Characterizing and predicting ccRCC-causing missense mutations in Von Hippel-Lindau disease

Mosaic Form of von Hippel-Lindau Syndrome: Case Report and Literature Review

von Hippel-Lindau syndrome (VHLS) is a hereditary cancer syndrome with CNS hemangioblastomas, clear cell renal carcinoma, pheochromocytoma, retinal angiomas, and a number of other manifestations. VHLS is caused by a mutation in the VHL gene and is inherited in an autosomal dominant manner. However, some cases of VHLS develop de novo, and among them, there are rare patients with a mosaic form of the disease. Genetic testing in mosaic patients is prone to false-negative results due to the low copy number of a mutant allele in DNA isolated from the blood. We describe a case of molecular genetic diagnostics of VHLS in a 39-year-old patient using various methods, including mutation analysis in asynchronous primary tumors and repeated DNA analysis from blood using NGS with high coverage for the mutant position. As a result, the patient was diagnosed with a mosaic form of VHLS caused by the variant c.481C>T (p.Arg161Ter), the proportion of which in the blood DNA was 2%. We also summarized the literature data on the mosaic form of VHLS: the severity of clinical manifestations, the features of differential diagnostics of VHLS with a negative result of routine molecular genetic VHL testing, and specific options of active surveillance and treatment for mutation carriers.

Exploring the effects of missense mutations on protein thermodynamics through structure-based approaches: findings from the CAGI6 challenges

Missense mutations are known contributors to diverse genetic disorders, due to their subtle, single amino acid changes imparted on the resultant protein. Because of this, understanding the impact of these mutations on protein stability and function is crucial for unravelling disease mechanisms and developing targeted therapies. The Critical Assessment of Genome Interpretation (CAGI) provides a valuable platform for benchmarking state-of-the-art computational methods in predicting the impact of disease-related mutations on protein thermodynamics. Here we report the performance of our comprehensive platform of structure-based computational approaches to evaluate mutations impacting protein structure and function on 3 challenges from CAGI6: Calmodulin, MAPK1 and MAPK3. Our stability predictors have achieved correlations of up to 0.74 and AUCs of 1 when predicting changes in ΔΔG for MAPK1 and MAPK3, respectively, and AUC of up to 0.75 in the Calmodulin challenge. Overall, our study highlights the importance of structure-based approaches in understanding the effects of missense mutations on protein thermodynamics. The results obtained from the CAGI6 challenges contribute to the ongoing efforts to enhance our understanding of disease mechanisms and facilitate the development of personalised medicine approaches.

Mitochondrial respiratory complex II is altered in renal carcinoma

BACKGROUND

Renal cell carcinoma (RCC) is a disease typified by anomalies in cell metabolism. The function of mitochondria, including subunits of mitochondrial respiratory complex II (CII), in particular SDHB, are often affected. Here we investigated the state and function of CII in RCC patients.

METHODS

We evaluated tumour tissue as well as the adjacent healthy kidney tissue of 78 patients with RCC of different histotypes, focusing on their mitochondrial function. As clear cell RCC (ccRCC) is by far the most frequent histotype of RCC, we focused on these patients, which were grouped based on the pathological WHO/ISUP grading system to low- and high-grade patients, indicative of prognosis. We also evaluated mitochondrial function in organoids derived from tumour tissue of 7 patients.

RESULTS

ccRCC tumours were characterized by mutated von Hippel-Lindau gene and high expression of carbonic anhydrase IX. We found low levels of mitochondrial DNA, protein and function, together with CII function in ccRCC tumour tissue, but not in other RCC types and non-tumour tissues. Mitochondrial content increased in high-grade tumours, while the function of CII remained low. Tumour organoids from ccRCC patients recapitulated molecular characteristics of RCC tissue.

CONCLUSIONS

Our findings suggest that the state of CII, epitomized by its assembly and SDHB levels, deteriorates with the progressive severity of ccRCC. These observations hold the potential for stratification of patients with worse prognosis and may guide the exploration of targeted therapeutic interventions.