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Review Open Access

Emerging insights into alternative end‑joining: Mechanisms, genome instability and therapeutic opportunities in cancer (Review)

  • Authors:
    • Nasir Azam
    • Xiangyu Liu
    • Xinghan Li
    • Lin Ma
    • Qi Liu
  • View Affiliations / Copyright

    Affiliations: Laboratory of Molecular Radiation Medicine, International Cancer Center, Shenzhen University, Shenzhen, Guangdong 518055, P.R. China, Department of Stomatology, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong 518055, P.R. China
    Copyright: © Azam et al. This is an open access article distributed under the terms of Creative Commons Attribution License.
  • Article Number: 103
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    Published online on: October 9, 2025
       https://doi.org/10.3892/ijo.2025.5809
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Abstract

Genome instability is a central hallmark of cancer, driven by aberrant DNA damage responses that facilitate tumor evolution and resistance to therapy. Although canonical non‑homologous end joining and homologous recombination are well‑characterized pathways for repairing DNA double‑strand breaks (DSBs), recent advances have revealed that cancer cells increasingly depend on alternative end‑joining (alt‑EJ) to survive persistent DNA damage that arises from intrinsic stresses or external therapies. Alt‑EJ, characterized by its reliance on microhomologous sequences at DSB sites, promotes mutation accumulation and chromosomal rearrangements, thereby driving genomic instability and tumor progression. Despite its pivotal role in cancer biology, the molecular regulation, contextual determinants and dualistic role of alt‑EJ in maintaining genome integrity compared with promoting instability remain incompletely understood. The present review integrated the latest mechanistic insights into alt‑EJ, elucidated its regulatory networks and interactions with canonical DSB repair pathways and discussed its consequences for cancer genome integrity and evolution. Furthermore, it highlighted the emerging potential of alt‑EJ as a therapeutic vulnerability for cancer, underscoring the urgent need to translate these discoveries into innovative treatment strategies aimed at overcoming therapy resistance and improving patient outcomes.
View Figures

Figure 1

Major pathways for DSB repair. NHEJ
begins with Ku70-Ku80 hetero-dimer attaching to DNA ends. DNA-PKcs
recruitment and auto-phosphorylation bring the DNA ends together
and allow ligation by XRCC4-LIG4 and XLF or PAXX. Resection by MRN
complex and CtIP promotes homology-directed repair. Long-range
resection creates RPA-coated ssDNA overhangs using BLM-DNA2
helicase-nuclease or EXO1 nucleases. HR occurs when BRCA1, PALB2
and BRCA2 facilitate loading RAD51 onto ssDNA and displace RPA.
RAD51 nucleoprotein filaments invade the DNA-synthesis template
sister chromatids. Alternatively, substantial resection generates a
substrate for SSA, where RAD52 promotes homologous sequence
annealing on each DNA end. ERCC1 and XPF handle 3'single-stranded
flaps for LIG1-mediated DNA ligation. DSB resection also activates
alt-EJ via PARP1, where POLQ anneals short homologous sequences,
synthesizes DNA and re-ligates DNA ends using LIG1 or LIG3. DSB,
DNA double-strand break; NHEJ, non-homologous end joining;
DNA-PKcs, DNA-dependent protein kinase catalytic subunit; ssDNA,
single-stranded DNA; HR, homologous recombination; alt-EJ,
alternative end-joining; PARP, poly (ADP-ribose) polymerase; XRCC4,
X-ray repair cross-complementing protein 4; LIG4, DNA ligase 4;
XLF, XRCC4-like factor; PAXX, paralogue of XRCC4 and XLF; CtIP,
c-terminal-binding protein-interacting protein; RPA, replication
protein A; BLM, Bloom syndrome helicase; DNA2, DNA replication
helicase/nuclease 2; EXO1, exonuclease 1; BRCA1/2, breast cancer
gene 1/2; PALB2, partner and localizer of BRCA2; SSA, single strand
annealing; ERCC1, excision repair cross complementation group 1;
XPF, xeroderma pigmentosum group F; POLQ, DNA polymerase theta;
LIG1/3, DNA ligase1/3; Ins/del, insertion or deletion; LOH, loss of
heterogeneity; nt, nucleotide.

Figure 2

Schematic illustration of alt-EJ
effectors. The alt-EJ pathway is influenced by several factors.
TGFβ signaling begins in the cytoplasm and activates Smad proteins
and non-canonical pathways to regulate DDR through miR-182 and
other mechanisms (24,25,78). Loss of TGFβ signaling, such as
with the effects induced by HPV, causes enhanced alt-EJ activity
(25,79). The HPV oncoprotein E7 directs DNA
repair to alt-EJ (83). PLK1
facilitate RHINO to accumulate in the M phase recruit POLQ to the
break site (69). APE2 interacts
with POLQ in an epistatic way for alt-EJ (63). CtIP, Mre11 and BLM proteins
regulate DNA end resection, which subsequently facilitates the
process of strand annealing and the coupling of fragmented DNA ends
through the annealing of microhomologies. alt-EJ, alternative
end-joining; DDR, DNA damage response; TGFβ, transforming growth
factor-beta; Smad, suppressor of mothers against decapentaplegic;
miR, microRNA; HPV, human papillomavirus; PLK1, polo-like kinase 1;
APE2, apurinic/apyrimidinic endodeoxyribonuclease 2; RHINO,
Rad9-Hus1-Rad1-interacting nuclear orphan; POLQ, DNA polymerase θ;
CtIP, c-terminal-binding protein-interacting protein; MRE11,
Meiotic recombination 11; BLM, Bloom syndrome helicase; PARP, poly
(ADP-ribose) polymerase.
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Copy and paste a formatted citation
Spandidos Publications style
Azam N, Liu X, Li X, Ma L and Liu Q: Emerging insights into alternative end‑joining: Mechanisms, genome instability and therapeutic opportunities in cancer (Review). Int J Oncol 67: 103, 2025.
APA
Azam, N., Liu, X., Li, X., Ma, L., & Liu, Q. (2025). Emerging insights into alternative end‑joining: Mechanisms, genome instability and therapeutic opportunities in cancer (Review). International Journal of Oncology, 67, 103. https://doi.org/10.3892/ijo.2025.5809
MLA
Azam, N., Liu, X., Li, X., Ma, L., Liu, Q."Emerging insights into alternative end‑joining: Mechanisms, genome instability and therapeutic opportunities in cancer (Review)". International Journal of Oncology 67.6 (2025): 103.
Chicago
Azam, N., Liu, X., Li, X., Ma, L., Liu, Q."Emerging insights into alternative end‑joining: Mechanisms, genome instability and therapeutic opportunities in cancer (Review)". International Journal of Oncology 67, no. 6 (2025): 103. https://doi.org/10.3892/ijo.2025.5809
Copy and paste a formatted citation
x
Spandidos Publications style
Azam N, Liu X, Li X, Ma L and Liu Q: Emerging insights into alternative end‑joining: Mechanisms, genome instability and therapeutic opportunities in cancer (Review). Int J Oncol 67: 103, 2025.
APA
Azam, N., Liu, X., Li, X., Ma, L., & Liu, Q. (2025). Emerging insights into alternative end‑joining: Mechanisms, genome instability and therapeutic opportunities in cancer (Review). International Journal of Oncology, 67, 103. https://doi.org/10.3892/ijo.2025.5809
MLA
Azam, N., Liu, X., Li, X., Ma, L., Liu, Q."Emerging insights into alternative end‑joining: Mechanisms, genome instability and therapeutic opportunities in cancer (Review)". International Journal of Oncology 67.6 (2025): 103.
Chicago
Azam, N., Liu, X., Li, X., Ma, L., Liu, Q."Emerging insights into alternative end‑joining: Mechanisms, genome instability and therapeutic opportunities in cancer (Review)". International Journal of Oncology 67, no. 6 (2025): 103. https://doi.org/10.3892/ijo.2025.5809
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