Developing a genetic testing panel for evaluation of morbidities in kidney transplant recipients.

Cardiovascular disease, infection, malignancy, and thromboembolism are major causes of morbidity and mortality in kidney transplant recipients (KTR). Prospectively identifying monogenic conditions associated with post-transplant complications may enable personalized management. Therefore, we developed a transplant morbidity panel (355 genes) associated with major post-transplant complications including cardiometabolic disorders, immunodeficiency, malignancy, and thrombophilia. This gene panel was then evaluated using exome sequencing data from 1590 KTR. Additionally, genes associated with monogenic kidney and genitourinary disorders along with American College of Medical Genetics (ACMG) secondary findings v3.2 were annotated. Altogether, diagnostic variants in 37 genes associated with Mendelian kidney and genitourinary disorders were detected in 9.9% (158/1590) of KTR; 25.9% (41/158) had not been clinically diagnosed. Moreover, the transplant morbidity gene panel detected diagnostic variants for 56 monogenic disorders in 9.1% KTRs (144/1590). Cardiovascular disease, malignancy, immunodeficiency, and thrombophilia variants were detected in 5.1% (81), 2.1% (34), 1.8% (29) and 0.2% (3) among 1590 KTRs, respectively. Concordant phenotypes were present in half of these cases. Reviewing implications for transplant care, these genetic findings would have allowed physicians to set specific risk factor targets in 6.3% (9/144), arrange intensive surveillance in 97.2% (140/144), utilize preventive measures in 13.2% (19/144), guide disease-specific therapy in 63.9% (92/144), initiate specialty referral in 90.3% (130/144) and alter immunosuppression in 56.9% (82/144). Thus, beyond diagnostic testing for kidney disorders, sequence annotation identified monogenic disorders associated with common post-transplant complications in 9.1% of KTR, with important clinical implications. Incorporating genetic diagnostics for transplant morbidities would enable personalized management in pre- and post-transplant care.

Sustained post-rituximab B-cell depletion is common in ANCA-associated vasculitis and is affected by sex and renal function.

OBJECTIVE: Despite the increasing use of rituximab in anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV), it remains unclear what the optimal dosing is, especially for maintenance of remission. A deeper understanding of post-rituximab B-cell repopulation patterns may aid better-tailored treatment. METHODS: This is a monocentric, retrospective study including ANCA-positive AAV patients receiving a single course of rituximab induction. CD19+ B cells were longitudinally monitored with flow cytometry. B-cell repopulation was defined as CD19+ >10 cells/µL. RESULTS: Seventy-one patients were included, the majority with microscopic polyangiitis (75%), myeloperoxidase-ANCA positivity (75%) and with renal involvement (79%). During a median follow-up of 54 months since the first rituximab infusion, 44 patients (62%) repopulated B cells, with a median time to repopulation of 39 months (range 7-102). Patients experiencing B-cell depletion lasting longer than the overall median time to repopulation (39 months) exhibited a lower risk of flare and higher risk of serious infection. In multivariate Cox regression, higher estimated glomerular filtration rate (eGFR) [hazard ratio (HR) 1.84, 95% confidence interval (CI) 1.13-2.98 per 30 mL/min/1.73 m2 eGFR] and female sex (HR 2.70, 95% CI 1.37-5.31) were independent predictors of increased rate of B-cell repopulation. CONCLUSION: A subset of AAV patients develop sustained post-rituximab B-cell depletion, which associates with reduced risk of flare and increased risk of serious infection in the long term. Preserved renal function and female sex are associated with faster B-cell repopulation. These observations further highlight the need to personalize immunosuppression to improve clinical outcomes.

Effect of Yogurt Enrichment with Wood Tannin during Shelf Life: Focus on Physicochemical, Microbiological, and Sensory Characteristics.

Six food-grade tannins obtained from different woods were used as a source of polyphenolic compounds at two concentrations (0.5% and 1% w/w) in yogurt formulations and monitored during 3 weeks of storage. Yogurt containing tannins showed significantly higher total phenolic content (+200%), antioxidant activity (+400%), and syneresis (+100%) than control. These changes were higher with fortification at 1%. Tannin origin also significantly influenced the yogurt composition and yogurt obtained from a Turkish gall showed higher values of total phenolic content (4 mg GAE/g) and antioxidant activity (17 µM Trolox/g). Yogurt color was evaluated by CIELab parameters, and their values were influenced by tannin origin and concentration. The addition of tannins did not significantly affect the number of lactic acid bacteria. Yogurt with a lower amount of tannins (0.5% w/w) received higher consumer acceptability but significant differences in preferences were due to tannin origin. In particular, yogurt added with tannin obtained from Quebracho wood at 1% w/w showed higher consumer preference. The obtained results would provide an opportunity for dairy producers to develop a novel dairy food with high nutritional quality.

Predictors of hypogammaglobulinemia in ANCA-associated vasculitis after a rituximab-based induction: a multicentre study.

OBJECTIVES: Rituximab has become the cornerstone of induction treatment in ANCA-associated vasculitis (AAV). B-cell depletion may increase the risk of hypogammaglobulinemia, potentially leading to severe infections. This study aims to assess factors associated with hypogammaglobulinemia in AAV patients treated with rituximab. METHODS: This retrospective cohort study included AAV patients treated with rituximab induction in 14 European centres. Severe adverse events (SAEs) were defined as episodes requiring hospitalization or intravenous antibiotics, malignancies, or death. Linear and logistic regression were used to identify predictors of IgG levels and of the risk of hypogammaglobulinemia, defined as IgG ≤7 g/l at 6 months. RESULTS: The study included 227 patients. IgG levels at 6 months were lower than baseline (P < 0.001). Patients requiring intravenous antibiotics during the first 6 months had lower IgG levels at 6 months (P = 0.004). Age [ß (95% CI): -0.23 (-0.38, -0.08) per 10 years, P = 0.003], oral glucocorticoid dose at induction [ß (95% CI): -0.37 (-0.51, -0.24) per sqrt-transformed mg prednisone, P < 0.001] and concomitant use of intravenous glucocorticoid pulses [ß (95% CI): -0.88 (-1.73, -0.02), P = 0.044] were associated with IgG levels at 6 months. Hypogammaglobulinemia was identified in 97 (42.7%) patients. In multivariable logistic regression, factors associated with the risk of hypogammaglobulinemia were age [OR (95% CI): 1.46 (1.15, 1.86) per 10 years, P = 0.002] and oral glucocorticoid dose at induction [OR (95% CI): 1.52 (1.23, 1.89) per 10 mg prednisone, P < 0.001]. CONCLUSIONS: In AAV patients treated with rituximab, hypogammaglobulinemia at 6 months after induction is common, and lower IgG levels are associated with serious infections. The risk of hypogammaglobulinemia in these patients increases with age and higher glucocorticoid doses.

The Role of Rituximab in Primary Focal Segmental Glomerular Sclerosis of the Adult.

Introduction: Primary focal segmental glomerular sclerosis (FSGS) is a rare, likely immune-mediated disease. Rituximab (RTX) may play a role in management, although data in adults are scanty. Methods: We collected cases of RTX-treated primary FSGS within the Italian Society of Nephrology Immunopathology Working Group and explored response rate (24-hour proteinuria <3.5 g and <50% compared with baseline, stable estimated glomerular filtration rate). Results: A total of 31 patients were followed for at least 12 months; further follow-up (median 17 months, interquartile range [IQR] 15-33.5) was available for 11. At first RTX administration, median creatinine and 24-hour proteinuria were 1.17 mg/dl (IQR 0.83-1.62) and 5.2 g (IQR 3.3-8.81), respectively. Response rate at 3, 6, and 12 months was 39%, 52%, and 42%, respectively. In the first 12 months, creatinine level remained stable whereas proteinuria and serum albumin level improved, with an increase in the proportion of patients tapering other immunosuppressants. There were 6 patients who were retreated with RTX within 12 months, either for proteinuria increase or refractory disease; only the 2 responders to the first RTX course experienced a further response. At univariate analysis, 6-month response was more frequent in steroid-dependent patients (odds ratio [OR] 7.7 [95% CI 1.16-52.17]) and those with proteinuria <5 g/24 h (OR 8.25 [1.45-46.86]). During long-term follow-up, 4 of 5 responders at 12 months maintained a sustained response, either without further immunosuppression (2 of 4) or with pre-emptive RTX (2 of 4); 1 relapsed and responded to RTX retreatment. Conclusion: RTX may be an option in primary FSGS, especially in steroid-dependent patients, with 24-hour proteinuria <5 g and previously responders to RTX. Optimal long-term management for responders is unclear, with some patients experiencing sustained remission and others requiring RTX retreatment, either preemptive or after rising proteinuria.

Coffee Silverskin as a Functional Ingredient in Vegan Biscuits: Physicochemical and Sensory Properties and In Vitro Bioaccessibility of Bioactive Compounds.

Coffee silverskin (CS), a by-product obtained by the coffee industry after the roasting process, is scientifically known to be a source of fiber and polyphenols, which could contribute to human health. In this work, the production of CS-enriched biscuits is proposed, where the CS from Arabica and Robusta type and a decaffeinated blend of the two were used at three different levels as a replacement for wheat flour. The biscuits were analyzed for their physicochemical properties, consumer acceptability, and the bioaccessibility of polyphenols after in vitro digestion was estimated in order to identify the formulation most appreciated by consumers and most promising in terms of nutritional and biofunctional potential. From the results, CS-based biscuits represent an interesting possibility to create a more sustainable coffee chain, thanks to the valorization of the silverskin, especially if a decaffeinated CS is considered. In fact, a 4% replacement of the wheat flour with decaffeinated CS is able to give a final product with a high content of accessible polyphenols and a biscuit appreciated by the consumer.

SARS-CoV-2 infection in dialysis and kidney transplant patients: immunological and serological response.

BACKGROUND: Dialysis and kidney transplant patients with moderate-severe COVID-19 have a high mortality rate, around 30%, that is similar in the two populations, despite differences in their baseline characteristics. In these groups, the immunology of the disease has been poorly explored. METHODS: Thirty-two patients on dialysis or with kidney transplant and SARS-CoV-2 infection requiring hospitalization (COV group) were included in our study. Lymphocyte subsets, dendritic cell (DC) counts and monocyte activation were studied. SARS-CoV-2 anti-spike/anti-nucleocapsid were monitored, and baseline cytokines and chemokines were measured in 10 patients. RESULTS: The COV group, compared to healthy subjects and uninfected dialysis/kidney transplant controls, showed lower numbers of CD4 + and CD8 + T cells, Natural-Killer (NK), B cells, plasmacytoid and myeloid DCs, while the proportion of terminally differentiated B-cells was increased. IL6, IL10, IFN-α and chemokines involved in monocyte and neutrophil recruitment were higher in the COV group, compared to uninfected dialysis/kidney transplant controls. Patients with severe disease had lower CD4 + , CD8 + and B-cell counts and lower monocyte HLA-DR expression. Of note, when comparing dialysis and kidney transplant patients with COVID-19, the latter group presented lower NK and pDC counts and monocyte HLA-DR expression. Up to 60 days after symptom onset, kidney transplant recipients showed lower levels of anti-spike antibodies compared to dialysis patients. CONCLUSIONS: During SARS-CoV-2 infection, dialysis and kidney transplant patients manifest immunophenotype abnormalities; these are similar in the two groups, however kidney transplant recipients show more profound alterations of the innate immune system and lower anti-spike antibody response.

Chromatin Velocity reveals epigenetic dynamics by single-cell profiling of heterochromatin and euchromatin.

Recent efforts have succeeded in surveying open chromatin at the single-cell level, but high-throughput, single-cell assessment of heterochromatin and its underlying genomic determinants remains challenging. We engineered a hybrid transposase including the chromodomain (CD) of the heterochromatin protein-1α (HP-1α), which is involved in heterochromatin assembly and maintenance through its binding to trimethylation of the lysine 9 on histone 3 (H3K9me3), and developed a single-cell method, single-cell genome and epigenome by transposases sequencing (scGET-seq), that, unlike single-cell assay for transposase-accessible chromatin with sequencing (scATAC-seq), comprehensively probes both open and closed chromatin and concomitantly records the underlying genomic sequences. We tested scGET-seq in cancer-derived organoids and human-derived xenograft (PDX) models and identified genetic events and plasticity-driven mechanisms contributing to cancer drug resistance. Next, building upon the differential enrichment of closed and open chromatin, we devised a method, Chromatin Velocity, that identifies the trajectories of epigenetic modifications at the single-cell level. Chromatin Velocity uncovered paths of epigenetic reorganization during stem cell reprogramming and identified key transcription factors driving these developmental processes. scGET-seq reveals the dynamics of genomic and epigenetic landscapes underlying any cellular processes.

Grape Pomace as a New Coagulant for Tofu Production: Physicochemical and Sensory Effects.

Tofu, one of the most important products made from soymilk, is obtained through a coagulation process performed with various coagulants (acids, salts and, enzymes). In this study, innovative tofu samples were produced using the grape pomace (GP) powders of different varieties (Barbera, Chardonnay, Moscato, and Pinot Noir) with different origins (fermented and distilled) at two concentration levels (2.5% and 5% w/v) as coagulants, and comparisons with traditional tofu were made. Physicochemical characteristics, phenolic contents, radical scavenging activity levels, textural properties, and consumer acceptability were evaluated. The moisture, protein content, and pH levels of GP tofu samples were slightly lower than those of traditional tofu. Regarding textural parameters, except for hardness, all other parameters were significantly lower in GP tofu samples, with differences due to GP concentration. The colours of GP tofu varied from amber-yellow to violet according to the GP origin. The blue-violet colours were observed predominantly in tofu samples obtained with Barbera and Pinot Noir GPs, while the other GP tofu samples showed amber-yellow colours. The concentrations of polyphenols were 2-10 times higher than in traditional tofu, while the radical scavenging activity levels were 9-80 times higher. The GP tofu samples were favoured by consumers, with small differences among the GP varieties.

[The complex etiopathogenesis of focal segmental glomerulosclerosis].

Focal segmental glomerulosclerosis (FSGS) is a pathological spectrum subtended by heterogeneous etiologies. A good knowledge of FSGS and its causes should be included in the nephrologists' clinical background, as it deeply influences the subsequent management of the affected patients. In fact, while immunosuppressive treatment should be considered in idiopathic FSGS, the treatment of secondary forms should primarily aim at curing or containing the underpinning etiologic factors. Furthermore, in contrast to secondary FSGS, idiopathic FSGS tends to relapse after kidney transplantation. Although FSGS has a wide spectrum of etiologies, several pathogenetic "moments" are shared. Furthermore, recent studies have identified a pool of glomerular cells potentially capable of regenerating lost podocytes; these cells might represent a promising therapeutic target. The primary aim of this review is to describe the etiologic factors associated with FSGS, with a focus on the main pathogenetic mechanisms involved in its development.

Update on ANCA-associated vasculitis: from biomarkers to therapy.

ANCA-associated vasculitis (AAV) are the prototype of a disease characterised by the presence of a biomarker; ANCA positivity in fact is recorded in 90% of cases of GPA and MPA. The role of ANCA in the management of AAV ranges from diagnostic to prognostic purposes with also therapeutic implications. Changes in clinical practice with the increased use of rituximab have drawn attention to B-cells as a biomarker able to contribute to patient management. Cytokines and other circulating factors, although still at a research stage, may represent future biomarkers of interest or even therapeutic options. From the point of view of renal involvement in AAV, proteinuria and microhematuria are still the biomarkers employed in everyday clinical practice with a proposed role for emerging ones (MCP1, CD163 and CD25). The aim of this review is to discuss the role of well-known biomarkers in everyday clinical management of AAV patients as well as future perspectives for those that are still at a research stage with attention to therapeutic implications.