Comparative transcriptome profiles of Schistosoma japonicum larval stages: Implications for parasite biology and host invasion

Schistosoma japonicum is prevalent in Asia with a wide mammalian host range, which leads to highly harmful zoonotic parasitic diseases. Most previous transcriptomic studies have been performed on this parasite, but mainly focus on stages inside the mammalian host. Moreover, few larval transcriptomic data are available in public databases. Here we mapped the detailed transcriptome profiles of four S. japonicum larval stages including eggs, miracidia, sporocysts and cercariae, providing a comprehensive development picture outside of the mammalian host. By analyzing the stage-specific/enriched genes, we identified functional genes associated with the biological characteristic at each stage: e.g. we observed enrichment of genes necessary for DNA replication only in sporocysts, while those involved in proteolysis were upregulated in sporocysts and/or cercariae. This data indicated that miracidia might use leishmanolysin and neprilysin to penetrate the snail, while elastase (SjCE2b) and leishmanolysin might contribute to the cercariae invasion. The expression profile of stem cell markers revealed potential germinal cell conversion during larval development. Additionally, our analysis indicated that tandem duplications had driven the expansion of the papain family in S. japonicum. Notably, all the duplicated cathepsin B-like proteases were highly expressed in cercariae. Utilizing our 3rd version of S. japonicum genome, we further characterized the alternative splicing profiles throughout these four stages. Taken together, the present study provides compressive gene expression profiles of S. japonicum larval stages and identifies a set of genes that might be involved in intermediate and definitive host invasion.

Improving prediction of core transcription factors for cell reprogramming and transdifferentiation

Identification of transcription factors (TFs) that could induce and direct cell conversion remains a challenge. Though several hundreds of TFs are usually transcribed in each cell type, the identity of a cell is controlled and can be achieved through the ectopic overexpression of only a small subset of so-called core TFs. Currently, the experimental identification of the core TFs for a broad spectrum of cell types remains challenging. Computational solutions to this problem would provide a better understanding of the mechanisms controlling cell identity during natural embryonic or malignant development, as well as give a foundation for cell-based therapy. Herein, we propose a computational approach based on over-enrichment of transcription factors binding sites (TFBS) in differentially accessible chromatin regions that could identify the potential core TFs for a variety of primary human cells involved in hematopoiesis. Our approach enables the integration of both transcriptomic (single-cell RNA sequencing, scRNA-seq) and epigenenomic (single-cell assay for transposable-accessible chromatin, scATAC-seq) data at the single-cell resolution to search for core TFs, and can be scalable to predict subsets of core TFs and their role in a given conversion between cells.

M-CSF-stimulated myeloid cells can convert into epithelial cells to participate in re-epithelialization and hair follicle regeneration during skin wound healing

Skin wound healing is a complex process which requires the interaction of many cell types and mediators in a highly sophisticated temporal sequence. Myeloid cells compose a significant proportion of the inflammatory cells recruited to a wound site and play important roles in clearance of damaged tissue and microorganisms. Myeloid cells have also been suggested to convert into fibro-blast-like cells and endothelial cells in participation of wound healing process. However, whether myeloid cells in wound skin can convert into epithelial cells and contribute to re-epithelialization and skin appendage regeneration is still unclear. In this study, we performed double immunofluorescent staining with antibodies for hematopoietic cells and keratinocytes as well as cell tracing technique to investigate hematopoietic cell conversion. The result show that during the healing process, some of the CD45-positive hematopoietic cells are overlapped with keratin 14, the markers of keratinocytes. Further, CD11b-positive myeloid cells seem the origin of converted epithelial cells. To confirm these results, we culture CD11b-posiitve myeloid cells from mouse splenocytes in a medium containing macrophage colony-stimulating factor (M-CSF) and dermal injection of these cells into the healthy skin when punch biopsy is created in mouse skin. Tracing injected labeled splenocyte-derived myeloid cells in skin, we confirm that myeloid cells able to convert into keratinocytes in repaired skin. Furthermore, our results from in vivo experiments provide new information on contribution of myeloid cells in hair follicle regeneration. In conclusion, this work highlights the myeloid cell contributions in wound repair and hair follicle regeneration in mice through conversion of M-CSF-stimulated CD11b+ myeloid cells into epithelial cells.

Production of d-Tagatose by Whole-Cell Conversion of Recombinant Bacillus subtilis in the Absence of Antibiotics

d-tagatose is a popular functional monosaccharide produced from lactose by β-galactosidase and arabinose isomerase. In this study, two d-alanine-deficient heterologous gene expression systems were constructed, B. subtilis 168 D1 and B. subtilis 168 D2, using overlapping extension PCR and the CRE/loxP system. The lacZ gene for β-galactosidase was integrated into a specific locus of the chassis B. subtilis 168 D2. A mutually complementary plasmid pMA5 with the alanine racemase gene alrA attached to it was constructed and used to assemble recombinant plasmids overexpressing β-galactosidase and arabinose isomerase. Afterward, an integrated recombinant was constructed by the plasmid expressing the arabinose isomerase gene araA of E. coli transform-competent B. subtilis 168 D2 cells. The co-expressing plasmids were introduced into alanine racemase knockout B. subtilis 168 D1. Whole-cell bioconversion was performed using the integrated recombinant with a maximum yield of 96.8 g/L d-tagatose from 500 g/L lactose, and the highest molar conversions were 57.2%. B. subtilis 168 D1/pMA5-alrA-araA-lacZ is capable of single-cell one-step production of d-tagatose. This study provides a new approach to the production of functional sugars.

Chemical induction of gut β-like-cells by combined FoxO1/Notch inhibition as a glucose-lowering treatment for diabetes

Lifelong insulin replacement remains the mainstay of type 1 diabetes treatment. Genetic FoxO1 ablation promotes enteroendocrine cell (EECs) conversion into glucose-responsive β-like cells. Here, we tested whether chemical FoxO1 inhibitors can generate β-like gut cells. Pan-intestinal epithelial FoxO1 ablation expanded the EEC pool, induced β-like cells, and improved glucose tolerance in Ins2Akita/+ mice. This genetic effect was phenocopied by small molecule FoxO1 inhibitor, Cpd10. Cpd10 induced β-like cells that released insulin in response to glucose in mouse gut organoids, and this effect was strengthened by the Notch inhibitor, DBZ. In Ins2Akita/+ mice, a five-day course of either Cpd10 or DBZ induced insulin-immunoreactive β-like cells in the gut, lowered glycemia, and increased plasma insulin levels without apparent adverse effects. These results provide proof of principle of gut cell conversion into β-like cells by a small molecule FoxO1 inhibitor, paving the way for clinical applications.

Acetone Ingestion Mimics a Fasting State to Improve Glucose Tolerance in a Mouse Model of Gestational Hyperglycemia

Gestational diabetes mellitus results, in part, from a sub-optimal β-cell mass (BCM) during pregnancy. Artemisinins were reported to increase BCM in models of diabetes by α- to β-cell conversion leading to enhanced glucose tolerance. We used a mouse model of gestational glucose intolerance to compare the effects of an artemisinin (artesunate) on glycemia of pregnant mice with vehicle treatment (acetone) or no treatment. Animals were treated daily from gestational days (GD) 0.5 to 6.5. An intraperitoneal glucose tolerance test was performed prior to euthanasia at GD18.5 or post-partum. Glucose tolerance was significantly improved in both pregnant and non-pregnant mice with both artesunate and vehicle-alone treatment, suggesting the outcome was primarily due to the acetone vehicle. In non-pregnant, acetone-treated animals, improved glucose tolerance was associated with a higher BCM and a significant increase in bihormonal insulin and glucagon-containing pancreatic islet cells, suggesting α- to β-cell conversion. BCM did not differ with treatment during pregnancy or post-partum. However, placental weight was higher in acetone-treated animals and was associated with an upregulation of apelinergic genes. Acetone-treated animals had reduced weight gain during treatment despite comparable food consumption to non-treated mice, suggesting transient effects on nutrient uptake. The mean duodenal and ileum villus height was reduced following exposure to acetone. We conclude that acetone treatment may mimic transient fasting, resulting in a subsequent improvement in glucose tolerance during pregnancy.

Central Memory T-Cell Differentiation Correlates with Depth of Response in Relapsed/Refractory Multiple Myeloma Patients Receiving Elotuzumab in Combination with Carfilzomib, Lenalidomide and Dexamethasone (Elo-KRd)

Introduction: The addition of elotuzumab (Elo), an anti SLAMF7 immunostimulatory antibody, to carfilzomib, lenalidomide and dexamethasone (KRd) can lead to synergistic anti-myeloma immune effects. Pre-clinical data showed that both Elo and KRd promote innate NK cell response and adaptive cytotoxic T cell response. Here we report longitudinal NK and T cell profiling data in relation to clinical response and MRD status in the context of an Elo-KRd Phase II study (NCT03361306). Methods: Patients with relapsed refractory multiple myeloma (RRMM) after first-line therapy who enrolled in this phase II study received treatment with 4 cycles of Elo-KRd induction followed by Elo-Rd maintenance. Peripheral blood (PB) specimens were collected pre-induction (n=15), after induction (n=14), and every other month during maintenance (n=10). Bone marrow (BM) aspirates were collected pre- and post-induction and at the time of CR confirmation. Minimal residual disease (MRD) was assessed by next-generation flow cytometry (MRD NGF, 10 -5 sensitivity) post-induction for patients achieving very good partial response or better (≥VGPR). PB and BM NK, CD4 and CD8 T cell subset distribution, activation and anergy status were assessed by flow cytometry. Longitudinal Elo-KRd immune modulatory effect was modelled by polynomial regression analyses. Wilcoxon signed rank tests were used for timepoints comparisons. Mann-Whitney U tests were used for response groups comparisons between. Population frequency data, among mononuclear cells, are presented as mean±SD unless otherwise noted. Results: We first investigated Elo-KRd immune modulatory activity during induction treatment. Immature / mature NK cell distribution in PB remained unaltered pre- and post-induction (iNK: 8.9±6.4 vs 8.6±3.5, p=0.808; mNK: 14.9±6.8 vs 13.1±6.1, p=0.463). No significant change in PB NK activation markers KIR2DS4, KIR3DL1, NKG2A, NKG2D or NKp46 was observed throughout Elo-KRd induction. A lack of NK cell maturation was also observed in the BM despite a rise of iNK NKG2D expression (iNK NKG2D+: 22.5±7.7 vs 30.1±8.8, p=0.0.039). The number of both PB effector T helper (CD4+ Th) and cytotoxic T cell (CD8+ CTL) significantly decreased post-induction (PB ThEff: 28.5±16.4 vs 14.4±10.6, p<0.001; PB CTLEff: 58.6±19.7 vs 39.0±13.9, p=0.005), whereas CTL central memory cell counts increased (PB CTLCM 11.7±11.2 vs, 15.9±11.4 p=0.058). A similar effector to central memory T cell conversion was observed in BM and was more pronounced among CTL (BM CTLEff/CM ratio: 21.6±54.8 vs 2.1±1.6, p= 0.002). Overall response rate on study was 80%, with 53.5% (8/15) achieving ≥VGPR. MRD negativity rate (at 10-5 sensitivity) post-induction was 20% (3/15). The subset of patients who achieved ≥VGPR had higher rates of Th and CTL CM cell differentiation at baseline [≥VGPR vs <VGPR; PB ThEff/CM ratio: median 1.0 (range 0.1 - 1.5) vs 3.1 (0.8 - 212.1); p=0.018; PB CTLEff/CM ratio: median 4.1 (range 0.7 - 16.3) vs 13.2 (4.3 - 10607.1); p=0.056]. Among the MRD negative group, one patient remained in sustained CR at 38 months follow up and retained a high Th/CTL CM conversion rate throughout. At the time of relapse, PB (n=6) and BM (n=2) specimens were collected. While no significant alterations in PB NK cell maturation or activation were observed, circulating CTL Eff / CM distribution reverted to baseline levels (baseline vs relapse; PB CTLEff/CM ratio: 743.6±2755.1 vs 282.7±672.0; p=0.156). BM CTL cell effector / central memory distribution also tends to return to pre-induction levels. Conclusions: Unlike preclinical data where Elo has shown to enhance NK cell activity, longitudinal immune profiling analysis in patients with RRMM treated with Elo-KRd revealed limited activation of NK cell and no effect on NK cell maturation. Instead, we noted several changes within T cell compartment, notably activation and subsequent loss of Th and CTL effector cells, along with gain of central memory phenotype. This observation was most apparent for patients achieving ≥VGPR who exhibited significant higher rate of Effector to CM T cell conversion. On relapse, CM CTL cell frequency in both PB and BM compartments decreased to baseline level. Taken together, our results suggest that higher CM conversion rate, typically associated with sustained antigen stimulation, was associated with response to study treatment. Disclosures Foureau: Cytognos: Honoraria; TeneoBio, Celgene: Research Funding. Bhutani: Amgen, BMS, Takeda: Speakers Bureau; Sanofi: Consultancy; Janssen, MedImmune, Takeda, Celgene, BMS, Cerecor, Celularity: Research Funding. Atrash: GSK: Research Funding; AMGEN: Research Funding; Jansen: Research Funding, Speakers Bureau. Paul: Regeneron: Membership on an entity's Board of Directors or advisory committees; AbbVie: Membership on an entity's Board of Directors or advisory committees; Genentech: Membership on an entity's Board of Directors or advisory committees; Janssen Pharmaceuticals Inc: Membership on an entity's Board of Directors or advisory committees; Amgen Inc.: Speakers Bureau; Bristol Myers Squibb: Divested equity in a private or publicly-traded company in the past 24 months. Symanowski: Eli Lilly: Consultancy, Other: DSMB Member; Immatics: Consultancy, Other: DSMB Member; Carsgen: Consultancy. Voorhees: Bristol-Myers Squibb Company.: Other: Data Safety & Monitoring; AbbVie Inc, Bristol-Myers Squibb Company; Consulting Agreement: GlaxoSmithKline, Novartis, Oncopeptides: Other: Advisory Committee. Usmani: EdoPharma: Consultancy; Janssen: Consultancy, Research Funding, Speakers Bureau; Amgen: Consultancy, Research Funding, Speakers Bureau; Array BioPharma: Consultancy, Research Funding; Abbvie: Consultancy; GSK: Consultancy, Research Funding; Celgene/BMS: Consultancy, Research Funding, Speakers Bureau; Sanofi: Consultancy, Research Funding, Speakers Bureau; Seattle Genetics: Consultancy, Research Funding; Pharmacyclics: Consultancy, Research Funding; Merck: Consultancy, Research Funding; Janssen Oncology: Consultancy, Research Funding; Takeda: Consultancy, Research Funding, Speakers Bureau; SkylineDX: Consultancy, Research Funding; Bristol-Myers Squibb: Research Funding.

Taiji-reprogram: a framework to uncover cell-type specific regulators and predict cellular reprogramming cocktails

Cellular reprogramming is a promising technology to develop disease models and cell-based therapies. Identification of the key regulators defining the cell type specificity is pivotal to devising reprogramming cocktails for successful cell conversion but remains a great challenge. Here, we present a systems biology approach called Taiji-reprogram to efficiently uncover transcription factor (TF) combinations for conversion between 154 diverse cell types or tissues. This method integrates the transcriptomic and epigenomic data to construct cell-type specific genetic networks and assess the global importance of TFs in the network. Comparative analysis across cell types revealed TFs that are specifically important in a particular cell type and often tightly associated with cell-type specific functions. A systematic search of TFs with differential importance in the source and target cell types uncovered TF combinations for desired cell conversion. We have shown that Taiji-reprogram outperformed the existing methods to better recover the TFs in the experimentally validated reprogramming cocktails. This work not only provides a comprehensive catalog of TFs defining cell specialization but also suggests TF combinations for direct cell conversion.

Engineering gallium phosphide nanostructures for efficient nonlinear photonics and enhanced spectroscopies

Optical resonances arising from quasi-bound states in the continuum (QBICs) have been recently identified in nanostructured dielectrics, showing ultrahigh quality factors accompanied by very large electromagnetic field enhancements. In this work, we design a periodic array of gallium phosphide (GaP) elliptical cylinders supporting, concurrently, three spectrally separated QBIC resonances with in-plane magnetic dipole, out-of-plane magnetic dipole, and electric quadrupole characters. We numerically explore this system for second-harmonic generation and degenerate four-wave mixing, demonstrating giant per unit cell conversion efficiencies of up to ∼ 2 W−1 and ∼ 60 W−2, respectively, when considering realistic introduced asymmetries in the metasurface, compatible with current fabrication limitations. We find that this configuration outperforms by up to more than four orders of magnitude the response of low-Q Mie or anapole resonances in individual GaP nanoantennas with engineered nonlinear mode-matching conditions. Benefiting from the straight-oriented electric field of one of the examined high-Q resonances, we further propose a novel nanocavity design for enhanced spectroscopies by slotting the meta-atoms of the periodic array. We discover that the optical cavity sustains high-intensity fields homogeneously distributed inside the slot, delivering its best performance when the elliptical cylinders are cut from end to end forming a gap, which represents a convenient model for experimental investigations. When placing an electric point dipole inside the added aperture, we find that the metasurface offers ultrahigh radiative enhancements, exceeding the previously reported slotted dielectric nanodisk at the anapole excitation by more than two orders of magnitude.

Increased NKX6.1 expression and decreased ARX expression in alpha cells accompany reduced beta-cell volume in human subjects

Pancreatic islet cells have plasticity, such as the abilities to dedifferentiate and transdifferentiate. Islet cell conversion to other characteristic cell is largely determined by transcription factors, but significance of expression patterns of these transcription factors in human islet cells remained unclear. Here, we present the NKX6.1-positive ratio of glucagon-positive cells (NKX6.1+/GCG+ ratio) and the ARX-negative ratio of glucagon-positive cells (ARX−/GCG+ ratio) in 34 patients who were not administered antidiabetic agents. Both of NKX6.1+/GCG+ ratio and ARX−/GCG+ ratio negatively associated with relative beta cell area. And these ratios did not have significant correlation with other parameters including age, body mass index, hemoglobin A1c, fasting plasma glucose level or relative alpha-cell area. Our data demonstrate that these expression ratios of transcription factors in glucagon-positive cells closely correlate with the reduction of beta-cell volume in human pancreas.