Treatment resistance to melanoma therapeutics on a single cell level.

Therapy targeting the BRAF-MEK cascade created a treatment revolution for patients with BRAF mutant advanced melanoma. Unfortunately, 80% patients treated will progress by 5 years follow-up. Thus, it is imperative we study mechanisms of melanoma progression and therapeutic resistance. We created a scRNA (single cell RNA) atlas of 128,230 cells from 18 tumors across the treatment spectrum, discovering melanoma cells clustered strongly by transcriptome profiles of patients of origins. Our cell-level investigation revealed gains of 1q and 7q as likely early clonal events in metastatic melanomas. By comparing patient tumors and their derivative cell lines, we observed that PD1 responsive tumor fraction disappears when cells are propagated in vitro. We further established three anti-BRAF-MEK treatment resistant cell lines using three BRAF mutant tumors. ALDOA and PGK1 were found to be highly expressed in treatment resistant cell populations and metformin was effective in targeting the resistant cells. Our study suggests that the investigation of patient tumors and their derivative lines is essential for understanding disease progression, treatment response and resistance.

Comparative transcriptome profiling reveals the key genes and molecular mechanisms involved in rice under blast infection.

The aim of this study was to analyze the resistance genes and molecular mechanisms involved in rice blast infection. The contents of seven hormones and eight biochemical indicators in the leaves and spikes were at dynamic levels after inoculation with rice blast strains over time. The mRNA and protein expression of the six genes were consistent with the transcriptome analysis results. In addition, KEGG enrichment analysis showed that Os03g0132000, Os06g0215600, and Os06g0215500 were significantly enriched in the alpha-linolenic acid metabolism KEGG pathway, whereas Os05g0311801 was significantly enriched in the zeatin biosynthesis KEGG pathway. Furthermore, Os03g0180900 and Os09g0439200 were significantly enriched in the plant hormone signal transduction KEGG pathways. Therefore, blast infection could alter the hormones, biochemical indicators, and traits of rice. Moreover, genes including Os03g0132000, Os03g0180900, and Os05g0311801 were identified as rice blast resistance genes, and the mechanism might involve alpha-linolenic acid metabolism, zeatin biosynthesis, and plant hormone signal transduction KEGG pathways.

Somatic mutation phasing and haplotype extension using linked-reads in multiple myeloma.

Somatic mutation phasing informs our understanding of cancer-related events, like driver mutations. We generated linked-read whole genome sequencing data for 23 samples across disease stages from 14 multiple myeloma (MM) patients and systematically assigned somatic mutations to haplotypes using linked-reads. Here, we report the reconstructed cancer haplotypes and phase blocks from several MM samples and show how phase block length can be extended by integrating samples from the same individual. We also uncover phasing information in genes frequently mutated in MM, including DIS3, HIST1H1E, KRAS, NRAS, and TP53, phasing 79.4% of 20,705 high-confidence somatic mutations. In some cases, this enabled us to interpret clonal evolution models at higher resolution using pairs of phased somatic mutations. For example, our analysis of one patient suggested that two NRAS hotspot mutations occurred on the same haplotype but were independent events in different subclones. Given sufficient tumor purity and data quality, our framework illustrates how haplotype-aware analysis of somatic mutations in cancer can be beneficial for some cancer cases.

Biologic and clinical analysis of childhood gamma delta T-ALL identifies LMO2/STAG2 rearrangements as extremely high-risk.

Acute lymphoblastic leukemia expressing the gamma delta T cell receptor (yo T-ALL) is a poorly understood disease. We studied 200 children with yo T-ALL from 13 clinical study groups to understand the clinical and genetic features of this disease. We found age and genetic drivers were significantly associated with outcome. yo T-ALL diagnosed in children under three years of age was extremely high-risk and enriched for genetic alterations that result in both LMO2 activation and STAG2 inactivation. Mechanistically, using patient samples and isogenic cell lines, we show that inactivation of STAG2 profoundly perturbs chromatin organization by altering enhancer-promoter looping, resulting in deregulation of gene expression associated with T-cell differentiation. High throughput drug screening identified a vulnerability in DNA repair pathways arising from STAG2 inactivation, which can be targeted by Poly(ADP-ribose) polymerase (PARP) inhibition. These data provide a diagnostic framework for classification and risk stratification of pediatric yo T-ALL.

Investigations of a 1018 nm gain-switched Yb-doped fiber oscillator.

In this paper, we investigate a 1018 nm gain-switched ytterbium-doped fiber oscillator at a low repetition rate in terms of theory and experiment. Theoretically, a numerical model applicable to a 1018 nm gain-switched ytterbium-doped fiber laser was established. The influence of the pump peak power and active fiber lengths on the 1018 nm gain-switched ytterbium-doped fiber laser was numerically simulated. Experimentally, a compact 1018 nm all-fiber-structured pulsed laser oscillator is constructed, in which a pulse width of 110 ns and a single-pulse energy of 0.1 mJ were obtained. Moreover, the experimental results are in agreement with the numerical simulation ones. To the best of our knowledge, this is the first time that gain-switching technology has been applied to 1018 nm fiber lasers to generate nanosecond pulsed lasers. The model and experimental results can provide a reference for the engineering design of the same type of low repetition rate fiber lasers below the kilohertz level.

All-fiber hectowatt radially polarized laser system.

A high-power all-fiber radially polarized laser system is demonstrated, in which an integrated nanograting mode convertor (S-wave plate) is used for the generation of radially polarized beam. Experimentally, a 1-W radially polarized beam was used as the seed laser, whose mode purity and mode extinction ratio (MER) were 96.5% and 98.3%, respectively. A single-stage few-mode fiber amplifier was employed to boost the 1-W seed laser to an average power of 113.2 W, when the pump power was 160 W. The corresponding slope efficiency and beam quality factor (M2) were approximately 72% and 2.3%, respectively. Moreover, the mode purity and MER of the amplified radially polarized laser were measured to be 95.7% and 97%, respectively. To the best of our knowledge, this is the highest output power from an all-fiber radially polarized laser system without obvious degradations of the mode purity and MER.

1.36 J nanosecond laser at 1 kHz repetition based on a slab amplifier chain.

A high beam quality diode-pumped Nd:YAG master oscillator power-amplifier (MOPA) laser with three end-pumped slab amplifiers is developed. The Q-swtiched side-pumped rod oscillator presented a pulse energy 3.1 mJ with beam quality factors of M x2=1.17 and M y2=1.15 at a repetition of 1 kHz. The MOPA system delivered a pulse energy of 1.36 J with a pulse width of 48.2 ns and an extraction efficiency of 44.8%. The beam quality factors of M x2=1.72 and M y2=3.85 are measured without any phase-conjugators or adaptive optics.

SINGLE CELL DISSECTION OF DEVELOPMENTAL ORIGINS AND TRANSCRIPTIONAL HETEROGENEITY IN B-CELL ACUTE LYMPHOBLASTIC LEUKEMIA.

Sequencing of bulk tumor populations has improved genetic classification and risk assessment of B-ALL, but does not directly examine intratumor heterogeneity or infer leukemia cellular origins. We profiled 89 B-ALL samples by single-cell RNA-seq (scRNA-seq) and compared them to a reference map of normal human B-cell development established using both functional and molecular assays. Intra-sample heterogeneity was driven by cell cycle, metabolism, differentiation, and inflammation transcriptional programs. By inference of B lineage developmental state composition, nearly all samples possessed a high abundance of pro-B cells, with variation between samples mainly driven by sub-populations. However, ZNF384- r and DUX4- r B-ALL showed composition enrichment of hematopoietic stem cells, BCR::ABL1 and KMT2A -r ALL of Early Lymphoid progenitors, MEF2D -r and TCF3::PBX1 of Pre-B cells. Enrichment of Early Lymphoid progenitors correlated with high-risk clinical features. Understanding variation in transcriptional programs and developmental states of B-ALL by scRNA-seq refines existing clinical and genomic classifications and improves prediction of treatment outcome.

Defining the condensate landscape of fusion oncoproteins.

Fusion oncoproteins (FOs) arise from chromosomal translocations in ~17% of cancers and are often oncogenic drivers. Although some FOs can promote oncogenesis by undergoing liquid-liquid phase separation (LLPS) to form aberrant biomolecular condensates, the generality of this phenomenon is unknown. We explored this question by testing 166 FOs in HeLa cells and found that 58% formed condensates. The condensate-forming FOs displayed physicochemical features distinct from those of condensate-negative FOs and segregated into distinct feature-based groups that aligned with their sub-cellular localization and biological function. Using Machine Learning, we developed a predictor of FO condensation behavior, and discovered that 67% of ~3000 additional FOs likely form condensates, with 35% of those predicted to function by altering gene expression. 47% of the predicted condensate-negative FOs were associated with cell signaling functions, suggesting a functional dichotomy between condensate-positive and -negative FOs. Our Datasets and reagents are rich resources to interrogate FO condensation in the future.

Coherent beam combining of cylindrical vector beams for power scaling.

Coherent beam combining (CBC) of cylindrical vector beams (CVBs) based on an active phase controller is proposed and demonstrated. Experimentally, two pieces of spatially variant wave plates (S-wave plate) were employed as vector mode convertors for two individual 1064-nm fiber amplifier channels. When the system was in a closed loop, a combined output power of 10 W and a CBC efficiency of higher than 94% were achieved, for both TM01 (radially polarized) mode and TE01 (azimuthally polarized) mode cases. Moreover, the laser system showed a high vector mode purity, which was measured to be ∼97.4% (TM01) and ∼97.3% (TE01). To the best of knowledge, this could possibly be the first demonstration of CBC of CVBs, which paves the way for power scaling of CVBs.

80-W single-frequency Innoslab µs-amplifier at 1319†nm with high efficiency.

A single-frequency quasi-continuous-wave partially end-pumped slab (Innoslab) laser amplifier at 1319 nm was demonstrated. The 3-W single-frequency all-fiber seed laser was amplified to a maximum average power of 80.1 W and the power stability was 0.52% in 10 minutes. The corresponding optical-optical efficiency was 16.1% under absorbed pump power of 478 W. The output pulse width was 131 µs at the repetition of 500 Hz. The beam quality factors of M2 were 1.3 in both the vertical and horizontal directions. To the best of our knowledge, this is the first report on single-frequency Nd:YAG Innoslab amplifier at 1319 nm with such high output power and efficiency.

Nonlinear spectral compression in high-power narrow-linewidth polarization maintaining fiber amplifiers for SBS suppression.

In this paper, we propose a method for narrowing the spectrum in high-power narrow-linewidth polarization-maintaining (PM) fiber amplifiers and investigate its potential for suppressing the stimulated Brillouin scattering (SBS). In this method, in addition to common phase modulation to suppress SBS, precisely designed amplitude modulation is induced to generate self-phase modulation in a high-power PM fiber amplifier. In this co-modulation way, the spectrum can be gradually compressed along the fiber. Compared to phase modulation alone or fiber-Bragg-gratings (FBGs) based narrow-linewidth fiber oscillator schemes, in which the spectrum remains the same or broadens, this scheme can achieve a higher SBS threshold for the same output spectral linewidth. Experiments on a ∼ 3 kW peak power quasi-continuous wave (QCW) fiber amplifier show that the co-modulation scheme can compress the spectrum from 0.25 nm to 0.084 nm as output peak power increases from 13 W to 3.2 kW and enhances the SBS threshold by ∼1.7 times compared to traditional FBGs-based fiber oscillator schemes, and by ∼1.4 times compared to common phase modulation schemes. This co-modulation scheme has the potential for mitigating SBS in high-power fiber amplifiers.

Mapping pediatric brain tumors to their origins in the developing cerebellum.

BACKGROUND: Distinguishing the cellular origins of childhood brain tumors is key for understanding tumor initiation and identifying lineage-restricted, tumor-specific therapeutic targets. Previous strategies to map the cell-of-origin typically involved comparing human tumors to murine embryonal tissues, which is potentially limited due to species-specific differences. The aim of this study was to unravel the cellular origins of the 3 most common pediatric brain tumors, ependymoma, pilocytic astrocytoma, and medulloblastoma, using a developing human cerebellar atlas. METHODS: We used a single-nucleus atlas of the normal developing human cerebellum consisting of 176 645 cells as a reference for an in-depth comparison to 4416 bulk and single-cell transcriptome tumor datasets, using gene set variation analysis, correlation, and single-cell matching techniques. RESULTS: We find that the astroglial cerebellar lineage is potentially the origin for posterior fossa ependymomas. We propose that infratentorial pilocytic astrocytomas originate from the oligodendrocyte lineage and MHC II genes are specifically enriched in these tumors. We confirm that SHH and Group 3/4 medulloblastomas originate from the granule cell and unipolar brush cell lineages. Radiation-induced gliomas stem from cerebellar glial lineages and demonstrate distinct origins from the primary medulloblastoma. We identify tumor genes that are expressed in the cerebellar lineage of origin, and genes that are tumor specific; both gene sets represent promising therapeutic targets for future study. CONCLUSION: Based on our results, individual cells within a tumor may resemble different cell types along a restricted developmental lineage. Therefore, we suggest that tumors can arise from multiple cellular states along the cerebellar "lineage of origin."

Stromal-induced epithelial-mesenchymal transition induces targetable drug resistance in acute lymphoblastic leukemia.

The bone marrow microenvironment (BME) drives drug resistance in acute lymphoblastic leukemia (ALL) through leukemic cell interactions with bone marrow (BM) niches, but the underlying mechanisms remain unclear. Here, we show that the interaction between ALL and mesenchymal stem cells (MSCs) through integrin ß1 induces an epithelial-mesenchymal transition (EMT)-like program in MSC-adherent ALL cells, resulting in drug resistance and enhanced survival. Moreover, single-cell RNA sequencing analysis of ALL-MSC co-culture identifies a hybrid cluster of MSC-adherent ALL cells expressing both B-ALL and MSC signature genes, orchestrated by a WNT/ß-catenin-mediated EMT-like program. Blockade of interaction between ß-catenin and CREB binding protein impairs the survival and drug resistance of MSC-adherent ALL cells in vitro and results in a reduction in leukemic burden in vivo. Targeting of this WNT/ß-catenin-mediated EMT-like program is a potential therapeutic approach to overcome cell extrinsically acquired drug resistance in ALL.

Understanding the cultivation mechanism for mental health education of college students in campus culture construction from the perspective of deep learning.

Nowadays, there is an increase in attention to the college student's mental health, and to enhance the awareness related to college students' mental health, colleges and universities have executed an immense range of mental health publicity activities. In order to better combine deep learning with classroom teaching, this paper puts forward a deep learning algorithm formulated on convolutional neural networks. The purpose of this research is to investigate the development and use of a cultivation mechanism for mental health education of college students in campus culture creation from the perspective of deep learning. The study's primary goal is to comprehend college students' mental health training in campus culture creation. The study's objective is to develop experimental outcomes of college students utilizing mental health education courses as an optional or mandatory course. Finally, investigations related to college students' mental health from the current situation in China, the investigation, statistics and analysis related to the college students in China are carried out in this situation. The experimental results of this study show that 62 of the 156 schools and universities assessed provide courses on mental health education for college students that are both obligatory and optional. According to the students questionnaire survey, 86.7% of respondents believe that it is critical to establish mental health related educational courses, 61.9% believe that compulsory courses should be established, and students want to add group guidance or activities to the teaching process to improve their experience and participation.

170-W Nd:YAG InnoSlab laser at 1319†nm.

In this paper, a continuous-wave Nd:YAG InnoSlab laser at 1319 nm with high output power and high beam quality is demonstrated. The maximum output power of 170 W at 1319-nm single wavelength is obtained with an optical-to-optical efficiency of 15.3% from absorbed pump power to laser output and the corresponding slope efficiency of 26.7%. The beam quality factors of M2 are 1.54 and 1.78 in the horizontal and vertical directions, respectively. To the best of our knowledge, this is the first report on Nd:YAG 1319-nm InnoSlab lasers with such high output power and good beam quality.

Linearly polarized fiber amplifier with narrow linewidth of 5†kW exhibiting a record output power and near-diffraction-limited beam quality.

In this work, a narrow-linewidth polarization-maintaining (PM) all-fiber amplifier with near-diffraction-limited beam quality and record output power is presented. First, a 4.45-kW PM fiber amplifier with a 3-dB linewidth of 0.08 nm and root mean square (rms) linewidth of 0.22 nm is achieved based on optimized phase modulation. However, the sideband of the spectrum broadens significantly during the amplification process, which is mainly caused by the additional intensity variation of the injected signal. Meanwhile, an up to 5.04-kW linearly polarized fiber laser with a relatively stable spectral bandwidth is achieved by effectively suppressing spectral broadening. At the maximum output power, the rms linewidth is 0.2 nm, the beam quality factor M2 is less than 1.3, the polarization extinction ratio (PER) is 16.5 dB, and the signal-to-noise ratio (SNR) is approximately 53 dB. The further power scaling of the amplifier is mainly limited by the pump power. To the best of our knowledge, this is the maximum output power of a narrow linewidth linearly polarized fiber amplifier to date.

The orally bioavailable GSPT1/2 degrader SJ6986 exhibits in vivo efficacy in acute lymphoblastic leukemia.

Advancing cure rates for high-risk acute lymphoblastic leukemia (ALL) has been limited by the lack of agents that effectively kill leukemic cells, sparing normal hematopoietic tissue. Molecular glues direct the ubiquitin ligase cellular machinery to target neosubstrates for protein degradation. We developed a novel cereblon modulator, SJ6986, that exhibits potent and selective degradation of GSPT1 and GSPT2 and cytotoxic activity against childhood cancer cell lines. Here, we report in vitro and in vivo testing of the activity of this agent in a panel of ALL cell lines and xenografts. SJ6986 exhibited similar cytotoxicity to the previously described GSPT1 degrader CC-90009 in a panel of leukemia cell lines in vitro, resulting in apoptosis and perturbation of cell cycle progression. SJ6986 was more effective than CC-90009 in suppressing leukemic cell growth in vivo, partly attributable to favorable pharmacokinetic properties, and did not significantly impair differentiation of human CD34+ cells ex vivo. Genome-wide CRISPR/Cas9 screening of ALL cell lines treated with SJ6986 confirmed that components of the CRL4CRBN complex, associated adaptors, regulators, and effectors were integral in mediating the action of SJ6986. SJ6986 is a potent, selective, orally bioavailable GSPT1/2 degrader that shows broad antileukemic activity and has potential for clinical development.