Efficacy and safety of sovleplenib (HMPL-523) in adult patients with chronic primary immune thrombocytopenia in China (ESLIM-01): a randomised, double-blind, placebo-controlled, phase 3 study.

BACKGROUND: Sovleplenib, a novel spleen tyrosine kinase (SYK) inhibitor, showed promising safety and activity in patients with primary immune thrombocytopenia in a phase 1b/2 trial. We aimed to evaluate the efficacy and safety of sovleplenib in patients with chronic primary immune thrombocytopenia. METHODS: This randomised, double-blind, placebo-controlled, phase 3 trial (ESLIM-01) was done in 34 clinical centres in China. Eligible patients, aged 18-75 years, had chronic primary immune thrombocytopenia, an Eastern Cooperative Oncology Group (ECOG) performance status of 0-1, and received one or more previous treatments. Patients were randomly assigned (2:1) to receive oral sovleplenib or placebo, 300 mg once daily, for 24 weeks. Randomisation was stratified by baseline platelet counts, previous splenectomy, and concomitant treatment for anti-immune thrombocytopenia at baseline. The primary endpoint was durable response rate (proportion of patients with a platelet count of ≥50 × 109/L on at least four of six scheduled visits between weeks 14 and 24, not affected by rescue treatment) assessed by intention-to-treat. The trial is registered with ClinicalTrials.gov, NCT05029635, and the extension, open-label phase is ongoing. FINDINGS: Between Sept 29, 2021, and Dec 31, 2022, 188 patients were randomly assigned to receive sovleplenib (n=126) or placebo (n=62). 124 (66%) were female, 64 (34%) were male, and all were of Asian ethnicity. Median previous lines of immune thrombocytopenia therapy were 4·0, and 134 (71%) of 188 patients had received previous thrombopoietin or thrombopoietin receptor agonist. The primary endpoint was met; durable response rate was 48% (61/126) with sovleplenib compared with zero with placebo (difference 48% [95% CI 40-57]; p<0·0001). The median time to response was 8 days with sovleplenib compared with 30 days with placebo. 125 (99%) of 126 patients in the sovleplenib group and 53 (85%) of 62 in the placebo group reported treatment-emergent adverse events (TEAEs), and most events were mild or moderate. Frequent TEAEs of grade 3 or higher for sovleplenib versus placebo were platelet count decreased (7% [9/126] vs 10% [6/62]), neutrophil count decreased (3% [4/126] vs 0% [0/62]), and hypertension (3% [4/126] vs 0% [0/62]). Incidences of serious TEAEs were 21% (26/126) in the sovleplenib group and 18% (11/62) in the placebo group. There were no deaths in the study. INTERPRETATION: Sovleplenib showed a clinically meaningful sustained platelet response in patients with chronic primary immune thrombocytopenia, with a tolerable safety profile and improvement in quality of life. Sovleplenib could be a potential treatment option for patients with immune thrombocytopenia who received one or more previous therapy. FUNDING: HUTCHMED and Science and Technology Commission of Shanghai Municipality.

Profiling novel lateral gene transfer events in the human microbiome.

Lateral gene transfer (LGT) is an important mechanism for genome diversification in microbial populations, including the human microbiome. While prior work has surveyed LGT events in human-associated microbial isolate genomes, the scope and dynamics of novel LGT events arising in personal microbiomes are not well understood, as there are no widely adopted computational methods to detect, quantify, and characterize LGT from complex microbial communities. We addressed this by developing, benchmarking, and experimentally validating a computational method (WAAFLE) to profile novel LGT events from assembled metagenomes. Applying WAAFLE to >2K human metagenomes from diverse body sites, we identified >100K putative high-confidence but previously uncharacterized LGT events (~2 per assembled microbial genome-equivalent). These events were enriched for mobile elements (as expected), as well as restriction-modification and transport functions typically associated with the destruction of foreign DNA. LGT frequency was quantifiably influenced by biogeography, the phylogenetic similarity of the involved taxa, and the ecological abundance of the donor taxon. These forces manifest as LGT networks in which hub species abundant in a community type donate unequally with their close phylogenetic neighbors. Our findings suggest that LGT may be a more ubiquitous process in the human microbiome than previously described. The open-source WAAFLE implementation, documentation, and data from this work are available at http://huttenhower.sph.harvard.edu/waafle.

Sovleplenib (HMPL-523), a novel Syk inhibitor, for patients with primary immune thrombocytopenia in China: a randomised, double-blind, placebo-controlled, phase 1b/2 study.

BACKGROUND: Spleen tyrosine kinase (Syk) inhibitor is a treatment option for primary immune thrombocytopenia. We aimed to evaluate the safety, tolerability, pharmacokinetics, preliminary activity, and recommended phase 2 dose of sovleplenib in patients with primary immune thrombocytopenia. METHODS: This randomised, double-blind, placebo-controlled, phase 1b/2 study was conducted at nine hospitals in China. Eligible patients were aged 18-75 years, had an ECOG performance score of 0-1, had primary immune thrombocytopenia for more than 6 months, and did not respond or relapsed after previous first-line treatment or had poor response or postoperative relapse after a splenectomy. Dose-escalation (100 mg, 200 mg, or 300 mg given orally once a day) and dose-expansion phases (recommended phase 2 dose) each consisted of an 8-week, double-blind, placebo-controlled period in which patients were randomly assigned (3:1) to receive sovleplenib or placebo with an interactive web response system followed by a 16-week, open-label period with sovleplenib. Patients, investigators, and the sponsor were masked to treatment allocation during the first 8 weeks. The main efficacy endpoint was the proportion of patients whose platelet count reached 30 × 109 platelets per L or higher and was double of the baseline at two consecutive visits during 0-8 weeks without rescue therapy. Efficacy was evaluated by intention-to-treat. This study is registered with ClinicalTrials.gov, NCT03951623. FINDINGS: Between May 30, 2019, and April 22, 2021, 62 patients were assessed for eligibility and 45 (73%) were randomly assigned. Patients received at least one dose of the study drug during the 8-week double-blind period (placebo [n=11] and sovleplenib 100 mg [n=6], 200 mg [n=6], 300 mg [n=16], and 400 mg [n=6]; this group was added following the observation of no protocol-specified safety events at the previous doses). All participants were Asian; 18 (40%) of 45 were male and 27 (60%) were female. The median age was 40·0 years (IQR 33·0-50·0). Ten (29%) of 34 patients in sovleplenib groups versus five (45%) of 11 in the placebo group received concomitant anti-primary immune thrombocytopenia therapy. The recommended phase 2 dose was determined as 300 mg once a day. The proportion of patients who met the main efficacy endpoint were three (50%; 95% CI 12-88) in the 100 mg group, three (50%; 12-88) in the 200 mg group, ten (63%; 35-85) in the 300 mg group, and two (33%; 4-78) in the 400 mg group compared with one (9%; 0-41) in the placebo group. The overall response rate in the 300 mg group was 80% (16 of 20 who received continuous sovleplenib plus those who crossed over from placebo) and the durable response rate was 31% (11-59; five of 16) in the continuous sovleplenib 300 mg and 75% (19-99; three of four) crossed from placebo to sovleplenib during 0-24 weeks. During the 28-day safety evaluation period, two grade 2 or worse treatment-related treatment-emergent adverse events occurred in the sovleplenib groups (hypertriglyceridaemia and anaemia). During 0-8 weeks, the most frequent treatment-emergent adverse events were an increase in blood lactate dehydrogenase, haematuria, and urinary tract infection (seven [21%] of 34 in sovleplenib groups vs one [9%] of 11 in the placebo group); and occult blood-positive and hyperuricaemia (four [12%] vs three [27%] for each). No fatal treatment-emergent adverse events were recorded. INTERPRETATION: Sovleplenib was well tolerated, and the recommended phase 2 dose showed a promising durable response in patients with primary immune thrombocytopenia, which provides evidence for future investigations. A phase 3 trial is ongoing (NCT05029635) to confirm the efficacy and safety of sovleplenib in patients with primary immune thrombocytopenia. FUNDING: HUTCHMED.

Loss of miR-31-5p drives hematopoietic stem cell malignant transformation and restoration eliminates leukemia stem cells in mice.

Leukemia stem cells (LSCs) propagate leukemia and are responsible for the high frequency of relapse of treated patients. The ability to target LSCs remains elusive, indicating a need to understand the underlying mechanism of LSC formation. Here, we report that miR-31-5p is reduced or undetectable in human LSCs compared to hematopoietic stem progenitor cells (HSPCs). Inhibition of miR-31-5p in HSPCs promotes the expression of its target gene FIH, encoding FIH [factor inhibiting hypoxia-inducing factor 1α (HIF-1α)], to suppress HIF-1α signaling. Increased FIH resulted in a switch from glycolysis to oxidative phosphorylation (OXPHOS) as the predominant mode of energy metabolism and increased the abundance of the oncometabolite fumarate. Increased fumarate promoted the conversion of HSPCs to LSCs and initiated myeloid leukemia-like disease in NOD-Prkdcscid IL2rgtm1/Bcgen (B-NDG) mice. We further demonstrated that miR-31-5p inhibited long- and short-term hematopoietic stem cells with a high frequency of LSCs. In combination with the chemotherapeutic agent Ara-C (cytosine arabinoside), restoration of miR-31-5p using G7 poly (amidoamine) nanosized dendriplex encapsulating miR-31-5p eliminated LSCs and inhibited acute myeloid leukemia (AML) progression in patient-derived xenograft mouse models. These results demonstrated a mechanism of HSC malignant transformation through altered energy metabolism and provided a potential therapeutic strategy to treat patients with AML.

Efficient prediction for high precision CO-N2 potential energy surface by stacking ensemble DNN.

High-dimensional potential energy surface (PES) for van der Waals systems with spectroscopic accuracy, is of great importance for quantum dynamics and an extremely challenge job. CO-N2 is a typical van der Waals system and its high-precision PES may help elucidate weak interaction mechanisms. Taking CO-N2 potential energies calculated by CCSD(T)-F12b/aug-cc-pVQZ as the benchmark, we establish an accurate, robust, and efficient machine learning model by using only four molecular structure descriptors based on 7966 benchmark potential energies. The highest accuracy is obtained by a stacking ensemble DNN (SeDNN). Its evaluation parameters MAE, RMSE, and R2 reach 0.096, 0.163, 0.9999 cm-1 , respectively, and the spectroscopic accuracy for vibration spectrum is achieved with predicted PES, which shows SeDNN superior goodness-of-fit and prediction performance. An elaborated PES with the reported global minimum has been predicted with the model, which perfectly reproduces CCSD(T) potential energies and the analytical MLR PES [PCCP, 2018, 20, 2036]. The critical points (global minimum, TSI, TSII, and their barriers), potential curve, and entire PES profile are remarkably consistent with CCSD(T) calculations. To further improve the usability of constructing PESs in practice, the size of the training set (energy points) for the model is reduced to 50%, 30%, and 20% of the database, respectively. The results show that even training with the smallest training set (1593 points), the PES only differs 2.555 cm-1 with the analytic MLR PES. Therefore, the proposed SeDNN is promisingly an alternative efficient tool to construct subtle PES for van der Waals systems.

Iterative subtractive binning of freshwater chronoseries metagenomes identifies over 400 novel species and their ecologic preferences.

Recent advances in sequencing technology and bioinformatic pipelines have allowed unprecedented access to the genomes of yet-uncultivated microorganisms from diverse environments. However, the catalogue of freshwater genomes remains limited, and most genome recovery attempts in freshwater ecosystems have only targeted specific taxa. Here, we present a genome recovery pipeline incorporating iterative subtractive binning, and apply it to a time series of 100 metagenomic datasets from seven connected lakes and estuaries along the Chattahoochee River (Southeastern USA). Our set of metagenome-assembled genomes (MAGs) represents >400 yet-unnamed genomospecies, substantially increasing the number of high-quality MAGs from freshwater lakes. We propose names for two novel species: 'Candidatus Elulimicrobium humile' ('Ca. Elulimicrobiota', 'Patescibacteria') and 'Candidatus Aquidulcis frankliniae' ('Chloroflexi'). Collectively, our MAGs represented about half of the total microbial community at any sampling point. To evaluate the prevalence of these genomospecies in the chronoseries, we introduce methodologies to estimate relative abundance and habitat preference that control for uneven genome quality and sample representation. We demonstrate high degrees of habitat-specialization and endemicity for most genomospecies in the Chattahoochee lakes. Wider ecological ranges characterized smaller genomes with higher coding densities, indicating an overall advantage of smaller, more compact genomes for cosmopolitan distributions.

von Willebrand Factor as a Predictor for Transplant-Associated Thrombotic Microangiopathy.

CONCLUSION: von Willebrand factor is a useful predictor and prognostic measure for TA-TMA, which may help clinicians identify and manage this life-threatening disease earlier.

Model-based Comparisons of the Abundance Dynamics of Bacterial Communities in Two Lakes.

Lake Lanier (Georgia, USA) is home to more than 11,000 microbial Operational Taxonomic Units (OTUs), many of which exhibit clear annual abundance patterns. To assess the dynamics of this microbial community, we collected time series data of 16S and 18S rRNA gene sequences, recovered from 29 planktonic shotgun metagenomic datasets. Based on these data, we constructed a dynamic mathematical model of bacterial interactions in the lake and used it to analyze changes in the abundances of OTUs. The model accounts for interactions among 14 sub-communities (SCs), which are composed of OTUs blooming at the same time of the year, and three environmental factors. It captures the seasonal variations in abundances of the SCs quite well. Simulation results suggest that changes in water temperature affect the various SCs differentially and that the timing of perturbations is critical. We compared the model results with published results from Lake Mendota (Wisconsin, USA). These comparative analyses between lakes in two very different geographical locations revealed substantially more cooperation and less competition among species in the warmer Lake Lanier than in Lake Mendota.

The Bacterial Symbionts of Closely Related Hydrothermal Vent Snails With Distinct Geochemical Habitats Show Broad Similarity in Chemoautotrophic Gene Content.

Symbiosis has evolved between a diversity of invertebrate taxa and chemosynthetic bacterial lineages. At the broadest level, these symbioses share primary function: the bacterial symbionts use the energy harnessed from the oxidation of reduced chemicals to power the fixation of inorganic carbon and/or other nutrients, providing the bulk of host nutrition. However, it is unclear to what extent the ecological niche of the host species is influenced by differences in symbiont traits, particularly those involved in chemoautotrophic function and interaction with the geochemical environment. Hydrothermal vents in the Lau Basin (Tonga) are home to four morphologically and physiologically similar snail species from the sister genera Alviniconcha and Ifremeria. Here, we assembled nearly complete genomes from their symbionts to determine whether differences in chemoautotrophic capacity exist among these symbionts that could explain the observed distribution of these snail species into distinct geochemical habitats. Phylogenomic analyses confirmed that the symbionts have evolved from four distinct lineages in the classes γ-proteobacteria or Campylobacteria. The genomes differed with respect to genes related to motility, adhesion, secretion, and amino acid uptake or excretion, though were quite similar in chemoautotrophic function, with all four containing genes for carbon fixation, sulfur and hydrogen oxidation, and oxygen and nitrate respiration. This indicates that differences in the presence or absence of symbiont chemoautotrophic functions does not likely explain the observed geochemical habitat partitioning. Rather, differences in gene expression and regulation, biochemical differences among these chemoautotrophic pathways, and/or differences in host physiology could all influence the observed patterns of habitat partitioning.

circMYBL2, a circRNA from MYBL2, regulates FLT3 translation by recruiting PTBP1 to promote FLT3-ITD AML progression.

Internal tandem duplication (ITD) mutations within FMS-like tyrosine kinase-3 (FLT3) occur in up to 30% of acute myeloid leukemia (AML) patients and confer a very poor prognosis. The oncogenic form of FLT3 is an important therapeutic target, and inhibitors specifically targeting FLT3 kinase can induce complete remission; however, relapse after remission has been observed due to acquired resistance with secondary mutations in FLT3, highlighting the need for new strategies to target FLT3-ITD mutations. Recent studies have reported that the aberrant formations of circular RNAs (circRNAs) are biological tumorigenesis-relevant mechanisms and potential therapeutic targets. Herein, we discovered a circRNA, circMYBL2, derived from the cell-cycle checkpoint gene MYBL2. circMYBL2 is more highly expressed in AML patients with FLT3-ITD mutations than in those without the FLT3-ITD mutation. We found that circMYBL2 knockdown specifically inhibits proliferation and promotes the differentiation of FLT3-ITD AML cells in vitro and in vivo. Interestingly, we found that circMYBL2 significantly influences the protein level of mutant FLT3 kinase, which contributes to the activation of FLT3-ITD-dependent signaling pathways. Mechanistically, circMYBL2 enhanced the translational efficiency of FLT3 kinase by increasing the binding of polypyrimidine tract-binding protein 1 (PTBP1) to FLT3 messenger RNA. Moreover, circMYBL2 knockdown impaired the cytoactivity of inhibitor-resistant FLT3-ITD+ cells, with a significant decrease in FLT3 kinase expression, followed by the inactivation of its downstream pathways. In summary, we are the first to reveal a circRNA that specifically influences FLT3-ITD AML and regulates FLT3 kinase levels through translational regulation, suggesting that circMYBL2 may be a potential therapeutic target for FLT3-ITD AML.

ORP4L Extracts and Presents PIP2 from Plasma Membrane for PLCß3 Catalysis: Targeting It Eradicates Leukemia Stem Cells.

Leukemia stem cells (LSCs) are a rare subpopulation of abnormal hematopoietic stem cells (HSCs) that propagates leukemia and are responsible for the high frequency of relapse in therapies. Detailed insights into LSCs' survival will facilitate the identification of targets for therapeutic approaches. Here, we develop an inhibitor, LYZ-81, which targets ORP4L with high affinity and specificity and selectively eradicates LCSs in vitro and in vivo. ORP4L is expressed in LSCs but not in normal HSCs and is essential for LSC bioenergetics and survival. It extracts PIP2 from the plasma membrane and presents it to PLCß3, enabling IP3 generation and subsequent Ca2+-dependent bioenergetics. LYZ-81 binds ORP4L competitively with PIP2 and blocks PIP2 hydrolysis, resulting in defective Ca2+ signaling. The results provide evidence that LSCs can be eradicated through the inhibition of ORP4L by LYZ-81, which may serve as a starting point of drug development for the elimination of LSCs to eventually cure leukemia.

A potent immunomodulatory role of exosomes derived from mesenchymal stromal cells in preventing cGVHD.

BACKGROUND: Mesenchymal stromal cells (MSCs) are a promising therapy for preventing chronic Graft-Versus-Host Disease (cGVHD) due to their potent immunomodulatory properties. However, the safety concerns regarding the use of MSCs remain unsolved, and conflicting effects are observed due to the heterogeneity of MSCs. Recently, exosomes were shown to mediate the paracrine effects of MSCs, making it a potential candidate for cell-free therapies. The aim of this study is to investigate the efficacy and safety of MSCs-derived exosomes (MSCs-exo) in an established cGVHD mouse model. METHODS: Bone marrow (BM)-derived MSCs were cultured, and the supernatants of these cultures were collected to prepare exosomes using ultracentrifugation. Exosomes from human dermal fibroblasts (Fib-exo) were used as a negative control. The cGVHD model was established, and tail vein injections of MSCs-exo or Fib-exo were administered once per week for 6 weeks. The symptoms and signs of cGVHD were monitored, and histopathological changes were detected by hematoxylin and eosin and Masson staining. The effects of MSCs-exo on Th17, Th1, and Treg were evaluated by flow cytometry, qPCR, and Luminex. In addition, human peripheral blood mononuclear cells (PBMCs) were stimulated and treated with MSCs-exo in vitro. IL-17-expressing Th17 and IL-10-expressing Treg were evaluated by flow cytometry, qPCR, and ELISA. RESULTS: We found that MSCs-exo effectively prolonged the survival of cGVHD mice and diminished the clinical and pathological scores of cGVHD. Fibrosis in the skin, lung, and liver was significantly ameliorated by MSCs-exo application. In MSCs-exo treated mice, activation of CD4+ T cells and their infiltration into the lung were reduced. Of note, MSCs-exo exhibited potent immunomodulatory effects via the inhibition of IL-17-expressing pathogenic T cells and induction of IL-10-expressing regulatory cells during cGVHD. The expressions of Th17 cell-relevant transcription factors and pro-inflammatory cytokines was markedly reduced after MSCs-exo treatment. In vitro, MSCs-exo blocked Th17 differentiation and improved the Treg phenotype in PBMCs obtained from healthy donors and patients with active cGVHD, further indicating the regulatory effect of MSCs-exo on GVHD effector T cells. CONCLUSIONS: Our data suggested that MSCs-exo could improve the survival and ameliorate the pathologic damage of cGVHD by suppressing Th17 cells and inducing Treg. This finding provides a novel alternative approach for the treatment of cGVHD.

Antigen discovery and specification of immunodominance hierarchies for MHCII-restricted epitopes.

Identifying immunodominant T cell epitopes remains a significant challenge in the context of infectious disease, autoimmunity, and immuno-oncology. To address the challenge of antigen discovery, we developed a quantitative proteomic approach that enabled unbiased identification of major histocompatibility complex class II (MHCII)-associated peptide epitopes and biochemical features of antigenicity. On the basis of these data, we trained a deep neural network model for genome-scale predictions of immunodominant MHCII-restricted epitopes. We named this model bacteria originated T cell antigen (BOTA) predictor. In validation studies, BOTA accurately predicted novel CD4 T cell epitopes derived from the model pathogen Listeria monocytogenes and the commensal microorganism Muribaculum intestinale. To conclusively define immunodominant T cell epitopes predicted by BOTA, we developed a high-throughput approach to screen DNA-encoded peptide-MHCII libraries for functional recognition by T cell receptors identified from single-cell RNA sequencing. Collectively, these studies provide a framework for defining the immunodominance landscape across a broad range of immune pathologies.

Emerging role of C5a/C5aR IL-17A axis in cGVHD.

Chronic graft-versus-host disease (cGVHD) manifests with features characteristic of autoimmune disease with organs attacked by pathogenic Th17 cells. However, the mechanism of Th17 cells generation in the setting of cGVHD is still unclear. Here we defined C5a/C5aR-IL-17Aaxis as a novel signaling that required in the pathologies of cGVHD. We firstly found a positive link between complement activation and the Th17 cells in patients with cGVHD. C5a, a critical component of complements, promoted the generation of Th17 cells in vitro and inhibition of the receptor for C5a (C5aR) reduced the Th17-bias response. Of note, C5aR blockade by PMX53 could suppress the generation of IL-17A-expressing Th17 cells and retard the onset and progression of cGVHD in vivo. Overall, our results provide new mechanistic insights that activation of C5a-C5aR signaling was required for IL-17A-induced immune responses in cGVHD and define novel molecular targets for developing effective therapeutics for cGVHD.

Coupled Hygro-Mechanical Finite Element Method on Determination of the Interlaminar Shear Modulus of Glass Fiber-Reinforced Polymer Laminates in Bridge Decks under Hygrothermal Aging Effects.

To investigate the mechanical degradation of the shear properties of glass fiber-reinforced polymer (GFRP) laminates in bridge decks under hygrothermal aging effects, short-beam shear tests were performed following the ASTM test standard (ASTM D790-10A). Based on the coupled hygro-mechanical finite element (FE) analysis method, an inverse parameter identification approach based on short-beam shear tests was developed and then employed to determine the environment-dependent interlaminar shear modulus of GFRP laminates. Subsequently, the shear strength and modulus of dry (0% Mt/M∞), moisture unsaturated (30% Mt/M∞ and 50% Mt/M∞), and moisture saturated (100% Mt/M∞) specimens at test temperatures of both 20 °C and 40 °C were compared. One cycle of the moisture absorption⁻desorption process was also investigated to address how the moisture-induced residual damage degrades the shear properties of GFRP laminates. The results revealed that the shear strength and modulus of moisture-saturated GFRP laminates decreased significantly, and the elevated testing temperature (40 °C) aggravated moisture-induced mechanical degradation. Moreover, an unrecoverable loss of shear properties for the GFRP laminates enduring one cycle of the moisture absorption⁻desorption process was evident.

Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation.

Intestinal colonization by bacteria of oral origin has been correlated with several negative health outcomes, including inflammatory bowel disease. However, a causal role of oral bacteria ectopically colonizing the intestine remains unclear. Using gnotobiotic techniques, we show that strains of Klebsiella spp. isolated from the salivary microbiota are strong inducers of T helper 1 (TH1) cells when they colonize in the gut. These Klebsiella strains are resistant to multiple antibiotics, tend to colonize when the intestinal microbiota is dysbiotic, and elicit a severe gut inflammation in the context of a genetically susceptible host. Our findings suggest that the oral cavity may serve as a reservoir for potential intestinal pathobionts that can exacerbate intestinal disease.

Indoleacrylic Acid Produced by Commensal Peptostreptococcus Species Suppresses Inflammation.

Host factors in the intestine help select for bacteria that promote health. Certain commensals can utilize mucins as an energy source, thus promoting their colonization. However, health conditions such as inflammatory bowel disease (IBD) are associated with a reduced mucus layer, potentially leading to dysbiosis associated with this disease. We characterize the capability of commensal species to cleave and transport mucin-associated monosaccharides and identify several Clostridiales members that utilize intestinal mucins. One such mucin utilizer, Peptostreptococcus russellii, reduces susceptibility to epithelial injury in mice. Several Peptostreptococcus species contain a gene cluster enabling production of the tryptophan metabolite indoleacrylic acid (IA), which promotes intestinal epithelial barrier function and mitigates inflammatory responses. Furthermore, metagenomic analysis of human stool samples reveals that the genetic capability of microbes to utilize mucins and metabolize tryptophan is diminished in IBD patients. Our data suggest that stimulating IA production could promote anti-inflammatory responses and have therapeutic benefits.

Gut Microbiome Function Predicts Response to Anti-integrin Biologic Therapy in Inflammatory Bowel Diseases.

The gut microbiome plays a central role in inflammatory bowel diseases (IBDs) pathogenesis and propagation. To determine whether the gut microbiome may predict responses to IBD therapy, we conducted a prospective study with Crohn's disease (CD) or ulcerative colitis (UC) patients initiating anti-integrin therapy (vedolizumab). Disease activity and stool metagenomes at baseline, and weeks 14, 30, and 54 after therapy initiation were assessed. Community α-diversity was significantly higher, and Roseburia inulinivorans and a Burkholderiales species were more abundant at baseline among CD patients achieving week 14 remission. Several significant associations were identified with microbial function; 13 pathways including branched chain amino acid synthesis were significantly enriched in baseline samples from CD patients achieving remission. A neural network algorithm, vedoNet, incorporating microbiome and clinical data, provided highest classifying power for clinical remission. We hypothesize that the trajectory of early microbiome changes may be a marker of response to IBD treatment.

Metagenomics of Two Severe Foodborne Outbreaks Provides Diagnostic Signatures and Signs of Coinfection Not Attainable by Traditional Methods.

Diagnostic testing for foodborne pathogens relies on culture-based techniques that are not rapid enough for real-time disease surveillance and do not give a quantitative picture of pathogen abundance or the response of the natural microbiome. Powerful sequence-based culture-independent approaches, such as shotgun metagenomics, could sidestep these limitations and potentially reveal a pathogen-specific signature on the microbiome that would have implications not only for diagnostics but also for better understanding disease progression and pathogen ecology. However, metagenomics have not yet been validated for foodborne pathogen detection. Toward closing these gaps, we applied shotgun metagenomics to stool samples collected from two geographically isolated (Alabama and Colorado) foodborne outbreaks, where the etiologic agents were identified by culture-dependent methods as distinct strains of Salmonella enterica subsp. enterica serovar Heidelberg. Metagenomic investigations were consistent with the culture-based findings and revealed, in addition, the in situ abundance and level of intrapopulation diversity of the pathogen, the possibility of coinfections with Staphylococcus aureus, overgrowth of commensal Escherichia coli, and significant shifts in the gut microbiome during infection relative to reference healthy samples. Additionally, we designed our bioinformatics pipeline to deal with several challenges associated with the analysis of clinical samples, such as the high frequency of coeluting human DNA sequences and assessment of the virulence potential of pathogens. Comparisons of these results to those of other studies revealed that in several, but not all, cases of diarrheal outbreaks, the disease and healthy states of the gut microbial community might be distinguishable, opening new possibilities for diagnostics. IMPORTANCE: Diagnostic testing for enteric pathogens has relied for decades on culture-based techniques, but a total of 38.4 million cases of foodborne illness per year cannot be attributed to specific causes. This study describes new culture-independent metagenomic approaches and the associated bioinformatics pipeline to detect and type the causative agents of microbial disease with unprecedented accuracy, opening new possibilities for the future development of health technologies and diagnostics. Our tools and approaches should be applicable to other microbial diseases in addition to foodborne diarrhea.

The Synergistic Effects of Decitabine Combined with Arsenic Trioxide (ATO) in the Human Myelodysplastic Syndrome Cell Line SKM-1.

Despite recent advances in the treatment of myelodysplastic syndrome (MDS), single-agent clinical effects remain unsatisfactory, and decitabine monotherapy is also associated with a relatively low rate of complete remission. To study the combined effects and mechanism of decitabine (DAC) and arsenic trioxide (ATO) on the human myelodysplastic cell line SKM-1,we used the MTS assay and CalcuSyn software to determine the cytotoxicity and potential synergistic effects, respectively. Furthermore, we determined apoptosis and measured the mRNA expression level of two genes that are considered main regulators of the apoptosis process. The results showed that DAC and/or ATO can inhibit the proliferation of SKM-1 cells and demonstrated significant synergy between the two agents (CI < 1). Additionally, combination of 2.5 µmol/L DAC and 5 µmol/L ATO led to a significantly higher apoptosis rate and more significantly decreased the Bcl2/Bax ratio than either compound alone (P < 0.001). Based on the observations of this study, we suggest that combined administration of these two drugs might be considered a novel therapeutic regimen for treating MDS.