Untreated Breast Cancer Patients Research Articles

Tumor-Infiltrating Lymphocyte Scoring in Neoadjuvant-Treated Breast Cancer.

Neoadjuvant chemotherapy (NAC) is now the standard of care for patients with locally advanced breast cancer (BC). TIL scoring is prognostic and adds predictive value to the residual cancer burden evaluation after NAC. However, NAC induces changes in the tumor, and the reliability of TIL scoring in post-NAC samples has not yet been studied. H&E- and dual CD3/CD20 chromogenic IHC-stained tissues were scored for stromal and intra-tumoral TIL by two experienced pathologists on pre- and post-treatment BC tissues. Digital TIL scoring was performed using the HALO® image analysis software (version 2.2). In patients with residual disease, we show a good inter-pathologist correlation for stromal TIL on H&E-stained tissues (CCC value 0.73). A good correlation for scoring with both staining methods (CCC 0.81) and the digital TIL scoring (CCC 0.77) was also observed. Overall concordance for TIL scoring in patients with a complete response was however poor. This study reveals there is good reliability for TIL scoring in patients with detectable residual tumors after NAC treatment, which is comparable to the scoring of untreated breast cancer patients. Based on the good consistency observed with digital TIL scoring, the development of a validated algorithm in the future might be advantageous.

Comprehensive multi-omics analysis of breast cancer reveals distinct long-term prognostic subtypes

Breast cancer (BC) is a leading cause of cancer-related death worldwide. The diverse nature and heterogeneous biology of BC pose challenges for survival prediction, as patients with similar diagnoses often respond differently to treatment. Clinically relevant BC intrinsic subtypes have been established through gene expression profiling and are implemented in the clinic. While these intrinsic subtypes show a significant association with clinical outcomes, their long-term survival prediction beyond 5 years often deviates from expected clinical outcomes. This study aimed to identify naturally occurring long-term prognostic subgroups of BC based on an integrated multi-omics analysis. This study incorporates a clinical cohort of 335 untreated BC patients from the Oslo2 study with long-term follow-up (>12 years). Multi-Omics Factor Analysis (MOFA+) was employed to integrate transcriptomic, proteomic, and metabolomic data obtained from the tumor tissues. Our analysis revealed three prominent multi-omics clusters of BC patients with significantly different long-term prognoses (p = 0.005). The multi-omics clusters were validated in two independent large cohorts, METABRIC and TCGA. Importantly, a lack of prognostic association to long-term follow-up above 12 years in the previously established intrinsic subtypes was shown for these cohorts. Through a systems-biology approach, we identified varying enrichment levels of cell-cycle and immune-related pathways among the prognostic clusters. Integrated multi-omics analysis of BC revealed three distinct clusters with unique clinical and biological characteristics. Notably, these multi-omics clusters displayed robust associations with long-term survival, outperforming the established intrinsic subtypes.

Abstract 756: Differences in composition, diversity, and function of the fecal microbiota of post-menopausal breast cancer patients compared to healthy, age-matched controls

Abstract Gut microbiota are a community of organisms that colonize the intestinal tract with essential roles in immune function, gut epithelial integrity, and metabolite production. Dysbiosis occurs when the gut microbiota environment is negatively altered causing detrimental changes to these functions, which may predispose an individual to breast cancer development. To understand the relationship between dysbiosis and breast cancer development, fecal microbiota samples were collected from 27 post-menopausal breast cancer patients of varying hormone receptor statuses (ER+HER2-, ER+Her2+, ER-HER2+, or ER-Her2-) prior to starting chemotherapeutic treatment. Samples were compared to 25 healthy controls, and all samples underwent 16srRNA sequencing. Samples from breast cancer patients and control groups were compared for significant differences (P<.05) in alpha (within sample) and beta (between sample) diversity. Using the Shannon Index and Generalized Least Squares Model, significant differences in alpha diversity were identified between all breast cancer types vs. controls (P=.0104), and between ER+HER2- breast cancer vs. controls (P=.00153). Healthy controls exhibited a higher mean Shannon Index than breast cancer patients, thus higher within sample diversity. Using principal coordinate analyses, significant differences in beta diversity were identified between all breast cancer types vs. controls (P = .01199), and ER+HER2- breast cancer vs. control (P = .008991). Further analyses identified significant taxa of microbiota with functions related to breast cancer development and progression. Of note, Lachnoclostridium, a genus of bacteria that can produce β-glucuronidase, which can deconjugate estrogen, was increased in all breast cancer types and ER+HER2- breast cancer when compared to controls. Deconjugation of estrogen can cause elevated blood estrogen levels, potentially increasing Estrogen Receptor binding in hormone-receptor-positive breast cancer. Additionally, Akkermansia, a genus implicated in gut barrier dysfunction, was decreased in ER+HER2- patients, while Parvimonas, a tumorigenic cell-cycle regulator, was increased. Elucidating if these effects are causative or reactionary may have important implications for understanding breast cancer etiology. Samples are currently undergoing additional metagenomic analyses using long-read sequencing to identify specific bacteria, viruses, fungi, parasites, and phages that may be contributing to dysbiosis. Overall, this study is the first, to our knowledge, to employ short and long-read sequencing to the fecal samples of untreated postmenopausal breast cancer patients. We provide mechanistic insight into the relationship between microbiota and breast cancer development, with the intent of informing future patient screening and prevention. Citation Format: Nadia Kabbej, Frederick Ashby, Erika Atencio, Erinn Rosenkrantz, Dominique Day, Khloe Dang, Josee Gauthier, Rachel Newsome, John Sommerville, Taqwa Naas, Raad Gharaibeh, Christian Jobin, Amira Quevedo, Coy D. Heldermon. Differences in composition, diversity, and function of the fecal microbiota of post-menopausal breast cancer patients compared to healthy, age-matched controls [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 756.

Abstract 4920: A nanopore sequencing approach characterizes cell-free DNA methylation-fragmentomics profiles indicative of breast cancer in a large cohort

Abstract The detection of breast cancer from cell-free DNA (cfDNA) offers a new approach with the potential to benefit individual screening and early detection. However, identifying breast cancer from cfDNA remains a major challenge when one uses conventional short-read sequencing. Methylation and DNA fragmentation characteristics provide highly informative biomarkers for detecting and monitoring cancer. To characterize these genomic features from cfDNA, we developed an approach using single molecule Nanopore sequencing. Single cfDNA molecules are sequenced intact with the methylation and fragment size directly extrapolated from Nanopore data. Moreover, our approach requires small amounts of cfDNA to discern specific genomic features from individual molecules. Thus, the use of Nanopore sequencing provides both methylation and fragment size as directly measured from native cfDNA without the use of any chemical processing or other molecular manipulation. We studied an extended breast cancer cohort with in total 1080 of samples, consisting of 440 untreated breast cancer patients and 640 healthy controls. Nanopore sequencing analysis of these cfDNA samples identified a range of 1 to 4 million CpG sites from 1 ml of plasma. Leveraging the cohort, we developed an ensemble classifier for breast cancer detection based on cfDNA methylation and fragmentation. The classifier leveraged a leave-one-out cross-validation (LOOCV) to generate predicted probability. We created nucleosome-specific methylation scores as the input features to the classifier, which scores quantified the similarity of each sample's methylation profile to a training set on a selected set of CpG sites associated with cancers. Furthermore, we also identified DNA fragmentation features, revealing distinct mono-nucleosome and di-nucleosome patterns that distinguish cancers from healthy controls. Aggregating the DNA nucleosome-specific scores and fragmentation features, we built an ensemble LOOCV random forest model. We applied the model to the breast cancer cohort and achieved a detection specificity of 74%, a sensitivity of 71%, and an overall accuracy of approximately 73%. The area under the receiver operating characteristic curve (AUROC) reached 80%. We validated the classifier with two external independent cohorts. Validation cohort 1 demonstrated as a specificity of 85%, a sensitivity of 80%, and overall accuracy of 83% with AUROC of 90%. Validation cohort 2 without controls demonstrated that the classifier achieved a sensitivity of 94%. Both validation sets confirm that our model can achieve excellent performance for early breast cancer detection. In summary, our findings demonstrate that nanopore sequencing provides cfDNA methylation and fragment profiling that enables breast cancer detection. This approach holds the potential to improve cancer diagnosis and treatment outcomes. Citation Format: Xiangqi Bai, Billy T. Lau, Alison Almada, Sue Grimes, Tianqi Chen, Hojoon Lee, Hanlee P. Ji. A nanopore sequencing approach characterizes cell-free DNA methylation-fragmentomics profiles indicative of breast cancer in a large cohort [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4920.

CORRELATION OF EPSTEIN-BARR VIRUS WITH BREAST CANCER: A CASE CONTROL STUDY

Background and aims: Epstein-Barr virus (EBV) is a gamma herpes virus and one of the most common infections globally. It has been linked to several health problems, including breast cancer, which is a leading cause of death among females worldwide. In Yemen, breast cancer is one of the top reported cancers in women. This study aimed to investigate the correlation between EBV and breast cancer among Yemeni women in Sana'a city. Methods: The study is a case-control study that included newly diagnosed, untreated breast cancer patients as cases and healthy women attending the National Cancer Control Foundation as controls. A total of 150 participants were tested for EBV (VCA) IgG using ELISA. Results: The association between EBV and BC in the case and control groups was found by the investigation. 48 women (64.0%) who tested positive for EBV IgG were included in the control group, whereas 71 women (94.7%) among the patients had the antibody identified. A substantial correlation between EBV and BC was found by statistical analysis; a chi-square value of 21.510 and a p-value of less than 0.001 supported this conclusion. With a 95% confidence interval, the odds ratio was 10.0 (3.3-30.4). Moreover, women above the age of thirty showed a higher risk than women under that age (p=0.006). In addition, compared to the control group, divorced and bereaved women had a significantly higher chance of contracting EBV (p= 0.002). Conclusions: According to the study's findings, there may be a link between EBV infection and a higher risk of breast cancer. To further understand the underlying mechanisms and potential strategies to reduce this risk, more research is required. Peer Review History: Received 1 December 2023; Revised 19 January 2024; Accepted 27 February; Available online 15 March 2024 Academic Editor: Dr. Muhammad Zahid Iqbal, AIMST University, Malaysia, drmmziqbal@gmail.com Average Peer review marks at initial stage: 6.0/10 Average Peer review marks at publication stage: 7.0/10 Reviewers: Dr. Andrzej Szymański, Poznan University of Technology, Poland, andrzej.szymanski@put.poznan.pl Dr. Fátima Morales Marín, University of Murcia, Spain, fatima.morales@um.es

A Retrospective Study on Previously Untreated Non-metastatic Breast Cancer Patients at a Tertiary Care Hospital

Introduction: The combination of adoxorubicin and cyclophosphamide (AC) followed by a taxane (Docetaxel or Paclitaxel) and epirubicin and cyclophosphamide (EC) followed by a taxane (Docetaxel or Paclitaxel) is a standard regimen for breast cancer patients. In this study, we compared the three-year overall survival (OS) and progression free survival (PFS) of a patient with previously untreated non-metastatic breast cancer patients. Objectives: To find out the overall survival and progression free survival among previously untreated non-metastatic breast cancer patients after standard chemotherapy. Methods: Fifty-six patients received four cycles of doxorubicin at a dose of 60mg/m2 and cyclophosphamide at a dose of 600 mg/m2 followed by four cycles of paclitaxel at a dose of 175mg/m2. Thirteen patients received AC followed by four cycles of docetaxel at a dose of 75mg/m2. Twenty-one patients received four cycles of epirubicin (75mg/m2) and cyclophosphamide (600mg/m2), followed by four cycles of paclitaxel (175mg/m2). Twelve patients were given EC followed by four cycles of docetaxel (75mg/m2). Results: The four groups of patients had similar characteristics. Overall survivalafter three years was 92% in AC followed by paclitaxel, 98% in AC followed by docetaxel, 95% and 97% in EC followed by paclitaxel and docetaxel respectively. One year of PFS in AC followed by paclitaxel and docetaxel was 98% and 100% respectively whereas in EC followed by paclitaxel and docetaxel were 98% and 98% respectively. The four arms had 96%, 98%, 97% and 96% PFS after two years respectively. This research also revealed that four chemotherapy regimens had three-year survival rates of 93%, 98%, 93% and 96% respectively. Conclusion: AC or EC followed by taxane regimens well suitable regimens for the population of patients with previously untreated non-metastatic breast cancer patients. The findings show the need for continued observation as well as taking into account the treatment of other patients throughout different periods. JAFMC Bangladesh. Vol 18, No 2 (December) 2022: 11-14

Assessment of genotoxic instability markers in peripheral blood lymphocytes of breast cancer patients: a case control study

Changes in genetic constitution of an individual leads to uncontrollable cell growth and tumour formation. The acquisition of genomic instability predisposes cells to accumulate stable genome mutations causing carcinogenesis. The cytokinesis-block micronucleus cytome assay (CBMN), a well-established marker assay for chromosomal mutagen sensitivity, was applied in this study enrolling breast cancer patients and age and sex-matched controls. This work aimed to assess the predictive value of the frequency of genotoxic markers in peripheral blood lymphocytes for the risk/susceptibility of breast cancer. Samples from a hundred untreated breast cancer patients and age and sex matched controls were enrolled in the study from Government Medical College, Alappuzha. The genomic instability was assessed using cytokinesis block micronucleus assay where cytome events were marked. The results showed a significant increase in the frequency of micronucleus, nucleoplasmic bridge, and buds in the binucleated cells of breast cancer patients compared to the control samples. The variability was assessed by CBMN Cyt assay. The frequency of Micronuclei and Nucleoplasmic buds was significantly higher in the patient groups than in the controls (p < 0.0001). In Breast cancer patients, the median (IQR) range of MNi was 12(6), the Nucleoplasmic bridge 3(3) and the Nuclear buds were 2(1) and, in the controls, it was 6(5), 1(2) and 1(1) respectively. A larger difference in the frequency of genetic markers in cancer patients over control cases support a significant role of these markers in the population screening of individuals at high risk of cancer. Communicated by Ramaswamy H. Sarma

Predicting Patient-Specific Tumor Dynamics: How Many Measurements Are Necessary?

Acquiring sufficient data is imperative to accurately predict tumor growth dynamics and effectively treat patients. The aim of this study was to investigate the number of volume measurements necessary to predict breast tumor growth dynamics using the logistic growth model. The model was calibrated to tumor volume data from 18 untreated breast cancer patients using a varying number of measurements interpolated at clinically relevant timepoints with different levels of noise (0-20%). Error-to-model parameters and the data were compared to determine the sufficient number of measurements needed to accurately determine growth dynamics. We found that without noise, three tumor volume measurements are necessary and sufficient to estimate patient-specific model parameters. More measurements were required as the level of noise increased. Estimating the tumor growth dynamics was shown to depend on the tumor growth rate, clinical noise level, and acceptable error of the to-be-determined parameters. Understanding the relationship between these factors provides a metric by which clinicians can determine when sufficient data have been collected to confidently predict patient-specific tumor growth dynamics and recommend appropriate treatment options.

Senescent mesenchymal stem/stromal cells in pre-metastatic bone marrow of untreated advanced breast cancer patients.

Breast cancer is the predominant form of carcinoma among women worldwide, with 70% of advanced patients developing bone metastases, with a high mortality rate. In this sense, the bone marrow (BM) mesenchymal stem/stromal cells (MSCs) are critical for BM/bone homeostasis, and failures in their functionality, transform the BM into a pre-metastatic niche (PMN). We previously found that BM-MSCs from advanced breast cancer patients (BCPs, infiltrative ductal carcinoma, stage III-B) have an abnormal profile. This work aims to study some of the metabolic and molecular mechanisms underlying MSCs shift from a normal to an abnormal profile in this group of patients. A comparative analysis was undertaken, which included self-renewal capacity, morphology, proliferation capacity, cell cycle, reactive oxygen species (ROS) levels, and senescence-associated β‑galactosidase (SA‑β‑gal) staining of BM-derived MSCs isolated from 14 BCPs and 9 healthy volunteers (HVs). Additionally, the expression and activity of the telomerase subunit TERT, as well as telomere length, were measured. Expression levels of pluripotency, osteogenic, and osteoclastogenic genes (OCT-4, SOX-2, M-CAM, RUNX-2, BMP-2, CCL-2, M-CSF, and IL-6) were also determined. The results showed that MSCs from BCPs had reduced ,self-renewal and proliferation capacity. These cells also exhibited inhibited cell cycle progression and phenotypic changes, such as an enlarged and flattened appearance. Additionally, there was an increase in ROS and senescence levels and a decrease in the functional capacity of TERT to preserve telomere length. We also found an increase in pro-inflammatory/pro-osteoclastogenic gene expression and a decrease in pluripotency gene expression. We conclude that these changes could be responsible for the abnormal functional profile that MSCs show in this group of patients.

Definition of a novel breast tumor-specific classifier based on secretome analysis

BackgroundDuring cancer development, the normal tissue microenvironment is shaped by tumorigenic events. Inflammatory mediators and immune cells play a key role during this process. However, which molecular features most specifically characterize the malignant tissue remains poorly explored.MethodsWithin our institutional tumor microenvironment global analysis (T-MEGA) program, we set a prospective cohort of 422 untreated breast cancer patients. We established a dedicated pipeline to generate supernatants from tumor and juxta-tumor tissue explants and quantify 55 soluble molecules using Luminex or MSD. Those analytes belonged to five molecular families: chemokines, cytokines, growth factors, metalloproteinases, and adipokines.ResultsWhen looking at tissue specificity, our dataset revealed some breast tumor-specific characteristics, as IL-16, as well as some juxta-tumor-specific secreted molecules, as IL-33. Unsupervised clustering analysis identified groups of molecules that were specific to the breast tumor tissue and displayed a similar secretion behavior. We identified a tumor-specific cluster composed of nine molecules that were secreted fourteen times more in the tumor supernatants than the corresponding juxta-tumor supernatants. This cluster contained, among others, CCL17, CCL22, and CXCL9 and TGF-β1, 2, and 3. The systematic comparison of tumor and juxta-tumor secretome data allowed us to mathematically formalize a novel breast cancer signature composed of 14 molecules that segregated tumors from juxta-tumors, with a sensitivity of 96.8% and a specificity of 96%.ConclusionsOur study provides the first breast tumor-specific classifier computed on breast tissue-derived secretome data. Moreover, our T-MEGA cohort dataset is a freely accessible resource to the biomedical community to help advancing scientific knowledge on breast cancer.

Cost-effectiveness of pembrolizumab plus chemotherapy as first-line treatment in PD-L1-positive metastatic triple-negative breast cancer.

Objective: This study evaluated the cost-effectiveness of pembrolizumab/chemotherapy combinations for previously untreated metastatic triple-negative breast cancer patients in the USA with PD-L1 combined positive score ≥10. Methods: A partitioned-survival model was developed to project health outcomes and direct medical costs over a 20-year time horizon. Efficacy and safety data were from randomized clinical trials. Comparative effectiveness of indirect comparators was assessed using network meta-analyses. A series of sensitivity analyses were performed to test the robustness of the results. Results: Pembrolizumab/chemotherapy resulted in total quality-adjusted life-year (QALY) gains of 0.70 years and incremental cost-effectiveness ratio of US$182,732/QALY compared with chemotherapy alone. The incremental cost-effectiveness ratio for pembrolizumab/nab-paclitaxel versus atezolizumab/nab-paclitaxel was US$44,157/QALY. Sensitivity analyses showed the results were robust over plausible values of model inputs. Conclusion: Pembrolizumab/chemotherapy is cost effective compared with chemotherapy as well as atezolizumab/nab-paclitaxel as first-line treatment for PD-L1-positive metastatic triple-negative breast cancer from a US payer perspective.

Abstract 5342: Identifying therapeutic targets in combination with PARP inhibitors using a 63-gene signature in triple-negative breast cancer

Abstract Triple-negative breast cancer (TNBC) is a difficult-to-treat breast cancer with limited therapeutic options. PARP inhibitors (PARPi) have emerged as a promising targeted therapeutic for TNBC patients with germline mutations in BRCA1/2, recently demonstrating inhibition of micrometastatic disease. However, studies have also suggested that PARPi may have efficacy in TNBC, regardless of BRCA mutation status. We have previously identified a 63-gene signature associated with the DNA damage response to PARPi, with an overall accuracy of 86% in a cohort of patient-derived xenografts and a predicted sensitivity to PARPi in 45% of untreated TNBC patients. Additionally, our 63-gene signature can be used to identify genes implicated in intrinsic resistance. Therefore, we hypothesize that genes from our 63-gene signature can be used to identify potential targets for combination therapies with PARPi. We selected six candidate genes from our 63-gene signature: BARD1, BUB1, FEN1, RRM2, EXO1, and USP1. For each of the selected genes, we performed siRNA knockdown experiments in MDAMB231, a TNBC cell line. Using flow cytometry, we found that talazoparib, a potent PARPi plus siBARD1, increased the proportion of cells in G2 phase, with 80% γ-H2AX-positive cells and 60% cleaved-caspase-3-positive cells. Interestingly, the DNA damage response was comparable to what was observed with the combination of talazoparib and carboplatin. Talazoparib + siBUB1 also induced DNA damage in 51% of cells (P&amp;lt;0.001), and apoptosis in 20% of cells (P=0.002). Similar effects for enhanced DNA damage and apoptosis with talazoparib was observed for siUSP1, siFEN1, and siEXO1. Furthermore, the combination of siBARD1 + talazoparib resulted in a 49% reduction in cell migration in comparison to siBARD1 alone (P=0.0008), and the combination of siBUB1 and talazoparib demonstrated a 44% reduction in cell migration in comparison to talazoparib alone (P=0.04). Moreover, we evaluated gene expression in different breast cancer subtypes, and correlated with prognosis in a cohort of 881 untreated breast cancer patients. We found elevated expression of RRM2, FEN1, and EXO1 amongst more aggressive breast cancer subtypes (basal and HER2), and that their overexpression were associated with a poorer 10-year distant metastasis-free survival (RRM2, P&amp;lt;0.00001; FEN1, P=0.00012; EXO1, P&amp;lt;0.00001). Taken together, genes from our 63-gene signature can be used to identify therapeutic targets that have demonstrated either enhanced DNA damage, cell death, or cell migration in combination with PARPi. With prognostic implications, these targets also demonstrate therapeutic potential in the clinic and warrant further investigation. Citation Format: Audrey Hubert, Alexia Cotte, Nelly Bechir, Takrima Haque, Saima N. Hassan. Identifying therapeutic targets in combination with PARP inhibitors using a 63-gene signature in triple-negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5342.

Comparison of the Metastasis Predictive Potential of mRNA and Long Non-Coding RNA Profiling in Systemically Untreated Breast Cancer.

Simple SummaryTo support health care providers in clinical decision-making for breast cancer (BC) patients, profiles of gene activity patterns have previously been developed, where the majority have been based on messenger RNAs (mRNAs), molecules coding for proteins. However, we and others have recently developed profiles based on functional molecules that do not code for proteins—e.g., long non-coding RNAs (lncRNAs)—demonstrating great prognostic potential. Unfortunately, studies comparing such profiles for predicting relapse in BC patients are very scarce. Therefore, we aimed to compare these two types of molecules (mRNAs and lncRNAs) to forecast relapse in low-risk BC patients using advanced machine learning methods with two different approaches. Regardless of approach, our data suggested that profiles based on lncRNAs improved prediction of relapse and demonstrated potential advantages for future profile development.Several gene expression signatures based on mRNAs and a few based on long non-coding RNAs (lncRNAs) have been developed to provide prognostic information beyond clinical evaluation in breast cancer (BC). However, the comparison of such signatures for predicting recurrence is very scarce. Therefore, we compared the prognostic utility of mRNAs and lncRNAs in low-risk BC patients using two different classification strategies. Frozen primary tumor samples from 160 lymph node negative and systemically untreated BC patients were included; 80 developed recurrence—i.e., regional or distant metastasis while 80 remained recurrence-free (mean follow-up of 20.9 years). Patients were pairwise matched for clinicopathological characteristics. Classification based on differential mRNA or lncRNA expression using seven individual machine learning methods and a voting scheme classified patients into risk-subgroups. Classification by the seven methods with a fixed sensitivity of ≥90% resulted in specificities ranging from 16–40% for mRNA and 38–58% for lncRNA, and after voting, specificities of 38% and 60% respectively. Classifier performance based on an alternative classification approach of balanced accuracy optimization also provided higher specificities for lncRNA than mRNA at comparable sensitivities. Thus, our results suggested that classification followed by voting improved prognostic power using lncRNAs compared to mRNAs regardless of classification strategy.

Soluble interleukin-2 receptor as a predictive and prognostic marker for patients with familial breast cancer.

The incidence of breast cancer increases annually, and it has become common within families of breast cancer patients. Interleukin-2 activates cytotoxic T lymphocytes, which are important for cancer immunity. To identify markers of increased familial breast cancer risk, soluble interleukin-2 receptor levels and immunologic factors were investigated in familial breast cancer and non-familial breast cancer patients. Of 106 untreated breast cancer patients in this study, 24 had familial breast cancer and 82 had non-familial breast cancer. The patients' soluble interleukin-2 receptor, interleukin-10, vascular endothelial growth factor, interleukin-17, regulatory T cell, myeloid-derived suppressor cell, white blood cell, and C-reactive protein levels, and their neutrophil-to-lymphocyte ratios were measured, and their prognoses were compared according to the soluble interleukin-2 receptor levels. Additionally, postoperative tissues from the patients with high soluble interleukin-2 receptor levels were stained with programmed cell death ligand 1 and cluster of differentiation 8. The soluble interleukin-2 receptor level in the familial breast cancer patients was significantly higher, and it showed significantly stronger correlations with the neutrophil-to-lymphocyte ratio and the interleukin-10, vascular endothelial growth factor, interleukin-17, regulatory T cell, myeloid-derived suppressor cell, white blood cell, and C-reactive protein levels, than in the non-familial breast cancer patients. The regulatory T cell and myeloid-derived suppressor cell levels were significantly higher in the patients with high soluble interleukin-2 receptor levels, and the overall survival and disease-free-survival rates were significantly worse for the familial breast cancer patients than for the non-familial breast cancer patients. Triple-negative breast cancer tissues from the familial breast cancer patients with high soluble interleukin-2 receptor levels stained well for programmed cell death ligand 1 and cluster of differentiation 8. Soluble interleukin-2 receptor levels can be used to predict the prognosis of familial breast cancer patients. Prospectively identifying patients who are less likely to have non-familial breast cancer is vital for improving their overall survival.

Increased resting-state cerebellar-cortical connectivity in breast cancer survivors with cognitive complaints after chemotherapy

Cognitive complaints after chemotherapy are common in breast cancer patients, but the neural bases for these complaints remain unclear. This pilot study explored resting-state functional connectivity (FC) as a marker of subtle cognitive changes in breast cancer patients who experience cognitive complaints. Chemotherapy-treated (n = 20, at least 6 months off therapy) and untreated (n = 17, disease-control) female breast cancer patients with cognitive complaints and healthy controls (n = 20) were recruited. The FC of the right dorsolateral prefrontal cortex was calculated, and any correlations between this FC and neuropsychological assessments were determined. Chemotherapy-treated patients with cognitive complaints displayed increased FC between the right dorsolateral prefrontal cortex and both the contralateral cerebellar lobule VII and the cerebellar vermis XI, compared to the disease-control and healthy-control groups, despite unimpaired neuropsychological performance. The increased FC was negatively correlated with executive function and attention in breast cancer survivors with cognitive complaints. Our pilot study findings provide evidence that cerebellar-cortical FC changes may be a pathophysiological basis for chemotherapy-related cognitive complaints. In addition, the FC changes have the potential to reflect minor or compensated cognitive function impairment in breast cancer patients.

9P BRCA1 promoter methylation confers a more favorable prognosis to systemically untreated young triple-negative breast cancer patients than tumour BRCA1 mutation

The prognoses of systemically treated, triple-negative breast cancer (TNBC) patients with a pathogenic tumor BRCA1 mutation (tBRCA1m) or BRCA1 promoter methylation (BRCA1 PM) have been widely studied. However, the prognosis for systemically untreated women remains unknown. This study investigates the prognosis of systemically untreated young N0 TNBC patients according to tumor BRCA1 status.

Metabolic syndrome and its related biochemical derangements in breast cancer patients who received neoadjuvant chemotherapy: A study from a tertiary care oncology centre from Puducherry, South India

Background and aimsComparison of the existence of metabolic syndrome, its components and their related biochemical complications between newly diagnosed and treated breast cancer patients. MethodsForty newly diagnosed untreated breast cancer patients and forty breast cancer patients who had received 7 cycles of neoadjuvant chemotherapy were recruited as group 1 and group 2 respectively. Height, weight, blood pressure, hormonal status, and tumor size were noted. The fasting blood glucose and lipid profile were estimated in AU 5811 Beckman coulter Clinical chemistry analyzer. Fasting insulin was estimated using Beckman Coulter access immunoassay system (UnicelDxI600). HbA1c assay was carried out in HPLC based ion exchange chromatography (Tosoh automated glycohemoglobin analyzer G8. Homeostasis Model Assessment 2-IR (HOMA 2-IR), HOMA-% B and HOMA-% S were calculated using an online calculator HOMA CALCULATOR [Oxford University]. Serum hsCRP and MDA were estimated by ELISA. FRAP assay was carried out manually to measure antioxidant status. ResultsThe existence of metabolic syndrome as well as type 2 diabetes was higher in the treated group when compared to the untreated patients. However, there were no significant differences in the indices of glucose homeostasis, low grade inflammation, oxidative stress and individual components of metabolic syndrome between the two groups. The triple negative patients were more prone to develop metabolic syndrome when compared to the triple positive patients. ConclusionSuitable therapeutic approaches may be planned out to address the metabolic syndrome and its related complications among breast cancer patients especially during the course of treatment.

Quantification of Immune Variables from Liquid Biopsy in Breast Cancer Patients Links Vδ2+ γδ T Cell Alterations with Lymph Node Invasion.

Simple SummaryVδ2+ γδ T cells have potent antitumor properties both in vitro and in murine preclinical models of breast cancers. However, in the context of human breast cancer, there is a lack of information for potential phenotypic alterations of this crucial immune cell subset. This is partly due to Vδ2+ γδ T cells scarcity in surgical specimens. To break this deadlock, we assessed Vδ2+ γδ T cell phenotypes using untreated breast cancer patients’ peripheral blood, so-called minimally invasive “liquid biopsy”. We show that circulating Vδ2+ γδ T cell phenotypic alterations are already established at diagnosis and related to tumor progression. Notably, terminally differentiated Vδ2+ γδ T cells expressing canonical markers of replicative senescence and exhaustion were significantly associated with tumor-draining lymph node invasion. Our results shed light on the interest of using liquid biopsy to monitor rare events and support Vδ2+ γδ T cell involvement in breast cancer pathogenesis and progression.The rationale for therapeutic targeting of Vδ2+ γδ T cells in breast cancer is strongly supported by in vitro and murine preclinical investigations, characterizing them as potent breast tumor cell killers and source of Th1-related cytokines, backing cytotoxic αβ T cells. Nonetheless, insights regarding Vδ2+ γδ T cell phenotypic alterations in human breast cancers are still lacking. This paucity of information is partly due to the challenging scarcity of these cells in surgical specimens. αβ T cell phenotypic alterations occurring in the tumor bed are detectable in the periphery and correlate with adverse clinical outcomes. Thus, we sought to determine through an exploratory study whether Vδ2+ γδ T cells phenotypic changes can be detected within breast cancer patients’ peripheral blood, along with association with tumor progression. By using mass cytometry, we quantified 130 immune variables from untreated breast cancer patients’ peripheral blood. Supervised analyses and dimensionality reduction algorithms evidenced circulating Vδ2+ γδ T cell phenotypic alterations already established at diagnosis. Foremost, terminally differentiated Vδ2+ γδ T cells displaying phenotypes of exhausted senescent T cells associated with lymph node involvement. Thereby, our results support Vδ2+ γδ T cells implication in breast cancer pathogenesis and progression, besides shedding light on liquid biopsies to monitor surrogate markers of tumor-infiltrating Vδ2+ γδ T cell antitumor activity.

CHRNA5 belongs to the secondary estrogen signaling network exhibiting prognostic significance in breast cancer.

Cholinergic signals can be important modulators of cellular signaling in cancer. We recently have shown that knockdown of nicotinic acetylcholine receptor subunit alpha 5, CHRNA5, diminishes the proliferative potential of breast cancer cells. However, modulation of CHRNA5 expression in the context of estrogen signaling and its prognostic implications in breast cancer remained unexplored. Meta-analyses of large breast cancer microarray cohorts were used to evaluate the association of CHRNA5 expression with estrogen (E2) treatment, estrogen receptor (ER) status and patient prognosis. The results were validated through RT-qPCR analyses of multiple E2 treated cell lines, CHRNA5 depleted MCF7 cells and across a breast cancer patient cDNA panel. We also calculated a predicted secondary (PS) score representing direct/indirect induction of gene expression by E2 based on a public dataset (GSE8597). Co-expression analysis was performed using a weighted gene co-expression network analysis (WGCNA) pipeline. Multiple other publicly available datasets such as CCLE, COSMIC and TCGA were also analyzed. Herein we found that CHRNA5 expression was induced by E2 in a dose- and time-dependent manner in breast cancer cell lines. ER- breast tumors exhibited higher CHRNA5 expression levels than ER+ tumors. Independent meta-analysis for survival outcome revealed that higher CHRNA5 expression was associated with a worse prognosis in untreated breast cancer patients. Furthermore, CHRNA5 and its co-expressed gene network emerged as secondarily induced targets of E2 stimulation. These targets were largely downregulated by exposure to CHRNA5 siRNA in MCF7 cells while the response of primary ESR1 targets was dependent on the direction ofthe PS-score. Moreover, primary and secondary target genes were uncoupled and clustered distinctly based on multiple public datasets. Our findings strongly associate increased expression of CHRNA5 and its co-expression network with secondary E2 signaling and a worse prognosis in breast cancer.

Expression of Serum IL-22, IL-23, and TLR9 as Tumor Markers in Untreated Breast Cancer Patients

Breast cancer (BC) is the most common cancer among women and is the most important cause of death among them. Breast cancer is a common malignancy, accounting for one-third of women cancers in Iraq. To the best of our knowledge, little literature information is available on the participation of Interleukin-22 (IL-22), interleukin-23 (IL-23), and Toll-like receptor 9 (TLR9) in BC patients. Thus, the evaluation of serum IL-22, IL-23, and TLR9 level changes can add new information on their roles in breast cancer development and progression. The present study aimed to evaluate the clinical usefulness of IL-22, IL-23, and TLR9 as tumor markers in BC. Levels of circulating interleukin-22, IL-23, and TLR9 were estimated by the enzyme-linked immunoassay method. The serum level of IL-22 was highly significantly elevated in patients compared to the benign and healthy control groups (317.53 ± 14.33 vs. 68.73 ± 12.38 and 62.67 ± 19.11 pg/mL, p ≤ 0.05), but the difference between the benign tumor and healthy control groups means was not significant. Also, these results indicated that the mean level of IL-23 was higher significantly in breast cancer patients in comparison with the benign and healthy controls (887.89 ± 199.04 vs. 146.86 ± 84.26 and 72.26 ± 12.76 pg/mL, p ≤ 0.05). So, no significant difference was revealed between a benign tumor and healthy control groups (146.86 ± 84.26 and 72.26 ± 12.76 pg/mL, p andgt; 0.05). Finally, a serum level of TLR9 was significantly elevated in breast cancer patients in comparison with the control groups (16.89 ± 0.75 vs. 9.97 ± 1.21 ng/mL, 9.06 ± 0.21 ng/mL, p less than 0.05). On estimating IL-22, IL-23, and TLR9, the results showed the concentrations of IL-22, IL-23, and TLR9 in the sera of breast cancer were significantly elevated as compared to those in the control groups. Expression of IL-22, IL-23, and TLR9 could be used as a diagnostic tumor biomarker.