Molecular targets of glucocorticoids that elucidate their therapeutic efficacy in aggressive lymphomas.

Glucocorticoids have been used for decades to treat lymphomas without an established mechanism of action. Using functional genomic, proteomic, and chemical screens, we discover that glucocorticoids inhibit oncogenic signaling by the B cell receptor (BCR), a recurrent feature of aggressive B cell malignancies, including diffuse large B cell lymphoma and Burkitt lymphoma. Glucocorticoids induce the glucocorticoid receptor (GR) to directly transactivate genes encoding negative regulators of BCR stability (LAPTM5; KLHL14) and the PI3 kinase pathway (INPP5D; DDIT4). GR directly represses transcription of CSK, a kinase that limits the activity of BCR-proximal Src-family kinases. CSK inhibition attenuates the constitutive BCR signaling of lymphomas by hyperactivating Src-family kinases, triggering their ubiquitination and degradation. With the knowledge that glucocorticoids disable oncogenic BCR signaling, they can now be deployed rationally to treat BCR-dependent aggressive lymphomas and used to construct mechanistically sound combination regimens with inhibitors of BTK, PI3 kinase, BCL2, and CSK.

Multi-omic profiling of follicular lymphoma reveals changes in tissue architecture and enhanced stromal remodeling in high-risk patients.

Follicular lymphoma (FL) is a generally incurable malignancy that evolves from developmentally blocked germinal center (GC) B cells. To promote survival and immune escape, tumor B cells undergo significant genetic changes and extensively remodel the lymphoid microenvironment. Dynamic interactions between tumor B cells and the tumor microenvironment (TME) are hypothesized to contribute to the broad spectrum of clinical behaviors observed among FL patients. Despite the urgent need, existing clinical tools do not reliably predict disease behavior. Using a multi-modal strategy, we examined cell-intrinsic and -extrinsic factors governing progression and therapeutic outcomes in FL patients enrolled onto a prospective clinical trial. By leveraging the strengths of each platform, we identify several tumor-specific features and microenvironmental patterns enriched in individuals who experience early relapse, the most high-risk FL patients. These features include stromal desmoplasia and changes to the follicular growth pattern present 20 months before first progression and first relapse.

Response to Bruton's tyrosine kinase inhibitors in aggressive lymphomas linked to chronic selective autophagy.

Diffuse large B cell lymphoma (DLBCL) is an aggressive, profoundly heterogeneous cancer, presenting a challenge for precision medicine. Bruton's tyrosine kinase (BTK) inhibitors block B cell receptor (BCR) signaling and are particularly effective in certain molecular subtypes of DLBCL that rely on chronic active BCR signaling to promote oncogenic NF-κB. The MCD genetic subtype, which often acquires mutations in the BCR subunit, CD79B, and in the innate immune adapter, MYD88L265P, typically resists chemotherapy but responds exceptionally to BTK inhibitors. However, the underlying mechanisms of response to BTK inhibitors are poorly understood. Herein, we find a non-canonical form of chronic selective autophagy in MCD DLBCL that targets ubiquitinated MYD88L265P for degradation in a TBK1-dependent manner. MCD tumors acquire genetic and epigenetic alterations that attenuate this autophagic tumor suppressive pathway. In contrast, BTK inhibitors promote autophagic degradation of MYD88L265P, thus explaining their exceptional clinical benefit in MCD DLBCL.

Identification, characterization and hypolipidemic effect of novel peptides in protein hydrolysate from Protaetia brevitarsis larvae.

The proteins were mainly derived from Protaetia brevitarsis larval extracts obtained using two empty intestine methods (traditional static method: TSM or salt immersion stress method: SISM) and extraction solvents (water: W or 50 % water-ethanol: W:E), and the proteins were used as objects to investigate the effect of emptying intestine methods on hypolipidemic peptides. The results revealed that the F-2 fractions of protein hydrolysate had stronger in vitro hypolipidemic activity, with the peptides obtained by SISM possessing a stronger cholesterol micelle solubility inhibition rate, especially in SISM-W:E-P. Moreover, a total of 106 peptides were tentatively identified, among which SISM identified more peptides with an amino acid number < 8. Meanwhile, five novel peptides (YPPFH, YPGFGK, KYPF, SPLPGPR and VPPP) exhibited good hypolipidemic activity in vitro and in vivo, among which YPPFH, VPPP and KYPF had strong inhibitory activities on pancreatic lipase (PL) and cholesteryl esterase (CE), and KYPF, SPLPGPR and VPPP could significantly reduce the TG content in Caenorhabditis elegans. Thus, P. brevitarsis can be developed as a naturally derived hypolipidemic component for the development and application in functional foods.

Analysis and therapeutic targeting of the IL-1R pathway in anaplastic large cell lymphoma.

Anaplastic large cell lymphoma (ALCL), a subgroup of mature T-cell neoplasms with an aggressive clinical course, is characterized by elevated expression of CD30 and anaplastic cytology. To achieve a comprehensive understanding of the molecular characteristics of ALCL pathology and to identify therapeutic vulnerabilities, we applied genome-wide CRISPR library screenings to both anaplastic lymphoma kinase positive (ALK+) and primary cutaneous (pC) ALK- ALCLs and identified an unexpected role of the interleukin-1R (IL-1R) inflammatory pathway in supporting the viability of pC ALK- ALCL. Importantly, this pathway is activated by IL-1α in an autocrine manner, which is essential for the induction and maintenance of protumorigenic inflammatory responses in pC-ALCL cell lines and primary cases. Hyperactivation of the IL-1R pathway is promoted by the A20 loss-of-function mutation in the pC-ALCL lines we analyze and is regulated by the nonproteolytic protein ubiquitination network. Furthermore, the IL-1R pathway promotes JAK-STAT3 signaling activation in ALCLs lacking STAT3 gain-of-function mutation or ALK translocation and enhances the sensitivity of JAK inhibitors in these tumors in vitro and in vivo. Finally, the JAK2/IRAK1 dual inhibitor, pacritinib, exhibited strong activities against pC ALK- ALCL, where the IL-1R pathway is hyperactivated in the cell line and xenograft mouse model. Thus, our studies revealed critical insights into the essential roles of the IL-1R pathway in pC-ALCL and provided opportunities for developing novel therapeutic strategies.

Targeting N-linked Glycosylation for the Therapy of Aggressive Lymphomas.

Diffuse large B-cell lymphoma (DLBCL) can be subdivided into the activated B-cell (ABC) and germinal center B cell-like (GCB) subtypes. Self-antigen engagement of B-cell receptors (BCR) in ABC tumors induces their clustering, thereby initiating chronic active signaling and activation of NF-κB and PI3 kinase. Constitutive BCR signaling is essential in some GCB tumors but primarily activates PI3 kinase. We devised genome-wide CRISPR-Cas9 screens to identify regulators of IRF4, a direct transcriptional target of NF-κB and an indicator of proximal BCR signaling in ABC DLBCL. Unexpectedly, inactivation of N-linked protein glycosylation by the oligosaccharyltransferase-B (OST-B) complex reduced IRF4 expression. OST-B inhibition of BCR glycosylation reduced BCR clustering and internalization while promoting its association with CD22, which attenuated PI3 kinase and NF-κB activation. By directly interfering with proximal BCR signaling, OST-B inactivation killed models of ABC and GCB DLBCL, supporting the development of selective OST-B inhibitors for the treatment of these aggressive cancers. SIGNIFICANCE: DLBCL depends on constitutive BCR activation and signaling. There are currently no therapeutics that target the BCR directly and attenuate its pathologic signaling. Here, we unraveled a therapeutically exploitable, OST-B-dependent glycosylation pathway that drives BCR organization and proximal BCR signaling. This article is highlighted in the In This Issue feature, p. 1749.

Evolutionary timescale of chalcidoid wasps inferred from over one hundred mitochondrial genomes.

Chalcidoidea is one of the most biologically diverse groups among Hymenoptera. Members are characterized by extraordinary parasitic lifestyles and extensive host ranges, among which several species attack plants or serve as pollinators. However, higher-level chalcidoid relationships remain controversial. Here, we performed mitochondrial phylogenomic analyses for major clades (18 out of 25 families) of Chalcidoidea based on 139 mitochondrial genomes. The compositional heterogeneity and conflicting backbone relationships in Chalcidoidea were assessed using various datasets and tree inferences. Our phylogenetic results supported the monophyly of 16 families and polyphyly of Aphelinidae and Pteromalidae. Our preferred topology recovered the relationship (Mymaridae+(Signiphoridae+Leucospidae)+(Chalcididae+((Perilampidae+Eucharitidae)+ remaining Chalcidoidea)))). The monophyly of Agaonidae and Sycophaginae was rejected, while the gall-associated ((Megastigmidae+Ormyridae)+(Ormocerinae+Eurytomidae)) relationship was supported in most results. A six-gene inversion may be a synapomorphy for most families, whereas other derived gene orders may introduce confusion in phylogenetic signals at deeper nodes. Dating estimates suggested that Chalcidoidea arose near the Jurassic/Cretaceous boundary and that two dynamic shifts in diversification occurred during the evolution of Chalcidoidea. We hypothesized that the potential codiversification between chalcidoids and their hosts may be crucial for accelerating the diversification of Chalcidoidea. Ancestral state reconstruction analyses supported the hypothesis that gall-inducers were mainly derived from parasitoids of gall-inducers, while other gall-inducers were derived from phytophagous groups. Taken together, these findings advance our understanding of mitochondrial genome evolution in the major interfamilial phylogeny of Chalcidoidea.

Appropriate oxygen vacancies and Mo-N bond synergistically modulate charge transfer dynamics of MoO3-x/S-CN for superior photocatalytic disinfection: Unveiling synergistic effects and disinfection mechanism.

Highly efficient charge transfer is a critical factor to modulate the photocatalytic activity. However, the conscious modulation of charge transfer efficiency is still a great challenge. Herein, a novel interfacial Mo-N bond and appropriate oxygen vacancies (OVs) modulated S-scheme MoO3-x/S-CN heterojunction was rationally fabricated for efficient photocatalytic disinfection. The results of characterizations and density functional theory (DFT) calculations suggested that the enhanced charge transfer dynamics is ascribed to the optimizing oxygen vacancies density and forming interfacial Mo-N bond. It can improve charge transfer efficiency from 36.4% (MoO3-x) to 52.5% (MoO3-x/S-CN) and produce more reactive oxygen species (ROS), achieving entirely inactivate of 7.60-log E. coli and S. aureus within 50 min and 75 min. Besides, MoO3-x/S-CN can well resist the disturbance from the coexisting substances, and can be applied in a wide pH range, and even authentic water bodies. Monitoring of bacterial antioxidant systems and membrane integrity revealed that bacterial inactivation begins with the oxidation of cell membrane and dies from leakage of intracellular substances and destruction of cell structure. This work provides an inspiration on consciously modulating S-scheme charge transfer efficiency by optimizing oxygen vacancies density and atomic-level interface control for promoting the photocatalytic antibacterial activity.

Characterization of bioactives and in vitro biological activity from Protaetia brevitarsis larval extracts obtained by different pretreatment extractions.

Intestinal contents affect the characterization of edible insect bioactive compounds. Two empty intestine methods, namely, traditional static method (TSM) or salt immersion stress method (SISM), associated with extraction solvents water (W), 50 % water-ethanol (W:E) or 100 % ethanol (E), were used to obtain six Protaetia brevitarsis larval extracts. The total flavonoid content (TFC) in the W:E extracts was significantly higher than that in the W and E extracts, with TSM-W:E the highest (p < 0.05). The relative contents of 132 bioactive compounds, especially p-hydroxyphenylacetic acid, citric acid, and dehydroepiandrosterone, were different between TSM-W and SISM-W. TSM-W:E had significantly higher 2,2-diphenyl-1-picrylhydroxy· (DPPH) scavenging and pancreatic lipase (PL) inhibitory activity than SISM-W:E (p < 0.05). DPPH scavenging and PL inhibitory activities were highly correlated with TFC and carbohydrates, respectively. Thus, bioactive compounds in P. brevitarsis extracts can be obtained selectively using pretreatment methods, which might be beneficial for high-value utilization of P. brevitarsis.

Oncogenic RAS commandeers amino acid sensing machinery to aberrantly activate mTORC1 in multiple myeloma.

Oncogenic RAS mutations are common in multiple myeloma (MM), an incurable malignancy of plasma cells. However, the mechanisms of pathogenic RAS signaling in this disease remain enigmatic and difficult to inhibit therapeutically. We employ an unbiased proteogenomic approach to dissect RAS signaling in MM. We discover that mutant isoforms of RAS organize a signaling complex with the amino acid transporter, SLC3A2, and MTOR on endolysosomes, which directly activates mTORC1 by co-opting amino acid sensing pathways. MM tumors with high expression of mTORC1-dependent genes are more aggressive and enriched in RAS mutations, and we detect interactions between RAS and MTOR in MM patient tumors harboring mutant RAS isoforms. Inhibition of RAS-dependent mTORC1 activity synergizes with MEK and ERK inhibitors to quench pathogenic RAS signaling in MM cells. This study redefines the RAS pathway in MM and provides a mechanistic and rational basis to target this mode of RAS signaling.

The gender-specific impact of starvation on mitotypes diversity in adults of Drosophila melanogaster.

In animals, starvation can increase the level of reactive oxygen species (ROS) in some tissues. Mitochondrial DNA (mtDNA) is more vulnerable to being attacked by ROS due to the lack of histone protection, leading to oxidative damage. However, whether starvation is associated with the genetic diversity of mtDNA remains unclear. Here, by using adult individuals of Drosophila melanogaster under three different feeding treatments (starvation, with the provision of only water, and normal feeding), based on the high-throughput sequencing results of the PCR amplicons of the partial sequences of the mitochondrial gene cytochrome c oxidase subunit I (mt-cox1), no significant difference in the mean number of mitochondrial haplotypes and the mean genetic distance of haplotypes within individuals were identified between the three treatment groups. Coupled with the low proportion of heterogeneous mt-cox1 sequences within each individual, it suggested that starvation had a limited impact on mitotype genetic diversity and mitochondrial function. Nevertheless, starvation could significantly increase the sequence number of haplotypes containing specific mutations, and for males with higher levels of mitochondrial heteroplasmy than females in the normal feeding group, starvation could further increase their mitochondrial heteroplasmy.

A Green Approach for High Oxidation Resistance, Flexible Transparent Conductive Films Based on Reduced Graphene Oxide and Copper Nanowires.

Copper nanowires (CuNWs)-based thin film is one of the potential alternatives to tin-doped indium oxide (ITO) in terms of transparent conductive films (TCFs). However, the severe problem of atmospheric oxidation restricts their practical applications. In this work, we develop a simple approach to fabricate highly stable TCFs through the dip-coating method using reduced graphene oxide (rGO) and CuNWs as the primary materials. Compared with previous works using toxic reduction agents, herein, the CuNWs are synthesized via a green aqueous process using glucose and lactic acid as the reductants, and rGO is prepared through the modified Hummers' method followed by a hydrogen-annealing process to form hydrogen-annealing-reduced graphene oxide (h-rGO). In the rGO/CuNWs films, the dip-coated graphene oxide layer can increase the adhesion of the CuNWs on the substrate, and the fabricated h-rGO/CuNWs can exhibit high atmospheric oxidation resistance and excellent flexibility. The sheet resistance of the h-rGO/CuNWs film only increased from 25.1 to 42.2 Ω/sq after exposure to ambient atmosphere for 30 days and remained almost unchanged after the dynamic bending test for 2500 cycles at a constant radius of 5.3 mm. The h-rGO/CuNWs TCF can be not only fabricated via a route with a superior inexpensive and safe method but also possessed competitive optoelectronic properties with high electrical stability and flexibility, demonstrating great opportunities for future optoelectronic applications.

Insights into the role of reactive oxygen species in photocatalytic H2O2 generation and OTC removal over a novel BN/Zn3In2S6 heterojunction.

Developing photocatalysts with superior performance to generate hydrogen peroxide (H2O2) and degrade oxytetracycline (OTC) is an effective strategy for the treatment of energy crisis and water purification. Herein, BN nanosheets were anchored onto the Zn3In2S6 microspheres for the research. Experimental and density functional theory (DFT) results demonstrate that due to different work functions and unique 2D/2D contact, the electron is spatially separated in BN/Zn3In2S6 nanocomposite, which increases the electron transfer efficiency from 43.7% (Zn3In2S6) to 55.6% (BN/ZIS-4). As a result, BN/ZIS-4 with optimal ratio of BN and Zn3In2S6 exhibits the highest OTC degradation efficiency (84.5%) and H2O2 generation rate (115.5 µmol L-1) under visible light illumination, which is 2.2 and 2.9 times than that of pristine Zn3In2S6. H2O2 generation is dominated by two pathways: two-step single-electron process (O2 → ∙O2- → H2O2) and another way (O2 → ∙O2- → 1O2 → H2O2). In the process of degrading OTC, ∙O2-, 1O2 and ∙OH are regarded as the main active species. This work offers a new insight for designing efficient, stable and reusable photocatalysts to solve current environmental conundrums.

Impact of mitotype diversity on metabarcoding biodiversity estimations in Insecta and Arachnida using different sample preparation strategies.

DNA barcoding and metabarcoding have been increasingly used in species delimitation and species diversity assessment, respectively, and the molecular markers used in animals are mainly derived from mitochondrial DNA. It is well known that the phenomenon of multiple mitochondrial haplotypes within the same specimen (hereafter referred to as "mitotype diversity") may have a negative impact on the proper assessment of biodiversity by metabarcoding. However, few studies have focused on the incidence of this phenomenon and its effects on metabarcoding results using different sample preparation strategies, such as mock community construction using pooled high-throughput sequencing (HTS) data, DNA-pooling and Tissue-pooling. In this study, we investigated mitotype diversity and its influence on metabarcoding based on 398 specimens from 66 species of Insecta and 82 specimens from 16 species of Arachnida by HTS of the mitochondrial cox1 gene fragment. The results revealed that mitotype diversity was common in the studied taxa and significantly increased the number of operational taxonomic units (OTUs) using the three sample preparation strategies. The results also showed that the bioinformatics pipeline based on authentic amplicon sequence variants was more reliable than the pipeline based on OTUs. Regarding the sample preparation strategies of DNA-pooling and Tissue-pooling commonly used in metabarcoding, our results revealed that their results of metabarcoding were quite similar, and the Tissue-pooling strategy was therefore preferred because of its simplicity. Our study calls for additional attention to the interference of mitotype diversity on the results of DNA metabarcoding in biodiversity assessment.

A highly accurate delta check method using deep learning for detection of sample mix-up in the clinical laboratory.

OBJECTIVES: Delta check (DC) is widely used for detecting sample mix-up. Owing to the inadequate error detection and high false-positive rate, the implementation of DC in real-world settings is labor-intensive and rarely capable of absolute detection of sample mix-ups. The aim of the study was to develop a highly accurate DC method based on designed deep learning to detect sample mix-up. METHODS: A total of 22 routine hematology test items were adopted for the study. The hematology test results, collected from two hospital laboratories, were independently divided into training, validation, and test sets. By selecting six mainstream algorithms, the Deep Belief Network (DBN) was able to learn error-free and artificially (intentionally) mixed sample results. The model's analytical performance was evaluated using training and test sets. The model's clinical validity was evaluated by comparing it with three well-recognized statistical methods. RESULTS: When the accuracy of our model in the training set reached 0.931 at the 22nd epoch, the corresponding accuracy in the validation set was equal to 0.922. The loss values for the training and validation sets showed a similar (change) trend over time. The accuracy in the test set was 0.931 and the area under the receiver operating characteristic curve was 0.977. DBN demonstrated better performance than the three comparator statistical methods. The accuracy of DBN and revised weighted delta check (RwCDI) was 0.931 and 0.909, respectively. DBN performed significantly better than RCV and EDC. Of all test items, the absolute difference of DC yielded higher accuracy than the relative difference for all methods. CONCLUSIONS: The findings indicate that input of a group of hematology test items provides more comprehensive information for the accurate detection of sample mix-up by machine learning (ML) when compared with a single test item input method. The DC method based on DBN demonstrated highly effective sample mix-up identification performance in real-world clinical settings.

Integrating the Z-scheme heterojunction and hot electrons injection into a plasmonic-based Zn2In2S5/W18O49 composite induced improved molecular oxygen activation for photocatalytic degradation and antibacterial performance.

The semiconductor-based photocatalysts with local surface plasmon resonance (LSPR) effect can extend light response to near-infrared region (NIR), as well as promote charge-carriers transfer, which provide a novel insight into designing light-driven photocatalyst with excellent photocatalytic performance. Here, we designed cost-effective wide-spectrum Zn2In2S5/W18O49 composite with enhanced photocatalytic performance based on a dual-channel charge transfer pathway. Benefiting from the synergistic effect of Z-scheme heterostructure and unique LSPR effect, the interfacial charge-carriers transfer rate and light-absorbing ability of Zn2In2S5/W18O49 were enhanced significantly under visible and NIR (vis-NIR) light irradiation. More reactive oxygen species (ROS) were formed by efficient molecular oxygen activation, which were the critical factors for both Escherichia coli (E. coli) photoinactivation and tetracycline (TC) photodegradation. The enhancement of molecular oxygen activation (MOA) ability was verified via quantitative analyses, which evaluated the amount of ROS through degrading nitrotetrazolium blue chloride (NBT) and p-phthalic acid (TA). By combining theoretical calculations with diverse experimental results, we proposed a credible photocatalytic reaction mechanism for antibiotic degradation and bacteria inactivation. This study develops a new insight into constructing promising photocatalysts with efficient photocatalytic activity in practical wastewater treatment.

Genome-wide CRISPR screen identifies CDK6 as a therapeutic target in adult T-cell leukemia/lymphoma.

Adult T-cell leukemia/lymphoma (ATLL) is an aggressive T-cell malignancy with a poor prognosis with current therapy. Here we report genome-wide CRISPR-Cas9 screening of ATLL models, which identified CDK6, CCND2, BATF3, JUNB, STAT3, and IL10RB as genes that are essential for the proliferation and/or survival of ATLL cells. As a single agent, the CDK6 inhibitor palbociclib induced cell cycle arrest and apoptosis in ATLL models with wild-type TP53. ATLL models that had inactivated TP53 genetically were relatively resistant to palbociclib owing to compensatory CDK2 activity, and this resistance could be reversed by APR-246, a small molecule activator of mutant TP53. The CRISPR-Cas9 screen further highlighted the dependence of ATLL cells on mTORC1 signaling. Treatment of ATLL cells with palbociclib in combination with mTORC1 inhibitors was synergistically toxic irrespective of the TP53 status. This work defines CDK6 as a novel therapeutic target for ATLL and supports the clinical evaluation of palbociclib in combination with mTORC1 inhibitors in this recalcitrant malignancy.

Tumor evolution selectively inactivates the core microRNA machinery for immune evasion.

Cancer cells acquire genetic heterogeneity to escape from immune surveillance during tumor evolution, but a systematic approach to distinguish driver from passenger mutations is lacking. Here we investigate the impact of different immune pressure on tumor clonal dynamics and immune evasion mechanism, by combining massive parallel sequencing of immune edited tumors and CRISPR library screens in syngeneic mouse tumor model and co-culture system. We find that the core microRNA (miRNA) biogenesis and targeting machinery maintains the sensitivity of cancer cells to PD-1-independent T cell-mediated cytotoxicity. Genetic inactivation of the machinery or re-introduction of ANKRD52 frequent patient mutations dampens the JAK-STAT-interferon-γ signaling and antigen presentation in cancer cells, largely by abolishing miR-155-targeted silencing of suppressor of cytokine signaling 1 (SOCS1). Expression of each miRNA machinery component strongly correlates with intratumoral T cell infiltration in nearly all human cancer types. Our data indicate that the evolutionarily conserved miRNA pathway can be exploited by cancer cells to escape from T cell-mediated elimination and immunotherapy.