protein 1) [NCBI Gene 7082] {aka ZO-1}, VSX2 (visual system homeobox 2) [NCBI Gene 338917] {aka CHX10, HOX10, MCOP2, MCOPCB3, RET1}, EYS (EGF-like photoreceptor maintenance factor) [NCBI Gene 346007] {aka C6orf178, C6orf179, C6orf180, EGFL10, EGFL11, RP25}, Cyp4v3 (cytochrome P450, family 4, subfamily v, polypeptide 3) [NCBI Gene 102294] {aka Cyp4v2}, PRPF31 (pre-mRNA processing factor 31) [NCBI Gene 26121] {aka NY-BR-99, PRP31, RP11, SNRNP61}, RPGR (retinitis pigmentosa GTPase regulator) [NCBI Gene 6103] {aka COD1, CORDX1, CRD, PCDX, RP15, RP3}, HES5 (hes family bHLH transcription factor 5) [NCBI Gene 388585] {aka bHLHb38}, TGFB1 (transforming growth factor beta 1) [NCBI Gene 7040] {aka CAEND1, CED, DPD1, IBDIMDE, LAP, TGF-beta1}, OAT (ornithine aminotransferase) [NCBI Gene 4942] {aka GACR, HOGA, OATASE, OKT}, WNT8B (Wnt family member 8B) [NCBI Gene 7479], GNAT2 (G protein subunit alpha transducin 2) [NCBI Gene 2780] {aka ACHM4, GNATC, HG1D}, WNT7B (Wnt family member 7B) [NCBI Gene 7477], THRB (thyroid hormone receptor beta) [NCBI Gene 7068] {aka C-ERBA-2, C-ERBA-BETA, ERBA2, GRTH, NR1A2, PRTH}, SOX1 (SRY-box transcription factor 1) [NCBI Gene 6656], Pou5f1 (POU domain, class 5, transcription factor 1) [NCBI Gene 18999] {aka NF-A3, Oct-3, Oct-3/4, Oct-4, Oct3, Oct3/4}, KLF4 (KLF transcription factor 4) [NCBI Gene 9314] {aka EZF, GKLF}, Cnga3 (cyclic nucleotide gated channel alpha 3) [NCBI Gene 12790] {aka CNG-3, CNG3}, RP2 (RP2 activator of ARL3 GTPase) [NCBI Gene 6102] {aka DELXp11.3, NM23-H10, NME10, TBCCD2, XRP2}, LRP2 (LDL receptor related protein 2) [NCBI Gene 4036] {aka DBS, GP330, LRP-2}, KCNJ13 (potassium inwardly rectifying channel subfamily J member 13) [NCBI Gene 3769] {aka KIR1.4, KIR7.1, LCA16, SVD}, RCVRN (recoverin) [NCBI Gene 5957] {aka RCV1}, POU4F2 (POU class 4 homeobox 2) [NCBI Gene 5458] {aka BRN3.2, BRN3B, Brn-3b}, RBPMS (RNA binding protein, mRNA processing factor) [NCBI Gene 11030] {aka HERMES}, CLN3 (CLN3 lysosomal/endosomal transmembrane protein, battenin) [NCBI Gene 1201] {aka BTN1, BTS, JNCL, RP101, SLC29B1}, LRRC8A (leucine rich repeat containing 8 VRAC subunit A) [NCBI Gene 56262] {aka AGM5, HsLRRC8A, LRRC8, SWELL1}, MIR204 (microRNA 204) [NCBI Gene 406987] {aka MIRN204, RDICC, miRNA204, mir-204}, MAK (male germ cell associated kinase) [NCBI Gene 4117] {aka RP62}, PRPF6 (pre-mRNA processing factor 6) [NCBI Gene 24148] {aka ANT-1, ANT1, C20orf14, Prp6, RP60, SNRNP102}, NRL (neural retina leucine zipper) [NCBI Gene 4901] {aka D14S46E, ESCS2, NRL-MAF, RP27}, RS1 (retinoschisin 1) [NCBI Gene 6247] {aka RS, XLRS1}, PRPH2 (peripherin 2) [NCBI Gene 5961] {aka AOFMD, AVMD, CACD2, DS, MDBS1, RDS}, RB1 (RB transcriptional corepressor 1) [NCBI Gene 5925] {aka OSRC, PPP1R130, RB, p105-Rb, p110-RB1, pRb}, CRB1 (crumbs cell polarity complex component 1) [NCBI Gene 23418] {aka CRB1-A, CRB1-B, CRB1-C, LCA8, RP12}, HTRA1 (HtrA serine peptidase 1) [NCBI Gene 5654] {aka ARMD7, CADASIL2, CARASIL, CARASIL2, HtrA, L56}, CHM (CHM Rab escort protein) [NCBI Gene 1121] {aka DXS540, GGTA, HSD-32, REP-1, TCD}, PRPH (peripherin) [NCBI Gene 5630] {aka NEF4, PRPH1}, NR2E3 (nuclear receptor subfamily 2 group E member 3) [NCBI Gene 10002] {aka ESCS, ESCS1, PNR, RNR, RP37, rd7}, C1QTNF5 (C1q and TNF related 5) [NCBI Gene 114902] {aka CTRP5, MFRP}, IGF1 (insulin like growth factor 1) [NCBI Gene 3479] {aka IGF, IGF-I, IGFI, MGF}, SOX2 (SRY-box transcription factor 2) [NCBI Gene 6657] {aka ANOP3, MCOPS3}, ARMS2 (age-related maculopathy susceptibility 2) [NCBI Gene 387715] {aka ARMD8}, LCA5 (lebercilin LCA5) [NCBI Gene 167691] {aka C6orf152}, CHML (CHM like Rab escort protein) [NCBI Gene 1122] {aka REP2}, PRPF8 (pre-mRNA processing factor 8) [NCBI Gene 10594] {aka HPRP8, PRP8, PRPC8, RP13, SNRNP220}, RPE65 (retinoid isomerohydrolase RPE65) [NCBI Gene 6121] {aka BCO3, LCA2, RP20, mRPE65, p63, rd12}, CRX (cone-rod homeobox) [NCBI Gene 1406] {aka CORD2, CRD, LCA7, OTX3}, WDR5 (WD repeat domain 5) [NCBI Gene 11091] {aka BIG-3, BIG3, CFAP89, SWD3}, WDR5B (WD repeat domain 5B) [NCBI Gene 54554], BCAR1 (BCAR1 scaffold protein, Cas family member) [NCBI Gene 9564] {aka CAS, CAS1, CASS1, CRKAS, P130Cas}
- **Diseases:** tumorigenic (MESH:D002471), Gyrate Atrophy of the Choroid and Retina (MESH:D015799), impaired rod function (MESH:D003072), inflammatory damage (MESH:D018746), muscular atrophy (MESH:D009133), Choroideremia (MESH:D015794), Achromatopsia (MESH:D003117), L-ORD (MESH:C565309), teratomas (MESH:D013724), X-linked disorder (MESH:D040181), drusen (MESH:D015593), lysosomal storage disorder (MESH:D016464), inherited and degenerative retinal diseases (MESH:D020271), LRP2 deficiency (MESH:D007153), non-syndromic retinitis pigmentosa (MESH:C537612), mitochondrial dysfunction (MESH:D028361), cone photoreceptor dysfunction (MESH:C566719), LCA type 4 (MESH:C536999), X-Linked Retinitis Pigmentosa (MESH:C567523), LCA type 16 (OMIM:614186), CORD (MESH:D000071700), optic nerve injury (MESH:D020221), injury to (MESH:D014947), ganglion cell layer abnormalities (MESH:D045888), RO (MESH:D012173), IRDs (MESH:D058499), LCA4 (MESH:C565778), photophobia (MESH:D020795), X-Linked Juvenile Retinoschisis (MESH:D041441), tumorigenesis (MESH:D063646), OA1 (MESH:C537863), ESCS (MESH:C564835), diabetic retinopathy (MESH:D003930), EOMD (OMIM:616118), chloride channel dysfunction (OMIM:160800), RPE degeneration (MESH:D012162), ARRP (MESH:D012174), pigmentation (MESH:D010859), SD (MESH:D000080362), BCD (MESH:C535440), SFD (MESH:C564992), Hyperornithinemia (MESH:C538380), CHM- RPE (MESH:C536309), inflammation (MESH:D007249), reduced vision (MESH:D015354), autosomal recessive disease (MESH:D030342), Batten disease (MESH:D009472), RGC degeneration (MESH:D009410), Retinoblastoma (MESH:D012175), AMD (MESH:D008268), nystagmus (MESH:D009759), blind (MESH:D001766), Usher syndrome (MESH:D052245), Retinal degenerative diseases (MESH:D012164), intraocular malignancy (MESH:C563596), cancer (MESH:D009369), eye disease (MESH:D005128), peripheral vision impairment (MESH:D014786), BD (MESH:D057826), LCA (MESH:D057130)
- **Chemicals:** adenine (MESH:D000225), cytosine (MESH:D003596), lipid (MESH:D008055), aldehyde (MESH:D000447), 4-HNE (-), calcium (MESH:D002118), oxygen (MESH:D010100), chloride (MESH:D002712), carbon (MESH:D002244), cGMP (MESH:D006152), carboplatin (MESH:D016190), retinoids (MESH:D012176), forskolin (MESH:D005576), silica (MESH:D012822), ROS (MESH:D017382), ceramide (MESH:D002518), ornithine (MESH:D009952), STOP (MESH:D014002), Eupatilin (MESH:C045325)
- **Species:** Streptococcus pyogenes (species) [taxon 1314], Homo sapiens (human, species) [taxon 9606], Adeno-associated virus (species) [taxon 272636], Francisella tularensis subsp. novicida (subspecies) [taxon 264], Streptococcus thermophilus (species) [taxon 1308], Staphylococcus aureus (species) [taxon 1280], Rodentia (rodent, order) [taxon 9989], Mus musculus (house mouse, species) [taxon 10090], Campylobacter jejuni (species) [taxon 197], Danio rerio (leopard danio, species) [taxon 7955], Bacteriophage sp. (species) [taxon 38018], Rattus norvegicus (brown rat, species) [taxon 10116], Adenoviridae (family) [taxon 10508], Oryctolagus cuniculus (domestic rabbit, species) [taxon 9986]
- **Mutations:** c.782A > C, c.835C>T, c.1205 T > C, c.2257C>T, c.163 C>A, Arg73Ser, c.4539+2001G>A, A69S, c.351-2A>G, c.828+3A>T, c.6901C>T, c.489C>A, p.Arg218Cys, P2301S, c.2991+1655A>G, c.291_291delAT, T2A, c.291delT, p.E125Vfs9, c.374_380del, p.P186S, p.P188T, c.6088C>T, c.221_222insAATTC, c.808C>T, c.834G>A, c.3211_3212insGT, c.1430A>G, c.4253+4C>T, p.Q279*, p.(Arg311Gln), p.Ala146Lys, c.229C>T, p.Asn296His, S-to-L, c.522_527+10del16, c.2480G>T, c.2276G>T, c.828+1G>A, g.25288G>A, p.R102W, c.269_273del, c.351-2A>6, c.2699 G>A, p.G261A, p.S190W, p.P23H, c.219G>C, p.(Gly1103Arg), c.2299delG, c.1685_1686delAT, G>T, c.278_288del11bp, c.2234_2235delGA, c.992G>A, c.1354dupT, p.G216C, Y236C, c.709_734dup, p.Gly1961Glu
- **Cell lines:** ESCs — Homo sapiens (Human), Embryonic stem cell (CVCL_UI95), -RPE — Homo sapiens (Human), Spontaneously immortalized cell line (CVCL_IQ82), C57BL/6J — Mus musculus (Mouse), Transformed cell line (CVCL_C0MW), ARPE-19 — Homo sapiens (Human), Spontaneously immortalized cell line (CVCL_0145), H9 — Homo sapiens (Human), Sezary syndrome, Cancer cell line (CVCL_1240), H1 — Homo sapiens (Human), Induced pluripotent stem cell (CVCL_HA53), fibroblasts — Mus musculus (Mouse), Spontaneously immortalized cell line (CVCL_0594), hESCs — Homo sapiens (Human), Telomerase immortalized cell line (CVCL_C464)

## Full text

_Full body text omitted from this summary view._ Fetch the complete paper as Markdown: https://tomesphere.com/paper/PMC13026061/full.md

## Figures

4 figures with captions in the complete paper: https://tomesphere.com/paper/PMC13026061/full.md

## References

224 references — full list in the complete paper: https://tomesphere.com/paper/PMC13026061/full.md

---
Source: https://tomesphere.com/paper/PMC13026061