Clinical laboratory characteristics and gene mutation spectrum of Ph-negative MPN patients with atypical variants of JAK2, MPL, or CALR.

OBJECTIVE: To evaluate the incidence, clinical laboratory characteristics, and gene mutation spectrum of Ph-negative MPN patients with atypical variants of JAK2, MPL, or CALR. METHODS: We collected a total of 359 Ph-negative MPN patients with classical mutations in driver genes JAK2, MPL, or CALR, and divided them into two groups based on whether they had additional atypical variants of driver genes JAK2, MPL, or CALR: 304 patients without atypical variants of driver genes and 55 patients with atypical variants of driver genes. We analyzed the relevant characteristics of these patients. RESULTS: This study included 359 patients with Ph-negative MPNs with JAK2, MPL, or CALR classical mutations and found that 55 (15%) patients had atypical variants of JAK2, MPL, or CALR. Among them, 28 cases (51%) were male, and 27 (49%) were female, with a median age of 64 years (range, 21-83). The age of ET patients with atypical variants was higher than that of ET patients without atypical variants [70 (28-80) vs. 61 (19-82), p = 0.03]. The incidence of classical MPL mutations in ET patients with atypical variants was higher than in ET patients without atypical variants [13.3% (2/15) vs. 0% (0/95), p = 0.02]. The number of gene mutations in patients with atypical variants of driver genes PV, ET, and Overt-PMF is more than in patients without atypical variants of PV, ET, and Overt-PMF [PV: 3 (2-6) vs. 2 (1-7), p < 0.001; ET: 4 (2-8) vs. 2 (1-7), p < 0.05; Overt-PMF: 5 (2-9) vs. 3 (1-8), p < 0.001]. The incidence of SH2B3 and ASXL1 mutations were higher in MPN patients with atypical variants than in those without atypical variants (SH2B3: 16% vs. 6%, p < 0.01; ASXL1: 24% vs. 13%, p < 0.05). CONCLUSION: These data indicate that classical mutations of JAK2, MPL, and CALR may not be completely mutually exclusive with atypical variants of JAK2, MPL, and CALR. In this study, 30 different atypical variants of JAK2, MPL, and CALR were identified, JAK2 G127D being the most common (42%, 23/55). Interestingly, JAK2 G127D only co-occurred with JAK2V617F mutation. The incidence of atypical variants of JAK2 in Ph-negative MPNs was much higher than that of the atypical variants of MPL and CALR. The significance of these atypical variants will be further studied in the future.

t(2;2;21;8)(p21;q37;q22;q22), a novel four-way complex translocation involving variant t(8;21) in case of acute myeloid leukemia : A case report and literature review.

Chromosomal translocation serves as a crucial diagnostic marker in the classification of acute myeloid leukemia. Among the most prevalent cytogenetic abnormalities is t(8;21)(q22;q22), typically associated with the FAB subtype AML-M2. On occasion, alternative forms of t(8;21) have been observed. This report presents a case of AML with RUNX1::RUNX1T1, wherein the karyotype revealed t(2;2;21;8)(p21;q37;q22;q22), representing the first instance of a variant t(8;21) involving both chromosomes 2. The combination of routine karyotype analysis and fluorescence in situ hybridization proves to be an effective method for identifying complex translocations of t(8;21).

The application of targeted RNA sequencing for the analysis of fusion genes, gene mutations, IKZF1 intragenic deletion, and CRLF2 overexpression in acute lymphoblastic leukemia.

INTRODUCTION: Acute lymphoblastic leukemia (ALL) is characterized by highly genetic heterogeneity, owing to recurrent fusion genes, gene mutations, intragenic deletion, and gene overexpression, which poses significant challenges in clinical detection. RNA sequencing (RNA-seq) is a powerful tool for detecting multiple genetic abnormalities, especially cryptic gene rearrangements, in a single test. METHODS: Sixty samples (B-ALL, n = 49; T-ALL, n = 9; mixed phenotype acute leukemia (MPAL), n = 2) and 20 controls were analyzed by targeted RNA-seq panel of 507 genes developed by our lab. Of these, 16 patients were simultaneously analyzed for gene mutations at the DNA level using a next-generation sequencing panel of 51 genes. Fusion genes, CRLF2 expression, and IKZF1 intragenic deletion were also detected by reverse transcription-polymerase chain reaction (RT-PCR). Karyotype analysis was performed using the R-banding and G-banding technique on bone marrow cells after 24 hours of culture. Partial fusion genes were analyzed using fluorescence in situ hybridization (FISH). RESULTS: Compared with the results of Karyotype analysis, FISH, and RT-PCR, the detection rate of fusion genes by targeted RNA-seq increased from 48.3% to 58.3%, and six unexpected fusion genes were discovered, along with one rare isoform of IKZF1 intragenic deletion (IK10). The DNA sequencing analysis of 16 ALL patients revealed that 96.2% (25/26) of gene mutations identified at the DNA level were also detectable at the RNA level, except for one mutation with a low variant allele fraction. The detection of CRLF2 overexpression exhibited complete concordance between RT-PCR and RNA-seq. CONCLUSION: The utilization of RNA-seq enables the identification of clinically significant genetic abnormalities that may go undetected through conventional detection methods. Its robust analytical performance might bring great application value for clinical diagnosis, prognosis, and therapy in ALL.

The first case of six-way complex translocation of t(4;7;9;22;8;14) in a patient with chronic myeloid leukemia.

In chronic myeloid leukemia (CML), patients exhibit the t(9;22)(q34.1;q11.2) translocation, resulting in the formation of a Philadelphia chromosome (Ph). However, a subset of CML patients display variant complex translocations, characterized by three-way, four-way, and five-way translocations, which have been occasionally associated with a poor prognosis. This case report presents the first case of a t(9;22) variant six-way complex translocation in CML. The R banding chromosome karyotyping technique was used to obtain preliminary karyotyping results, and the multi-probe FISH technique was used to assist in the verification of chromosome results. Both FISH and PCR proved the existence of fusion genes. A 45-year-old male patient admitted to our hospital due to elevated WBC and anemia. Bone marrow smears revealed a significant proliferation of mature granulocytes, accompanied by an increase in eosinophils and basophils. Karyotype analysis indicated abnormalities in six chromosomes, including 4, 7, 8, 9, 14, and 22. Further analysis using FISH technology demonstrated the presence of the BCR::ABL1 fusion gene, as well as the mapping of the BCR (22q11), MYC (8q24), IGH (14q32), D4S163 (4q35.1), and D7S486 (7q31) genes to new chromosomes. Ultimately, the karyotype findings were described as t(4;7;9;22;8;14)(q27;q22;q34;q11;q22;q12). PCR showed that BCR::ABL1 was p210. After treatment with imatinib for 4 months, the patient achieved complete cytogenetic response (CCyR) and early molecular response (EMR). This is the first report of complex chromosomal karyotype involving six-way translocation in CML; the combination of chromosome analysis and FISH techniques is an effective strategy in determining the karyotype result.

Oxysterol-Binding Protein: new insights into lipid transport functions and human diseases.

Oxysterol-binding protein (OSBP) mediates lipid exchange between organelles at membrane contact sites, thereby regulating lipid dynamics and homeostasis. How OSBP's lipid transfer function impacts health and disease remain to be elucidated. In this review, we first summarize the structural characteristics and lipid transport functions of OSBP, and then focus on recent progresses linking OSBP with fatty liver disease, diabetes, lysosome-related diseases, cancer and viral infections, with the aim of discovering novel therapeutic strategies for common human diseases.

Identification of novel mutations in patients with Diamond-Blackfan anemia and literature review of RPS10 and RPS26 mutations.

INTRODUCTION: Diamond-Blackfan anemia (DBA) is a rare congenital bone marrow failure syndrome characterized by erythroid aplasia, physical malformation, and cancer predisposition. Twenty ribosomal protein genes and three non-ribosomal protein genes have been identified associated with DBA. METHODS: To investigate the presence of novel mutations and gain a deeper understanding of the molecular mechanisms of disease, targeted next-generation sequencing was performed in 12 patients with clinically suspected DBA. Literatures were retrieved with complete clinical information published in English by November 2022. The clinical features, treatment, and RPS10/RPS26 mutations were analyzed. RESULTS: Among the 12 patients, 11 mutations were identified and 5 of them were novel (RPS19, p.W52S; RPS10, p.P106Qfs*11; RPS26, p.R28*; RPL5, p.R35*; RPL11, p.T44Lfs*40). Including 2 patients in this study, 13 patients with RPS10 mutations and 38 patients with RPS26 mutations were reported from 4 and 6 countries, respectively. The incidences of physical malformation in patients with RPS10 and RPS26 mutations (22% and 36%, respectively) were lower than the overall incidence in DBA patients (~50%). Patients with RPS26 mutations had a worse response rate of steroid therapy than RPS10 (47% vs. 87.5%), but preferred RBC transfusions (67% vs. 44%, p = 0.0253). CONCLUSION: Our findings add to the DBA pathogenic variant database and demonstrate the clinical presentations of the DBA patients with RPS10/RPS26 mutations. It shows that next-generation sequencing is a powerful tool for the diagnosis of genetic diseases such as DBA.

Effects of genetic polymorphisms on methotrexate levels and toxicity in Chinese patients with acute lymphoblastic leukemia.

Methotrexate (MTX) has an antitumor effect when used for the treatment of acute lymphoblastic leukemia (ALL). This study aims at evaluating the associations between 14 polymorphisms of six genes involved in MTX metabolism with serum MTX concentration and toxicity accompanying high-dose MTX. Polymorphisms in 183 Chinese patients with ALL were analyzed using TaqMan single nucleotide polymorphism genotyping assay. The serum MTX concentration was determined using homogeneous enzyme immunoassay. MTX-related toxicities were also evaluated. Renal toxicity was significantly associated with higher serum MTX concentrations at 24, 48, and 72 hours, and MTX elimination delay (P = 0.001, P < 0.001, P < 0.001, and P < 0.001, respectively), whereas SLCO1B1 rs4149056 was associated with serum MTX concentrations at 48 and 72 hours, and MTX elimination delay in candidate polymorphisms (P = 0.014, P = 0.019, and P = 0.007, respectively). SLC19A1 rs2838958 and rs3788200 were associated with serum MTX concentrations at 24 hours (P = 0.016, P = 0.043, respectively). MTRR rs1801394 was associated with serum MTX concentrations at 72 hours (P = 0.045). Neutropenia was related to SLC19A1 rs4149056 (odds ratio [OR]: 3.172, 95% confidence interval [CI]: 1.310-7.681, P = 0.011). Hepatotoxicity was associated with ABCC2 rs2273697 (OR: 3.494, 95% CI: 1.236-9.873, P = 0.018) and MTRR rs1801394 (OR: 0.231, 95% CI: 0.084-0.632, P = 0.004). Polymorphisms of SLCO1B1, SLC19A1, ABCC2, and MTRR genes help predict higher risk of increased MTX levels or MTX-related toxicities in adult ALL patients.

An NGS based MRD evaluation from acute myeloid leukemia patients.

INTRODUCTION: Measurable residual disease (MRD) is a prognostic factor for acute myeloid leukemia (AML). A next-generation sequencing (NGS) based MRD panel was developed and the results were validated. METHODS: The NGS sequencing data was collected from 1003 Chinese AML patients. RESULTS: The sequencing data from 586 newly diagnosed AML patients showed that NRAS mutation was most common (20.8%), followed by NPM1 (19.4%), FLT3-ITD (18.5%), and DNMT3A (15.4%). NPM1 and FLT3-ITD mutations were less in Chinese than in Caucasian AML patients, and the result of KRAS mutation was opposite. A new panel named "AML NGS-MRD hot-spot panel" was designed, containing 178 hot-spot exons from 52 mutated genes and only 62.8 Kb in size. With this hot-spot panel, 92.5% newly diagnosed AML patients were found to carry ≥1 mutations. To verify the performance of this panel, additional 205 newly diagnosed AML patients and 212 post-treatment AML patients were evaluated, and the hot-spot panel achieved a similar detection rate (91.2% for newly diagnosed AML patients and 89.2% for post-treatment AML patients). Finally, this study found that the mutation frequencies of signaling pathway genes (e.g., KRAS, NRAS, FLT3-ITD, KIT) were significantly reduced in post-treatment AML. CONCLUSION: The "AML NGS-MRD hot-spot panel" detected the mutations from relapsed AML patients with minimal panel size, and was a reliable and cost-effective panel for AML patients.

A rare case of fluid overload-associated large B-cell lymphoma and antigen loss at relapse.

Fluid overload-associated large B-cell lymphoma (FO-LBCL) is a new addition to the list of large B-cell lymphomas in the 5th edition of the World Health Organization Classification of Haematolymphoid Tumours (WHO-HAEM5). This report presents an unusual case of FO-LBCL with partial B cell antigen loss at relapse and reviews the characteristics, treatment, and prognosis of these patients to enhance our understanding of this disease. Immunophenotyping was performed through immunohistochemistry and flow cytometry. Immunoglobulin gene rearrangements were analyzed using BIOMED-2 multiplex primers. MYC, BCL2, and BCL6 gene rearrangements were detected by fluorescent in situ hybridization (FISH). Cell-free DNA (cfDNA) from pleural effusion and peripheral blood was subjected to somatic mutation evaluation using next-generation sequencing (NGS). In 2020, the patient was initially diagnosed with tuberculous pleurisy and received anti-tuberculous drugs. Subsequent testing of the pleural effusion cell block revealed that the large cells to be positive for CD10, CD20, CD79a, PAX5, MUM1, Bcl-2, Bcl-6, and c-myc and negative for CD3, CD30, Cyclin D1, and HHV8. In situ hybridization for Epstein-Barr virus (EBV)-associated mRNA (EBER-ISH) was negative. Additionally, a clonal rearrangement of immunoglobulin heavy locus (IGH) FR2-JH was detected; the results of MYC, BCL2, and BCL6 gene rearrangements were all negative. Following pleural drainage treatment, the patient achieved symptom remission and was diagnosed with large B-cell lymphoma (HHV8-unrelated PEL-like lymphoma). In 2022, the patient was readmitted due to the recurrence of pleural effusion. The pleural effusion cell block revealed a distinct immunophenotype compared to previous findings, positivity for PAX5 and negativity for CD20, CD10, CD3, CD5, CD30, CD38, CD138, CD79a, MUM1, Bcl-2, Bcl-6, Cyclin D1, c-myc, ALK, and HHV8. Identical IGH FR2-JH clonal rearrangement suggested the recurrence of the original clone. CfDNA analysis showed mutations in CD79B, MYD88, CCND3, and DTX1. The patient was ultimately diagnosed with FO-LBCL based on the WHO-HAEM5 classification. Diagnosis of FO-LBCL should be differentiated from primary effusion lymphoma (PEL). The features of this case align with the description of "FO-LBCL" in WHO-HAEM5 and "HHV8 and EBV-negative primary effusion-based lymphoma" in International Consensus Classification (ICC). FO-LBCL patients generally have a more favorable prognosis compared to PEL. In this case, the patient exhibited a favorable prognosis for over 22 months without additional treatment apart from pleural drainage.

Mutational landscape of chronic myelomonocytic leukemia in Chinese patients.

BACKGROUND: Chronic myelomonocytic leukemia (CMML) is a rare and heterogeneous hematological malignancy. It has been shown that the molecular abnormalities such as ASXL1, TET2, SETBP1, and SRSF2 mutations are common in Caucasian population. METHODS: We retrospectively analyzed 178 Chinese CMML patients. The targeted next generation sequencing (NGS) was used to evaluate 114 gene variations, and the prognostic factors for OS were determined by COX regression analysis. RESULTS: The CMML patients showed a unique mutational spectrum, including TET2 (36.5%), NRAS (31.5%), ASXL1 (28.7%), SRSF2 (24.7%), and RUNX1 (21.9%). Of the 102 patients with clonal analysis, the ancestral events preferentially occurred in TET2 (18.5%), splicing factors (16.5%), RAS (14.0%), and ASXL1 (7.8%), and the subclonal genes were mainly ASXL1, TET2, and RAS. In addition, the secondary acute myeloid leukemia (sAML) transformed from CMML often had mutations in DNMT3A, ETV6, FLT3, and NPM1, while the primary AML (pAML) demonstrated more mutations in CEBPA, DNMT3A, FLT3, IDH1/2, NPM1, and WT1. It was of note that a series of clones were emerged during the progression from CMML to AML, including DNMT3A, FLT3, and NPM1. By univariate analysis, ASXL1 mutation, intermediate- and high-risk cytogenetic abnormality, CMML-specific prognostic scoring system (CPSS) stratifications (intermediate-2 and high group), and treatment options (best supportive care) predicted for worse OS. Multivariate analysis revealed a similar outcome. CONCLUSIONS: The common mutations in Chinese CMML patients included epigenetic modifiers (TET2 and ASXL1), signaling transduction pathway components (NRAS), and splicing factor (SRSF2). The CMML patients with DNMT3A, ETV6, FLT3, and NPM1 mutations tended to progress to sAML. ASXL1 mutation and therapeutic modalities were independent prognostic factors for CMML.

The Diagnosis of Chronic Myeloid Leukemia with Deep Adversarial Learning.

Chronic myeloid leukemia (CML) is a clonal proliferative disorder of granulocytic lineage, with morphologic evaluation as the first step for a definite diagnosis. This study developed a conditional generative adversarial network (cGAN)-based model, CMLcGAN, to segment megakaryocytes from myeloid cells in bone marrow biopsies. After segmentation, the statistical characteristics of two types of cells were extracted and compared between patients and controls. At the segmentation phase, the CMLcGAN was evaluated on 517 images (512 × 512) which achieved a mean pixel accuracy of 95.1%, a mean intersection over union of 71.2%, and a mean Dice coefficient of 81.8%. In addition, the CMLcGAN was compared with seven other available deep learning-based segmentation models and achieved a better segmentation performance. At the clinical validation phase, a series of seven-dimensional statistical features from various cells were extracted. Using the t-test, five-dimensional features were selected as the clinical prediction feature set. Finally, the model iterated 100 times using threefold cross-validation on whole slide images (58 CML cases and 31 healthy cases), and the final best AUC was 84.93%. In conclusion, a CMLcGAN model was established for multiclass segmentation of bone marrow cells that performed better than other deep learning-based segmentation models.

Novel cytoplasmic lncRNA IKBKBAS promotes lung adenocarcinoma metastasis by upregulating IKKß and consequential activation of NF-κB signaling pathway.

NF-κB signaling pathway is a critical link between inflammation and cancer. Emerging evidence suggested that long non-coding RNAs (lncRNAs) were involved in dysregulation of NF-κB. Herein, we reported a novel lncRNA IKBKBAS that activated NF-κB in lung adenocarcinoma (LUAD) by upregulating IKKß, a key member of NF-κB signaling pathway, thereby promoting the metastasis of LUAD both in vitro and in vivo. The upregulated IKBKBAS functioned as a competing endogenous RNA (ceRNA) via competing with IKKß mRNA for binding miR-4741, consequently leading to upregulation and activation of IKKß, and ultimately activation of NF-κB. The abnormally elevated IKBKBAS in LUAD was mainly resulted from the extremely decrease of miR-512-5p that targeting IKBKBAS. Furthermore, we identified a positive feedback loop between NF-κB and IKBKBAS, in which NF-κB activation induced by overexpression of IKBKBAS could promote the transcription of IKBKBAS by binding the κB sites within IKBKBAS promoter. Our studies revealed that IKBKBAS was involved in the activation of NF-κB signaling by upregulating the expression of IKKß, which made it serve as a potential novel target for therapies to LUAD.

Identification of acquired PIGA mutations and additional variants by next-generation sequencing in paroxysmal nocturnal hemoglobinuria.

INTRODUCTION: Paroxysmal Nocturnal Hemoglobinuria (PNH) is an acquired clonal disease of hematopoietic stem cells. It is caused by somatic mutation of the X-linked PIGA gene, resulting in a deficient expression of glycosylphosphatidylinositol-anchored proteins (GPI-APs). In this study, we aimed to explore the diagnostic value of next-generation sequencing (NGS) and potential molecular basis in PNH patients. METHODS: Genomic DNA of 85 PNH patients was analyzed by a 114-gene NGS panel. RESULTS: Mutational analysis of PIGA identified 124 mutations in 92% PNH patients, including 101 distinct mutations and 23 recurrent mutations. Among them, 102 mutations were newly reported. Most mutations were located in exon 2 of PIGA gene, and truncated mutation was the most common one. Other mutations were detected in 26 out of 85 cases, including five cases of DNMT3A variants, four cases of ASXL1 variants, and four cases of U2AF1 variants. Clonal analysis was performed in one case and outlined a linear evolution pattern in classic PNH. There was a positive correlation between number of PIGA mutations and fraction of GPI-APs deficient granulocytes. CONCLUSION: The detection of PIGA mutations and additional variants by targeted NGS not only shed light on the genetic characteristics of PNH, but also provided an important reference value in the diagnosis of PNH at molecular level.

Identification of new mutations in patients with hereditary spherocytosis by next-generation sequencing.

Hereditary spherocytosis (HS) is the most common inherited hemolytic anemia characterized by the presence of spherical-shaped erythrocytes on the peripheral blood smear, hemolysis, splenomegaly, jaundice, and gallstones. To date, mutations in at least five genes (ANK1, EPB42, SLC4A1, SPTA1, and SPTB) have been found to be associated with different subtypes of HS. Here, we aim to investigate the presence of novel as well as known mutations in 35 Chinese patients with clinically suspected HS. Whole-exome sequencing (WES) has identified 3 patients with SLC4A1, 16 patients with ANK1, and 16 patients with SPTB mutations, including 5 splicing, 12 nonsense, 9 frameshift, 7 missense, and 1 start-loss mutation, indicating that SPTB and ANK1 are the most frequently mutated genes in Chinese HS patients. Among 34 mutations identified, 21 were novel. Most of SPTB and ANK1 mutations were nonsense (8/16) and frameshift (6/16) mutations. By trio analysis of eight families we have confirmed six de novo mutations. In addition, genotype-phenotype analysis was also performed by comparing clinical manifestations among three groups of patients with SPTB, ANK1, and SLC4A1 mutations. It revealed that patients with ANK1 mutations had a significantly higher level of MCV and MCH but lower percentage of spherocytes compared with those carrying SPTB mutations. In conclusion, our results suggested that molecular diagnosis by next-generation sequencing (NGS) is a fast, economic, and accurate way to detect and identify pathogenic alterations of inherited diseases, highlighting the potential usage of NGS in clinical practice.

Insights into mechanisms of pranoprofen-induced apoptosis and necroptosis in human corneal stromal cells.

Pranoprofen (PPF) is a wildly used anti-inflammatory ophthalmic drug. It was reported that PPF could decrease early epithelialization of scrape wounds in rabbit cornea and could reduce cell activities of cultured human corneal endothelial cells. However, effects of PPF on corneal stromal cells playing important roles in corneal wound healing remain unknown. In this study,in vitro model of cultured human corneal stomal (HCS) cells and in vivo model of rabbit corneas were used to investigate the effects and underlying mechanisms of PPF. Our findings showed that high concentrations of PPF treatment (0.1 % to 0.0125 %) caused limited chromatin condensation and quickly decreased cell viability that was proved to initiate necroptosis in HCS cells through activating receptor interacting protein kinase (RIPK) and mixed lineage kinase domain-like (MLKL). While low concentrations of PPF treatment (0.00625 %) induced DNA fragmentation, apoptotic body formation, ROS generation, activation of caspases and increase in cytoplasmic content of Bad, Bax and cytoplasmic cytochrome c that suggested apoptosis happened through ROS-mediated caspase-dependent and caspase-independent pathways. Studies of rabbit corneas treated with 0.1 % PPF (the clinical concentration) showed that PPF could induce apoptosis of rabbit corneal stromal cells. This work would be helpful for better understanding cytotoxic effects PPF on human corneal cells.