High-throughput scNMT protocol for multiomics profiling of single cells from mouse brain and pancreatic organoids.

Single-cell nucleosome, methylome, and transcriptome (scNMT) sequencing is a recently developed method that allows multiomics profiling of single cells. In this scNMT protocol, we describe profiling of cells from mouse brain and pancreatic organoids, using liquid handling platforms to increase throughput from 96-well to 384-well plate format. Our approach miniaturizes reaction volumes and incorporates the latest Smart-seq3 protocol to obtain higher numbers of detected genes and genomic DNA (gDNA) CpGs per cell. We outline normalization steps to optimally distribute per-cell sequencing depth. For complete details on the use and execution of this protocol, please refer to Clark (2019), Clark et al. (2018), and Clark et al., 2018, Hagemann-Jensen et al., 2020a, Hagemann-Jensen et al., 2020b.

Cdk4 and Cdk6 Couple the Cell-Cycle Machinery to Cell Growth via mTORC1.

Cell growth is coupled to cell-cycle progression in mitotically proliferating mammalian cells, but the underlying molecular mechanisms are not well understood. CyclinD-Cdk4/6 is known to phosphorylate RB to promote S-phase entry, but recent work suggests they have additional functions. We show here that CyclinD-Cdk4/6 activates mTORC1 by binding and phosphorylating TSC2 on Ser1217 and Ser1452. Pharmacological inhibition of Cdk4/6 leads to a rapid, TSC2-dependent reduction of mTORC1 activity in multiple human and mouse cell lines, including breast cancer cells. By simultaneously driving mTORC1 and E2F, CyclinD-Cdk4/6 couples cell growth to cell-cycle progression. Consistent with this, we see that mTORC1 activity is cell cycle dependent in proliferating neural stem cells of the adult rodent brain. We find that Cdk4/6 inhibition reduces cell proliferation partly via TSC2 and mTORC1. This is of clinical relevance, because Cdk4/6 inhibitors are used for breast cancer therapy.

Guided tissue organization and disease modeling in a kidney tubule array.

Three-dimensional (3D) in vitro kidney tubule models have either largely relied on the self-morphogenetic properties of the mammalian cells or used an engineered microfluidic platform with a monolayer of cells cultured on an extracellular matrix (ECM) protein coated porous membrane. These systems are used to understand critical processes during kidney development and transport properties of renal tubules. However, high variability and lack of kidney tubule-relevant geometries among engineered structures limit their utility in disease research and pre-clinical drug testing. Here, we report a novel bioengineered guided kidney tubule (gKT) array system that incorporates in vivo-like physicochemical cues in 3D culture to reproducibly generate homogeneous kidney tubules. The system utilizes a unique 3D micro-molded ECM platform in human physiology-scale dimensions (50-µm diameter) and relevant shapes to guide cells towards formation of mature tubule structures. The guided kidney tubules in our array system display enhanced tubule homogeneity with in vivo-like structural and functional features as evaluated by marker protein localization and epithelial transport analysis. Furthermore, the response of gKT structures to forskolin treatment exhibits characteristic tissue transformations from tubules to expanding cysts. Moreover, acute cisplatin injury causes induction of Kidney Injury Molecule-1 (KIM-1) expression as well as tubular necrosis and apoptosis. Thus the gKT array system offers enhanced structural uniformity with accurate in vivo-like tissue architecture, and will have broad applications in kidney tubule disease pathophysiology (including ciliopathies and drug-induced acute kidney injury), and will enhance pre-clinical drug screening studies.

Netrin 1 and Alpha-Methyl Acylcoenzim-A Racemase in diagnosis of prostate cancer.

OBJECTIVES: To investigate serum and urine levels of Alpha-methylacyl-CoA-racemase (AMACR) and Netrin 1 in patients with and without prostate cancer and to determine whether these markers could be used as alternatives in diagnosis of prostate cancer instead of serum prostate specific antigen (PSA) levels. METHODS: One hundred and seventy five patients between 45-75 years to whom transrectal ultrasound guided biopsies were performed for abnormal serum PSA levels or digital rectal examinations were included. The levels of AMACR and Netrin 1 levels of blood and urine samples of 5 mL those were taken prior to biopsies were measured. . RESULTS: The mean age of the patients was 62.7 ±6.4 years. Prostate cancer was detected in 40 patients (22.8%) while 135 of them (77.2%) were diagnosed as benign prostate hyperplasia (BPH). In BPH group, serum and urine levels of AMACR and Netrin 1 were 13.4 ±16.9 ng/mL; 7.1 ±3.4 ng/mL; 164.1±46 pg/mL and 19.5 ±5.0 pg/mL respectively. The levels of serum and urine levels of AMACR and Netrin 1 were 10.2 ±9.8 ng/mL; 6.8 ±2.5 ng/mL; 159.1 ±44.1 pg/mL and 20.1 ±5.3 pg/mL respectively in prostate cancer group. There was no statistically significant difference or correlation between these two groups serum and urine AMACR and Netrin 1 results. CONCLUSIONS: Serum and urine levels of AMACR and Netrin 1 were not found to be alternatives for serum PSA levels in the diagnosis of prostate cancer in this study.

OBJETIVOS: Investigar los niveles de alfa-metil acilcoenzima-A y Netrina 1 en pacientes con y sin cáncer de próstata y determinar si estos marcadores pueden ser usados como una alternativa en el diagnóstico de cáncer de próstata en lugar del antígeno prostático específico en suero (PSA). MÉTODOS: Fueron incluidos 175 pacientes entre 45-75 años, a quienes se les realizó una biopsia de próstata guiada por ultrasonido por presentar un nivel anormal de PSA en el suero o un tacto rectal. Se tomó una muestra de 5 mL de sangre y orina para medir los niveles de alfa-metil acilcoenzima-A y Netrina 1. Estos niveles se midieron antes del análisis de la biopsia. RESULTADOS: La edad media de los pacientes fue de 62.7±6.4 años. Se detectó cander en 40 pacientes (22.8%), mientras que a 135 de ellos (77.2%) se les diagnóstico una hiperplasia benigna de próstata (HBP). En el grupo HBP los niveles en suero y orina de alfa-metil acilcoenzima-A y Netrina 1 fueron 13.4 ±16.9 ng/mL; 7.1 ±3.4 ng/mL; 164.1 ±46 pg/mL y 19.5 ±5.0 pg/mL respectivamente. En el grupo con cáncer de próstata los niveles en suero y orina de alfa-metil acilcoenzima-A y Netrina 1 fueron 10.2 ±9.8 ng/mL; 6.8 ±2.5 ng/mL; 159.1 ±44.1 pg/mL y 20.1 ±5.3 pg/mL respectivamente. No hubo una diferencia significativa o una correlación entre los niveles de alfa-metil acilcoenzima-A y Netrina 1 en suero y orina al comparar estos dos grupos de pacientes. CONCLUSIONES: Los niveles de alfa-metil acilcoenzima-A y Netrina 1 en suero y orina no son una alternativa para reemplazar el PSA en suero para el diagnóstico de cáncer de próstata.

Netrin 1 and Alpha-Methyl Acylcoenzim-A Racemase in diagnosis of prostate cancer / Netrina 1 y Alfa Metil-Acil coenzima-A Racemasa para el diagnóstico de cáncer de próstata

Abstract Objectives: To investigate serum and urine levels of Alpha-methylacyl-CoA-racemase (AMACR) and Netrin 1 in patients with and without prostate cancer and to determine whether these markers could be used as alternatives in diagnosis of prostate cancer instead of serum prostate specific antigen (PSA) levels. Methods: One hundred and seventy five patients between 45-75 years to whom transrectal ultrasound guided biopsies were performed for abnormal serum PSA levels or digital rectal examinations were included. The levels of AMACR and Netrin 1 levels of blood and urine samples of 5 mL those were taken prior to biopsies were measured. . Results: The mean age of the patients was 62.7 ±6.4 years. Prostate cancer was detected in 40 patients (22.8%) while 135 of them (77.2%) were diagnosed as benign prostate hyperplasia (BPH). In BPH group, serum and urine levels of AMACR and Netrin 1 were 13.4 ±16.9 ng/mL; 7.1 ±3.4 ng/mL; 164.1±46 pg/mL and 19.5 ±5.0 pg/mL respectively. The levels of serum and urine levels of AMACR and Netrin 1 were 10.2 ±9.8 ng/mL; 6.8 ±2.5 ng/mL; 159.1 ±44.1 pg/mL and 20.1 ±5.3 pg/mL respectively in prostate cancer group. There was no statistically significant difference or correlation between these two groups serum and urine AMACR and Netrin 1 results Conclusions: Serum and urine levels of AMACR and Netrin 1 were not found to be alternatives for serum PSA levels in the diagnosis of prostate cancer in this study.

Resumen Objetivos: Investigar los niveles de alfa-metil acilcoenzima-A y Netrina 1 en pacientes con y sin cáncer de próstata y determinar si estos marcadores pueden ser usados como una alternativa en el diagnóstico de cáncer de próstata en lugar del antígeno prostático específico en suero (PSA). Métodos: Fueron incluidos 175 pacientes entre 45-75 años, a quienes se les realizó una biopsia de próstata guiada por ultrasonido por presentar un nivel anormal de PSA en el suero o un tacto rectal. Se tomó una muestra de 5 mL de sangre y orina para medir los niveles de alfa-metil acilcoenzima-A y Netrina 1. Estos niveles se midieron antes del análisis de la biopsia. Resultados: La edad media de los pacientes fue de 62.7±6.4 años. Se detectó cander en 40 pacientes (22.8%), mientras que a 135 de ellos (77.2%) se les diagnóstico una hiperplasia benigna de próstata (HBP). En el grupo HBP los niveles en suero y orina de alfa-metil acilcoenzima-A y Netrina 1 fueron 13.4 ±16.9 ng/mL; 7.1 ±3.4 ng/mL; 164.1 ±46 pg/mL y 19.5 ±5.0 pg/mL respectivamente. En el grupo con cáncer de próstata los niveles en suero y orina de alfa-metil acilcoenzima-A y Netrina 1 fueron 10.2 ±9.8 ng/mL; 6.8 ±2.5 ng/mL; 159.1 ±44.1 pg/mL y 20.1 ±5.3 pg/mL respectivamente. No hubo una diferencia significativa o una correlación entre los niveles de alfa-metil acilcoenzima-A y Netrina 1 en suero y orina al comparar estos dos grupos de pacientes. Conclusiones: Los niveles de alfa-metil acilcoenzima-A y Netrina 1 en suero y orina no son una alternativa para reemplazar el PSA en suero para el diagnóstico de cáncer de próstata.

Evaluation of Ves-Matic Cube 200 for erythrocyte sedimentation rate determination.

BACKGROUND: International Council for Standardization in Haematology suggested Westergren method as the reference method to analyze erythrocyte sedimentation rate (ESR). However, in recent years closed automated systems that measure ESR directly from a capped EDTA blood sample tube have been developed. We evaluated the analytic performance of one of these new methods, the Ves-Matic Cube 200. METHODS: K(2) EDTA and citrated blood samples were taken from 101 randomly selected outpatients in Ankara Numune Education and Research Hospital. The ESR results using Ves-Matic Cube 200 and Westergren as reference method from 101 patients were compared and interference studies were performed. RESULTS: We found the mean difference between the two methods as 0.19 ± 15.85 mm/hr (-3.317 to 2.940 mm/hr, 95% confidence interval). Regression analysis yielded the equation "y = -2.59 + 1.15x" between the two methods (r = 0.82). CONCLUSIONS: Ves-Matic Cube 200 should be monitored carefully for good quality control. Temperature correction should be applied to study control material as recommended by the manufacturer. Ves-Matic Cube 200 device should be monitored carefully, performance studies should be performed, and the results should be checked in order to eliminate the random errors during the routine studies.