Cystic Adventitial Disease of the (ilio) Femoral Artery with a Connection to the Hip Joint: Case Report and a Review of the Literature.

Objective: Cystic adventitial disease (CAD) is an uncommon non-atherosclerotic peripheral vessel disease, most often seen in the popliteal artery. Only a small number of cases involving the (ilio) femoral artery have been reported. The case of a 48 year old female with CAD of the left femoral artery with a connection of the disease to the hip joint on pre-operative imaging confirmed during surgery is described. A literature review of CAD of the (ilio) femoral artery with patient demographic data, symptoms, management, presence of a joint connection, and long term outcomes was performed. Methods: Multiple databases (Medline, CINAHL, EMBASE) were searched and each article was cross referenced to collect the literature on CAD of the (ilio) femoral artery. Case studies or series of CAD of the (ilio) femoral artery in English between 1995 and 2021 were included. Results: Sixteen case reports with 17 patients were included; 71% were male. CAD was unilateral in all case reports, with 53% on the right side. Patients presented with vascular symptoms including claudication (88%), a palpable pulsating mass (18%), acute limb ischaemia (6%) or limb swelling (8%). Computed tomography angiography (CTA) (76%) and duplex ultrasonography (47%) were the most commonly used imaging modalities. The common femoral artery was the most affected site (88%). Reported treatments were cyst resection and autologous vein reconstruction (six, one recurrence), cyst resection and patch repair (five, one recurrence), cyst resection with synthetic graft reconstruction (three, no recurrence), cyst resection (two, one recurrence), and cyst incision and decompression (one, one recurrence). In 18% of the cases, a connection between the CAD and hip joint was seen. Conclusion: Cyst resection and ligation with interposition of an autologous vein graft, synthetic graft or patch repair (in only locally affected arteries) seems to be the preferred treatment, with a low reported recurrence rate. CTA and magnetic resonance imaging are the imaging modalities of choice when suspecting CAD to determine an appropriate pre-operative plan and identify joint connections.

Precancerous liver diseases do not cause increased mutagenesis in liver stem cells.

Inflammatory liver disease increases the risk of developing primary liver cancer. The mechanism through which liver disease induces tumorigenesis remains unclear, but is thought to occur via increased mutagenesis. Here, we performed whole-genome sequencing on clonally expanded single liver stem cells cultured as intrahepatic cholangiocyte organoids (ICOs) from patients with alcoholic cirrhosis, non-alcoholic steatohepatitis (NASH), and primary sclerosing cholangitis (PSC). Surprisingly, we find that these precancerous liver disease conditions do not result in a detectable increased accumulation of mutations, nor altered mutation types in individual liver stem cells. This finding contrasts with the mutational load and typical mutational signatures reported for liver tumors, and argues against the hypothesis that liver disease drives tumorigenesis via a direct mechanism of induced mutagenesis. Disease conditions in the liver may thus act through indirect mechanisms to drive the transition from healthy to cancerous cells, such as changes to the microenvironment that favor the outgrowth of precancerous cells.

GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing.

GRIDSS2 is the first structural variant caller to explicitly report single breakends-breakpoints in which only one side can be unambiguously determined. By treating single breakends as a fundamental genomic rearrangement signal on par with breakpoints, GRIDSS2 can explain 47% of somatic centromere copy number changes using single breakends to non-centromere sequence. On a cohort of 3782 deeply sequenced metastatic cancers, GRIDSS2 achieves an unprecedented 3.1% false negative rate and 3.3% false discovery rate and identifies a novel 32-100 bp duplication signature. GRIDSS2 simplifies complex rearrangement interpretation through phasing of structural variants with 16% of somatic calls phasable using paired-end sequencing.

Optimizing Nanopore sequencing-based detection of structural variants enables individualized circulating tumor DNA-based disease monitoring in cancer patients.

Here, we describe a novel approach for rapid discovery of a set of tumor-specific genomic structural variants (SVs), based on a combination of low coverage cancer genome sequencing using Oxford Nanopore with an SV calling and filtering pipeline. We applied the method to tumor samples of high-grade ovarian and prostate cancer patients and validated on average ten somatic SVs per patient with breakpoint-spanning PCR mini-amplicons. These SVs could be quantified in ctDNA samples of patients with metastatic prostate cancer using a digital PCR assay. The results suggest that SV dynamics correlate with and may improve existing treatment-response biomarkers such as PSA. https://github.com/UMCUGenetics/SHARC .

Amplatzer Vascular Plug Embolization in Two Patients with Ruptured Infrarenal Aortic Aneurysm and Aortoiliac Occlusive Disease.

Mortality for ruptured abdominal aortic aneurysm (AAA) is known to be high. When left untreated, it is nearly always fatal. Standard treatment options include open surgery and endovascular aneurysm repair (EVAR), but both techniques have limitations. Owing to comorbidities and anatomical constraints, some patients are deemed unsuitable for both open surgery and EVAR. In these patients, alternative treatment strategies can be of special interest. To our knowledge, these are the first two cases reported using an Amplatzer Vascular Plug II for aortic embolization in patients with coexisting aneurysmatic and aorto-bi-iliac occlusive disease requiring urgent treatment for contained AAA rupture. Successful aneurysm exclusion was noted at follow-up ranging from 5 months to 3 years, and no procedure-related complications occurred. We therefore believe that in selected patients, this could be an elegant alternative in life-threatening situations with sustained occlusion in the mid-term.

The mutational impact of culturing human pluripotent and adult stem cells.

Genetic changes acquired during in vitro culture pose a risk for the successful application of stem cells in regenerative medicine. To assess the genetic risks induced by culturing, we determined all mutations in individual human stem cells by whole genome sequencing. Individual pluripotent, intestinal, and liver stem cells accumulate 3.5 ± 0.5, 7.2 ± 1.1 and 8.3 ± 3.6 base substitutions per population doubling, respectively. The annual in vitro mutation accumulation rate of adult stem cells is nearly 40-fold higher than the in vivo mutation accumulation rate. Mutational signature analysis reveals that in vitro induced mutations are caused by oxidative stress. Reducing oxygen tension in culture lowers the mutational load. We use the mutation rates, spectra, and genomic distribution to model the accumulation of oncogenic mutations during typical in vitro expansion, manipulation or screening experiments using human stem cells. Our study provides empirically defined parameters to assess the mutational risk of stem cell based therapies.

5-Fluorouracil treatment induces characteristic T>G mutations in human cancer.

5-Fluorouracil (5-FU) is a chemotherapeutic drug commonly used for the treatment of solid cancers. It is proposed that 5-FU interferes with nucleotide synthesis and incorporates into DNA, which may have a mutational impact on both surviving tumor and healthy cells. Here, we treat intestinal organoids with 5-FU and find a highly characteristic mutational pattern that is dominated by T>G substitutions in a CTT context. Tumor whole genome sequencing data confirms that this signature is also identified in vivo in colorectal and breast cancer patients who have received 5-FU treatment. Taken together, our results demonstrate that 5-FU is mutagenic and may drive tumor evolution and increase the risk of secondary malignancies. Furthermore, the identified signature shows a strong resemblance to COSMIC signature 17, the hallmark signature of treatment-naive esophageal and gastric tumors, which indicates that distinct endogenous and exogenous triggers can converge onto highly similar mutational signatures.

Deficiency of nucleotide excision repair is associated with mutational signature observed in cancer.

Nucleotide excision repair (NER) is one of the main DNA repair pathways that protect cells against genomic damage. Disruption of this pathway can contribute to the development of cancer and accelerate aging. Mutational characteristics of NER-deficiency may reveal important diagnostic opportunities, as tumors deficient in NER are more sensitive to certain treatments. Here, we analyzed the genome-wide somatic mutational profiles of adult stem cells (ASCs) from NER-deficient Ercc1 -/Δ mice. Our results indicate that NER-deficiency increases the base substitution load twofold in liver but not in small intestinal ASCs, which coincides with the tissue-specific aging pathology observed in these mice. Moreover, NER-deficient ASCs of both tissues show an increased contribution of Signature 8 mutations, which is a mutational pattern with unknown etiology that is recurrently observed in various cancer types. The scattered genomic distribution of the base substitutions indicates that deficiency of global-genome NER (GG-NER) underlies the observed mutational consequences. In line with this, we observe increased Signature 8 mutations in a GG-NER-deficient human organoid culture, in which XPC was deleted using CRISPR-Cas9 gene-editing. Furthermore, genomes of NER-deficient breast tumors show an increased contribution of Signature 8 mutations compared with NER-proficient tumors. Elevated levels of Signature 8 mutations could therefore contribute to a predictor of NER-deficiency based on a patient's mutational profile.

MutationalPatterns: comprehensive genome-wide analysis of mutational processes.

BACKGROUND: Base substitution catalogues represent historical records of mutational processes that have been active in a cell. Such processes can be distinguished by various characteristics, like mutation type, sequence context, transcriptional and replicative strand bias, genomic distribution and association with (epi)-genomic features. RESULTS: We have created MutationalPatterns, an R/Bioconductor package that allows researchers to characterize a broad range of patterns in base substitution catalogues to dissect the underlying molecular mechanisms. Furthermore, it offers an efficient method to quantify the contribution of known mutational signatures within single samples. This analysis can be used to determine whether certain DNA repair mechanisms are perturbed and to further characterize the processes underlying known mutational signatures. CONCLUSIONS: MutationalPatterns allows for easy characterization and visualization of mutational patterns. These analyses willsupport fundamental research into mutational mechanisms and may ultimately improve cancer diagnosis and treatment strategies. MutationalPatterns is freely available at http://bioconductor.org/packages/MutationalPatterns .

Measuring mutation accumulation in single human adult stem cells by whole-genome sequencing of organoid cultures.

Characterization of mutational processes in adult stem cells (ASCs) will improve our understanding of aging-related diseases, such as cancer and organ failure, and may ultimately help prevent the development of these diseases. Here, we present a method for cataloging mutations in individual human ASCs without the necessity of using error-prone whole-genome amplification. Single ASCs are expanded in vitro into clonal organoid cultures to generate sufficient DNA for accurate whole-genome sequencing (WGS) analysis. We developed a data-analysis pipeline that identifies with high confidence somatic variants that accumulated in vivo in the original ASC. These genome-wide mutation catalogs are valuable resources for the characterization of the underlying mutational mechanisms. In addition, this protocol can be used to determine the effects of culture conditions or mutagen exposure on mutation accumulation in ASCs in vitro. Here, we describe a protocol for human liver ASCs that can be completed over a period of 3-4 months with hands-on time of ∼5 d.