Section E6.1-6.6 of the American College of Medical Genetics and Genomics (ACMG) Technical Laboratory Standards: Cytogenomic studies of acquired chromosomal abnormalities in neoplastic blood, bone marrow, and lymph nodes.

Cytogenomic analyses of acquired clonal chromosomal abnormalities in neoplastic blood, bone marrow, and/or lymph nodes are instrumental in the clinical management of patients with hematologic neoplasms. Cytogenetic analyses assist in the diagnosis of such disorders and can provide important prognostic information. Furthermore, cytogenetic studies can provide crucial information regarding specific genetically defined subtypes of these neoplasms that may have targeted therapies. At time of relapse, cytogenetic analysis can confirm recurrence of the original neoplasm, detect clonal disease evolution, or uncover a new unrelated neoplastic process. This section deals specifically with the technical standards applicable to cytogenomic studies of acquired clonal chromosomal abnormalities in neoplastic blood, bone marrow, and/or lymph nodes. This updated Section E6.1-6.6 supersedes the previous Section E6 in Section E: Clinical Cytogenetics of the American College of Medical Genetics and Genomics Technical Standards for Clinical Genetics Laboratories.

Section E6.7-6.12 of the American College of Medical Genetics and Genomics (ACMG) Technical Laboratory Standards: Cytogenomic studies of acquired chromosomal abnormalities in solid tumors.

Clinical cytogenomic studies of solid tumor samples are critical to the diagnosis, prognostication, and treatment selection for cancer patients. An overview of current cytogenomic techniques for solid tumor analysis is provided, including standards for sample preparation, clinical and technical considerations, and documentation of results. With the evolving technologies and their application in solid tumor analysis, these standards now include sequencing technology and optical genome mapping, in addition to the conventional cytogenomic methods, such as G-banded chromosome analysis, fluorescence in situ hybridization, and chromosomal microarray analysis. This updated Section E6.7-6.12 supersedes the previous Section E6.5-6.8 in Section E: Clinical Cytogenetics of the American College of Medical Genetics and Genomics Standards for Clinical Genetics Laboratories.

Effects of Mineralocorticoid Receptor Antagonists for Chronic Kidney Disease: A Systemic Review and Meta-Analysis.

BACKGROUND: Mineralocorticoid receptor blockade could be a potential approach for the inhibition of chronic kidney disease (CKD) progression. The benefits and harms of different mineralocorticoid receptor antagonists (MRAs) in CKD are inconsistent. OBJECTIVES: The aim of the study was to summarize the benefits and harms of MRAs for CKD patients. METHODS: We searched MEDLINE, EMBASE, and the Cochrane databases for trials assessing the effects of MRAs on non-dialysis-dependent CKD populations. Treatment and adverse effects were summarized using meta-analysis. RESULTS: Fifty-three trials with 6 different MRAs involving 22,792 participants were included. Compared with the control group, MRAs reduced urinary albumin-to-creatinine ratio (weighted mean difference [WMD], -90.90 mg/g, 95% CI, -140.17 to -41.64 mg/g), 24-h urinary protein excretion (WMD, -0.20 g, 95% CI, -0.28 to -0.12 g), estimated glomerular filtration rate (eGFR) (WMD, -1.99 mL/min/1.73 m2, 95% CI, -3.28 to -0.70 mL/min/1.73 m2), chronic renal failure events (RR, 0.86, 95% CI, 0.79-0.93), and cardiovascular events (RR, 0.84, 95% CI, 0.77-0.92). MRAs increased the incidence of hyperkalemia (RR, 2.04, 95% CI, 1.73-2.40) and hypotension (RR, 1.80, 95% CI, 1.41-2.31). MRAs reduced the incidence of peripheral edema (RR, 0.65, 95% CI, 0.56-0.75) but not the risk of acute kidney injury (RR, 0.94, 95% CI, 0.79-1.13). Nonsteroidal MRAs (RR, 0.66, 95% CI, 0.57-0.75) but not steroidal MRAs (RR, 0.20, 95% CI, 0.02-1.68) significantly reduced the risk of peripheral edema. Steroidal MRAs (RR, 5.68, 95% CI, 1.26-25.67) but not nonsteroidal MRAs (RR, 0.52, 95% CI, 0.22-1.22) increased the risk of breast disorders. CONCLUSIONS: In the CKD patients, MRAs, particularly in combination with angiotensin-converting enzyme inhibitor/angiotensin receptor blocker, reduced albuminuria/proteinuria, eGFR, and the incidence of chronic renal failure, cardiovascular and peripheral edema events, whereas increasing the incidence of hyperkalemia and hypotension, without the augment of acute kidney injury events. Nonsteroidal MRAs were superior in the reduction of more albuminuria with fewer peripheral edema events and without the augment of breast disorder events.

Development and application of an indirect ELISA for detection of antibodies against emerging atypical porcine pestivirus.

BACKGROUND: Atypical porcine pestivirus (APPV) is a newly discovered swine pestivirus, which can cause congenital tremor and high mortality in newborn piglets and subclinical infection in adult pigs, leading to significant impacts on the pig industry. Currently, there is no approved serological method to assess APPV infection status in pig farms. METHODS: In this study, the envelope glycoprotein E2 of APPV was highly expressed in suspension HEK293 cells, and further an indirect enzyme-linked immunosorbent assay based on the recombinant E2 protein (E2-iELISA) was developed and evaluated. RESULTS: The reaction parameters of the E2-iELISA were optimized, and the cutoff value was determined to be 0.2 by analyzing S/P values of 165 negative sera against APPV that were confirmed by virus neutralization test (VNT). Specificity test showed that the method had no cross-reaction with other common swine viruses. The E2-iELISA was evaluated using a panel of swine sera, and showed high sensitivity (113/120, 94.2%) and specificity (65/70, 92.9%), and the agreement rate with VNT was 93.7% (178/190). Subsequently, the E2-iELISA was utilized to investigate the seroprevalence of APPV in pig herds of China. When detecting 1368 pig serum samples collected from nine provinces in China, the overall seroprevalence of APPV was 73.9% (1011/1368). CONCLUSION: Our findings suggest that the E2-iELISA is specific and sensitive, and could be a valuable tool for serological surveillance of APPV infection in pigs.

Association of peripheral eosinophil count with chronic kidney disease progression risk: a retrospective cohort study in Chinese population.

BACKGROUND: The role of peripheral eosinophils in chronic kidney disease (CKD) requires further evaluation. We aimed to determine whether an eosinophil count increase is related to the occurrence of end-stage renal disease (ESRD). METHODS: This single-center, observational, retrospective cohort study was conducted between January 2016 and December 2018 in Hangzhou, China, and included 3163 patients, categorized into four groups according to peripheral eosinophil count (PEC) quartile values. The main outcome was ESRD development during follow-up. We evaluated the relationship between the serum eosinophil count, demographic and clinical information, and ESRD incidence. Cox proportional hazards models and Kaplan-Meier survival curves were used. RESULTS: A total of 3163 patients with CKD were included in this cohort, of whom 1254 (39.6%) were females. The median (interquartile range [IQR]) age was 75 [64, 85] years, and the median (IQR) estimated glomerular filtration rate was 55.16 [45.19, 61.19] mL/min/1.73 m2. The median PEC was 0.1224 × 109/L (IQR, 0.0625-0.212). Among the 3163 patients with CKD, 273 (8.6%) developed ESRD during a median follow-up time of 443.8 [238.8, 764.9] days. Individuals in the highest PEC quartile had a 66.2% higher ESRD risk than those in the lowest quartile (hazard ratio, 1.662; 95% confidence interval, 1.165-2.372). The results from the Kaplan-Meier survival curves confirmed the conclusion. CONCLUSIONS: Alongside traditional risk factors, patients with CKD and an elevated PEC are more likely to develop ESRD. Therefore, more attention should be paid to those patients with CKD who have a high PEC.

Development, validation, and visualization of a web-based nomogram for predicting chronic kidney disease incidence at health examination centers.

PURPOSE: To develop and validate a web-based nomogram for predicting new incident chronic kidney disease (CKD) within 4 years in a cohort undergoing routine physical examination from two health examination centers. METHODS: One center was utilized for training and internal validation of a nomogram model involving 6515 patients, while a separate center was employed for external validation with 3152 patients. Sixteen candidate predictors, including patient demographics, medical histories, physical examination, and laboratory test data, were included in this study to ascertain factors linked to new incident CKD. A nomogram was created to predict CKD risks using a logistic model. The nomogram's performance was assessed using the area under the receiver operating characteristic curve (AUC), calibration plot, and decision curve analysis. RESULTS: Out of the 9667 healthy individuals included in the study with mean age of 46 years, sex ratio (male/female) of 1.69 (6075/3592), 118 (2.59%), 51 (2.61%), and 60 (1.90%) individuals developed CKD in the training (n = 4563), internal validation (n = 1952), and external validation (n = 3152) datasets, respectively. Age, history of diabetes mellitus, systolic blood pressure, serum creatinine, albumin, and triglyceride levels were used to build the nomogram, which yielded excellent discrimination ability (training cohort, AUC = 0.8806, 95% confidence interval [CI] 0.8472-0.9141; internal validation cohort, AUC = 0.8506, 95% CI 0.7856-0.9156; external validation cohort, AUC = 0.9183, 95% CI 0.8698-0.9669). We further developed a web-based calculator for convenient application (https://luochuxuan.shinyapps.io/dynnomapp/). CONCLUSION: Our web-based nomogram accurately predicted CKD risks in Chinese health individuals and can be easily used in clinical settings.

Osteoblast Jmjd3 regulates osteoclastogenesis via EphB4 and RANKL signalling.

BACKGROUND: Osteoblasts suppress osteoclastogenesis during the reversal phase of bone remodelling and the mechanism needs to be further investigated. Here, we investigated the role of histone demethylase Jumonji domain-containing 3 (Jmjd3) in osteoblasts on regulating osteoclastogenesis. METHODS: Jmjd3 expression was silenced in osteoblasts. Osteoblasts and osteoclasts were co-cultured in direct or indirect contact ways, and osteoclastogenesis was determined by tartrate-resistant acid phosphatase (TRAP) staining and Western blotting. Additionally, Ephrin receptor B4 (EphB4) and receptor activator of nuclear factor-kappa Β ligand (RANKL) expression were quantified in osteoblasts via real-time PCR, Western blotting, and enzyme-linked immunosorbent assay. Subsequently, EphB4 was overexpressed in osteoblasts and RANKL expression and osteoclastogenesis was quantified. RESULTS: Osteoclastogenesis and marker protein expression levels was promoted when osteoclasts were co-cultured with Jmjd3-silenced osteoblasts. Silencing of Jmjd3 expression in osteoblasts decreased EphB4 expression, owing to suppression of demethylation of H3K27me3 on the promoter region of EphB4. Whereas RANKL expression was upregulated in Jmjd3-silenced osteoblasts. Overexpression of EphB4 in osteoblasts inhibited osteoclastogenesis and RANKL expression. CONCLUSION: Jmjd3 in osteoblasts is a crucial regulator of osteoblast-to-osteoclast communication through EphB4-EphrinB2, RANKL-RANK and EphB4-RANKL signalling axes, suggesting the pivotal role of Jmjd3 in bone remodelling process in bone destruction disease such as chronic apical periodontitis.

A study on the factors influencing the utilization of public health services by China's migrant population based on the Shapley value method.

BACKGROUND: The health of migrants has received significant global attention, and it is a particularly significant concern in China, which has the largest migrant population in the world. Analyzing data on samples from the Chinese population holds practical significance. For instance, one can delve into an in-depth analysis of the factors impacting (1) the health records of residents in distinct regions and (2) the current state of family doctor contracts. This study explores the barriers to access these two health services and the variations in the effects and contribution magnitudes. METHODS: This study involved data from 138,755 individuals, extracted from the 2018 National Migration Population Health and Family Planning Dynamic Monitoring Survey database. The theoretical framework employed was the Anderson health service model. To investigate the features and determinants of basic public health service utilization among the migrant population across different regions of China, including the influence of enabling resources and demand factors, x2 tests and binary logistic regression analyses were conducted. The Shapley value method was employed to assess the extent of influence of each factor. RESULTS: The utilization of various service types varied among the migrant population, with significant regional disparities. The results of the decomposition of the Shapley value method highlighted variations in the mechanism underlying the influence of propensity characteristics, enabling resources, and demand factors between the two health service types. Propensity characteristics and demand factors were found to be the primary dimensions with the highest explanatory power; among them, health education for chronic disease prevention and treatment was the most influential factor. CONCLUSION: To better meet the health needs of the migrant population, regional barriers need to be broken down, and the relevance and effectiveness of publicity and education need to be improved. Additionally, by considering the education level, demographic characteristics, and mobility characteristics of the migrant population, along with the relevant health policies, the migrant population needs to be guided to maintain the health records of residents. They should also be encouraged to sign a contract with a family doctor in a more effective manner to promote the equalization of basic health services for the migrant population.

Acute kidney injury in patients with cancer receiving anti-PD-1/PD-L1 antibodies: incidence, risk factors, and prognosis.

Anti-PD-1/PD-L1 antibodies are widely used in anti-cancer therapy. While they have improved cancer prognoses, immune-related adverse events, which can cause acute kidney injury (AKI), cannot be ignored. The purpose of this retrospective cohort study was to assess the incidence, risk factors, and prognosis of AKI associated with anti-PD-1/PD-L1 antibodies. Patients who received anti-PD-1/PD-L1 antibody treatment at our hospital between January 2018 and December 2022 were enrolled. Clinical information, combined medications, concomitant diseases, tumor types, and laboratory indicators were collected from patient records, and the incidence of AKI was determined. The risk factors for AKI were assessed using univariate and multivariate logistic regression analyses. Overall, 1418 patients were enrolled. The median follow-up time was 112 days and 92 (6.5%) developed AKI. The median time from the initial anti-PD-1/PD-L1 antibody treatment to AKI was 99.85 days. Head and neck cancer and combined use of diuretics, non-steroidal anti-inflammatory drugs (NSAIDs), lower hemoglobin level, and other types of chemotherapeutic drugs were independent risk factors for AKI. The complete recovery, partial recovery, non-recovery, and unknown AKI rates were 7.6%, 28.3%, 52.2%, and 11.9%, respectively. Kidney biopsies were performed on two patients with AKI and pathology confirmed diagnosis of acute tubulointerstitial nephritis. In this cohort, AKI was not uncommon in patients treated with anti-PD-1/PD-L1 antibodies; therefore, it is necessary to monitor renal function and identify AKI early, especially in patients with head and neck tumors. Improving anemia and minimizing the use of diuretics, NSAIDs, and chemotherapeutics may reduce AKI.

Plasma D-dimer levels are associated with disease progression in diabetic nephropathy: a two-center cohort study.

BACKGROUND: This study aimed to investigate the relationship between plasma D-dimer levels, clinicopathological features, and clinical outcomes in patients with biopsy-proven diabetic nephropathy (DN). METHODS: A total of 137 patients with biopsy-proven DN were enrolled in this two-center cohort study. Patients were stratified into tertiles based on plasma D-dimer levels. We investigated the relationship between plasma D-dimer levels and clinical outcomes, including a composite of death, a 40% decline in estimated glomerular filtration rate (e-GFR) from baseline, or end-stage renal disease (ESRD) (defined as e-GFR < 15 mL/min/1.73 m2 or need for renal replacement therapy including hemodialysis, peritoneal dialysis, or kidney transplantation), assessed using Cox regression models with adjustment for confounders. RESULTS: At baseline, the mean age was 52.61 ± 11.63 years, and the mean e-GFR was 58.02 ± 28.77 mL/min/1.73 m2. During a median 26-month follow-up period, 65 (47% of patients) achieved clinical outcomes. Compared with the low plasma D-dimer level group, those with higher plasma D-dimer levels were more likely to have higher 24-h proteinuria (p = .002), lower e-GFR (p = .001), lower hemoglobin (p = .001), a higher glomerular lesion class (p = .03), and higher interstitial fibrosis and tubular atrophy (IFTA) scores (p = .002). After adjustment for demographic, DN-specific covariates, and treatments, it was observed that a higher tertile of plasma D-dimer was nonlinearly associated with an increased risk of the clinical outcomes (Hazard Ratio (HR) for tertile 2 vs. 1, 1.7; 95% Confidence Interval (CI), 0.80-3.75; HR for tertile 3 vs. 1, 2.2; 95% CI, 0.93-5.27; p for trend = .001) in the Cox proportional hazards models. CONCLUSION: In this study, DN patients with higher levels of plasma D-dimer had higher 24-h proteinuria, lower e-GFR, a higher glomerular lesion class, and higher IFTA scores. Furthermore, a high level of plasma D-dimer was nonlinearly associated with DN progression.

ERG amplification is a secondary recurrent driver event in myeloid malignancy with complex karyotype and TP53 mutations.

ERG is a transcription factor encoded on chromosome 21q22.2 with important roles in hematopoiesis and oncogenesis of prostate cancer. ERG amplification has been identified as one of the most common recurrent events in acute myeloid leukemia with complex karyotype (AML-CK). In this study, we uncover three different modes of ERG amplification in AML-CK. Importantly, we present evidence to show that ERG amplification is distinct from intrachromosomal amplification of chromosome 21 (iAMP21), a hallmark segmental amplification frequently encompassing RUNX1 and ERG in a subset of high-risk B-lymphoblastic leukemia. We also characterize the association with TP53 aberrations and other chromosomal aberrations, including chromothripsis. Lastly, we show that ERG amplification can initially emerge as subclonal events in low-grade myeloid neoplasms. These findings demonstrate that ERG amplification is a recurrent secondary driver event in AML and raise the tantalizing possibility of ERG as a therapeutic target.

Association of central arterial blood pressure and left ventricular hypertrophy in patients with chronic kidney disease.

AIMS: In the general population, central arterial blood pressure has proved to be more closely related to left ventricular hypertrophy (LVH) than brachial arterial blood pressure. We aimed to investigate whether this relationship was true in patients with chronic kidney disease (CKD). METHODS: In this retrospective study, we reviewed the medical records of 289 adult patients with CKD from the Zhejiang Provincial People's Hospital in Zhejiang, China. Demographic, echocardiographic and brachial and central blood pressure parameters were retrieved from medical records. Central blood pressure was measured using the SphygmoCor® CvMS (AtCor, Australia) device and its corresponding software. Multivariate logistic regression analyses were performed to identify independent predictors of LVH. Receiver operating characteristic curves were used to determine the ability of central and brachial blood pressure to predict LVH. RESULTS: The left ventricular mass index was positively associated with both central and brachial blood pressures. However, multiple logistic regression analysis demonstrated that a central pulse pressure (CPP) ≥ 58 mm Hg was an independent risk factor for LVH (OR = 5.597, 95%CI 2.363-13.259, p < .001). Brachial pulse pressure is not superior to CPP in predicting LVH (area under the curve [AUC] = 0.695, 95%CI 0.634-0.756, p < .001 vs. AUC = 0.687, 95%CI: 0.626-0.748, p < .001, respectively; p = .4824). CONCLUSION: Our results suggested that, similarly to the general population, CPP is a better parameter for predicting the occurrence of LVH in patients with CKD.

LASSO-derived nomogram predicting new-onset diabetes mellitus in patients with kidney disease receiving immunosuppressive drugs.

WHAT IS KNOWN AND OBJECTIVE: Patients with kidney disease receiving immunosuppressive drugs (ISDs) (tacrolimus, cyclosporine and glucocorticoids) have a high risk of developing new-onset diabetes mellitus (NODM). We aimed to establish a precise and convenient model for predicting NODM in patients receiving immunosuppressive drugs. METHODS: This retrospective study recruited 1883 patients receiving ISDs between January 2010 and October 2018. The occurrence of NODM was the primary endpoint. The patients were randomly divided into training (n = 1318) and validation cohorts (n = 565) at a 7:3 ratio. A nomogram was established based on a least absolute shrinkage and selection operator (LASSO)-derived logistic regression model. The nomogram's discrimination and calibration abilities were evaluated in both cohorts using the Hosmer-Lemeshow test and calibration curves. Decision curve analysis (DCA) was used to evaluate the net benefit of the predictive efficacy. RESULTS AND DISCUSSION: Amongst the 1883 patients with kidney disease receiving immunosuppressive drugs, 375 (28.5%) and 169 (29.9%) developed NODM in the training (n = 1318) and validation cohorts (n = 565), respectively. Nine clinic predictors were included in this LASSO-derived nomogram, which is easy to be operated clinically. The discriminative ability, determined by the area under the receiver operating characteristic curve (AUC), was 0.816 (95% confidence interval [CI] 0.790-0.841) and 0.831 (95%CI 0.796-0.867) in the training and validation cohorts, respectively. Calibration was confirmed with the Hosmer-Lemeshow test in the training and validation cohorts (p = 0.238, p = 0.751, respectively). WHAT IS NEW AND CONCLUSION: Nearly one-third of patients with kidney disease receiving immunosuppressive drugs developed NODM. The nomogram established in this study may aid in predicting the occurrence of NODM in patients with kidney disease receiving immunosuppressive drugs.

Single nucleotide polymorphism array and cytogenetic analyses of ovarian teratomas in children.

Teratomas are the most common tumors in the ovary during childhood. Previous studies suggested that they may be derived from germ cells at any developmental stage from premeiotic oogonia through meiotic oocytes to post-meiotic ova. The majority of mature teratomas reveal normal karyotypes and immature teratomas show higher frequency of chromosomal abnormalities. We analyzed fresh tissue samples from 25 primary ovarian teratomas and three extraovarian deposits using whole genome single nucleotide polymorphism (SNP) array and karyotype. SNP array detected five patterns of copy neutral loss of heterozygosity (CN-LOH): failure of meiosis I (type I) in 12 tumors, failure of meiosis II (type II) in six tumors, endoreduplication of a haploid ovum (type III) in two tumors, premeiotic error (type IV) in four tumors, and both meiotic I and meiotic II errors in one tumor (type V). Three tumors with type I error had a single chromosome showing meiotic II error, and two tumors with type II error had a single chromosome showing premature sister-chromatid separation in meiosis I. Lack of recombination in multiple chromosomes in meiosis I were common, chromosomes 17, 7, 8, 21, and 22 were most commonly involved. Abnormal karyotypes were observed in four teratomas including +3, del(3q), +7, +8, +12, and i(18q). The extraovarian deposits revealed the same CN-LOH pattern as the primary teratoma. In summary, SNP array reveals the origin of ovarian teratoma and we propose a new mechanism that consecutive meiotic I and II errors occur frequently in ovarian teratomas.

Myelodysplastic syndrome with t(6;9)(p22;q34.1)/DEK-NUP214 better classified as acute myeloid leukemia? A multicenter study of 107 cases.

t(6;9)(p22;q34.1)/DEK-NUP214 is a recurrent genetic abnormality that occurs in 1-2% of patients with acute myeloid leukemia (AML), and rarely in myelodysplastic syndrome (MDS). It has been suggested by others that all myeloid neoplasms with t(6;9)/DEK-NUP214 may be considered as AML, even when blast count is <20%. In this study, we compared the clinicopathologic features of 107 patients with myeloid neoplasms harboring t(6;9)/DEK-NUP214: 33 MDS and 74 AML. Compared with patients with AML, patients with MDS were older (p = 0.10), had a lower white blood cell count (p = 0.0017), a lower blast count in the peripheral blood (p < 0.0001) and bone marrow (p < 0.0001), a higher platelet count (p = 0.022), and a lower frequency of FLT3-ITD mutation (p = 0.01). In addition, basophilia was not a common feature in the patients of this cohort. Although there was no difference in overall survival between MDS and AML patients (p = 0.18) in the entire cohort, the survival curves did show a trend toward favorable survival in MDS patients. Multivariate analyses showed that initial diagnosis of MDS vs. AML and allogeneic hematopoietic stem cell transplantation were prognostic factors for survival of patients with t(6;9)/DEK-NUP214 (p = 0.008 and p < 0.0001, respectively). Our data suggest that MDS with t(6;9)/DEK-NUP214 is prognostically not equivalent to AML with t(6;9)/DEK-NUP214. These data also show that stem cell transplantation greatly improves the survival of MDS and AML patients with myeloid neoplasms associated with t(6;9)/DEK-NUP214.

TRIM63 is a sensitive and specific biomarker for MiT family aberration-associated renal cell carcinoma.

Microphthalmia-associated transcription factor (MiT) family aberration-associated renal cell carcinoma (MiTF-RCC) is a subtype of renal cell carcinoma harboring recurrent chromosomal rearrangements involving TFE3 or TFEB genes. MiTF-RCC is morphologically diverse, can histologically resemble common RCC subtypes like clear cell RCC and papillary RCC, and often poses a diagnostic challenge in genitourinary clinical and pathology practice. To characterize the MiTF-RCC at the molecular level and identify biomarker signatures associated with MiTF-RCC, we analyzed RNAseq data from MiTF-RCC, other RCC subtypes and benign kidney. Upon identifying TRIM63 as a cancer-specific biomarker in MiTF-RCC, we evaluated its expression independently by RNA in situ hybridization (RNA-ISH) in whole tissue sections from 177 RCC cases. We specifically included 31 cytogenetically confirmed MiTF-RCC cases and 70 RCC cases suspicious for MiTF-RCC in terms of clinical and morphological features, to evaluate and compare TRIM63 RNA-ISH results with the results from TFE3/TFEB fluorescence in situ hybridization (FISH), which is the current clinical standard. We confirmed that TRIM63 mRNA was highly expressed in all classes of MiTF-RCC compared to other renal tumor categories, where it was mostly absent to low. While the TRIM63 RNA-ISH and TFE3/TFEB FISH results were largely concordant, importantly, TRIM63 RNA-ISH was strongly positive in TFE3 FISH false-negative cases with RBM10-TFE3 inversion. In conclusion, TRIM63 can serve as a diagnostic marker to distinguish MiTF-RCC from other renal tumor subtypes with overlapping morphology. We suggest a combination of TFE3/TFEB FISH and TRIM63 RNA-ISH assays to improve the accuracy and efficiency of MiTF-RCC diagnosis. Accurate diagnosis of MiTF-RCC and other RCC subtypes would enable effective targeted therapy and avoid poor therapeutic response due to tumor misclassification.

Chromosomal microarray analysis, including constitutional and neoplastic disease applications, 2021 revision: a technical standard of the American College of Medical Genetics and Genomics (ACMG).

Chromosomal microarray technologies, including array comparative genomic hybridization and single-nucleotide polymorphism array, are widely applied in the diagnostic evaluation for both constitutional and neoplastic disorders. In a constitutional setting, this technology is accepted as the first-tier test for the evaluation of chromosomal imbalances associated with intellectual disability, autism, and/or multiple congenital anomalies. Furthermore, chromosomal microarray analysis is recommended for patients undergoing invasive prenatal diagnosis with one or more major fetal structural abnormalities identified by ultrasonographic examination, and in the evaluation of intrauterine fetal demise or stillbirth when further cytogenetic analysis is desired. This technology also provides important genomic data in the diagnosis, prognosis, and therapy of neoplastic disorders, including both hematologic malignancies and solid tumors. To assist clinical laboratories in the validation of chromosomal microarray methodologies for constitutional and neoplastic applications, the American College of Medical Genetics and Genomics (ACMG) Laboratory Quality Assurance Committee has developed these updated technical laboratory standards, which replace the ACMG technical standards and guidelines for microarray analysis in constitutional and neoplastic disorders previously published in 2013.

Lactobacillus rhamnosus GG defense against Salmonella enterica serovar Typhimurium infection through modulation of M1 macrophage polarization.

Lactobacillus rhamnosus GG (LGG), a model probiotic strain, plays an important role in immune regulatory activity to prevent and treat intestinal inflammation or diarrhea. However, the effect of the immune modulation of LGG on macrophages to prevent Salmonella infection has not been thoroughly studied. In this study, C57BL/6 mice were pre-administered LGG for 7 days continuously, and then infected with Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium). The results of the in vivo study indicated that LGG could reduce body weight loss, death rate and intestinal inflammatory response caused by S. Typhimurium. LGG also limited S. Typhimurium dissemination to liver and spleen, and thereby protected against infection. In vitro study, we observed that LGG enhanced the phagocytic and bactericidal ability of macrophages and upregulated M1 macrophage characters (e.g. iNOS, NO and IL-12) against S. Typhimurium. In addition, LGG also elevated IL-10 secretion, which was helpful to ameliorate intestinal inflammatory injury caused by S. Typhimurium. In conclusion, LGG could modulate M1 macrophage polarization and offer protective effects against S. Typhimurium infection.

Genetic reduction of cilium length by targeting intraflagellar transport 88 protein impedes kidney and liver cyst formation in mouse models of autosomal polycystic kidney disease.

Polycystin-1 (PC1) and -2 (PC2), products of the PKD1 and PKD2 genes, are mutated in autosomal dominant polycystic kidney disease (ADPKD). They localize to the primary cilia; however, their ciliary function is in dispute. Loss of either the primary cilia or PC1 or PC2 causes cyst formation. However, loss of both cilia and PC1 or PC2 inhibits cyst growth via an unknown pathway. To help define a pathway, we studied cilium length in human and mouse kidneys. We found cilia are elongated in kidneys from patients with ADPKD and from both Pkd1 and Pkd2 knockout mice. Cilia elongate following polycystin inactivation. The role of intraflagellar transport proteins in Pkd1-deficient mice is also unknown. We found that inactivation of Ift88 (a gene expressing a core component of intraflagellar transport) in Pkd1 knockout mice, as well as in a new Pkd2 knockout mouse, shortened the elongated cilia, impeded kidney and liver cystogenesis, and reduced cell proliferation. Multi-stage in vivo analysis of signaling pathways revealed ß-catenin activation as a prominent, early, and sustained event in disease onset and progression in Pkd2 single knockout but not in Pkd2.Ift88 double knockout mouse kidneys. Additionally, AMPK, mTOR and ERK pathways were altered in Pkd2 single knockout mice but only AMPK and mTOR pathway alteration were rescued in Pkd2.Ift88 double knockout mice. Thus, our findings advocate an essential role of polycystins in the structure and function of the primary cilia and implicate ß-catenin as a key inducer of cystogenesis downstream of the primary cilia. Our data suggest that modulating cilium length and/or its associated signaling events may offer novel therapeutic approaches for ADPKD.

Cytogenomic array detects a subset of myelodysplastic syndrome with increased risk that is invisible to conventional karyotype.

Conventional karyotyping is essential standard practice in the initial evaluation of myelodysplastic syndrome (MDS) and is the most impactful single component of the Revised International Prognostic Scoring System (IPSS-R). While single nucleotide polymorphism array (SNP-A) has demonstrated the ability to detect chromosomal defects with greater sensitivity than conventional karyotype, widespread adoption is limited by the unknown additional prognostic impact of SNP-A analysis. Here, we investigate the significance of additional SNP-A abnormalities in the setting of MDS and demonstrate differences in survival of patients with additional abnormalities, even those initially characterized as relatively lower risk either by cytogenetic score or IPSS-R. Our findings identify specific abnormalities, particularly KMT2A partial tandem duplication, that are invisible to conventional karyotype and potentially contribute to the poor prognosis of MDS patients. Furthermore, these results demonstrate the added value of SNP-A analysis in identifying patients who may benefit from more aggressive therapy, particularly those who would otherwise be classified into lower risk categories.