Minimally invasive biopsy-based diagnostics in support of precision cancer medicine

Precision cancer medicine (PCM) to support the treatment of solid tumors requires minimally invasive diagnostics. Here, we describe the development of fine-needle aspiration biopsy-based (FNA) molecular cytology which will be increasingly important in diagnostics and adaptive treatment. We provide support for FNA-based molecular cytology having a significant potential to replace core needle biopsy (CNB) as a patient-friendly potent technique for tumor sampling for various tumor types. This is not only because CNB is a more traumatic procedure and may be associated with more complications compared to FNA-based sampling, but also due to the recently developed molecular methods used with FNA. Recent studies show that image-guided FNA in combination with ultrasensitive molecular methods also offers opportunities for characterization of the tumor microenvironment which can aid therapeutic decisions. Here we provide arguments for an increased implementation of molecular FNA-based sampling as a patient-friendly diagnostic method, which may, due to its repeatability, facilitate regular sampling that is needed during different treatment lines, to provide tumor information, supporting treatment decisions, shortening lead times in healthcare, and benefit healthcare economics.

Multiplex protein analysis and ensemble machine learning methods of fine needle aspirates from prostate cancer patients reveal potential diagnostic signatures associated with tumour grade

BACKGROUND

Improved molecular diagnosis is needed in prostate cancer (PC). Fine needle aspiration (FNA) is a minimally invasive biopsy technique, less traumatic compared to core needle biopsy, and could be useful for diagnosis of PC. Molecular biomarkers (BMs) in FNA-samples can be assessed for prediction, eg of immunotherapy efficacy before treatment as well as at treatment decision time points during disease progression.

METHODS

In the present pilot study, the expression levels of 151 BM proteins were analysed by proximity extension assay in FNA-samples from 16 patients, including benign prostate lesions (n = 3) and cancers (n = 13). An ensemble data analysis strategy was applied using several machine learning models.

RESULTS

Twelve potentially predictive BM proteins correlating with International Society of Urological Pathology grade groups were identified, among them vimentin, tissue factor pathway inhibitor 2, and integrin beta-5. The validity of the results was supported by network analysis that showed functional associations between most of the identified putative BMs. We also showed that multiple immune checkpoint targets can be assessed (eg PD-L1, CD137, and Galectin-9), which may support the selection of immunotherapy in advanced PC. Results are promising but need further validation in a larger cohort.

CONCLUSIONS

Our pilot study represents a "proof of concept" and shows that multiplex profiling of potential diagnostic and predictive BM proteins is feasible on tumour material obtained by FNA sampling of prostate cancer. Moreover, our results demonstrate that an ensemble data analysis strategy may facilitate the identification of BM signatures in pilot studies when the patient cohort is limited.

Fast, streamlined fluorescence nanoscopy resolves rearrangements of SNARE and cargo proteins in platelets co-incubated with cancer cells

BACKGROUND

Increasing evidence suggests that platelets play a central role in cancer progression, with altered storage and selective release from platelets of specific tumor-promoting proteins as a major mechanism. Fluorescence-based super-resolution microscopy (SRM) can resolve nanoscale spatial distribution patterns of such proteins, and how they are altered in platelets upon different activations. Analysing such alterations by SRM thus represents a promising, minimally invasive strategy for platelet-based diagnosis and monitoring of cancer progression. However, broader applicability beyond specialized research labs will require objective, more automated imaging procedures. Moreover, for statistically significant analyses many SRM platelet images are needed, of several different platelet proteins. Such proteins, showing alterations in their distributions upon cancer progression additionally need to be identified.

RESULTS

A fast, streamlined and objective procedure for SRM platelet image acquisition, analysis and classification was developed to overcome these limitations. By stimulated emission depletion SRM we imaged nanoscale patterns of six different platelet proteins; four different SNAREs (soluble N-ethylmaleimide factor attachment protein receptors) mediating protein secretion by membrane fusion of storage granules, and two angiogenesis regulating proteins, representing cargo proteins within these granules coupled to tumor progression. By a streamlined procedure, we recorded about 100 SRM images of platelets, for each of these six proteins, and for five different categories of platelets; incubated with cancer cells (MCF-7, MDA-MB-231, EFO-21), non-cancer cells (MCF-10A), or no cells at all. From these images, structural similarity and protein cluster parameters were determined, and probability functions of these parameters were generated for the different platelet categories. By comparing these probability functions between the categories, we could identify nanoscale alterations in the protein distributions, allowing us to classify the platelets into their correct categories, if they were co-incubated with cancer cells, non-cancer cells, or no cells at all.

CONCLUSIONS

The fast, streamlined and objective acquisition and analysis procedure established in this work confirms the role of SNAREs and angiogenesis-regulating proteins in platelet-mediated cancer progression, provides additional fundamental knowledge on the interplay between tumor cells and platelets, and represent an important step towards using tumor-platelet interactions and redistribution of nanoscale protein patterns in platelets as a basis for cancer diagnostics.

PITX2 DNA-Methylation: Predictive versus Prognostic Value for Anthracycline-Based Chemotherapy in Triple-Negative Breast Cancer Patients

Background

PITX2 DNA methylation has been shown to predict outcomes in high-risk breast cancer patients after anthracycline-based chemotherapy. To determine its prognostic versus predictive value, the impact of PITX2 DNA methylation on outcomes was studied in an untreated cohort vs. an anthracycline-treated triple-negative breast cancer (TNBC) cohort.

Material and Methods

The percent DNA methylation ratio (PMR) of paired-like homeodomain transcription factor 2 (PITX2) was determined by a validated methylation-specific real-time PCR test. Patient samples of routinely collected archived formalin-fixed paraffin-embedded (FFPE) tissue and clinical data from 144 TNBC patients of 2 independent cohorts (i.e., 66 untreated patients and 78 patients treated with anthracycline-based chemotherapy) were analyzed.

Results

The risk of 5- and 10-year overall survival (OS) increased continuously with rising PITX2 DNA methylation in the anthracycline-treated population, but it increased only slightly during 10-year follow-up time in the untreated patient population. PITX2 DNA methylation with a PMR cutoff of 2 did not show significance for poor vs. good outcomes (OS) in the untreated patient cohort (HR = 1.55; p = 0.259). In contrast, the PITX2 PMR cutoff of 2 identified patients with poor (PMR >2) vs. good (PMR ≤2) outcomes (OS) with statistical significance in the anthracycline-treated cohort (HR = 3.96; p = 0.011). The results in the subgroup of patients who did receive anthracyclines only (no taxanes) confirmed this finding (HR = 5.71; p = 0.014).

Conclusion

In this hypothesis-generating study PITX2 DNA methylation demonstrated predominantly predictive value in anthracycline treatment in TNBC patients. The risk of poor outcome (OS) correlates with increasing PITX2 DNA methylation.

Hard wiring of normal tissue-specific chromosome-wide gene expression levels is an additional factor driving cancer type-specific aneuploidies

Background

Many carcinomas have recurrent chromosomal aneuploidies specific to the tissue of tumor origin. The reason for this specificity is not completely understood.

Methods

In this study, we looked at the frequency of chromosomal arm gains and losses in different cancer types from the The Cancer Genome Atlas (TCGA) and compared them to the mean gene expression of each chromosome arm in corresponding normal tissues of origin from the Genotype-Tissue Expression (GTEx) database, in addition to the distribution of tissue-specific oncogenes and tumor suppressors on different chromosome arms.

Results

This analysis revealed a complex picture of factors driving tumor karyotype evolution in which some recurrent chromosomal copy number reflect the chromosome arm-wide gene expression levels of the their normal tissue of tumor origin.

Conclusions

We conclude that the cancer type-specific distribution of chromosomal arm gains and losses is potentially “hardwiring” gene expression levels characteristic of the normal tissue of tumor origin, in addition to broadly modulating the expression of tissue-specific tumor driver genes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13073-021-00905-y.

Genome Instability Profiles Predict Disease Outcome in a Cohort of 4,003 Patients with Breast Cancer

PURPOSE

The choice of therapy for patients with breast cancer is often based on clinicopathologic parameters, hormone receptor status, and HER2 amplification. To improve individual prognostication and tailored treatment decisions, we combined clinicopathologic prognostic data with genome instabilty profiles established by quantitative measurements of the DNA content.

EXPERIMENTAL DESIGN

We retrospectively assessed clinical data of 4,003 patients with breast cancer with a minimum postoperative follow-up period of 10 years. For the entire cohort, we established genome instability profiles. We applied statistical methods, including correlation matrices, Kaplan-Meier curves, and multivariable Cox proportional hazard models, to ascertain the potential of standard clinicopathologic data and genome instability profiles as independent predictors of disease-specific survival in distinct subgroups, defined clinically or with respect to treatment.

RESULTS

In Cox regression analyses, two parameters of the genome instability profiles, the S-phase fraction and the stemline scatter index, emerged as independent predictors in premenopausal women, outperforming all clinicopathologic parameters. In postmenopausal women, age and hormone receptor status were the predominant prognostic factors. However, by including S-phase fraction and 2.5c exceeding rate, we could improve disease outcome prediction in pT1 tumors irrespective of the lymph node status. In pT3-pT4 tumors, a higher S-phase fraction led to poorer prognosis. In patients who received adjuvant endocrine therapy, chemotherapy or radiotherapy, or a combination, the ploidy profiles improved prognostication.

CONCLUSIONS

Genome instability profiles predict disease outcome in patients with breast cancer independent of clinicopathologic parameters. This applies especially to premenopausal patients. In patients receiving adjuvant therapy, the profiles improve identification of high-risk patients.

High Levels of Chromosomal Copy Number Alterations and TP53 Mutations Correlate with Poor Outcome in Younger Breast Cancer Patients

Prognosis in young patients with breast cancer is generally poor, yet considerable differences in clinical outcomes between individual patients exist. To understand the genetic basis of the disparate clinical courses, tumors were collected from 34 younger women, 17 with good and 17 with poor outcomes, as determined by disease-specific survival during a follow-up period of 17 years. The clinicopathologic parameters of the tumors were complemented with DNA image cytometry profiles, enumeration of copy numbers of eight breast cancer genes by multicolor fluorescence in situ hybridization, and targeted sequence analysis of 563 cancer genes. Both groups included diploid and aneuploid tumors. The degree of intratumor heterogeneity was significantly higher in aneuploid versus diploid cases, and so were gains of the oncogenes MYC and ZNF217. Significantly more copy number alterations were observed in the group with poor outcome. Almost all tumors in the group with long survival were classified as luminal A, whereas triple-negative tumors predominantly occurred in the short survival group. Mutations in PIK3CA were more common in the group with good outcome, whereas TP53 mutations were more frequent in patients with poor outcomes. This study shows that TP53 mutations and the extent of genomic imbalances are associated with poor outcome in younger breast cancer patients and thus emphasize the central role of genomic instability vis-a-vis tumor aggressiveness.

Abstract P3-08-65: PITX2 DNA methylation: A prognostic/predictive biomarker for anthracycline-based chemotherapy

Background: Published data on the basis of a research-use-only PITX2 methylation assay using fresh-frozen tissue showed that the PITX2 DNA methylation may be a predictive marker for response to (neo) adjuvant anthracycline-based chemotherapy in breast cancer patients, including high-risk lymph node positive, estrogen receptor-positive, HER2-negative breast cancer and triple-negative breast cancer (TNBC). A retrospective study showed that high-risk ER-positive patients with a high PITX2 methylation ratio (PMR>12) had a poor outcome after anthracycline-based chemotherapy [HR 2,28; 95%-Cl 1,49 - 3,49; p<0.001, median DFS 71 months] compared to patients with low PITX2 methylation ratios [PMR≤12, median DFS 105 months]. Nevertheless, the question regarding the prognostic versus predictive value of PITX2 methylation for anthracycline therapy remained unanswered so far. Within an exploratory study using archived tissue specimen, this question was addressed by comparing the impact of PITX2 methylation on outcome in an untreated versus treated TNBC population. Methods: Patient samples and clinical data from 144 TNBC patients of 2 cohorts were analyzed: 1) 66 untreated patients from the Karolinska Institute in Sweden (primary diagnosis 1971-1976) and 2) 78 patients treated with anthracycline-based chemotherapy from the Comprehensive Cancer Center TUM in Germany (primary diagnosis 1996 to 2014). The main eligibility criteria were as follows: ER-negative, PR-negative, HER2-negative breast cancer (TNBC); no endocrine therapy; untreated collective: no further therapy besides surgery and radiation therapy; treated collective: surgery followed by anthracycline based chemotherapy. Samples were assessed for PITX2 methylation using a CE marked PITX2 RGQ PCR Test. The study was designed to determine the PITX2 PMR cut-off value in the untreated population (n=66, prognostic value) and to subsequently determine if this cut-off provides statistical significance in the treated population (n=78, prognostic & predictive value) as well. If no statistically significant cut-off value can be determined in the untreated population, cut-off determination was performed in the treated population and the cut-off was applied in the untreated population. The primary clinical endpoint for all cut-offs was 10-years DFS, secondary clinical endpoints were DFS censored at 5-years and OS censored at 5- and 10-years. Results: The untreated TNBC study population demonstrated a higher event rate at 10-years DFS/OS compared to the anthracycline-treated population [36 DFS/28 OS events vs 28 DFS/14 OS events]. Anthracycline treatment improved significantly overall survival [HR=0.42; p=0.008]. Risk recurrence increased continuously over 5 year and 10 years DFS/OS with increasing PITX2 DNA methylation in the anthracycline-treated population but not in the untreated patients over 5 years DFS/OS and only marginally over 10 years DFS/OS. PITX2 methylation identifies at the cut-off of PMR 2 a patient population with poor vs good overall survival with statistical significance [HR=3.96, p=0.011] in the treated patient cohort but did not identify patients with poor vs good outcome in the untreated patient cohort [HR=1.55, p=0.259].

Summary: In this hypothesis generating study DNA-methylation of PITX2 identifies with high statistical significance anthracycline-treated patients with poor vs good survival. Recurrence risk increases with increasing PITX2 DNA-methylation. PITX2 DNA-methylation shows no prognostic, but significant predictive value for anthracycline treatment in TNBC patients in this study. To confirm conclusively the predictive value of PITX2 DNA-methylation, the results warrant a confirmatory study with tumor specimens from a prospective trial of anthracycline-treated patients vs. anthracycline-free treated patients.

Citation Format: Marion Kiechle, Gabriele Schricker, Rudolf Napieralski, Michaela Aubele, Gert Auer, Kurt Ulm, Jonathan Perkins, Stefan Paepke, Moritz Hamann, Olaf G. Wilhelm. PITX2 DNA methylation: A prognostic/predictive biomarker for anthracycline-based chemotherapy [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P3-08-65.

Super-resolution microscopy can identify specific protein distribution patterns in platelets incubated with cancer cells

Protein contents in platelets are frequently changed upon tumor development and metastasis. However, how cancer cells can influence protein-selective redistribution and release within platelets, thereby promoting tumor development, remains largely elusive. With fluorescence-based super-resolution stimulated emission depletion (STED) imaging we reveal how specific proteins, implicated in tumor progression and metastasis, re-distribute within platelets, when subject to soluble activators (thrombin, adenosine diphosphate and thromboxane A2), and when incubated with cancer (MCF-7, MDA-MB-231, EFO21) or non-cancer cells (184A1, MCF10A). Upon cancer cell incubation, the cell-adhesion protein P-selectin was found to re-distribute into circular nano-structures, consistent with accumulation into the membrane of protein-storing alpha-granules within the platelets. These changes were to a significantly lesser extent, if at all, found in platelets incubated with normal cells, or in platelets subject to soluble platelet activators. From these patterns, we developed a classification procedure, whereby platelets exposed to cancer cells, to non-cancer cells, soluble activators, as well as non-activated platelets all could be identified in an automatic, objective manner. We demonstrate that STED imaging, in contrast to electron and confocal microscopy, has the necessary spatial resolution and labelling efficiency to identify protein distribution patterns in platelets and can resolve how they specifically change upon different activations. Combined with image analyses of specific protein distribution patterns within the platelets, STED imaging can thus have a role in future platelet-based cancer diagnostics and therapeutic monitoring. The presented approach can also bring further clarity into fundamental mechanisms for cancer cell-platelet interactions, and into non-contact cell-to-cell interactions in general.

Protein profiling of fine-needle aspirates reveals subtype-associated immune signatures and involvement of chemokines in breast cancer

There are increasing demands for informative cancer biomarkers, accessible via minimally invasive procedures, both for initial diagnostics and for follow-up of personalized cancer therapy, including immunotherapy. Fine-needle aspiration (FNA) biopsy provides ready access to relevant tissue samples; however, the minute amounts of sample require sensitive multiplex molecular analysis to be of clinical biomarker utility. We have applied proximity extension assays (PEA) to analyze 167 proteins in FNA samples from patients with breast cancer (BC; n = 25) and benign lesions (n = 32). We demonstrate that the FNA BC samples could be divided into two main clusters, characterized by differences in expression levels of the estrogen receptor (ER) and the proliferation marker Ki67. This clustering corresponded to some extent to established BC subtypes. Our analysis also revealed several proteins whose expression levels differed between BC and benign lesions (e.g., CA9, GZMB, IL-6, VEGFA, CXCL11, PDL1, and PCD1), as well as several chemokines correlating with ER and Ki67 status (e.g., CCL4, CCL8, CCL20, CXCL8, CXCL9, and CXCL17). Finally, we also identified three signatures that could predict Ki67 status, ER status, and tumor grade, respectively, based on a small subset of proteins, which was dominated by chemokines. To our knowledge, expression profiles of CCL13 in benign lesions and BC have not previously been described but were shown herein to correlate with proliferation (P = 0.00095), suggesting a role in advanced BC. Given the broad functional range of the proteins analyzed, immune-related proteins were overrepresented among the observed alterations. Our pilot study supports the emerging role of chemokines in BC progression. Due to the minimally traumatic sampling and clinically important molecular information for therapeutic decisions, this methodology is promising for future immunoscoring and monitoring of treatment efficacy in BC.

A fine-needle aspiration-based protein signature discriminates benign from malignant breast lesions

There are increasing demands for informative cancer biomarkers, accessible via minimally invasive procedures, both for initial diagnostics and to follow-up personalized cancer therapy. Fine-needle aspiration (FNA) biopsy provides ready access to relevant tissues; however, the minute sample amounts require sensitive multiplex molecular analysis to achieve clinical utility. We have applied proximity extension assays (PEA) and NanoString (NS) technology for analyses of proteins and of RNA, respectively, in FNA samples. Using samples from patients with breast cancer (BC, n = 25) or benign lesions (n = 33), we demonstrate that these FNA-based molecular analyses (a) can offer high sensitivity and reproducibility, (b) may provide correct diagnosis in shorter time and at a lower cost than current practice, (c) correlate with results from routine analysis (i.e., benchmarking against immunohistochemistry tests for ER, PR, HER2, and Ki67), and (d) may also help identify new markers related to immunotherapy. A specific 11-protein signature, including FGF binding protein 1, decorin, and furin, distinguished all cancer patient samples from all benign lesions in our main cohort and in smaller replication cohort. Due to the minimally traumatic sampling and rich molecular information, this combined proteomics and transcriptomic methodology is promising for diagnostics and evaluation of treatment efficacy in BC.

Abstract 2189: Genomic dynamics in breast cancer progression analyzed by miFISH analysis

Our previous studies of synchronous Ductal Carcinomas in Situ (DCIS) and Invasive Ductal Carcinomas (IDC) often showed a high degree of chromosomal instability already in DCIS, and frequently a direct clonal evolution from DCIS to IDC. We now asked the question whether this degree of instability is also present in DCIS that did not progress to IDC. In collaboration with Englewood Hospital and Medical Center, we are therefore conducting a retrospective study analyzing FFPE material from 20 DCIS patients with low-grade or high-grade DCIS who did not present with invasive breast carcinoma during their follow-up (5-10 years) and compared the findings to 10 DCIS patients who presented with synchronous IDC. Using our novel multiplex interphase FISH (miFISH) assay, we are able to determine copy number changes of five oncogenes (COX2, MYC, CCND1, HER2, ZNF217) and three tumor suppressor genes (DBC2, CDH1, TP53) and assessed intratumor heterogeneity (ITH) and clonal evolution during disease progression.

The miFISH analysis showed that low-grade DCIS displayed mostly stable patterns of gene copy numbers in a diploid genome, while high-grade DCIS frequently had increased nuclear DNA content (ploidy) associated with a higher degree of ITH. However, some low-grade DCIS exhibited complex and unstable patterns with higher ploidy. Also, a few high-grade DCIS were defined by few copy number changes, e.g., the gain of a whole chromosome 8 (DBC and MYC), resulting in a clonal population with a low instability index. DCIS and their synchronous IDC often displayed very similar miFISH patterns indicating direct expansion of dominant clones. Of note, the DCIS cells of one case were defined by the well described 1q gain/16q loss pattern and acquired subsequently a chromosome 8 gain in the IDC, confirming our previous observation that the gain of MYC is a pivotal step in breast cancer progression. Our data also show that DCIS with or without synchronous IDC exhibited similar patterns. This could indicate that DCIS in general, regardless of grading, should be treated as lesions with progressive potential. Phylogenetic tree modeling with our custom FISHtrees software will further elucidate the dynamics of DCIS lesions.

In summary, miFISH analysis and phylogenetic tree modeling allow an in-depth characterization of precursor lesions and their evolutionary trajectory. We anticipate that this approach will ultimately help to stratify progression risk in patients with DCIS.

Citation Format: Irianna Marie Torres, Leanora Hernandez, Jausheng Tzeng, Russell Schwartz, Alejandro Schaffer, Edward Michael Gertz, Daniela Hirsch, Steven Brower, Miguel Sanchez, Gert Auer, Kerstin Heselmeyer-Haddad, Thomas Ried. Genomic dynamics in breast cancer progression analyzed by miFISH analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2189.

Aneuploidy, TP53 mutation, and amplification of MYC correlate with increased intratumor heterogeneity and poor prognosis of breast cancer patients

The clinical course of breast cancer varies from one patient to another. Currently, the choice of therapy relies on clinical parameters and histological and molecular tumor features. Alas, these markers are informative in only a subset of patients. Therefore, additional predictors of disease outcome would be valuable for treatment stratification. Extensive studies showed that the degree of variation of the nuclear DNA content, i.e., aneuploidy, determines prognosis. Our aim was to further elucidate the molecular basis of aneuploidy. We analyzed five diploid and six aneuploid tumors with more than 20 years of follow-up. By performing FISH with a multiplexed panel of 10 probes to enumerate copy numbers in individual cells, and by sequencing 563 cancer-related genes, we analyzed how aneuploidy is linked to intratumor heterogeneity. In our cohort, none of the patients with diploid tumors died of breast cancer during follow-up in contrast to four of six patients with aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however, TP53 mutations were not observed in diploid tumors, but in all aneuploid tumors in our collective. We conclude that quantitative measurements of intratumor heterogeneity by multiplex FISH, detection of MYC amplification and TP53 mutation could augment prognostication in breast cancer patients.

Platelet protein biomarker panel for ovarian cancer diagnosis

BACKGROUND

Platelets support cancer growth and spread making platelet proteins candidates in the search for biomarkers.

METHODS

Two-dimensional (2D) gel electrophoresis, Partial Least Squares Discriminant Analysis (PLS-DA), Western blot, DigiWest.

RESULTS

PLS-DA of platelet protein expression in 2D gels suggested differences between the International Federation of Gynaecology and Obstetrics (FIGO) stages III-IV of ovarian cancer, compared to benign adnexal lesions with a sensitivity of 96% and a specificity of 88%. A PLS-DA-based model correctly predicted 7 out of 8 cases of FIGO stages I-II of ovarian cancer after verification by western blot. Receiver-operator curve (ROC) analysis indicated a sensitivity of 83% and specificity of 76% at cut-off >0.5 (area under the curve (AUC) = 0.831, p < 0.0001) for detecting these cases. Validation on an independent set of samples by DigiWest with PLS-DA differentiated benign adnexal lesions and ovarian cancer, FIGO stages III-IV, with a sensitivity of 70% and a specificity of 83%.

CONCLUSION

We identified a group of platelet protein biomarker candidates that can quantify the differential expression between ovarian cancer cases as compared to benign adnexal lesions.

Protein levels of clusterin and glutathione synthetase in platelets allow for early detection of colorectal cancer

Colorectal cancer (CRC) is one of the most frequent malignancies in the Western world. Early tumor detection and intervention are important determinants on CRC patient survival. During early tumor proliferation, dissemination and angiogenesis, platelets store and segregate proteins actively and selectively. Hence, the platelet proteome is a potential source of biomarkers denoting early malignancy. By comparing protein profiles of platelets between healthy volunteers (n = 12) and patients with early- (n = 7) and late-stage (n = 5) CRCs using multiplex fluorescence two-dimensional gel electrophoresis (2D-DIGE), we aimed at identifying differentially regulated proteins within platelets. By inter-group comparisons, 94 differentially expressed protein spots were detected (p < 0.05) between healthy controls and patients with early- and late-stage CRCs and revealed distinct separations between all three groups in principal component analyses. 54 proteins of interest were identified by mass spectrometry and resulted in high-ranked Ingenuity Pathway Analysis networks associated with Cellular function and maintenance, Cellular assembly and organization, Developmental disorder and Organismal injury and abnormalities (p < 0.0001 to p = 0.0495). Target proteins were validated by multiplex fluorescence-based Western blot analyses using an additional, independent cohort of platelet protein samples [healthy controls (n = 15), early-stage CRCs (n = 15), late-stage CRCs (n = 15)]. Two proteins-clusterin and glutathione synthetase (GSH-S)-featured high impact and were subsequently validated in this independent clinical cohort distinguishing healthy controls from patients with early- and late-stage CRCs. Thus, the potential of clusterin and GSH-S as platelet biomarkers for early detection of CRC could improve existing screening modalities in clinical application and should be confirmed in a prospective multicenter trial.

Abstract 2908: Single-cell genetic analysis of ductal carcinoma in situ with and without synchronous invasive breast cancer by multiplex FISH delineates specific patterns of tumor clonality and heterogeneity

We previously studied synchronous Ductal Carcinomas in Situ (DCIS) and Invasive Ductal Carcinomas (IDC) using a novel approach of multiplexing FISH probes that allows us to simultaneously assess the copy numbers of up to 20 loci within intact nuclei providing new insights into tumor clonality and heterogeneity. A high degree of chromosomal instability already in DCIS, and frequently, but not always, a direct clonal evolution from DCIS to IDC was detected. We now ask whether this degree of instability is also present in DCIS that did not progress to IDC and are therefore analyzing FFPE material from 20 patients with either low-grade and high-grade DCIS who did not present with invasive breast carcinoma during their follow-up (5-10 years), in addition to 10 patients who presented with synchronous IDC. The multiplex FISH assay used targets five oncogenes (COX2, MYC, CCND1, HER2, ZNF217) and three tumor suppressor genes (DBC2, CDH1, TP53) frequently altered in breast carcinomas. To date, we have analyzed two paired cases of synchronous DCIS and IDC, DCIS-IDC 3 and 4, and three cases of DCIS without IDC, OP-DCIS 1, 4 and 5. The paired cases exhibited very similar aberration patterns for synchronous DCIS and IDC indicating the invasive carcinoma is closely related to the DCIS lesion. Specifically, the major clones in DCIS 3 (low-grade) and IDC 3 showed a diploid tumor cell population with a gain of COX2, and losses of DBC2, MYC, TP53, and HER2. Of note, the only difference observed was a gain of ZNF217 in the DCIS which was not seen in the major clone of the invasive carcinoma. The other paired case, DCIS 4 (high-grade) and IDC 4, showed major clones of triploid tumor cell populations with gains of COX2, CCND1 and MYC and losses of DBC2, CDH1, TP53 and ZNF217. The three DCIS cases without synchronous or subsequent IDC exhibited varying degrees of aberration and complexity patterns in their clonal populations. Case OP-DCIS 1, a high-grade DCIS, revealed a tetraploid cell population which showed a major clone with an amplification of CCND1 and a MYC gain combined with losses of DBC2, CDH1, TP53 and HER2. A low-grade DCIS, OP-DCIS 4, exhibited a diploid cell population with a major clone showing loss of CDH1 as the only aberration. The third case OP-DCIS 5 (low-grade DCIS) exhibited a diploid cell population with one major clone showing losses of CDH1, MYC, DBC2, TP53, HER2 and CCND1. Our preliminary observations show a tendency of diploid lesions with a predominance of loss patterns for low-grade DCIS, while high-grade DCIS seem to reveal higher ploidy with more complex gain and loss patterns. However, also low-grade DCIS with mainly loss patterns progress to invasive cancers as seen in case DCIS-IDC3. We expect that the analysis of the remaining cases will further elucidate the dynamics of DCIS lesions which will hopefully help to assess and stratify progression risk in patients with DCIS.

Citation Format: Irianna Marie Torres, Leanora Hernandez, Jausheng Tzeng, Russell Schwartz, Alejandro Schaffer, Edward Gertz, Stephen Brower, Miguel Sanchez, Gert Auer, Kerstin Heselmeyer-Haddad, Ried Thomas. Single-cell genetic analysis of ductal carcinoma in situ with and without synchronous invasive breast cancer by multiplex FISH delineates specific patterns of tumor clonality and heterogeneity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2908. doi:10.1158/1538-7445.AM2017-2908

Patterns of acute inflammatory symptoms prior to cancer diagnosis

Although many studies have examined the role of chronic inflammation in cancer development, few studies discuss the patterns of acute inflammation prior to cancer diagnosis. Patients with lung, colorectal, prostate, or breast cancer between 1 July 2006 and 31 December 2009 and their metastatic status at diagnosis were determined through the Swedish Cancer Register. Non-steroidal anti-inflammatory drugs (NSAIDs) use in the year prior to cancer diagnosis was assessed through the Swedish Prescribed Drug Register. There were 13,945 patients identified with breast cancer, 6501 with prostate cancer, 5508 with lung cancer, and 12,723 with colon cancer. For metastatic patients, there is strong evidence of higher NSAIDs use 1–3 months compared to 10–12 months prior to diagnosis (breast odds ratio (OR) = 3.54, 95% CI 2.26–5.54; prostate OR = 3.90, 95% CI 3.10–4.90; lung OR = 2.90 95% CI 2.44–3.44; colorectal OR = 1.67, 95% CI 1.36–2.05). For non-metastatic patients, increased NSAIDs use 1–3 months prior to diagnosis was also observed, but only to a smaller extent for lung and prostate cancer (prostate OR = 1.48, 95% CI 1.27–1.72; lung 1.41, 95% CI 1.19–1.67). In conclusion, if NSAIDs use reflects underlying inflammatory symptoms, there is support for the hypothesis that advanced cancer was associated with an acute inflammatory process.

A new method to gently place biopsy needles or treatment electrodes into tissues with high target precision

We present a new core needle biopsy and treatment electrode precision placement technique which, regardless of needle size, target lesion hardness and elasticity, makes it possible to precisely place an image guided device inside the abnormal tissue. Once inside the abnormal lesion, multiple tissue samples can be collected using a dedicated trocar and collecting system. Our unique "Fourier" driver substitutes the commonly used spring-loaded device or complements the jerky insertion technique used by experienced interventional physicians. It enables the physician to precisely and with extreme tactility maneuver even large diameter core needles or treatment-electrodes into the lesion using only a diminutive external force. This is achieved by applying supporting servo-controlled mechanical high-acceleration micro-pulses, proportional to the average vector directed by the physician. The Fourier-needle or Fourier-electrode stands completely non-moving when the system automatically goes into full idling. This means that the angle of attack successively and arbitrary can be aligned to hit the target, becoming successively symmetrically inserted into even small tumors to be treated as well as exactly hit any point outlined by real time ultrasound guiding. This kind of biopsy needle or treatment electrode placement results in a uniquely accurate and less traumatic procedure. Due to the risk of disseminating viable tumor cells the precision placement device can be combined with a computer controlled anti-seeding system, denaturizing tumor cells detached during penetration of the biopsy needle or treatment electrode.

Phylogenetic analysis of multiple FISH markers in oral tongue squamous cell carcinoma suggests that a diverse distribution of copy number changes is associated with poor prognosis

Oral tongue squamous cell carcinoma (OTSCC) is associated with poor prognosis. To improve prognostication, we analyzed four gene probes (TERC, CCND1, EGFR and TP53) and the centromere probe CEP4 as a marker of chromosomal instability, using fluorescence in situ hybridization (FISH) in single cells from the tumors of sixty-five OTSCC patients (Stage I, n = 15; Stage II, n = 30; Stage III, n = 7; Stage IV, n = 13). Unsupervised hierarchical clustering of the FISH data distinguished three clusters related to smoking status. Copy number increases of all five markers were found to be correlated to non-smoking habits, while smokers in this cohort had low-level copy number gains. Using the phylogenetic modeling software FISHtrees, we constructed models of tumor progression for each patient based on the four gene probes. Then, we derived test statistics on the models that are significant predictors of disease-free and overall survival, independent of tumor stage and smoking status in multivariate analysis. The patients whose tumors were modeled as progressing by a more diverse distribution of copy number changes across the four genes have poorer prognosis. This is consistent with the view that multiple genetic pathways need to become deregulated in order for cancer to progress.

A standardized method for quantifying proliferation by Ki-67 and cyclin A immunohistochemistry in breast cancer

Immunohistochemical analysis of proliferation markers such as Ki-67 and cyclin A is widely used in clinical evaluation as a prognostic factor in breast cancer. The proliferation status of tumors is guiding the decision of whether or not a patient should be treated with chemotherapy because low-proliferative tumors are less sensitive by such treatment. However, the lack of optimal cutoff points and selection of tumor areas hamper its use in clinical practice. This study was performed to compare the Ki-67 and cyclin A expression counted in hot-spot vs average counting based on 5 to 14 random tumor areas in 613 breast carcinomas. We correlated the findings with 10-year follow-up in order to standardize the evaluation of proliferation markers in clinical practice. A significant correlation was found between the percentage of positive cells estimated by Ki-67 and cyclin A both by hot-spot and by average counting. Both methods showed that high expression of Ki-67 and cyclin A is associated with more adverse tumor stage. The cutoff value for Ki-67 for distant metastases was set to 22% and to 15%, using hot-spot and average counting, respectively. For cyclin A, the values were set to 14% and 8% using the respective methods. Survival curves revealed that patients with a high hot-spot proliferation index had a significantly greater risk of shorter tumor-free survival. Our findings suggest that the determination of proliferation markers in breast cancer should be standardized to hot-spot counting and that specific cutoff values for proliferation could be useful as prognostic markers in clinical practice. Moreover, we suggest that expression levels of cyclin A could be used as a complementary marker to estimate the proliferation status in tumors, especially those with "borderline" expression levels of Ki-67, in order to more accurately estimate the proliferations status of the tumors.

Distinct effects of anti-inflammatory and anti-thrombotic drugs on cancer characteristics at diagnosis

BACKGROUND

A previous study showed that regular use of low-dose aspirin was associated with smaller tumour size and fewer metastases for colorectal and lung cancer. We aim to explain these distinct effects in terms of the anti-inflammatory and anti-thrombotic properties of aspirin.

METHODS

From the Swedish Cancer Register, we identified patients diagnosed with colorectal and lung cancers between 1st October 2006 and 31st December 2009; each cancer was assessed in terms of tumour size/extent (T), lymph-node (N) and metastatic (M) status. Linkage with the Swedish Prescribed Drug Register was performed to obtain information on the use of low-dose aspirin, anti-inflammatory and anti-thrombotic drugs prior to cancer diagnosis.

RESULTS

We identified 14,743 individuals with colorectal cancer and 5888 with lung cancer. For low-dose aspirin users we observed a statistically significant association with smaller tumour size and fewer metastases. For both cancers, the use of non-aspirin anti-inflammatory drugs was associated with smaller tumour size in all categories T2-T4 odds ratio (OR = 0.76, 95% confidence interval (CI) 0.63-0.92 for T2 versus T1 in colorectal cancer), but not with metastatic status (OR = 0.94, 95% CI 0.84-1.06 in colorectal cancer). In contrast, anti-thrombotic drug use was associated with fewer metastases, but not with tumour categories T2 and T3.

CONCLUSIONS

The results suggest that the use of anti-inflammatories is associated with tumour-growth inhibition at the primary site, while the use of anti-thrombotics is associated with restriction of cancer-cell metastasising capability. These have clinical implications on the potential use of these drugs for chemoprevention or chemotherapy.

Genetic Instability and Disease Prognostication

Genetic instability is a striking feature of human cancers, with an impact on the genesis, progression and prognosis. The clinical importance of genomic instability and aneuploidy is underscored by its association with poor patient outcome in multiple cancer types, including breast and colon cancer. Interestingly, there is growing evidence that prognostic gene expression signatures simply reflect the degree of genomic instability. Additionally, also the proteome is affected by aneuploidy and has therefore become a powerful tool to screen for new targets for therapy, diagnosis and prognostication. In this context, the chapter presents the impact of genomic instability on disease prognostication occurring in human cancers.

Multicolor fluorescence nanoscopy by photobleaching: concept, verification, and its application to resolve selective storage of proteins in platelets

Fluorescence nanoscopy provides means to discern the finer details of protein localization and interaction in cells by offering an order of magnitude higher resolution than conventional optical imaging techniques. However, these super resolution techniques put higher demands on the optical system and the fluorescent probes, making multicolor fluorescence nanoscopy a challenging task. Here we present a new and simple procedure, which exploits the photostability and excitation spectra of dyes to increase the number of simultaneous recordable targets in STED nanoscopy. We use this procedure to demonstrate four-color STED imaging of platelets with ≤40 nm resolution and low crosstalk. Platelets can selectively store, sequester, and release a multitude of different proteins, in a manner specific for different physiological and disease states. By applying multicolor nanoscopy to study platelets, we can achieve spatial mapping of the protein organization with a high resolution for multiple proteins at the same time and in the same cell. This provides a means to identify specific platelet activation states for diagnostic purposes and to understand the underlying protein storage and release mechanisms. We studied the organization of the pro- and antiangiogenic proteins VEGF and PF-4, together with fibrinogen and filamentous actin, and found distinct features in their respective protein localization. Further, colocalization analysis revealed only minor overlap between the proteins VEGF and PF-4 indicating that they have separate storage and release mechanisms, corresponding well with their opposite roles as pro- and antiangiogenic proteins, respectively.

Anticoagulant medication at time of needle biopsy for breast cancer in relation to risk of lymph node metastasis

Anticoagulant treatment might enhance the natural defense against tumor cell dissemination caused by diagnostic needle biopsy by counteracting thrombocyte coating of such cells. To clarify whether women using anticoagulant treatment at the time of biopsy have a lower occurrence of lymph node metastasis, we conducted a nationwide Swedish cohort study of 26,528 female incident breast cancer patients in 2006-2011. Point risk ratio (RR) of risk of lymph node metastasis among users of anticoagulant treatment adjusted for age, T-stage, socioeconomic factors, and concomitant medication was RR = 0.94, (95% CI: 0.87-1.03), and lower in younger women (RR = 0.80, 95% CI 0.50-1.29). Although nonsignificant, these associations may underestimate a true negative association since women using anticoagulant treatment are likely to have more concomitant diseases, lead an unhealthier lifestyle, and have lower participation in mammography screening. These findings provide some support for the hypothesis that anticoagulant medications might counteract breast cancer spread caused by needle biopsy.

Abstract A046: MiR-221 and -222 expression elevates cell invasion and allows distinction between different prognostic groups in advanced breast cancers

Introduction: The expression of miR-221 and -222 is frequently altered in invasive breast cancer and in breast cancer cell lines. We aimed to determine the prognostic and/or therapeutic impact of miR-221/222 expression and its association with tumor progression and metastasizing processes.

Experimental procedures: We investigated the expression of miR-221 and -222 in 86 formalin-fixed, paraffin-embedded (FFPE) tissue specimens from invasive ductal breast carcinomas (IDC) using quantitative RT-PCR. The prognostic impact of miRNA expression was analyzed using univariate and multivariable analysis for distant metastasis-free survival of patients. Immunohistochemistry (IHC) of the tissue samples was performed for oncoprotein HER2 and proliferation marker Ki-67, and in addition for p27KIP1, estrogen receptor (ER), and PTEN which were already described as targets of these miRNAs. In vitro studies and in silico target analyses were performed for breast cancer cell lines T47D and SKBR3. Here lentiviral particles were produced for overexpression of miRNAs as described (Anastasov, Rad Oncol 7:206,2012) with packaging plasmids and lentiviral precursor expression vectors for miR-221 and miR-222. After viral infection, the cells were analyzed for several signaling markers by Western blot, for cell proliferation, migration, and invasion compared to the corresponding untreated cell lines.

Summary of results: Our results demonstrate a statistically significant direct association between miR-222 and HER1/HER3 expression (p=0.003), and inverse correlations of miR-221 and HER4 (p=0.006), miR-222 and ER (p=0.016), and miR-222 and p27KIP1 (p=0.048). Nuclear grade of tumors was directly associated with Ki-67 expression (p≥0.001) and inversely with p27KIP1 (p=0.03). Both miRNAs are significantly associated with distant metastasis-free survival of patients; in particular miR-221 expression is a powerful discriminator in defining prognostic subgroups in HER2-positive and lymph node-positive breast cancer patients. To further substantiate these results, miR-221 and miR-222 were overexpressed in cell lines (T47D, SKBR3). Here, we could confirm association of the two miRNAs with p27Kip1, ER, and PTEN expression, which have been described as targets of miR-221 and -222. Upregulation of these miRNAs strongly increased tumor cell proliferation and invasion in vitro. Additional in silico and in vitro analyses revealed that tumor invasion processes are influenced by miR-221 and -222 via targeting the soluble variant of the urokinase-type plasminogen activator receptor (uPAR / CD87).

Statement and conclusions: We could demonstrate that elevated expression of miR-221 and miR-222 in ductal breast cancer allows distinguishing between different prognostic subgroups. Our in vitro results following miR-221/-222 overexpression in breast cancer tumor cell lines demonstrated a strong association between miRNAs and cellular invasion. From our in silico analysis there is also a clear hint that this process is modified by targeting of an uPAR isoform.

Citation Format: Natalie Falkenberg, Jr., Natasa Anastasov, Jr., Herbert Braselmann, Gert Auer, Michaela Huber, Manfred Schmitt, Heinz Höfler, Michaela Aubele. MiR-221 and -222 expression elevates cell invasion and allows distinction between different prognostic groups in advanced breast cancers. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research: Genetics, Biology, and Clinical Applications; Oct 3-6, 2013; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2013;11(10 Suppl):Abstract nr A046.

The impact of pre-analytical conditions on the serum proteome: heat-stabilization versus nitrogen storage

CONTEXT

Biological material reflecting the in vivo composition of markers provides a high potential for biomarker discovery.

OBJECTIVE

We compared the serum proteome following heat- and nitrogen-preservation, with and without subsequent storage at room temperature.

MATERIALS AND METHODS

Serum samples were collected, treated and analysed by two-dimensional gel electrophoresis. Protein spots were identified and confirmed by two mass spectrometry approaches (MALDI & ESI) and subjected to Ingenuity Pathway Analysis.

RESULTS

We revealed 24 differentially expressed proteins (p ≤ 0.05) between nitrogen and heat preservation, and 87 between nitrogen and heat preservation with subsequent storage for 120 h at room-temperature. Mass spectrometry identified 25 polypeptides. Pathway analysis resulted in networks maintaining Cellular Assembly and Organization, Movement and Maintenance.

CONCLUSION

Heat-stabilization does not substantially change the short-term proteome composition of serum compared with nitrogen treatment. However, heat-stabilization alone seems insufficient for long-term sample preservation for serum samples. We identified transthyretin and apolipoprotein A-IV as sample quality markers.

The impact of cysteine-rich intestinal protein 1 (CRIP1) in human breast cancer

Background

CRIP1 (cysteine-rich intestinal protein 1) has been found in several tumor types, its prognostic impact and its role in cellular processes, particularly in breast cancer, are still unclear.

Methods

To elucidate the prognostic impact of CRIP1, we analyzed tissues from 113 primary invasive ductal breast carcinomas using immunohistochemistry. For the functional characterization of CRIP1, its endogenous expression was transiently downregulated in T47D and BT474 breast cancer cells and the effects analyzed by immunoblotting, WST-1 proliferation assay and invasion assay.

Results

We found a significant correlation between CRIP1 and HER2 (human epidermal growth factor receptor 2) expression levels (p = 0.016) in tumor tissues. In Kaplan Meier analyses, CRIP1 expression was significantly associated with the distant metastases-free survival of patients, revealing a better prognosis for high CRIP1 expression (p = 0.039). Moreover, in multivariate survival analyses, the expression of CRIP1 was an independent negative prognostic factor, along with the positive prognosticators nodal status and tumor size (p = 0.029). CRIP1 knockdown in the T47D and BT474 breast cancer cell lines led to the increased phosphorylation of MAPK and Akt, to the reduced phosphorylation of cdc2, and to a significantly elevated cell proliferation in vitro (p < 0.001). These results indicate that reduced CRIP1 levels may increase cell proliferation and activate cell growth. In addition, CRIP1 knockdown increased cell invasion in vitro.

Conclusions

Because the lack of CRIP1 expression in breast cancer tissue is significantly associated with a worse prognosis for patients and low endogenous CRIP1 levels in vitro increased the malignant potential of breast cancer cells, we hypothesize that CRIP1 may act as a tumor suppressor in proliferation and invasion processes. Therefore, CRIP1 may be an independent prognostic marker with significant predictive power for use in breast cancer therapy.

Chromosomal aneuploidy affects the global proteome equilibrium of colorectal cancer cells

BACKGROUND

Chromosomal aneuploidy has been identified as a prognostic factor in the majority of sporadic carcinomas. However, it is not known how chromosomal aneuploidy affects chromosome-specific protein expression in particular, and the cellular proteome equilibrium in general.

OBJECTIVE

The aim was to detect chromosomal aneuploidy-associated expression changes in cell clones carrying trisomies found in colorectal cancer.

METHODS

We used microcell-mediated chromosomal transfer to generate three artificial trisomic cell clones of the karyotypically stable, diploid, yet mismatch-deficient, colorectal cancer cell line DLD1--each of them harboring one extra copy of either chromosome 3, 7 or 13. Protein expression differences were assessed by two-dimensional gel electrophoresis and mass spectrometry, compared to whole-genome gene expression data, and evaluated by PANTHER classification system and Ingenuity Pathway Analysis (IPA).

RESULTS

In total, 79 differentially expressed proteins were identified between the trisomic clones and the parental cell line. Up-regulation of PCNA and HMGB1 as well as down-regulation of IDH3A and PSMB3 were revealed as trisomy-associated alterations involved in regulating genome stability.

CONCLUSIONS

These results show that trisomies affect the expression of genes and proteins that are not necessarily located on the trisomic chromosome, but reflect a pathway-related alteration of the cellular equilibrium.

Radiation resistance due to high expression of miR-21 and G2/M checkpoint arrest in breast cancer cells

Background

There is evidence that the extent of the G2/M arrest following irradiation is correlated with tumour cell survival and hence therapeutic success. We studied the regulation of cellular response to radiation treatment by miR-21-mediated modulation of cell cycle progression in breast cancer cells and analysed miR-21 expression in breast cancer tissue samples with long-term follow up.

Methods

The miR-21 expression levels were quantified (qRT-PCR) in a panel of 86 cases of invasive breast carcinomas in relation to metastasis free survival. The cellular radiosensitivity of human breast cancer cells after irradiation was determined comparing two cell lines (T47D and MDA-MB-361) by cell proliferation and colony forming assays. The influence of miR-21 overexpression or downregulation on cell cycle progression and G2/M checkpoint arrest after irradiation was assessed by flow cytometric analysis.

Results

The expression of miR-21 was transiently increased 8 hours after irradiation in the radioresistant T47D cells and significantly changed with lower extent in radiosensitive MDA-MB-361 cells. Anti-miR-21 treated breast cancer cells failed to exhibit the DNA damage-G2 checkpoint increase after irradiation. Apoptotic activity was significantly enhanced from 7% to 27% in T47D cells and from 18% to 30% in MDA-MB-361 cells 24 hours after 5 Gy irradiation. Additionally, we characterized expression of miR-21 in invasive breast carcinomas. In comparison to non-cancerous adjacent breast tissue, tumours samples had increased miR-21 expression that inversely correlated with the distant metastases-free survival of patients (p = 0.029).

Conclusions

Our data indicate that miR-21 expression in breast cancer cells contributes to radiation resistance by compromising cell cycle progression. These data point to the potential of combining radiotherapy with an anti-miR-21 as a potent G2/M check point inhibitor in overcoming radiation resistance of tumours.

Fluorescence nanoscopy of platelets resolves platelet-state specific storage, release and uptake of proteins, opening up future diagnostic applications

Dysregulation of how platelets store, sequester and release specific proteins seems to be implicated in many disease states, including cancer. Dual-color immunofluorescence stimulated emission depletion (STED) microscopy with 40 nm resolution is used to map pro-angiogenic VEGF, anti-angiogenic PF-4 and fibrinogen in >300 individual platelets. This reveals that these proteins are stored in a segmented, zonal manner within regional clusters, significantly smaller than the size of an α-granule. No colocalization between the different proteins is observed. Upon platelet activation by thrombin or ADP, the proteins undergo significant spatial rearrangements, including alterations in the size and number of the protein clusters, and specific for a certain protein and the type of activation induced. Following these observations, a simple assignment procedure is used to show that the three distinct states of platelets (non-, ADP- and thrombin-activated) can be identified based on the average size, number and peripheral localization profiles of the regional protein clusters within the platelets. Thus, high-resolution spatial mapping of specific proteins is a useful procedure to detect and characterize deviations in the selective storage, release and uptake of these proteins in the platelets. Since these deviations seem to be specific for, and may even underlie, certain patophysiological states, these findings may have interesting diagnostic and therapeutic implications.

Nuclear-DNA content and p53 immunostaining in oral squamous-cell carcinoma - an analysis of a consecutive 10-year material

In a retrospective analysis of 91 consecutive oral carcinomas we reviewed all patient records and weighed clinicopathological parameters against the results of image DNA cytometry and p53 immunhistochemical staining of the initial diagnostic biopsies. Eighty-seven percent of the biopsies were either aneuploid or nondiploid and there was a significant correlation between poorly differentiated tumours and aneuploidy. Sixty-nine percent of the tumours were p53 positive. DNA aberration or p53 positivity had no significant impact on prediction of survival or susceptibility to radiotherapy. In a multivariate analysis, T category had the greatest predictive value concerning survival. There was no correlation between p53 positivity and smoking.

Protein expression changes in ovarian cancer during the transition from benign to malignant

Epithelial ovarian carcinoma has in general a poor prognosis since the vast majority of tumors are genomically unstable and clinically highly aggressive. This results in rapid progression of malignancy potential while still asymptomatic and thus in late diagnosis. It is therefore of critical importance to develop methods to diagnose epithelial ovarian carcinoma at its earliest developmental stage, that is, to differentiate between benign tissue and its early malignant transformed counterparts. Here we present a shotgun quantitative proteomic screen of benign and malignant epithelial ovarian tumors using iTRAQ technology with LC-MALDI-TOF/TOF and LC-ESI-QTOF MS/MS. Pathway analysis of the shotgun data pointed to the PI3K/Akt signaling pathway as a significant discriminatory pathway. Selected candidate proteins from the shotgun screen were further confirmed in 51 individual tissue samples of normal, benign, borderline or malignant origin using LC-MRM analysis. The MRM profile demonstrated significant differences between the four groups separating the normal tissue samples from all tumor groups as well as perfectly separating the benign and malignant tumors with a ROC-area of 1. This work demonstrates the utility of using a shotgun approach to filter out a signature of a few proteins only that discriminates between the different sample groups.

Proteomic profiling of follicular and papillary thyroid tumors

OBJECTIVE

Thyroid proteomics is a new direction in thyroid cancer research aiming at etiological understanding and biomarker identification for improved diagnosis.

METHODS

Two-dimensional electrophoresis was applied to cytosolic protein extracts from frozen thyroid samples (ten follicular adenomas, nine follicular carcinomas, ten papillary carcinomas, and ten reference thyroids). Spots with differential expression were revealed by image and multivariate statistical analyses, and identified by mass spectrometry.

RESULTS

A set of 25 protein spots significant for discriminating between the sample groups was identified. Proteins identified for nine of these spots were studied further including 14-3-3 protein beta/alpha, epsilon, and zeta/delta, peroxiredoxin 6, selenium-binding protein 1, protein disulfide-isomerase precursor, annexin A5 (ANXA5), tubulin alpha-1B chain, and α1-antitrypsin precursor. This subset of protein spots carried the same predictive power in differentiating between follicular carcinoma and adenoma or between follicular and papillary carcinoma, as compared with the larger set of 25 spots. Protein expression in the sample groups was demonstrated by western blot analyses. For ANXA5 and the 14-3-3 proteins, expression in tumor cell cytoplasm was demonstrated by immunohistochemistry both in the sample groups and an independent series of papillary thyroid carcinomas.

CONCLUSION

The proteins identified confirm previous findings in thyroid proteomics, and suggest additional proteins as dysregulated in thyroid tumors.

P3-03-04: Targeted Modulation of HER Receptor Signaling in Breast Cancer Using miR-21

Introduction: MicroRNAs (miRNAs) are multifunctional nucleic acids that regulate the stability and translational efficiency of targeted messenger RNAs. Endogenously altered miRNA levels have been linked in breast cancer to acquired chemoresistance and changed radiosensitivity. Thus the modification of miRNA expression represents an attractive therapeutic strategy. We now show that the targeted inhibition of miR-21 can modify expression of the HER2 receptor in breast cancer.

Materials and Methods: Using TaqMan-based technology the expression of five selected miRNAs (miR-7b, miR-10a, miR-17-5p, miR-125a, and miR-21) was investigated in formalin-fixed, paraffin-embedded breast carcinoma tissues expressing different levels of HER2 (n=60). Possible regulation of HER2 was explored in cell lines using lentivirus to stably downregulate or upregulate HER2 and miR-21 expressions. The effects were analyzed using qRT-PCR, Western blots, proliferation and migration assays.

Results: In tumor tissues we identified overexpression of miR-10a and miR-21, and underexpression of miR-17-5p and miR-125a in most of the tumor tissue samples. Significant associations (p≤0.05) were found between HER receptor expression and the expression of miR-17-5p and miR-125a, and miR-21 showed correlation with expression of ER and PR. Furthermore, analysis of miR-21 downregulation in breast cancer cell lines showed inhibition of cellular proliferation and HER2 protein synthesis. Additionally, downregulation of HER2 expression decreased miR-21 expression and showed moderate change in cellular proliferation activity.

Conclusions: Based on these results we conclude that there is tight interplay between HER2 and miR-21 expression in breast cancer cells. Because miRNAs modulate gene expression we suggest that modulation of miR-21 has the potential to impact tumor therapy by interference with specific signaling pathways.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P3-03-04.

Genomic instability influences the transcriptome and proteome in endometrial cancer subtypes

BACKGROUND

In addition to clinical characteristics, DNA aneuploidy has been identified as a prognostic factor in epithelial malignancies in general and in endometrial cancers in particular. We mapped ploidy-associated chromosomal aberrations and identified corresponding gene and protein expression changes in endometrial cancers of different prognostic subgroups.

METHODS

DNA image cytometry classified 25 endometrioid cancers to be either diploid (n = 16) or aneuploid (n = 9), and all uterine papillary serous cancers (UPSC) to be aneuploid (n = 8). All samples were subjected to comparative genomic hybridization and gene expression profiling. Identified genes were subjected to Ingenuity pathway analysis (IPA) and were correlated to protein expression changes.

RESULTS

Comparative genomic hybridization revealed ploidy-associated specific, recurrent genomic imbalances. Gene expression analysis identified 54 genes between diploid and aneuploid endometrioid carcinomas, 39 genes between aneuploid endometrioid cancer and UPSC, and 76 genes between diploid endometrioid and aneuploid UPSC to be differentially expressed. Protein profiling identified AKR7A2 and ANXA2 to show translational alterations consistent with the transcriptional changes. The majority of differentially expressed genes and proteins belonged to identical molecular functions, foremost Cancer, Cell Death, and Cellular Assembly and Organization.

CONCLUSIONS

We conclude that the grade of genomic instability rather than the histopathological subtype correlates with specific gene and protein expression changes. The identified genes and proteins might be useful as molecular targets for improved diagnostic and therapeutic intervention and merit prospective validation.

Genomic instability and oncogene amplifications in colorectal adenomas predict recurrence and synchronous carcinoma

Individual colorectal adenomas have different propensities to progress to invasive disease. In this study, we explored whether these differences could be explained by gene copy number alterations. We evaluated 18 adenomas of patients without synchronous or subsequent carcinoma (6.5 years follow-up), 23 adenomas of carcinoma patients, and 6 related carcinomas. All samples were measured for their DNA ploidy status. Centromere probes for chromosomes 17 and 18, as well as gene-specific probes for SMAD7, EGFR, NCOA3, TP53, MYC, and RAB20 were assessed by multicolor fluorescence in situ hybridization. An increased genomic instability index of CEP17, SMAD7, and EGFR, as well as TP53 deletions and MYC amplifications defined adenomas of patients with synchronous carcinoma (P<0.05). Diploid NCOA3 signal counts were associated with longer adenoma recurrence-free surveillance (P=0.042). In addition, NCOA3, MYC, EGFR, and RAB20 amplifications, as well as TP53 deletions correlated with increased DNA stem line values and/or aneuploidy in adenomas (P<0.05). Furthermore, aberrations of NCOA3, MYC, and RAB20 were associated with histopathologically defined high-risk adenomas (P<0.05). RAB20 amplifications were also correlated with high-grade dysplastic adenomas (P=0.002). We conclude that genomic instability in colorectal adenomas is reflected by EGFR, MYC, NCOA3, and RAB20 amplifications that do correlate with histomorphological features and are indicative for adenoma recurrence and the presence of synchronous carcinomas.

Axillary lymph node metastasis and survival in breast cancer patients with concurrent cardio-cerebral-vascular disease

Objectives

Dissemination of tumour cells occurring both spontaneously or caused by diagnostic biopsy procedures is the most serious complication of solid malignancies. In the present work we focus on local tumour spread and how this complication of cancer disease can be counteracted.

Design

From a cohort of 864 breast cancer patients we selected those who died of their primary cancer and those who died because of a simultaneously existing cardio-cerebral-vascular disease (CCVD) and were exposed to anticoagulants.

Setting

The study was based on breast cancer patients diagnosed at Karolinska University Hospital during 1991 (n = 519) and 1997–1998 (n = 345).

Main outcome measures

Axillary lymph node metastasis (ALNM) and survival of breast cancer patients with concurrent CCVD.

Results

Breast cancer patients belonging to the group that died of CCVD showed ALNM at the time of tumour diagnosis in 27% of the cases compared with 68% diagnosed in the group that died of their breast cancer (p < 0.0001). Likewise we observed a highly significant (p < 0.0001) difference in mean survival time with an average of 102 months in the group of breast cancer patients who died of CCVD and an average of 61 months in the group who died of breast cancer.

Conclusion

The data presented herein indicate that breast cancer patients regularly involved in treatment with anticoagulants because of simultaneously existing CCVD develop ALNM significantly less frequently and have an increased average survival time compared with breast cancer patients not suffering from CCVD.

HDAC2 and TXNL1 distinguish aneuploid from diploid colorectal cancers

DNA aneuploidy has been identified as a prognostic factor for epithelial malignancies. Further understanding of the translation of DNA aneuploidy into protein expression will help to define novel biomarkers to improve therapies and prognosis. DNA ploidy was assessed by image cytometry. Comparison of gel-electrophoresis-based protein expression patterns of three diploid and four aneuploid colorectal cancer cell lines detected 64 ploidy-associated proteins. Proteins were identified by mass spectrometry and subjected to Ingenuity Pathway Analysis resulting in two overlapping high-ranked networks maintaining Cellular Assembly and Organization, Cell Cycle, and Cellular Growth and Proliferation. CAPZA1, TXNL1, and HDAC2 were significantly validated by Western blotting in cell lines and the latter two showed expression differences also in clinical samples using a tissue microarray of normal mucosa (n=19), diploid (n=31), and aneuploid (n=47) carcinomas. The results suggest that distinct protein expression patterns, affecting TXNL1 and HDAC2, distinguish aneuploid with poor prognosis from diploid colorectal cancers.

Differential expression of ANXA6, HSP27, PRDX2, NCF2, and TPM4 during uterine cervix carcinogenesis: diagnostic and prognostic value

Background:

Cytology-based diagnostics of squamous cervical cancer (SCC) precursor lesions is subjective and can be improved by objective markers.

Methods:

IHC-based analysis of ANXA6, HSP27, peroxiredoxin 2 (PRDX2), NCF2, and tropomyosin 4 (TPM4) during SCC carcinogenesis.

Results:

Expression of ANXA6, HSP27, PRDX2, and NCF2 in the cytoplasm of dysplastic cells increased from cervical intraepithelial neoplasia 2/3 (CIN2/3) to microinvasive cancer. Invasive SCC showed lower expression of TPM4 than CIN and normal epithelium. CIN2/3 with the highest sensitivity and specificity differed from normal epithelium by cytoplasmic expression of HSP27. Patients with cytoplasmic HSP27 expression in SCC deviating from that observed in normal epithelium had worse relapse-free (P=0.019) and overall (P=0.014) survival. Invasive SCC with the highest sensitivity and specificity differed from normal epithelium by expression of PRDX2 and TPM4 in the cytoplasm, from CIN2/3 by the expression of ANXA6 and TPM4 in the cytoplasm, and from microinvasive SCC by the expression of PRDX2 and ANXA6 in the cytoplasm. The number of sporadic ANXA6+ cells between the atypical cells increased from CIN2/3 to invasive SCC.

Conclusion:

Detection of expression changes of the proteins ANXA6, HSP27, PRDX2, NCF2, and TPM4 in SCC precursor lesions may aid current cytological and pathological diagnostics and evaluation of prognosis.

Prevention of tumour cell dissemination in diagnostic needle procedures

BACKGROUND

A side effect of diagnostic needle biopsies is the possibility to disseminate tumour cells into the needle track, which may cause concern in certain malignant tumour types.

METHODS

In order to prevent tumour cell dissemination we developed a technology that uses radiofrequency (RF) pulses to sterilise the needle track and denaturate tumour cells. To determine feasibility, we applied this technology to fine needle aspiration biopsy (FNAB) and used breast cancer as a model tumour. Routine FNAB was performed in 88 patients with adenocarcinoma and blood droplets passing the skin orifice were cytomorphologically analysed for the presence of tumour cells.

RESULTS

The analysis showed the presence of tumour cells in 65/88 cases (74%). When using an experimental anti-seeding device in a subset of patients viable tumour cells were found in 0/31 cases (P<0.001). In all 31 patients blood passing the skin orifice was sparse. No degrading effect on the cytological sample inside the needle was detected and pain caused by the RF pulses was comparable to that of the biopsy procedure itself.

CONCLUSION

The herein presented method has the potential to prevent the dissemination of viable tumour cells in the needle track and minimize bleeding without additional pain or degradation of the aspirate.

SELDI-TOF serum proteomics and colorectal cancer: a current overview

Surface enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS) is a widely used technology platform for diagnostic biomarker discovery in tissue, plasma and serum. High-throughput and simplicity of experimental procedures have allowed this technology to become an important research tool for biomarker discovery during the last years. This review provides an overview of SELDI-TOF functionality, its advantages and drawbacks and gives a current literature overview of colorectal cancer based serum biomarker detection. Further improvements in instrumentation sensitivity and labelling chemistries will enable detection of novel, tissue-leakage biomarkers in serum. However, major emphasis should be given on subsequent identification of differentially observed protein peaks detected by SELDI-TOF. Clinical validation in large patient cohorts will then allow transferring novel biomarkers into clinical use.

Multivariate meta-analysis of proteomics data from human prostate and colon tumours

Background

There is a vast need to find clinically applicable protein biomarkers as support in cancer diagnosis and tumour classification. In proteomics research, a number of methods can be used to obtain systemic information on protein and pathway level on cells and tissues. One fundamental tool in analysing protein expression has been two-dimensional gel electrophoresis (2DE). Several cancer 2DE studies have reported partially redundant lists of differently expressed proteins. To be able to further extract valuable information from existing 2DE data, the power of a multivariate meta-analysis will be evaluated in this work.

Results

We here demonstrate a multivariate meta-analysis of 2DE proteomics data from human prostate and colon tumours. We developed a bioinformatic workflow for identifying common patterns over two tumour types. This included dealing with pre-processing of data and handling of missing values followed by the development of a multivariate Partial Least Squares (PLS) model for prediction and variable selection. The variable selection was based on the variables performance in the PLS model in combination with stability in the validation. The PLS model development and variable selection was rigorously evaluated using a double cross-validation scheme. The most stable variables from a bootstrap validation gave a mean prediction success of 93% when predicting left out test sets on models discriminating between normal and tumour tissue, common for the two tumour types. The analysis conducted in this study identified 14 proteins with a common trend between the tumour types prostate and colon, i.e. the same expression profile between normal and tumour samples.

Conclusions

The workflow for meta-analysis developed in this study enabled the finding of a common protein profile for two malign tumour types, which was not possible to identify when analysing the data sets separately.