Genomic landscape of liquid biopsy mutations in TP53 and DNA damage genes in cancer patients.

Next-generation sequencing (NGS) assays based on plasma cell-free DNA (cfDNA) are increasingly used for clinical trials inclusion. Their optimized limit of detection applied to a large number of genes leads to the identification of mutations not confirmed in tissue. It becomes essential to describe the characteristics and consequences of these liquid biopsy-only mutations. In the STING protocol (Gustave Roussy, NCT04932525), 542 patients with advanced solid cancer had cfDNA-based and tissue-based NGS analysis (performed by FoundationOne® Liquid CDx and FoundationOne CDx™, respectively). Mutations identified in the liquid biopsy but not in the paired tissue were considered as liquid biopsy-only mutations irrespective of their variant allelic frequency (VAF). Out of 542 patients, 281 (51.8%) harbored at least one liquid biopsy-only mutation. These patients were significantly older, and more heavily pretreated. Liquid biopsy-only mutations occurring in TP53, and in DDR genes (ATM, CHEK2, ATR, BRCA2, and BRCA1) accounted for 90.8% of all the mutations. The median VAF of these mutations was generally low (0.37% and 0.40% for TP53 and DDR genes respectively). The variant type repartition depended on the gene. Liquid biopsy-only mutations affected hotspot in TP53 codon 273, 125, 195, 176, 237 or 280 and ATM codon 2891 and 3008. In a subset of 37 patients, 75.0%, 53.5% and 83.3% of the liquid biopsy-only mutations occurring respectively in ATM, TP53, and CHEK2 were confirmed in the matching whole blood sample. Although liquid biopsy-only mutations makes the interpretation of liquid biopsy results more complex, they have distinct characteristics making them more easily identifiable.

Next-Generation Sequencing on Circulating Tumor DNA in Advanced Solid Cancer: Swiss Army Knife for the Molecular Tumor Board? A Review of the Literature Focused on FDA Approved Test.

FDA-approved next-generation sequencing assays based on cell-free DNA offers new opportunities in a molecular-tumor-board context thanks to the noninvasiveness of liquid biopsy, the diversity of analyzed parameters and the short turnaround time. It gives the opportunity to study the heterogeneity of the tumor, to elucidate complex resistance mechanisms and to adapt treatment strategies. However, lowering the limit of detection and increasing the panels' size raise new questions in terms of detection of incidental germline alterations, occult malignancies and clonal hematopoiesis of indeterminate potential mutations. In this review, after a technological discussion and description of the common problematics encountered, we establish recommendations in properly using these FDA-approved tests in a molecular-tumor-board context.

Li-Fraumeni syndrome in Tunisian carriers with different and rare tumor phenotype: genotype-phenotype correlation.

BACKGROUND: Li-Fraumeni syndrome (LFS) is a rare autosomal hereditary predisposition to multiples cancers, mainly affecting young individuals. It is characterized by a broad tumor spectrum. To our best knowledge, only one Tunisian study with a confirmed LFS was published. METHODS: Our study focused on the clinical, histopathological and genetic results of two patients with rare tumor phenotype and tried to establish genotype-phenotype correlation. The clinical diagnosis was based on Chompret-Bonaiti criteria relative to LFS. Molecular study was assessed using Sanger sequencing of the hotspot germline variants of TP53 gene. RESULTS: We report 2 Tunisian families fulfilling the clinical criteria of Chompret-Bonaiti. The tumor phenotype was bilateral breast cancer (BC) in 27-year-old woman and multiple tumors for the second proband, with an onset age of 14, 35 and 36 yo for osteosarcoma, BC and esophageal cancer respectively. Each of them had a rare histological type of breast cancer associated with LFS, phyllode tumor and intralobular carcinoma. Both patients had cancer family history. The molecular study showed deleterious heterozygous germline TP53 variants in each index case: The first had a well-known hotspot missense variation c.742C>T p.(R248W) with a rare histological association, explaining genotype phenotype correlation. The second case had a nonsense variation c.159G>A p.(W53*), rare worldwide, extending the phenotype spectrum in LFS. Immunohistochemistry study in tumor samples confirmed the lack of p53 protein expression. CONCLUSIONS: Conclusively, germline TP53 testing is primordial in patients with a family history suggestive of LFS for clinical practice avoiding genotoxic treatments and adapting the surveillance. National database in LFS listing clinical and mutational data is important to set, particularly for variants rarely reported worldwide. Experience from different countries must be integrated to harmonize global protocols for cancer surveillance in LFS.

Posterior Microphthalmos Pigmentary Retinopathy Syndrome with Angle-Closure Glaucoma: A Case Report.

Purpose: To describe a particular form of posterior microphthalmos pigmentary retinopathy syndrome (PMPRS) with an atypical clinical presentation of pigment retinal dystrophy and an association to an inconstant complication which is angle-closure glaucoma (ACG). Methods: A 40-year-old male patient with ACG on maximal topical treatment was referred to our department for uncontrolled intraocular pressure. Best-corrected visual acuity was 2/10 in the right eye and light perception in the left eye. Intraocular pressure was 36 mmHg bilaterally. He had 360° peripheral anterior synechiae on gonioscopy. Fundus examination revealed total cupping with pale retinal lesions in both eyes and a few pigment deposits in the midperiphery of the right eye. Multimodal imaging was done. Results: Fundus autofluorescence revealed patchy areas of hypoautofluorescence. Optical coherence tomography (OCT) showed bilateral foveoschisis and macular folds. Anterior segment OCT showed a circumferential iridocorneal angle closure. Axial length measured with ultrasound biomicroscopy was 18.4 mm in the right eye and 18.1 in the left eye. Electroretinogram revealed attenuated scotopic responses. The patient was diagnosed with nanophthalmos-retinitis pigmentosa (RP)-foveoschisis syndrome complicated with ACG. A combined surgery with phacoemulsification - anterior vitrectomy - intraocular lens implantation and trabeculectomy was performed in both eyes with a satisfactory outcome. Conclusions: In its typical forms, PMPR syndrome is an association of nanophthalmos - RP - foveoschisis and optic nerve head (ONH) drusen. Incomplete phenotypes may lack ONH drusen or foveoschisis. Patients with PMPRS have to be screened for iridocorneal angle synechia and ACG.

Optical Coherence Tomography Angiography in idiopathic retinal vasculitis, aneurysms and neuroretinitis (IRVAN) syndrome: A case report.

PURPOSE: Since its first description by Chang et al. in 1995, the diagnosis of Idiopathic retinal vasculitis, aneurysms and neuroretinitis (IRVAN) syndrome has been based on the findings of Fundus Fluorescein Angiography (FFA). Our purpose was to describe the utility of optical coherence tomography angiography (OCT-A) in its diagnosis and management. CASE DESCRIPTION: A 40-year-old female presented with bilateral blurred vision. Her best corrected visual acuity was at 8/10. Fundus examination revealed blurred disc margins, perivascular exudates, arterial sheaths and retinal hemorrhages bilaterally. FFA showed staining of the optic disc with dye leakage in the right eye, a punctuate hyperfluorescence of the temporosuperior artery in the left eye, bilateral vascular sheathing and capillary dropout. OCT-A showed simultaneous presence of papillary aneurysm and neovascularization of the optic nerve head in the right eye, a papillary aneurysm in the left eye and bilateral capillary non-perfusion. Our patient was diagnosed with IRVAN syndrome. Oral steroids associated with panretinal laser photocoagulation and intravitreal injection of bevacizumab in the right eye resulted in vanishing of the papillary neovascularization with no recurrence on OCT-A at 10-month follow-up. CONCLUSIONS: OCT-A is an additional tool to FFA for visualization of arterial macroaneurysms and retinal neovascularization without the interference of dye leakage. It well demarcates nonperfused areas and ensures follow-up of retinal neovascularization. Its limitations are the limited field of view and the low sensitivity in detecting arteriolar dilations. Thus, OCT-A is unable to outplace FFA but should be considered alternately with it for non-invasive follow-up of IRVAN syndrome.

JAK2 p.(V617F) mutation in Tunisian myeloproliferative neoplasms and its genotype-phenotype correlation.

Myeloproliferative neoplasms (MPNs) comprise polycythemia vera (PV), essential thrombocythemia (ET) and primary myelofibrosis (PMF). The relationship between JAK2 p.(V617F) mutation and MPNs was first described in 2005. The purpose of this study was to determine the prevalence of JAK2 p.(V617F) mutation in Tunisian patients assessed for MPNs and try to set a genotype-phenotype correlation. A retrospective study was conducted between January 2015 and April 2019. We collected the clinical data of all patients with MPNs suspicion or atypical splanchnic vein thrombosis (SVT). JAK2 p.(V617F) mutation was detected by allele specific real-time quantitative fluorescence PCR (AS-qPCR). We gathered 974 patients who underwent molecular analysis, 55.5% of them were male and 44.5% were female. The median age of all studied patients was 56 years. JAK2 p.(V617F) was found in 349 (35.8%) of total enrolled cases. It was reported in 44%, 37%, 29% and 25% of all patients diagnosed as having respectively ET, PV, PMF and atypical SVT. JAK2 p.(V617F) was negative in 62.2% of patients addressed for suspicion of PV. There was a significant positive correlation between the JAK2 p.(V617F) mutation status, age, gender, white blood cell counts and platelet counts. To our best knowledge, this is the first vast investigation of JAK2 p.(V617F) variant in Tunisia and North Africa with the lowest mutation rate in entire cohort and MPNs subgroups, underlying a specific presentation of this mutation. It is considered as an essential marker of MPNs' diagnosis and prognosis and is associated with differences in the phenotype of these disorders, helpful for the follow-up of these patients.

Beckwith-Wiedemann syndrome: Clinical, histopathological and molecular study of two Tunisian patients and review of literature.

BACKGROUND: Beckwith-Wiedemann syndrome (BWS) is a rare overgrowth syndrome characterized by congenital malformations and predisposition to embryonic tumors. Loss of methylation of imprinting center 2 (IC2) is the most frequent alteration and rarely associated with tumors compared to paternal uniparental disomy of chromosome 11 (UPD(11)pat) and gain of methylation of imprinting center 1. METHODS: Our study aimed to describe the clinical, histopathological and genetic characteristics of two patients and establish genotype-phenotype correlations. The clinical diagnosis was based on the criteria defined by the international expert consensus of BWS. Molecular study of 11p15.5 methylation status was assessed using methylation-specific-multiplex ligation probe amplification (MS-MLPA). RESULTS: Patients were aged 12 months and 3 months and fulfilled the clinical score of BWS. MS-MLPA showed molecular alterations consisting of loss of methylation in IC2 (IC2-LOM) at the maternal allele for one patient and a mosaic UPD(11)pat for the second patient in whom follow-up at 6months revealed adrenocortical carcinoma (ACC) with low grade of malignancy. Molecular subtypes guide the follow-up and tumor surveillance, our major concern. CONCLUSION: We have to take into account the psychological impact of a possible tumor whatever the underlying mechanism is. Nevertheless, the tumor risk remains high for UPD(11)pat. Our study extended the phenotype of BWS with absence of macrosomia in Tunisian patients, contrasting with literature, and added a supplementary case of ACC in the tumor spectrum of BWS patients with UPD(11)pat.

Quantitative Analysis of Microvascular Network with Optical Coherence Tomography Angiography and its Correlation with Visual Acuity in Retinal Vein Occlusion.

PURPOSE: To analyze the macular microvascular network and the correlations between visual acuity and quantitative parameters using optical coherence tomography angiography (OCTA) in eyes with retinal vein occlusion (RVO). METHODS: We conducted a prospective cross-sectional study including patients with unilateral RVO. We performed 4.5 mm × 4.5 mm macular OCTA angiograms for assessment of quantitative parameters in both superficial and deep capillary plexuses (SCP, DCP). Area of foveal avascular zone (FAZ), vascular density (VD), skeleton density (SD), fractal dimension (FD), vessel diameter index (VDI), and lacunarity (LAC) were analyzed. RESULTS: Seventy eyes of 35 patients were enrolled. As compared to fellow eyes, OCTA analysis in eyes with RVO showed larger FAZ, lower VD, lower SD, lower FD, higher VDI, and increased LAC in both plexuses (All P < 0.05). The enlargement of FAZ in the SCP was associated with visual loss (P = 0.025, r = 0.378). In the DCP, visual acuity was negatively correlated with parafoveal VD, SD, and FD (P = 0.004, r = -0.472; P = 0.003, r = -0.482 and P = 0.036, r = -0.308, respectively). Stepwise multivariate regression analysis showed that lower SD and lower FD in the DCP remained correlated with poorer visual acuity (P = 0.04, r = -0.261 and P = 0.032, r = -0.264, respectively). CONCLUSIONS: OCTA provides quantitative parameters to analyze retinal microvasculature in eyes with RVO. These OCTA biomarkers could be used to predict the impact of macular ischemia and capillary dropout on visual acuity in RVO.

Skeletal phenotype/genotype in progressive pseudorheumatoid chondrodysplasia.

BACKGROUND: Axial and extra-axial deceleration in function and progressive joint pain with subsequent development of antalgic gait associated with swellings, and stiffness of the joints with loss of the physiological spine biomechanics were the natural history in this group of patients. Clinical and radiological phenotypes have been analysed carefully to further understand the aetiology behind. METHODS: Seven patients (three children around the age of 9-11 and one child of 17 years old). Three adults aging 25, 30, 33 and 40 years old were seen and examined. The paediatric group of patients were initially diagnosed with myopathy followed later by juvenile rheumatoid arthritis in other institutions. Clinical and imaging documentation were collected in our departments, followed by mutation screening, was carried out by bidirectional sequencing of the WISP3 gene. RESULTS: Clinical and radiological phenotypic studies confirmed the diagnosis of progressive pseudorheumatoid chondrodysplasia. A constellation of abnormalities such as early senile hyperostosis of the spine (Forestier disease), osteoarthritis of the hips showed progressive diminution and irregularities of the hip joint spaces associated with progressive capital femoral epiphyseal dysplasia and coxa vara have been encountered. Loss-of-function homozygous mutations (c.667T>G, p.Cys223Gly) and (c.170C>A, p.Ser57*) in the WISP3 gene were identified in our patients. CONCLUSION: The definite diagnosis was not defined via vigorous myopathic and rheumatologic investigations. Detailed clinical examination and skeletal survey, followed by genotypic confirmation, were our fundamental pointers to rule out the false diagnosis of juvenile rheumatoid arthritis and rheumatoid polyarthritis in the adult group of patients. We wish to stress that the clinical/radiological phenotype is the baseline tool to establish a definite diagnosis and to guide the geneticist toward proper genotype.Key Points•Joint pain and difficulties in walking/climbing the stairs are characteristic features encountered in early childhood. False diagnosis of juvenile rheumatoid arthritis can be made at this point.•False positive-like muscular wasting resembling myopathy results in ensuing vigorous troublesome investigations.•Flattened vertebral bodies associated with defective ossification of the anterior end plates are characteristic features of progressive pseudorheumatoid chondrodysplasia.•Joint expansions, which are usually accompanied by narrowing of the articular ends of the appendicular skeletal system, show a clear radiological phenotype of pseudorheumatoid chondrodysplasia.

Granular type I corneal dystrophy in a large consanguineous Tunisian family with homozygous p.R124S mutation in the TGFBI gene.

Purpose: We report the clinical features and the mutational analysis in a large Tunisian family with granular corneal dystrophy type I (GCD1). Patients and Methods: Thirty-three members of the Tunisian family underwent a complete ophthalmologic examination. DNA extraction and direct Sanger sequencing of the exons 4 and 12 of transforming growth factor ß Induced (TGFBI) gene was performed for 42 members. For the molecular modeling of TGFBI protein, we used pGenTHREADER method to identify templates, 3D-EXPRESSO program to align sequences, MODELLER to get a homology model for the FAS1 (fasciclin-like) domains and finally NOMAD-ref web server for the energy minimization. Results: The diagnosis of GCD1 was clinically and genetically confirmed. Sequencing of exon 4 of TGFBI gene revealed the p.[R124S] mutation at heterozygous and homozygous states in patients with different clinical severities. Visual acuity was severely affected in the homozygous patients leading to a first penetrating keratoplasty. Recurrence occurred rapidly, began in the seat of the corneal stitches and remained superficial up to 40 years after the graft. For heterozygous cases, visual acuity ranged from 6/10 to 10/10. Corneal opacities were deeper and predominating in the stromal center. According to bioinformatic analysis, this mutation likely perturbs the protein physicochemical properties and reduces its solubility without structural modification. Conclusions: Our study describes for the first time phenotype-genotype correlation in a large Tunisian family with GCDI and illustrates for the first time clinical and histopathological presentation of homozygous p.[R124S] mutation. These results help to understand pathophysiology of the disease.