Genomic and transcriptomic analysis of breast cancer identifies novel signatures associated with response to neoadjuvant chemotherapy.

BACKGROUND: Neoadjuvant chemotherapy (NAC) has become a standard treatment strategy for breast cancer (BC). However, owing to the high heterogeneity of these tumors, it is unclear which patient population most likely benefit from NAC. Multi-omics offer an improved approach to uncovering genomic and transcriptomic changes before and after NAC in BC and to identifying molecular features associated with NAC sensitivity. METHODS: We performed whole-exome and RNA sequencing on 233 samples (including matched pre- and post-treatment tumors) from 50 BC patients with rigorously defined responses to NAC and analyzed changes in the multi-omics landscape. Molecular features associated with NAC response were identified and validated in a larger internal, and two external validation cohorts, as well as in vitro experiments. RESULTS: The most frequently altered genes were TP53, TTN, and MUC16 in both pre- and post-treatment tumors. In comparison with pre-treatment tumors, there was a significant decrease in C > A transversion mutations in post-treatment tumors (P = 0.020). NAC significantly decreased the mutation rate (P = 0.006) of the DNA repair pathway and gene expression levels (FDR = 0.007) in this pathway. NAC also significantly changed the expression level of immune checkpoint genes and the abundance of tumor-infiltrating immune and stroma cells, including B cells, activated dendritic cells, γδT cells, M2 macrophages and endothelial cells. Furthermore, there was a higher rate of C > T substitutions in NAC nonresponsive tumors than responsive ones, especially when the substitution site was flanked by C and G. Importantly, there was a unique amplified region at 8p11.23 (containing ADGRA2 and ADRB3) and a deleted region at 3p13 (harboring FOXP1) in NAC nonresponsive and responsive tumors, respectively. Particularly, the CDKAL1 missense variant P409L (p.Pro409Leu, c.1226C > T) decreased BC cell sensitivity to docetaxel, and ADGRA2 or ADRB3 gene amplifications were associated with worse NAC response and poor prognosis in BC patients. CONCLUSIONS: Our study has revealed genomic and transcriptomic landscape changes following NAC in BC, and identified novel biomarkers (CDKAL1P409L, ADGRA2 and ADRB3) underlying chemotherapy resistance and poor prognosis, which could guide the development of personalized treatments for BC.

Integrated Multi-Omics Analysis Model to Identify Biomarkers Associated With Prognosis of Breast Cancer.

Background: With the rapid development and wide application of high-throughput sequencing technology, biomedical research has entered the era of large-scale omics data. We aim to identify genes associated with breast cancer prognosis by integrating multi-omics data. Method: Gene-gene interactions were taken into account, and we applied two differential network methods JDINAC and LGCDG to identify differential genes. The patients were divided into case and control groups according to their survival time. The TCGA and METABRIC database were used as the training and validation set respectively. Result: In the TCGA dataset, C11orf1, OLA1, RPL31, SPDL1 and IL33 were identified to be associated with prognosis of breast cancer. In the METABRIC database, ZNF273, ZBTB37, TRIM52, TSGA10, ZNF727, TRAF2, TSPAN17, USP28 and ZNF519 were identified as hub genes. In addition, RPL31, TMEM163 and ZNF273 were screened out in both datasets. GO enrichment analysis shows that most of these hub genes were involved in zinc ion binding. Conclusion: In this study, a total of 15 hub genes associated with long-term survival of breast cancer were identified, which can promote understanding of the molecular mechanism of breast cancer and provide new insight into clinical research and treatment.

Worldwide review with meta-analysis of women's awareness about breast cancer.

OBJECTIVE: To summarize the awareness levels of breast cancer (BC) worldwide and investigate factors associated with BC awareness to determine differences in awareness between China and other countries. METHODS: This systematic review followed the PRISMA guidelines and included 92 articles up to July, 2021. We calculated percentages for BC awareness levels and conducted subgroup analysis and cumulative meta-analysis. RESULTS: A total 84% (95% confidence interval [95%CI]: 78-90%) of women knew about BC; however, only 51% (95%CI: 37-66%) and 40% (95%CI: 24-56%) of women were aware of BC symptoms and BC risk factors, respectively. The most commonly known BC symptom was breast lump (71%, 95%CI: 62-80%), and BC family history was the most well-known BC risk factor (61%, 95%CI: 54-69%). Subgroup analysis showed lower awareness levels among Chinese and Asian women than women from other countries. Cumulative meta-analysis showed no obvious progress in BC awareness levels over time. We investigated 15 awareness-related factors, the most frequent of which were education level (61.8%), occupation (29.4%), and age (26.5%). CONCLUSION: BC awareness levels remain low. Improving BC awareness is critical, especially in developing countries. PRACTICE IMPLICATIONS: Effective education programs are urgently needed to improve women's BC awareness.

Relationship Between Lifestyle Habits and Health-Related Quality of Life of Recently Diagnosed Breast Cancer Patients: A Comparison Between Younger and Older Women in China.

Objective: The aim of this study was to evaluate the relationship between lifestyle habits and health-related quality of life (HRQoL) among different ages who were initially diagnosed with breast cancer (within the first 2 weeks) and to determine the contribution of lifestyle habits factors on HRQoL. Methods: Patients with breast cancer were recruited from 22 hospitals in 11 provinces or municipalities in northern and eastern China. The Functional Assessment of Cancer Therapy-Breast Cancer (FACT-B) was used to measure HRQoL. Chi-square test, ANOVA, and multivariable generalized linear models were conducted to identify the differences in HRQoL between two age groups (age <50 years and ≥50 years) and to evaluate the contribution of lifestyle habits factors on HRQoL of patients with breast cancer. Results: About 1,199 eligible patients with breast cancer were used for analysis. Younger women (aged <50 years) appeared to show lower scores than older women (aged ≥50 years) in HRQoL subscales, including emotional well-being (p = 0.003), functional well-being (p = 0.006), breast cancer subscale (p = 0.038), and FACT-B Total scores (p = 0.028). Tea and alcohol consumption and being very satisfied with sleep and current life were the strongest predictors of higher HRQoL in younger group. Meanwhile, no coffee consumption, frequent participation in physical activities, high sleep satisfaction, and current life satisfaction were the key predictors of higher HRQoL in older women with breast cancer. Conclusion: The relationship of the nine lifestyle habit items with HRQoL differed among younger and older women. The associated variable of low HRQoL can help clinicians take intervention early in order to improve the prognosis of patients with breast cancer.

High Spatiotemporal Resolution Mapping of Surface Water in the Southwest Poyang Lake and Its Responses to Climate Oscillations.

Accurately quantifying spatiotemporal changes in surface water is essential for water resources management, nevertheless, the dynamics of Poyang Lake surface water areas with high spatiotemporal resolution, as well as its responses to climate change, still face considerable uncertainties. Using the time series of Sentinel-1 images with 6- or 12-day intervals, the Sentinel-1 water index (SWI), and SWI-based water extraction model (SWIM) from 2015 to 2020 were used to document and study the short-term characteristics of southwest Poyang Lake surface water. The results showed that the overall accuracy of surface water area was satisfactory with an average of 91.92%, and the surface water area ranged from 129.06 km2 on 2 March 2017 to 1042.57 km2 on 17 July 2016, with significant intra- and inter-month variability. Within the 6-day interval, the maximum change of lake area was 233.42 km2 (i.e., increasing from 474.70 km2 up to 708.12 km2). We found that the correlation coefficient between the water area and the 45-day accumulated precipitation reached to 0.75 (p < 0.001). Moreover, a prediction model was built to predict the water area based on climate records. These results highlight the significance of high spatiotemporal resolution mapping for surface water in the erratic southwest Poyang Lake under a changing climate. The automated water extraction algorithm proposed in this study has potential applications in delineating surface water dynamics at broad geographic scales.

Adipocyte-derived SFRP5 inhibits breast cancer cells migration and invasion through Wnt and epithelial-mesenchymal transition signaling pathways.

OBJECTIVE: Obesity is closely associated with metastasis in breast cancer patients. Secreted frizzled-related protein 5 (SFRP5), one of the novel adipokines with anti-inflammatory properties, is associated with obesity. This study aims to study the role of SFRP5 in the crosstalk between obesity and breast cancer metastasis and identify the underlying mechanism. METHODS: 3T3-L1 pre-adipocytes were differentiated to mature adipocytes and a hypertrophic adipocyte model was induced with palmitic acid (PA). Cell motility was measured in MDA-MB-231 and MCF-7 breast cancer cells co-cultured with adipocytes conditioned medium (CM) with or without SFRP5 protein. Wnt and epithelial-mesenchymal transition (EMT) signal pathways were investigated by western blot. Circulating SFRP5 level in 218 breast cancer patients and the association with clinicopathologic characteristics of breast cancer were further determined. Online databases ENCORI and PREDICT Plus were used to exam the link between SFRP5 and prognosis. RESULTS: Reduced SFRP5 level was detected in the hypertrophic adipocyte model. Recombinant SFRP5 protein inhibited MDA-MB-231 and MCF-7 cells invasion and migration induced by PA-treated adipocyte CM, and SFRP5 inhibition by specific antibody reversed the effect of SFRP5. Furthermore, SFRP5 significantly inhibited Wnt and downstream EMT in breast cancer cells. Low circulating SFRP5 level correlated with body mass index (BMI), lymph node (LN) metastasis, TNM stage and high Ki67 expression in breast cancer patients. Increased SFRP5 level was associated with favorable predicted survival. Kaplan-Meier curves showed high SFRP5 level in tumor tissue was associated with better outcome of breast cancer patients. CONCLUSIONS: Our findings demonstrated SFRP5 is a vital adipokine that mediates the crosslink between obesity and the metastatic potential of breast cancer. Promotion of SFRP5 expression in the adipose microenvironment may represent a novel approach for preventing breast cancer metastasis.

Impact of phosphorylated insulin-like growth factor-1 receptor on the outcome of breast cancer patients and the prognostic value of its alteration during neoadjuvant chemotherapy.

The expression of insulin-like growth factor-1 receptor (IGF-1R), which is involved in the genesis and progression of breast cancer, is thought to be associated with the overall survival (OS) of patients. However, the predictive and prognostic significance of the IGF-1R expression in breast cancer remains controversial. The present study aimed to identify the factors associated with the levels of phosphorylated (p)-IGF-1R in breast cancer, their impact on the outcomes of breast cancer patients, and the prognostic value of alterations of p-IGF-1R during neoadjuvant chemotherapy (NAC). The present study included 348 female breast cancer patients whose paraffin-embedded tumor tissue sections had been collected by biopsy and/or resection, among which the pre-NAC and post-NAC sections were available from 40 patients. Human epidermal growth factor receptor 2 (HER2) positivity and molecular subtype were significantly associated with the presence of p-IGF-1R in the tumor tissue (P<0.05). Patients with p-IGF-1R present in the tumor tissue had a shorter OS (P=0.003). The p-IGF-1R levels in the tumor after NAC differed significantly from those prior to NAC (P=0.005); however, this alteration in p-IGF-1R levels was not associated with a shorter OS. In parallel with HER2, p-IGF-1R appears to be a promising indicator for predicting clinical outcomes and may be an attractive target for improving the efficacy of antitumor therapy, particularly for patients with HER2-negative, estrogen receptor-positive and luminal B tumors.

Rapid detection of collagens using a closed-tube LAMP method.

Identification methods of collagens and gelatins have been studied many years due to religious and food safety issues. Some researchers detected the collagen while others took up their study based on DNA at the first time. In this work, we used a closed-tube loop-mediated isothermal amplification (LAMP) technique to differentiate collagen and gelatin samples. DNA was extracted by DNeasy mericon Food Kit and was dissolved in 30 µl elution buffer, optimum concentration of Mg2+, deoxyribonucleoside triphosphates(dNTPs), betaine in LAMP reaction is 6.0 mmol/L, 2.0 mmol/L, and 0.8 mmol/L, respectively. After LAMP reaction, samples being detected changed their initial color to green, others' were colorless or brown slightly. The research offered a simple, fast detection technique to differentiate collagen and gelatin samples derived from porcine, bovine and channel catfish (Ictalurus punctatus) , the collagens' species can be determined by color variation in reaction tubes within two hour.

Factors associated with insufficient awareness of breast cancer among women in Northern and Eastern China: a case-control study.

OBJECTIVES: To investigate the awareness and knowledge level of breast cancer among Chinese participants. DESIGN: Case-control study. SETTINGS: This study was based on the database of the minister-affiliated hospital key project of the Ministry of Health of the People's Republic of China that included 21 Chinese hospitals between April 2012 and April 2013. PARTICIPANTS: Matched study was designed among 2978 participants with Han ethnicity aged between 25 and 70. PRIMARY AND SECONDARY OUTCOME MEASURES: Student's t-test, Pearson's χ2 test, reliability analysis, exploratory factor analysis, and univariate and multivariate logistic regression analyses were performed to know the level of breast cancer knowledge and find the breast cancer awareness-associated factors. RESULTS: 80.0% (2383/2978) of the participants had poor awareness level of breast cancer. In-depth knowledge of breast cancer such as early symptoms and risk factors was poorly found among them. Television broadcast and relatives or friends with breast cancers were the main sources of information about breast cancer. Of all participants, 72.8% (2167/2978) had heard about breast cancer as a frequent cancer affecting women, and 63.3% (1884/2978) knew that family history of breast cancer was a risk factor for breast cancer. Over half of them were aware that a breast lump could be a symptom of breast cancer. Multivariate analysis identified the following variables that predicted awareness of breast cancer: young age (OR=0.843, 95% CI 0.740 to 0.961), occupation (agricultural worker) (OR=12.831, 95% CI 6.998 to 23.523), high household social status (OR=0.644, 95% CI 0.531 to 0.780), breast hyperplasia history (OR=1.684, 95% CI 1.273 to 2.228), high behavioural prevention score (OR=4.407, 95% CI 3.433 to 5.657). CONCLUSION: Most women were aware of breast cancer as a disease, but their in-depth knowledge of it was poor. More publicity and education programmes to increase breast cancer awareness are necessary and urgent, especially for the ageing women and agricultural workers.

A case-control study on risk factors of breast cancer in Han Chinese women.

This study aimed to investigate risk factors associated with breast cancer among Han Chinese women in northern and eastern China. A matched case-control study involving 1489 patients with breast cancer and 1489 controls was conducted across 21 hospitals in 11 provinces in China, from April 2012 to April 2013. We developed a structured questionnaire to record information from face-to-face interviews with participants. Student's t-tests, Pearson's chi-square tests, and univariate and multivariate conditional logistic regression analyses were used to identify variables with significant differences between the case and control groups. Ten variables were identified (P<0.05): location, economic status, waist-to-hip ratio, menopause, family history of breast cancer, present life satisfaction, sleep satisfaction, milk products, behavior prevention scores, and awareness of breast cancer. We identified a comprehensive range of factors related to breast cancer, among which several manageable factors may contribute to breast cancer prevention. Further prospective studies concerning psychological interventions, sleep regulation, health guidance, and physical exercise are required. A screening model for high-risk populations should be put on the agenda.

Differentiating collagens based on mitochondrion 12SrRNA gene.

Aquatic collagens are one of the main collagens sold in the market due to superior physicochemical and biological activities. In this work, the species of three types of aquatic and commercial collagens were identified by molecular biotechnology. After isolating DNA from bovine, porcine and three types of aquatic animals, DNA was dissolved in a storage buffer. The animals' mitochondrion 12SrRNA sequences were downloaded from the GenBank database, and three pairs of primers that can be used to detect the aquatic collagens were designed by Primer Premier 6 and evaluated by Oligo 7. Analysis of the polymerase chain reaction and agarose electrophoresis showed that the fragments were 440, 307, 112 and 270bp, respectively, thereby enabling successful detection of the collagen species. Results indicate that PCR-based detection methods can also suitably trace the species of aquatic collagens.

Effects of foliar dressing of selenite and silicate alone or combined with different soil ameliorants on the accumulation of As and Cd and antioxidant system in Brassica campestris.

This study was conducted to investigate the possibility of using a combined technology to synchronously reduce As and Cd accumulation in the edible parts of Brassica campestris. The results showed that a foliar application of selenite (Se) and silicon (Si) combined with soil ameliorants (including Ca-Mg-P fertilizer, sodium silicate and red mud) showed limited effects on the growth of B. campestris. The As concentration in the leaves of B. campestris in all treatments was below the Chinese safety standard. When sodium silicate and Ca-Mg-P fertilizer were added to the soil, the additional foliar application of Se and Si could in some cases help further reduce the concentrations of As and Cd in the leaves of B. campestris. However, when red mud was applied to the soil, the foliar application of Se and Si enhanced the Cd concentration in the leaves of B. campestris. In most cases, high levels of soil ameliorants plus foliar application of Se and Si significantly enhanced the As concentrations in both the soil solution and the roots of B. campestris but reduced the soil solution Cd concentration and the leaf As concentration. Most of the treatments reduced the thiobarbituric acid reactive substances (TBARS) concentration in the leaves of B. campestris, and the foliar application of Se and Si helped the soil ameliorants alleviate the oxidative stress resulting from As and Cd exposure. In this study, several treatments significantly increased the activities of superoxide dismutase (SOD) and ascorbate peroxidase (APX). However, the enzymes peroxidase (POD) and catalase (CAT) were not induced by most treatments. In summary, the combined treatment of 1gkg-1 Ca-Mg-P fertilizer plus foliar spraying 2mmolL-1 sodium selenite was most effective in reducing the Cd concentration and a rather strong ability to reduce the As concentration and trigger the activities of SOD and APX in the leaves of B. campestris.

A dietary polyphenol resveratrol acts to provide neuroprotection in recurrent stroke models by regulating AMPK and SIRT1 signaling, thereby reducing energy requirements during ischemia.

Polyphenol resveratrol (RSV) has been associated with Silent Information Regulator T1 (SIRT1) and AMP-activated protein kinase (AMPK) metabolic stress sensors and probably responds to the intracellular energy status. Our aim here was to investigate the neuroprotective effects of RSV and its association with SIRT1 and AMPK signaling in recurrent ischemia models. In this study, elderly male Wistar rats received a combination of two mild transient middle cerebral artery occlusions (tMCAOs) as an in vivo recurrent ischemic model. Primary cultured cortical neuronal cells subjected to combined oxygen-glucose deprivation (OGD) were used as an in vitro recurrent ischemic model. RSV administration significantly reduced infarct volumes, improved behavioral deficits and protected neuronal cells from cell death in recurrent ischemic stroke models in vivo and in vitro. RSV treatments significantly increased the intracellular NAD(+) /NADH ratio, AMPK and SIRT1 activities, decreased energy assumption and restored cell energy ATP level. SIRT1 and AMPK inhibitors and specific small interfering RNA (siRNA) for SIRT1 and AMPK significantly abrogated the neuroprotection induced by RSV. AMPK-siRNA and inhibitor decreased SIRT1 activities; however, SIRT1-siRNA and inhibitor had no impact on phospho-AMPK (p-AMPK) levels. These results indicated that the neuroprotective effects of RSV increased the intracellular NAD(+) /NADH ratio as well as AMPK and SIRT1 activities, thereby reducing energy ATP requirements during ischemia. SIRT1 is a downstream target of p-AMPK signaling induced by RSV in the recurrent ischemic stroke model.