Monitoring Chronic Myeloid Leukemia: How Molecular Tools May Drive Therapeutic Approaches

More than 15 years ago, imatinib entered into the clinical practice as a "magic bullet"; from that point on, the prognosis of patients affected by chronic myeloid leukemia (CML) became comparable to that of aged-matched healthy subjects. The aims of treatment with tyrosine kinase inhibitors (TKIs) are for complete hematological response after 3 months of treatment, complete cytogenetic response after 6 months, and a reduction of the molecular disease of at least 3 logs after 12 months. Patients who do not reach their goal can switch to another TKI. Thus, the molecular monitoring of response is the main consideration of management of CML patients. Moreover, cases in deep and persistent molecular response can tempt the physician to interrupt treatment, and this "dream" is possible due to the quantitative PCR. After great international effort, today the BCR-ABL1 expression obtained in each laboratory is standardized and expressed as "international scale." This aim has been reached after the establishment of the EUTOS program (in Europe) and the LabNet network (in Italy), the platforms where biologists meet clinicians. In the field of quantitative PCR, the digital PCR is now a new and promising, sensitive and accurate tool. Some authors reported that digital PCR is able to better classify patients in precise "molecular classes," which could lead to a better identification of those cases that will benefit from the interruption of therapy. In addition, digital PCR can be used to identify a point mutation in the ABL1 domain, mutations that are often responsible for the TKI resistance. In the field of resistance, a prominent role is played by the NGS that enables identification of any mutation in ABL1 domain, even at sub-clonal levels. This manuscript reviews how the molecular tools can lead the management of CML patients, focusing on the more recent technical advances

Case Report: Decrypting an interchromosomal insertion associated with Marfan’s syndrome: how optical genome mapping emphasizes the morbid burden of copy-neutral variants

Optical genome mapping (OGM), which allows analysis of ultra-high molecular weight (UHMW) DNA molecules, represents a response to the restriction created by short-read next-generation-sequencing, even in cases where the causative variant is a neutral copy-number-variant insensitive to quantitative investigations. This study aimed to provide a molecular diagnosis to a boy with Marfan syndrome (MFS) and intellectual disability (ID) carrying a de novo translocation involving chromosomes 3, 4, and 13 and a 1.7 Mb deletion at the breakpoint of chromosome 3. No FBN1 alteration explaining his Marfan phenotype was highlighted. UHMW gDNA was isolated from both the patient and his parents and processed using OGM. Genome assembly was followed by variant calling and annotation. Multiple strategies confirmed the results. The 3p deletion, which disrupted ROBO2, (MIM*602431) included three copy-neutral insertions. Two came from chromosome 13; the third contained 15q21.1, including the FBN1 from intron-45 onwards, thus explaining the MFS phenotype. We could not attribute the ID to a specific gene variant nor to the reshuffling of topologically associating domains (TADs). Our patient did not have vesicular reflux-2, as reported by missense alterations of ROBO2 (VUR2, MIM#610878), implying that reduced expression of all or some isoforms has a different effect than some of the point mutations. Indeed, the ROBO2 expression pattern and its role as an axon-guide suggests that its partial deletion is responsible for the patient’s neurological phenotype. Conclusion: OGM testing 1) highlights copy-neutral variants that could remain invisible if no loss of heterozygosity is observed and 2) is mandatory before other molecular studies in the presence of any chromosomal rearrangement for an accurate genotype-phenotype relationship

Valorization of an Underutilized Waste from Olive Oil Production by Recovery of Hydroxytyrosol

Hydroxytyrosol (HT) is one of the most powerful natural antioxidants, mainly contained in olive oil and its by-products. Here, a procedure for the preparation of an HT-enriched sample is described. An acidic aqueous extract (pH 1.25) from Olive Oil Dregs (OOD), a by-product from oil mills, was prepared by incubation at 37 °C for 1 h. The total phenolic content and HT amount were 6.24 ± 0.10 mg gallic acid equivalent/g OOD and 532.98 ± 5.78 μg/g OOD, respectively. Amberlite XAD16N and XAD7HP resins were used for the recovery of HT from the raw extract. Several elution conditions were tested with both resins, and elution with 25% ethanol provided the highest HT recovery (92.50% from XAD7HP). Antioxidant activities were assessed in the pool containing the highest quantity of HT. The results were compared with those of the raw extract. Ferric reducing antioxidant power values were comparable (95.71 ± 2.50 and 96.64 ± 13.47 μg ascorbic acid equivalent/mg for HT-enriched pool and raw extract, respectively), while the radical scavenging activity was higher for the pool (92.83% ± 0.44 and 44.12% ± 1.82, respectively). The results reported here demonstrate that HT can be recovered with a high yield from OOD, providing a preparation with high radical scavenging power. In addition, it is proved that this by-product, poorly considered up to now, can be usefully exploited

DataSheet1_Case Report: Decrypting an interchromosomal insertion associated with Marfan’s syndrome: how optical genome mapping emphasizes the morbid burden of copy-neutral variants.pdf

Optical genome mapping (OGM), which allows analysis of ultra-high molecular weight (UHMW) DNA molecules, represents a response to the restriction created by short-read next-generation-sequencing, even in cases where the causative variant is a neutral copy-number-variant insensitive to quantitative investigations. This study aimed to provide a molecular diagnosis to a boy with Marfan syndrome (MFS) and intellectual disability (ID) carrying a de novo translocation involving chromosomes 3, 4, and 13 and a 1.7 Mb deletion at the breakpoint of chromosome 3. No FBN1 alteration explaining his Marfan phenotype was highlighted. UHMW gDNA was isolated from both the patient and his parents and processed using OGM. Genome assembly was followed by variant calling and annotation. Multiple strategies confirmed the results. The 3p deletion, which disrupted ROBO2, (MIM*602431) included three copy-neutral insertions. Two came from chromosome 13; the third contained 15q21.1, including the FBN1 from intron-45 onwards, thus explaining the MFS phenotype. We could not attribute the ID to a specific gene variant nor to the reshuffling of topologically associating domains (TADs). Our patient did not have vesicular reflux-2, as reported by missense alterations of ROBO2 (VUR2, MIM#610878), implying that reduced expression of all or some isoforms has a different effect than some of the point mutations. Indeed, the ROBO2 expression pattern and its role as an axon-guide suggests that its partial deletion is responsible for the patient’s neurological phenotype. Conclusion: OGM testing 1) highlights copy-neutral variants that could remain invisible if no loss of heterozygosity is observed and 2) is mandatory before other molecular studies in the presence of any chromosomal rearrangement for an accurate genotype-phenotype relationship.</p

Discovering a familial Xp11.4 microduplication: Does the mother matter?

Interstitial duplications of the short arm of the X chromosome have been rarely described, especially in males. Usually boys present mental retardation, multiple congenital abnormalities and short stature. We describe two sons one with a 2q37.3 deletion and a Xp11.4 duplication and the other with Xp11.4 duplication only, identified by array-CGH. They both presented a phenotype characterized by poor growth, mild facial dysmorphisms, autism and developmental delay. The 2q37.3 identified chromosomal anomaly was inherited from the healthy father and included approximately 8 known genes, while the Xp11.4 duplication resulted inherited from the healthy mother and involved 13 known genes. Of these TSPAN7 and CASK, localized on Xp11.4, genes are of special interest. The alteration on the X chromosome could be more related to the clinical feature presented by the two brothers, while the anomaly on the chromosome 2 is more likely a polymorphism or might influence the phenotype correlated to the Xp11.4 duplication. The healthy phenotype of the mother could be explained by X chromosome inactivation (XCI) phenomenon

Nurses' Physical and Psychological Symptoms During the first COVID-19 Lockdown in Italy: a Nationwide Cross-Sectional Study in Stem Cell Transplantation Setting

Northern Italy was one of the first European territories to deal with the Coronavirus Disease 2019 (COVID-19) outbreak. Drastic emergency restrictions were introduced to contain the spread and limit pressure on healthcare facilities. However, nurses were at high risk of developing physical, mental, and working issues due to professional exposure. The aim of this cross-sectional study was to investigate these issues among nurses working in Italian hematopoietic stem cell transplant (HSCT) centers during the COVID-19 pandemic

Prospective assessment of NGS-detectable mutations in CML patients with non-optimal response: the NEXT-in-CML study

In chronic myeloid leukemia (CML) patients, tyrosine kinase inhibitors (TKIs) may select for drug-resistant BCR-ABL1 kinase domain (KD) mutants. Although Sanger sequencing (SS) is considered the gold standard for BCR-ABL1 KD mutation screening, next generation sequencing (NGS) has recently been assessed in retrospective studies. We conducted a prospective, multicenter study ('NEXT-in-CML') to assess the frequency and clinical relevance of low level mutations and the feasibility, cost and turnaround times of NGS-based BCR-ABL1 mutation screening in a routine setting. A series of 236 consecutive CML patients with Failure (F; n=124) or Warning (W; n=112) response to TKI therapy were analyzed in parallel by SS and by NGS in one of four reference laboratories. Fifty-one patients (22 F, 29 W) who were negative for mutations by SS had low level mutations detectable by NGS. Moreover, 29 (27F, 2W) of 60 patients who were positive for mutations by SS showed additional low level mutations. Thus, mutations undetectable by SS were identified in 80/236 (34%) patients, of whom 42 (18% of the total) had low level mutations somehow relevant for clinical decision-making. Prospective monitoring of mutation kinetics demonstrated that TKI-resistant low level mutations are invariably selected if the patients are not switched to another TKI or if they are switched to a inappropriate TKI or TKI dose. The NEXT-in-CML study provides for the first time robust demonstration of the clinical relevance of low level mutations, supporting the incorporation of NGS-based BCR-ABL1 KD mutation screening results in the clinical decision algorithms