Maveropepimut-S, a DPX-based immune-educating therapy, shows promising and durable clinical benefit in patients with recurrent ovarian cancer, a phase 2 trial

PURPOSE

Patients with platinum resistant ovarian cancer (OvCa) respond poorly to existing therapies. Hence there is a need for more effective treatments.

METHODS

The DeCidE1 trial is a multicenter, randomized, open-label, single-arm phase 2 study to evaluate the safety and effectiveness of maveropepimut-S (MVP-S) with cyclophosphamide (CPA) in patients with recurrent ovarian cancer. Median follow-up for evaluable subjects was 4.4 months. Data were collected from March 2019 to June 2021. Subjects received two injections of 0.25 mL MVP-S 3 weeks apart, followed by one 0.1 mL doses, every 8 weeks up to progression. Oral CPA, 50 mg twice daily, was administered in repeating weekly on and off cycles.

RESULTS

Twenty-two patients were enrolled. Median age was 58 years (38-78 years). Among the evaluable population, ORR was 21% (90% CI, 7.5%-41.9%), with a DCR of 63% (90% CI, 41.8%-81.3%), including 4 (21%) patients with partial responses, 8 (42%) stable disease, and 7 (37%) progressive disease. The ORRs were consistent across subgroups based on platinum-sensitivity, and DCR was higher in the platinum-resistant subpopulation. Four stable disease patients maintained clinical benefit up to 25 months. Most treatment related adverse events (TRAEs) were grade 1 and 2 (87% of unique events). Most common AEs were injection site reactions. Eight subjects reported grade 3 and no grade 4 AEs. Survivin-specific T cell responses were observed in treated patients with clinical benefit.

CONCLUSIONS

MVP-S with intermittent low-dose CPA is well-tolerated, with clinical benefit for patients with recurrent OvCa. Observed responses are irrespective of the platinum status.

Reverse Translating Molecular Determinants of Anti-Programmed Death 1 Immunotherapy Response in Mouse Syngeneic Tumor Models

Targeting the programmed death 1/programmed death ligand 1 (PD-1/PD-L1) pathway with immunotherapy has revolutionized the treatment of many cancers. Somatic tumor mutational burden (TMB) and T-cell-inflamed gene expression profile (GEP) are clinically validated pan-tumor genomic biomarkers that can predict responsiveness to anti-PD-1/PD-L1 monotherapy in many tumor types. We analyzed the association between these biomarkers and the efficacy of PD-1 inhibitor in 11 commonly used preclinical syngeneic tumor mouse models using murinized rat anti-mouse PD-1 DX400 antibody muDX400, a surrogate for pembrolizumab. Response to muDX400 treatment was broadly classified into three categories: highly responsive, partially responsive, and intrinsically resistant to therapy. Molecular and cellular profiling validated differences in immune cell infiltration and activation in the tumor microenvironment of muDX400-responsive tumors. Baseline and on-treatment genomic analysis showed an association between TMB, murine T-cell-inflamed gene expression profile (murine-GEP), and response to muDX400 treatment. We extended our analysis to investigate a canonical set of cancer and immune biology-related gene signatures, including signatures of angiogenesis, myeloid-derived suppressor cells, and stromal/epithelial-to-mesenchymal transition/TGFβ biology previously shown to be inversely associated with the clinical efficacy of immune checkpoint blockade. Finally, we evaluated the association between murine-GEP and preclinical efficacy with standard-of-care chemotherapy or antiangiogenic agents that previously demonstrated promising clinical activity, in combination with muDX400. Our profiling studies begin to elucidate the underlying biological mechanisms of response and resistance to PD-1/PD-L1 blockade represented by these models, thereby providing insight into which models are most appropriate for the evaluation of orthogonal combination strategies.

Abstract 1685: Genomics based studies of gastric tumors identify ICOS as potential target for therapeutic intervention

JTX-2011, an ICOS agonist antibody, is the first clinical program to emerge from Jounce's Translational Science Platform, which couples the choice of target mechanism to potential predictive biomarkers of response. ICOS (Inducible T cell CO-Stimulator), a co-stimulatory molecule expressed primarily on T lymphocytes, was prioritized as a target based on preclinical and clinical data suggesting that it plays an important role in the immune response to cancer. Fundamental data from our preclinical studies shows that tumor reduction occurs only in animals when a certain percentage of ICOS positive immune cells are resident within the tumor or in combination with a PD-1 inhibitor. Thus ICOS expression is a key element of our biomarker-driven approach in the ICONIC clinical trial. Based on this biomarker approach, we have identified gastric cancer as a cancer of potential interest for an ICOS-targeted immunotherapy approach.

Gastric adenocarcinoma was identified as a tumor of interest based on the integrated analysis of RNA, DNA and clinical data from the Cancer Genome Atlas (TCGA). This analysis was performed within stomach adenocarcinoma (STAD) to understand the context in which ICOS is expressed. ICOS levels were correlated to gene signatures of immune infiltrate as well as other clinical attributes and molecular markers. ICOS and PD-L1 levels were assessed by IHC in human tumor samples and in biopsies from ICONIC participants.IHC and RNA analyses reveals a dynamic range of ICOS expression across gastric adenocarcinoma tumors, with high prevalence in both EBV+ and MSI-H tumors as well as a subset of EBV-/MSS tumors. While there is a correlation between ICOS, ICOS signature, PD-L1 and IFNγ signatures, RNA analysis indicates that a subpopulation of gastric tumors with lower levels of PD-L1 expression may be ICOS positive. Integrative analysis of tumors identifies gastric cancer as an attractive indication for exploration of JTX-2011 plus a PD-1 inhibitor based on the relatively high frequency of ICOS expression within this tumor type. Since ICOS expression has a dynamic range of expression, an ICOS IHC biomarker is being used to enrich for patients in a gastric cancer cohort, as well as other tumor-specific cohorts in the Phase 2 portion of the ICONIC clinical study.

Citation Format: Heather A. Hirsch, Jason Reeves, Tong Zi, Alexander Needham, Edward Stack, David Lee, Emma Lees, Deborah A. Law, Elizabeth Trehu. Genomics based studies of gastric tumors identify ICOS as potential target for therapeutic intervention [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 1685.

Abstract 1307: Assessment of gene expression in peripheral blood from patients with advanced melanoma using RNA-seq before and after treatment with anti-PD-1 therapy with pembrolizumab (MK-3475)

Pembrolizumab (MK-3475) is a humanized monoclonal IgG4 antibody against programmed death receptor 1 (PD-1) that is currently being studied in clinical trials across more than 30 types of cancer. Gene expression profiling was used to explore a less invasive method for gaining new insights into the pembrolizumab mechanism of action and to assess the potential for blood-based predictive biomarkers. RNA-seq data were obtained from the whole blood of 44 patients with advanced melanoma enrolled in the phase 1 KEYNOTE-001 clinical study before and after the first cycle of treatment with pembrolizumab. Objective response rates (ORR) were assessed per RECIST v1.1 by independent central review. The pembrolizumab dose and treatment schedule varied among the patients studied and included 10 mg/kg given once every 3 weeks (Q3W) (n = 21), 10 mg/kg Q2W (n = 12), and 2 mg/kg Q3W (n = 11). Among the 44 patients with melanoma included in the analysis, 75% received previous ipilimumab treatment. The ORR was 32%. Significant posttreatment changes in gene expression were confirmed for the target, PD-1, and its key ligand, programmed death ligand 1 (PD-L1). Changes in PD-1 and PD-L1 gene expression did not, however, show a significant association with ORR. Statistically significant posttreatment changes for an interferon-gamma (IFNG)-related 10-gene signature were observed (P < 0.002, upregulated in 70% of patients), and these changes were also associated with improved clinical outcome in terms of ORR (P = 0.042) and progression-free survival (P = 0.010). There appeared to be a possible association between IFNG gene signature posttreatment changes in blood in tumors with higher PD-L1 expression at baseline. There were no clear differences between posttreatment changes in the IFNG gene signature according to previous ipilimumab treatment. Baseline blood expression levels for PD-1, PD-L1, and the IFNG 10-gene signature were not found to be associated with clinical outcome. Additional post hoc analyses of baseline expression in combination with pathway analysis showed that the more highly ranked genes were linked to oxidative phosphorylation, suggesting that for patients whose tumors are not responding to pembrolizumab, their T cells may not be engaged with glycolysis, which is important for the transcriptional regulation of IFNG. The observation that nonresponders showed a lack of ability to induce activation of IFNG signaling suggests a possible link to defective T-cell effector function and may provide a means by which to monitor patient response to anti-PD-1 therapy.

Citation Format: Mark D. Ayers, Michael Nebozhyn, Heather A. Hirsch, Razvan Cristescu, Erin E. Murphy, S. Peter Kang, Scot W. Ebbinghaus, Terrill K. McClanahan, Andrey Loboda, Jared K. Lunceford. Assessment of gene expression in peripheral blood from patients with advanced melanoma using RNA-seq before and after treatment with anti-PD-1 therapy with pembrolizumab (MK-3475). [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1307. doi:10.1158/1538-7445.AM2015-1307

Abstract 256: Identification of additional cancers likely to respond to anti-PD-1 therapy (pembrolizumab): Evaluation of PD-L1 expression in a large molecular tumor profiling gene expression database

Increased PD-L1 expression has been associated with clinical activity of anti-PD-1/PD-L1 therapies in both melanoma and non-small cell lung cancer (NSCLC). Our objective was to identify other cancers that show increased PD-L1 expression in order to target them for treatment with the PD-1 inhibitor pembrolizumab (MK-3475). A collaboration between Merck and the Moffitt Cancer Center was previously established to build a molecular profiling database of >16,000 primary and >3000 metastatic tumors representing 25 different cancers. All tumor samples were profiled on a standardized platform (Affymetrix-Merck Custom GeneChip). For each profiled sample, the PD-L1 cutpoint determined for positivity was defined as the Affymetrix pan-cancer 75th percentile of PD-L1 probes mean. This cutpoint was projected for each specific tumor type and percentages of tumors with PD-L1 above the cutpoint were determined. Cancer indications were rank ordered from highest to lowest percentage of PD-L1 positivity. The analysis identified NSCLC (42% PD-L1+) and melanoma (41% PD-L1+) among the top indications for which single-agent clinical activity of anti-PD1/PD-L1 therapies has been reported. At the bottom of the rankings were prostate cancer (14% PD-L1+) and pancreatic cancer (4% PD-L1+), indications for which limited clinical activity had been reported. This observation confirmed that ranking tumor types by PD-L1 expression across the profiling database could be used to identify other cancers that may respond to anti-PD-1 therapy. Of interest were the tumor types with high PD-L1 expression for which no clinical studies evaluating an anti-PD-1/PD-L1 agent had been initiated. Among the indications with high PD-L1 expression were head and neck (59% PD-L1+), urothelial (42% PD-L1+), and triple-negative (TN) breast (29% PD-L1+) cancer; these indications were chosen for evaluation with pembrolizumab in the KEYNOTE-012 study. By accessing cohorts of Asian patients with lung, liver, and gastric cancer and use of similar gene expression microarray profiling, we were able to extrapolate the PD-L1 rankings for these cancers; this resulted in the addition of gastric cancer to KEYNOTE-012. Recently, clinical results from KEYNOTE-012 have shown strong clinical activity for pembrolizumab in all 4 selected indications: head and neck, 20% ORR; urothelial, 21% ORR; TN breast, 18% ORR; and gastric, 31% ORR. The strategy of using a tumor profiling gene expression database for evaluation of PD-L1 expression enabled rapid expansion of pembrolizumab development into indications for which the likelihood of demonstrating clinical activity was high. In turn, this should help accelerate the approval of pembrolizumab for additional indications and, ultimately, provide help to patients suffering from cancer.

Citation Format: Mark D. Ayers, Michael Nebozhyn, Razvan Cristescu, Terrill K. McClanahan, Heather A. Hirsch, Jonathan D. Cheng, Andrey Loboda. Identification of additional cancers likely to respond to anti-PD-1 therapy (pembrolizumab): Evaluation of PD-L1 expression in a large molecular tumor profiling gene expression database. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 256. doi:10.1158/1538-7445.AM2015-256

Preclinical evaluation of the WEE1 inhibitor MK-1775 as single-agent anticancer therapy

Inhibition of the DNA damage checkpoint kinase WEE1 potentiates genotoxic chemotherapies by abrogating cell-cycle arrest and proper DNA repair. However, WEE1 is also essential for unperturbed cell division in the absence of extrinsic insult. Here, we investigate the anticancer potential of a WEE1 inhibitor, independent of chemotherapy, and explore a possible cellular context underlying sensitivity to WEE1 inhibition. We show that MK-1775, a potent and selective ATP-competitive inhibitor of WEE1, is cytotoxic across a broad panel of tumor cell lines and induces DNA double-strand breaks. MK-1775-induced DNA damage occurs without added chemotherapy or radiation in S-phase cells and relies on active DNA replication. At tolerated doses, MK-1775 treatment leads to xenograft tumor growth inhibition or regression. To begin addressing potential response markers for MK-1775 monotherapy, we focused on PKMYT1, a kinase functionally related to WEE1. Knockdown of PKMYT1 lowers the EC(50) of MK-1775 by five-fold but has no effect on the cell-based response to other cytotoxic drugs. In addition, knockdown of PKMYT1 increases markers of DNA damage, γH2AX and pCHK1(S345), induced by MK-1775. In a post hoc analysis of 305 cell lines treated with MK-1775, we found that expression of PKMYT1 was below average in 73% of the 33 most sensitive cell lines. Our findings provide rationale for WEE1 inhibition as a potent anticancer therapy independent of a genotoxic partner and suggest that low PKMYT1 expression could serve as an enrichment biomarker for MK-1775 sensitivity.

Metformin decreases the dose of chemotherapy for prolonging tumor remission in mouse xenografts involving multiple cancer cell types

Metformin, the first-line drug for treating diabetes, selectively kills the chemotherapy resistant subpopulation of cancer stem cells (CSC) in genetically distinct types of breast cancer cell lines. In mouse xenografts, injection of metformin and the chemotherapeutic drug doxorubicin near the tumor is more effective than either drug alone in blocking tumor growth and preventing relapse. Here, we show that metformin is equally effective when given orally together with paclitaxel, carboplatin, and doxorubicin, indicating that metformin works together with a variety of standard chemotherapeutic agents. In addition, metformin has comparable effects on tumor regression and preventing relapse when combined with a four-fold reduced dose of doxorubicin that is not effective as a monotherapy. Finally, the combination of metformin and doxorubicin prevents relapse in xenografts generated with prostate and lung cancer cell lines. These observations provide further evidence for the CSC hypothesis for cancer relapse, an experimental rationale for using metformin as part of combinatorial therapy in a variety of clinical settings, and for reducing the chemotherapy dose in cancer patients.

Loss of miR-200 inhibition of Suz12 leads to polycomb-mediated repression required for the formation and maintenance of cancer stem cells

In an inducible oncogenesis model, the miR-200 family is inhibited during CSC formation but not transformation, and inhibition of miR-200b increases CSC formation. Interestingly, miR-200b directly targets Suz12, a subunit of a polycomb repressor complex (PRC2). Loss of miR-200 during CSC formation increases Suz12 expression, Suz12 binding, H3-K27 trimethylation, and Polycomb-mediated repression of the E-cadherin gene. miR-200b expression or Suz12 depletion blocks the formation and maintenance of mammospheres, and in combination with chemotherapy suppresses tumor growth and prolongs remission in mouse xenografts. Conversely, ectopic expression of Suz12 in transformed cells is sufficient to generate CSCs. The miR-200b-Suz12-cadherin pathway is important for CSC growth and invasive ability in genetically distinct breast cancer cells, and its transcriptional signature is observed in metastatic breast tumors. The interaction between miR-200 and Suz12 is highly conserved, suggesting that it represents an ancient regulatory mechanism to control the growth and function of stem cells.

STAT3 activation of miR-21 and miR-181b-1 via PTEN and CYLD are part of the epigenetic switch linking inflammation to cancer

A transient inflammatory signal can initiate an epigenetic switch from nontransformed to cancer cells via a positive feedback loop involving NF-kappaB, Lin28, let-7, and IL-6. We identify differentially regulated microRNAs important for this switch and putative transcription factor binding sites in their promoters. STAT3, a transcription factor activated by IL-6, directly activates miR-21 and miR-181b-1. Remarkably, transient expression of either microRNA induces the epigenetic switch. MiR-21 and miR-181b-1, respectively, inhibit PTEN and CYLD tumor suppressors, leading to increased NF-kappaB activity required to maintain the transformed state. These STAT3-mediated regulatory circuits are required for the transformed state in diverse cell lines and tumor growth in xenografts, and their transcriptional signatures are observed in colon adenocarcinomas. Thus, STAT3 is not only a downstream target of IL-6 but, with miR-21, miR-181b-1, PTEN, and CYLD, is part of the positive feedback loop that underlies the epigenetic switch that links inflammation to cancer.

A transcriptional signature and common gene networks link cancer with lipid metabolism and diverse human diseases

Transcriptional profiling of two isogenic models of transformation identifies a gene signature linking cancer with inflammatory and metabolic diseases. In accord with this common transcriptional program, many drugs used for treatment of diabetes and cardiovascular diseases inhibit transformation and tumor growth. Unexpectedly, lipid metabolism genes are important for transformation and are upregulated in cancer tissues. As in atherosclerosis, oxidized LDL and its receptor OLR1 activate the inflammatory pathway through NF-kappaB, leading to transformation. OLR1 is important for maintaining the transformed state in developmentally diverse cancer cell lines and for tumor growth, suggesting a molecular connection between cancer and atherosclerosis. We suggest that the interplay between this common transcriptional program and cell-type-specific factors gives rise to phenotypically disparate human diseases.

An epigenetic switch involving NF-kappaB, Lin28, Let-7 MicroRNA, and IL6 links inflammation to cell transformation

Inflammation is linked clinically and epidemiologically to cancer, and NF-kappaB appears to play a causative role, but the mechanisms are poorly understood. We show that transient activation of Src oncoprotein can mediate an epigenetic switch from immortalized breast cells to a stably transformed line that forms self-renewing mammospheres that contain cancer stem cells. Src activation triggers an inflammatory response mediated by NF-kappaB that directly activates Lin28 transcription and rapidly reduces let-7 microRNA levels. Let-7 directly inhibits IL6 expression, resulting in higher levels of IL6 than achieved by NF-kappaB activation. IL6-mediated activation of the STAT3 transcription factor is necessary for transformation, and IL6 activates NF-kappaB, thereby completing a positive feedback loop. This regulatory circuit operates in other cancer cells lines, and its transcriptional signature is found in human cancer tissues. Thus, inflammation activates a positive feedback loop that maintains the epigenetic transformed state for many generations in the absence of the inducing signal.

Metformin selectively targets cancer stem cells, and acts together with chemotherapy to block tumor growth and prolong remission

The cancer stem cell hypothesis suggests that, unlike most cancer cells within a tumor, cancer stem cells resist chemotherapeutic drugs and can regenerate the various cell types in the tumor, thereby causing relapse of the disease. Thus, drugs that selectively target cancer stem cells offer great promise for cancer treatment, particularly in combination with chemotherapy. Here, we show that low doses of metformin, a standard drug for diabetes, inhibits cellular transformation and selectively kills cancer stem cells in four genetically different types of breast cancer. The combination of metformin and a well-defined chemotherapeutic agent, doxorubicin, kills both cancer stem cells and non-stem cancer cells in culture. Furthermore, this combinatorial therapy reduces tumor mass and prevents relapse much more effectively than either drug alone in a xenograft mouse model. Mice seem to remain tumor-free for at least 2 months after combinatorial therapy with metformin and doxorubicin is ended. These results provide further evidence supporting the cancer stem cell hypothesis, and they provide a rationale and experimental basis for using the combination of metformin and chemotherapeutic drugs to improve treatment of patients with breast (and possibly other) cancers.

Zur Wirksamkeit der perioperativen Antibiotikaprophylaxe bei Hysterektomien und abdominalen Schnittentbindungen

All controlled studies which were available by computer search from the literature were evaluated regarding the efficiency of preventive antibiotics for post-operative infections following hysterectomies and Cesarian sections. All controlled studies were evaluated by identical criteria. In 41 out of 46 studies (89.1%) on vaginal hysterectomies, febrile morbidity showed a significant decrease. In abdominal hysterectomies, 15 of 26 studies (57.7%) and in Cesarian sections 47 of 53 studies (88.7%) showed a significant decrease. Following vaginal hysterectomies and Cesarian sections, the preventive antibiotics decreased the febrile morbidity by 26 or 26.9 percentage points and pelvic or uterine infections by about 20 percentage points. In abdominal hysterectomies, the decrease was only 10.4 or 4.4 percentage points. Cesarian sections after the onset of labour and or rupture of the membranes have a high risk of infection and show the best decrease of febrile morbidity following preventive antibiotics.

Differential analysis for high density tiling microarray data

Background

High density oligonucleotide tiling arrays are an effective and powerful platform for conducting unbiased genome-wide studies. The ab initio probe selection method employed in tiling arrays is unbiased, and thus ensures consistent sampling across coding and non-coding regions of the genome. These arrays are being increasingly used to study the associated processes of transcription, transcription factor binding, chromatin structure and their association. Studies of differential expression and/or regulation provide critical insight into the mechanics of transcription and regulation that occurs during the developmental program of a cell. The time-course experiment, which comprises an in-vivo system and the proposed analyses, is used to determine if annotated and un-annotated portions of genome manifest coordinated differential response to the induced developmental program.

Results

We have proposed a novel approach, based on a piece-wise function – to analyze genome-wide differential response. This enables segmentation of the response based on protein-coding and non-coding regions; for genes the methodology also partitions differential response with a 5' versus 3' versus intra-genic bias.

Conclusion

The algorithm built upon the framework of Significance Analysis of Microarrays, uses a generalized logic to define regions/patterns of coordinated differential change. By not adhering to the gene-centric paradigm, discordant differential expression patterns between exons and introns have been identified at a FDR of less than 12 percent. A co-localization of differential binding between RNA Polymerase II and tetra-acetylated histone has been quantified at a p-value < 0.003; it is most significant at the 5' end of genes, at a p-value < 10^-13. The prototype R code has been made available as supplementary material [see Additional file 1].

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.

Rank-statistics based enrichment-site prediction algorithm developed for chromatin immunoprecipitation on chip experiments

BACKGROUND

High density oligonucleotide tiling arrays are an effective and powerful platform for conducting unbiased genome-wide studies. The ab initio probe selection method employed in tiling arrays is unbiased, and thus ensures consistent sampling across coding and non-coding regions of the genome. Tiling arrays are increasingly used in chromatin immunoprecipitation (IP) experiments (ChIP on chip). ChIP on chip facilitates the generation of genome-wide maps of in-vivo interactions between DNA-associated proteins including transcription factors and DNA. Analysis of the hybridization of an immunoprecipitated sample to a tiling array facilitates the identification of ChIP-enriched segments of the genome. These enriched segments are putative targets of antibody assayable regulatory elements. The enrichment response is not ubiquitous across the genome. Typically 5 to 10% of tiled probes manifest some significant enrichment. Depending upon the factor being studied, this response can drop to less than 1%. The detection and assessment of significance for interactions that emanate from non-canonical and/or un-annotated regions of the genome is especially challenging. This is the motivation behind the proposed algorithm.

RESULTS

We have proposed a novel rank and replicate statistics-based methodology for identifying and ascribing statistical confidence to regions of ChIP-enrichment. The algorithm is optimized for identification of sites that manifest low levels of enrichment but are true positives, as validated by alternative biochemical experiments. Although the method is described here in the context of ChIP on chip experiments, it can be generalized to any treatment-control experimental design. The results of the algorithm show a high degree of concordance with independent biochemical validation methods. The sensitivity and specificity of the algorithm have been characterized via quantitative PCR and independent computational approaches.

CONCLUSION

The algorithm ranks all enrichment sites based on their intra-replicate ranks and inter-replicate rank consistency. Following the ranking, the method allows segmentation of sites based on a meta p-value, a composite array signal enrichment criterion, or a composite of these two measures. The sensitivities obtained subsequent to the segmentation of data using a meta p-value of 10-5, an array signal enrichment of 0.2 and a composite of these two values are 88%, 87% and 95%, respectively.

Distinct mechanisms for repression of RNA polymerase III transcription by the retinoblastoma tumor suppressor protein

The retinoblastoma (RB) protein represses global RNA polymerase III transcription of genes that encode nontranslated RNAs, potentially to control cell growth. However, RNA polymerase III-transcribed genes exhibit diverse promoter structures and factor requirements for transcription, and a universal mechanism explaining global repression is uncertain. We show that RB represses different classes of RNA polymerase III-transcribed genes via distinct mechanisms. Repression of human U6 snRNA (class 3) gene transcription occurs through stable promoter occupancy by RB, whereas repression of adenovirus VAI (class 2) gene transcription occurs in the absence of detectable RB-promoter association. Endogenous RB binds to a human U6 snRNA gene in both normal and cancer cells that maintain functional RB but not in HeLa cells whose RB function is disrupted by the papillomavirus E7 protein. Both U6 promoter association and transcriptional repression require the A/B pocket domain and C region of RB. These regions of RB contribute to U6 promoter targeting through numerous interactions with components of the U6 general transcription machinery, including SNAP(C) and TFIIIB. Importantly, RB also concurrently occupies a U6 promoter with RNA polymerase III during repression. These observations suggest a novel mechanism for RB function wherein RB can repress U6 transcription at critical steps subsequent to RNA polymerase III recruitment.

The small nuclear RNA-activating protein 190 Myb DNA binding domain stimulates TATA box-binding protein-TATA box recognition

Human U6 small nuclear RNA (snRNA) gene transcription by RNA polymerase III requires cooperative promoter binding involving the snRNA-activating protein complex (SNAP(c)) and the TATA-box binding protein (TBP). To investigate the role of SNAP(c) for TBP function at U6 promoters, TBP recruitment assays were performed using full-length TBP and a mini-SNAP(c) containing SNAP43, SNAP50, and a truncated SNAP190. Mini-SNAP(c) efficiently recruits TBP to the U6 TATA box, and two SNAP(c) subunits, SNAP43 and SNAP190, directly interact with the TBP DNA binding domain. Truncated SNAP190 containing only the Myb DNA binding domain is sufficient for TBP recruitment to the TATA box. Therefore, the SNAP190 Myb domain functions both to specifically recognize the proximal sequence element present in the core promoters of human snRNA genes and to stimulate TBP recognition of the neighboring TATA box present in human U6 snRNA promoters. The SNAP190 Myb domain also stimulates complex assembly with TBP and Brf2, a subunit of a snRNA-specific TFIIIB complex. Thus, interactions between the DNA binding domains of SNAP190 and TBP at juxtaposed promoter elements define the assembly of a RNA polymerase III-specific preinitiation complex.

The retinoblastoma tumor suppressor protein targets distinct general transcription factors to regulate RNA polymerase III gene expression

The retinoblastoma protein (RB) represses RNA polymerase III transcription effectively both in vivo and in vitro. Here we demonstrate that the general transcription factors snRNA-activating protein complex (SNAP(c)) and TATA binding protein (TBP) are important for RB repression of human U6 snRNA gene transcription by RNA polymerase III. RB is associated with SNAP(c) as detected by both coimmunoprecipitation of endogenous RB with SNAP(c) and cofractionation of RB and SNAP(c) during chromatographic purification. RB also interacts with two SNAP(c) subunits, SNAP43 and SNAP50. TBP or a combination of TBP and SNAP(c) restores efficient U6 transcription from RB-treated extracts, indicating that TBP is also involved in RB regulation. In contrast, the TBP-containing complex TFIIIB restores adenovirus VAI but not human U6 transcription in RB-treated extracts, suggesting that TFIIIB is important for RB regulation of tRNA-like genes. These results suggest that different classes of RNA polymerase III-transcribed genes have distinct general transcription factor requirements for repression by RB.

[Episiotomy and its complications]

1. Many benefits claimed for episiotomy are not sufficiently proven. In recent literature, some of them are questioned and some have been disproven. 2. Episiotomy, especially median episiotomy, has a higher risk of third-degree lacerations. Mediolateral episiotomy is more often followed by postpartum pain and impaired wound-healing. 3. Typical, albeit rare complications of episiotomy and third-degree lacerations are incontinence for stool and flatus, and-very seldom-fistula formation. 4. Complications of episiotomy as well as the failure to perform an episiotomy have had forensic consequences. 5. For good healing of an episiotomy or a perineal laceration suturing with an adequate technique and the use of non-reactive suture material is mandatory.

[Perforation of surgical gloves in gynecologic operations and abdominal Cesarean section]

The aim of the study was to determine the incidence of glove perforation during gynaecological operations and Caesarean section, and to assess the value of double gloving. For this purpose the surgical gloves used in 415 procedures were tested for perforations by the water leak test. For laparotomy and breast surgery, two pairs of gloves (brand A) were worn; for vaginal and other surgery, only a single pair of thicker gloves (brand B) was used. As controls, 75 pairs of unused gloves of each brand were tested. This revealed 6 (4%) perforations in brand A gloves and 2 (1.3%) perforations in brand B gloves. Most perforations (20-40%) occurred during hysterectomy, Caesarean section, and other types of laparotomy. The gloves worn by the scrub nurse or technician were most often perforated (43.5% after vaginal hysterectomy), followed by the surgeon's gloves (29% after laparotomy). Perforations were most often located at the tip of the index finger (16.8%) and thumb (16.2%) of the nondominant hand. If two pairs of gloves were worn, and perforation occurred, only 26.7% had perforations at identical sites on the outer and inner gloves. Consequently, since three quarters of the perforations were limited to the outer glove, double gloving reduced the risk of exposure to blood by a factor of 4. The results of this study support the recommendation that two pairs of gloves be worn, at least during major surgical procedures and Caesarean section. Furthermore, the alternative operative techniques and methods of handling surgical instruments proposed for reducing the incidence of glove perforation should be tested.

Delivery of very premature infants: does the caesarean section rate relate to mortality, morbidity, or long-term outcome?

A retrospective analysis of obstetric factors influencing mortality and morbidity of very premature infants (1500 g, less than or equal to 32 weeks' gestation) was undertaken. The study included 275 such infants born in the Department of Obstetrics of the University of Tübingen during the period January 1977 to June 1987. The caesarean section rate of very preterm infants increased from 28% during the period 1977-1982 to 87% during the period 1982-1987 (P less than 0.005), accompanied by an increase in survival rate from 63% to 70%. The improvement in survival rate was statistically significant for the group with birth weight 751-1000 g (P less than 0.01). The overall mortality rate was 31% after caesarean section and 36% after vaginal delivery. Amongst the causes of death of the non-survivors, acidosis was more frequent and amniotic infection syndrome less frequent in the infants delivered vaginally than in those delivered abdominally. The proportion of children with normal development at two years of age was significantly (P less than 0.02) greater amongst those born in 1982-1987 than in those born in 1977-1981. The interpretation of these findings is by no means clear but must include the hypothesis that the increased caesarean section rate may be incidental and in no way related to the improved outcome.

[Prevention of vaginal prolapse in hysterectomy by suspension of the vaginal stump]

For prophylaxis of enterocele and of prolapse of the vagina following hysterectomy, the vaginal stump is fixed in at-risk patients to the sacro-uterine ligaments (known as McCall's suture) or to the sacro-spinal ligament (Amreich-Richter method). We report on the indications and results obtained in 101 sacro-spinal fixations and 211 McCall sutures in vaginal hysterectomy and 118 McCall sutures in abdominal hysterectomy. From 1975 to 1981 sacro-spinal fixation was only occasionally employed in prophylaxis of enterocele. After introduction of the McCall suture in 1982, the use of this method has been steadily increasing and has largely replaced sacrospinal fixation for prophylactic purposes. Nevertheless we are still using this often in cases of total prolapse, since in that situation, the fixation of the vaginal stump to the sacrouterine ligaments (in most cases weakly developed) is insufficient and does not offer enough support. Of a total of 350 McCall sutures performed to date, postrenal anuria occurred twice after kinking of the ureters, a typical complication that requires removal of the McCall suture. In a total of 174 sacro-spinal fixations of the vaginal stump for prophylactic or therapeutic indications, pronounced intraoperative haemorrhage took place in about 5% of the cases, whereas in one case, there was an abscess formation due to an infected haematoma. Technical details on both methods and on avoiding complications are discussed.

[Prevention of HIV infections in surgical gynecology and obstetrics]

In professionally conditioned HIV infections of medical personnel, blood has so far been the only source of infection that is of any importance. Hence, measures to prevent such infections must primarily aim at avoiding any contact with blood from HIV-infected patients. Since the HIV status of the patients and possibly alos other infections transmitted by blood (hepatitis) are often unknown, the following protective measures must be applied in all patients as a matter of routine. Fundamentally, gloves must always be worn when coming into contact with blood, body fluids, mucosa and non-intact skin. In operative procedures and deliveries, barrier methods must be employed to protect the eyes, nose, mouth and skin, as well as technical procedures during surgery and organisational measures to prevent any possible injuries or lesions caused by operative interventions and to reduce the number of persons exposed to risk. So far, needle pricks have been the most frequent mode of infection. Hence, used cannules should be treated with utmost care; do not return them into their protective cover but throw them directly into solid waste containers. After contamination, blood and other body fluids should be eliminated immediately. In case of massive contamination with material containing HIV, chemoprophylaxis should be given careful consideration.

[Fertility following tubal pregnancy: comparison of tube-saving surgery and salpingectomy]

391 patients were operated during 1980 to 1987 at the Department of Gynaecology of the University of Tübingen for extrauterine pregnancy. A questionnaire was circulated to inquire, how many of these women wanted to become pregnant again. 176 answered positively, the return quota being 82%. After surgery, performed to preserve the Fallopian tubes, 64% of these patients had an intrauterine pregnancy, compared with only 41% after salpingectomy or segmental resection without anastomosis. In women without the characteristic factors which reduce fertility, such as primary sterility, surgery concerning sterility or refertilization, or other kinds of abdominal surgery, a greater proportion of intrauterine pregnancies was seen after surgery preserving the Fallopian tubes (79%), than in women with the above mentioned risk factors (53%). The incidence of repeat extrauterine pregnancies was approximately equal after Fallopian tube-preserving surgery and after salpingectomy (20% and 18%, respectively).

[Late complications of episiotomy]

By means of a questionnaire and partly by phone calls 467 women who delivered at the Universitäts-Frauenklinik Tübingen 1-5 years ago were interviewed regarding perineal discomfort, wound healing and anal incontinence. 106 women have had a mediolateral episiotomy, 250 a median episiotomy (including 115 complete perineotomies) and 111 women have had no episiotomy. Dyspareunia was reported in 47% of the primiparous woman and by 22% of multiparous women with episiotomy; by contrast without episiotomy, this problem occurred only in 7% and 8% of primiparous and multiparous patients respectively (p less than 0.01). Perineal pain while sitting on a chair was reported by 30% of women with mediolateral episiotomy as compared to 19% of those with median episiotomy or complete perineotomy and 4.5% without episiotomy (median episiotomy vs. mediolateral episiotomy: p less than 0.05, episiotomy vs. no episiotomy: p less than 0.001). Occasional involuntary passage of flatus occurred in 18%, 22% and 14% respectively (differences not significant); involuntary passage of faeces in 7%, 9% and 1% respectively (episiotomy vs. no episiotomy: p less than 0.01). The occasional involuntary passage of faeces persisted for more than 6 months in 2 of 106 women with mediolateral episiotomy and in 3 of 250 women with median episiotomy. Because of the good healing of adequately reconstructed perineal tears and the better outcome of median episiotomy as compared to mediolateral episiotomy the authors advocate to use episiotomy restrictively and, if enlargement of the vaginal outlet is indicated, to use median rather than mediolateral episiotomy. If necessary, median episiotomy may be extended to complete perineotomy.

Clinical evaluation of terconazole. European experience

Terconazole is a new topical antifungal agent that differs structurally and functionally from the imidazoles. European clinical trials were conducted to determine (1) the lowest effective dose for a given treatment period, (2) which formulation should be tested further, and (3) how terconazole compares with other topical antifungal agents in terms of safety and efficacy. The results of dose-response studies demonstrated that 80- and 240-mg suppositories and 0.4% cream were the most effective formulations. Data from multicenter studies of pregnant and nonpregnant women in Belgium and Luxembourg indicate that the efficacy of terconazole cream is superior to that of miconazole nitrate cream and clotrimazole cream. Terconazole cream is also more effective than clotrimazole cream in terms of lower relapse rates.

[Results of organ-saving therapy in tubal pregnancy]

Worldwide, the incidence of nonruptured tubal pregnancy has increased, and so has the feasibility of conservative management of this condition. Following conservative surgery the rate of intrauterine pregnancy is significantly higher than after salpingectomy. The rate of ectopic pregnancy has not (or hardly) increased. For a surgeon skilled in this technique, the laparoscopic approach has advantages because it avoids laparotomy. For the time being, medical treatment of ectopic pregnancy with methotrexate, prostaglandins, and antiprogesterone should be confined to clinical studies. For nonviable, nonruptured tubal pregnancy with decreasing HCG titers expectant management seems possible; following conservative treatment, monitoring of HCG until it becomes undetectable is mandatory.

[Comparison of the results of preoperative studies with imaging procedures with the surgical status of ovarian cancer]

Optimal cytoreductive surgery of ovarian cancer is based on the preoperative diagnosis and assessment of tumour spread. Of 147 patients who underwent staging laparotomy at the Department of Gynaecology of the University of Tübingen, intraoperative staging was compared retrospectively with the results of sonography, computed tomography, double-contrast enema and urography. Ultrasound and computed tomography were comparable concerning accuracy of the diagnosis in 86 and 79% of the cases, respectively. Combined application of both methods resulted in an accuracy of 90%. Involvement of colon was diagnosed by double-contrast enema in only 41% of the cases in which enterotomy had to be performed. Involvement of bladder and ureter was observed in 80% of the cases by intravenous urography. According to our results abdominal ultrasound and urography should be performed in patients with palpable pelvic masses. The application of computed tomography as an additional method is indicated in patients with tumour classified as benign by sonographic examination. Double-contrast enema is of limited value in the diagnosis of colon involvement.

Effect of cesarean section on outcome in high- and low-risk very preterm infants

The effect of mode of delivery on the survival and morbidity of 24- to 32-week infants (500-1500 g) was studied in 262 consecutive deliveries. The study population was divided into high-risk (e.g., hypertension) and low-risk (e.g., incompetence of the cervix) groups by evaluation of risk factors. 194 very preterm newborn were classified as high risk and 68 as low risk. In both groups the perinatal outcome of vaginal delivery and cesarean section delivery was compared. Cesarean section was associated with a highly significantly improved survival rate in the high-risk group, but was not associated with differences in fetal outcome in the low-risk group. The results of this study do not support primary cesarean section as the method of delivery for all very preterm fetuses.

[Incidence and significance of pathogen detection in Douglas fluid in non-inflammatory genital diseases]

Between 1976 and 1986 the secretions from the pouch of Douglas of 1,219 patients with non-inflammatory genital diseases were microbiologically studied. Microorganisms were detected in 3.4%. In the majority of cases they were physiological skin organisms, with a count of less than 10 per ml of Douglas fluid. These findings support the view, that secondary contamination of the specimens occurred during removal, transportation, or laboratory processing.

[Laparoscopic findings in suspected adnexitis]

Between 1976 and 1985 laparoscopy was performed on a total of 768 patients in whom adnexitis was suspected. In accordance with conventional usage they were initially designated as "acute" and "chronic" cases of adnexitis on the basis of clinical criteria. The tentative diagnosis of an active infection was confirmed by laparoscopy in 62.7% of the patients with the clinically acute form and 14.5% of those with "chronic" adnexitis. Although high temperature, leukocytosis, and an increased ESR were more common among patients with laparoscopically confirmed adnexitis, high levels of inflammatory reaction were also found in patients with other conditions. In 164 patients (21%) no pathological findings were found in the genital and abdominal regions. The results confirm the importance of laparoscopy in the diagnosis of adnexitis.

[Maternal morbidity following cesarean section: effect of infection control and preventive use of antibiotics]

1. Between 1976 and 1986, data were collected prospectively by a nurse specializing in hygiene on postoperative infections in the 3508 low cervical cesarean sections carried out at the University Gynecological Clinic in Tübingen. Over the past four years, this has also included data on noninfectious complications. During this 11-year period, the rate of sections rose from 10.3% to 18.2%. 2. During the first seven years, in which only hygienic, organizational, and surgical measures were used to prevent infection, the rate of patients with postoperative infections decreased from 28.2% to 11.9% (-58%), while the rate of feverish standard morbidity decreased from 27.2% to 9.7% (-64%). 3. Over the past four years, in which 60% of the patients received a perioperative antibiotics prophylaxis consisting of three doses of a cephalosporin, the number of patients with infections has decreased further to 8.6% (-28%), and the number of those with feverish morbidity to 3.7% (-62%). Over the total period, the reduction in the named parameters was 70% and 86%. 4. The most frequent infections were urinary tract infections (mainly cases of asymptomatic bacteriuria), infections of the abdominal wound, and endomyometritis and phlebitis of the arm owing to intravenous applications. Only the reductions in the number of cases of bacteriuria (-77%), wound infections (-72%), and endomyometritis (-73%) reached statistic significance. 5. As a result of antibiotics prophylaxis, the rate of infections in the case of primary section decreased from 15.3% to 9.0%, and in the case of secondary section from 15.1% to 8.2%; feverish standard morbidity decreased from 9.1% to 3.5% and from 9.4% to 4.9%.(ABSTRACT TRUNCATED AT 250 WORDS)

[Maternal morbidity following cesarean section. Comparison of isthmo-corpus longitudinal section and isthmian transverse section in premature labor]

In an increasing number of cases of the Caesarean delivery of small premature babies (length of gestation less than 32 weeks or an estimated weight of less than 1501 g) between April 1983 and March 1987, the uterus was opened by an isthmo-corporeal longitudinal section if the lower uterine segment appeared too narrow for a gentle delivery via an isthmian transverse incision. A comparison of 67 Caesarean deliveries of this type with 116 Caesarean deliveries of the same small premature babies using an isthmian transverse incision did not reveal any difference with regard to postoperative infections, feverish standard morbidity, or other noninfectious complications. In comparison with Caesarean deliveries of older babies, the Caesarean deliveries of small premature babies had significantly more infectious and noninfectious complications, such as cases of phlebitis of the arm owing to intravenous application (2.7% as against 1.0%), posthemorrhaging and hematomas (3.8% as against 0.8%), and blood transfusions (3.3% as against 0.8%). The number of infectious complications was significantly reduced by a perioperative antibiotics prophylaxis. The question of late complications as a result of the isthmo-corporeal longitudinal section, especially the danger of rupture of the uterine scar in the event of a subsequent vaginal delivery, has not yet been resolved.

[Fetal outcome following cesarean section in premature labor. Isthmocorpus longitudinal section or isthmian transverse section?]

Little is known about the comparative safety of the isthmocorporal versus the low transverse uterine incision for Caesarean delivery of the very low birthweight infant. To address this question, the fetal outcome of 59 deliveries by isthmocorporal incision and 76 by low transverse incision were analysed. The incidences of a 5-min-Apgar score of 6 or lower and UA-pH were not significantly different. No correlation was evident between early intraventricular hemorrhage and type of incision. The number of neonatal deaths weighing less than 1000 g associated with vertical incision (27%) was lower than that associated with the low transverse incision (47%). Nevertheless the difference was not statistically significant. The decision for the type of incision should be made intraoperatively by an experienced surgeon. This factor is probably more important than the choice of a particular incision.

[Diagnostic and therapeutic interventions in extrauterine pregnancy]

Between 1969 and 1985 surgery was performed in 456 cases of extrauterine pregnancy (EUP) at Tübingen University Gynecological Clinic. The average number of such operations performed annually rose from 11 in the first six years to 61 in the last three years. As a result of early detection and treatment of EUP, tubal ruptures and severe intraabdominal hemorrhages have become increasingly rare. In the last six years, blood transfusions were only necessary in 6% of the patients who underwent surgery. In 28% no blood at all was found in the abdomen at surgery. For this reason, puncture of the pouch of Douglas was increasingly--and finally completely--supplanted by laparoscopy. Up to 1977 the affected tube was always removed; subsequently it was ever more frequently preserved. From 1983 to 1985 preservation of the tube was already being requested by 83% of the patients and it was possible to achieve this in 90% of them. In a total of 202 patients in whom the affected tube was preserved the following surgical procedures were employed: salpingotomies in 61%, salpingostomies in 4%, segmental resections with and without anastomoses in 22%, and expression or removal of a tubal abortion in 10%. The principal complications were continued growth of the tubal pregnancy following expression and salpingotomy in one case each, and occurrence of a hematosalpinx with the tentative diagnosis of continued pregnancy. Therefore, it is imperative to check the drop in the beta-HCG level after procedures in which the tube is preserved.

[Decrease in nosocomial infection based on continuous monitoring and control. 7 years' experience in a women's clinic]

During a seven-year programme of surveillance and control of infection data were collected by a specialist hygiene nurse on 47 551 gynaecological, obstetric and post-partum patients. The infection rate was highest (40.5%) after major surgical procedures. Infection rate after cesarian section was 16%, eight times the rate after vaginal delivery (2%). The most frequent type of infection was of the urinary tract (70%), usually asymptomatic bacteriuria. Next most frequent were pelvic infections, abdominal wound infections, and phlebitis via an intravenous entry in long-term parenteral nutrition. During the period of observation bacteriuria rate decreased by 75%, the other nosocomial infections by 64%, febrile standard morbidity by 81%. The decrease is largely due to the infection surveillance programme with the employment of a specialist hygiene nurse.

[4 tubal pregnancies in the same patient: advantages and disadvantages of tube-saving operation]

In comparison with salpingectomy conservative procedures for the treatment of tubal pregnancy increase the chance for a living child, but also the risk of further tubal pregnancies. After unilateral salpingectomy the risk of the next pregnancy being tubal is 11%; after conservative surgery it is also 11%. If the patient has only one Fallopian tube, conservative surgery alone offers a chance of an intrauterine pregnancy. On average there is a 54% likelihood of this. In such cases the risk of a recurrence of tubal pregnancy is 16%. The advantages and disadvantages of conservative procedures are illustrated with reference to two patients, each of whom had altogether four tubal pregnancies. One of these patients, after two tubal pregnancies, conceived an intrauterine pregnancy through the remaining tube, from which a tubal pregnancy had also been eliminated; thus, conservative surgery provided the possibility of this further pregnancy resulting in the woman's only living child.