Breast Lesions Detected via Molecular Breast Imaging: Physiological Parameters Affecting Interpretation

Rationale and Objectives: To evaluate correlations between molecular breast imaging (MBI) descriptor characteristics and positive predictive value (PPV) in detecting breast cancer. Materials and Methods: A retrospective review was performed on 193 suspicious findings from 153 women (31-81 years) with positive MBI examinations. We assessed associations between: (i) lesion pattern (mass vs. non-mass) and PPV; (ii) lesion pattern and suspected likelihood of cancer (low vs. moderate vs. high); (iii) background parenchymal uptake (BPU) (homogeneous vs. heterogeneous) and PPV; (iv) breast density (dense vs. non-dense) and PPV; (v) BPU and density. Results: One hundred ten of 153 patients were diagnosed with malignancy or high-risk pathology (PPV1 = 71.9%), and 130/193 biopsies resulted in malignant or high-risk lesions (PPV3 = 67.4%). Biopsies of mass vs. non-mass findings had comparable PPV3 (71.7% vs 61.3%; p = 0.0717). Mass findings were correlated with higher suspicion for cancer than non-mass findings (p \u3c 0.001). There was no significant difference in PPV3 when comparing biopsies from homogeneous vs. heterogeneous BPU (72.5% vs 60.7%; p = 0.103). No association was found between patients\u27 BPU and diagnosed cancer or high-risk lesions (p = 0.513). Biopsies from non-dense breasts demonstrated higher PPV3 than biopsies from dense breasts (85.4% vs 60.6%; p = 0.0025); patients with non-dense breasts were more likely to be diagnosed with cancer or high-risk pathology (PPV1 = 87.8% vs 66.0%; p = 0.00844). Dense breasts had a greater association with heterogeneous BPU (p = 0.0844). Conclusion: Neither variability in mass or non-mass positive MBI findings, nor variability in BPU on MBI were significant determinants for the probability of malignancy. Dense breasts were associated with lower predictability and heterogeneous BPU on MBI

Inferring evolutionary histories of pathway regulation from transcriptional profiling data

One of the outstanding challenges in comparative genomics is to interpret the evolutionary importance of regulatory variation between species. Rigorous molecular evolution-based methods to infer evidence for natural selection from expression data are at a premium in the field, and to date, phylogenetic approaches have not been well-suited to address the question in the small sets of taxa profiled in standard surveys of gene expression. We have developed a strategy to infer evolutionary histories from expression profiles by analyzing suites of genes of common function. In a manner conceptually similar to molecular evolution models in which the evolutionary rates of DNA sequence at multiple loci follow a gamma distribution, we modeled expression of the genes of an \emph{a priori}-defined pathway with rates drawn from an inverse gamma distribution. We then developed a fitting strategy to infer the parameters of this distribution from expression measurements, and to identify gene groups whose expression patterns were consistent with evolutionary constraint or rapid evolution in particular species. Simulations confirmed the power and accuracy of our inference method. As an experimental testbed for our approach, we generated and analyzed transcriptional profiles of four \emph{Saccharomyces} yeasts. The results revealed pathways with signatures of constrained and accelerated regulatory evolution in individual yeasts and across the phylogeny, highlighting the prevalence of pathway-level expression change during the divergence of yeast species. We anticipate that our pathway-based phylogenetic approach will be of broad utility in the search to understand the evolutionary relevance of regulatory change.Comment: 30 pages, 12 figures, 2 tables, contact authors for supplementary table

Current and future directions of breast mri

Magnetic resonance imaging (MRI) is the most sensitive exam for detecting breast cancer. The American College of Radiology recommends women with 20% or greater lifetime risk of developing breast cancer be screened annually with MRI. However, other high-risk populations would also benefit. Hartmann et al. reported women with atypical hyperplasia have nearly a 30% incidence of breast cancer at 25-year follow-up. Women with dense breast tissue have up to a 4-fold increased risk of breast cancer when compared to average-risk women; their cancers are more likely to be mammographically occult. Because multiple cohorts of women are at high risk for developing breast cancer, there has been a movement to develop an abbreviated MRI (abMRI) protocol to expand the availability of MRI screening. Studies on abMRI effectiveness have been promising, with Weinstein et al. demonstrating a cancer detection rate of 27.4/1000 in women with dense breasts after a negative digital breast tomosynthesis. Breast MRI is also used to evaluate the extent of disease as part of preoperative assessment in women with newly diagnosed breast cancer, and to assess a patient’s response to neoadjuvant chemotherapy. This paper aims to explore the current uses of MRI and propose future indications and directions

Local Regulatory Variation in Saccharomyces cerevisiae

Naturally occurring sequence variation that affects gene expression is an important source of phenotypic differences among individuals within a species. We and others have previously shown that such regulatory variation can occur both at the same locus as the gene whose expression it affects (local regulatory variation) and elsewhere in the genome at trans-acting factors. Here we present a detailed analysis of genome-wide local regulatory variation in Saccharomyces cerevisiae. We used genetic linkage analysis to show that nearly a quarter of all yeast genes contain local regulatory variation between two divergent strains. We measured allele-specific expression in a diploid hybrid of the two strains for 77 genes showing strong self-linkage and found that in 52%–78% of these genes, local regulatory variation acts directly in cis. We also experimentally confirmed one example in which local regulatory variation in the gene AMN1 acts in trans through a feedback loop. Genome-wide sequence analysis revealed that genes subject to local regulatory variation show increased polymorphism in the promoter regions, and that some but not all of this increase is due to polymorphisms in predicted transcription factor binding sites. Increased polymorphism was also found in the 3′ untranslated regions of these genes. These findings point to the importance of cis-acting variation, but also suggest that there is a diverse set of mechanisms through which local variation can affect gene expression levels

Expression Profiling of the Wheat Pathogen Zymoseptoria tritici Reveals Genomic Patterns of Transcription and Host-Specific Regulatory Programs

Host specialization by pathogens requires a repertoire of virulence factors as well as fine-tuned regulation of gene expression. The fungal wheat pathogen Zymoseptoria tritici (synonym Mycosphaerella graminicola) is a powerful model system for the discovery of genetic elements that underlie virulence and host specialization. We transcriptionally profiled the early stages of Z. tritici infection of a compatible host (wheat) and a noncompatible host (Brachypodium distachyon). The results revealed infection regulatory programs common to both hosts and genes with striking wheat-specific expression, with many of the latter showing sequence signatures of positive selection along the Z. tritici lineage. Genes specifically regulated during infection of wheat populated two large clusters of coregulated genes that may represent candidate pathogenicity islands. On evolutionarily labile, repeat-rich accessory chromosomes (ACs), we identified hundreds of highly expressed genes with signatures of evolutionary constraint and putative biological function. Phylogenetic analyses suggested that gene duplication events on these ACs were rare and largely preceded the diversification of Zymoseptoria species. Together, our data highlight the likely relevance for fungal growth and virulence of hundreds of Z. tritici genes, deepening the annotation and functional inference of the genes of this model pathogen

Neutrophils promote CXCR3-dependent itch in the development of atopic dermatitis.

Chronic itch remains a highly prevalent disorder with limited treatment options. Most chronic itch diseases are thought to be driven by both the nervous and immune systems, but the fundamental molecular and cellular interactions that trigger the development of itch and the acute-to-chronic itch transition remain unknown. Here, we show that skin-infiltrating neutrophils are key initiators of itch in atopic dermatitis, the most prevalent chronic itch disorder. Neutrophil depletion significantly attenuated itch-evoked scratching in a mouse model of atopic dermatitis. Neutrophils were also required for several key hallmarks of chronic itch, including skin hyperinnervation, enhanced expression of itch signaling molecules, and upregulation of inflammatory cytokines, activity-induced genes, and markers of neuropathic itch. Finally, we demonstrate that neutrophils are required for induction of CXCL10, a ligand of the CXCR3 receptor that promotes itch via activation of sensory neurons, and we find that that CXCR3 antagonism attenuates chronic itch

Circulating miRNA Biomarkers in Early Breast Cancer Detection following Mammography

The currently accepted stepwise model of breast tumorigenesis assumes a gradual transition from normal breast epithelial cells to atypical ductal hyperplasia (ADH), to ductal carcinoma in situ (DCIS) and then to invasive ductal carcinoma (IDC). Percutaneous core needle biopsy (CNB) is the standard technique following an abnormal mammographic finding. However, CNB is less reliable in differentiating simple ADH (sADH) from ADH component coexisted with advanced lesions such as DCIS and/or IDC (cADH). Therefore, to identify and validate novel reliable molecular biomarkers is essential in order to improve the efficiency of therapeutic recommendations, as well as to minimize anxiety and unnecessary procedures. miRNAs function as tumor suppressors or oncogenes and play a critical role in cancer initiation and progression by regulating their target genes. Unlike messenger RNAs (mRNAs), which could be easily degraded, miRNAs are found to be stable not only in body fluid, but also in Formalin-Fixed, Paraffin-Embedded (FFPE) tissues. The stability of miRNAs in FFPE and blood samples suggests that they may be the ideal biomarkers for the early diagnosis and prognosis of cancer, including breast cancer. The goal of this research is to use FFPE and blood samples from the two different groups of patients, analyze the candidate miRNAs to differentiating simple sADH from cADH. In our published studies, we identified a series of miRNAs that are differentially expressed during stepwise transition of breast carcinogenesis, including miR-671-5p. In this study, we showed that the expression of miR-671-5p and miR-638 decreases in ADH, DCIS, and IDC compared with the matched adjacent normal tissues. In addition, we examined the candidate miRNA expression in two groups of ADH blood samples: 28 sADHs and 32 cADHs by qRT-PCR. We found that miR-671-5p expression was decreased in cADHs, but not in sADHs, compared with their matched normal controls. Our recent publication demonstrated that miR-671-5p functions as a tumor suppressor miRNA during breast cancer progression by regulating FOXM1 expression. Using NanoString technology, we found another miRNA, miR-545-3p to be significantly overexpressed in cADHs compared with sADH. miR-545-3p is related to Snai2, which is a member of Snail family transcription factor, encoding a transcription repressor involving in epithelial-mesenchymal transitions (EMT). Our data suggest that miRNAs, such as miR-671-5p and miR-545-3p may be potential circulating biomarkers for early breast cancer detection following mammography and CNB

miRNAs as potential biomarkers in early breast cancer detection following mammography

Breast cancer is the most common cancer among American women, except for skin cancers. About 12 % women in the United States will develop invasive breast cancer during their lifetime. Currently one of the most accepted model/theories is that ductal breast cancer (most common type of breast cancer) follows a linear progression: from normal breast epithelial cells to ductal hyperplasia to atypical ductal hyperplasia (ADH) to ductal carcinoma in situ (DCIS), and finally to invasive ductal carcinoma (IDC). Distinguishing pure ADH diagnosis from DCIS and/or IDC on mammography, and even combined with follow-up core needle biopsy (CNB) is still a challenge. Therefore subsequent surgical excision cannot be avoided to make a definitive diagnosis. MicroRNAs (miRNAs) are a highly abundant class of endogenous non-coding RNAs, which contribute to cancer initiation and progression, and are differentially expressed between normal and cancer tissues. They can function as either tumor suppressors or oncogenes. With accumulating evidence of the role of miRNAs in breast cancer progression, including our own studies, we sought to summarize the nature of early breast lesions and the potential use of miRNA molecules as biomarkers in early breast cancer detection. In particular, miRNA biomarkers may potentially serve as a companion tool following mammography screening and CNB. In the long-term, a better understanding of the molecular mechanisms underlying the miRNA signatures associated with breast cancer development could potentially result in the development of novel strategies for disease prevention and therapy