# Single amino-acid differences define H2B variants and modify chromatin accessibility to induce EMT in breast cancer

**Authors:** Hejer Dhahri, Kin H. Lau, Wesley N. Saintilnord, Elisson Lopes, Hannah N. Damico, Youssef A. Hegazy, Flavio R. Palma, Daniël P. Melters, Darrell P. Chandler, Yamini Dalal, Jonathan D. Licht, Marcelo G. Bonini, Yvonne N. Fondufe-Mittendorf

PMC · DOI: 10.1038/s41388-025-03636-1 · Oncogene · 2026-01-24

## TL;DR

This paper shows that specific H2B histone variants, like H2B1O, are linked to worse breast cancer outcomes and can drive cancer progression by altering chromatin structure and promoting EMT.

## Contribution

The study identifies H2B1O as a novel onco-histone variant associated with breast cancer subtype-specific dysregulation and chemotherapy resistance.

## Key findings

- H2B1O overexpression is more common in certain breast cancer subtypes and populations, correlating with worse prognosis.
- H2B1O compacts nucleosome structure and activates pro-inflammatory and oncogenic pathways, inducing EMT and chemotherapy resistance.
- H2B variant expression is proposed as a prognostic biomarker and potential therapeutic target in breast cancer.

## Abstract

Histones scaffold genomic DNA and regulate access to the transcriptional machinery. However, naturally occurring histone variants can alter histone-DNA interactions, DNA and histone modifications, and the chromatin interactome. Hence, alterations in histone variant deposition can disrupt chromatin, and are increasingly recognized as a way to trigger various disease, including cancer. While significant attention has been placed on the biochemical and functional roles of H2A, H3, and H4 histone variants, the variants of H2B remain largely understudied. Here, we show that H2B variants are dysregulated in breast cancer and that certain variants are associated with specific breast cancer subtypes. HIST1H2BO overexpression (in particular) is more common in Asian, African American/Black, and young female populations and is associated with a worse prognosis. In vitro studies show that H2B1O compacts nucleosome structure. Incorporating H2B1O into chromatin activates pro-inflammatory and oncogenic pathways, induces epithelial-to-mesenchymal transition (EMT), and generates resistance to first-line chemotherapeutic agents. Thus, H2B1O acts much like an onco-histone, with H2B variant expression being a prognostic biomarker for breast cancer and a potential new target for drug therapies to enhance treatment efficacy.

## Linked entities

- **Genes:** H2BC17 (H2B clustered histone 17) [NCBI Gene 8348]
- **Proteins:** H2BC21 (H2B clustered histone 21)
- **Diseases:** breast cancer (MONDO:0004989)

## Full-text entities

- **Genes:** TLR6 (toll like receptor 6) [NCBI Gene 10333] {aka CD286}, H3C3 (H3 clustered histone 3) [NCBI Gene 8352] {aka H3.1, H3/c, H3FC, HIST1H3C}, TBP (TATA-box binding protein) [NCBI Gene 6908] {aka GTF2D, GTF2D1, HDL4, SCA17, TBP1, TFIID}, H2BC6 (H2B clustered histone 6) [NCBI Gene 8344] {aka H2B.h, H2B/h, H2BC10, H2BC4, H2BC7, H2BC8}, H2BC17 (H2B clustered histone 17) [NCBI Gene 8348] {aka H2B.2, H2B/n, H2BFN, HIST1H2BO, dJ193B12.2}, DNASE1 (deoxyribonuclease 1) [NCBI Gene 1773] {aka DNL1, DRNI}, Junb (jun B proto-oncogene, AP-1 transcription factor subunit) [NCBI Gene 16477], BRCA1 (BRCA1 DNA repair associated) [NCBI Gene 672] {aka BRCAI, BRCC1, BROVCA1, FANCS, IRIS, PNCA4}, H2BC4 (H2B clustered histone 4) [NCBI Gene 8347] {aka H2B.1, H2B/l, H2BC10, H2BC6, H2BC7, H2BC8}, H2BC5 (H2B clustered histone 5) [NCBI Gene 3017] {aka H2B.1B, H2B/a, H2B/b, H2B/g, H2B/h, H2B/k}, EGF (epidermal growth factor) [NCBI Gene 1950] {aka HOMG4, URG}, OR2B6 (olfactory receptor family 2 subfamily B member 6) [NCBI Gene 26212] {aka OR2B1, OR2B1P, OR2B5, OR2B6P, OR5-40, OR5-41}, LIPC (lipase C, hepatic type) [NCBI Gene 3990] {aka HDLCQ12, HL, HTGL}, TLR4 (toll like receptor 4) [NCBI Gene 7099] {aka ARMD10, CD284, TLR-4, TOLL}, H2BC12 (H2B clustered histone 12) [NCBI Gene 85236] {aka H2B/S, H2BFAiii, H2BFT, H2BK, HIST1H2BK}, H2bc4 (H2B clustered histone 4) [NCBI Gene 68024] {aka 2610022J01Rik, H2bc6, H2bc8, H2bfs, Hist1h2bc}, PGR (progesterone receptor) [NCBI Gene 5241] {aka NR3C3, PR}, H3-3B (H3.3 histone B) [NCBI Gene 3021] {aka BRYLIB2, H3.3B, H3F3B}, Tnfaip3 (tumor necrosis factor, alpha-induced protein 3) [NCBI Gene 21929] {aka A20, Tnfip3}, ERBB2 (erb-b2 receptor tyrosine kinase 2) [NCBI Gene 2064] {aka CD340, HER-2, HER-2/neu, HER2, MLN 19, MLN-19}, TLR2 (toll like receptor 2) [NCBI Gene 7097] {aka CD282, TIL4}, Batf (basic leucine zipper transcription factor, ATF-like) [NCBI Gene 53314] {aka B-ATF, SFA-2}, Cxcl1 (C-X-C motif chemokine ligand 1) [NCBI Gene 14825] {aka Fsp, Gro1, KC, Mgsa, N51, Scyb1}, EREG (epiregulin) [NCBI Gene 2069] {aka EPR, ER, Ep}, H2BC13 (H2B clustered histone 13) [NCBI Gene 8340] {aka H2B/c, H2BFC, HIST1H2BL, dJ97D16.4}, TGFB1 (transforming growth factor beta 1) [NCBI Gene 7040] {aka CAEND1, CED, DPD1, IBDIMDE, LAP, TGF-beta1}, H2bc9 (H2B clustered histone 9) [NCBI Gene 319182] {aka H2b-221, Hist1h2bh}, NPS (neuropeptide S) [NCBI Gene 594857], FN1 (fibronectin 1) [NCBI Gene 2335] {aka CIG, ED-B, FINC, FN, FNZ, GFND}, MMP2 (matrix metallopeptidase 2) [NCBI Gene 4313] {aka CLG4, CLG4A, MMP-2, MMP-II, MONA, TBE-1}, SPINK1 (serine peptidase inhibitor Kazal type 1) [NCBI Gene 6690] {aka PCTT, PSTI, Spink3, TATI, TCP}, UPP1 (uridine phosphorylase 1) [NCBI Gene 7378] {aka UDRPASE, UP, UPASE, UPP}, H2BC19P (H2B clustered histone 19, pseudogene) [NCBI Gene 337874] {aka H2B/o, H2B/s, H2BFO, HIST2H2BD}, CDH2 (cadherin 2) [NCBI Gene 1000] {aka ACOGS, ADHD8, ARVD14, CD325, CDHN, CDw325}, GAPDH (glyceraldehyde-3-phosphate dehydrogenase) [NCBI Gene 2597] {aka G3PD, GAPD, HEL-S-162eP}, Cxcl2 (C-X-C motif chemokine ligand 2) [NCBI Gene 20310] {aka CINC-2a, GROb, Gro2, MIP-2, MIP-2a, Mgsa-b}, ZHX2 (zinc fingers and homeoboxes 2) [NCBI Gene 22882] {aka AFR1, RAF}, Fosb (Fos B proto-oncogene, AP-1 transcription factor subunit) [NCBI Gene 14282], INS (insulin) [NCBI Gene 3630] {aka IDDM, IDDM1, IDDM2, ILPR, IRDN, MODY10}, COL8A1 (collagen type VIII alpha 1 chain) [NCBI Gene 1295] {aka C3orf7}, Zhx2 (zinc fingers and homeoboxes 2) [NCBI Gene 387609] {aka Afr-1, Afr1, Raf, mKIAA0854}, MTOR (mechanistic target of rapamycin kinase) [NCBI Gene 2475] {aka FRAP, FRAP1, FRAP2, RAFT1, RAPT1, SKS}, Fosl1 (fos-like antigen 1) [NCBI Gene 14283] {aka Fra1, fra-1}, H2BC9 (H2B clustered histone 9) [NCBI Gene 8345] {aka H2B/j, H2BFJ, HIST1H2BH}, STK33 (serine/threonine kinase 33) [NCBI Gene 65975] {aka SPGF93}, H2BC11 (H2B clustered histone 11) [NCBI Gene 8970] {aka H2B/r, H2BFR, H2BJ, HIST1H2BJ}, Jun (Jun proto-oncogene, AP-1 transcription factor subunit) [NCBI Gene 16476] {aka AP-1, Junc, c-jun}, ST8SIA4 (ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4) [NCBI Gene 7903] {aka PST, PST1, SIAT8-D, SIAT8D, ST8SIA-IV, ST8SiaIV}, H2BC21 (H2B clustered histone 21) [NCBI Gene 8349] {aka GL105, H2B, H2B-GL105, H2B.1, H2BE, H2BFQ}, MAP2K7 (mitogen-activated protein kinase kinase 7) [NCBI Gene 5609] {aka JNKK2, MAPKK7, MEK, MEK 7, MKK7, PRKMK7}, MAPK1 (mitogen-activated protein kinase 1) [NCBI Gene 5594] {aka ERK, ERK-2, ERK2, ERT1, MAPK2, NS13}, Txnrd1 (thioredoxin reductase 1) [NCBI Gene 50493] {aka TR, TR1, TrxR1}, H4C3 (H4 clustered histone 3) [NCBI Gene 8364] {aka H4/g, H4FG, HIST1H4C, TEBIVANED1, TEVANED1, dJ221C16.1}, H2AZ1 (H2A.Z variant histone 1) [NCBI Gene 3015] {aka H2A.Z-1, H2A.z, H2A/z, H2AFZ, H2AZ}, H1-1 (H1.1 linker histone, cluster member) [NCBI Gene 3024] {aka H1.1, H1A, H1F1, HIST1, HIST1H1A}, Mdk (midkine) [NCBI Gene 17242] {aka MK, Mek}, Stk33 (serine/threonine kinase 33) [NCBI Gene 117229] {aka 4921505G21Rik}, Tgfb1 (transforming growth factor, beta 1) [NCBI Gene 21803] {aka TGF-beta1, TGFbeta1, Tgfb, Tgfb-1}, Kras (Kras proto-oncogene, GTPase) [NCBI Gene 16653] {aka K-Ras, K-Ras 2, K-ras, Ki-ras, Kras-2, Kras2}, H2AC18 (H2A clustered histone 18) [NCBI Gene 8337] {aka H2A, H2A.2, H2A/O, H2A/q, H2AFO, H2a-615}
- **Diseases:** lung squamous cell carcinoma (MESH:D002294), herpes simplex virus 1 infection (MESH:D006561), colon adenocarcinoma (MESH:D003110), lymph node metastasis (MESH:D008207), THCA thyroid carcinoma (MESH:D013964), infection (MESH:D007239), HND (MESH:D006250), toxicity (MESH:D064420), stomach adenocarcinoma (MESH:D013274), bladder urothelial carcinoma (MESH:D001749), systemic lupus erythematosus (MESH:D008180), inflammatory breast cancer (MESH:D058922), prostate adenocarcinoma (MESH:D000230), Luminal B (MESH:D006509), tumorigenic (MESH:D002471), basal tumor (MESH:D009369), liver hepatocellular carcinoma (MESH:D006528), oncogenic (MESH:D000074723), COAD (MESH:D029424), aneuploidy (MESH:D000782), viral carcinogenesis (MESH:D014777), metastasis (MESH:D009362), lung adenocarcinoma (MESH:D000077192), Metastatic (MESH:D000092182), uterine corpus endometrial carcinoma (MESH:D016889), oncogenesis (MESH:D063646), TNBC (MESH:D064726), Breast cancer (MESH:D001943), inflammation (MESH:D007249), mycoplasma (MESH:D009175), kidney renal clear cell carcinoma (MESH:D002292)
- **Chemicals:** hydrocortisone (MESH:D006854), agarose (MESH:D012685), salt (MESH:D012492), HCl (MESH:D006851), DAPI (MESH:C007293), methanol (MESH:D000432), glucose (MESH:D005947), mica (MESH:C011934), SDS (MESH:D012967), phenol red (MESH:D010637), formaldehyde (MESH:D005557), sodium acetate (MESH:D019346), Paclitaxel (MESH:D017239), puromycin (MESH:D011691), Doxorubicin (MESH:D004317), Alexa Fluor  647 (MESH:C569686), MgCl2 (MESH:D015636), EdU (MESH:C022811), acrylamide (MESH:D020106), guanidinium (MESH:D019791), butanol (MESH:D000440), Alexa Fluor  594 (-), benzamidine hydrochloride (MESH:C032157), Coomassie blue (MESH:C048139), DPM (MESH:C064754), EGTA (MESH:D004533), sucrose (MESH:D013395), F12 (MESH:C007782), glycerol (MESH:D005990), urea (MESH:D014508), calcium chloride (MESH:D002122), DMSO (MESH:D004121), EDTA (MESH:D004492), ethanol (MESH:D000431), streptomycin (MESH:D013307), Tween 20 (MESH:D011136), silicon (MESH:D012825), penicillin (MESH:D010406), Triton X-100 (MESH:D017830), TE (MESH:D013691), chloroform (MESH:D002725), water (MESH:D014867), KCl (MESH:D011189), ammonium acetate (MESH:C018824), NaCl (MESH:D012965), SYBR green (MESH:C098022), Olaparib (MESH:C531550), HEPES (MESH:D006531), 32P (MESH:C000615311), Crystal violet (MESH:D005840), dithiothreitol (MESH:D004229), Orange G (MESH:C008710), phenol (MESH:D019800), polyacrylamide (MESH:C016679), CO2 (MESH:D002245), bisacrylamide (MESH:C021221)
- **Species:** Human betaherpesvirus 5 (no rank) [taxon 10359], Escherichia coli (E. coli, species) [taxon 562], Homo sapiens (human, species) [taxon 9606]
- **Mutations:** E76K, C for 5-6, arginine residues at positions 2, C into 0
- **Cell lines:** S2 — Drosophila melanogaster (Fruit fly), Spontaneously immortalized cell line (CVCL_Z232), MDA-MB-231 — Homo sapiens (Human), Breast adenocarcinoma, Cancer cell line (CVCL_0062), C6 — Rattus norvegicus (Rat), Rat malignant glioma, Cancer cell line (CVCL_0194), MCF7 — Homo sapiens (Human), Invasive breast carcinoma of no special type, Cancer cell line (CVCL_0031), MCF10A — Homo sapiens (Human), Spontaneously immortalized cell line (CVCL_0598), T47D — Homo sapiens (Human), Invasive breast carcinoma of no special type, Cancer cell line (CVCL_0553), BT474 — Homo sapiens (Human), Invasive breast carcinoma of no special type, Cancer cell line (CVCL_0179)

## Full text

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## Figures

9 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12867764/full.md

## References

2 references — full list in the complete paper: https://tomesphere.com/paper/PMC12867764/full.md

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Source: https://tomesphere.com/paper/PMC12867764