Abundance In Patients Research Articles

Quantitative pharmacology of dual-targeted bicistronic CAR-T-cell therapy using multiscale mechanistic modeling.

Despite the initial success of single-targeted chimeric-antigen receptor (CAR) T-cell therapy in hematological malignancies, its long-term effectiveness is often hindered by antigen heterogeneity and escape. As a result, there is a growing interest in cell therapies targeting multiple antigens (≥2). However, the dose-exposure-response relationship and specific factors influencing the pharmacology of dual-targeted CAR-T-cell therapy remain unclear. In this study, we have developed a multiscale cellular kinetic-pharmacodynamic (CK-PD) model using case studies from CD19/CD22 and GPRC5D/BCMA autologous CAR-Ts. Initially, an invitro tumor-killing model characterized the impact of individual binder affinities and their contribution to overall potency across varying (1) effector: target (ET) ratios and (2) tumor-associated antigen (TAA) expressing cell lines. Subsequently, an integrated CK-PD model was developed in pediatric acute lymphoblastic leukemia (ALL) patients, which accounted for CAR-T-cell product composition and relative antigen abundance in patients' tumor burden to characterize patient-level multiphasic cellular kinetics using multiple bioanalytical assays (e.g., flow and qPCR-based readouts). Global sensitivity analysis highlighted relative antigen expression, maximum killing rate constant, and CAR-T expansion rate constant as major determinants for observed exposure of dual-targeted CAR-T-cell therapy. This modeling framework could facilitate dose-optimization and construct refinement for dual-targeted bicistronic CAR-T-cell therapies, serving as a valuable tool for both forward and reverse translation in drug development.

169P Alteration of LARGE1 abundance in patients and a mouse model of 5q-associated spinal muscular atrophy

169P Alteration of LARGE1 abundance in patients and a mouse model of 5q-associated spinal muscular atrophy

Potential Trimethylamine (TMA)-Producing Bacteria in patients with chronic kidney disease undergoing hemodialysis.

Trimethylamine (TMA), produced by gut microbiota, is the precursor of trimethylamine-N-oxide (TMAO), a uremic toxin that accumulates in patients with chronic kidney disease (CKD). Elevated TMAO plasma levels are associated with cardiovascular complications and CKD progression. To evaluate the association between gut microbiota composition and TMAO plasma levels in CKD patients undergoing hemodialysis (HD). This is a cross-sectional study with 25 patients evaluated (60% female, 53 (18) years, body mass index (BMI) 25.8 (6.75)Kg/m2). They were divided into two groups according to their TMAO plasma levels: normal (≤ 7.4μM) and high (> 7.4μM). Uremic toxins such as indoxyl sulfate (IS), p-cresyl sulfate (pCS), and indol acetic acid (IAA) were measured with RP-HPLC, and TMAO plasma levels were quantified using LC-MS/MS. Fecal DNA was extracted with a commercial kit, PCR amplified the V4 region of the 16S rRNA gene, and short-read sequencing was performed on the Illumina platform. Dietary intake, anthropometric measurements, and inflammation markers were also evaluated. Nrf2, NF-κB, IL-1β, and NLRP3 mRNA expressions were measured from peripheral blood mononuclear cells (PBMC) using quantitative real-time polymerase chain reaction (qPCR). There were significant positive correlations between TMAO and plasma levels of pCS, NLPR3 inflammasome mRNA expression, serum phosphorus levels, and negative correlations with dietary lipid intake. The group with TMAO > 7.4μM showed an increase in the microbiome abundance of Saccharibacteria (genus incertae sedis), Colidextribacter, Dorea, and Staphylococci genera, and a decrease in abundance in the genera Lachnospira, Lactobacilli, and Victivallis. TMAO plasma level was positively correlated with the abundance of bacteria of the genera Colidextribacter and Helicobacter and was negatively correlated with Sphingomanos, Lachnospira, Streptomyces, and Bacillus genera. Saccharibacteria (genus incertae sedis), Colidextribacter, Dorea, and Staphylococci genera showed higher abundance in patients with high TMAO levels. In addition, we observed that elevated plasma TMAO levels are associated with inflammation markers, dietary lipid intake, and serum phosphorus levels in patients undergoing HD.

Periodontal treatment causes a longitudinal increase in nitrite-producing bacteria.

The oral microbiome-dependent nitrate (NO3 -)-nitrite (NO2 -)-nitric oxide (NO) pathway may help regulate blood pressure. NO2 --producing bacteria in subgingival plaque are reduced in relative abundance in patients with untreated periodontitis compared with periodontally healthy patients. In periodontitis patients, the NO2 --producing bacteria increase several months after periodontal treatment. The early effects of periodontal treatment on NO2 --producing bacteria and the NO3 --NO2 --NO pathway remain unknown. The aim of this study was to determine how periodontal treatment affects the oral NO2 --producing microbiome and salivary NO3 - and NO2 - levels over time. The subgingival microbiota of 38 periodontitis patients was analysed before (baseline [BL]) and 1, 7 and 90 days after periodontal treatment. Changes in NO2 --producing bacteria and periodontitis-associated bacteria were determined by 16s rRNA Illumina sequencing. Saliva samples were collected at all-time points to determine NO3 - and NO2 - levels using gas-phase chemiluminescence. A significant increase was observed in the relative abundance of NO2 --producing species between BL and all subsequent timepoints (all p<0.001). Periodontitis-associated species decreased at all timepoints, relative to BL (all p<0.02). NO2 --producing species negatively correlated with periodontitis-associated species at all timepoints, with this relationship strongest 90 days post-treatment (ρ=-0.792, p<0.001). Despite these findings, no significant changes were found in salivary NO3 - and NO2 - over time (all p>0.05). Periodontal treatment induced an immediate increase in the relative abundance of health-associated NO2 --producing bacteria. This increase persisted throughout periodontal healing. Future studies should test the effect of periodontal treatment combined with NO3 - intake on periodontal and cardiovascular health.

Influence of Mycobiota in the Nasopharyngeal Tract of COVID-19 Patients.

The nasopharyngeal tract contains a complex microbial community essential to maintaining host homeostasis. Recent studies have shown that SARS-CoV-2 infection changes the microbial composition of the nasopharynx. Still, little is known about how it affects the fungal microbiome, which could provide valuable insights into disease pathogenesis. Nasopharyngeal swabs were collected from 55 patients, during three distinct COVID-19 waves that occurred in the Campania Region (southern Italy). An RNA-seq-based analysis was performed to evaluate changes in mycobiota diversity, showing variations depending on the disease's severity and the sample collection wave. The phyla Basidiomycota and Ascomycota were shown to have higher abundance in patients with severe symptoms. Furthermore, the diversity of the fungal population was greater in the second wave. Conclusion: According to our research, COVID-19 induces significant dysbiosis of the fungal microbiome, which may contribute to disease pathogenesis, and understanding its underlying mechanisms could contribute to developing effective treatments.

Altered gut microbe metabolites in patients with alcohol‑induced osteonecrosis of the femoral head: An integrated omics analysis.

Excessive alcohol consumption is considered to be a major risk factor of alcohol-induced osteonecrosis of the femoral head (AONFH). The gut microbiota (GM) has been reported to aid in the regulation of human physiology and its composition can be altered by alcohol consumption. The aim of the present study was to improve the understanding of the GM and its metabolites in patients with AONFH. Metabolomic sequencing and 16S rDNA analysis of fecal samples were performed using liquid chromatography-mass spectrometry to characterize the GM of patients with AONFH and healthy normal controls (NCs). Metagenomic sequencing of fecal samples was performed to identify whether GM changes on the species level were associated with the expression of gut bacteria genes or their associated functions in patients with AONFH. The abundance of 58 genera was found to differ between the NC group and the AONFH group. Specifically, Klebsiella, Holdemanella, Citrobacter and Lentilactobacillus were significantly more abundant in the AONFH group compared with those in the NC group. Metagenomic sequencing demonstrated that the majority of the bacterial species that exhibited significantly different abundance in patients with AONFH belonged to the genus Pseudomonas. Fecal metabolomic analysis demonstrated that several metabolites were present at significantly different concentrations in the AONFH group compared with those in the NC group. These metabolites were products of vitamin B6 metabolism, retinol metabolism, pentose and glucuronate interconversions and glycerophospholipid metabolism. In addition, these changes in metabolite levels were observed to be associated with the altered abundance of specific bacterial species, such as Basidiobolus, Mortierella, Phanerochaete and Ceratobasidium. According to the results of the present study, a comprehensive landscape of the GM and metabolites in patients with AONFH was revealed, suggesting the existence of interplay between the gut microbiome and metabolome in AONFH pathogenesis.

Alteration of Gut Microbiota Composition and Diversity in Acute and/or Chronic Graft-versus-Host Disease Following Hematopoietic Stem Cell Transplantation: A Prospective Cohort Study.

Changes in gut microbiome composition have been implicated in the pathogenesis of graft-versus-host disease (GvHD) after allogeneic hematopoietic stem cell transplantation (allo-HSCT). Our objective was to explore the microbial abundance in patients with GvHD after allo-HSCT. We conducted a single-center, prospective study in patients who underwent allo-HSCT and developed grade II or higher acute GvHD and/or moderate or severe chronic GvHD, to explore the microbial abundance of taxa at the phylum, family, genus, and species level, and we utilized alpha and beta diversity indices to further describe our findings. We collected fecal specimens at -2 to +2 (T1), +11 to +17 (T2), +25 to +30 (T3), +90 (T4), and +180 (T5) days to assess changes in gut microbiota, with day 0 being the day of allo-HSCT. We included 20 allo-HSCT recipients in the study. Compared with timepoint T1, at timepoint T4 we found a significant decrease in the abundance of Proteobacteria phylum (14.22% at T1 vs. 4.07% at T4, p = 0.01) and Enterobacteriaceae family (13.3% at T1 vs. <0.05% at T4, p < 0.05), as well as a significant increase in Enterococcus species (0.1% at T1 vs. 12.8% at T4, p < 0.05) in patients who developed acute GvHD. Regarding patients who developed chronic GvHD after allo-HSCT, there was a significant reduction in the abundance of Eurobactereaceae family (1.32% at T1 vs. 0.53% at T4, p < 0.05) and Roseruria genus (3.97% at T1 vs. 0.09% at T4, p < 0.05) at T4 compared with T1. Alpha and beta diversity analyses did not reveal a difference in the abundance of bacteria at the genus level in GvHD patients at T4 compared with T1. Our study reinforces results from previous studies regarding changes in gut microbiota in patients with acute GvHD and provides new data regarding the gut microbiome changes in chronic GvHD. Future studies will need to incorporate clinical parameters in their analyses to establish their association with specific changes in gut microbiota in patients with GvHD after allo-HSCT.

Volatilomic profiles of gastric juice in gastric cancer patients

Volatilomics is a powerful tool capable of providing novel biomarkers for the diagnosis of gastric cancer. The main objective of this study was to characterize the volatilomic signatures of gastric juice in order to identify potential alterations induced by gastric cancer. Gas chromatography with mass spectrometric detection, coupled with headspace solid phase microextraction as the pre-concentration technique, was used to identify volatile organic compounds (VOCs) released by gastric juice samples collected from 78 gastric cancer patients and two cohorts of controls (80 and 96 subjects) from four different locations (Latvia, Ukraine, Brazil, and Colombia). 1440 distinct compounds were identified in samples obtained from patients and 1422 in samples provided by controls. However, only 6% of the VOCs exhibited an incidence higher than 20%. Amongst the volatiles emitted, 18 showed differences in their headspace concentrations above gastric juice of cancer patients and controls. Ten of these (1-propanol, 2,3-butanedione, 2-pentanone, benzeneacetaldehyde, 3-methylbutanal, butylated hydroxytoluene, 2-pentyl-furan, 2-ethylhexanal, 2-methylpropanal and phenol) appeared at significantly higher levels in the headspace of the gastric juice samples obtained from patients; whereas, eight species showed lower abundance in patients than found in controls. Given that the difference in the volatilomic signatures can be explained by cancer-related changes in the activity of certain enzymes or pathways, the former set can be considered potential biomarkers for gastric cancer, which may assist in developing non-invasive breath tests for the diagnosis of this disease. Further studies are required to elucidate further the mechanisms that underlie the changes in the volatilomic profile as a result of gastric cancer.

Alteration of LARGE1 abundance in patients and a mouse model of 5q-associated spinal muscular atrophy

Spinal muscular atrophy (SMA) is a neuromuscular disorder caused by recessive pathogenic variants affecting the survival of motor neuron (SMN1) gene (localized on 5q). In consequence, cells lack expression of the corresponding protein. This pathophysiological condition is clinically associated with motor neuron (MN) degeneration leading to severe muscular atrophy. Additionally, vulnerability of other cellular populations and tissues including skeletal muscle has been demonstrated. Although the therapeutic options for SMA have considerably changed, treatment responses may differ thus underlining the persistent need for validated biomarkers. To address this need and to identify novel marker proteins for SMA, we performed unbiased proteomic profiling on cerebrospinal fluid derived (CSF) from genetically proven SMA type 1–3 cases and afterwards performed ELISA studies on CSF and serum samples to validate the potential of a novel biomarker candidates in both body fluids. To further decipher the pathophysiological impact of this biomarker, immunofluorescence studies were carried out on spinal cord and skeletal muscle derived from a 5q-SMA mouse model. Proteomics revealed increase of LARGE1 in CSF derived from adult patients showing a clinical response upon treatment with nusinersen. Moreover, LARGE1 levels were validated in CSF samples of further SMA patients (type 1–3) by ELISA. These studies also unveiled a distinguishment between groups in improvement of motor skills: adult patients do present with lowered level per se at baseline visit while no elevation upon treatment in the pediatric cohort can be observed. ELISA-based studies of serum samples showed no changes in the pediatric cohort but unraveled elevated level in adult patients responding to future intervention with nusinersen, while non-responders did not show a significant increase. Additional immunofluorescence studies of LARGE1 in MN and skeletal muscle of a SMA type 3 mouse model revealed an increase of LARGE1 during disease progression. Our combined data unraveled LARGE1 as a protein dysregulated in serum and CSF of SMA-patients (and in MN and skeletal muscle of SMA mice) holding the potential to serve as a disease marker for SMA and enabling to differentiate between patients responding and non-responding to therapy with nusinersen.

Long-term beneficial effect of faecal microbiota transplantation on colonisation of multidrug-resistant bacteria and resistome abundance in patients with recurrent Clostridioides difficile infection

BackgroundMultidrug-resistant (MDR) bacteria are a growing global threat, especially in healthcare facilities. Faecal microbiota transplantation (FMT) is an effective prevention strategy for recurrences of Clostridioides difficile infections and can also be useful for other microbiota-related diseases.MethodsWe study the effect of FMT in patients with multiple recurrent C. difficile infections on colonisation with MDR bacteria and antibiotic resistance genes (ARG) on the short (3 weeks) and long term (1–3 years), combining culture methods and faecal metagenomics.ResultsBased on MDR culture (n = 87 patients), we notice a decrease of 11.5% in the colonisation rate of MDR bacteria after FMT (20/87 before FMT = 23%, 10/87 3 weeks after FMT). Metagenomic sequencing of patient stool samples (n = 63) shows a reduction in relative abundances of ARGs in faeces, while the number of different resistance genes in patients remained higher compared to stools of their corresponding healthy donors (n = 11). Furthermore, plasmid predictions in metagenomic data indicate that patients harboured increased levels of resistance plasmids, which appear unaffected by FMT. In the long term (n = 22 patients), the recipients’ resistomes are still donor-like, suggesting the effect of FMT may last for years.ConclusionsTaken together, we hypothesise that FMT restores the gut microbiota to a composition that is closer to the composition of healthy donors, and potential pathogens are either lost or decreased to very low abundances. This process, however, does not end in the days following FMT. It may take months for the gut microbiome to re-establish a balanced state. Even though a reservoir of resistance genes remains, a notable part of which on plasmids, FMT decreases the total load of resistance genes.

Lower airway microbiota in COPD and healthy controls

BackgroundThe lower airway microbiota in patients with chronic obstructive pulmonary disease (COPD) are likely altered compared with the microbiota in healthy individuals. Information on how the microbiota is affected by...

Abstract A057: Decreased plasma linoleic acid and increased oleic acid associated with obesity in pancreatic cancer

Abstract Background: Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy that interferes with absorption of nutrients including fats. Obesity is a key risk factor for PDAC and confers metabolic dysfunction associated with changes in fatty acid (FA) metabolism, including FAs in the linoleic acid and palmitic acid pathways. In turn, FAs can influence the molecular signaling in pancreatic cells. Changes in blood FA abundance induced by PDAC could be amplified by obesity and influence PDAC-associated outcomes. Therefore, we investigated plasma FA abundance in patients with treatment-naïve PDAC compared with control participants and explored how obesity status affects the linoleic acid and palmitic acid pathways in cancer. Methods: Blood and clinical characteristics were collected from participants with resectable tumors (rPDAC, n=52) or metastatic disease (mPDAC, r=55) that were treatment-naïve and 22 controls. Plasma samples were analyzed for relative FA abundance using gas chromatography and levels were compared between controls, rPDAC and mPDAC. Changes in FA abundance due to obesity (body mass index ≥30 kg/m2) were assessed in all groups. All FA abundance changes were analyzed using a two-way ANOVA with the appropriate parametric or non-parametric test, and p-values were adjusted using the Bonferroni correction. Results: Compared with controls, both rPDAC and mPDAC were associated with increased FA abundance of palmitic acid and decreased abundance of linoleic acid, γ-linolenic acid, and dihomo-γ-linolenic acid, regardless of obesity status (p&amp;lt;0.05). Plasma FA abundance of linoleic acid was increased in mPDAC versus rPDAC, regardless of obesity status (p&amp;lt;0.05). Decreased abundance of linoleic acid was noted in rPDAC and mPDAC participants with obesity versus participants without obesity, while there was an increased abundance of oleic acid observed in mPDAC among participants with obesity versus participants without obesity (p&amp;lt;0.05). Conclusions: Plasma FA levels are dysregulated in all PDAC stages versus controls. The results suggest that obesity-associated metabolic dysregulation influences linoleic acid and oleic acid abundances of participants with treatment-naïve PDAC. By improving our understanding of how obesity influences FA abundance in PDAC, we can identify novel mechanistic targets for treatment specific to PDAC stage and obesity status. Citation Format: Kaylin M. Chasser, Martha A. Belury, Jordan M. Cloyd, Rachel M. Cole, Stacey Culp, Mary E. Dillhoff, Aslam Ejaz, Kristyn Gumpper-Fedus, Phil A. Hart, Lauren Kanzaki, Andrei V. Manilchuk, Anne M. Noonan, Timothy M. Pawlik, Mitchell Ramsey, Zobeida Cruz-Monserrate. Decreased plasma linoleic acid and increased oleic acid associated with obesity in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr A057.

Gut microbiota changes in patients with Alzheimer's disease spectrum based on 16S rRNA sequencing: a systematic review and meta-analysis.

The gut microbiota (GM) is hypothesized to play roles in Alzheimer's disease (AD) pathogenesis. In recent years, many GM composition and abundance investigations in AD patients have been conducted; however, despite this work, some results remain controversial. Therefore, we conducted a systematic review and meta-analysis using 16S ribosomal RNA (16S rRNA) sequencing to explore GM alterations between patients with AD spectrum and healthy controls (HCs). A systematic and comprehensive literature search of PubMed, Web of Science, Embase, the Cochrane Library, China National Knowledge Infrastructure, China Biology Medicine disc database, WanFang database and Social Sciences Citation Index databases was conducted from inception to January 2023. Inclusion and exclusion criteria were strictly defined, and two researchers independently screened and extracted information from selected studies. Data quality were evaluated according to the "Cochrane system evaluator manual" and pooled data were comprehensively analyzed using Stata 14 software with standardized mean differences (SMDs) and 95% confidence intervals (95% CIs) used to measure effect sizes. Also, geographical heterogeneity effects (related to cohorts) on GM abundance were examined based on subgroup meta-analyses if sufficient studies reported outcomes. Finally, publication bias was assessed using funnel plots. Out of 1566 articles, 13 studies involving 581 patients with AD spectrum and 445 HCs were deemed eligible and included in our analysis. In summary, a decreased microbiota alpha diversity and a significantly distinct pattern of clustering with regard to beta diversity were observed in AD spectrum patients when compared with HCs. Comparative analyses revealed a decreased Ruminococcus, Faecalibacterium, Lachnospira, Dialister, Lachnoclostridium, and Roseburia abundance in AD spectrum patients while Phascolarctobacterium, Lactobacillus, and Akkermansia muciniphila were more enriched in patients when compared to HCs. Furthermore, regional variations may have been in play for intestinal microbes such as Bacteroides, Bifidobacterium, and Alistipes. Our meta-analysis identified alterations in GM abundance in patients with AD spectrum, with 12 genera from four major phyla significantly associated with AD. Moreover, we provided evidence for region-specific alterations in Bacteroides, Bifidobacterium, and Alistipes abundance. These findings may have profound implications for the development of innovative GM-based strategies to prevent and treat AD. https://doi.org/10.37766/inplasy2024.6.0067, identifier INPLASY202460067.

Implications of the microbiome and metabolic intermediaries produced by bacteria in breast cancer.

The breast microbiome presents a diverse microbial community that could affects health and disease states, in the context of breast cancer. Sequencing technologies have allowed describing the diversity and abundance of microbial communities among individuals. The complex tumoral microenvironment that includes the microbial composition could influence tumor growth. The imbalance of diversity and abundance inside the microbial community, known as dysbiosis plays a crucial role in this context. One the most prevalent bacterial genera described in breast invasive carcinoma are Bacillus, Pseudomonas, Brevibacillus, Mycobacterium, Thermoviga, Acinetobacter, Corynebacterium, Paenibacillus, Ensifer, and Bacteroides. Paenibacills genus shows a relation with patient survival. When the Paenibacills genus increases its abundance in patients with breast cancer, the survival probability decreases. Within this dysbiotic environment, various bacterial metabolites could play a pivotal role in the progression and modulation of breast cancer. Key bacterial metabolites, such as cadaverine, lipopolysaccharides (LPS), and trimethylamine N-oxide (TMAO), have been found to exhibit potential interactions within breast tissue microenvironments. Understanding the intricate relationships between dysbiosis and these metabolites in breast cancer may open new avenues for diagnostic biomarkers and therapeutic targets. Further research is essential to unravel the specific roles and mechanisms of these microbial metabolites in breast cancer progression.

HOXC6: A promising biomarker linked to an immunoevasive microenvironment in colorectal cancer based on TCGA analysis and cohort validation

HOXC6 plays an essential part of the carcinogenesis of solid tumors, but its functional relevance within the immune contexture in patients with colorectal cancer (CRC) is still uncertain. We intended to investigate the predictive value of HOXC6 expression for survival outcomes and its correlation with immune contexture in CRC patients by utilizing the Cancer Genome Atlas database (n = 619). Validation was performed in cohorts from Zhongshan Hospital (n = 200) and Shanghai Cancer Center (n = 300). Immunohistochemical (IHC) staining was utilized to compare the levels of immunocytes infiltrating the tumor between the groups with high and low expression of HOXC6. Elevated levels of HOXC6 expression in CRC tissues were linked to malignant progression and poor prognosis. HOXC6 as a risk factor for survival of CRC patients was confirmed. Receiver operating characteristic analysis confirmed its diagnostic value, and a reliable prognostic nomogram was constructed. KEGG analysis and GSEA showed that HOXC6 participated in immune regulation, and its expression was tightly linked to the abundance of infiltrating immunocytes. HOXC6 was upregulated in patients diagnosed with CRC within the two cohorts, and high HOXC6 levels were correlated with a worse prognosis. The high-HOXC6 expression group showed increased infiltration of Treg cells, CD68+ macrophages, CD66b+ neutrophils, and CD8+ T-cells and elevated levels of PD-L1 and PD-1, but decreased levels of granzyme B and perforin. These findings suggest that HOXC6 abundance in patients with CRC determines a poor prognosis, promotes an immunoevasive environment, and directs CD8+ T-cell dysfunction. HOXC6 is expected to become a prospective biomarker for the outcome of CRC.

Microbiomes in Post–Digital Rectal Exam Urine Samples are Linked to Prostate Cancer Risk

Abstract Purpose: Bacterial species including Cutibacterium acnes (C. acnes) have been associated with different inflammatory and neoplastic conditions in prostate cancer (PCa) tissue samples, but their clinical impact is unknown. Using next-generation sequencing (NGS)–based clinical reports, we investigated the differential abundance and incidence of microbiomes in post–digital rectal exam (DRE) urine samples from patients with PCa and a matched control group at low risk of PCa. Materials and Methods: A total of 200 post-DRE urine samples were analyzed, 100 from patients with histopathologically confirmed PCa and 100 from men at very low risk of PCa with PSA &lt;1.5 ng/mL as controls. Bacterial and fungal communities were characterized by NGS of 16S and internal transcribed spacer (ITS) loci, respectively, with species' relative abundances provided on physicians' clinical reports. The differential abundance and incidence of species between cancer and control groups were evaluated. Results: Microbes were reported in 39% and 56% of PCa and control group samples, respectively. C. acnes had a significantly higher relative abundance in patients with PCa vs controls (P &lt; .05), and C. acnes incidence rates were also nominally higher in patients with PCa as compared with controls (12.82% and 7.27%, respectively). By contrast, Finegoldia magna (F. magna) had a significantly higher relative abundance (P &lt; .05) and incidence rate (P &lt; .05) in controls as compared with patients with PCa. Conclusions: C. acnes was among the most prevalent bacterial species in PCa urine samples. F. magna identified in the low-risk group is responsible for production of equol, a soy metabolite associated with lowering risk of PCa, suggesting a role in prostate cancer chemoprevention.

Gut Microbiome Faecalibacterium Abundance in Patients with Plasma Cell Disorders Undergoing Autologous Hematopoietic Stem Cell Transplant Is Associated with Progression Free Survival

Background: Different aspects of the gut microbiota (GM), including diversity, abundance, and functionality, have been linked to the development, progression, response, and adverse events to therapy in plasma cell neoplasms (PCN). The primary goal of this study was to further investigate the relationship between the composition of the GM, focusing on the genus Faecalibacterium that contains the most common anaerobic commensal bacterium in the GM ( Faecalibacterium prausnitzii), and clinical outcomes of patients with PCN undergoing autologous hematopoietic stem cell transplant (HSCT). Methods: GM samples were collected prospectively between 2017 and 2021 at our institution as part of a phase III, randomized clinical trial including patients with malignant hematologic diseases undergoing either chemotherapy or transplant. Fecal samples were obtained at pre (baseline), mid (defined as at 1 week from baseline), and end (defined as at engraftment, absolute neutrophil count &amp;gt; 500 cells/mm 3) autologous HSCT and processed by 16S rDNA sequencing (V1-V3) using Illumina MiSeq to determine Faecalibacterium abundance at each prespecified time point. Progression free survival (PFS) and overall survival (OS) were computed via Kaplan-Meier estimate. Results: 83 evaluable patients underwent autologous HSCT for PCN, 54 (65%) as part of frontline therapy. 79 (95%) of the transplant recipients carried a diagnosis of Multiple Myeloma. Melphalan was used as the conditioning regimen, with 54 (65%) of the patients receiving a dose of 200 mg/m 2 (versus 140 mg/m 2). The median age of the patients was 64 (range, 31-79) years and 50 (60%) were men. With median time to follow up for survivors (n= 82, alive &amp;gt; 1 month post HSCT) of 32 (range, 0.7-61) months, the median PFS was 40 months and median OS was not reached. Faecalibacterium relative abundance was 3.5%, 1.7%, and 2% of the GM at pre, mid, and end transplant, respectively. Higher baseline Faecalibacterium abundance was significantly associated with superior PFS (n= 79) (HR= 0.92, p= 0.01) and OS (HR= 0.88, p= 0.008). Patients were partitioned into 2 groups, those with pre-transplant Faecalibacterium abundance above median and below median, to generate representative Kaplan-Meier curves for PFS (Figure 1). Greater reduction in Faecalibacterium abundance during transplant, and especially from pre to mid transplant, were significantly associated with worse PFS (n= 75) (HR= 1.08, p= 0.007; HR= 1.10, p= 0.004, respectively) and OS (HR= 1.09, p= 0.021; HR= 1.09, p= 0.04, respectively). There was no significant relationship between Faecalibacterium abundance and PFS at mid (n= 83) (HR= 1, p= 1), end (n= 83) (HR= 1.01, p= 0.7), or notably mid to end transplant (n= 75) (HR= 1, p= 0.9). Levels of the bacteria also did not associate with OS from mid to end transplant (n= 75) (HR 1.01, p= 0.8). Conclusions: Our study indicated that Faecalibacterium abundance in the GM changed rapidly early after autologous HSCT in patients with PCN likely due to melphalan administration. Higher baseline levels and smaller reduction in Faecalibacterium abundance predicted superior PFS. Further follow up with more mature data is needed to confirm OS associations. These findings support the need for further investigation into the role of GM and possible interventions to modify GM to improve outcomes to autologous transplant in patients with PCN.

The Ig Superfamily Ligand B7H6 Subjects Activated T Cells to NK Cell Surveillance and Limits CAR T Cell Persistence

Understanding the mechanisms that regulate T cell immunity is critical for the development of effective therapies for diseases associated with T cell dysfunction. Co-inhibitory ‘checkpoint molecules’ are tightly connected to T cell activation and balance excessive or prolonged immune activation by suppressing clonal expansion. Previous studies have suggested that NK cells might also suppress lymphocyte expansion, but the specific ligands enabling T cell recognition by natural cytotoxicity receptors (NCRs) remain unknown. In this study, we describe the physiological expression of the immunoglobulin superfamily ligand B7H6 on activated T cells and elucidated the functional and clinical implication of its recognition by autologous NK cells. In a targeted proteomics screen for mediators of NK cell recognition on T cells, we identified the Ig superfamily ligand B7H6 ( NCR3LG1) to be highly expressed by T cells upon activation. We show that, unlike other checkpoint molecules, B7H6 mediates NKp30-dependent recognition and subsequent cytolysis of activated T cells by autologous NK cells. Time-resolved deep RNA-sequencing of anti-CD3/CD28-stimulated peripheral blood-derived T cells from n=24 human donors revealed that NCR3LG1 transcript expression changes dynamically upon stimulation and that B7H6 surface protein recognition by NK cells initiates Granzyme B-mediated ‘fratricide’ as early as 8 hours post T cell stimulation. Genomic knockout of NCR3LG1 rendered activated T cells resistant to NK cell-mediated killing without affecting their viability or proliferative capacity. By analyzing transcriptomic profiles of 313,303 CD8+ and 283.930 CD4+ T cells in datasets of multiple sclerosis (MS, n = 62 patients), inflammatory bowel disease (IBD, n = 4 patients), hepatitis B virus infection (HBV, n = 23 patients) and 9 different cancer entities (n = 47 patients), we found a conserved B7H6+ T cell population that is prevalent in the tissue and blood of most individuals at 1-5% frequency. In line with our experimental data, B7H6 positivity was coupled to a highly activated cell state of T cells. Considering CAR T cell manufacturing involves robust activation and clonal expansion, we hypothesized the B7H6-NKp30 axis is a yet unknown, but relevant factor in limiting CAR T cell persistence. Clinical-grade CD19.CD28.4-1BBzeta-CAR T cell products as well as circulating CAR T cells in lymphoma patients indeed uniformly expressed NCR3LG1 transcripts and B7H6 surface protein and were lysed by autologous NK cells in vitro. We then co-injected CD19.CAR T cells and patient-autologous NK cells in leukemia-engrafted mice and observed reduced CAR T cell persistence in the peripheral blood of mice with NK cell co-injection. Co-injection of NK cells further increased tumor burden and resulted in significantly decreased survival in leukemia-bearing mice treated with CD19-recognizing CAR-T cells, while these effects could be minimized by NKp30 antibody blockade or prior genetic editing of NCR3LG1 on CAR T cells. Given the physiological coupling T cell activation and B7H6 expression, any T cell-directed immunotherapy regimen might trigger the B7H6-NKp30-cytolysis mechanism. We therefore analyzed tissue of patients that were treated with nivolumab and ipilimumab (NCT03416244). In contrast to the previous notion of largely tumor-targeting NK cell function, we observed an increased NK cell abundance in patients that failed to respond to treatment. Notably, we found both B7H6+ CD8+ and CD4+ T cells in situ and that their abundance and a high NK/T ratio was associated with reduced progression-free survival (PFS), even in initial clinical responders, and experimentally deducted a NKp30 dependent cytolysis of these T cells. Together, our data demonstrates a mechanism that couples T cell expansion to eventual clearance by NK cells. This concept differs from the previously known immune checkpoints, as those molecules act through intracellular downstream signaling in T cells. We show that NK cell surveillance via B7H6 counteracts anti-tumor activity of CAR-T cells in vivo and that the genetic or antibody-mediated inhibition of B7H6 enhances T cell persistence. We therefore suggest an alternative immune checkpoint that limits T cell expansion and persistence in physiological and cellular engineering contexts. Targeting the B7H6-NKp30 axis may offer a means to modulate T cell immunity across multiple disease entities.

IL-3 receptor signalling suppresses chronic intestinal inflammation by controlling mechanobiology and tissue egress of regulatory T cells

IL-3 has been reported to be involved in various inflammatory disorders, but its role in inflammatory bowel disease (IBD) has not been addressed so far. Here, we determined IL-3 expression...

Profiling gut microbiota signatures associated with the deficit subtype of schizophrenia: Findings from a case-control study

BackgroundPrevious studies have reported a variety of gut microbiota alterations in patients with schizophrenia. However, none of these studies has investigated gut microbiota in patients with the deficit subtype of schizophrenia (D-SCZ) that can be characterized by primary and enduring negative symptoms. Therefore, in this study we aimed to profile gut microbiota of individuals with D-SCZ, compared to those with non-deficit schizophrenia (ND-SCZ) and healthy controls (HCs). MethodsA total of 115 outpatients (44 individuals with D-SCZ and 71 individuals with ND-SCZ) during remission of positive and disorganization symptoms as well as 120 HCs were enrolled. Gut microbiota was analyzed using the 16 rRNA amplicon sequencing. Additionally, the levels of C-reactive protein (CRP), glucose and lipid metabolism markers were determined in the peripheral blood samples. ResultsAltogether 14 genera showed differential abundance in patients with D-SCZ compared to ND-SCZ and HCs, including Candidatus Soleaferrea, Eubacterium, Fusobacterium, Lachnospiraceae UCG-002, Lachnospiraceae UCG-004, Lachnospiraceae UCG-010, Libanicoccus, Limosilactobacillus, Mogibacterium, Peptococcus, Prevotella, Prevotellaceae NK3B31 group, Rikenellaceae RC9 gut group, and Slackia after adjustment for potential confounding factors. Observed alterations were significantly associated with cognitive performance in both groups of patients. Moreover, several significant correlations of differentially abundant genera with the levels of CRP, lipid profile parameters, glucose and insulin were found across all subgroups of participants. ConclusionFindings from the present study indicate that individuals with D-SCZ show a distinct profile of gut microbiota alterations that is associated with cognitive performance, metabolic parameters and subclinical inflammation.