TAF15–ZNF384 fusion gene in childhood mixed phenotype acute leukemia

Studies of Genetic and Proteomic Risk Factors of Amyotrophic Lateral Sclerosis Inspire Biomarker Development and Gene Therapy

Amyotrophic lateral sclerosis (ALS) is an incurable neurodegenerative disease affecting the upper and lower motor neurons, leading to muscle weakness, motor impairments, disabilities and death. Approximately 5-10% of ALS cases are associated with positive family history (familial ALS or fALS), whilst the remainder are sporadic (sporadic ALS, sALS). At least 50 genes have been identified as causative or risk factors for ALS. Established pathogenic variants include superoxide dismutase type 1 (SOD1), chromosome 9 open reading frame 72 (c9orf72), TAR DNA Binding Protein (TARDBP), and Fused In Sarcoma (FUS); additional ALS-related genes including Charged Multivesicular Body Protein 2B (CHMP2B), Senataxin (SETX), Sequestosome 1 (SQSTM1), TANK Binding Kinase 1 (TBK1) and NIMA Related Kinase 1 (NEK1), have been identified. Mutations in these genes could impair different mechanisms, including vesicle transport, autophagy, and cytoskeletal or mitochondrial functions. So far, there is no effective therapy against ALS. Thus, early diagnosis and disease risk predictions remain one of the best options against ALS symptomologies. Proteomic biomarkers, microRNAs, and extracellular vehicles (EVs) serve as promising tools for disease diagnosis or progression assessment. These markers are relatively easy to obtain from blood or cerebrospinal fluids and can be used to identify potential genetic causative and risk factors even in the preclinical stage before symptoms appear. In addition, antisense oligonucleotides and RNA gene therapies have successfully been employed against other diseases, such as childhood-onset spinal muscular atrophy (SMA), which could also give hope to ALS patients. Therefore, an effective gene and biomarker panel should be generated for potentially "at risk" individuals to provide timely interventions and better treatment outcomes for ALS patients as soon as possible.

MethReg: estimating the regulatory potential of DNA methylation in gene transcription

Epigenome-wide association studies often detect many differentially methylated sites, and many are located in distal regulatory regions. To further prioritize these significant sites, there is a critical need to better understand the functional impact of CpG methylation. Recent studies demonstrated that CpG methylation-dependent transcriptional regulation is a widespread phenomenon. Here, we present MethReg, an R/Bioconductor package that analyzes matched DNA methylation and gene expression data, along with external transcription factor (TF) binding information, to evaluate, prioritize and annotate CpG sites with high regulatory potential. At these CpG sites, TF-target gene associations are often only present in a subset of samples with high (or low) methylation levels, so they can be missed by analyses that use all samples. Using colorectal cancer and Alzheimer's disease datasets, we show MethReg significantly enhances our understanding of the regulatory roles of DNA methylation in complex diseases.

Clinical Characteristics And Outcome Of Biphenotypic Acute Leukemia: 10 Case Reports And Literature Review

Background

Biphenotypic acute leukemia (BAL), or mixed-phenotype acute leukemia (MPAL) represents a rare subgroup of acute leukemia which co-expresses markers for either more than one lineage in a homogenous blast population or the coexistence of two blast populations of different lineages. Proper diagnosis and classification of BAL are extremely important for patients' outcome since BAL usually has a poor prognosis.

Purpose

The objective of this study was to identify the incidence of biphenotypic acute leukemia, their clinical characteristics and outcome of BAL patients with the chemotherapy treatment and Hematopoietic Stem Cell Transplantation (HSCT) after initial complete remission.

Patients and methods

Ten cases of biphenotypic acute leukemia were analyzed for their clinical characteristics, immunological phenotypes, chemotherapy methods for induction initial complete remission and outcome data, including induction chemotherapy, complete remission (CR) and the overall survival time, relapse and death. This study was an observational, retrospective, and descriptive study of the clinical aspects of BAL. Cytogenetics and fusion genes analysis were also done with bone marrow samples using G-banding analysis and karyotyped according to the International System for Human Cytogenetic Nomenclature. The fusion genes' mutational status was determined by real-time PCR (RT-PCR). Gene mutation analyses were conducted with next-generation sequencing method.

Results

Among 10 BAL patients, 4 cases carried B/Myeloid phenotype, 4 cases carried T/Myeloid phenotype and 2 cases carried T/B phenotype. Cytogenetic analysis showed that 3 of the 10 cases had clonal abnormalities. Of the four cases of fusion gene aberration, two patients had RUNX1 gene mutation, one patient had BCR/ABL fusion gene mutation, and one patient had JAK1, JAK3, FBXW7 mutation. Overall, 5 of 8 (62.5%) BAL patients with chemotherapy achieved complete remission (CR) after their initial induction therapy. In the AML-directed therapy group, 1 of 2 (50%) patients achieved CR. Meanwhile, 4 of 6 (66.7%) patients achieved CR after ALL-directed induction chemotherapy. Two patients received Hematopoietic Stem Cell Transplantation (HSCT) after initial CRs, one patient died two months after transplantation due to pulmonary infection, and another patient is still alive. With an average of 14.3 (4.0-42.0) months' follow-ups, the median survival time was 7 months. Although patients achieved CR after initial chemotherapy, the relapse rate was very high and the CR rate after relapse was very low.

Conclusion

Our results confirmed that BAL is a rare malignancy with a very poor prognosis. Patients with ALL-directed chemotherapy achieved a better CR rate compared to those with AML-directed chemotherapy. Patients should receive HSCT after initial CR whenever it is possible.

PHF6 and DNMT3A mutations are enriched in distinct subgroups of mixed phenotype acute leukemia with T-lineage differentiation

The genetic aberrations that drive mixed phenotype acute leukemia (MPAL) remain largely unknown, with the exception of a small subset of MPALs harboring BCR -ABL1 and MLL translocations. We performed clinicopathologic and genetic evaluation of 52 presumptive MPAL cases at Memorial Sloan Kettering Cancer Center. Only 29 out of 52 (56%) cases were confirmed to be bona fide MPAL according to the 2016 World Heath Organization classification. We identified PHF6 and DNMT3A mutations as the most common recurrent mutations in MPAL, each occurring in 6 out of 26 (23%) cases. These mutations are mutually exclusive of each other and BCR-ABL1/MLL translocations. PHF6- and DNMT3A-mutated MPAL showed marked predilection for T-lineage differentiation (5/6 PHF6 mutated, 6/6 DNMT3A mutated). PHF6-mutated MPAL occurred in a younger patient cohort compared with DNMT3A-mutated cases (median age, 27 years vs 61 years, P < .01). All 3 MPAL cases with both T- and B-lineage differentiation harbored PHF6 mutations. MPAL with T-lineage differentiation was associated with nodal or extramedullary involvement (9/15 [60%] vs 0, P = .001) and a higher relapse incidence (78% vs 22%, P = .017) compared with those without T-lineage differentiation. Sequencing studies on flow-cytometry-sorted populations demonstrated that PHF6 mutations are present in all blast compartments regardless of lineage differentiation with high variant allele frequency, implicating PHF6 as an early mutation in MPAL pathogenesis. In conclusion, PHF6 and DNMT3A mutations are the most common somatic alterations identified in MPAL and appear to define 2 distinct subgroups of MPAL with T-lineage differentiation with inferior outcomes.

Overexpression and mutation of ZNF384 is associated with favorable prognosis in breast cancer patients

Background

To search for genes with high sensitivity and to explore its application value related to clinical prognostic prediction, so as to provide important foundation for the preventive intervention, early diagnosis, treatment and prognosis evaluation for breast cancer.

Methods

Tissue samples from ten clinical breast cancer patients were collected to search for the common mutant genes among various samples, and to explore the enrichment degree of mutant genes at both disease and signaling pathway levels using the whole exome sequencing (WES). Subsequently, targets genes with changes in expression levels that showed high correlations with mutation were screened from the above common genes using The Cancer Genome Atlas (TCGA) database. On this basis, differences in the mutation and expression levels of the screened target genes between breast cancer tissues and para-carcinoma tissues, as well as their correlations with patient survival were analyzed using the gene expression and mutation data in TCGA database, together with the clinical information. Finally, the potential regulatory pathways and potential downstream targets of the target genes were predicted through gene set enrichment analysis (GSEA) using Multi-Experiment Matrix (MEM) software.

Results

A total of 23 common mutant genes were discovered from the tissue samples from ten breast cancer patients, which were mostly enriched in the cancer, PI3K/Akt and cAMP signaling pathways. Among these 23 genes, only the changes in the expression levels of ZNF384 and PDE4DIP had displayed over 15% consistency with mutation. Besides, it was discovered through TCGA database analysis that, the expression level of ZNF384 gene in breast cancer tissues with ZNF384 mutation was far higher than that in those with no ZNF384 mutation. Moreover, such gene mutation and high expression had shown significantly positive correlation with the patient survival (P<0.05). In addition, GSEA indicated that, tissues with high ZNF384 expression were associated with enrichments related to cell cycle signaling pathway and mitosis metaphase pathway, while this series of effects might be correlated with its regulation on the level and activity of its downstream gene CXCL14.

Conclusions

ZNF384 mutation and up-regulated ZNF384 expression level in breast cancer tissues is significantly positively correlated with patient survival. Therefore, ZNF384 can serve as a molecular marker for the diagnosis and prognostic prediction of breast cancer as well as a potential therapeutic target.