Smad7 Deficiency in Myeloid Cells Does Not Affect Liver Injury, Inflammation or Fibrosis after Chronic CCl4 Exposure in Mice.

Myeloid cells play an essential role in the maintenance of liver homeostasis, as well as the initiation and termination of innate and adaptive immune responses. In chronic hepatic inflammation, the production of transforming growth factor beta (TGF-ß) is pivotal for scarring and fibrosis induction and progression. TGF-ß signalling is tightly regulated via the Smad protein family. Smad7 acts as an inhibitor of the TGF-ß-signalling pathway, rendering cells that express high levels of it resistant to TGF-ß-dependent signal transduction. In hepatocytes, the absence of Smad7 promotes liver fibrosis. Here, we examine whether Smad7 expression in myeloid cells affects the extent of liver inflammation, injury and fibrosis induction during chronic liver inflammation. Using the well-established model of chronic carbon tetrachloride (CCl4)-mediated liver injury, we investigated the role of Smad7 in myeloid cells in LysM-Cre Smadfl/fl mice that harbour a myeloid-specific knock-down of Smad7. We found that the chronic application of CCl4 induces severe liver injury, with elevated serum alanine transaminase (ALT)/aspartate transaminase (AST) levels, centrilobular and periportal necrosis and immune-cell infiltration. However, the myeloid-specific knock-down of Smad7 did not influence these and other parameters in the CCl4-treated animals. In summary, our results suggest that, during long-term application of CCl4, Smad7 expression in myeloid cells and its potential effects on the TGF-ß-signalling pathway are dispensable for regulating the extent of chronic liver injury and inflammation.

Activating ERBB2/HER2 mutations indicate susceptibility to pan-HER inhibitors in Lynch and Lynch-like colorectal cancer.

OBJECTIVE: Microsatellite instability (MSI) is detected in approximately 15% of all colorectal cancers (CRC) and virtually in all cases with Lynch syndrome. The MSI phenotype is caused by dysfunctional mismatch repair (MMR) and leads to accumulation of DNA replication errors. Sporadic MSI CRC often harbours BRAF(V600E); however, no consistent data exist regarding targeted treatment approaches in BRAF(wt) MSI CRC. DESIGN: Mutations and quantitative MSI were analysed by deep sequencing in 196 formalin fixed paraffin embedded (FFPE) specimens comprising Lynch and Lynch-like CRCs from the German Hereditary Nonpolyposis Colorectal Cancer registry. Functional relevance of recurrent ERBB2/HER2 mutations was investigated in CRC cell lines using reversible and irreversible HER-targeting inhibitors, EGFR-directed antibody cetuximab, HER2-directed antibody trastuzumab and siRNA-mediated ERBB2/HER2 knockdown. RESULTS: Quantification of nucleotide loss in non-coding mononucleotide repeats distinguished microsatellite status with very high accuracy (area under curve=0.9998) and demonstrated progressive losses with deeper invasion of MMR-deficient colorectal neoplasms (p=0.008). Characterisation of BRAF(wt) MSI CRC revealed hot-spot mutations in well-known oncogenic drivers, including KRAS (38.7%), PIK3CA (36.5%), and ERBB2 (15.0%). L755S and V842I substitutions in ERBB2 were highly recurrent. Functional analyses in ERBB2-mutated MSI CRC cell lines revealed a differential response to HER-targeting compounds and superiority of irreversible pan-HER inhibitors. CONCLUSIONS: We developed a high-throughput deep sequencing approach for concomitant MSI and mutational analyses in FFPE specimens. We provided novel insights into clinically relevant alterations in MSI CRC and a rationale for targeting ERBB2/HER2 mutations in Lynch and Lynch-like CRC.

Mutational analysis of pulmonary tumours with neuroendocrine features using targeted massive parallel sequencing: a comparison of a neglected tumour group.

BACKGROUND: Lung cancer is the leading cause of cancer-related deaths worldwide. The typical and atypical carcinoid (TC and AC), the large-cell neuroendocrine carcinoma (LCNEC) and the small-cell lung cancers (SCLC) are subgroups of pulmonary tumours that show neuroendocrine differentiations. With the rising impact of molecular pathology in routine diagnostics the interest for reliable biomarkers, which can help to differentiate these subgroups and may enable a more personalised treatment of patients, grows. METHODS: A collective of 70 formalin-fixed, paraffin-embedded (FFPE) pulmonary neuroendocrine tumours (17 TCs, 17 ACs, 19 LCNECs and 17 SCLCs) was used to identify biomarkers by high-throughput sequencing. Using the Illumina TruSeq Amplicon-Cancer Panel on the MiSeq instrument, the samples were screened for alterations in 221 mutation hot spots of 48 tumour-relevant genes. RESULTS: After filtering >26 000 detected variants by applying strict algorithms, a total of 130 mutations were found in 29 genes and 49 patients. Mutations in JAK3, NRAS, RB1 and VHL1 were exclusively found in SCLCs, whereas the FGFR2 mutation was detected in LCNEC only. KIT, PTEN, HNF1A and SMO were altered in ACs. The SMAD4 mutation corresponded to the TC subtype. We prove that the frequency of mutations increased with the malignancy of tumour type. Interestingly, four out of five ATM-mutated patients showed an additional alteration in TP53, which was by far the most frequently altered gene (28 out of 130; 22%). We found correlations between tumour type and IASLC grade for ATM- (P=0.022; P=0.008) and TP53-mutated patients (P<0.001). Both mutated genes were also associated with lymph node invasion and distant metastasis (P⩽0.005). Furthermore, PIK3CA-mutated patients with high-grade tumours showed a reduced overall survival (P=0.040) and the mutation frequency of APC and ATM in high-grade neuroendocrine lung cancer patients was associated with progression-free survival (PFS) (P=0.020). CONCLUSIONS: The implementation of high-throughput sequencing for the analysis of the neuroendocrine lung tumours has revealed that, even if these tumours encompass several subtypes with varying clinical aggressiveness, they share a number of molecular features. An improved understanding of the biology of neuroendocrine tumours will offer the opportunity for novel approaches in clinical management, resulting in a better prognosis and prediction of therapeutic response.

Identification of specific nuclear structural protein alterations in human breast cancer.

Breast cancer is the most commonly diagnosed type of cancer and a major cause of death in women. Reliable biomarkers are urgently needed to improve early detection or to provide evidence of the prognosis for each individual patient through expression levels in tumor tissue or body fluids. This proteomic analysis focused on the nuclear structure of human breast cancer tissue, which has been shown to be a promising tool for cancer biomarker development. The nuclear matrix composition of human breast cancer (n = 14), benign controls (n = 2), and healthy controls (n = 2) was analyzed by high-resolution two-dimensional gel electrophoresis and mass spectrometry. Validation studies were performed in an individual sample set consisting of additional breast cancer tissues (n = 3) and additional healthy control tissues (n = 2) by one-dimensional immunoblot. In this setting, we identified five proteins that were upregulated in human breast cancer tissue, but absent in the healthy and benign controls (P < 0.001). These spots were also present in the investigated human breast cancer cell lines, but absent in the MCF10a cell line, which represents normal human epithelial breast cells. Two of the breast cancer-specific proteins have been confirmed to be calponin h2 and calmodulin-like protein 5 by one-dimensional immunoblot. This is the first study demonstrating the expression of both proteins in human breast cancer tissue. Further studies are required to investigate the potential role of these proteins as biomarkers for early diagnosis or prognosis in human breast cancer.

Androgen receptor coactivators lysine-specific histone demethylase 1 and four and a half LIM domain protein 2 predict risk of prostate cancer recurrence.

Prostate cancer biology varies from locally confined tumors with low risk for relapse to tumors with high risk for progression even after radical prostatectomy. Currently, there are no reliable biomarkers to predict tumor relapse and poor clinical outcome. In this study, we correlated expression patterns of the androgen receptor (AR) coactivators lysine-specific histone demethylase 1 (LSD1) and four and a half LIM-domain protein 2 (FHL2), AR, Gleason score, Gleason grade, and p53 expression in clinically organ confined prostate cancers with relapse after radical prostatectomy. Our data reveal that high levels of LSD1, nuclear expression of the FHL2 coactivator, high Gleason score and grade, and very strong staining of nuclear p53 correlate significantly with relapse during follow-up. No correlation exists with relapse and the expression of AR and cytoplasmic expression of FHL2. To confirm these data, we did quantitative reverse transcription-PCR and Western blot analyses in a subset of tumor specimens. Consistently, both LSD1 mRNA and protein levels were significantly up-regulated in high-risk tumors. We previously identified LSD1 and FHL2 as nuclear cofactors interacting specifically with the AR in prostate cells and showed that both stimulate androgen-dependent gene transcription. Our present study suggests that LSD1 and nuclear FHL2 may serve as novel biomarkers predictive for prostate cancer with aggressive biology and point to a role of LSD1 and FHL2 in constitutive activation of AR-mediated growth signals.

Gene expression profiling identifies new biological markers of neoplastic germ cells.

BACKGROUND: There is only limited knowledge about gene expression in human testicular germ cell tumors of adolescents and adults (TGCTs), and, in particular in its preinvasive stage intratubular germ cell neoplasia unclassified (IGCNU). MATERIALS AND METHODS: Global gene expression was studied in 10 invasive human testicular germ cell tumors (TGCTs), 7 intratubular germ cell neoplasia unclassified (IGCNU) and 3 normal testes. The pattern of expression of several genes was studied by immunohistochemistry on tissue microarrays containing 126 TGCTs, IGCNU, normal testes and in 5 fetal testes. RESULTS: RAS-related genes (KRAS2, RALA, RAB39B) and various core markers of embryonic stem cells were overexpressed in IGCNU compared to normal testes. CD9, PODXL and centromere-specific histone-H3-like protein CENPA were specifically identified in IGCNU, seminomas, embryonal carcinomas and in fetal gonocytes. Embryonic stem cell regulator SOX2 and downstream targets of the Nodal pathway were up-regulated in embryonal carcinoma only but not in IGCNU/seminoma. Preliminary data revealed that the expression profile of IGCNU is dependent on the histology of the adjacent invasive tumor. CONCLUSION: Our study determined the genes involved in early pathogenetic events of neoplastic germ cell formation, provided new insights into genetic pathways driving the transition of embryonal carcinoma and seminoma from IGCNU and identified new biomarkers of neoplastic germ cells such as CD9, CENPA and PODXL.

Genome-wide expression profiling reveals new insights into pathogenesis and progression of testicular germ cell tumors.

Testicular germ cell tumors (GCT) are the most frequent malignancy in young adults and arise from intratubular germ cell neoplasia undetermined (IGCNU, also referred to as carcinoma in situ, CIS). To determine the transcriptional programs involved in the transition from normal germ cells to GCT, and to further elucidate genetic differences between seminomas and non-seminomatous GCT the global expression profile of 12 neoplastic and 3 normal testicular tissues were investigated by whole genome cDNA microarrays. Transcriptional differences between seminomas and embryonal carcinomas were determined and gene signatures characterizing histological subtypes of GCT were identified. The most significant difference between seminomas and embryonal carcinomas was the expression of spermatogenesis-associated genes (PRAME, MAGEA4, SPAG1, HPX) in seminomas and regulatory genes DNMT3B and SOX2 as well as small molecular weight keratins KRT8, KRT18 in embryonal carcinomas. The expression of several selected genes (CK18, MAGE-A4, SOX2, DNMT3B, CD30, KIT) was studied by immunohistochemistry or reverse transcriptase-polymerase chain reaction (RT-PCR) in a large collective of GCT. In summary, our data identified tumor type-specific gene signatures of GCT and provided new insights into genetic pathways driving the transition to seminomas and embryonal carcinomas from their respective precursor lesions.

Comprehensive Analysis of Disease-Related Genes in Chronic Lymphocytic Leukemia by Multiplex PCR-Based Next Generation Sequencing.

BACKGROUND: High resolution molecular studies have demonstrated that the clonal acquisition of gene mutations is an important mechanism that may promote rapid disease progression and drug resistance in chronic lymphocytic leukemia (CLL). Therefore, the early and sensitive detection of such mutations is an important prerequisite for future predictive CLL diagnostics in the clinical setting. MATERIAL & METHODS: Here, we describe a novel, target-specific next generation sequencing (NGS) approach, which combines multiplex PCR-based target enrichment and library generation with ultra-deep high-throughput parallel sequencing using a MiSeq platform. We designed a CLL specific target panel, covering hotspots or complete coding regions of 15 genes known to be recurrently mutated and/or related to B-cell receptor signaling. RESULTS: High-throughput sequencing was performed using as little as 40 ng of peripheral blood B-cell DNA from 136 CLL patients and a dilution series of two ATM- or TP53-mutated cell lines, the latter of which demonstrated a limit of mutation detection below 5%. Using a stringent functional assessment algorithm, 102 mutations in 8 genes were identified in CLL patients, including hotspot regions of TP53, SF3B1, NOTCH1, ATM, XPO1, MYD88, DDX3X and the B-cell receptor signaling regulator PTPN6. The presence of mutations was significantly associated with an advanced disease status und molecular markers of an inferior prognosis, such as an unmutated IGHV mutation status or positivity for ZAP70 by flow cytometry. CONCLUSION: In summary, targeted sequencing using an amplicon based library technology allows a resource-efficient and sensitive mutation analysis for diagnostic or exploratory purposes and facilitates molecular subtyping of patient sets with adverse prognosis.

Marked clinical and histologic improvement in a patient with type-1 Gaucher's disease following long-term glucocerebroside substitution. A case report and review of current diagnosis and management.

Type-1 Gaucher's disease represents the most common lysosomal storage disorder. With the introduction of enzyme replacement therapy, many of the clinical manifestations can be controlled. The functional deficiency of the lysosomal beta-glucocerebrosidase leads to deposition of glycosylceramide in the liver, spleen, and bone marrow. We report the clinical and pathologic presentation of a patient with a florid type-1 Gaucher's disease who received long-term enzyme replacement therapy, which led to marked clinical improvement. A repeat liver biopsy performed at the time of a cholecystectomy several years after initiation of enzyme replacement therapy revealed complete resolution of Gaucher cells.

Comparison of pre-analytical FFPE sample preparation methods and their impact on massively parallel sequencing in routine diagnostics.

Over the last years, massively parallel sequencing has rapidly evolved and has now transitioned into molecular pathology routine laboratories. It is an attractive platform for analysing multiple genes at the same time with very little input material. Therefore, the need for high quality DNA obtained from automated DNA extraction systems has increased, especially to those laboratories which are dealing with formalin-fixed paraffin-embedded (FFPE) material and high sample throughput. This study evaluated five automated FFPE DNA extraction systems as well as five DNA quantification systems using the three most common techniques, UV spectrophotometry, fluorescent dye-based quantification and quantitative PCR, on 26 FFPE tissue samples. Additionally, the effects on downstream applications were analysed to find the most suitable pre-analytical methods for massively parallel sequencing in routine diagnostics. The results revealed that the Maxwell 16 from Promega (Mannheim, Germany) seems to be the superior system for DNA extraction from FFPE material. The extracts had a 1.3-24.6-fold higher DNA concentration in comparison to the other extraction systems, a higher quality and were most suitable for downstream applications. The comparison of the five quantification methods showed intermethod variations but all methods could be used to estimate the right amount for PCR amplification and for massively parallel sequencing. Interestingly, the best results in massively parallel sequencing were obtained with a DNA input of 15 ng determined by the NanoDrop 2000c spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). No difference could be detected in mutation analysis based on the results of the quantification methods. These findings emphasise, that it is particularly important to choose the most reliable and constant DNA extraction system, especially when using small biopsies and low elution volumes, and that all common DNA quantification techniques can be used for downstream applications like massively parallel sequencing.

Regulation of protein tyrosine kinases in tumour cells by the transcription factor Ets-1.

Tyrosine phosphorylation is one of the key covalent modifications that occurs in multicellular organisms as a result of intercellular communication. The family of tyrosine kinases (PTKs) are responsible for part of the cellular phosphorylation and are involved in a broad variety of cellular functions including differentiation, proliferation, migration, invasion, angiogenesis and survival under physiological as well as pathological conditions. Aberration in PTK signalling occurs in inflammatory diseases and diabetes, and aberrant expression can lead to benign proliferative conditions as well as to various forms of cancer. Indeed, more than 70% of the known oncogenes and proto-oncogenes involved in cancer code for PTKs. Therefore, these enzymes are now used as targets in the treatment of different tumours. Ets-1 is a transcription factor expressed in a number of human malignancies with demonstrated roles within both neoplastic cells and tumour stroma. These roles include stimulation of tumour cell proliferation and invasion as well as tumour angiogenesis. Database searches have revealed that ETS binding sites are present in several promoters of PTK-encoding genes. We investigated the role of Ets-1 in transcriptional regulation of a panel of 89 PTKs in epithelial HeLa tumour cells. In this study, HeLa cells stably overexpressing and underexpressing Ets-1 were used for real-time PCR analysis of all known human PTKs. The results suggest that Ets-1 is an essential transcription factor that cannot be substituted by other members of the ETS family. Transcription of most PTKs was found to be increased by Ets-1. In contrast Ets-1 seems to act as a transcriptional repressor of other PTKs. The data presented here underscore the importance of Ets-1 in tumour development and progression.

Saturation biopsy improves preoperative Gleason scoring of prostate cancer.

We evaluated the differences between conventional needle biopsy (CB) and saturation biopsy (SB) techniques with regard to the prediction of Gleason score, tumor stage, and insignificant prostate cancer. Data from a total number of 240 patients were analyzed. The main group, consisting of 185 patients, was diagnosed according to a saturation prostate needle biopsy protocol (SB), by which more than 12 cores were taken per biopsy. The control group was diagnosed using CB, by which 12 or less than 12 cores were taken per biopsy (n=55). In the main group, the Gleason score of the biopsy was confirmed in 19.5%, in the control group in 23.5% according to the prostatectomy specimen (p=0.50). Upgrading after the operation was found in 56.7% in the main group and in 60% in the control group (p=0.24). Downgrading after the operation was found in 23.9% in the main group and in 16.3% in the control group (p=0.24). If the Gleason score of the postoperative specimens differed by only one point from the biopsy, we considered this a minor deviation. In the main group, 59% of the carcinomas were preoperatively classified correctly or revealed minor deviation in Gleason scores. In contrast, only 47% of the carcinomas in the control group were assessed correctly or with minor deviation in Gleason scores. Thus, the main group demonstrated a better rate of preoperative prediction in tumor grading assessed by Gleason score (p=0.05). In addition, the Gleason scores of both protocols were assigned to three groups (Gleason <7; Gleason 7; Gleason >7), and the group changes from the biopsy to the prostatectomy specimen were found to be significantly more frequent in the CB group (p=0.04). There was no significant difference between the two types of biopsy techniques regarding tumor stage or the detection of insignificant carcinomas. The advantage of the extensive prostate needle biopsy technique (SB) is a better preoperative prediction of the Gleason score as well as the risk groups with Gleason scores <7, equal to 7, or >7. Both techniques fail to detect insignificant prostate cancer.

Uterine tumor resembling an ovarian sex cord tumor associated with metastasis.

Uterine tumors resembling ovarian sex-cord tumors (UTROSCT) are very rare, usually benign uterine tumors, and are probably derived from uterine mesenchymal stem cells. In this case report, a unique case of a malignant UTROSCT is described. Four years after a diagnosis of UTROSCT of the uterine corpus, the patient developed obstructive ileus due to a large infiltrating tumor within the small bowel with the same morphology and expression pattern as the previously diagnosed UTROSCT. In addition, 2 benign gastrointestinal stromal tumors were detected in the same patient. This case indicates that although the majority of UTROSCT are benign tumors, some of them might undergo malignant transformation and have a metastatic potency.

Orofaciodigital syndrome type IV (Mohr-Majewski syndrome): report of a family with two affected siblings.

We report on sibling fetuses with orofaciodigital syndrome (OFDS) type IV (Mohr-Majewski syndrome). The 1st was a 13-week-old fetus with hypertelorism; a median cleft defect of the upper lip, soft palate, and uvula; a polypoid lower lip and multiple frenula of the tongue adherent to the mandible; a congenital heart defect; pre- and postaxial polydactyly of the upper and preaxial polydactyly of the lower limbs; and an intersex genitalia. However, the shortening of both arms and forearms was particularly striking, with shortening of the ulna and ulnar deviation of both hands. The 2nd fetus was of the same parents, was 11 weeks old, and presented with a similar spectrum of malformations. The features of both fetuses showed a transitional phenotype between the OFDS type II (Mohr syndrome) and the short rib-polydactyly syndrome type II (Majewski syndrome), thus extending the known spectrum of the OFDS type IV.