# mRNA Isoforms and Variants in Health and Disease

**Authors:** Sharmin Shila, Vinesh Dahiya, Charles Hisle, Elizabeth Bahadursingh, Ramkumar Thiyagarajan, Patrick E. Fields, M. A. Karim Rumi

PMC · DOI: 10.3390/ijms26199356 · International Journal of Molecular Sciences · 2025-09-25

## TL;DR

This paper discusses how different mRNA isoforms affect health and disease, highlighting the importance of studying them for better understanding of biological processes.

## Contribution

The paper emphasizes the need to detect mRNA isoforms to improve understanding of physiological and pathological conditions.

## Key findings

- Genes typically express more than three mRNA isoforms, each with unique functions.
- Pathological states alter transcript variant expression, which can contribute to disease or recovery.
- Current gene expression studies often miss mRNA isoforms due to preference for simpler analyses.

## Abstract

Cellular gene expression varies in different physiological or pathological conditions. Conventional gene expression analysis assumes that each gene produces a single mRNA, which is not accurate. On average, genes express more than three mRNA isoforms. A particular cell type expresses different mRNA isoforms from a specific gene depending on its developmental or differentiation state. Different isoforms encode distinct proteins or noncoding regulatory RNAs, each with its own unique functions. Pathological states also alter the expression of transcript variants, which can either cause a disease or facilitate recovery. Still, the detection of mRNA isoforms or variants is not preferred to avoid complex analyses. As a result, gene expression studies often fail to identify the actual mRNA isoforms or variants associated with pathophysiology. In this article, we summarize the data on mRNA isoforms and disease-associated variants identified in various physiological and pathological conditions. These findings emphasize the importance of detecting mRNA isoforms for a better understanding of physiological or pathological conditions.

## Full-text entities

- **Genes:** NOP53 (NOP53 ribosome biogenesis factor) [NCBI Gene 29997] {aka GLTSCR2, PICT-1, PICT1}, MAPT (microtubule associated protein tau) [NCBI Gene 4137] {aka DDPAC, FTD1, FTDP-17, MAPTL, MSTD, MTBT1}, HNRNPC (heterogeneous nuclear ribonucleoprotein C) [NCBI Gene 3183] {aka HNRNP, HNRPC, MRD74, SNRPC}, CDKN1A (cyclin dependent kinase inhibitor 1A) [NCBI Gene 1026] {aka CAP20, CDKN1, CIP1, MDA-6, P21, SDI1}, CDKN2A (cyclin dependent kinase inhibitor 2A) [NCBI Gene 1029] {aka ARF, CAI2, CDK4I, CDKN2, CMM2, INK4}, FOXP4 (forkhead box P4) [NCBI Gene 116113] {aka hFKHLA}, HBB (hemoglobin subunit beta) [NCBI Gene 3043] {aka CD113t-C, ECYT6, beta-globin}, ARHGEF10L (Rho guanine nucleotide exchange factor 10 like) [NCBI Gene 55160] {aka GrinchGEF}, FGFR2 (fibroblast growth factor receptor 2) [NCBI Gene 2263] {aka BBDS, BEK, BFR-1, CD332, CEK3, CFD1}, SMS (spermine synthase) [NCBI Gene 6611] {aka MRSR, MRXSSR, SPMSY, SRS, SpS}, ERG (ETS transcription factor ERG) [NCBI Gene 2078] {aka LMPHM14, erg-3, p55}, TSHR (thyroid stimulating hormone receptor) [NCBI Gene 7253] {aka CHNG1, LGR3, hTSHR-I}, RUNX1 (RUNX family transcription factor 1) [NCBI Gene 861] {aka AML1, AML1-EVI-1, AMLCR1, CBF2alpha, CBFA2, EVI-1}, COA1 (cytochrome c oxidase assembly factor 1) [NCBI Gene 55744] {aka C7orf44, MITRAC15}, ADORA2B (adenosine A2b receptor) [NCBI Gene 136] {aka ADORA2}, HMGA2 (high mobility group AT-hook 2) [NCBI Gene 8091] {aka BABL, HMGI-C, HMGIC, LIPO, SRS5, STQTL9}, CYP27B1 (cytochrome P450 family 27 subfamily B member 1) [NCBI Gene 1594] {aka CP2B, CYP1, CYP1alpha, CYP27B, P450c1, PDDR}, CTLA4 (cytotoxic T-lymphocyte associated protein 4) [NCBI Gene 397286], TMPRSS2 (transmembrane serine protease 2) [NCBI Gene 7113] {aka PRSS10}, ZHX2 (zinc fingers and homeoboxes 2) [NCBI Gene 22882] {aka AFR1, RAF}, CFTR (CF transmembrane conductance regulator) [NCBI Gene 1080] {aka ABC35, ABCC7, CF, CFTR/MRP, MRP7, TNR-CFTR}, APOE (apolipoprotein E) [NCBI Gene 348] {aka AD2, APO-E, ApoE4, LDLCQ5, LPG}, Tia1 (cytotoxic granule-associated RNA binding protein 1) [NCBI Gene 21841] {aka 2310050N03Rik, TIA-1, mTIA-1}, H2az1 (H2A.Z variant histone 1) [NCBI Gene 51788] {aka H2A.Z, H2A.Z1, H2a.z-1, H2afz}, RBM39 (RNA binding motif protein 39) [NCBI Gene 100049658], TPO (thyroid peroxidase) [NCBI Gene 7173] {aka MSA, TDH2A, TPX}, Rab8b (RAB8B, member RAS oncogene family) [NCBI Gene 235442] {aka 5930437D16, D330025I23Rik}, TPX2 (TPX2 microtubule nucleation factor) [NCBI Gene 22974] {aka C20orf1, C20orf2, DIL-2, DIL2, FLS353, GD:C20orf1}, ESRP2 (epithelial splicing regulatory protein 2) [NCBI Gene 80004] {aka RBM35B}, ADAM33 (ADAM metallopeptidase domain 33) [NCBI Gene 80332] {aka C20orf153, DJ964F7.1}, SRP19 (signal recognition particle 19) [NCBI Gene 6728], PRMT5 (protein arginine methyltransferase 5) [NCBI Gene 100294711], INS (insulin) [NCBI Gene 3630] {aka IDDM, IDDM1, IDDM2, ILPR, IRDN, MODY10}, KLF4 (KLF transcription factor 4) [NCBI Gene 9314] {aka EZF, GKLF}, DMD (dystrophin) [NCBI Gene 1756] {aka BMD, CMD3B, DXS142, DXS164, DXS206, DXS230}, VDR (vitamin D receptor) [NCBI Gene 7421] {aka NR1I1, PPP1R163}, EP300 (EP300 lysine acetyltransferase) [NCBI Gene 2033] {aka KAT3B, MKHK2, RSTS2, p300}, ACY1 (aminoacylase 1) [NCBI Gene 95] {aka ACY-1, ACY1D, HEL-S-5}, MYC (MYC proto-oncogene, bHLH transcription factor) [NCBI Gene 4609] {aka MRTL, MYCC, bHLHe39, c-Myc}, Dscam1 (Down syndrome cell adhesion molecule 1) [NCBI Gene 35652] {aka 43Bc, CG17800, CT39257, DSCAM, DScam, DmDscam}, FOS (Fos proto-oncogene, AP-1 transcription factor subunit) [NCBI Gene 2353] {aka AP-1, C-FOS, p55}, MIA3 (MIA SH3 domain ER export factor 3) [NCBI Gene 375056] {aka D320, ODCD2, TANGO, TANGO1, UNQ6077}, f11r.1 (F11 receptor, tandem duplicate 1) [NCBI Gene 323696] {aka JAM, f11r, jam1a, wu:fc07c05, zgc:103642}, CD44 (CD44 molecule (IN blood group)) [NCBI Gene 960] {aka CDW44, CSPG8, ECM-III, ECMR-III, H-CAM, HCELL}, AKT1 (AKT serine/threonine kinase 1) [NCBI Gene 207] {aka AKT, PKB, PKB-ALPHA, PRKBA, RAC, RAC-ALPHA}, PAH (phenylalanine hydroxylase) [NCBI Gene 5053] {aka PH, PKU, PKU1}, TET2 (tet methylcytosine dioxygenase 2) [NCBI Gene 54790] {aka IMD75, KIAA1546, MDS}, TNNT2 (troponin T2, cardiac type) [NCBI Gene 7139] {aka CMD1D, CMH2, CMPD2, LVNC6, RCM3, TnTC}, IRF5 (interferon regulatory factor 5) [NCBI Gene 3663] {aka SLEB10}, HNRNPLL (heterogeneous nuclear ribonucleoprotein L like) [NCBI Gene 100622737] {aka HNRPLL}, Sf3b1 (splicing factor 3b, subunit 1) [NCBI Gene 81898] {aka 155kDa, 2810001M05Rik, Prp10, SAP155, SF3b155, TA-8}, Myocd (myocardin) [NCBI Gene 214384] {aka BSAC2A, Srfcp}, APP (amyloid beta precursor protein) [NCBI Gene 351] {aka AAA, ABETA, ABPP, AD1, APPI, CTFgamma}, TBX20 (T-box transcription factor 20) [NCBI Gene 57057] {aka ASD4}, Cirbp (cold inducible RNA binding protein) [NCBI Gene 12696] {aka Cirp}, Hsp70Ab (Heat shock protein 70 Ab) [NCBI Gene 44920] {aka 87A7 hsp70, CG18743, DMHSP7A2, Dm-hsp70, Dmel\CG18743, GRP78}, ATG13 (autophagy related 13) [NCBI Gene 9776] {aka KIAA0652, PARATARG8}, Nr5a1 (nuclear receptor subfamily 5, group A, member 1) [NCBI Gene 26423] {aka Ad4BP, ELP, ELP-3, Ftz-F1, Ftzf1, SF-1}, HIF1A (hypoxia inducible factor 1 subunit alpha) [NCBI Gene 3091] {aka HIF-1-alpha, HIF-1A, HIF-1alpha, HIF1, HIF1-ALPHA, MOP1}, DYRK1A (dual specificity tyrosine phosphorylation regulated kinase 1A) [NCBI Gene 1859] {aka DYRK, DYRK1, HP86, MNB, MNBH, MRD7}
- **Diseases:** Duchenne muscular dystrophy (MESH:D020388), Metabolic Diseases (MESH:D008659), Genetic Diseases (MESH:D030342), hematological malignancies (MESH:D019337), Graves' disease (MESH:D006111), Thalassemia (MESH:D013789), celiac disease (MESH:D002446), SLE (MESH:D008180), brachyphalangy (MESH:C535432), neurofibrillary tangles (MESH:D055956), Systemic Diseases (MESH:D034721), liver steatosis (MESH:D005234), Autoimmune Diseases (MESH:D001327), Obesity (MESH:D009765), Neurological Diseases (MESH:D020271), skin cancer (MESH:D012878), COPD (MESH:D029424), paralysis (MESH:D010243), retinopathy (MESH:D058437), beta-thalassemia (MESH:D017086), hyperthyroidism (MESH:D006980), tumorigenesis (MESH:D063646), tibial aplasia syndrome (MESH:C536482), AD (MESH:D000544), ACYl (MESH:D054069), neuropsychiatric disorders (MESH:D001523), lung cancer (MESH:D008175), non-alcoholic fatty liver disease (MESH:D065626), disorders of sex determination (MESH:D012735), diabetes mellitus (MESH:D003920), muscle weakness (MESH:D018908), Down Syndrome (MESH:D004314), uterine cancer (MESH:D014594), adrenal insufficiency (MESH:D000309), Tumor (MESH:D009369), Sjogren's syndrome (MESH:D012859), spinal muscular atrophy (MESH:D009134), cystic fibrosis (MESH:D003550), emphysema (MESH:D004646), asthma (MESH:D001249), schizophrenia (MESH:D012559), congenital myasthenic syndromes (MESH:D020294), injury to (MESH:D014947), neurodegeneration (MESH:D019636), airway inflammation (MESH:D007249), muscle atrophy (MESH:D009133), prostate cancer (MESH:D011471), congenital defects (MESH:D000013), melanoma (MESH:D008545), fibrosis (MESH:D005355), loss (MESH:D016388), metabolic syndrome (MESH:D024821), autism spectrum disorder (MESH:D000067877), influenza infection (MESH:D007251), Chronic respiratory diseases (MESH:D012140), developmental abnormalities (MESH:D006130), Genitourinary Diseases (MESH:D000091642), diabetic nephropathy (MESH:D003928), HIV infection (MESH:D015658), liver cancer (MESH:D006528)
- **Chemicals:** oligonucleotides (MESH:D009841), N6-methyladenosine (MESH:C010223), vitamin D (MESH:D014807), glucose (MESH:D005947), calcium (MESH:D002118), m6A (MESH:C005955), lipid (MESH:D008055), FLASH (-)
- **Species:** Human immunodeficiency virus 1 (no rank) [taxon 11676], Trichophyton rubrum (species) [taxon 5551], Mus musculus (house mouse, species) [taxon 10090], Caenorhabditis elegans (species) [taxon 6239], Drosophila melanogaster (fruit fly, species) [taxon 7227], Mycobacterium tuberculosis (species) [taxon 1773], Homo sapiens (human, species) [taxon 9606], Listeria monocytogenes (species) [taxon 1639], Danio rerio (leopard danio, species) [taxon 7955]
- **Mutations:** 500 C to G, 540 C to T, ASP of 95, rs9573096
- **Cell lines:** S2 — Drosophila melanogaster (Fruit fly), Spontaneously immortalized cell line (CVCL_Z232)

## Full text

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## Figures

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## References

275 references — full list in the complete paper: https://tomesphere.com/paper/PMC12524470/full.md

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Source: https://tomesphere.com/paper/PMC12524470