Rapid diagnosis of acute promyelocytic leukemia with the PML-RARA fusion gene using a combination of droplet-reverse transcription-polymerase chain reaction and instant-quality fluorescence in situ hybridization

Harnessing intermolecular G-quadruplex-based spatial confinement effect for accelerated activation of CRISPR/Cas12a empowers ultra-sensitive detection of PML/RARA fusion genes

Accurate detection and classification of the three isoforms of PML/RARA genomic fragments are crucial for predicting disease progression, stratifying risk, and administering precise drug therapies in acute promyelocytic leukemia (APL). In this study, we have developed a highly specific nucleic acid detection platform capable of quantifying the long isoform of the three main PML-RARA isoforms at a constant temperature. This platform integrates the strengths of the CRISPR/Cas12a nuclease-based method and the rolling circle amplification (RCA) technique. Notably, the RCA-assisted CRISPR/Cas12a trans-cleavage system incorporates a spatial confinement effect by utilizing intermolecular G-quadruplex structures. This innovative design effectively enhances the local concentration of CRISPR/Cas12a, thereby accelerating its cleaving efficiency towards reporter nucleic acids and enabling the detection of PML/RARA fusion gene expression through spectroscopy. The robust detection of PML/RARA fusion gene from human serum samples validates the reliability and potential of this platform in the screening, diagnosis, and prognosis of APL cases. Our findings present an approach that holds significant potential for the further development of the robust CRISPR/Cas sensor system, offering a rapid and adaptable paradigm for APL diagnosis.

The translational values of TRIM family in pan-cancers: From functions and mechanisms to clinics

Cancer is the second leading cause of human death across the world. Tripartite motif (TRIM) family, with E3 ubiquitin ligase activities in majority of its members, is reported to be involved in multiple cellular processes and signaling pathways. TRIM proteins have critical effects in the regulation of biological behaviors of cancer cells. Here, we discussed the current understanding of the molecular mechanism of TRIM proteins regulation of cancer cells. We also comprehensively reviewed published studies on TRIM family members as oncogenes or tumor suppressors in the oncogenesis, development, and progression of a variety of types of human cancers. Finally, we highlighted that certain TRIM family members are potential molecular biomarkers for cancer diagnosis and prognosis, and potential therapeutic targets.

Development and validation of a droplet digital PCR assay for the evaluation of PML-RARα fusion transcripts in acute promyelocytic leukemia

Acute promyelocytic leukemia (APL) is an aggressive disease that requires prompt treatment. Promyelocytic leukemia protein-retinoic acid receptor α (PML-RARα) fusion genes resulting from reciprocal translocation are considered a molecular basis for diagnosing APL. Moreover, PML-RARα fusion gene testing is an essential tool for monitoring the response to therapy via minimal residual disease and providing a diagnosis before rapid disease progression in APL. The present study developed a novel droplet digital PCR (ddPCR) assay to rapidly detect two PML-RARα variants (bcr1 and bcr3) and compared its limit of detection (LOD) with quantitative PCR (qPCR). It was demonstrated that the LOD of ddPCR for PML-RARα reached 0.001%, and the evaluation of high copy number samples of PML-RARα by ddPCR correlated well with qPCR. Furthermore, clinical sample testing with ddPCR found that 34 and 24% samples were bcr-1-positive and bcr3-positive, respectively. However, according to qPCR, 30% of the samples were bcr1-positive and 20% were bcr3-positive. In addition, the concordance rate between ddPCR and qPCR reaction was 86%. While monitoring minimal residual disease, the PML-RARα mutation rate of three patients who recovered well decreased to 0.34%. However, one patient who was bcr3-positive and relapsed had a mutation rate of 13% while in remission, indicating that the bcr3 isoform may be an adverse prognostic factor affecting recovery. Therefore, the present results suggested that this novel ddPCR assay may be useful for monitoring and evaluating the treatment effects and prognosis of APL.

The prognostic value of CD2, CD4, and HLA-DR expression and FLT3-ITD mutation in adult acute promyelocytic leukemia

In order to explore the prognostic value of CD2, CD4, and human leucocyte antigen-DR (HLA-DR) expression and Fms-like tyrosine kinase 3-internal tandem duplication (FLT3-ITD) mutation in leukemia cells in the bone marrow of patients with acute promyelocytic leukemia (APL), we retrospectively collected and analyzed the immunophenotype, molecular features and clinical characteristics of 219 newly diagnosed adult patients with APL in Henan Provincial People's Hospital from January 2010 to December 2019. It turned out that the relapse rates of patients with CD2, CD4, or HLA-DR expression and the early mortality rates of patients with CD2 expression, HLA-DR expression, or FLT3-ITD mutation were higher than those of their counterparts. Moreover, reduced overall survival was found for patients who showed CD2 expression, HLA-DR expression or FLT3-ITD mutation. Therefore, CD2 expression, HLA-DR expression and FLT3-ITD mutation were adverse prognostic factors in adults with APL.

A simple non-toxic ethylene carbonate fluorescence in situ hybridization (EC-FISH) for simultaneous detection of repetitive DNA sequences and fluorescent bands in plants

The major drawbacks of standard plant fluorescence in situ hybridization (FISH) designed for double-stranded DNA probes include requirement for experimentally determined heat denaturation of chromosomes at high temperatures and at least overnight hybridization. Consequently, processing with chromosomal preparations may easily result in heat-induced deterioration of chromosomal structural details, is time-consuming, and involves the use of toxic formamide and formaldehyde. Here, I have described a simple and appealing non-toxic procedure with ethylene carbonate (EC)-a formamide-substituting solvent and double-stranded repetitive DNA probes. Applying EC as a component of the hybridization solution at 46 °C not only allowed successful overnight hybridization but also gave a possibility to reduce the hybridization time to 3 h, hence converting the technique into a 1-day procedure. Importantly, the EC-FISH tended to preserve well chromosome structural details, e.g., DAPI-positive bands, thus facilitating simultaneous FISH mapping and chromosome banding on the same slide. The procedure requires no formaldehyde and RNA-se treatment of chromosomes, and no heat denaturation of chromosomal DNA. The key condition is to obtain high-quality cytoplasm-free preparations. The method was reproducible in all the plants studied (Allium, Nigella, Tradescantia, Vicia), giving a species-specific signal pattern together with clear DAPI bands on chromosomes. The procedure described here is expected to give a positive stimulus for improving gene-mapping approaches in plants.

Early treatment of acute promyelocytic leukaemia is accurately guided by the PML protein localisation pattern: real-life experience from a tertiary New Zealand centre

Current guidelines recommend that a rapid test be used to assist diagnosis of acute promyelocytic leukaemia (APL), but the choice of an assay is discretionary. PML immunofluorescence (PML IF) identifies the microparticulate pattern of the PML protein localisation, highly specific for APL. The aim of this study was to evaluate clinical utility of PML IF in a real-life setting based on a retrospective records review for all patients who had PML IF performed in our centre between 2000 and 2017. Final analysis included 151 patients, 70 of whom had APL. PML IF was reported on average 3 days faster than cytogenetics. Compared with genetic results, PML IF showed sensitivity of 96% and specificity of 100%. PML IF accurately predicted APL in four APL cases with cryptic karyotype/FISH and excluded APL in 98% cases tested based on the suspicious immunophenotype alone, 21/28 of whom had mutated NPM1. Results of PML IF influenced decision to start ATRA in 25 (36%) APL patients and led to its termination in six non-APL patients. In conclusion, PML IF is a fast and reliable test that facilitates accurate treatment decisions when APL is suspected. This performance of PML IF remains hard to match in a real-life setting.

A simple surface plasmon resonance biosensor for detection of PML/RARα based on heterogeneous fusion gene-triggered nonlinear hybridization chain reaction

In this work, a simple and enzyme-free surface plasmon resonance (SPR) biosensing strategy has been developed for highly sensitive detection of two major PML/RARα (promyelocytic leukemia, retinoic acid receptor alpha) subtypes based on the heterogeneous fusion gene-triggered nonlinear hybridization chain reaction (HCR). On the gold chip surface, the cascade self-assembly process is triggered after the introduction of PML/RARα. The different fragments of PML/RARα can specifically hybridize with capture probes (Cp) immobilized on the chip and the hybridization DNA₁ (H₁). Then, the nonlinear HCR is initiated by the complex of Cp-PML/RARα-H₁ with the introduction of two hybridization DNA chains (H₂ and H₃). As a result, a dendritic nanostructure is achieved on the surface of chip, leading to a significant SPR amplification signal owing to its high molecular weight. The developed method shows good specificity and high sensitivity with detection limit of 0.72 pM for "L" subtype and 0.65 pM for "S" subtype. Moreover, this method has been successfully applied for efficient identification of clinical positive and negative PCR samples of the PML/RARα subtype. Thus, this developed biosensing strategy presents a potential platform for analysis of fusion gene and early diagnosis of clinical disease.

[The analysis of prognosis-associated factors in adults with acute promyelocytic leukemia]

Objective: To explore the prognostic value of CD34, CD2, CD56 expressions and FLT3-ITD mutation in adults with acute promyelocytic leukemia (APL) . Methods: The immuno-phenotypic and molecular characteristics of 137 adult patients with APL (from January 2010 to March 2016, in Henan Provincial People's Hospital) were investigated. And the relationships between CD34, CD2, CD56 expressions, FLT3-ITD mutation and the outcomes of high WBC counts at onset, complete remission (CR) rate, early mortality, relapse rate (RR) , overall survival (OS) , disease free survival (DFS) were explored. Results: ①Among the 137 patients, the positive ratios of CD34, CD2, CD56 expressions and mutation rate of FLT3-ITD were 26.3%, 25.5%, 10.2% and 17.5%, respectively. The morbidities of positive CD34, CD2, CD56 expressions and FLT3-ITD mutation in the high-risk group were 43.2%, 47.7%, 18.2% and 27.3% respectively, while those in the low-/intermediate-risk groups were 18.3%, 15.1%, 6.5% and 12.9%, respectively (P<0.05) . ②At a median follow-up of 41 months, the total CR rate of the 137 adults APL patients was 96.9%, early mortality 6.6% and relapse rate 7.3% respectively. And RR of positive CD34 or CD2 expression patients was higher than negative CD34/CD2 expression ones (18.8% vs 3.3%, χ(2)=8.462, P=0.004; 16.1% vs 4.3%, χ(2)=4.382, P=0.028, respectively) . In addition, the early mortality of patients with positive CD56 expression or FLT3-ITD mutation was extremely higher than in negative ones (21.4% vs 4.9%, χ(2)=5.610, P=0.018; 16.7% vs 4.4%, χ(2)=4.833, P=0.028, respectively) . ③The whole OS and DFS were 88.3% and 84.7%, respectively. Wherein, OS and DFS in patients with CD34(+), CD56(+) or FLT3-ITD mutation were worse (P<0.05) . Conclusions: Positive CD34, CD2, CD56 expression and FLT3-ITD mutation were latent poor prognostic factors in adults with APL.

[Efficacy of combination of ATRA, ATO and anthracyclines induction therapy in patients with acute promyelocytic leukemia]

Objective: To explore the efficacies of regimens of three-drug induction therapy (ATRA+ATO+anthracyclines) versus two-drug induction therapy (ATRA+ATO) in patients with acute promyelocytic leukemia (APL). Methods: Of 184 patients diagnosed with APL from January 2009 to March 2016, 58 patients underwent three-drug induction therapy, while the rest were treated with two-drug induction therapy. Three-drug induction therapy was of ATRA (20 mg·m(-2)·d(-1), d(1-28)) + ATO (0.16 mg·kg(-1)·d(-1), d(1-28)) + Idarubicin (8 mg·m(-2)·d(-1), d(3-5)) /daunorubicin (40 mg·m(-2)·d(-1), d(3-5)) , while two-drug induction therapy ATRA+ATO with the same doses and methods as above. Of 184 cases, 69 cases accompanied with WBC counts>10×10(9)/L, 115 cases with WBC counts≤10×10(9)/L at onset. Results: ①Short-term efficacy: After one cycle induction therapy, the rates of hematologic remission, genetic remission, molecular remission and induced differentiation syndrome (DS) in three-drug regimen group were 98.3%, 87.9%, 72.4% and 0 respectively, while those in two-drug regimen group were 87.3%, 65.9%, 51.6% and 12.7% respectively. In patients with WBC >10×10(9)/L, DS rate and early mortality in three-drug regimen group were lower than in two-drug regimen group (0 vs 15.6%, 4.2% vs 15.6%, respectively). In patients with WBC≤10×10(9)/L, DS rate in three-drug regimen group was also lower than in two-drug regimen group (0 vs 12.3%) , but there were no statistical differences in terms of relapse and early mortality. ② Long-term efficacy: The relapse rate, overall survival (OS) and disease free survival (DFS) in three-drug regimen group were 0, 98.5%, 96.6% respectively, while those in two-drug regimen group were 8.6%, 86.5% and 84.1% respectively; the advantages of three-drug over two-drug regimen, especially in cases of WBC >10×10(9)/L were observed. ③ Side effects: the incidences of gastrointestinal reaction, liver dysfunction, myocardial damage and headache in three-drug regimen group hardly increased. Conclusion: The efficacies of three-drug induction therapy were superior to two-drug one.

A novel, rapid point-of-care test for lung cancer patients to detect epidermal growth factor receptor gene mutations by using real-time droplet-PCR and fresh liquid cytology specimens

Epidermal growth factor receptor gene (EGFR) mutations are associated with response to tyrosine kinase inhibitors (TKIs) in patients with non-small cell lung cancer (NSCLC). We developed a novel, rapid EGFR mutation assay using a real-time droplet-polymerase chain reaction machine (EGFR d-PCR assay). The purpose of this study was to validate the performance of the EGFR d-PCR assay using fresh liquid cytology specimens. We analyzed three major EGFR mutations (L858R in exon 21, E746_A750del in exon 19 and T790M in exon 20) in 80 fresh liquid cytology specimens of adenocarcinoma (ADC) or NSCLC-not otherwise specified (NOS) via the EGFR d-PCR assay and conventional real-time PCR assay using the therascreen® EGFR RGQ PCR kit (Therascreen assay). In addition, we performed sensitivity assays using cell lines with EGFR mutations. The EGFR d-PCR assay detected 16 L858Rs, 8 E746_A750dels and 1 T790M mutation and the Therascreen assay detected 16 L858Rs, 11 deletions in exon 19 and 1 T790M mutation. The results were concordant between the two assays. The reaction time of the EGFR d-PCR assay was 8 min and 10 sec, but that of the Therascreen assay was 1 h and 45 min. Sensitivity, as assessed by the detection limit of the EGFR d-PCR assay was 0.5, 0.05 and 0.5% for L858R, E746_A750del and T790M, respectively. The EGFR d-PCR assay markedly reduced the detection time of major EGFR mutations with high sensitivity compared with the conventional Therascreen assay and is expected to expedite EGFR-TKI therapy for lung cancer patients, especially those in advanced stages.

Molecular biomarkers in acute myeloid leukemia

Acute myeloid leukemia (AML) is the most common acute leukemia in adults. The pathophysiology of this disease is just beginning to be understood at the cellular and molecular level, and currently cytogenetic markers are the most important for risk stratification and treatment of AML patients. However, with the advent of new technologies, the detection of other molecular markers such as point mutations and characterization of epigenetic and proteomic profiles, have begun to play an important role in how the disease is approached. Recent evidence shows that the identification of new AML biomarkers contributes to a better understanding of the molecular basis of the disease, is significantly useful in screening, diagnosis, prognosis and monitoring of AML, as well as the possibility of predicting each individual's response to treatment. This review summarizes the most relevant molecular (genetic, epigenetic, and protein) biomarkers associated with acute myeloid leukemia and discusses their clinical importance in terms of risk prediction, diagnosis and prognosis.