HOTAIR Gene Variant Linked to Higher Cholangiocarcinoma Risk in Egyptian Patients

A genetic variant within a long non-coding RNA gene called HOTAIR appears to be associated with an increased risk of cholangiocarcinoma, a rare and aggressive cancer of the bile ducts, according to a cross-sectional study conducted in Egypt. The research, published in the Egyptian Liver Journal, found that Egyptian patients carrying the GG genotype at a specific position in the HOTAIR gene, known as rs4759314, had markedly higher odds of cholangiocarcinoma compared with patients who had the AA genotype. The finding points to a possible genetic biomarker for a cancer that is notoriously difficult to detect early and is often diagnosed only at an advanced stage, when curative surgery is no longer an option.

Cholangiocarcinoma arises from the epithelial cells lining the biliary tract and is classified by anatomical location as intrahepatic, perihilar, or distal. The disease is described in the study as rare, aggressive, and increasingly prevalent, characterized by late-stage diagnosis and resistance to chemotherapy. Surgical intervention remains the only potentially curative treatment, but it is frequently precluded because the disease has already advanced by the time patients present. Patients typically show symptoms of biliary obstruction, elevated cholestatic liver enzymes, and raised levels of tumor markers such as CEA and CA19-9, yet the role of these markers in prognosis remains unclear because of their low sensitivity and specificity. These challenges underscore the need for new biomarkers and therapeutic targets, which motivated the research team to investigate whether inherited variation in HOTAIR might influence susceptibility to the disease.

HOTAIR, which stands for HOX transcript antisense intergenic RNA, is a 2.2 kilobase non-coding RNA produced from the homeobox C gene locus on chromosome 12q13.13. Long non-coding RNAs are RNA molecules exceeding 200 nucleotides in length that do not encode proteins but can affect numerous biological processes, and they may function as either oncogenes or tumor suppressors. HOTAIR has been identified as a regulator of cancer, playing a role in the genesis and progression of numerous human malignancies and serving as a diagnostic and prognostic biomarker. It functions as a molecular scaffold that modulates chromatin state to facilitate transcriptional silencing and can also act as a competing endogenous RNA, sponging microRNAs and altering downstream gene expression. In numerous cancers, increased HOTAIR expression correlates with resistance to therapy and reduced overall survival. Prior to this study, however, the authors noted a lack of data regarding HOTAIR polymorphisms and their correlation with the risk of cholangiocarcinoma.

The research team, led by Basma Nabil Zakie Abo-Elhassan of the National Liver Institute at Menoufia University, enrolled 150 participants between April 2024 and March 2025, recruited from the outpatient clinic and inpatient departments of Hepatology and Gastroenterology at the National Liver Institute Hospital in Egypt. The cohort comprised three groups of 50 participants each: patients with a confirmed diagnosis of cholangiocarcinoma, with a mean age of 55.66 years and 70 percent males; patients with non-malignant biliary obstruction, with a mean age of 53.82 years and 68 percent males; and 50 age- and gender-matched healthy volunteers serving as controls, with a mean age of 52.20 years and 54 percent males. Individuals with hepatocellular carcinoma or metastatic focal liver lesions of non-cholangiocarcinoma origin were excluded. Cholangiocarcinoma diagnosis was confirmed according to British Society of Gastroenterology guidelines based on laboratory findings, radiological studies including triphasic CT, MRI with MRCP, and ERCP, and histopathological confirmation according to the American Joint Committee on Cancer classification. Non-malignant obstruction was confirmed with MRCP and ERCP findings showing absence of focal lesions.

Genotyping was performed using a polymerase chain reaction-restriction fragment-length polymorphism, or PCR-RFLP, technique. The researchers targeted two single-nucleotide polymorphisms: rs4759314, an A-to-G substitution, and rs920778, a T-to-C variant. For rs4759314, the resulting fragments were identified as 124 base pairs for the G allele and 98 and 25 base pairs for the A allele, while for rs920778 the fragments were 140 base pairs for the T allele and 113 and 27 base pairs for the C allele. The sample size was calculated using G*Power software, with a minimum requirement of 133 participants estimated at 80 percent power and an effect size of 0.30; 150 participants were recruited to account for possible missing data or failed genotyping. Clinical data, including CA19.9 levels, were recorded alongside the genetic results.

The results showed that the AA genotype was the most frequent form of rs4759314 across all study groups, but the GG genotype was notably more frequent in the cholangiocarcinoma group, and the G allele also appeared at a higher frequency in that group. Statistical analysis indicated that the GG genotype was associated with an increased risk of cholangiocarcinoma compared with the AA genotype, with an odds ratio of 4.18, a 95 percent confidence interval of 1.19 to 14.60, and a p-value of 0.025 when comparing the cancer group to the non-malignant biliary obstruction group. Against the healthy control group, the GG genotype carried an odds ratio of 5.28, with a 95 percent confidence interval of 1.33 to 20.87 and a p-value of 0.018. The G allele was associated with an elevated risk of cholangiocarcinoma compared with the A allele, with an odds ratio of 2.95, and the dominant genetic model also indicated a significant association, with an odds ratio of 3.16 and a 95 percent confidence interval of 1.35 to 7.43. No significant differences in genotype distribution or allele frequency were observed between the non-malignant biliary obstruction group and the healthy control group, and the AG genotype did not significantly influence disease risk.

In contrast, the rs920778 polymorphism showed no significant association with cholangiocarcinoma susceptibility. The CT genotype was the most frequent among all groups, and there were no significant differences in the genotypes and allele frequencies of this variant across the study groups. This absence of association is notable because prior research has linked rs920778 to cancer susceptibility in other populations: a recent meta-analysis found the variant significantly associated with increased cancer risk, particularly in Asian populations and digestive cancers, and research in Chinese populations has connected rs920778 to ovarian cancer susceptibility and prognosis. The authors also noted that their rs4759314 genotype distribution aligned with a prior Egyptian study that examined these variants in relation to breast cancer, in which the A-to-G variation showed a significant association with increased risk across dominant, co-dominant, and over-dominant genetic models.

To test whether the rs4759314 genotype remained relevant beyond standard clinical parameters, the researchers constructed a multivariate logistic regression model. Univariate analysis had identified hemoglobin values, platelet count, ALT, albumin concentration, INR, bilirubin, CA19-9 levels, amylase and lipase values, and the rs4759314 AG-plus-GG genotype as potential risk factors for cholangiocarcinoma. The final multivariate model included CA19.9, total bilirubin, and lipase, and demonstrated good fit according to the Hosmer-Lemeshow test, with a p-value greater than 0.05, and avoided multicollinearity, with a variance inflation factor below 1.3. After adjusting for these confounders, the rs4759314 genotype remained a significant predictor of cholangiocarcinoma, with an adjusted odds ratio of 3.387, a 95 percent confidence interval of 1.038 to 11.048, and a p-value of 0.043. Within the cancer group, the genotype also showed significant differences regarding white blood cell count, platelet count, and C-reactive protein levels, as well as associations with the presence of hepatic focal lesions, lymph node metastasis, and the number of focal lesions; patients with the GG genotype exhibited a greater frequency of lymph node metastasis and a higher number of focal lesions, and focal lesions affecting both lobes occurred more frequently in GG carriers. The authors described these comparisons as preliminary and warranting further investigation.

The study’s radiological findings underscored the advanced presentation typical of the disease: 82 percent of cholangiocarcinoma patients exhibited hepatic focal lesions, 72 percent presented with lymph node metastasis, while the majority showed normal spleen size, at 92 percent, and absence of ascites, at 56 percent. The authors concluded that the findings suggest the HOTAIR rs4759314 polymorphism may have a potential association with increased susceptibility to cholangiocarcinoma, indicating that the G allele could serve as a potential genetic biomarker, while emphasizing that further research is warranted to validate its clinical utility. They also acknowledged several limitations: histopathological confirmation was not obtained for all cases, the study lacks representative CT imaging findings for the cholangiocarcinoma and non-malignant cases, and the single-center design with 50 patients per group limits statistical power. The authors recommended that future multicenter trials prioritize larger cohorts and comprehensive imaging to validate these findings. As a cross-sectional study, the work establishes associations rather than causal effects, and the wide confidence intervals around the odds ratios reflect the modest sample size, leaving open the question of how this variant will perform as a biomarker in broader and more diverse populations.

Subject of Research: Association between HOTAIR gene polymorphisms and susceptibility to cholangiocarcinoma in Egyptian patients

Article Title: The association of polymorphism within the HOX transcript antisense intergenic RNA (HOTAIR) gene with cholangiocarcinoma in Egyptian patients

Article References: Abo-Elhassan, B. N. Z., elsameea, E. A., El-Aarag, B., & El-Abd, M. G. (2026). The association of polymorphism within the HOX transcript antisense intergenic RNA (HOTAIR) gene with cholangiocarcinoma in Egyptian patients. Egyptian Liver Journal, 16(1), Article 78. https://doi.org/10.1186/s43066-026-00558-9

Image Credits: AI Generated

DOI: 10.1186/s43066-026-00558-9

Keywords: cholangiocarcinoma, HOTAIR, long non-coding RNA, single-nucleotide polymorphism, rs4759314, rs920778, genetic biomarker, PCR-RFLP, biliary tract cancer, Egypt, case-control association study, liver institute Menoufia University