Ameliorative effects of Lactobacillus against Aflatoxin B1

Lactobacilli are probiotics with Aflatoxin (AF) detoxification ability, found in fermented products, GIT of animals and environment. Purpose of this study was to investigate the ability of broiler isolates of Lactobacillus against Aflatoxin B1 (AFB1). For this purpose, 5 isolates of Lactobacillus from broiler gut were incubated with 100 ppb AFB1 in aqueous environment and effect of different parameters (cell fractions, time, temperature, pH) on detoxification was determined by HPLC. The ameliorative effect of Lactobacillus salivarius (LS) against AFB1 was studied in broiler. The results revealed that LS (CR. 4) showed the best results (in vitro) as compared to other isolates (L. salivarius (CR. 3, CR, 4), L. agilis (CE. 2.1, CE. 3.1) and L. crispatus (CE. 28). Cell debris of CR. 4 showed significantly higher detoxification (P<0.05). Maximum amount of AFB1 was detoxified at 30°C (97%), pH 4.0 (99%) and 6 h (99.97%). In vivo study showed that AFB1 decreased weight gain (1,269 ± 0.04 gm/ bird), feed consumed (2,161 ± 0.08 gm/ bird), serum total protein (2.42 ± 0.34 gm/ dl), serum albumin (0.5 ± 0.2 2 gm/dl) and antibody titer (4.2 ± 0.83). Liver function enzymes were found (alanine transaminase (ALT): 32 ± 10.7 U/L) and aspartate transaminase (AST): 314.8 ± 27 U/L) elevated in AFB1 fed broilers. Treatment with 1% LS not only decreased the toxic effects of AFB1 (group D) but also improved the overall health of broilers due to its probiotic effects (p<0.05) as compared to control negative (group A). The detoxification ability of LS was better than commercial binder (CB) (0.2% Protmyc). It was concluded that detoxification of AFB1 by Lactobacillus was strain, temperature, pH and time dependent. LS has detoxification ability against AFB1 in vivo.

Immunology and Immunotherapy of Endometriosis

Endometriosis is one of the most common gynecological and systemic diseases, with a remarkable immune background. Patients suffer from pain and fertility reduction. Due to the distinct immune component, an immunotherapeutic approach may gain importance in the future. In endometriosis, shifts in the cell fractions of the immune system are well known. Moreover, hypoxia concomitant with inflammation causes a disturbed immune response. The removal of endometriosis has a therapeutic effect, normalizes the immune disorders, and remains the most effective causative treatment in terms of pain and infertility. A key issue is whether a similar effect can be achieved for fertility with non-invasive immunotherapy where surgery is inadvisable or cannot be performed for various reasons. Numerous immunotherapy trials, including vaccines, were conducted on animals only, although the research is encouraging. Among the promising methods of non-specific immunotherapy is the administration of an ethiodized oil contrast. Moreover, due to the significant successes of immunotherapy in oncology, the possibility of immunotherapy affecting NK cells has been postulated. NK cells are responsible for the surveillance and apoptosis of ectopic cells. Expanding the arsenal of endometriosis treatment by immunotherapy is promising due to the significant contribution of immunological factors and the limitations of current treatment methods.

Immunological Profiles of The Breast Cancer Microenvironment Represented by Tumor-Infiltrating Lymphocytes and PD-L1 Expression

Purpose: Histologically assessed tumor-infiltrating lymphocytes and programmed cell death 1 ligand 1 (hPD-L1) are established prognostic or predictive biomarkers in certain subsets of breast cancer. However, the association with immune response complexity is not fully understood. In this study, the immune cell fractions in breast cancer tissue and blood were evaluated to analyze their association with histologically assessed tumor-infiltrating lymphocytes and PD-L1. Methods: Forty-five tumor and 18 blood samples were collected from patients with breast cancer. Total leukocyte counts, proportions of 11 types of immune cells, and PD-L1 expression in each cell fraction were evaluated using multicolor flow cytometry. Histologically assessed tumor-infiltrating lymphocytes and PD-L1 were evaluated using hematoxylin and eosin staining and immunohistochemistry, respectively. Results: The immune cell composition of blood was partly correlated with that of tumor tissue but the abundance ratio of each fraction was different between them. A higher histologically assessed tumor-infiltrating lymphocyte proportion was associated with increased leukocyte infiltration, a higher proportion of CD4+ and CD8+ T cells, and a lower proportion of natural killer cells and natural killer T cells. PD-L1 was highly expressed in the non-B-cell antigen-presenting cell fractions (monocyte/macrophage, nonclassical monocyte, myeloid-derived suppressor, dendritic, and myeloid dendritic cell) in tumors. Histologically assessed PD-L1 positivity reflected PD-L1 expression well in these fractions, as well as increased leukocyte infiltration in tumors. Conclusion: Our results indicate that histologically assessed tumor-infiltrating lymphocytes reflect differences in immune responses in the tumor microenvironment. Non-B-cell antigen-presenting cell fractions are primarily involved in the PD-L1 pathway in breast cancer microenvironments.

An adaptive method of defining negative mutation status for multi-sample comparison using next-generation sequencing

Background Multi-sample comparison is commonly used in cancer genomics studies. By using next-generation sequencing (NGS), a mutation's status in a specific sample can be measured by the number of reads supporting mutant or wildtype alleles. When no mutant reads are detected, it could represent either a true negative mutation status or a false negative due to an insufficient number of reads, so-called "coverage". To minimize the chance of false-negative, we should consider the mutation status as "unknown" instead of "negative" when the coverage is inadequately low. There is no established method for determining the coverage threshold between negative and unknown statuses. A common solution is to apply a universal minimum coverage (UMC). However, this method relies on an arbitrarily chosen threshold, and it does not take into account the mutations' relative abundances, which can vary dramatically by the type of mutations. The result could be misclassification between negative and unknown statuses. Methods We propose an adaptive mutation-specific negative (MSN) method to improve the discrimination between negative and unknown mutation statuses. For a specific mutation, a non-positive sample is compared with every known positive sample to test the null hypothesis that they may contain the same frequency of mutant reads. The non-positive sample can only be claimed as “negative” when this null hypothesis is rejected with all known positive samples; otherwise, the status would be “unknown”. Results We first compared the performance of MSN and UMC methods in a simulated dataset containing varying tumor cell fractions. Only the MSN methods appropriately assigned negative statuses for samples with both high- and low-tumor cell fractions. When evaluated on a real dual-platform single-cell sequencing dataset, the MSN method not only provided more accurate assessments of negative statuses but also yielded three times more available data after excluding the “unknown” statuses, compared with the UMC method. Conclusions We developed a new adaptive method for distinguishing unknown from negative statuses in multi-sample comparison NGS data. The method can provide more accurate negative statuses than the conventional UMC method and generate a remarkably higher amount of available data by reducing unnecessary “unknown” calls.

The Immune Infiltration in HNSCC and Its Clinical Value: A Comprehensive Study Based on the TCGA and GEO Databases

Background. Being potential field of research for tumor immunological therapy, the head and neck squamous cell carcinoma (HNSCC) is one of most discussed types of tumor. Recently, some clinical trials have also used immunological therapy and demonstrated a subset of HNSCC patients who have shown a clear longer survival time. Objective. To conduct further studies and deeper research in the immunological oncology of HNSCC, a more detailed description and comprehending of the complicated landscape of immune infiltrative may be required. Methods. Firstly, we have described the fraction of different infiltrating immune cells in the HNSCC tumor and then compared it to the normal tissue, and secondly, we have explored the clinical implications of various infiltrated immune cell fractions meticulously. The gene expression profiles of HNSCC tissue were obtained from databases of TCGA and GEO and utilized the deconvolution algorithm (CIBERSORT) to presume the fractions of 22 several immune sensitive cells. Results. Our results indicated that the immune infiltrating cell fractions were considerably different between HNSCC tumor tissue and paired normal tissue, but at the same time, we found a potential internal correlation among the immune cells and also showed the association between immune infiltrating cells and their clinical characteristics. It is worth noting that the resting dendritic cells and M1 macrophages were linked with a favorable prognosis, while the CD4+ T cells with a poorer outcome. Conclusion. Fractions of immune cell percentage were also associated with tumors’ pathological grade, age, and TNM stage.

Identification of a Novel Proliferating Cell Fraction in Chronic Lymphocytic Leukaemia with High Expression of IgM and Chemokine Receptors

Chronic lymphocytic leukaemia (CLL) is characterised by the accumulation of malignant CD5+ B cells in the peripheral blood (PB), secondary lymphoid tissues and bone marrow. Currently considered an incurable disease, B cell receptor (BCR) signalling plays a key role in the disease aetiology as evidenced by the therapeutic success of BCR signalling inhibitors such as ibrutinib. Previous studies using incorporation of 2H-labelling of DNA in vivo demonstrated sub-clonal heterogeneity in PB CLL cell fractions sorted based on reciprocal densities of chemokine C-X-C motif receptor 4 (CXCR4) and CD5. The CXCR4 loCD5 hi fraction was shown to be enriched in recently born proliferating cells while the CXCR4 hiCD5 lo fraction consists of resting, quiescent cells thought to reflect their migratory and BCR signalling histories in tissue. Whilst these proliferating/resting fractions have since been more closely examined, the remaining bulk PB CLL population has been left relatively unexplored leaving other therapeutically relevant cell fractions undetected. Here, we have comprehensively analysed the phenotype of subpopulations of PB cells from 11 CLL patients using flow cytometry to identify activated and proliferating cell fractions. CD19 +CD5 +cells were divided into 9 fractions based on CXCR4/CD5 densities and to permit comparisons between fractions, each cell fraction was defined as containing 1-2% of the total clonal CD19 +CD5 + population. Surprisingly, we detected enrichment for Ki67+ proliferating cells and high expression of AID in the cell fraction with highest expression levels of both CXCR4 and CD5 (CXCR4 hiCD5 hi), demonstrating that CXCR4 loCD5 hi cells are not the only proliferating fraction in the blood. Moreover, we could detect mitotic cells in the CXCR4 hiCD5 hi fraction using imaging flow cytometry of a nuclear stain. This CXCR4 hiCD5 hi fraction showed the highest surface expression levels of IgM, CD86, CCR7, CXCR3 and CXCR5 of all the fractions assessed (p&lt;0.05), indicating they are highly activated and primed for migration to lymph nodes (LNs) for further activation and proliferation. Proliferation of CLL cells is highest in secondary lymphoid tissues, however the phenotype of proliferating cells in tissue is unknown. To examine the phenotype of proliferating CLL cells in LNs, we analysed a fine-needle aspirate obtained from an enlarged cervical node using flow cytometry and compared this to a matched PB sample. Flow cytometric gates set on the PB sample were used to define and quantify LN cell fractions. Expression levels of both Ki67 and surface IgM were highest in the CXCR4 hiCD5 hi fraction which was expanded to 20% of the CD19 +CD5 + population in the LN whilst CXCR4 loCD5 hi cells (accounting for 2% of the bulk LN population) expressed very low surface IgM and Ki67 levels, suggesting CXCR4 hiCD5 hi cells may be the most proliferative cells in CLL. The CXCR4 loCD5 hi cell fraction has been shown to be a key target of ibrutinib, however the impact of ibrutinib on the CXCR4 hiCD5 hi fraction is unknown. Administration of ibrutinib to PB CLL cells for 48hr in vitro resulted in selective targeted depletion of the CXCR4 loCD5 hi fraction, as evidenced by induction of apoptotic markers in this compartment; conversely, persistent cells after 48hr ibrutinib administration in vitro were exclusively of the CXCR4 hi phenotype. In conclusion, we have identified a potentially dangerous fraction of proliferating cells in the PB of CLL patients with high expression of CXCR4, CD5, IgM, CCR7, CXCR3 and CXCR5 open for both migration to tissue and reception of BCR signals. Furthermore, CXCR4 hiCD5 hi cells in the periphery may closely mirror tissue-resident activated cell phenotypes and may represent critical targets for therapeutic intervention, particularly in high-risk CLL patients refractory to BCR inhibitor therapies. Disclosures Patten: ROCHE: Research Funding; GILEAD SCIENCES: Honoraria, Research Funding; NOVARTIS: Honoraria; JANSSEN: Honoraria; ASTRA ZENECA: Honoraria; ABBVIE: Honoraria.

Characterization of Somatic Mosaicism and Mutational Profiling of Clonal Hematopoiesis Compared to MDS and sAML Depicts Diversities of Clonal Evolution

Background: Clonal hematopoiesis (CH) describes the presence of genetic alterations and expansion of clonal cell populations in the peripheral blood (PB) of individuals without clinical manifestation of a hematologic malignancy. CH is a common, age-related state. However, individuals carrying CH are at greater risk for hematologic cancer. It has been shown that presence of TP53- and other high-risk mutations, variant allele frequency (VAF) &gt;10% or multiple mutations in CH carriers may confer a higher risk of preleukemic development and transformation to myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML). Nevertheless, further insights into the role of CH in clonal evolution towards leukemia and elaborating features that are predictive of leukemic progression are needed. Aims: We have recently shown that CH is common in individuals undergoing hip replacement surgery (Hecker, Hartmann et al., Blood 2021). Here, we compared mutational spectrum in these CH individuals to MDS and secondary AML (sAML) cohorts. Additionally, we analyzed spatial and lineage distribution of CH and longitudinally monitored CH and MDS clones over time. Methods: Samples from individuals without known hematologic disease undergoing hip replacement surgery (n=288 samples from 261 individuals), patients with MDS (n=92) or sAML (n=123) were screened for variants in 68 leukemia-associated genes using a targeted sequencing approach (VAF cut off, 1%). Follow-up (FU) PB samples were available for 21 individuals with CH and 16 untreated low-risk MDS patients, 6-24 months after screening. n=5 CH bone marrow (BM) samples carrying six ASXL1-mutations were sorted for seven different cell fractions. Results: At screening, variants were detected in 127/261 (49%) healthy individuals, 84/92 (91%) MDS and 117/123 (95%) sAML patients, with median VAFs of 2.7% (ranging from 1-44%), 18.8% (1.1-87%) and 37.1% (1-99%), respectively. Individuals with CH had a median number of 1 variant per individual, whereas median detected variants per patient increased with clonal evolution with 3 variants in the MDS and 4 variants per patient in the sAML cohort. CH, MDS and sAML showed entity-specific mutation profiles (Figure 1A). Most variants in CH affected epigenetic modifiers, while mutations in splicing factors, signaling pathways and transcription factors increased with clonal progression. During FU, untreated low-risk MDS patients more frequently gained additional mutations compared to CH individuals (7/16 vs 2/21, respectively; p=0.024). However, we did not observe significant changes in clone sizes over time. In 17 hip replacement individuals both femoral heads were removed simultaneously, allowing paired analysis of two different hematopoietic sites. CH prevalence in this subgroup was 70.6% (12/17). Ten individuals showed identical mutation patterns in BM obtained from the right and left femoral head, with little differences in VAFs (Table 1). In contrast, two other individuals showed significant differences in variant detection comparing one to the other side: ASXL1-mutations were only present in one hip sample, whereas all the other variants were detectable in both sides (p&lt;0.001), indicating possible spatial heterogeneity of CH clones in the BM compartment. To further characterize ASXL1 mosaicism across hematopoietic lineages and differentiation stages, we sorted and sequenced n=5 CH BM samples carrying six ASXL1-mutations for seven different hematopoietic cell fractions. In all cases ASXL1-mutations were identified in CD34 +CD38 -CD90 + hematopoietic stem cells (HSC). VAFs of ASXL1-mutations were differentially distributed (p=0.0049, Kruskal Wallis test): detected VAFs were significantly higher in HSC and common myeloid progenitors (CMP) compared to VAFs in T-cells (p=0.045 and p=0.011, respectively; Dunn´s multiple comparison test; Figure 1B). Conclusions: CH, MDS and sAML show characteristic mutation profiles that remained stable over a 6-24-month period. Gains of additional variants and clonal expansion associated with disease progression. Cellular distribution analysis of ASXL1 CH variants revealed characteristic repartition patterns within the hematopoietic differentiation tree. Additionally, differences in variant detection between cellular BM compartments indicates spatial heterogeneity of CH clones warranting further investigation. J.S.H. and L.H. contributed equally. Figure 1 Figure 1. Disclosures Platzbecker: Geron: Honoraria; Takeda: Honoraria; AbbVie: Honoraria; Celgene/BMS: Honoraria; Janssen: Honoraria; Novartis: Honoraria. Goetze: BMS/Celgene: Other: Advisory Board, Research Funding; Abbvie: Other: Advisory Board.

Sub-Cellular Metabolomics Contributes Mitochondria-Specific Metabolic Insights to a Mouse Model of Leigh Syndrome

Direct injury of mitochondrial respiratory chain (RC) complex I by Ndufs4 subunit mutations results in complex I deficiency (CID) and a progressive encephalomyopathy, known as Leigh syndrome. While mitochondrial, cytosolic and multi-organelle pathways are known to be involved in the neuromuscular LS pathogenesis, compartment-specific metabolomics has, to date, not been applied to murine models of CID. We thus hypothesized that sub-cellular metabolomics would be able to contribute organelle-specific insights to known Ndufs4 metabolic perturbations. To that end, whole brains and skeletal muscle from late-stage Ndufs4 mice and age/sex-matched controls were harvested for mitochondrial and cytosolic isolation. Untargeted 1H-NMR and semi-targeted LC-MS/MS metabolomics was applied to the resulting cell fractions, whereafter important variables (VIPs) were selected by univariate statistics. A predominant increase in multiple targeted amino acids was observed in whole-brain samples, with a more prominent effect at the mitochondrial level. Similar pathways were implicated in the muscle tissue, showing a greater depletion of core metabolites with a compartment-specific distribution, however. The altered metabolites expectedly implicate altered redox homeostasis, alternate RC fueling, one-carbon metabolism, urea cycling and dysregulated proteostasis to different degrees in the analyzed tissues. A first application of EDTA-chelated magnesium and calcium measurement by NMR also revealed tissue- and compartment-specific alterations, implicating stress response-related calcium redistribution between neural cell compartments, as well as whole-cell muscle magnesium depletion. Altogether, these results confirm the ability of compartment-specific metabolomics to capture known alterations related to Ndufs4 KO and CID while proving its worth in elucidating metabolic compartmentalization in said pathways that went undetected in the diluted whole-cell samples previously studied.

In vitro biosynthesis of organic selenium by Lactobacillus casei from inorganic selenium forms

The bioconversion of selenium in the form of sodium selenite (Na2 SeO3 ) (SeIV) or sodium selenate (Na2 SeO4 ) (SeVI) to organic form by Lactobacillus casei (L. casei) was investigated in vitro. MRS media was supplemented with 1, 2, 5, 10 or 20 ppm of Se, inoculated with 2% starter culture with about 105 cfu/ ml of L. casei and then incubated up to 24 hrs at 37o C. Increasing of selenite “Se(IV)” concentrations in the media markedly reduced the bacterial growth compared to selenate “Se(VI)” indicating cytotoxic effect of selenite. The media supplemented with 5 ppm or more of Se(IV) became reddish after 24 hr of incubation as a result of the formation of 100-200 nanometer particles of selenium (SeNPs). Se speciation of the cultured media supernatants and its corresponding cell fractions was carried out by HPLC-ICP-MS technique. The bioconversion rate of Se to organic form by L. casei was extremely higher in Se(IV) than Se(VI) in both fractions, however the media supernatant contained the highest content. Increasing the media Se content resulted in gradual increase of organic Se concentration in both cells and supernatant fractions. The medium supplemented with 1 ppm Se(IV) was completely depleted from the inorganic Se as it completely converted to organic form. Although the cell fractions from all Se(VI) supplemented media contained only organic Se, the media supernatant contained significant residual amount of the inorganic form. Our results demonstrate the ability of L. casei to convert Se(IV) or Se(VI) up to 20 ppm to organic form(s) either in the cultured media or inside the bacterial cells. However, Se(IV) but not Se(VI), at a limit concentration of 1 ppm, was completely converted and accumulated in an organic form in the cell fraction and the cultured medium.

Administration of breast milk cell fractions to neonates with birthweight equal to or less than 1800 g: a randomized controlled trial

Background Most premature and very low birthweight infants cannot tolerate breast milk feeding in the first few days of life and are deprived of its benefits. This study evaluates the clinical outcomes of administering breast milk cell fractions to neonates with a birthweight of ≤1800 g. Methods We conducted a randomized controlled trial on 156 infants in the neonatal intensive care unit of Mahdieh Maternity Hospital in Tehran, Iran, from May 2019 to April 2020. All neonates with a birthweight ≤1800 g were enrolled and divided into intervention and control groups using stratified block randomization. Neonates in the intervention group received the extracted breast milk cell fractions (BMCFs) of their own mother’s milk after being centrifuged in the first 6 to 12 h after birth. The control group received routine care, and breastfeeding was started as soon as tolerated in both groups. Study outcomes were necrotizing enterocolitis (NEC), death, and in-hospital complications. Results We divided participants into two groups: 75 neonates in the intervention group and 81 neonates in the control group. The mean birthweight of neonates was 1390.1 ± 314.4 g, and 19 (12.2%) neonates deceased during their in-hospital stay. The incidence of NEC was similar in both groups. After adjustment for possible confounders in the multivariable model, receiving BMCFs were independently associated with lower in-hospital mortality (5 [26.3%] vs. 70 (51.1%]; odds ratio (OR): 0.24; 95% confidence interval [CI] 0.07, 0.86). Also, in a subgroup analysis of neonates with birthweight less than 1500 g, in-hospital mortality was significantly lower in the intervention group (4 [9.5%] vs. 13 [30.2%]; OR: 0.24; 95% CI 0.07, 0.82). There were no differences in major complications such as bronchopulmonary dysplasia and retinopathy of prematurity between the two groups. No adverse effects occurred. Conclusions Our research demonstrated a significantly lower mortality rate in neonates (with a birthweight of ≤1800 g) who received breast milk cell fractions on the first day of life. Since this is a novel method with minimal intervention, we are looking forward to developing and evaluating this method in larger studies. Trial registration IIranian Registry of Clinical Trials. Registered 25 May 2019, IRCT20190228042868N1.