Primary ciliary dyskinesia (PCD) is a rare genetic disorder characterized by impaired ciliary motility that leads to respiratory symptoms, laterality defects, and other systemic abnormalities. Despite significant advancements in genetic research identifying over 50 causative genes and enabling genetic diagnosis in approximately 90% of cases, comprehensive phenotypic characterization remains underexplored. We investigated two respiratory asymptomatic individuals (sisters) who exhibited laterality defects in a three-generation family, both of whom harbored novel compound heterozygous mutations (NM_001372.4:c.308del and NM_001372.4:c.11845G > A) in the
dynein axonemal heavy chain 9
(
DNAH9
) gene associated with primary ciliary dyskinesia-40 (CILD40). Structural modeling and western blotting analysis of HEK-293T cells demonstrated that the frameshift mutation abolished DNAH9 stability, whereas the missense mutation disrupted hydrogen bonds, leading to partial protein destabilization. Peripheral blood RNA sequencing revealed extensive dysregulation of axonemal and intraflagellar transport genes, implicating defects in microtubule-based motility in the two affected siblings with biallelic DNAH9 mutations, but not in their heterozygous family members or one unaffected relative. Plasma proteomic analysis of patients with CILD40 identified significant enrichment of pathways related to platelet activation, complement and coagulation cascades. Further comparative analysis with a patient with PCD caused by a CCDC40 mutation (CILD15 subtype) revealed differential signatures in CILD40, highlighting the potential of plasma proteomics for understanding distinct pathogenic mechanisms across PCD subtypes. These findings underscore the critical role of
DNAH9
compound heterozygous mutations in CILD40 and provide new insights into the genetic, transcriptional, and proteomic phenotypic heterogeneity of PCD.
Siming Kong, Mingshuo Wang, Xuedong Wang et al.· Phenomics· 0 citations
308
Background:
Cholangiocarcinoma (CCA) is a lethal malignancy with limited understanding of its early developmental mechanisms. A significant subset of CCA harbors gain-of-function mutations in
IDH1
(e.g., R132C), which promotes accumulation of the oncometabolite 2-hydroxyglutarate (2-HG). A major barrier in dissecting early events is the lack of models that faithfully recapitulate human physiology. Patient-derived organoids (PDOs) retain the genetic and phenotypic diversity of the original tissue. Base editing now enables the introduction of specific nucleotide mutations into physiologically relevant models to study causal driver events. However, the oncogenic impact of IDH1 mutations on normal and pre-diseased cholangiocytes, and their synergy with factors like bile acids, are poorly defined.
Methods:
Normal and dilated cholangiocyte organoids were derived from clinical specimens. Cytosine base editing installed the IDH1 R132C mutation. Phenotypes (proliferation, invasion, CEA/CA19-9 secretion) and 2-HG levels were assessed, with/without bile acid challenge. Integrated transcriptomics and metabolomics delineated underlying reprogramming.
Results:
Introduction of the
IDH1
R132C mutation into both normal and dilated cholangiocyte organoids induced a pro-oncogenic phenotype, including enhanced proliferation, invasion, and secretion of CEA/CA19-9, concomitant with 2-HG accumulation. Mechanistically, multi-omics analysis revealed that IDH1 R132C, particularly in dilated cholangiocytes, drives a transcriptional program characteristic of early biliary transformation, involving dysregulation of pathways governing cell fate (e.g., Hippo/YAP suppression) and metabolism (e.g., upregulated glutaminolysis). Crucially, bile acids acted as a potent synergistic cofactor, amplifying phenotypes and rewiring the metabolic network to create a dependency on specific biosynthetic pathways. This combination effectively locked organoids into a proliferative, precursor-like state.
Conclusions:
We have established a novel, physiologically relevant in vitro model that recapitulates the synergistic oncogenesis driven by
IDH1
mutation and microenvironmental stress in early CCA. Our study moves beyond phenomenology to identify the critical early molecular and metabolic nodes activated during this transformation. Importantly, by targeting a key identified metabolic vulnerability (e.g., with a glutaminase inhibitor or a mutant IDH1 inhibitor), we were able to significantly attenuate the observed hyperproliferative and invasive phenotypes, and reduce tumor marker secretion. This work provides a preclinical platform for identifying and testing interceptive strategies aimed at reversing or halting early cholangiocarcinogenesis in high-risk settings.
Ziye Chen, Qingru Song, Jinxin Wang et al.· Journal of Clinical Oncology· 0 citations