Single-cell transcriptome analyses reveal critical roles of RNA splicing during leukemia progression.

Leukemogenesis is proposed to be a multistep process by which normal hematopoietic stem and progenitor cells are transformed into full-blown leukemic cells, the details of which are not fully understood. Here, we performed serial single-cell transcriptome analyses of preleukemic and leukemic cells (PLCs) and constructed the cellular and molecular transformation trajectory in a Myc-driven acute myeloid leukemia (AML) model in mice, which represented the transformation course in patients. We found that the Myc targets were gradually up-regulated along the trajectory. Among them were splicing factors, which showed stage-specific prognosis for AML patients. Furthermore, we dissected the detailed gene network of a tipping point for hematopoietic stem and progenitor cells (HSPCs) to generate initiating PLCs, which was characterized by dramatically increased splicing factors and unusual RNA velocity. In the late stage, PLCs acquired explosive heterogeneity through RNA alternative splicing. Among them, the Hsp90aa1hi subpopulation was conserved in both human and mouse AML and associated with poor prognosis. Exon 4 skipping of Tmem134 was identified in these cells. While the exon skipping product Tmem134ß promoted the cell cycle, full-length Tmem134α delayed tumorigenesis. Our study emphasized the critical roles of RNA splicing in the full process of leukemogenesis.

Integration of Ultrathin Hafnium Oxide with a Clean van der Waals Interface for Two-Dimensional Sandwich Heterostructure Electronics.

Integrating high-κ dielectrics with a small equivalent oxide thickness (EOT) with two-dimensional (2D) semiconductors for low-power consumption van der Waals (vdW) heterostructure electronics remains challenging in meeting both interface quality and dielectric property requirements. Here, we demonstrate the integration of ultrathin amorphous HfOx sandwiched within vdW heterostructures by the selective thermal oxidation of HfSe2 precursors. The self-cleaning process ensures a high-quality interface with a low interface state density of 1011-1012 cm-2 eV-1. The synthesized HfOx displays excellent dielectric properties with an EOT of ∼1.5 nm, i.e., a high κ of ∼16, an ultralow leakage current of 10-6 A/cm2, and an impressively high breakdown field of 9.5 MV/cm. This facilitates low-power consumption vdW heterostructure MoS2 transistors, demonstrating steep switching with a low subthreshold swing of 61 mV/decade. This one-step integration of high-κ dielectrics into vdW sandwich heterostructures holds immense potential for developing low-power consumption 2D electronics while meeting comprehensive dielectric requirements.

Venetoclax overcomes resistance to all-trans retinoic acid in a variant acute promyelocytic leukemia with TNRC18::RARA fusion.

Acute promyelocytic leukemia (APL) is generally driven by PML::RARA, but approximately 2% of variant APL patients do not contain this fusion gene and pose challenges in diagnosis and treatment. Here, we reported an aggressive APL patient with variant TNRC18::RARA fusion gene, who was resistant to standard differentiation induction therapy consisting of all-trans retinoic acid (ATRA) and arsenic trioxide but achieved complete remission with venetoclax plus ATRA. Mechanistically, venetoclax possesses synergistic effects in ATRA-induced TNRC18::RARA-positive cell differentiation.

DNMT3AR882H accelerates angioimmunoblastic T-cell lymphoma in mice.

DNA methylation-related genes, including TET2, IDH2, and DNMT3A are highly frequently mutated in angioimmunoblastic T-cell lymphoma (AITL), an aggressive malignancy of T follicular helper (Tfh) cells associated with aberrant immune features. It has been shown that TET2 loss cooperates with RHOAG17V to promote AITL in mice but the functional role of DNMT3A mutations in AITL remains unclear. Here, we report that DNMT3AR882H, the most common mutation of DNMT3A in AITL, accelerates the development of Tet2-/-; RHOAG17V AITL in mice, indicated by the expansion of malignant Tfh cells and aberrant B cells, skin rash, and significantly shortened disease-free survival. To understand the underlying cellular and molecular mechanisms, we performed single-cell transcriptome analyses of lymph nodes of mice transplanted with Tet2-/-, Tet2-/-; RHOAG17V or DNMT3AR882H; Tet2-/-; RHOAG17V hematopoietic stem and progenitor cells. These single-cell landscapes reveal that DNMT3A mutation further activates Tfh cells and leads to rapid and terminal differentiation of B cells, probably through enhancing the interacting PD1/PD-L1, ICOS/ICOSL, CD28/CD86, and ICAM1/ITGAL pairs. Our study establishes the functional roles of DNMT3A mutation in AITL and sheds light on the molecular mechanisms of this disease.

Efficacy and safety of histone deacetylase inhibitors in peripheral T-cell lymphoma: a systematic review and meta-analysis on prospective clinical trials.

Background: The overall survival of peripheral T-cell lymphoma (PTCL) is dismal. Histone deacetylase (HDAC) inhibitors have exhibited promising treatment outcomes for PTCL patients. Therefore, this work aims to systematically evaluate the treatment outcome and safety profile of HDAC inhibitor-based treatment for untreated and relapsed/refractory (R/R) PTCL patients. Methods: The prospective clinical trials of HDAC inhibitors for the treatment of PTCL were searched on the Web of Science, PubMed, Embase, ClinicalTrials.gov, and Cochrane Library database. The pooled overall response rate, complete response (CR) rate, and partial response rate were measured. The risk of adverse events was evaluated. Moreover, the subgroup analysis was utilized to assess the efficacy among different HDAC inhibitors and efficacy in different PTCL subtypes. Results: For untreated PTCL, 502 patients in seven studies were involved, and the pooled CR rate was 44% (95% CI, 39-48%). For R/R PTCL patients, there were 16 studies included, and the CR rate was 14% (95% CI, 11-16%). The HDAC inhibitor-based combination therapy exhibited better efficacy when compared with HDAC inhibitor monotherapy for R/R PTCL patients (P = 0.02). In addition, the pooled CR rate was 17% (95% CI, 13-22%), 10% (95% CI, 5-15%), and 10% (95% CI, 5-15%) in the romidepsin, belinostat, and chidamide monotherapy subgroups, respectively. In the R/R angioimmunoblastic T-cell lymphoma subgroup, the pooled ORR was 44% (95% CI, 35-53%), higher than other subtypes. A total of 18 studies were involved in the safety assessment of treatment-related adverse events. Thrombocytopenia and nausea were the most common hematological and non-hematological adverse events, respectively. Conclusion: This meta-analysis demonstrated that HDAC inhibitors were effective treatment options for untreated and R/R PTCL patients. The combination of HDAC inhibitor and chemotherapy exhibited superior efficacy to HDAC inhibitor monotherapy in the R/R PTCL setting. Additionally, HDAC inhibitor-based therapy had higher efficacy in angioimmunoblastic T-cell lymphoma patients than that in other subtypes.

KMT2D Deficiency Promotes Myeloid Leukemias which Is Vulnerable to Ribosome Biogenesis Inhibition.

KMT2C and KMT2D are the most frequently mutated epigenetic genes in human cancers. While KMT2C is identified as a tumor suppressor in acute myeloid leukemia (AML), the role of KMT2D remains unclear in this disease, though its loss promotes B cell lymphoma and various solid cancers. Here, it is reported that KMT2D is downregulated or mutated in AML and its deficiency, through shRNA knockdown or CRISPR/Cas9 editing, accelerates leukemogenesis in mice. Hematopoietic stem and progenitor cells and AML cells with Kmt2d loss have significantly enhanced ribosome biogenesis and consistently, enlarged nucleolus, increased rRNA and protein synthesis rates. Mechanistically, it is found that KMT2D deficiency leads to the activation of the mTOR pathway in both mouse and human AML cells. Kmt2d directly regulates the expression of Ddit4, a negative regulator of the mTOR pathway. Consistent with the abnormal ribosome biogenesis, it is shown that CX-5461, an inhibitor of RNA polymerase I, significantly restrains the growth of AML with Kmt2d loss in vivo and extends the survival of leukemic mice. These studies validate KMT2D as a de facto tumor suppressor in AML and reveal an unprecedented vulnerability to ribosome biogenesis inhibition.

Safety and efficacy of dual PI3K-δ, γ inhibitor, duvelisib in patients with relapsed or refractory lymphoid neoplasms: A systematic review and meta-analysis of prospective clinical trials.

Background: Duvelisib is the first FDA-approved oral dual inhibitor of phosphatidylinositol-3-kinase PI3K-delta (PI3K-δ) and PI3K-gamma (PI3K-γ). Although many clinical studies support the efficacy of duvelisib, the safety of duvelisib remains with great attention. This systematic review and meta-analysis aimed to evaluate the safety and efficacy of duvelisib in treating different relapsed or refractory (RR) lymphoid neoplasm types. Methods: We searched prospective clinical trials from PUBMED, EMBASE, Cochrane Library, and ClinicalTrials.gov. For efficacy analysis, Overall response rate (ORR), complete response rate (CR), partial response rate (PR), rate of stable disease (SDR), rate of progressive disease (PDR), median progression-free survival (mPFS), 12-/24-month PFS, and 12-month overall survival (OS) were assessed. For safety analysis, the incidences of any grade and grade ≥3 adverse events (AEs), serious AEs, and treatment-related discontinuation and death were evaluated. Subgroup analysis based on the disease type was performed. Results: We included 11 studies and 683 patients, including 305 chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL), 187 B-cell indolent non-Hodgkin lymphoma (iNHL), 39 B-cell aggressive non-Hodgkin lymphoma (aNHL), and 152 T-cell non-Hodgkin lymphoma (T-NHL) patients. The pooled ORR in CLL/SLL, iNHL, aNHL and T-NHL was 70%, 70%, 28% and 47%, respectively. Additionally, the pooled ORR in CLL/SLL patients with or without TP53 mutation/17p-deletion (62% vs. 74%, p=0.45) and in follicular lymphoma (FL) or other iNHL (69% vs. 57%, p=0.38) had no significant differences. Mantle cell lymphoma (MCL) patients had higher pooled ORR than other aNHL (68% vs. 17%, p=0.04). Angioimmunoblastic TCL (AITL) patients had higher pooled ORR than other PTCL patients (67% vs. 42%, p=0.01). The pooled incidence of any grade, grade ≥3, serious AEs, treatment-related discontinuation and death was 99%, 79%, 63%, 33% and 3%, respectively. The most frequent any-grade AEs were diarrhea (47%), ALT/AST increase (39%), and neutropenia (38%). The most frequent grade ≥3 AEs were neutropenia (25%), ALT/AST increased (16%), diarrhea (12%), and anemia (12%). Conclusion: Generally, duvelisib could offer favorable efficacy in patients with RR CLL/SLL, iNHL, MCL, and AITL. Risk and severity in duvelisib treatment may be mitigated through proper identification and management.

RIPK1 inhibition enhances the therapeutic efficacy of chidamide in FLT3-ITD positive AML, both in vitro and in vivo.

Acute myeloid leukemia (AML) with FLT3-ITD mutation accounts for a large proportion of relapsed/refractory AML with poor prognosis. RIPK1 is a known key regulator of necroptosis and RIPK1 inhibition shows anti-AML effects in vitro. Chidamide is a histone deacetylase inhibitor (HDACi) with proven ability to induce apoptosis in FLT3-ITD positive AML cells. In the present study, we evaluated the effects of the combination of 22b, a novel RIPK1 inhibitor, and chidamide on proliferation and apoptosis in FLT3-ITD positive AML cell lines and primary cells. The results showed that 22b could significantly enhance the anti-leukemia effect of low-dose chidamide both on cell lines and primary cells. In a subcutaneous xenograft AML model, the combination of 22b and chidamide exhibited obviously elevated anti-tumor activity. In conclusion, our results support that the combination of RIPK1 inhibitor 22b and chidamide may be a novel therapeutic avenue for FLT3-ITD positive AML patients.

Reconfigurable Quasi-Nonvolatile Memory/Subthermionic FET Functions in Ferroelectric-2D Semiconductor vdW Architectures.

The functional reconfiguration of transistors and memory in homogenous ferroelectric devices offers significant opportunities for implementing the concepts of in-memory computing and logic-memory monolithic integration. Thus far, reconfiguration is realized through programmable doping profiles in the semiconductor channel using multiple-gate operation. This complex device architecture limits further scaling to match the overall chip requirements. Here, reconfigurable memory/transistor functionalities in a ferroelectric-gated van der Waals transistor by controlling the behavior of ferroelectric oxygen vacancies at the interface are demonstrated. Short- and long-term memory functions are demonstrated by modulating the border oxygen vacancy distribution and the associated charge dynamics. The quasi-nonvolatile long-term memory exhibits data retention of over 105 s and endurance of up to 5 × 105 cycles, verifying its applicability as a potential device platform for neuromorphic networks. More importantly, by modulating the ferroelectricity of the interfacial domains with the interactions of oxygen vacancies, a hysteresis-free logic transistor is realized with a subthermionic subthreshold swing down to 46 mV dec-1 , which resembles a negative-capacitance field-effect transistor. The new concept of achieving functional reconfiguration with prior device performance in a single-gate ferroelectric field-effect transistor is of great advantage in future integrated circuit applications.

Interfacial Ammonia Selectivity, Atmospheric Passivation, and Molecular Identification in Graphene-Nanopored Activated Carbon Molecular-Sieve Gas Sensors.

Graphene's inherent nonselectivity and strong atmospheric doping render most graphene-based sensors unsuitable for atmospheric applications in environmental monitoring of pollutants and breath detection of biomarkers for noninvasive medical diagnosis. Hence, demonstrations of graphene's gas sensitivity are often in inert environments such as nitrogen, consequently of little practical relevance. Herein, target gas sensing at the graphene-activated carbon interface of a graphene-nanopored activated carbon molecular-sieve sensor obtained via the postlithographic pyrolysis of Novolac resin residues on graphene nanoribbons is shown to simultaneously induce ammonia selectivity and atmospheric passivation of graphene. Consequently, 500 parts per trillion (ppt) ammonia sensitivity in atmospheric air is achieved with a response time of ∼3 s. The similar graphene and a-C workfunctions ensure that the ambipolar and gas-adsorption-induced charge transfer characteristics of pristine graphene are retained. Harnessing the van der Waals bonding memory and electrically tunable charge-transfer characteristics of the adsorbed molecules on the graphene channel, a molecular identification technique (charge neutrality point disparity) is developed and demonstrated to be suitable even at parts per billion (ppb) gas concentrations. The selectivity and atmospheric passivation induced by the graphene-activated carbon interface enable atmospheric applications of graphene sensors in environmental monitoring and noninvasive medical diagnosis.

An Epigenetic Mechanism Underlying Chromosome 17p Deletion-Driven Tumorigenesis.

Chromosome copy-number variations are a hallmark of cancer. Among them, the prevalent chromosome 17p deletions are associated with poor prognosis and can promote tumorigenesis more than TP53 loss. Here, we use multiple functional genetic strategies and identify a new 17p tumor suppressor gene (TSG), plant homeodomain finger protein 23 (PHF23). Its deficiency impairs B-cell differentiation and promotes immature B-lymphoblastic malignancy. Mechanistically, we demonstrate that PHF23, an H3K4me3 reader, directly binds the SIN3-HDAC complex through its N-terminus and represses its deacetylation activity on H3K27ac. Thus, the PHF23-SIN3-HDAC (PSH) complex coordinates these two major active histone markers for the activation of downstream TSGs and differentiation-related genes. Furthermore, dysregulation of the PSH complex is essential for the development and maintenance of PHF23-deficient and 17p-deleted tumors. Hence, our study reveals a novel epigenetic regulatory mechanism that contributes to the pathology of 17p-deleted cancers and suggests a susceptibility in this disease. SIGNIFICANCE: We identify PHF23, encoding an H3K4me3 reader, as a new TSG on chromosome 17p, which is frequently deleted in human cancers. Mechanistically, PHF23 forms a previously unreported histone-modifying complex, the PSH complex, which regulates gene activation through a synergistic link between H3K4me3 and H3K27ac.This article is highlighted in the In This Issue feature, p. 1.

Conductance Tunable Suspended Graphene Nanomesh by Helium Ion Beam Milling.

This paper demonstrates that the electrical properties of suspended graphene nanomesh (GNM) can be tuned by systematically changing the porosity with helium ion beam milling (HIBM). The porosity of the GNM is well-controlled by defining the pitch of the periodic nanopores. The defective region surrounding the individual nanopores after HIBM, which limits the minimum pitch achievable between nanopores for a certain dose, is investigated and reported. The exponential relationship between the thermal activation energy (EA) and the porosity is found in the GNM devices. Good EA tuneability observed from the GNMs provides a new approach to the transport gap engineering beyond the conventional nanoribbon method.

Research on the Hydrophobicity of Square Column Structures on Monocrystalline Silicon Fabricated Using Micro-Machining.

The theoretical prediction models of contact angle were constructed by considering the interface free energy. Then, the square column structure on monocrystalline silicon was fabricated using micro-milling. The rationality of prediction models was validated by regulating the parameters of the square column. It should be mentioned that the whole construction process was facile and efficient. After processing, the hydrophobicity of monocrystalline silicon with the square column structure was improved. The static contact angle of the processed monocrystalline silicon reached 165.8° when the side length of the square column was 60 µm. In addition, the correctness of the prediction models was verified from the perspective of molecular dynamics. The prediction models of contact angle were of great value for the practical application.

Quantum Dot Formation in Controllably Doped Graphene Nanoribbon.

We introduce the controllable doping from hydrogen silsesquioxane (HSQ) to graphene by changing its electron-beam exposure dose. Using HSQ as the dopant, a fine-resolution electron-beam resist allows us to selectively dope graphene with an extremely high spatial resolution of a few nanometers. Therefore, we can design and demonstrate the single quantum dot (QD)-like transport in the graphene nanoribbon (GNR) with the opening of the energy gap. Moreover, we suggest a rough geometric design rule in which a relatively short and wide GNR is required for observing the single QD-like transport. We envisage that this method can be utilized for other materials and for other applications, such as p-n junctions and tunnel field-effect transistors.