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KMT2A-rearranged (KMT2A-r) infant acute lymphoblastic leukemia (ALL) is a devastating malignancy with a dismal outcome, and younger age at diagnosis is associated with increased risk of relapse. To discover age-specific differences and critical drivers that mediate poor outcome in KMT2A-r ALL, we subjected KMT2A-r leukemias and normal hematopoietic cells from patients of different ages to single-cell multiomics analyses. We uncovered the following critical new insights: leukemia cells from patients

The adoptive transfer of chimeric antigen receptor (CAR) T cells represents a breakthrough in clinical oncology, yet both between- and within-patient differences in autologously derived T cells are a major contributor to therapy failure. To interrogate the molecular determinants of clinical CAR T-cell persistence, we extensively characterized the premanufacture T cells of 71 patients with B-cell malignancies on trial to receive anti-CD19 CAR T-cell therapy. We performed RNA-sequencing analysis on sorted T-cell subsets from all 71 patients, followed by paired Cellular Indexing of Transcriptomes and Epitopes (CITE) sequencing and single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) on T cells from six of these patients. We found that chronic IFN signaling regulated by IRF7 was associated with poor CAR T-cell persistence across T-cell subsets, and that the TCF7 regulon not only associates with the favorable naïve T-cell state, but is maintained in effector T cells among patients with long-term CAR T-cell persistence. These findings provide key insights into the underlying molecular determinants of clinical CAR T-cell function.Significance:To improve clinical outcomes for CAR T-cell therapy, there is a need to understand the molecular determinants of CAR T-cell persistence. These data represent the largest clinically annotated molecular atlas in CAR T-cell therapy to date, and significantly advance our understanding of the mechanisms underlying therapeutic efficacy.This article is highlighted in the In This Issue feature, p. 2113

Supplementary Table S3. Gene sets for the TCF7 regulon and interferon response. For each gene set, three annotations are provided: the Ensembl gene id, the Entrez gene id, and HGNC symbol based on annotation from Ensembl version 94.

Supplementary tables 1-4 and figures 1-11

Supplementary Methods

The adoptive transfer of chimeric antigen receptor (CAR) T cells represents a breakthrough in clinical oncology, yet both between- and within-patient differences in autologously derived T cells are a major contributor to therapy failure. To interrogate the molecular determinants of clinical CAR T-cell persistence, we extensively characterized the premanufacture T cells of 71 patients with B-cell malignancies on trial to receive anti-CD19 CAR T-cell therapy. We performed RNA-sequencing analysis on sorted T-cell subsets from all 71 patients, followed by paired Cellular Indexing of Transcriptomes and Epitopes (CITE) sequencing and single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) on T cells from six of these patients. We found that chronic IFN signaling regulated by IRF7 was associated with poor CAR T-cell persistence across T-cell subsets, and that the TCF7 regulon not only associates with the favorable naïve T-cell state, but is maintained in effector T cells among patients with long-term CAR T-cell persistence. These findings provide key insights into the underlying molecular determinants of clinical CAR T-cell function. Significance: To improve clinical outcomes for CAR T-cell therapy, there is a need to understand the molecular determinants of CAR T-cell persistence. These data represent the largest clinically annotated molecular atlas in CAR T-cell therapy to date, and significantly advance our understanding of the mechanisms underlying therapeutic efficacy. This article is highlighted in the In This Issue feature, p. 2113

The Chinese H{\alpha} Solar Explorer (CHASE), dubbed "Xihe" - Goddess of the Sun, was launched on October 14, 2021 as the first solar space mission of China National Space Administration (CNSA). The CHASE mission is designed to test a newly developed satellite platform and to acquire the spectroscopic observations in the H{\alpha} waveband. The H{\alpha} Imaging Spectrograph (HIS) is the scientific payload of the CHASE satellite. It consists of two observational modes: raster scanning mode and continuum imaging mode. The raster scanning mode obtains full-Sun or region-of-interest spectral images from 6559.7 to 6565.9 {\AA} and from 6567.8 to 6570.6 {\AA} with 0.024 {\AA} pixel spectral resolution and 1 minute temporal resolution. The continuum imaging mode obtains photospheric images in continuum around 6689 {\AA} with the full width at half maximum of 13.4 {\AA}. The CHASE mission will advance our understanding of the dynamics of solar activity in the photosphere and chromosphere. In this paper, we present an overview of the CHASE mission including the scientific objectives, HIS instrument overview, data calibration flow, and first results of on-orbit observations., Comment: 9 pages, 6 figures

Dissolved organic matter (DOM) derived from various composts can promote significant changes of soil properties. However, little is known about the DOM compositions and their similarities and differences at the molecular level. In this study, the molecular compositions of DOM derived from kitchen waste compost (KWC), green waste compost (GWC), manure waste compost (MWC), and sewage sludge compost (SSC) were characterized by electrospray ionization coupled with Fourier transform ion cyclotron resonance mass spectrometry (ESI FT-ICR MS). The molecular formulas were classified into four subcategories: CHO, CHON, CHOS, and CHONS. The KWC, MWC, and SSC DOM represented the highest fraction (35.8%-47.4%) of CHON subcategory, while the GWC DOM represented the highest fraction (68.4%) of CHO subcategory. The GWC DOM was recognized as the nitrogen- and sulfur-deficient compounds that were less saturated, more aromatic, and more oxidized compared with other samples. Further analysis of the oxygen, nitrogen-containing (N-containing), and sulfur-containing (S-containing) functional groups in the four subcategories revealed higher organic molecular complexity. Comparison of the similarities and differences of the four samples revealed 22.8% ubiquitous formulas and 17.4%, 11.1%, 10.7%, and 6.3% unique formulas of GWC, KWC, SSC, and MWC DOM, respectively, suggesting a large proportion of ubiquitous DOM as well as unique, source-specific molecular signatures. The findings presented herein provide new insight into the molecular characterization of DOM derived from various composts and demonstrated the potential role of these different compounds for agricultural utilization.

Crucial transitions in cancer-including tumor initiation, local expansion, metastasis, and therapeutic resistance-involve complex interactions between cells within the dynamic tumor ecosystem. Transformative single-cell genomics technologies and spatial multiplex in situ methods now provide an opportunity to interrogate this complexity at unprecedented resolution. The Human Tumor Atlas Network (HTAN), part of the National Cancer Institute (NCI) Cancer Moonshot Initiative, will establish a clinical, experimental, computational, and organizational framework to generate informative and accessible three-dimensional atlases of cancer transitions for a diverse set of tumor types. This effort complements both ongoing efforts to map healthy organs and previous large-scale cancer genomics approaches focused on bulk sequencing at a single point in time. Generating single-cell, multiparametric, longitudinal atlases and integrating them with clinical outcomes should help identify novel predictive biomarkers and features as well as therapeutically relevant cell types, cell states, and cellular interactions across transitions. The resulting tumor atlases should have a profound impact on our understanding of cancer biology and have the potential to improve cancer detection, prevention, and therapeutic discovery for better precision-medicine treatments of cancer patients and those at risk for cancer.

DNA methylation is an epigenetic mark that has vital importance in both development and disease. Single cell bisulfite sequencing technologies enable profiling of the methylome at high resolution, providing the basis for dissecting the heterogeneity and dynamics of DNA methylation in complex tissues and over time. Despite the rapid increase in the number of experimental protocols for methylome sequencing, analytical tools designed specifically for single-cell data are lacking. We developed a computational tool, SINBAD, for efficient and standardized pre-processing, quality assessment and analysis of single cell methylation data. Starting from multiplexed sequencing reads, major analysis modules of SINBAD include preprocessing, read mapping, methylation quantification, multivariate analysis, and gene signature profiling. SINBAD provides a flexible platform to implement interoperable and robust processing of single-cell methylome data.

Semiconductor photocatalysis is an extremely promising technology to deal with the far-reaching issues we need to face, such as the shortage of renewable-energy resources and the increasingly serious worldwide environmental problems. Ag3PO4 is an excellent visible-light-driven photocatalyst, showing an extraordinary photoactivity for oxygen evolution in water splitting and degradation of pollutant in aqueous solution. However, due to the uncontrollable photocorrosion phenomenon, the Ag3PO4-based photocatalysis is still at laboratory scale. To remove the obstacles for practical application and to further improve its photocatalytic performance, this review summarized the achievements that have been made in this field. We began with an effort to introduce the reasons for Ag3PO4 exhibiting excellent photocatalytic performance. Subsequently, the different synthesis methods of Ag3PO4 were discussed. Finally, we outlined the barriers that hindered the practical application of Ag3PO4 and proposed the ways to remove these barriers. This review also underlined the crucial problems that should be addressed prior to practical applications.

A highly efficient and new ternary TCPP/rGO/Bi2WO6 Z-scheme heterojunction was designed and fabricated via a facile hydrothermal approach and a liquid ultrasonic route in sequence. The crystal structures, morphologies, microstructures, chemical compositions, elemental states, optical and photo-electrochemical properties of the heterojunction were characterized. This Z-scheme TCPP/rGO/Bi2WO6 photocatalyst has significantly enhanced photocatalytic activity for the tetracycline (TC) degradation under the irradiation of visible light (λ > 420 nm) within 60 min, as compared to pure Bi2WO6, rGO/Bi2WO6 and TCPP/Bi2WO6 composites. The effects of the photocatalyst dosages, pollutant concentrations, coexisting ions and illumination conditions on the photodegradation were investigated. According to the trapping experiments and electron spin resonance analyses, the hole (h+) and superoxide radical ( O2−) mainly contribute to the TC decomposition in the TCPP/rGO/Bi2WO6 photocatalytic system. The photodegradation process in the TCPP/rGO/Bi2WO6 ternary composites can be well described by the proposed Z-scheme mechanism. The results indicate that more efficient charge separation, better light absorption, and larger surface area from the developed photocatalyst collectively contribute to the excellent photocatalytic performances. Besides, the photocatalyst has great stability and recyclability with a removal efficiency of 79.27% even after five times of repeated treatment. This work reports a new strategy for the preparation of Z-scheme heterojunction photocatalyst with high photocatalytic activity and provides an alternative for the effective removal of antibiotic wastewater through photocatalysis.

The adoptive transfer of T lymphocytes reprogrammed to target tumour cells has demonstrated potential for treatment of various cancers

Neuroblastoma is a childhood cancer originating from embryonic neuronal progenitor cells and is the most common cancer diagnosed in infants. Although the majority of patients respond to initial chemotherapy, most high-risk patients suffer relapse due to therapy resistance. Here, we generated single-cell transcriptome and bulk whole-genome sequencing data of diagnosis and post-therapy samples from 23 patients diagnosed with high-risk neuroblastoma. We found two distinct adrenergic populations in the patient samples. Most tumor cells showed a mature sympathoblast phenotype whereas a small fraction was in an undifferentiated state with activation of protein translation, unfolded protein, and oxidative phosphorylation pathways. We found that therapy-resistant tumor cells in these two subpopulations had distinct characteristics. The more mature resistant subpopulation upregulated genes associated with epithelial-to-mesenchymal transition, including TWIST1, PLCB1 and CD276. The undifferentiated resistant subpopulation upregulated Ras signal transduction and TP53 pathway genes. Analysis of the immune microenvironment revealed that most tumor-associated macrophages became more immunosuppressive post-therapy via multiple newly gained signaling interactions including the complement signaling pathway. We discovered a limited infiltration of T lymphocytes in the tumor microenvironment, and chemotherapy induced an effector state with upregulated mTOR signaling and metabolism. Overall, our study revealed subpopulations of tumor cells in neuroblastoma that responded differently to induction chemotherapy. Our findings uncovered distinct molecular signatures of the resistant cells and their interactions with the immune microenvironment, paving the way for developing novel therapies for high-risk neuroblastoma. Citation Format: Yasin Uzun, Liron D. Grossmann, Chia-Hui Chen, Anusha Thadi, Chi-Yun Wu, Peng Gao, Dinh Diep, Lea Surrey, Daniel Martinez, Tasleema Patel, Qi Qiu, Sarah Johnson, Wenbao Yu, Shane Drabings, Changya Chen, Yuxuan Hu, Gregory Chen, Derek A. Oldridge, Kun Zhang, Hao Wu, Kathrin Bernt, Nancy Zhang, John M. Maris, Kai Tan. Longitudinal single-cell sequencing of high-risk neuroblastoma tumors reveals intrinsic and extrinsic mechanisms of therapy resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6051.

SummaryInfant ALL is a devastating malignancy caused by rearrangements of the KMT2A gene (KMT2A-r) in approximately 70% of patients. The outcome is dismal and younger age at diagnosis is associated with increased risk of relapse. To discover age-specific differences and critical drivers that mediate the poor outcome in KMT2A-r ALL, we subjected KMT2A-r leukemias and normal hematopoietic cells from patients of different ages to multi-omic single cell analysis using scRNA-Seq, scATAC-Seq and snmC-Seq2. We uncovered the following critical new insights: Leukemia cells from infants younger than 6 months have a greatly increased lineage plasticity and contain a hematopoietic stem and progenitor-like (HSPC-like) population compared to older infants. We identified an immunosuppressive signaling circuit between the HSPC-like blasts and cytotoxic lymphocytes in younger patients. Both observations offer a compelling explanation for the ability of leukemias in young infants to evade chemotherapy and immune mediated control. Our analysis also revealed pre-existing lymphomyeloid primed progenitor and myeloid blasts at initial diagnosis of B-ALL. Tracking of leukemic clones in two patients whose leukemia underwent a lineage switch documented the evolution of such clones into frank AML. These findings provide critical insights into KMT2A-r ALL and have potential clinical implications for targeted inhibitors or multi-target immunotherapy approaches. Beyond infant ALL, our study demonstrates the power of single cell multi-omics to detect tumor intrinsic and extrinsic factors affecting rare but critical subpopulations within a malignant population that ultimately determines patient outcome.

Hematopoietic stem and progenitor cells (HSPCs) in the bone marrow are derived from a small population of hemogenic endothelial (HE) cells located in the major arteries of the mammalian embryo. HE cells undergo an endothelial to hematopoietic cell transition, giving rise to HSPCs that accumulate in intra-arterial clusters (IAC) before colonizing the fetal liver. To examine the cell and molecular transitions between endothelial (E), HE, and IAC cells, and the heterogeneity of HSPCs within IACs, we profiled ∼40 000 cells from the caudal arteries (dorsal aorta, umbilical, vitelline) of 9.5 days post coitus (dpc) to 11.5 dpc mouse embryos by single-cell RNA sequencing and single-cell assay for transposase-accessible chromatin sequencing. We identified a continuous developmental trajectory from E to HE to IAC cells, with identifiable intermediate stages. The intermediate stage most proximal to HE, which we term pre-HE, is characterized by increased accessibility of chromatin enriched for SOX, FOX, GATA, and SMAD motifs. A developmental bottleneck separates pre-HE from HE, with RUNX1 dosage regulating the efficiency of the pre-HE to HE transition. A distal candidate Runx1 enhancer exhibits high chromatin accessibility specifically in pre-HE cells at the bottleneck, but loses accessibility thereafter. Distinct developmental trajectories within IAC cells result in 2 populations of CD45+ HSPCs; an initial wave of lymphomyeloid-biased progenitors, followed by precursors of hematopoietic stem cells (pre-HSCs). This multiomics single-cell atlas significantly expands our understanding of pre-HSC ontogeny.

Joint analysis of genomic and transcriptomic data reveals diverse noncoding mutation landscapes in five types of pediatric cancers., Interpreting the function of noncoding mutations in cancer genomes remains a major challenge. Here, we developed a computational framework to identify putative causal noncoding mutations of all classes by joint analysis of mutation and gene expression data. We identified thousands of SNVs/small indels and structural variants as putative causal mutations in five major pediatric cancers. We experimentally validated the oncogenic role of CHD4 overexpression via enhancer hijacking in B-ALL. We observed a general exclusivity of coding and noncoding mutations affecting the same genes and pathways. We showed that integrated mutation profiles can help define novel patient subtypes with different clinical outcomes. Our study introduces a general strategy to systematically identify and characterize the full spectrum of noncoding mutations in cancers.

Early T-Cell Precursor Acute Lymphoblastic Leukemia (ETP-ALL) is a treatment resistant type of pediatric leukemia whose biology is poorly understood, and new therapies are badly needed. While there are ongoing efforts to profile ETP-ALL using bulk and targeted genomics methods, these technologies fail to capture sub-clonal patterns in ETP-ALL, which may be pertinent to understanding its biology. To synergize with current efforts to use bulk-genomics to characterize ETP-ALL, we performed single cell transcriptomics (scRNA-seq) and single cell chromatin accessibility (scATAC-seq) profiling on 30 ETP-ALL patients: 10 of which had excellent response to induction therapy (Day 29 minimal residual disease (MRD) 20%), and 10 of which responded to initial therapy but relapsed later. As additional comparator groups, we also profiled 10 typical T-ALL patients, and 10 Mixed Phenotype Acute Leukemia (MPAL) patients. We mapped leukemic cells back to a healthy transcriptomic and epigenetic references, which we assembled using scRNA-seq and scATAC-seq of healthy pediatric bone marrow and thymus. We found that leukemic cells from different subtypes of ALL projected to different stages in healthy hematopoietic development. Non-ETP T-ALL patients had the highest proportions of cells projecting to more mature T-cell states, such as ab T cells, and MPAL patients had the highest proportions of cells projecting to myeloid progenitor cells (GMPs). However, the dominant projected population of ETP-ALL and MPAL were both lymphoid (CLP/LMPP) progenitors, supporting a high degree of overlap between these two treatment resistant cancers. Despite clear overall patterns, we found that there was both a large amount of inter-tumoral and intra-tumoral heterogeneity, with leukemic blasts from different patients and different populations within any one patient projecting to different cell states. We then asked if any cell types were enriched in ETP-ALL patients that responded poorly to induction therapy (Day 29 MRD > 20%). We found that non-responders have a higher proportion of LMPP/HSPC (multi-potent) progenitor-like cells and that progenitor-like populations are transcriptomically and epigenetically different between non-responders and responders, with 100+ differentially expressed genes (DEGs) and 50+ differentially accessible chromatin regions. DEGs and enriched chromatin regions are enriched for transcription factor motifs known to regulate hematopoietic differentiation, such as BCL11A/B, MEF2A/B/C (non-responders enriched), TCF7, IRF9 (responders enriched). We established patient derived xenograft (PDX) models for the patients in our dataset (28 of 50 have successfully engrafted thus far) by injection of primary blasts into immunodeficient (NSG) mice. We profiled 12 PDX models using scRNA-seq and found that blasts have a subtle, patient-specific transcriptomic shift upon engraftment, with 25-150 differentially expressed genes between patient and PDX. Interestingly, we found that cells in S/G2M cell cycle phase from PDX and patient are similar, while G1 cells have the largest transcriptomic shift, suggesting that a pool of cycling cells engrafts before settling in a subtly shifted transcriptomic state. Despite these observations, we found that the overall transcriptomic hierarchy is maintained in PDX, with engrafted cells from 5/6 PDX projecting to near-identical stages of arrest along our healthy hematopoietic trajectory, with preserved expression of key differentially expressed genes and transcription factors between non-responders and responders. Our single cell multi-omics analysis reveals a large degree of intra and inter-tumoral transcriptomic and epigenetic heterogeneity in T-ALL, in which non-responding ETP-ALL patients have a higher proportion of blasts arrested in a HSPC/LMPP-like state. On-going mechanistic analyses are being performed using PDX models to assess the role of the progenitor-like cell populations in resistant disease and these analyses will be presented at ASH. *CC and JX, as well as, DTT and KT contributed equally to this work Figure 1 Figure 1. Disclosures No relevant conflicts of interest to declare.

KMT2A-rearranged (KMT2A-r) infant ALL is a devastating malignancy with a dismal outcome, and younger age at diagnosis is associated with increased risk of relapse. To discover age-specific differences and critical drivers that mediate poor outcome in KMT2A-r ALL, we subjected KMT2A-r leukemias and normal hematopoietic cells from patients of different ages to single cell multi-omics analyses. We uncovered the following critical new insights: leukemia cells from patients younger than 6 months have significantly increased lineage plasticity. Steroid response pathways are downregulated in the most immature blasts from younger patients. We identify a hematopoietic stem and progenitor-like (HSPC-like) population in the blood of younger patients that contains leukemic blasts and form an immunosuppressive signaling circuit with cytotoxic lymphocytes. These observations offer a compelling explanation for the ability of leukemias in young patients to evade chemotherapy and immune mediated control. Our analysis also revealed pre-existing lymphomyeloid primed progenitors and myeloid blasts at initial diagnosis of B-ALL. Tracking of leukemic clones in two patients whose leukemia underwent a lineage switch documented the evolution of such clones into frank AML. These findings provide critical insights into KMT2A-r ALL and have clinical implications for molecularly targeted and immunotherapy approaches. Beyond infant ALL, our study demonstrates the power of single cell multi-omics to detect tumor intrinsic and extrinsic factors affecting rare but critical subpopulations within a malignant population that ultimately determines patient outcome. Disclosures Bernt: Merck: Other: Spouse is an employee of Merck.; Syndax: Research Funding.

Infant ALL is a devastating malignancy caused by rearrangements of the KMT2A gene (KMT2A-r) in approximately 70% of patients. The outcome is dismal and younger age at diagnosis is associated with increased risk of relapse. To discover age-specific differences and critical drivers that mediate the poor outcome in KMT2A-r ALL, we subjected KMT2A-r leukemias and normal hematopoietic cells from patients of different ages to multi-omic single cell analysis using scRNA-Seq, scATAC-Seq and snmC-Seq2. We uncovered the following critical new insights: Leukemia cells from infants younger than 6 months have a greatly increased lineage plasticity and contain a hematopoietic stem and progenitor-like (HSPC-like) population compared to older infants. We identified an immunosuppressive signaling circuit between the HSPC-like blasts and cytotoxic lymphocytes in younger patients. Both observations offer a compelling explanation for the ability of leukemias in young infants to evade chemotherapy and immune mediated control. Our analysis also revealed pre-existing lymphomyeloid primed progenitor and myeloid blasts at initial diagnosis of B-ALL. Tracking of leukemic clones in two patients whose leukemia underwent a lineage switch documented the evolution of such clones into frank AML. These findings provide critical insights into KMT2A-r ALL and have potential clinical implications for targeted inhibitors or multitarget immunotherapy approaches. Beyond infant ALL, our study demonstrates the power of single cell multi-omics to detect tumor intrinsic and extrinsic factors affecting rare but critical subpopulations within a malignant population that ultimately determines patient outcome.

The aim of this research work was to determine the molecular compositional changes of dissolved organic matter (DOM) taken from different phases of the hyperthermophilic composting (HTC) process. The DOM samples were extracted by the standard protocol of C18 extraction methodology, and then analyzed by electrospray ionization coupled with Fourier transform ion cyclotron resonance mass spectrometry (ESI FT-ICR MS). The profiles of negative ion mass spectrum and DOM molecular formulas of four compost samples were reported. Data related to the molecular compositional changes of DOM during HTC were also presented. Further interpretation and discussion on these datasets can be found in the related article entitled “Molecular insights into the transformation of dissolved organic matter during hyperthermophilic composting using ESI FT-ICR MS” [1]. Keywords: FT-ICR MS, HTC, DOM transformation, Molecular compound, Molecular formula

Hematopoietic stem cell (HSC) ontogeny is accompanied by dynamic changes in gene regulatory networks. We performed RNA-Seq and histone mark ChIP-Seq to define the transcriptomes and epigenomes of cells representing key developmental stages of HSC ontogeny in the mouse. The five populations analyzed were embryonic day 10.5 (E10.5) endothelium and hemogenic endothelium from the major arteries (dorsal aorta, umbilical and vitelline), an enriched population of pre-hematopoietic stem cells (pre-HSCs), fetal liver HSCs, and adult bone marrow HSCs. We observed dynamic and combinatorial epigenetic changes that mark regulatory DNA sequences including gene promoters and enhancers. Using epigenetic signatures, we identified enhancers for each developmental stage. Only 12% of enhancers are primed, and 78% are active, suggesting the vast majority of enhancers are establishedde novoat the developmental stages where they are required to control their target genes, without prior priming in earlier stages. We constructed developmental-stage-specific transcriptional regulatory networks during HSC ontogeny by linking enhancers and predicted bound transcription factors to their target promoters using a novel computational algorithm. Our computational analyses predicted known transcriptional regulators for the endothelial-to-hematopoietic transition, validating our overall approach, and identified putative novel transcription factors whose regulon activities correlate with the emergence of pre-HSCs. We validated roles for the broadly expressed transcription factors SP3 and MAZ in arterial hemogenic endothelium. Our data and computational analyses provide a useful resource for uncovering regulators of HSC formation.

Ratiometric electrochemiluminescence (ECL) has attracted great attention in the field of electrochemical analysis. In this study, a dual-signal-output ratiometric ECL sensor was developed for the detection of nicotinamide adenine dinucleotide (NADH). Nitrogen-doped graphene quantum dots (NGQDs) exhibit double ECL signal output capability, without the requirement of additional coreactants. NADH can amplify the anodic ECL response of NGQDs, while it can diminish the cathodic ECL response of NGQDs. Based on the principle between relative enhancing ECL intensity ratio and NADH concentrations, the constructed ratiometric ECL sensor was applied to NADH assays, with a wide concentration range of 10–400 μM and a low limit of detection (LOD) of 2.5 μM (S/N = 3). Furthermore, the proposed method was applied for the determination of spiked NADH, which was proved to be feasible in the biological sample matrix. The proposed strategy of modulating multiple-ECL signals of the single NGQD emitter not only provides a new ECL system for the accurate detection of NADH but also broadens the design pathway for ratiometric sensing fabrication.

Fast, robust and technology-independent computational methods are needed for supervised cell type annotation of single-cell RNA sequencing data. We present SciBet, a Bayesian classifier that accurately predicts cell identity for newly sequenced cells or cell clusters. We enable web client deployment of SciBet for rapid local computation without uploading local data to the server. This user-friendly and cross-platform tool can be widely useful for single cell type identification.

Biodegradable plastics attract public attention as promising substitute for non-degradable plastics that trigger serious plastic pollution, and they are claimed to be environmentally harmless and biodegradable by microorganisms. However, not all biodegradable plastics are completely degradable under natural conditions. Some of them may be disintegrated into microplastics more rapidly than conventional plastics, emerging as another threat to soil environments. As a part of microplastics, biodegradable microplastics may pose stronger negative effects on several soil species than oil-based microplastics under some conditions. Currently, there is a fiercely increasing trend to replace nondegradable plastic commodities with biodegradable ones. Therefore, to discuss the ecological safety of biodegradable plastics is essential before promoting wide application of them during commercial use. This review provided a brief introduction on biodegradable plastics and summarized their deterioration behaviors in terrestrial environments, together with evidences on releases of additives and biodegradable microplastics. Then, potential adverse effects of biodegradable microplastics in soil ecosystems, including responses on soil properties, microbial communities, and several soil species were discussed, suggesting biodegradable microplastics as a potential threat to ecological safety of soil ecosystems. By this token, biodegradable plastics might not be a panacea to the existing “white pollution” and need further exploring.

Differentiation of effector and memory CD8+ T cells is accompanied by extensive changes in the transcriptome and histone modifications at gene promoters; however, the enhancer repertoire and associated gene regulatory networks are poorly defined. Using histone mark chromatin immunoprecipitation coupled with deep sequencing, we mapped the enhancer and super-enhancer landscapes in antigen-specific naive, differentiated effector, and central memory CD8+ T cells during LCMV infection. Epigenomics-based annotation revealed a highly dynamic repertoire of enhancers, which were inherited, de novo activated, decommissioned and re-activated during CD8+ T cell responses. We employed a computational algorithm to pair enhancers with target gene promoters. On average, each enhancer targeted three promoters and each promoter was regulated by two enhancers. By identifying enriched transcription factor motifs in enhancers, we defined transcriptional regulatory circuitry at each CD8+ T cell response stage. These multi-dimensional datasets provide a blueprint for delineating molecular mechanisms underlying functional differentiation of CD8+ T cells.

Chimeric Antigen Receptor (CAR) T-cell therapy has been a major success for B-cell Acute Lymphoblastic Leukemia (B-ALL), yet recent clinical trials suggest that approximately 20% of patients do not respond to therapy and 40% of initial responders relapse within a year. We hypothesize that intrinsic T-cell factors are a major contributor to early therapeutic failure to CAR T-cell therapy. In particular, since most protocols do not select for T-cell subtypes, the heterogeneity in T-cell composition likely plays a major role in CAR T-cell engineering and confounds functional and clinical correlative studies. In order to characterize the molecular phenotypes of T-cells underlying therapeutic response, we performed subtype-specific transcriptomic profiling of clinical T-cell populations in 71 patients treated with CAR T-cell therapy at the Children's Hospital of Philadelphia. We obtained clinical T-cells via clinical leukapheresis prior to CAR T-cell engineering, used FACS to separate T-cells into five subtypes per patient (Naive, Stem Cell Memory, Central Memory, Effector Memory, and Effector), and performed RNA-Sequencing on all 355 samples. To our knowledge, this is the largest and most comprehensive transcriptomic profiling of clinical T-cells in CAR T-cell therapy to date. We found that a higher proportion of CCR7+CD62L+ naive and early memory T-cell phenotypes associates with longer clinical T-cell persistence (HR: 3.25 [1.37-7.89], P = 0.006), and that combining proportions of these populations with CCR7-CD62L-CD45RO+CD95+ effector memory T-cells has the greatest prognostic value (HR: 4.82 [1.89-12.32], P < 0.001). Apoptotic signaling pathways were enriched in effector and effector memory T-cell lineages (FDR < 0.001), suggesting that programmed cell death limits the contribution of these phenotypes to long-term CAR T-cell persistence. Maintenance of naive and early memory T-cell phenotypes associates positively with expression of transcription factors TCF7 and LEF1 (FDR < 0.001) and negatively with TBX21, EOMES, and ZEB2 (FDR < 0.001). Within T-cell subtypes, mixed-effects regression and integrative network analysis identified genes and network modules that discriminate between clinical responders and non-responders. We found that higher expression of CRTAM and SLAMF6 in naive and stem cell memory T-cells associates positively with clinical CAR T-cell persistence (FDR = 0.0088-0.019), suggesting that these lineage-determining factors direct T-cell fates toward effective CAR T-cell lineages. Finally, we identify an enrichment of type I interferon response pathways among patients with poor CAR T-cell persistence (F-test P < 0.001), suggesting a role of the chronic interferon response network in T-cell dysfunction. Together, these data shed light on the critical role of pre-infusion T-cell populations in CAR T-cell therapy, and may inform clinical prognosis and the development of improved CAR T-cell therapies. Citation Format: Gregory M. Chen, Changya Chen, Rajat K. Das, Yang-Yang Ding, Bing He, Hannah Kim, David M. Barrett, Kai Tan. A subtype-specific T-cell transcriptomic atlas reveals determinants of T-cell dysfunction in CAR T-cell therapy resistance [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4236.

Chimeric antigen receptor (CAR) T-cell therapy has been a major breakthrough in B-cell acute lymphoblastic leukemia (B-ALL), yet therapeutic resistance remains an important clinical challenge. Given that approximately 20% of patients do not respond to therapy and 40% of initial responders relapse within a year, there is a pressing need to understand the basis of therapy resistance in order to identify prognostic biomarkers and improve the therapeutic modality. We hypothesize that intrinsic T-cell factors are a major contributor to early therapeutic failure to CAR T-cell therapy. Most protocols do not select for specific T-cell subtypes, leading to the use of heterogeneous T-cell populations for CAR T-cell engineering. In order to characterize the molecular phenotypes of T cells underlying therapeutic response, we performed subtype-specific transcriptomic profiling of clinical T-cell populations in patients subsequently treated with anti-CD19 CAR T-cell therapy. We identified 71 patients with B-ALL treated with CAR T-cell therapy at the Children’s Hospital of Philadelphia, and obtained T cells via clinical leukapheresis prior to CAR T-cell engineering. We used FACS to separate T cells into five subtypes per patient (Naive, Stem Cell Memory, Central Memory, Effector Memory, and Effector), and performed bulk RNA-sequencing on all 355 samples. To our knowledge, this is the largest and most comprehensive transcriptomic profiling of clinical T cells in CAR T-cell therapy to date. We find that a higher proportion of CCR7+CD62L+ naive and early memory T-cell phenotypes associates with longer clinical T-cell persistence (HR=3.25 [1.37-7.89], p=0.006), and that combining proportions of these populations with CCR7−CD62L−CD45RO+CD95+ effector memory T cells has the greatest prognostic value (HR: 4.82 [1.89-12.32]; p This abstract is also being presented as Poster A65. Citation Format: Gregory M. Chen, Changya Chen, Rajat K. Das, Yang-Yang Ding, Bing He, Hannah Kim, David M. Barrett, Kai Tan. Development of a transcriptomic T-cell atlas highlights the differential role of T-cell subpopulations in CAR T-cell therapy resistance [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2019 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2020;8(3 Suppl):Abstract nr PR3.

A highly efficient and new ternary TCPP/rGO/Bi

The transcription factor RUNX1 is required in the embryo for formation of the adult hematopoietic system. Here we describe the seminal findings that led to the discovery of RUNX1 and of its critical role in blood cell formation in the embryo from hemogenic endothelium. We also present RNA-Seq data demonstrating that hemogenic endothelial cells in different anatomic sites, which produce hematopoietic progenitors with dissimilar differentiation potentials, are molecularly distinct. Hemogenic and non-hemogenic endothelial cells in the yolk sac are more closely related to each other than either are to hemogenic or non-hemogenic endothelial cells in the major arteries. Thus, a major driver of the different lineage potentials of the committed erythro-myeloid progenitors that emerge in the yolk sac, versus hematopoietic stem cells that originate in the major arteries, is likely to be the distinct molecular properties of the hemogenic endothelial cells from which they are derived. We use bioinformatics analyses to predict signaling pathways active in arterial hemogenic endothelium, which include the functionally validated pathways Notch, Wnt, and Hedgehog. We also use a novel bioinformatics approach to assemble transcriptional regulatory networks and predict transcription factors that may be specifically involved in hematopoietic cell formation from arterial hemogenic endothelium, which is the origin of the adult hematopoietic system.

The aim of this work was to investigate the effect of different surfactants on the removal efficiency of heavy metals in sewage sludge treated by a method combining bio-acidification with Fenton oxidation. Four surfactants were adopted such as anionic surfactant (sodium dodecyl benzene sulfonate, SDBS), nonionic surfactants (tween-20 and tween-60) and cationic surfactant (hexadecyl trimethyl ammonium chloride, HTAC), respectively. The indigenous sulfur-oxidizing bacteria in bio-acidification phase were enriched and cultured from fresh activated sludge obtained from a wastewater treatment plant. It is shown that different surfactants exhibited distinct effect on the removal efficiency of heavy metals from sewage sludge. The nonionic surfactants, especially tween-60, promotes the solubilization of heavy metals, while the anionic and cationic surfactants hinder the removal of heavy metals. Copper is efficiently leached. The removal efficiency of cadium is relatively lower than that of Cu due to the demand for rigorous pH value. Lead is leached with a low efficiency as the formation of low soluble PbSO4 precipitates.

Hematopoietic stem and progenitor cells (HSPCs) in the bone marrow are derived from a small population of hemogenic endothelial (HE) cells located in the yolk sac and major caudal arteries of the mammalian embryo. HE cells undergo an endothelial to hematopoietic cell transition, giving rise to HSPCs that accumulate in intra-arterial clusters before colonizing the fetal liver. To examine the molecular transitions between endothelial cells, HE, and intra-arterial cluster cells, and the heterogeneity of HSPCs within the intra-arterial clusters, we profiled ~40,000 cells from the caudal arteries (dorsal aorta, umbilical, vitelline) of embryonic day 9.5 to 11.5 mouse embryos by single-cell RNA sequencing (scRNA-seq) and single-cell chromatin accessibility sequencing (scATAC-Seq). A continuous developmental trajectory leads from endothelial cells to intra-arterial cluster cells, with identifiable intermediate stages between endothelial cells and HE. The intermediate endothelial stages most proximal to HE are characterized by elevated expression of genes regulated by GATA and SOX transcription factors. Developmental bottlenecks separate endothelial cells from HE cells, with the efficiency of transit through one of the last bottleneck regulated by RUNX1 dosage. Distinct developmental trajectories within intra-arterial cluster cells result in two populations of CD45+HSPCs; an initial wave of multi-lineage committed progenitors followed by precursors of hematopoietic stem cells (pre-HSCs). These and other insights gained from single cell analyses of HSPC formation from arterial endothelium will be presented. Disclosures No relevant conflicts of interest to declare.

Water Cycle Observation Mission (WCOM) is a mission dedicated to synergetic observations of global water cycle parameters, with emphasis on soil moisture, ocean surface salinity, snow water equivalent and frozen/thaw. WCOM implements its observation requirements by measurement of microwave emission/scattering of both the frequencies sensitive to the key parameters and also the auxiliary frequencies providing necessary atmospheric and surface roughness corrections. In order to satisfy this measurement requirements, WCOM is equipped with payloads with combination of active and passive microwave sounding capabilities of frequency from L-band to W-band. In addition to the multiple frequency requirement, the requirement for spatial resolutions and swath width leads to large aperture antennas and scanning of antenna beams, the accommodation of the three payloads becomes the major challenge for the design of the WCOM satellite. In order to satisfy the temporal resolution requirement, the design of data downlink and ground segment are also discussed. In this presentation, a preliminary design for WCOM satellite is provided, some technical issues need further investigation are also discussed.

Differentiation of effector and memory CD8+ T cells is accompanied by extensive changes in the transcriptome and histone modifications at gene promoters; however, the enhancer repertoire and associated gene regulatory networks are poorly defined. Using histone mark chromatin immunoprecipitation coupled with deep sequencing, we mapped the enhancer and super-enhancer landscapes in antigen-specific naïve, differentiated effector, and central memory CD8+ T cells during LCMV infection. Epigenomics-based annotation revealed a highly dynamic repertoire of enhancers, which were inherited, de novo activated, decommissioned and re-activated during CD8+ T cell responses. We employed a computational algorithm to pair enhancers with target gene promoters. On average, each enhancer targeted three promoters and each promoter was regulated by two enhancers. By identifying enriched transcription factor motifs in enhancers, we defined transcriptional regulatory circuitries at each CD8+ T-cell response stage. These multi-dimensional datasets provide a blueprint for delineating molecular mechanisms underlying functional differentiation of CD8+ T cells.

SUMMARY Fetal hematopoietic stem cells (HSCs) undergo a developmental switch to become adult HSCs with distinct functional properties. To better understand the molecular mechanisms underlying the developmental switch, we have conducted deep sequencing of the 3D genome, epigenome, and transcriptome of fetal and adult HSCs in mouse. We find that chromosomal compartments and topologically associating domains (TADs) are largely conserved between fetal and adult HSCs. However, there is a global trend of increased compartmentalization and TAD boundary strength in adult HSCs. In contrast, intra-TAD chromatin interactions are much more dynamic and wide-spread, involving over a thousand gene promoters and distal enhancers. These developmental-stage-specific enhancer-promoter interactions are mediated by different sets of transcription factors, such as TCF3 and MAFB in fetal HSCs, versus NR4A1 and GATA3 in adult HSCs. Loss-of-function studies of TCF3 confirm the role of TCF3 in mediating condition-specific enhancer-promoter interactions and gene regulation in fetal HSCs., In Brief A developmental transition occurs between fetal and adult hematopoietic stem cells. How the 3D genome folding contributes to this transition is poorly understood. Chen et al. show global genome organization is largely conserved, but a large fraction of enhancer-promoter interactions is reorganized and regulate genes contributing to the phenotypic differences., Graphical Abstract