Landscape analysis of adjacent gene rearrangements reveals BCL2L14-ETV6 gene fusions in more aggressive triple-negative breast cancer.

Triple-negative breast cancer (TNBC) accounts for 10 to 20% of breast cancer, with chemotherapy as its mainstay of treatment due to lack of well-defined targets, and recent genomic sequencing studies have revealed a paucity of TNBC-specific mutations. Recurrent gene fusions comprise a class of viable genetic targets in solid tumors; however, their role in breast cancer remains underappreciated due to the complexity of genomic rearrangements in this cancer. Our interrogation of the whole-genome sequencing data for 215 breast tumors catalogued 99 recurrent gene fusions, 57% of which are cryptic adjacent gene rearrangements (AGRs). The most frequent AGRs, BCL2L14-ETV6, TTC6-MIPOL1, ESR1-CCDC170, and AKAP8-BRD4, were preferentially found in the more aggressive forms of breast cancers that lack well-defined genetic targets. Among these, BCL2L14-ETV6 was exclusively detected in TNBC, and interrogation of four independent patient cohorts detected BCL2L14-ETV6 in 4.4 to 12.2% of TNBC tumors. Interestingly, these fusion-positive tumors exhibit more aggressive histopathological features, such as gross necrosis and high tumor grade. Amid TNBC subtypes, BCL2L14-ETV6 is most frequently detected in the mesenchymal entity, accounting for ∼19% of these tumors. Ectopic expression of BCL2L14-ETV6 fusions induce distinct expression changes from wild-type ETV6 and enhance cell motility and invasiveness of TNBC and benign breast epithelial cells. Furthermore, BCL2L14-ETV6 fusions prime partial epithelial-mesenchymal transition and endow resistance to paclitaxel treatment. Together, these data reveal AGRs as a class of underexplored genetic aberrations that could be pathological in breast cancer, and identify BCL2L14-ETV6 as a recurrent gene fusion in more aggressive form of TNBC tumors.

[Effects of long non-coding RNA RP1-90L14.1 on the biological behaviors of cancer prostate LNCaP cells and its regulating mechanisms].

OBJECTIVE: To investigate the effects of long non-coding RNA RP1-90L14.1 on the proliferation, migration and invasion of prostate cancer LNCaP cells and the expressions of GRIN2A and BACE2. METHODS: Using RT-PCR, we detected the expression of RP1-90L14.1 in LNCaP and LNCaP-AI cells, transiently transfected the RP1-90L14.1 overexpression plasmid (the RP1-90L14.1 group) and vector plasmid (the LNCaP-NC group) into the LNCaP cells, and cultured the two groups of cells with ordinary medium and phenol red-free activated carbon adsorption medium (PRF-ACA). Then we examined the proliferation, migration and invasiveness of the cells by CCK-8 and Transwell, and determined the mRNA and protein expressions of GRIN2A and BACE2 by RT-PCR and Western blot. RESULTS: The expression of RP1-90L14.1 was significantly higher in the LNCaP-AI than in the LNCaP cells (8.49 ± 0.43 vs 2.53 ± 0.95, P < 0.05), and so was that of LNCaP-RP1-90L14.1 in the RP1-90L14.1 than in the LNCaP-NC group after transfection (0.71 ± 0.22 vs 0.02 ± 0.01, P < 0.05). The optical densities (OD) of the cells were 51.95% and 50.69% higher in the RP1-90L14.1 than in the LNCaP-NC group after 72 hours of culture with ordinary medium and phenol red-free ACA (1.22 ± 0.08 vs 0.08 ± 0.05, P < 0.05; 0.79 ± 0.02 vs 0.53 ± 0.05, P < 0.05), and 51.72% and 60.23% higher in the former than in the latter after 96 hours (1.72 ± 0.07 vs 1.13 ± 0.05, P < 0.05; 1.18 ± 0.05 vs 0.73 ± 0.08, P < 0.05). The numbers of the migrating cells cultured with common medium and PRF-ACA were markedly higher in the RP1-90L14.1 than in the LNCaP-NC group after transfection (682.0 ± 42.7 vs 422.0 ± 37.1, P < 0.05; 419.0 ± 42.9 vs 251.0 ± 25.9, P < 0.05), and so were those of the invading cells (507.0 ± 22.2 vs 274.0 ± 19.6, P < 0.05; 352.0 ± 14.1 vs 216.0 ± 14.3, P < 0.05). Statistically significant differences were observed between the RP1-90L14.1 and LNCaP-NC groups in the mRNA and protein expressions of GRIN2A (5.13 ± 0.89 vs 2.09 ± 0.54, P < 0.05; 5.88 ± 0.29 vs 2.03 ± 0.22, P < 0.05) and BACE2 (5.82 ± 0.50 vs 2.53 ± 0.30, P < 0.05; 4.89 ± 0.19 vs 3.37 ± 0.13, P < 0.05). CONCLUSIONS: 　lncRNA RP1-90L14.1 may play important roles in the proliferation, migration and invasiveness of prostate cancer cells. RP1-90L14.1 can promote the expressions of GRIN2A and BACE2 and may have an endogenous competitive relation with GRIN2A and BACE2.

DNA methylation and whole-genome transcription analysis in CD4+ T cells from systemic lupus erythematosus patients with or without renal damage.

BACKGROUND: Lupus nephritis (LN) is the most common cause of kidney injury in systemic lupus erythematosus (SLE) patients and is associated with increased mortality. DNA methylation, one of the most important epigenetic modifications, has been reported as a key player in the pathogenesis of SLE. Hence, our article aimed to explore DNA methylation in CD4+ T cells from LNs to identify additional potential biomarkers and pathogenic genes involved in the progression of LN. METHODS: Our study enrolled 46 SLE patients with or without kidney injury and 23 healthy controls from 2019 to 2022. CD4+ T cells were sorted for DNA methylation genotyping and RNA-seq. Through bioinformatics analysis, we identified the significant differentially methylated CpG positions (DMPs) only in the LN group and validated them by Bisulfite PCR. Integration analysis was used to screen for differentially methylated and expressed genes that might be involved in the progression of LN, and the results were analyzed via cell experiments and flow cytometry. RESULTS: We identified 243 hypomethylated sites and 778 hypermethylated sites only in the LN cohort. Three of these DMPs, cg08332381, cg03297029, and cg16797344, were validated by Bisulfite PCR and could be potential biomarkers for LN. Integrated analysis revealed that the expression of BCL2L14 and IFI27 was regulated by DNA methylation, which was validated by azacytidine (5-aza) treatment. The overexpression of BCL2L14 in CD4+ T cells might induce renal fibrosis and inflammation by regulating the differentiation and function of Tfh cells. CONCLUSION: Our study identified novel aberrant DMPs in CD4+ T cells only in LN patients and DNA methylation-regulated genes that could be potential LN biomarkers. BCL2L14 is likely involved in the progression of LN and might be a treatment target.

The Impact of Organizational Boundaries on Healthcare Coordination and Utilization.

We measure organizational concentration-the distribution of a patient's healthcare across organizations-to examine how firm boundaries affect healthcare efficiency. First, when patients move to regions where outpatient visits are typically concentrated within a small set of firms, their healthcare utilization falls. Second, for patients whose PCPs exit the market, switching to a PCP with 1 standard deviation higher organizational concentration reduces utilization by 21%. This finding is robust to controlling for the spread of healthcare across providers. Increases in organizational concentration predict improvements in diabetes care and are not associated with greater use of emergency department or inpatient care.

Dietary polyphenols and their relationship to the modulation of non-communicable chronic diseases and epigenetic mechanisms: A mini-review.

Chronic Non-Communicable Diseases (NCDs) have been considered a global health problem, characterized as diseases of multiple factors, which are developed throughout life, and regardless of genetics as a risk factor of important relevance, the increase in mortality attributed to the disease to environmental factors and the lifestyle one leads. Although the reactive species (ROS/RNS) are necessary for several physiological processes, their overproduction is directly related to the pathogenesis and aggravation of NCDs. In contrast, dietary polyphenols have been widely associated with minimizing oxidative stress and inflammation. In addition to their antioxidant power, polyphenols have also drawn attention for being able to modulate both gene expression and modify epigenetic alterations, suggesting an essential involvement in the prevention and/or development of some pathologies. Therefore, this review briefly explained the mechanisms in the development of some NCDs, followed by a summary of some evidence related to the interaction of polyphenols in oxidative stress, as well as the modulation of epigenetic mechanisms involved in the management of NCDs.

Drug Diffusion Through Peer Networks: The Influence of Industry Payments.

Pharmaceutical companies market to physicians through individual detailing accompanied by monetary or in-kind transfers. Large compensation payments to a small number of physicians account for most of this promotional spending. Studying US promotional payments and prescriptions for anticoagulant drugs, we investigate how peer influence broadens the payments' reach. Following a compensation payment, prescriptions for the marketed drug increase by both the paid physician and the paid physician's peers. Payments increase prescriptions to both recommended and contraindicated patients. Over three years, marketed anticoagulant prescriptions rose 23 percent due to payments, with peer spillovers contributing a quarter of the increase.

LncRNA RP11-551L14.4 suppresses breast cancer development by inhibiting the expression of miR-4472.

Background: Previous studies have been reported that long non-coding RNA (lncRNA) can regulate the expression of genes which are involved in many important cellular processes The potential role of lncRNA RP11-551L14.4 in the development of breast cancer and the possible regulatory mechanisms was investigated. Methods: Quantitative real-time polymerase chain reaction (qRT-PCR) was conducted to analyze RP11-551L14.4 expression in 36 paired breast cancer tissues and adjacent tissues. The expression of RP11-551L14.4 in multiple breast cancer cell lines was detected by qRT-PCR. Meanwhile, overexpression of RP11-551L14.4 models was established using lentivirus in BT474 and T47D breast cancer cells. Cell counting kit-8 (CCK-8), cell colony formation and cell cycle assays were performed to detect the effects of RP11-551L14.4 on the biological function of breast cancer cells. Besides, bioinformatics techniques, dual luciferase reporter gene assay and rescue experiments were used to investigate the potential mechanisms. Results: RP11-551L14.4 expression was negatively associated with the advanced tumor stage. Breast cancer patients with low RP11-551L14.4 expression manifested a poorer prognosis. The results of qRT-PCR showed that RP11-551L14.4 expression in breast cancer tissues was significantly lower than in adjacent tissues. Meanwhile, overexpression of RP11-551L14.4 significantly decreased the cell proliferation and cell cycle. Bioinformatics technology showed that RP11-551L14.4 could complementarily bind to miR-4472. qRT-PCR results indicated that the expression levels of miR-4472 and RP11-551L14.4 in breast cancer were negatively correlated. Luciferase reporter gene assay showed that miR-4472 remarkably decreased the relative luciferase activity of the wild-type RP11-551L14.4 vector. miR-4472 is a direct target gene of RP11-551L14.4. miR-4472 levels were reduced, and repulsive guidance molecule A (RGMA) mRNA or protein levels were increased after overexpression of RP11-551L14.4 in the breast cancer cells. miR-4472 reversed the effects caused by RP11-551L14.4 in breast cancer cells. Conclusion: RP11-551L14.4 expression was remarkably decreased in breast cancer tissues and cells. RP11-551L14.4 may inhibit the malignant progression of breast cancer by regulating miR-4472 expression.

Quantitative Proteomic Analysis of Plasma Exosomes to Identify the Candidate Biomarker of Imatinib Resistance in Chronic Myeloid Leukemia Patients.

BACKGROUND: Imatinib (IM), a tyrosine kinase inhibitor (TKI), has markedly improved the survival and life quality of chronic myeloid leukemia (CML) patients. However, the lack of specific biomarkers for IM resistance remains a serious clinical challenge. Recently, growing evidence has suggested that exosome-harbored proteins were involved in tumor drug resistance and could be novel biomarkers for the diagnosis and drug sensitivity prediction of cancer. Therefore, we aimed to investigate the proteomic profile of plasma exosomes derived from CML patients to identify ideal biomarkers for IM resistance. METHODS: We extracted exosomes from pooled plasma samples of 9 imatinib-resistant CML patients and 9 imatinib-sensitive CML patients by ultracentrifugation. Then, we identified the expression levels of exosomal proteins by liquid chromatography-tandem mass spectrometry (LC-MS/MS) based label free quantification. Bioinformatics analyses were used to analyze the proteomic data. Finally, the western blot (WB) and parallel reaction monitoring (PRM) analyses were applied to validate the candidate proteins. RESULTS: A total of 2812 proteins were identified in plasma exosomes from imatinib-resistant and imatinib-sensitive CML patients, including 279 differentially expressed proteins (DEPs) with restricted criteria (fold change≥1.5 or ≤0.667, p<0.05). Compared with imatinib-sensitive CML patients, 151 proteins were up-regulated and 128 proteins were down-regulated. Bioinformatics analyses revealed that the main function of the upregulated proteins was regulation of protein synthesis, while the downregulated proteins were mainly involved in lipid metabolism. The top 20 hub genes were obtained using STRING and Cytoscape, most of which were components of ribosomes. Moreover, we found that RPL13 and RPL14 exhibited exceptional upregulation in imatinib-resistant CML patients, which were further confirmed by PRM and WB. CONCLUSION: Proteomic analysis of plasma exosomes provides new ideas and important information for the study of IM resistance in CML. Especially the exosomal proteins (RPL13 and RPL14), which may have great potential as biomarkers of IM resistance.

Functional analysis of candidate genes from genome-wide association studies of hearing.

The underlying causes of age-related hearing loss (ARHL) are not well understood, but it is clear from heritability estimates that genetics plays a role in addition to environmental factors. Genome-wide association studies (GWAS) in human populations can point to candidate genes that may be involved in ARHL, but follow-up analysis is needed to assess the role of these genes in the disease process. Some genetic variants may contribute a small amount to a disease, while other variants may have a large effect size, but the genetic architecture of ARHL is not yet well-defined. In this study, we asked if a set of 17 candidate genes highlighted by early GWAS reports of ARHL have detectable effects on hearing by knocking down expression levels of each gene in the mouse and analysing auditory function. We found two of the genes have an impact on hearing. Mutation of Dclk1 led to late-onset progressive increase in ABR thresholds and the A430005L14Rik (C1orf174) mutants showed worse recovery from noise-induced damage than controls. We did not detect any abnormal responses in the remaining 15 mutant lines either in thresholds or from our battery of suprathreshold ABR tests, and we discuss the possible reasons for this.

Upregulation of miR-496 decreases cerebral ischemia/reperfusion injury by negatively regulating BCL2L14.

Neurological functions were seriously impaired by cerebral ischemia-reperfusion (I/R) injury following ischemic stroke and its molecular mechanism is still not fully understood. MicroRNA-496 (miR-496) has been reported to be deregulated in several diseases but it still remains unknown about the function of miR-496 in cerebral I/R injury. Here, Middle cerebral artery occlusion/reperfusion (MCAO/R) was performed to induce cerebral I/R injury in rats. Then, neurological deficits were assessed by Bederson and Longa score system. The 2,3,5-triphenyltetrazolium chloride (TTC) and terminal deoxynucleotidyltransferase UTP nick end labeling (TUNEL) staining were used to evaluate the rat brain pathology. The oxygen-glucose deprivation and reperfusion (OGD/R) induced in vitro I/R injury was constructed in SH-SY5Y cells. The expression of miR-496 was determined using Real-time PCR. Bioinformatics analysis and dual luciferase reporter assay were utilized to confirm the target gene of miR-496. CCK-8, EdU staining, flow cytometry and Hoechst 33258 staining were respectively utilized to measure cell viability, proliferation and apoptosis. The results showed the expression of miR-496 was found to be down-regulated by cerebral I/R in rats and OGD/R-inducedSH-SY5Y cell model. MiR-496 overexpression alleviated the OGD/R-induced injury in SH-SY5Y cells. In addition, pro-apoptosis factor Bcl-2-like protein 14 (BCL2L14) was predicted and verified as the direct target of miR-496 and suppressed by miR-496. Furthermore, BCL2L14 knockdown exhibited similar effects similar to those of miR-496 overexpression, and the restored BCL2L14expression reversed the protective effects of miR-496 on SH-SY5Y cells. In conclusions, our results suggest that miR-496 alleviates cerebral I/R injury possibly via inhibiting BCL2L14 expression.

The differences in the relationship between obstructive sleep apnea severity and trabecular bone score in men and women with type 2 diabetes.

AIMS: Type 2 diabetes mellitus (T2DM) and obstructive sleep apnea (OSA) may adversely affect bone. Gender is a well-established factor influencing bone health. We investigated the impact of OSA on bone mineral density (BMD) and trabecular bone score (TBS) in T2DM. METHODS: Eighty-one T2DM patients [33 men and 48 women] participated. OSA was diagnosed using an overnight monitor, with its severity assessed by an apnea hypopnia index (pAHI). The measurements of hypoxia, including the percentage of total sleep time in which oxygen saturation remains below 90% (pT90), the oxygen desaturation index (pODI) and minimum O2 (min O2), were reported. Lumbar spine (L1-4) and femoral neck (FN) BMD were measured using dual-energy X-ray absorptiometry (DXA). TBS was computed from DXA images. RESULTS: Sixty-five patients (80.2%) had OSA. pAHI, pT90, pODI and min O2 were not correlated to L1-4 BMD, FN BMD or TBS in all participants by multiple regression analyses adjusting for age, gender and BMI. However, an interaction between gender and pAHI, and gender and pODI were significantly associated with TBS (b = 0.003, p = 0.034 and b = 0.004, p = 0.046, respectively). We therefore reassessed an association between pAHI or pODI and TBS separately between men and women. After adjusting for age and BMI, more severe OSA (higher pAHI) and higher pODI significantly associated with lower TBS (b = -0.002, p = 0.034 and b = -0.003, p = 0.021, respectively) in men. On the other hand, higher pAHI non-significantly associated with better trabecular microarchitecture as indicated by higher TBS (b = 0.002, p = 0.059) in women. When considered only postmenopausal (n = 33), higher pAHI and higher pODI were significantly associated with higher TBS (b = 0.004, p = 0.003 and b = 0.004, p = 0.008, respectively). CONCLUSIONS: In T2DM patients, there is a complex interrelationship among OSA severity, gender and TBS. More severe OSA predicted lower TBS in men, but predicted higher TBS in postmenopausal women.

Biological welfare and the commons: A natural experiment in the Alps, 1765-1845.

In the late 18th century hundreds self-governing alpine communities in Northern Italy came under the direct control of centralized states (Austria and France) at different times. We exploit the timing and location of these interventions in a DD type design to investigate the effects of removing CPR institutions on biological welfare. We find a significant and persistent increase in infant mortality rates and a more modest decrease in birth rates as a result of state centralization. We provide evidence that these demographic changes reflect a critical loss of natural resource income caused by the disruption of communal institutions. Impacts are most severe in communities that have no prior experience with formal institutions.

Synthesis of α-l-Fucose-l-14 C (6-Deoxy-l-galactose-l-14 C).

α-l-Fucose-l-14 C was synthesized in a radiochemical yield of 30 percent. The synthesis involved degradation of nonradioactive l'fuconic acid to 5-deoxy-l-lyxose and synthesis from this of α-l-fucose-l-l4 C by use of 14C-labeled cyanide in the cyanohydrin reaction. The resulting epimeric, 14C-labeled aldonic acids were separated as either the barium or the sodium salts. Both salts of l-fuconic acid crystallize more readily than the corresponding salts of the epimeric 6-deoxy-l-talonic acid. The preparation of barium l-fuconate by the electrolytic oxidation of l-fucose in the presence of barium carbonate and barium bromide is described.