Search

Recent findings indicate that the microbiota is involved in the development of lung cancer by inducing inflammatory responses and generating genome damage. This study aimed to compare sputum microbiomes from the mouth and oropharynx in non-small cell lung carcinoma (NSCLC) patients. A second goal was to search for bacterial taxonomic units that behave differently in the microbiome of NSCLC patients and healthy subjects. In the study, the taxonomic composition of the sputum and oropharyngeal microbiomes of 23 male patients with untreated NSCLC and 20 healthy subjects were compared. Next-generation sequencing of bacterial 16S rRNA genes was used to determine the taxonomic composition of the respiratory microbiome. Using the Kruskal-Wallis test, increased alpha diversity was observed in the sputum microbiome compared to that of the oropharynx, but this was evident only in NSCLC patients and not in healthy subjects. Using the Robust Aitchison PCA test, differences in beta diversity were found between sputum and oropharynx samples, and these differences were significant both for NSCLC patients (p = 0.045) and healthy controls (p = 0.009). However, no significant statistical differences were detected using the Robust Aitchison PCA when only comparing oropharyngeal samples from NSCLC patients and controls, nor when comparing sputum samples alone. Analysis of differences in the relative percentage of individual bacterial taxa using the Mann-Whitney U-test, and taking into account the FDR correction, showed an increase in the genus Rothia in oropharyngeal samples of NSCLC patients, as compared to control subjects (4.98 ± 6.33 vs 2.21 ± 6.28; p = 0.0008). However, linear discriminant analysis using LefSe did not show Rothia as a differentially regulated feature between NSCLC and controls in the oropharynx. Thus, more research is needed to identify possible bacterial NSCLC biomarkers in the oropharynx.

Purpose The cause of the piriformis-related pelvic and extra-pelvic pain syndromes is still not well understood. Usually, the piriformis syndrome is seen as extra-pelvic sciatica caused by the entrapment of the sciatic nerve by the piriformis in its crossing through the greater sciatic foramen. However, the piriformis muscle may compress additional nerve structures in other regions and cause idiotypic pelvic pain, pelvic visceral pain, pudendal neuralgia, and pelvic organ dysfunction. There is still a lack of detailed description of the muscle origin, topography, and its possible relationships with the anterior branches of the sacral spinal nerves and with the sacral plexus. In this research, we aimed to characterize the topographic relationship of the piriformis with its surrounding anatomical structures, especially the anterior branches of the sacral spinal nerves and the sacral plexus in the pelvic cavity, as well as to estimate the possible role of anatomical piriformis variants in pelvic pain and extra-pelvic sciatica. Methods Human cadaveric material was used accordingly to the Swiss Academy of Medical Science Guidelines adapted in 2021 and the Federal Act on Research involving Human Beings (Human Research ACT, HRA, status as 26, May 2021). All body donors gave written consent for using their bodies for teaching and research. 14 males and 26 females were included in this study. The age range varied from 64 to 97 years (mean 84 ± 10.7 years, median 88). Results three variants of the sacral origin of the piriformis were found when referring to the relationship between the muscle and the anterior sacral foramen. Firstly, the medial muscle origin pattern and its complete covering of the anterior sacral foramen by the piriformis muscle is the most frequent anatomical variation (43% in males, 70% in females), probably with the most relevant clinical impact. This pattern may result in the compression of the anterior branches of the sacral spinal nerves when crossing the muscle. Conclusions These new anatomical findings may provide a better understanding of the complex piriformis and pelvic pain syndromes due to compression of the sacral spinal nerves with their somatic or autonomous (parasympathetic) qualities when crossing the piriformis.

Renal cell carcinoma (RCC) occurs in a number of cancer predisposition syndromes, but the genetic architecture of susceptibility to RCC is not well defined. We investigated the frequency of pathogenic and likely pathogenic (P/LP) germline variants in cancer susceptibility genes (CSGs) within a large series of unselected RCC participants. Whole-genome sequencing data on 1336 RCC participants and 5834 controls recruited to the UK 100 000 Genomes Project, a nationwide multicentre study, was analyzed to identify rare P/LP short variants (single nucleotide variants and insertions/deletions ranging from 1 to 50 base pairs) and structural variants in 121 CSGs. Among 1336 RCC participants [mean: 61.3 years (±12 SD), range: 13–88 years; 64% male], 85 participants [6.4%; 95% CI (5.1, 7.8)] had one or more P/LP germline variant in a wider range of CSGs than previously recognized. A further 64 intragenic variants in CSGs previously associated with RCC were classified as a variant of uncertain significance (VUS) (24 ‘hot VUSs’) and were considered to be of potential clinical relevance as further evaluation might results in their reclassification. Most patients with P variants in well-established CSGs known to predispose to renal cell carcinoma (RCC-CSGs) were aged

The results of measurements of the velocity and absorption coefficient of ultrasound in a nematic phase oriented by a magnetic field are presented. Within the framework of the hydrodynamics of the nematic phase, the coefficients of the bulk and shear viscosity of the nematic phase are calculated. The temperature dependence of the shear viscosity coefficients is exponential. The nature of the sharp increase in the bulk viscosity coefficients with an increase in the temperature of the nematic phase in the region of the phase transition nematic liquid crystal - isotropic phase is analyzed. The analysis of the temperature dependence of the ultrasound velocity in the nematic phase, carried out under the assumption of the existence of two processes responsible for the propagation of ultrasound, allowed us to identify the critical component and calculate the relaxation time of the critical contribution. In the vicinity to the phase transition, the dependence on the temperature of the relaxation time of the critical contribution increases sharply with a divergence index equal to 1.03. The relationship between the critical contribution to the absorption and the speed of ultrasound has been established. An array of data necessary for the calculation of liquid crystal technical devices has been obtained.

Microglia are the resident immune cells of the central nervous system contributing substantially to health and disease. There is increasing evidence that inflammatory microglia may induce or accelerate brain aging, by interfering with physiological repair and remodeling processes. Many viral infections affect the brain and interfere with microglia functions, including human immune deficiency virus, flaviviruses, SARS-CoV-2, influenza, and human herpes viruses. Especially chronic viral infections causing low-grade neuroinflammation may contribute to brain aging. This review elucidates the potential role of various neurotropic viruses in microglia-driven neurocognitive deficiencies and possibly accelerated brain aging.

Introduction The best way to teach human gross anatomy to medical students has often been debated, although recent studies emphasize on the benefits of dissection‐based courses (DOI 10.1002/ase.1859). Prosection and model‐based courses, online and virtual reality approaches have been introduced over time, due to reduction in teaching time, and due to economic reasons with decreasing budget. In 2020, we were challenged by the pandemic of SARS‐CoV‐2 and corresponding COVID‐19 public health measures. We had to change and adapt several times anatomy teaching and learning over the two semesters for the cohort of 112 first/second year undergraduate medical students. With the experience of this student cohort with various anatomy learning approaches, we wanted to know what anatomy teaching method was best perceived by the students. Methods 112 medical students were asked about their learning experience with various anatomy teaching approaches for 2020, including 1) dissection‐based learning, 2) prosections and models‐based demonstrations, 3) structured self‐directed learning using written instructions and corresponding anatomical material, 4) structured self‐directed learning using online instructions via Moodle and an online anatomy program (https://e‐learn.anatomy.uzh.ch/Anatomy/Anatomy.html; German version). All students agreed to participate in the study. The questionnaire was administered by https://www.surveymonkey.com and done anonymously. To date 66/112 (59%) students replied. Results The majority of the students (92%) preferred the dissection course as their main anatomy learning method, 80% of students were happy with a demonstration course using prosections and anatomical models. Only a minority liked to have structured self‐directed learning with either anatomical specimens and models (42%) or with online material (36%). Rather few students preferred learning with an online course (18%) or through unstructured self‐directed learning using their own resources (12%). For the dissection course the students appreciated the 3 dimensional aspect (92%), the real size appearance of the structures (90%), the active explorative approach (81%), the topographical relationship of the structures (81%) and anatomical variability (72%). During complete lock‐down of the COVID‐19 measures when the students had to stay isolated at home for several weeks, the majority of students thought that the offered online structured self‐directed course was most adequate under those circumstances (55%), but would otherwise not be the preferred replacement of a dissection course (55%). Conclusion Evaluation of student experience with a variety of anatomy learning methods clearly indicate that a structured dissection‐based course with additional anatomical demonstration would be preferred by the majority of our students. Online material would be beneficial as additional learning support. However, the majority of students agreed that, under strict COVID‐19 stay‐at‐home measures, the structured self‐directed online course was the best way to learn anatomy. When going back to normal, we will offer the newly developed online material for guided self‐directed learning, in addition to the established dissection course.

INTRODUCTION: The innervation pattern of the clavicular head of the deltoid muscle and its corresponding topography were investigated via cadaveric dissection in the present study, focusing on the lateral pectoral nerve. MATERIALS AND METHODS: Fifty-eight upper extremities were dissected and the nerve supplies to the deltoid muscle and the variability of the lateral pectoral and axillary nerves, including their topographical patterns, were noted. RESULTS: The clavicular portion of the deltoid muscle received a deltoid branch from the lateral pectoral nerve in 86.2% of cases. Two topographical patterns of the lateral pectoral nerve were observed, depending on the branching level from the brachial plexus: a proximal variant, where the nerve entered the pectoral region undern the clavicle, and a distal variant, where the nerve entered the pectoral region from the axillary fossa around the caudal border of the pectoralis minor. These dissection findings were supported by histological confirmation of peripheral nerve tissue entering the clavicular part of the deltoid muscle. CONCLUSION: The topographical variations of the lateral pectoral nerve are relevant for orthopedic and trauma surgeons and neurologists. These new data could revise the interpretation of deltoid muscle atrophy and of thoracic outlet and pectoralis minor compression syndromes. They could also explain the residual anteversion function of the arm after axillary nerve injury and deficiency, which is often thought to be related to biceps brachii muscle function.

The NPHS2 gene, encoding the slit diaphragm protein podocin, accounts for genetic and sporadic forms of nephrotic syndrome (NS). Patients with NS often present symptoms of volume retention, such as oedema formation or hypertension. The primary dysregulation in sodium handling involves an inappropriate activation of the epithelial sodium channel, ENaC. Plasma proteases in a proteinuria‐dependent fashion have been made responsible; however, referring to the timeline of symptoms occurring and underlying mechanisms, contradictory results have been published. Characterizing the mouse model of podocyte inactivation of NPHS2 (Nphs2∆pod) with respect to volume handling and proteinuria revealed that sodium retention, hypertension and gross proteinuria appeared sequentially in a chronological order. Detailed analysis of Nphs2∆pod during early sodium retention, revealed increased expression of full‐length ENaC subunits and αENaC cleavage product with concomitant increase in ENaC activity as tested by amiloride application, and augmented collecting duct Na+/K+‐ATPase expression. Urinary proteolytic activity was increased and several proteases were identified by mass spectrometry including cathepsin B, which was found to process αENaC. Renal expression levels of precursor and active cathepsin B were increased and could be localized to glomeruli and intercalated cells. Inhibition of cathepsin B prevented hypertension. With the appearance of gross proteinuria, plasmin occurs in the urine and additional cleavage of γENaC is encountered. In conclusion, characterizing the volume handling of Nphs2∆pod revealed early sodium retention occurring independent to aberrantly filtered plasma proteases. As an underlying mechanism cathepsin B induced αENaC processing leading to augmented channel activity and hypertension was identified.

Renal proximal tubular cells constantly recycle nutrients to ensure minimal loss of vital substrates into the urine. Although most of the transport mechanisms have been discovered at the molecular level, little is known about the factors regulating these processes. Here, we show that mTORC1 and mTORC2 specifically and synergistically regulate PTC endocytosis and transport processes. Using a conditional mouse genetic approach to disable nonredundant subunits of mTORC1, mTORC2, or both, we showed that mice lacking mTORC1 or mTORC1/mTORC2 but not mTORC2 alone develop a Fanconi-like syndrome of glucosuria, phosphaturia, aminoaciduria, low molecular weight proteinuria, and albuminuria. Interestingly, proteomics and phosphoproteomics of freshly isolated kidney cortex identified either reduced expression or loss of phosphorylation at critical residues of different classes of specific transport proteins. Functionally, this resulted in reduced nutrient transport and a profound perturbation of the endocytic machinery, despite preserved absolute expression of the main scavenger receptors, MEGALIN and CUBILIN. Our findings highlight a novel mTOR–dependent regulatory network for nutrient transport in renal proximal tubular cells.

Summary Background Germline pathogenic variants in the E-cadherin gene ( CDH1 ) are strongly associated with the development of hereditary diffuse gastric cancer. There is a paucity of data to guide risk assessment and management of families with hereditary diffuse gastric cancer that do not carry a CDH1 pathogenic variant, making it difficult to make informed decisions about surveillance and risk-reducing surgery. We aimed to identify new candidate genes associated with predisposition to hereditary diffuse gastric cancer in affected families without pathogenic CDH1 variants. Methods We did whole-exome sequencing on DNA extracted from the blood of 39 individuals (28 individuals diagnosed with hereditary diffuse gastric cancer and 11 unaffected first-degree relatives) in 22 families without pathogenic CDH1 variants. Genes with loss-of-function variants were prioritised using gene-interaction analysis to identify clusters of genes that could be involved in predisposition to hereditary diffuse gastric cancer. Findings Protein-affecting germline variants were identified in probands from six families with hereditary diffuse gastric cancer; variants were found in genes known to predispose to cancer and in lesser-studied DNA repair genes. A frameshift deletion in PALB2 was found in one member of a family with a history of gastric and breast cancer. Two different MSH2 variants were identified in two unrelated affected individuals, including one frameshift insertion and one previously described start-codon loss. One family had a unique combination of variants in the DNA repair genes ATR and NBN . Two variants in the DNA repair gene RECQL5 were identified in two unrelated families: one missense variant and a splice-acceptor variant. Interpretation The results of this study suggest a role for the known cancer predisposition gene PALB2 in families with hereditary diffuse gastric cancer and no detected pathogenic CDH1 variants. We also identified new candidate genes associated with disease risk in these families. Funding UK Medical Research Council (Sackler programme), European Research Council under the European Union's Seventh Framework Programme (2007–13), National Institute for Health Research Cambridge Biomedical Research Centre, Experimental Cancer Medicine Centres, and Cancer Research UK.

Purpose Aromatase inhibitors (AIs) have an established role in the treatment of breast cancer. Response rates are only 50% to 70% in the neoadjuvant setting and lower in advanced disease. Accurate biomarkers are urgently needed to predict response in these settings and to determine which individuals will benefit from adjuvant AI therapy. Patients and Methods Pretreatment and on-treatment (after 2 weeks and 3 months) biopsies were obtained from 89 postmenopausal women who had estrogen receptor–alpha positive breast cancer and were receiving neoadjuvant letrozole for transcript profiling. Dynamic clinical response was assessed with use of three-dimensional ultrasound measurements. Results The molecular response to letrozole was characterized and a four-gene classifier of clinical response was established (accuracy of 96%) on the basis of the level of two genes before treatment (one gene [IL6ST] was associated with immune signaling, and the other [NGFRAP1] was associated with apoptosis) and the level of two proliferation genes (ASPM, MCM4) after 2 weeks of therapy. The four-gene signature was found to be 91% accurate in a blinded, completely independent validation data set of patients treated with anastrozole. Matched 2-week on-treatment biopsies were associated with improved predictive power as compared with pretreatment biopsies alone. This signature also significantly predicted recurrence-free survival (P = .029) and breast cancer –specific survival (P = .009). We demonstrate that the test can also be performed with use of quantitative polymerase chain reaction or immunohistochemistry. Conclusion A four-gene predictive model of clinical response to AIs by 2 weeks has been generated and validated. Deregulated immune and apoptotic responses before treatment and cell proliferation that is not reduced 2 weeks after initiation of treatment are functional characteristics of breast tumors that do not respond to AIs.

ABSTRACT Kyoto Breast Cancer Consensus Conference, Kyoto, Japan, 18–20 February 2014 The loco-regional management of breast cancer is increasingly complex with application of primary systemic therapies, oncoplastic techniques and genetic testing for breast cancer susceptibility. Personalization of loco-regional treatment is integral to optimization of breast cancer care. Clinical and pathological tumor stage, biological features and host factors influence loco-regional treatment strategies and extent of surgical procedures. Key issues including axillary staging, axillary treatment, radiation therapy, primary systemic therapy (PST), preoperative hormonal therapy and genetic predisposition were identified and discussed at the Kyoto Breast Cancer Consensus Conference (KBCCC2014). In the first of a two part conference scene, consensus recommendations for axillary management are presented and focus on the following topics: indications for completion axillary lymph node dissection in primary surgical patients with ≤2 macrometastases or any sentinel nodal deposits after PST; the timing of sentinel lymph node biopsy in the context of PST; use of axillary irradiation as a component of primary treatment plans and the role of intraoperative node assessment in the post-Z0011 era.

ABSTRACT Kyoto Breast Cancer Consensus Conference, Kyoto, Japan, 18–20 February 2014 The loco-regional management of breast cancer is increasingly complex with application of primary systemic therapies, oncoplastic techniques and genetic testing for breast cancer susceptibility. Personalization of loco-regional treatment is integral to optimization of breast cancer care. Clinical and pathological tumor stage, biological features and host factors influence loco-regional treatment strategies and extent of surgical procedures. Key issues including axillary staging, axillary treatment, radiation therapy, primary systemic therapy (PST), preoperative hormonal therapy and genetic predisposition were identified and discussed at the Kyoto Breast Cancer Consensus Conference (KBCCC2014). In the second of a two part conference scene, consensus recommendations for radiation treatment, primary systemic therapies and management of genetic predisposition are reported and focus on the following topics: influence of both clinical response to PST and stage at presentation on recommendations for postmastectomy radiotherapy; use of regional nodal irradiation in selected node-positive patients and those with adverse pathological factors; extent of surgical resection following downstaging of tumors with PST; use of preoperative hormonal therapy in premenopausal women with larger, node-negative luminal A-like tumors and managing increasing demands for contralateral prophylactic mastectomy in patients with a unilateral sporadic breast cancer.

The median survival of patients with human epidermal growth factor receptor 2 (HER2)-positive metastatic breast cancer (MBC) has more than doubled, since the discovery of HER2-targeted treatments: it rose from less than 2 years in 2001 (prior introduction of trastuzumab) to more than 4 years in 2017. The initial generation of HER2-targeted therapies included trastuzumab with taxanes in the first line, followed by the addition of lapatinib and by a switch to another cytotoxic agent after progression. Results of CLEOPATRA, EMILIA, and TH3RESA trials have changed this clinical practice. The current consensus includes horizontal dual blockade (trastuzumab + pertuzumab) with taxanes or vinorelbine in the first line, followed by trastuzumab-emtansine (T-DM1) in the second line, with addition of lapatinib in the later lines of treatment. However, the fast and simultaneous development of new drugs led to a relative shortage of clinical evidence to support this sequence. Triple-positive breast cancers (TPBC), which express both hormonal receptors and HER2, constitute nearly half of HER2-positive cases. For these tumors, the current consensus is to add endocrine therapy after completion of cytotoxic treatment. Again, this consensus is not fully evidence-based. In view of the recent progress in treatment of estrogen-receptor positive breast cancers, a series of trials is evaluating addition of CDK4/6 inhibitors, aromatase inhibitors or fulvestrant to HER2-targeted and cytotoxic chemotherapy in TPBC patients. Despite the remarkable progress in treatment of HER2-positive breast cancer, metastatic disease is still incurable in the majority of patients. A wide range of novel therapies are under development to prevent and overcome resistance to current HER2-targeted agents. This review discusses pivotal clinical trials that have shaped current clinical practices, the current consensus recommendations, and the new experimental treatments in metastatic HER2-positive breast cancer.

The article’s purpose is the analysis of the evolution process and all its main aspects in the history of Moscow Slavonic-greek-latin Academy of the specified period. At the beginning of the XVIII century Moscow Academy was found on a basis of European «pre-classical» university pattern and became the first higher institute for all social estates in Russia. After the Peter’s the Great death the Academy experiences reduction of material security and contraction of the students’ social estate. Another tendency is also observed - the penetration of European university modernization ideas in Russia provokes the start of several national university projects. During the Catherine’s the Second reign these ideas influence on the evolution of the Academy as well as already generated Academy educational tradition influences the specified university projects. This reciprocal effect leads the creation of separate higher educational systems: secular, under the Ministry of National Enlightenment, and theological, under the Holy Synod. The sources allow tracking the participation of higher state and church fi gures working together on both structures. As a result Moscow Academy served as a sample for other theological academies and thus has become the foundation of the whole theological education system

To the Editor. Sweat duct proliferations and related cutaneous tumours pose a challenge for diagnosis and treatment due to the presence of multiple overlapping histopathological features (Schaller et al. 2010). In 1961 Nicolau and Balus described individuals with benign cutaneous lesions including atrophodermia vermiculata, multiple syringomata and milia which become known as Nicolau-Balus syndrome and was characterised by irregular distribution of elastin fibres (Nicolau and Balus 1961). A similar phenotype was later described as Rombo syndrome by Michaelsson et al (Michaelsson et al. 1981), with elastin distribution in these cases appearing like “swathes of steel wool” in some areas of the dermis (Van Steensel et al. 2001). In 2010, Schaller et al described several cases with the same abnormal elastin distribution, with the additional feature of sweat duct proliferations that appear morphologically similar to those found in microcystic adnexal carcinoma (MAC) patients, but (unlike MAC) were not invasive and did not require surgical resection (Schaller et al. 2010). In this study we describe five families with clinical and histopathological features that show similarities to Nicolau-Balus and Rombo syndromes with some cases also showing MAC-like ductal proliferations (figure S1). We provide evidence that these syndromes are caused by germline pathogenic variants in MYH9. Accordingly, we propose the term MALTA (MYH9 Associated eLasTin Aggregation) syndrome to reflect the common underlying genetic basis of this disease.

In a search for new breast cancer (BC) predisposing genes, we performed a whole exome sequencing analysis using six patient samples of familial BC and identified a germline inactivating mutation c.183delG [p. Arg61fs] in an orphan G protein-coupled receptor GPRC5A. An extended case-control study revealed a tenfold enrichment for this mutation in BC patients carrying the 5382insC allele of BRCA1, the major founder mutation in the Russian population, compared to wild-type BRCA1 BC cases [6/117 (5.1%) vs. 8/1578 (0.5%), p = 0.0002]. In mammary tumors (n = 60), the mRNA expression of GPRC5A significantly correlated with that of BRCA1 (p = 0.00018). In addition, the amount of GPRC5A transcript was significantly lower in BC obtained from BRCA1 mutation carriers (n = 17) compared to noncarriers (n = 93) (p = 0.026). Accordingly, a siRNA-mediated knockdown of either BRCA1 or GPRC5A in the MDA-MB-231 human BC cell line reduced expression of GPRC5A or BRCA1, respectively. Knockdown of GPRC5A also attenuated radiation-induced BRCA1- and RAD51-containing nuclear DNA repair foci. Taken together, these data suggest that GPRC5A is a modifier of BC risk in BRCA1 mutation carriers and reveals a functional interaction of these genes.

Background 10% of all breast cancers are HER2+/ER+ and these cancers exhibit both intrinsic and acquired resistance to endocrine therapy. They have a worse prognosis than HER2-/ER+ cancers. Aims 1. To investigate the role of HER2 in response to neoadjuvant Letrozole. 2. To predict which HER2+ cancers do not respond to Letrozole. Methods 23 postmenopausal women with large, operable, locally advanced HER2+/ER+ breast cancer treated with neoadjuvant Letrozole had response assessed by periodic 3D ultrasound. Core biopsies taken at 0, 14 days and 3 months of treatment. RNA were extracted, amplified, labelled and hybridised to Illumina HT-12 whole genome beadarrays. A group of patients with ER+/HER2- disease were identified to compare clinical and molecular response. Results 13 (57%) HER2+/ER+ patients responded (R) and 10 (43%) patients did not (NR). HER2 expression was significantly higher at baseline in the NR group (p = 0.005). There were differences in gene expression between HER2+/ER+ R and NR and between the HER2+/ER+ and HER2-/ER+ NR groups. In the HER2+/ER+ NR group, there was virtually no change in gene expression during treatment with Letrozole. Table 1 Up Regulated GenesDown Regulated Genes n0-14 days14 days-3 months0-3 months0-14 days14 days-3 months0-3 monthsHER2-ve Responders43122833505127213HER2-ve Non Responders1588361432340129HER2+ve Responders13541272703831125HER2+ve Non Responders10851117106 Considerable gene changes with overlap in the genes that changed most was evident in HER2+/ER+ and HER2-/ER+ responders. Analysis of 55 estrogen sensitive proliferation genes revealed significantly less reduction in the HER2+/ER+ NR group than in the HER2+/ER+ R group (AUC = 10.57 vs 27.93 respectively; p The HER2+/ER+ NR group had significantly less reduction in these 55 estrogen sensitive proliferation genes when compared to the HER2-/ER+ NR group at 14 days (AUC = 17.94 vs 18.05 respectively; p = 0.0007) and by 3 months (AUC = 10.57 vs 26.26; p In logistic regression analysis, HER2 status was predictive of disease progression (p = 0.048). A single gene classifier predicted response to endocrine therapy in the ER+/HER2+ group. This was accurate in 94% of patients in the test set (n = 23). This classifier was also predictive of progression free survival (p = 0.006) in HER2+/ER+ patients. Conclusions In this large cohort of patients treated with neoadjuvant letrozole: • HER2+/ER+ cancers have a low rate of response. • Changes in gene expression are similar in HER2+/ER+ and HER2-/ER+ responders. • HER2+/ER+ cancers that do not respond to letrozole have few gene changes and little reduction in estrogen signalling pathways. • In contrast HER2-/ER+ non responders show significant gene changes and reduced expression of estrogen sensitive proliferation genes. • A single gene classifier at diagnosis in ER+/HER2+ has been identified which predicts response to Letrozole with 94% accuracy. • Validation continues. This single gene classifier may provide a simple test to predict which HER2+/ER+ cancers are endocrine resistant. Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P5-09-01.

Background: Approximately 75% of older postmenopausal patients with large operable or locally advanced oestrogen receptor positive breast cancer respond to treatment with neoadjuvant letrozole. Prediction of response is required as approximately 25% fail to respond. The aim of this study was to design a response predicting classifier with two data sets, one published previously [1] and secondly a new dataset. Methods: Patients were treated with Letrozole (Femara, 2.5 mg daily) and tissues were collected before treatment, 2 or 3 weeks on treatment, and between 3 and 5 months on treatment. Response was based on a 3D ultrasound, with response being classified as a 50% reduction in tumour volume at 3 months. To ensure biological relevance of the response groups we also separated patients into Quick Stable Responders (QSR) and Long-Term Non-responders (LNR), as summarised in Table 1. Illumina HT-12 BeadArrays were used for gene expression profiling, allowing platform-independent cross-validation with our previous study using Affymetrix HGU-133 chips [1]. The probe IDs were re-annotated to Ensemble gene IDs and XPN batch correction has been applied to make the datasets directly comparable. A combination of Rank-Product, SAM and Random Forrest analyses have been used to design several alternative signatures separating extreme response groups, the patients who responded rapidly vs those who did not respond for a long time. One of the best performing signatures included 48 informative features: 24 at baseline, 12 at 2-weeks and 12 changes between 0 and 2 weeks. This signature was validated on the independent previously published test set by classifying extreme responses (quick stable responders vs long term non responders) using Support vector machines (SVM) with different kernel functions. Results Are summarised in Table 2. Conclusions – A new sample series has been collected to study neo-adjuvant endocrine response. It can be used for independent validation of previous results [1] and for design of new platform-independent response predictors.– Multi-gene predictors based upon change in gene expression outperform those from baseline or 14 day measurements alone. The best classifiers include all 3 time points.– A classifier has been derived with a 91% accuracy rate of predicting extreme response group in 21 of 23 patients. References [1] Miller 2009 J Clin Oncol 27:1382. Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P3-06-23.

Virtually all known tumor predisposing genes have been identified via the analysis of familial cancer cases. Here we argue that this approach is likely to miss recessively acting cancer genes and suggest the analysis of family history-negative patients with multiple primary malignancies for identifying homozygous at-risk genotypes. We performed calculations showing that the homozygous carriers of rare recessive cancer predisposing alleles are unlikely to report a family history of the disease. We further revealed that the c.2515_2519delAAGTT homozygous mutation in a Holliday junction resolvase, GEN1, was overrepresented in women with bilateral breast cancer (BC) as compared to healthy controls [11/360 (3.1 %) vs. 18/1305 (1.4 %); odds ratio (OR) = 2.25 (1.02-4.75); p = 0.031], although this trend was not maintained in unilateral BC patients [23/1851 (1.2 %)]. Noticeably, presence of biallelic c.2515_2519delAAGTT mutation was associated with the absence of BC in mother both in bilateral and unilateral BC cases [7/239 (3.0 %) vs. 0/41 (0 %) and 21/1,558 (1.3 %) vs. 0/215 (0 %), respectively; Mantel-Haenszel p = 0.041]. Thus, this study suggests that identification of dominant and recessive cancer predisposing genes may require distinct study groups.

Background: Unlike recurrences with other therapies, ER+ breast cancers (BC) can recur ≥10 yrs after an apparent successful period of adjuvant endocrine therapy. The molecular basis for this pattern of resistance is unresolved. We addressed the hypothesis that early recurrences during tamoxifen (TAM) treatment exhibit different biological characteristics than those that recur years later by assessing for variation in their respective transcriptomes. Methods: Appropriate tumors were identified from a set (BC030280) of snap-frozen tumor biopsies collected in Edinburgh from subjects with stage I-III BC before starting TAM (no chemotherapy); all had ≥10 yrs follow-up. Using rigorous standard operating procedures, high quality total RNA was extracted from samples with ≥50% malignant epithelium and arrayed on Affymetrix U133 Plus 2.0 GeneChips. Raw data were normalized using PLIER and analyzed with an adapted validated training and internal cross-validation workflow to avoid gene selection bias. A published dataset (Loi) was used for independent classifier validation that best fit our criteria for sample size, treatment (TAM only), data quality, and recurrence distribution. Early (E) vs late (L) recurrences were defined as distant relapse ≤3 vs ≥10 yrs from diagnosis. To explore putative mechanistic associations driving the transcriptome differences, a novel computational procedure was developed to integrate gene expression data with protein-protein interaction (PPI) data and create a statistical network model of the signaling. Metropolis sampling, a Markov Chain Monte Carlo method that can be implemented as a modified random walk procedure, identified ER network topology represented by the genes (nodes) and their predicted interconnections (edges). Results: A support vector machine with recursive feature elimination was used for the binary classification tasks on the BC030280 dataset. The optimized classifier for E vs L recurrence was independently tested on the Loi dataset with high levels of accuracy, specificity, and sensitivity. Classifier validation is supported by the respective survival curves (not shown). Gene set enrichment analysis reveals the top PPIs are primarily related to apoptosis (23/50; p=2.9e-13) and proliferation (14/50; p=6.8e-5). Substantial overlap of the network features and topology was seen between datasets. Specifically, increased relative expression of ESR1, ESR2, EGFR, BCL2, and AR was seen in L vs E recurrent tumors, and increased expression of CALM1, CALM2, CALM3, SRC, CDK1, and MAPK1 was seen in E vs L recurrent tumors. Several hubs (nodes with ≥5 edges) independently predicted for recurrence in additional public datasets of ER+ BC. Discussion: Our work provides clear evidence that robust molecular differences exist between ER+ BC that recur early vs. much later despite adjuvant TAM. Exploiting these differences will improve our understanding of involved signaling pathways, allow for the reliable prediction of early treatment failure, and guide use of novel therapeutics specifically directed at preventing E vs L recurrences on endocrine therapy. Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr S1-8.

The BLM gene belongs to the RecQ helicase family and has been implicated in the maintenance of genomic stability. Its homozygous germline inactivation causes Bloom syndrome, a severe genetic disorder characterized by growth retardation, impaired fertility and highly elevated cancer risk. We hypothesized that BLM is a candidate gene for breast cancer (BC) predisposition. Sequencing of its entire coding region in 95 genetically enriched Russian BC patients identified two heterozygous carriers of the c.1642 C>T (Q548X) mutation. The extended study revealed this allele in 17/1,498 (1.1%) BC cases vs. 2/1,093 (0.2%) healthy women (p = 0.004). There was a suggestion that BLM mutations were more common in patients reporting first-degree family history of BC (6/251 (2.4%) vs. 11/1,247 (0.9%), p = 0.05), early-onset cases (12/762 (1.6%) vs. 5/736 (0.7%), p = 0.14) and women with bilateral appearance of the disease (2/122 (1.6%) vs. 15/1376 (1.1%), p = 0.64). None of the BLM-associated BC exhibited somatic loss of heterozygosity at the BLM gene locus. This study demonstrates that BLM Q548X allele is recurrent in Slavic subjects and may be associated with BC risk.

Protocols employing primary systemic therapy provide important basic knowledge about tumor behavior/response to therapy, but major challenges remain in how to obtain and use this information practically in the clinical setting.

Introduction Rhabdomyosarcomas (RMS) are the most prevalent form of paediatric soft tissue sarcomas. They arise from skeletal muscle progenitor cells and are divided predominantly into two subtypes, embryonic and alveolar, with relatively poor prognosis. The alveolar subtype appears to be driven by an oncogenic fusion gene protein, typically but not exclusively FOXO1-PAX3 or FOXO1-PAX7. Fusion negative tumours better define the embryonal subtype, with occasional RMS cases where both subtypes histologically appear to coincide. Previously published work on somatic RMS variants associate embryonal RMS with hits in the RAS/AKT pathway (KRAS, NRAS, HRAS, NF1, PIK3CA, PTEN) alongside other cancer-related genes (TP53, FGFR4, FBXW7, BCOR). In this study we generate new whole exome sequencing data and integrate with previously published datasets to study germline predisposition to RMS. Material and methods The study includes 3 published datasets (Shern 2014 – 120 samples; Seki 2015 – 16 samples and Zhang 2015 – 30 samples) in addition to our in-house set (36 tumour-normal pairs of both RMS subtypes, collected in collaboration with the Children’s Cancer and Leukaemia Group tissue bank). Our primary samples were processed using Illumina’s Nextera Rapid Capture kit and sequenced on HiSeq NGS machines. The combined analysis cohort consists of 202 cases of paediatric RMS. Results and discussions A customised bioinformatics pipeline was used for integration of the studied datasets: from raw fastqs through BWA-MEM alignment and GATK-HC joint variant calling. Germline variants passing several quality control filters were pruned for a MAF Conclusion We explored the potential for germline predisposition to RMS as genetic inheritance is common in a number of paediatric cancers. The relative rarity of paediatric RMS prevents sufficiently powered single-centre studies and requires the consolidation of all available data to make meaningful conclusions. We employ this approach to identify new candidate predisposition genes. Expanding our understanding of genes predisposing to rhabdomyosarcomas, could assist earlier diagnosis and therapy for these children, ultimately improving their survival.

Transcriptomic screens in breast cancer cell lines have identified a protein named anterior gradient-2 (AGR2) as a potentially novel oncogene overexpressed in estrogen receptor (ER) positive tumours. As targeting the ER is responsible for major improvements in cure rates and prevention of breast cancers, we have evaluated the pro-oncogenic function of AGR2 in anti-hormone therapeutic responses. We show that AGR2 expression promotes cancer cell survival in clonogenic assays and increases cell proliferation and viability in a range of cancer cell lines. Chromatin immunoprecipitation and reporter assays indicate that AGR2 is transcriptionally activated by estrogen through ERalpha. However, we also found that AGR2 expression is elevated rather than inhibited in response to tamoxifen, thus identifying a novel mechanism to account for an agonistic effect of the drug on a specific pro-oncogenic pathway. Consistent with these data, clinical analysis indicates that AGR2 expression is related to treatment failure in ERalpha-positive breast cancers treated with tamoxifen. In contrast, AGR2 is one of the most highly suppressed genes in cancers of responding patients treated with the anti-hormonal drug letrozole. These data indicate that the AGR2 pathway represents a novel pro-oncogenic pathway for evaluation as anti-cancer drug developments, especially therapies that by-pass the agonist effects of tamoxifen.

Endocrine therapy is a major treatment modality for hormone-dependent breast cancer. It has a relatively low morbidity, and there is evidence that antihormonal treatments have had a significant effect in reducing mortality for breast cancer. Despite this, resistance to endocrine therapy, either primary or acquired during treatment, occurs in the majority of patients, and is a major obstacle to optimal clinical management. There is therefore an urgent need to identify, on an individual basis, those tumors that are most likely to respond to endocrine therapy (so sparing patients with resistant tumors the needless side effects of ineffective therapy), and the mechanisms of resistance in tumors that are nonresponsive to treatment (so these can be bypassed). These needs are the focus of this review, which discusses the particular issues encountered when investigating the potential of multigene expression signatures as predictive factors for response to aromatase inhibitors, which have recently become front-line endocrine therapies for postmenopausal patients with breast cancer.

Some breast cancers have been shown to contain a small fraction of cells characterized by CD44 + /CD24 −/low cell-surface antigen profile that have high tumor-initiating potential. In addition, breast cancer cells propagated in vitro as mammospheres (MSs) have also been shown to be enriched for cells capable of self-renewal. In this study, we have defined a gene expression signature common to both CD44 + /CD24 −/low and MS-forming cells. To examine its clinical significance, we determined whether tumor cells surviving after conventional treatments were enriched for cells bearing this CD44 + /CD24 −/low -MS signature. The CD44 + /CD24 −/low -MS signature was found mainly in human breast tumors of the recently identified “claudin-low” molecular subtype, which is characterized by expression of many epithelial-mesenchymal-transition (EMT)-associated genes. Both CD44 + /CD24 −/low -MS and claudin-low signatures were more pronounced in tumor tissue remaining after either endocrine therapy (letrozole) or chemotherapy (docetaxel), consistent with the selective survival of tumor-initiating cells posttreatment. We confirmed an increased expression of mesenchymal markers, including vimentin ( VIM ) in cytokeratin-positive epithelial cells metalloproteinase 2 ( MMP 2), in two separate sets of postletrozole vs. pretreatment specimens. Taken together, these data provide supporting evidence that the residual breast tumor cell populations surviving after conventional treatment may be enriched for subpopulations of cells with both tumor-initiating and mesenchymal features. Targeting proteins involved in EMT may provide a therapeutic strategy for eliminating surviving cells to prevent recurrence and improve long-term survival in breast cancer patients.

Purpose Endocrine agents, such as letrozole, are established in the treatment of hormone-dependent breast cancer. However, response rates are only 50% to 70% in the neoadjuvant setting and lower in advanced disease. Thus there is a need to identify novel markers predicting for response and to understand molecular mechanisms of resistance. Patients and Methods Sequential tumor biopsies were taken before and after 10 to 14 days of neoadjuvant treatment with letrozole in patients with estrogen receptor–rich breast cancer. Expression profiles on high-density microarray chips were then related to clinical responses as assessed from tumor volume measurements after 3 months of treatment. Results Of 52 patients, 37 (71%) were classified as having a clinical response to letrozole and 15 being clinically resistant. Bioinformatic analysis identified 205 covariables (69 baseline expression, 45 day 14 expression, and 91 change in expression with treatment) which differentiated between clinical responders and nonresponders. Hierarchical clustering using the variables separated responders and nonresponders into two distinct groups. Ontological assessment indicated that discriminating genes were enriched toward cellular biosynthetic processes. In particular, functional gene assessment showed ribosomal protein probes to have higher baseline expression in tumors responsive to letrozole and increased expression with treatment in nonresponding cases. Conclusion To our knowledge, this is the first study to describe genetic covariables and molecular processes discriminating between tumors clinically responsive and resistant to an aromatase inhibitor. The understanding of such molecular phenotypes will be important in optimizing the clinical use of aromatase inhibitors, both in terms of identifying responsive breast cancers and developing new agents to target resistance pathways.

While estrogens have been shown to modulate EGFR/HER-1 and HER-2/neu expression in experimental systems, the effects of estrogen deprivation on expression levels of the HER-receptors and the neuregulin (NRG)1 ligand in breast cancers remain unknown. Here, we measured EGFR/HER-1-4 and NRG1 mRNA in ER positive tumors from 85 postmenopausal breast cancer patients before and after two weeks (n=64) and three months (n=85) of primary treatment with an aromatase inhibitor (AI). In tumors lacking HER-2/neu amplification, quantitative real-time PCR analyses revealed EGFR/HER-1 and NRG1 to vary significantly between the three time points (before therapy, after 2 weeks and after 3 months on treatment; P≤0.001 for both). Pair-wise comparison revealed a significant increase in EGFR/HER-1 already during the first two weeks of treatment (P=0.049) with a further increase for both EGFR/HER-1 and NRG1 after 3 months on treatment (P≤0.001 and P=0.001 for both comparing values at 3 months to values at baseline and 2 weeks respectively). No difference between tumors responding versus non-responders was recorded. Further, no significant change in any parameter was observed among HER-2/neu amplified tumors. Analyzing components of the HER-2/neu PI3K/Akt downstream pathway, the PIK3CA H1047R mutation was associated with treatment response (P=0.035); however no association between either AKT phosphorylation status or PIK3CA gene mutations and EGFR/HER-1 or NRG1 expression levels were observed. Our results indicate primary AI treatment to modulate expression of HER-family members and the growth factor NRG1 in HER-2/neu non-amplified breast cancers in vivo. Potential implications to long term sensitivity warrants further investigations.

Neo-adjuvant endocrine therapy has an established place in the treatment of post-menopausal oestrogen-receptor positive breast cancers. However, a number of clinical questions still need to be addressed to realise the full potential of the neo-adjuvant endocrine treatment. Thus, there is a shortage of data about direct comparison between endocrine and cytotoxic neo-adjuvant treatments in ER+ve patients. Other questions under investigation include optimal duration of therapy, utility of neo-adjuvant endocrine therapy in pre-menopause, selection between different endocrine agents and predicting and overcoming resistance. The latter attracts most of the translational attention. Significant effort has been directed toward (i) development of response-predictive bio-markers, (ii) understanding molecular diversity of resistance in clinical samples and (iii) development of new treatments targeting the resistance mechanisms (such as combination of m-TOR and aromatase inhibitors). The recent response prediction studies included re-analysis of established molecular markers (ER, PgR, HER2, Ki67) and development of new multi-gene signatures. Some of the transcriptional signatures initially developed for the adjuvant setting are being studied in neo-adjuvant endocrine context (e.g. Oncotype DX). Despite being able to improve response prediction, these signatures still provide limited information about the individual mechanisms of resistance. New analytical methods, new trial designs and new bioinformatics resources are being employed to overcome this limitation and to develop a panel of mechanism-focused tests for guiding future neo-adjuvant endocrine therapies in breast cancer.

Introduction Aromatase inhibitors (AIs) are a vital component of estrogen receptor positive (ER+) breast cancer treatment. De novo and acquired resistance, however, is common. The aims of this study were to relate patterns of copy number aberrations to molecular and proliferative response to AIs, to study differences in the patterns of copy number aberrations between breast cancer samples pre- and post-AI neoadjuvant therapy, and to identify putative biomarkers for resistance to neoadjuvant AI therapy using an integrative analysis approach. Methods Samples from 84 patients derived from two neoadjuvant AI therapy trials were subjected to copy number profiling by microarray-based comparative genomic hybridisation (aCGH, n = 84), gene expression profiling (n = 47), matched pre- and post-AI aCGH (n = 19 pairs) and Ki67-based AI-response analysis (n = 39). Results Integrative analysis of these datasets identified a set of nine genes that, when amplified, were associated with a poor response to AIs, and were significantly overexpressed when amplified, including CHKA, LRP5 and SAPS3. Functional validation in vitro, using cell lines with and without amplification of these genes (SUM44, MDA-MB134-VI, T47D and MCF7) and a model of acquired AI-resistance (MCF7-LTED) identified CHKA as a gene that when amplified modulates estrogen receptor (ER)-driven proliferation, ER/estrogen response element (ERE) transactivation, expression of ER-regulated genes and phosphorylation of V-AKT murine thymoma viral oncogene homolog 1 (AKT1). Conclusions These data provide a rationale for investigation of the role of CHKA in further models of de novo and acquired resistance to AIs, and provide proof of concept that integrative genomic analyses can identify biologically relevant modulators of AI response. Electronic supplementary material The online version of this article (doi:10.1186/s13058-015-0532-0) contains supplementary material, which is available to authorized users.

Aromatase inhibitors (AIs) are major treatment options for the management of patients with breast cancer. The drugs are effective and response rates can be high. However, resistance, either primary or acquired during treatment, may occur. Optimal clinical management requires accurate predictors of response to identify those tumours, which are most likely to respond (so sparing patients with resistant tumours needless side-effects of ineffective therapy). Currently, oestrogen receptor (ER) status is the only factor used routinely to select for treatment with aromatase inhibitors, but a substantial proportion of ER-positive tumours fails treatment. There is, therefore, an urgent need to identify additional markers by which accurately to predict clinical response on an individual basis. Whilst other markers (such as progesterone receptors or HER2) have some predictive powers, individually they have limited utility for routine use. The hope is that discovery strategies based on genome-wide searches will identify novel markers that can be used as predictive indices. Molecular phenotyping of individual tumours could then be used to decide not only which patients should be treated with AIs but whether AIs should be used alone or in combination or in sequence with other targeted agents in order that clinical benefits are maximized. This chapter will focus on utility of routinely assessed biomarkers, multi-component indices and gene signatures and outline the future perspectives in studies aimed to AI response prediction.

Invasive lobular carcinoma (ILC) accounts for approximately 10% to 15% of breast carcinomas, and although it responds poorly to neoadjuvant chemotherapy, it appears to respond well to endocrine therapy. Pre- and on-treatment (after 2 weeks and 3 months) biopsies and surgical samples were obtained from 14 postmenopausal women with estrogen receptor–positive (ER+) histologically confirmed ILC who responded to 3 months of neoadjuvant letrozole and were compared with a cohort of 14 responding invasive ductal carcinomas (IDC) matched on clinicopathologic features. RNA was extracted and processed for whole human genome expression microarray. Dynamic clinical response was assessed using periodic three-dimensional ultrasound measurements performed during treatment and defined as a reduction of >70% in tumor volume by 3 months. Pretreatment profiles of ILC and IDC tumors showed distinctive expression of genes associated with E-cadherin signaling, epithelial adhesion, and stromal rearrangement. The changes in gene expression in response to letrozole were highly similar between responding ILC and IDC tumors; genes involved in proliferation were downregulated and those involved with immune function and extracellular matrix remodeling were upregulated. However, molecular differences between the histologic subtypes were maintained upon treatment. This is the first study of molecular changes in ILC in response to endocrine therapy to date. The genes that change on letrozole are highly consistent between ILC and IDC. Differences in gene expression between ILC and IDC at diagnosis are maintained at each time point on treatment. Cancer Res; 74(19); 5371–6. ©2014 AACR.

The precise place of local estrogen production in mammary cancer is still controversial. In this investigation localization of aromatase (the key enzyme of estrogen biosynthesis) was studied in breast cancer tissue by immunohistochemical method using polyclonal rabbit antibodies. The cytoplasmic staining was found in different cell types, but the most intensive specific staining was found in malignant cells and it was stronger (P

The epithelial-to-mesenchymal transition (EMT) is a widely studied program of development of cells characterized by loss of cell adhesion, repression of E-cadherin expression, and increased cell mobility. Microarrays have become a well-established technique for simultaneously measuring the expression of thousands of transcripts encoded by the genome. In this chapter, we demonstrate how microarray analysis can be used to assess the role of EMT-genes associated with a collagen invading phenotype by generating a gene expression signature and relating this to cell line and tumor datasets from published microarray studies.

The activity of aromatase (estrogen synthetase) in tumor tissue of breast cancer patients was investigated by biochemical and immunohistochemical methods. The detection of medium or high enzyme activity in tumor tissue was virtually the same for both methods. According to immunohistochemical analysis, aromatase activity was localized mainly in malignant epithelial cells, being reliably higher in the tumors of patients in menopause than in those whose cycle was intact. Doubts about the biological role of aromatase in breast cancer tissue may be dispelled if the tissue topography of the enzyme and the individual ratio of epithelial to stromal cellular elements in individual neoplasms of the breast are taken into account.

Background Affymetrix GeneChips and Illumina BeadArrays are the most widely used commercial single channel gene expression microarrays. Public data repositories are an extremely valuable resource, providing array-derived gene expression measurements from many thousands of experiments. Unfortunately many of these studies are underpowered and it is desirable to improve power by combining data from more than one study; we sought to determine whether platform-specific bias precludes direct integration of probe intensity signals for combined reanalysis. Results Using Affymetrix and Illumina data from the microarray quality control project, from our own clinical samples, and from additional publicly available datasets we evaluated several approaches to directly integrate intensity level expression data from the two platforms. After mapping probe sequences to Ensembl genes we demonstrate that, ComBat and cross platform normalisation (XPN), significantly outperform mean-centering and distance-weighted discrimination (DWD) in terms of minimising inter-platform variance. In particular we observed that DWD, a popular method used in a number of previous studies, removed systematic bias at the expense of genuine biological variability, potentially reducing legitimate biological differences from integrated datasets. Conclusion Normalised and batch-corrected intensity-level data from Affymetrix and Illumina microarrays can be directly combined to generate biologically meaningful results with improved statistical power for robust, integrated reanalysis.

This paper reviews the effects of oestrogen deprivation by third generation aromatase inhibitors on molecular profiles in breast cancers. It particularly focuses on results obtained as a result of pre-operative and neoadjuvant therapy in which primary breast cancers have been biopsied or excised before and during treatment with letrozole, anastrozole or exemestane. Studies may be subdivided into those evaluating early (10–14 days) or late (3–4 months) changes; a single investigation charted sequential changes. Early changes involved downregulation of genes classically induced by oestrogen or associated with cell cycle and proliferation. In contrast, expressions of genes associated with stromal signatures were upregulated. Considerably more genes were changed at later time-points; these probably represent not only primary effects on cellular expression but secondary consequences of cell death and clonal selection. Thus, after 3–4 months of treatment mitochondrial-related genes and those associated with cell cycle and cell division were downregulated whereas genes associated with extracellular matrix (ECM) remodelling, vascularization, inflammatory responses and cell adhesion were upregulated. Recently, observations have been reported from a study in which tumours were sequentially sampled to include pretreatment and both early and later time-points. This allowed direct monitoring of the dynamic changes in gene expression. Different patterns of changes in gene expression were identified which were also associated with general differences in sub-cellular distribution of corresponding proteins. The effect of treatment on expression of specific genes and processes such as aromatase, oestrogen receptor (ER), oestrogen-regulated genes, HER2, p53, ribosomal proteins, markers of proliferation, oxidative phosphorylation and stromal response are summarized.