A transcriptome-based signature of pathological angiogenesis predicts breast cancer patient survival

Liposome-encapsulated zoledronate increases inflammatory macrophage population in TNBC tumours

BACKGROUND

Tumour associated macrophages (TAMs) are important players in breast tumour progression and metastasis. Clinical and preclinical evidence suggests a role for zoledronate (ZOL) in breast cancer metastasis prevention. Further, zoledronate is able to induce inflammatory activation of monocytes and macrophages, which can be favourable in cancer treatments. The inherent bone tropism of zoledronate limits its availability in soft tissues and tumours. In this study we utilised an orthotopic murine breast cancer model to evaluate the possibility to use liposomes (EMP-LIP) to target zoledronate to tumours to modify TAM activation.

METHODS

Triple-negative breast cancer 4T1 cells were inoculated in the 4th mammary fat pad of female Balb/c mice. Animals were divided according to the treatment: vehicle, ZOL, EMP-LIP and liposome encapsulated zoledronate (ZOL-LIP). Treatment was done intravenously (with tumour resection) and intraperitoneally (without tumour resection). Tumour growth was followed by bioluminescence in vivo imaging (IVIS) and calliper measurements. Tumour-infiltrating macrophages were assessed by immunohistochemical and immunofluorescence staining. Protein and RNA expression levels of inflammatory transcription factors and cytokines were measured by Western Blotting and Taqman RT-qPCR.

RESULTS

Liposome encapsulated zoledronate (ZOL-LIP) treatment suppressed migration of 4T1 cell in vitro. Tumour growth and expression of the angiogenic marker CD34 were reduced upon both ZOL and ZOL-LIP treatment in vivo. Long-term ZOL-LIP treatment resulted in shift towards M1-type macrophage polarization, increased CD4 T cell infiltration and activation of NF-κB indicating changes in intratumoural inflammation, whereas ZOL treatment showed similar but non-significant trends. Moreover, ZOL-LIP had a lower bisphosphonate accumulation in bone compared to free ZOL.

CONCLUSION

Results show that the decreased bisphosphonate accumulation in bone promotes the systemic anti-tumour effect of ZOL-LIP by increasing inflammatory response in TNBC tumours via M1-type macrophage activation.

Oxygen-induced pathological angiogenesis promotes intense lipid synthesis and remodeling in the retina

The retina is a notable tissue with high metabolic needs which relies on specialized vascular networks to protect the neural retina while maintaining constant supplies of oxygen, nutrients, and dietary essential fatty acids. Here we analyzed the lipidome of the mouse retina under healthy and pathological angiogenesis using the oxygen-induced retinopathy model. By matching lipid profiles to changes in mRNA transcriptome, we identified a lipid signature showing that pathological angiogenesis leads to intense lipid remodeling favoring pathways for neutral lipid synthesis, cholesterol import/export, and lipid droplet formation. Noteworthy, it also shows profound changes in pathways for long-chain fatty acid production, vital for retina homeostasis. The net result is accumulation of large quantities of mead acid, a marker of essential fatty acid deficiency, and a potential marker for retinopathy severity. Thus, our lipid signature might contribute to better understand diseases of the retina that lead to vision impairment or blindness.

Transcriptomics for Clinical and Experimental Biology Research: Hang on a Seq

Sequencing the human genome empowers translational medicine, facilitating transcriptome-wide molecular diagnosis, pathway biology, and drug repositioning. Initially, microarrays are used to study the bulk transcriptome; but now short-read RNA sequencing (RNA-seq) predominates. Positioned as a superior technology, that makes the discovery of novel transcripts routine, most RNA-seq analyses are in fact modeled on the known transcriptome. Limitations of the RNA-seq methodology have emerged, while the design of, and the analysis strategies applied to, arrays have matured. An equitable comparison between these technologies is provided, highlighting advantages that modern arrays hold over RNA-seq. Array protocols more accurately quantify constitutively expressed protein coding genes across tissue replicates, and are more reliable for studying lower expressed genes. Arrays reveal long noncoding RNAs (lncRNA) are neither sparsely nor lower expressed than protein coding genes. Heterogeneous coverage of constitutively expressed genes observed with RNA-seq, undermines the validity and reproducibility of pathway analyses. The factors driving these observations, many of which are relevant to long-read or single-cell sequencing are discussed. As proposed herein, a reappreciation of bulk transcriptomic methods is required, including wider use of the modern high-density array data-to urgently revise existing anatomical RNA reference atlases and assist with more accurate study of lncRNAs.

Transcriptome analysis of AAV-induced retinopathy models expressing human VEGF, TNF-α, and IL-6 in murine eyes

Retinopathies are multifactorial diseases with complex pathologies that eventually lead to vision loss. Animal models facilitate the understanding of the pathophysiology and identification of novel treatment options. However, each animal model reflects only specific disease aspects and understanding of the specific molecular changes in most disease models is limited. Here, we conducted transcriptome analysis of murine ocular tissue transduced with recombinant Adeno-associated viruses (AAVs) expressing either human VEGF-A, TNF-α, or IL-6. VEGF expression led to a distinct regulation of extracellular matrix (ECM)-associated genes. In contrast, both TNF-α and IL-6 led to more comparable gene expression changes in interleukin signaling, and the complement cascade, with TNF-α-induced changes being more pronounced. Furthermore, integration of single cell RNA-Sequencing data suggested an increase of endothelial cell-specific marker genes by VEGF, while TNF-α expression increased the expression T-cell markers. Both TNF-α and IL-6 expression led to an increase in macrophage markers. Finally, transcriptomic changes in AAV-VEGF treated mice largely overlapped with gene expression changes observed in the oxygen-induced retinopathy model, especially regarding ECM components and endothelial cell-specific gene expression. Altogether, our study represents a valuable investigation of gene expression changes induced by VEGF, TNF-α, and IL-6 and will aid researchers in selecting appropriate animal models for retinopathies based on their agreement with the human pathophysiology.

Angiogenesis goes computational - The future way forward to discover new angiogenic targets?

Multi-omics technologies are being increasingly utilized in angiogenesis research. Yet, computational methods have not been widely used for angiogenic target discovery and prioritization in this field, partly because (wet-lab) vascular biologists are insufficiently familiar with computational biology tools and the opportunities they may offer. With this review, written for vascular biologists who lack expertise in computational methods, we aspire to break boundaries between both fields and to illustrate the potential of these tools for future angiogenic target discovery. We provide a comprehensive survey of currently available computational approaches that may be useful in prioritizing candidate genes, predicting associated mechanisms, and identifying their specificity to endothelial cell subtypes. We specifically highlight tools that use flexible, machine learning frameworks for large-scale data integration and gene prioritization. For each purpose-oriented category of tools, we describe underlying conceptual principles, highlight interesting applications and discuss limitations. Finally, we will discuss challenges and recommend some guidelines which can help to optimize the process of accurate target discovery.

Prediction of pathological complete response to neoadjuvant chemotherapy in patients with breast cancer using a combination of contrast-enhanced ultrasound and dynamic contrast-enhanced magnetic resonance imaging

This study aimed to evaluate the value of dynamic contrast-enhanced ultrasound (CEUS) combined with dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) in predicting pathological complete response (pCR) in patients with breast cancer receiving neoadjuvant chemotherapy (NAC). Fifty-seven female patients with breast cancer (mean age, 50.46 years; range, 32-66 years) scheduled for NAC were recruited. CEUS and DCE-MRI were performed before and after NAC. Imaging features and their changes were compared with postoperative pathological results. After the clinical differences were balanced using propensity score matching, univariate and multiple logistic regression analyses were used to derive the characteristics independently associated with pCR. Receiver operating characteristic curve analysis was performed to assess diagnostic performance. After six to eight cycles of NAC, 24 (42.1%) patients achieved pCR, while 33 (57.9%) did not. Multivariate analysis showed that enhancement order on CEUS and DCE-MRI before NAC, reduction in diameter and enhancement shape on CEUS, maximum diameter on DCE-MRI, and the type of progressive dynamic contrast enhancement after NAC were independently associated with pCR after NAC. The area under the receiver operating characteristic curve for CEUS+DCE-MRI was 0.911 (95% confidence interval, 0.826-0.997), and the specificity and positive predictive values were 87.0% and 87.5%. CEUS and DCE-MRI have the potential for assessing the pathological response to NAC in patients with breast cancer; their combination showed the best diagnostic performance. CEUS+DCE-MRI has proved beneficial for comprehensive assessment and personalizing treatment strategies for patients with breast cancer.

DMDRMR promotes angiogenesis via antagonizing DAB2IP in clear cell renal cell carcinoma

Clear cell renal cell carcinoma (ccRCC) patients are highly angiogenic and treated by targeted therapies against VEGFA/VEGFR signaling pathway. However, tumors with such targeted therapies remain a significant clinic challenge. Understanding the underlying mechanism against angiogenesis is highly desired. Here, we demonstrated that the lncRNA DMDRMR serves as a sponge of miR-378a-5p to increase EZH2 and SMURF1 expression, thus promoting EZH2-mediated transcriptional repression of DAB2IP and SMURF1-mediated degradation of DAB2IP. Consequently, this axis activates VEGFA/VEGFR2 signaling pathway, resulting in angiogenesis and resistance of tumor cells to sunitinib in ccRCC. Moreover, the competing endogenous RNA regulatory axis of DMDRMR is clinically relevant to ccRCC pathogenesis and prognosis of patients with ccRCC. Our results support that the DMDRMR/miR-378a-5p/DAB2IP axis may serve as a novel target for combination diagnosis or therapy of ccRCC patients. Our findings may have highly clinical relevance for future translation to develop the targeted therapies for patients with ccRCC.

Molecular Characterization of Limited Ulcerative Colitis Reveals Novel Biology and Predictors of Disease Extension

BACKGROUND AND AIMS

Disease extent varies in ulcerative colitis (UC) from proctitis to left-sided colitis to pancolitis and is a major prognostic factor. When the extent of UC is limited there is often a sharp demarcation between macroscopically involved and uninvolved areas and what defines this or subsequent extension is unknown. We characterized the demarcation site molecularly and determined genes associated with subsequent disease extension.

METHODS

We performed RNA sequence analysis of biopsy specimens from UC patients with endoscopically and histologically confirmed limited disease, of which a subset later extended. Biopsy specimens were obtained from the endoscopically inflamed upper (proximal) limit of disease, immediately adjacent to the uninvolved colon, as well as at more proximal, endoscopically uninflamed colonic segments.

RESULTS

Differentially expressed genes were identified in the endoscopically inflamed biopsy specimens taken at each patient's most proximal diseased site relative to healthy controls. Expression of these genes in the more proximal biopsy specimens transitioned back to control levels abruptly or gradually, the latter pattern supporting the concept that disease exists beyond the endoscopic disease demarcation site. The gradually transitioning genes were associated with inflammation, angiogenesis, glucuronidation, and homeodomain pathways. A subset of these genes in inflamed biopsy specimens was found to predict disease extension better than clinical features and were responsive to biologic therapies. Network analysis revealed critical roles for interferon signaling in UC inflammation and poly(ADP-ribose) polymerase 14 (PARP14) was a predicted key driver gene of extension. Higher PARP14 protein levels were found in inflamed biopsy specimens of patients with limited UC that subsequently extended.

CONCLUSION

Molecular predictors of disease extension reveal novel strategies for disease prognostication and potential therapeutic targeting.

A Review on Silver Nanoparticles: Classification, Various Methods of Synthesis, and Their Potential Roles in Biomedical Applications and Water Treatment

Recent developments in nanoscience have appreciably modified how diseases are prevented, diagnosed, and treated. Metal nanoparticles, specifically silver nanoparticles (AgNPs), are widely used in bioscience. From time to time, various synthetic methods for the synthesis of AgNPs are reported, i.e., physical, chemical, and photochemical ones. However, among these, most are expensive and not eco-friendly. The physicochemical parameters such as temperature, use of a dispersing agent, surfactant, and others greatly influence the quality and quantity of the synthesized NPs and ultimately affect the material’s properties. Scientists worldwide are trying to synthesize NPs and are devising methods that are easy to apply, eco-friendly, and economical. Among such strategies is the biogenic method, where plants are used as the source of reducing and capping agents. In this review, we intend to debate different strategies of AgNP synthesis. Although, different preparation strategies are in use to synthesize AgNPs such as electron irradiation, optical device ablation, chemical reduction, organic procedures, and photochemical methods. However, biogenic processes are preferably used, as they are environment-friendly and economical. The review covers a comprehensive discussion on the biological activities of AgNPs, such as antimicrobial, anticancer anti-inflammatory, and anti-angiogenic potentials of AgNPs. The use of AgNPs in water treatment and disinfection has also been discussed in detail.

Gene expression profile of the murine ischemic retina and its response to Aflibercept (VEGF-Trap)

Ischemic retinal dystrophies are leading causes of acquired vision loss. Although the dysregulated expression of the hypoxia-responsive VEGF-A is a major driver of ischemic retinopathies, implication of additional VEGF-family members in their pathogenesis has led to the development of multivalent anti-angiogenic tools. Designed as a decoy receptor for all ligands of VEGFR1 and VEGFR2, Aflibercept is a potent anti-angiogenic agent. Notwithstanding, the molecular mechanisms mediating Aflibercept's efficacy remain only partially understood. Here, we used the oxygen-induced retinopathy (OIR) mouse as a model system of pathological retinal vascularization to investigate the transcriptional response of the murine retina to hypoxia and of the OIR retina to Aflibercept. While OIR severely impaired transcriptional changes normally ensuing during retinal development, analysis of gene expression patterns hinted at alterations in leukocyte recruitment during the recovery phase of the OIR protocol. Moreover, the levels of Angiopoietin-2, a major player in the progression of diabetic retinopathy, were elevated in OIR tissues and consistently downregulated by Aflibercept. Notably, GO term, KEGG pathway enrichment, and expression dynamics analyses revealed that, beyond regulating angiogenic processes, Aflibercept also modulated inflammation and supported synaptic transmission. Altogether, our findings delineate novel mechanisms potentially underlying Aflibercept's efficacy against ischemic retinopathies.

PCDHB17P/miR-145-3p/MELK/NF-κB Feedback Loop Promotes Metastasis and Angiogenesis of Breast Cancer

Breast cancer is one of the most common life-threatening cancers, mainly because of its aggressiveness and metastasis. Accumulating evidence indicates that long non-coding RNAs (lncRNAs) participate in the development and progression of breast cancer. Nevertheless, the function and expression level of lncRNAs in breast cancer are still not fully understood. Here, we demonstrated that lncRNA PCDHB17P was up-expressed in human breast cancer tissues and cell lines. Knockdown of PCDHB17P remarkably suppressed migration and invasion, as well as tube formation ability of breast cancer cells. MiR-145-3p was significantly decreased in breast cancer samples, which was negatively correlated to the expression of PCDHB17P. In addition, we identified that MELK was a direct target gene of miR-145-3p, which was higher expressed in breast cancer tissues than that in adjacent normal tissues. Mechanistic investigation indicated that PCDHB17P acted as a cancer-promoting competing endogenous RNA (ceRNA) by binding miR-145-3p and upregulating MELK. Interestingly, MELK could in turn increase the promoter activity and expression of PCDHB17P via NF-κB, thus forming a positive feedback loop that drives the metastasis and angiogenesis of breast cancer. Overall, the results demonstrated that the constitutive activation of PCDHB17P/miR-145-3p/MELK/NF-κB feedback loop promotes the metastasis and angiogenesis of breast cancer, suggesting that this lncRNA might be a promising prognostic biomarker and therapeutic target for breast cancer.