Accurate detection of tumor-specific gene fusions reveals strongly immunogenic personal neo-antigens

Cancer-associated gene fusions are a potential source for highly immunogenic neoantigens, but the lack of computational tools for accurate, sensitive identification of personal gene fusions has limited their targeting in personalized cancer immunotherapy. Here we present EasyFuse, a machine learning computational pipeline for detecting cancer-specific gene fusions in transcriptome data obtained from human cancer samples. EasyFuse predicts personal gene fusions with high precision and sensitivity, outperforming previously described tools. By testing immunogenicity with autologous blood lymphocytes from patients with cancer, we detected pre-established CD4⁺ and CD8⁺ T cell responses for 10 of 21 (48%) and for 1 of 30 (3%) identified gene fusions, respectively. The high frequency of T cell responses detected in patients with cancer supports the relevance of individual gene fusions as neoantigens that might be targeted in personalized immunotherapies, especially for tumors with low mutation burden.

Human immunodeficiency virus type 1 impairs sumoylation

The HIV type 1 dampens host cell sumoylation in vitro and reduces the expression of UBA2 protein, a subunit of the SUMO E1–activating enzyme. In vivo, infection in patients is associated with diminished global leukocyte sumoylation activity.

During infection, the human immunodeficiency virus type 1 (HIV-1) manipulates host cell mechanisms to its advantage, thereby controlling its replication or latency, and evading immune responses. Sumoylation is an essential post-translational modification that controls vital cellular activities including proliferation, stemness, or anti-viral immunity. SUMO peptides oppose pathogen replication and mediate interferon-dependent anti-viral activities. In turn, several viruses and bacteria attack sumoylation to disarm host immune responses. Here, we show that HIV-1 impairs cellular sumoylation and targets the host SUMO E1–activating enzyme. HIV-1 expression in cultured HEK293 cells or in CD4⁺ Jurkat T lymphocytes diminishes sumoylation by both SUMO paralogs, SUMO1 and SUMO2/3. HIV-1 causes a sharp and specific decline in UBA2 protein levels, a subunit of the heterodimeric SUMO E1 enzyme, which likely serves to reduce the efficiency of global protein sumoylation. Furthermore, HIV-1–infected individuals display a significant reduction in total leukocyte sumoylation that is uncoupled from HIV-induced cytopenia. Because sumoylation is vital for immune function, T-cell expansion and activity, loss of sumoylation during HIV disease may contribute to immune system deterioration in patients.

Sumoylation of Cas9 at lysine 848 regulates protein stability and DNA binding

Cas9 is sumoylated and ubiquitylated in human cells. K848 is the major SUMO2/3 modification site, but multiple lysines are ubiquitylated, precipitating proteasomal degradation. Preventing Cas9 sumoylation by K848 ablation or by pharmacologic means reduces Cas9 half-life and DNA binding ability.

CRISPR/Cas9 is a popular genome editing technology. Although widely used, little is known about how this prokaryotic system behaves in humans. An unwanted consequence of eukaryotic Cas9 expression is off-target DNA binding leading to mutagenesis. Safer clinical implementation of CRISPR/Cas9 necessitates a finer understanding of the regulatory mechanisms governing Cas9 behavior in humans. Here, we report our discovery of Cas9 sumoylation and ubiquitylation, the first post-translational modifications to be described on this enzyme. We found that the major SUMO2/3 conjugation site on Cas9 is K848, a key positively charged residue in the HNH nuclease domain that is known to interact with target DNA and contribute to off-target DNA binding. Our results suggest that Cas9 ubiquitylation leads to decreased stability via proteasomal degradation. Preventing Cas9 sumoylation through conversion of K848 into arginine or pharmacologic inhibition of cellular sumoylation enhances the enzyme’s turnover and diminishes guide RNA-directed DNA binding efficacy, suggesting that sumoylation at this site regulates Cas9 stability and DNA binding. More research is needed to fully understand the implications of these modifications for Cas9 specificity.

An assessment of the urban water footprint and blue water scarcity: A case study for Van (Turkey)

Today, most of the world's population faces water scarcity, while global warming, urbanization, industrialization and population increases continue to increase the severity of the pressure on water resources. Management of water resources plays a key role in the sustainability of agricultural production. The water footprint (WF) is different in comparison to other water statistics because it takes direct and indirect water consumption into account, and helps in the management of water resources. Within this context, the WF of Van province, which is Turkey's most easterly located arid region, was calculated from 2004 to 2019. The study area covers lake Van, which is Turkey's largest lake, and the Van basin with an area of 23.334 km2 and a population of 1.136.757 (2019). In the calculations, crop (WFcrop), livestock (WFlivestock), and domestic and industrial water footprints (WFdomestic+industrial) were evaluated separately, and blue and green water footprints (WFblue and WFgreen) were analyzed in detail. According to the results, the average WF of Van province was found to be 8.73 billion m3 year-1. Throughout the province, 87.6% of the WF is composed of WFcrop, 4.9% is WFlivestock and 7.5% is WFdomestic+industrial. Of the WFcrop, 62.5% depends on WFblue, i.e., freshwater. Most of the WFlivestock consisted of dairy cattle (49%) and sheep (38%). The average WFdomestic+industrial for 2004 to 2019 was 0.64 billion m3 year-1. The average per capita water footprint of Van province was found to be 889.9 m3 year-1 capita-1. In addition, the province is classified as severe water scarcity (257%). This study is one of the first province-based calculations of WF in Turkey and is the first study to bring a different aspect to published literature by including residual soil moisture from the winter months. As a result of this study, the WFblue of the WFcrop is above the worldwide average and should be reduced by changing the crop pattern or synchronizing the planting and harvest dates of the crops to a period that benefits from precipitation. In addition, this study is expected to contribute to new studies for calculating the provincial scale WF and will have positive effects on agricultural planning, water allocation and the sustainability of water resources.

FAST: a randomised phase II study of zolbetuximab (IMAB362) plus EOX versus EOX alone for first-line treatment of advanced CLDN18.2-positive gastric and gastro-oesophageal adenocarcinoma

BACKGROUND

Claudin 18.2 (CLDN18.2) is contained within normal gastric mucosa epithelial tight junctions; upon malignant transformation, CLDN18.2 epitopes become exposed. Zolbetuximab, a chimeric monoclonal antibody, mediates specific killing of CLDN18.2-positive cells through immune effector mechanisms.

PATIENTS AND METHODS

The FAST study enrolled advanced gastric/gastro-oesophageal junction and oesophageal adenocarcinoma patients (aged ≥18 years) with moderate-to-strong CLDN18.2 expression in ≥40% tumour cells. Patients received first-line epirubicin + oxaliplatin + capecitabine (EOX, arm 1, n = 84) every 3 weeks (Q3W), or zolbetuximab + EOX (loading dose, 800 mg/m² then 600 mg/m² Q3W) (arm 2, n = 77). Arm 3 (exploratory) was added after enrolment initiation (zolbetuximab + EOX 1000 mg/m² Q3W, n = 85). The primary endpoint was progression-free survival (PFS) and overall survival (OS) was a secondary endpoint.

RESULTS

In the overall population, both PFS [hazard ratio (HR) = 0.44; 95% confidence interval (CI), 0.29-0.67; P < 0.0005] and OS (HR = 0.55; 95% CI, 0.39-0.77; P < 0.0005) were significantly improved with zolbetuximab + EOX (arm 2) compared with EOX alone (arm 1). This significant PFS benefit was retained in patients with moderate-to-strong CLDN18.2 expression in ≥70% of tumour cells (HR = 0.38; 95% CI, 0.23-0.62; P < 0.0005). Significant improvement in PFS was also reported in the overall population of arm 3 versus arm 1 (HR = 0.58; 95% CI, 0.39-0.85; P = 0.0114) but not in high CLDN18.2-expressing patients; no significant improvement in OS was observed in either population. Most adverse events (AEs) related to zolbetuximab + EOX (nausea, vomiting, neutropenia, anaemia) were grade 1-2. Grade ≥3 AEs showed no substantial increases overall (zolbetuximab + EOX versus EOX alone).

CONCLUSIONS

In advanced gastric/gastro-oesophageal junction and oesophageal adenocarcinoma patients expressing CLDN18.2, adding zolbetuximab to first-line EOX provided longer PFS and OS versus EOX alone. Zolbetuximab + EOX was generally tolerated and AEs were manageable. Zolbetuximab 800/600 mg/m² is being evaluated in phase III studies based on clinical benefit observed in the overall population and in patients with moderate-to-strong CLDN18.2 expression in ≥70% of tumour cells.

Investigation of the clonal associations in Acinetobacter Baumannii strains isolated from the respiratory samples of patients in a tertiary research hospital

Objective

The blaOXA resistance genes and ISAba1 were examined in 70 samples from lower respiratory tract of hospitalized patients.

Materials and Methods

Of the 67 isolates obtained, almost half (46.3%) of them were from endotracheal aspirate, and most were collected from the intensive care units of the reanimation (37.3%) and internal medicine (32.8%) units.

Results

Three samples from the internal medicine intensive care unit had positive cultures. Of the multidrug resistant (MDR) samples, 70 isolates (>50%) were moderately sensitive, while fewer (10%) were resistant to tigecycline. In contrast, 100% were sensitive to colistin. All strains were found to be positive for blaOXA-23-like and blaOXA-51-like genes, whereas no blaOXA-40-like and blaOXA-58-like genes were detected. The ISAba1 positivity rate was 90.0%. Pattern 5 was mainly identified among the 22 different patterns. Of note, 50% of Pattern 5 was found in the patients of the internal medicine intensive care unit, and a third was associated with ventilator-associated pneumonia. Importantly, the internal medicine unit's equipment was found to be culture positive.

Conclusion

Findings obtained from this study suggest that isolates can easily spread through the hospital via isolate cross-contamination caused by health personnel. These contaminating isolates may be able to maintain their presence within the hospital for a long time.

A multicentre, phase IIa study of zolbetuximab as a single agent in patients with recurrent or refractory advanced adenocarcinoma of the stomach or lower oesophagus: the MONO study

BACKGROUND

Claudin 18.2 (CLDN18.2) is physiologically confined to gastric mucosa tight junctions; however, upon malignant transformation, perturbations in cell polarity lead to CLDN18.2 epitopes being exposed on the cancer cell surface. The first-in-class monoclonal antibody, zolbetuximab (formerly known as IMAB362), binds to CLDN18.2 and can induce immune-mediated lysis of CLDN18.2-positive cells.

PATIENTS AND METHODS

Patients with advanced gastric, gastro-oesophageal junction (GEJ) or oesophageal adenocarcinomas with moderate-to-strong CLDN18.2 expression in ≥50% of tumour cells received zolbetuximab intravenously every 2 weeks for five planned infusions. At least three patients were enrolled in two sequential cohorts (cohort 1300 mg/m2; cohort 2600 mg/m2); additional patients were enrolled into a dose-expansion cohort (cohort 3600 mg/m2). The primary end point was the objective response rate [ORR: complete and partial response (PR)]; secondary end points included clinical benefit [ORR+stable disease (SD)], progression-free survival, safety/tolerability, and zolbetuximab pharmacokinetic profile.

RESULTS

From September 2010 to September 2012, 54 patients were enrolled (cohort 1, n = 4; cohort 2, n = 6; cohort 3, n = 44). Three patients in cohort 1 and 25 patients in cohorts 2/3 received at least 5 infusions. Antitumour activity data were available for 43 patients, of whom 4 achieved PR (ORR 9%) and 6 (14%) had SD for a clinical benefit rate of 23%. In a subgroup of patients with moderate-to-high CLDN18.2 expression in ≥70% of tumour cells, ORR was 14% (n = 4/29). Treatment-related adverse events occurred in 81.5% (n = 44/54) patients; nausea (61%), vomiting (50%), and fatigue (22%) were the most frequent.

CONCLUSIONS

Zolbetuximab monotherapy was well tolerated and exhibited antitumour activity in patients with CLDN18.2-positive advanced gastric or GEJ adenocarcinomas, with response rates similar to those reported for single-agent targeted agents in gastric/GEJ cancer trials.

CLINICALTRIALS.GOV NUMBER

NCT01197885.

A molecule inducing androgen receptor degradation and selectively targeting prostate cancer cells

A new molecule induces AR sumoylation and degradation resulting in selective growth inhibition in AR-dependent prostate cancer cells, but its activity is blunted by interference with proteasomes.

Aberrant androgen signaling drives prostate cancer and is targeted by drugs that diminish androgen production or impede androgen–androgen receptor (AR) interaction. Clinical resistance arises from AR overexpression or ligand-independent constitutive activation, suggesting that complete AR elimination could be a novel therapeutic strategy in prostate cancers. IRC117539 is a new molecule that targets AR for proteasomal degradation. Exposure to IRC117539 promotes AR sumoylation and ubiquitination, reminiscent of therapy-induced PML/RARA degradation in acute promyelocytic leukemia. Critically, ex vivo, IRC117539-mediated AR degradation induces prostate cancer cell viability loss by inhibiting AR signaling, even in androgen-insensitive cells. This approach may be beneficial for castration-resistant prostate cancer, which remains a clinical issue. In xenograft models, IRC117539 is as potent as enzalutamide in impeding growth, albeit less efficient than expected from ex vivo studies. Unexpectedly, IRC117539 also behaves as a weak proteasome inhibitor, likely explaining its suboptimal efficacy in vivo. Our studies highlight the feasibility of AR targeting for degradation and off-target effects’ importance in modulating drug activity in vivo.

Abstract OT2-06-01: Highly innovative personalized RNA-immunotherapy for patients with triple negative breast cancer

Background: The treatment of triple negative breast cancer (TNBC) is hampered by the lack of established therapeutic targets such as hormone receptors or HER-2. Chemotherapy and radiotherapy is the standard of care, yet survival rates in TNBC remain poor. Approaches tailored to the patient's individual tumor signature may lead to improved therapeutic outcome. We have set up a clinical workflow covering drug development (from target discovery to manufacturing) and drug release providing a custom-made investigational medicinal product (IMP) for each individual patient.

Trial Design: A phase I/II trial assesses the feasibility, safety and biological efficacy of this personalized immunotherapy in three clinical sites in Germany and Sweden. TNBC patients (pT1cN0M0 – TxNxM0) after completion of initial standard of care therapy will be allocated to one of two study arms. Patients in ARM1 receive 8 vaccination cycles with a personalized combination of shared tumor-associated antigens, selected based on each patient tumor's antigen-expression profile out of a WAREHOUSE of pre-manufactured mRNA vaccine. Patients in ARM2 receive the personalized mRNA WAREHOUSE vaccine followed by 8 vaccination cycles of an on-demand manufactured mRNA MUTANOME vaccine encoding up to twenty unique neo-epitopes of the individual patient identified by next generation sequencing. The mRNAs are administered intravenously as a nanoparticulate lipoplex formulation, which protects RNA from degradation, activates innate immunity, transfects APCs and consequently induces highly potent antigen-specific T-cell responses. The treatment of 12 patients in ARM1 is completed and enrolment of patients for ARM2 has started. Preliminary data show that the RNA-WAREHOUSE approach is feasible and can be applied safely. Biomarker analysis is ongoing. This approach is promising as it addresses the heterogeneity of TNBC.

The TNBC-MERIT trial was initially funded by the EU Commission's FP7 and led by BioNTech AG.

Citation Format: Schmidt M, Bolte S, Frenzel K, Heesen L, Derhovanessian E, Bukur V, Diken M, Gruetzner J, Kreiter S, Klein A, Kuhn A, Langer D, Loewer M, Lindman H, Schneeweiss A, Tuereci O, Sahin U. Highly innovative personalized RNA-immunotherapy for patients with triple negative breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr OT2-06-01.

Abstract P2-07-08: Standardized prediction of Oncotype DX® risk classes by local RT-qPCR

Background: Recent results from the prospective validation of the Oncotype DX® recurrence score (RS) have underlined the clinical validity of the assay for the prediction of chemotherapy benefit in ER+/HER2- early stage breast cancer patients. Due to health economic restrictions, some patients have no easy access to the test. A pre-selection of tumor samples may help identify patients with a high likelihood to be spared chemotherapy. Histology and semi-quantitative IHC are hence used to select samples for Oncotype testing, but these suffer from intra- and inter-observer variability, especially for Ki-67 which is a main factor in most RS prediction algorithms. We have established and validated a tool for the prediction of RS risk classes (TAILORx cutoff RS ≤25) based on highly standardized, reproducible and locally performed RT-qPCR measurements of ERBB2, ESR1, PGR and MKI67 mRNA using the CE-marked IVD MammaTyper®.

Methods: Total RNA was extracted from whole surface 10μm sections from FFPE breast cancer samples with a known RS result and a tumor cell content ≥20%. ERBB2, ESR1, PGR and MKI67 mRNA expression was measured by RT-qPCR on a CFX96 qPCR cycler using the MammaTyper® kit. A prediction model for an RS ≤25 result was established using multivariable logistic regression. Based on this model and the training data two cutoffs for confident prediction of low chemotherapy benefit patients in a clinical setting were established at 95% and 97.5% specificity. The model and the cutoffs were then fixed and validated in a second, separate set of breast cancer samples. ROC analysis was used to characterize predictive power of the continuous values resulting from the prediction model. Positive and negative predictive values for detection of an RS ≤25 result were also determined on the validation samples using the two pre-defined cutoffs.

Results: The sample set for training of the prediction model encompassed 202 samples including 29 samples (14.4%) with an RS &gt;25. In an initial multivariable model with all four markers, PGR and MKI67 were the strongest predictors while the influence of ESR in the model was lower, but still significant. ERBB2 was no significant predictor in this set of ERBB2 negative samples and was therefore excluded from the final model which was based on three markers only. This three marker model achieved an AUC of 0.920 (95% CI: 0.871-0.968) in the training samples. When applying the fixed model from the training dataset to a second separately collected set of 104 samples containing 20 samples (19.2%) with an RS &gt;25, an AUC of 0.883 (95% CI: 0.810-0.955) was documented. When further applying the two predefined cutoffs established in the training set, 45 and 36 of the 104 validation samples (43.3% and 34.6%) had a predicted low chemotherapy benefit result (RS ≤25). Even with the less stringent cutoff, not a single one of the RS &gt;25 cases from the validation cohort was falsely predicted as RS ≤25 sample.

Conclusion: We have established a highly reliable method for prediction of Oncotype DX® low chemotherapy benefit results based on local and cost effective mRNA measurements. This method enables local pathologies to pre-assess routine samples using a highly precise molecular tool and thereby reserve the Oncotype DX® test for cases with ambiguous cancer biology.

Citation Format: Lehr H-A, Aulmann S, Etzrodt A, Laible M, Hartmann K, Gürtler C, Wirtz RM, Sahin U, Varga Z. Standardized prediction of Oncotype DX® risk classes by local RT-qPCR [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P2-07-08.

Abstract P1-06-11: Prediction of oncotype DX® results based on local gene expression measurements by MammaTyper®

Background: Oncotype DX® recurrence score (RS) has emerged as a recommended risk classifier for patients with ER+/HER2- early-stage breast cancer. While RS is one of the most rigorously studied risk scores, it is also one of the most expensive tests, thus remaining beyond reach for a many patients.

The necessity for an affordable method for estimating risk of recurrence has motivated investigations on the correlation between RS and traditional parameters such as IHC for ER, PR and Ki67. However, semi-quantitative IHC lacks standardization across different laboratories especially for Ki67.

In this study we therefore investigated whether the standardized assessment of HER2, ER, PR, and Ki67 on mRNA level could better serve for prediction of low risk RS cases.

Methods: ERBB2, ESR1, PGR and MKI67 mRNA expression was measured by RT-qPCR in extracts from FFPE breast cancer samples using the MammaTyper® test. Complete data for RS, IHC, grading and mRNA measurement was available for 198 samples. Tumor subtypes according to St Gallen surrogate definition from 2013 were assigned based on binary mRNA marker classification (pos/neg) according to pre-defined cut-offs. Subtype results were compared to RS risk classes based on commercial and TAILORx-trial cut-offs. RS low risk classification (RS ≤25) based on four IHC markers and grading was estimated using the online tool breastrecurrenceestimator.onc.jhmi.edu and compared to observed RS classes.

Finally, the prediction of continuous RS values by mRNA or semi-quantitative IHC measurement was compared by linear regression and subsequent ROC analysis of prediction models.

Results: The distribution of RS risk classes in the set of samples with full data was 21% RS 0-10, 39% RS 11-17, 27% RS 18-25, 7% RS 26-30 and 7% RS &gt;30. MammaTyper® called 38% (76) of the samples as Luminal A-like. From these samples 70% and 99% had RS values below 18 and 25 respectively. Only 1 MammaTyper® Luminal A-like sample had an RS &gt;30.

Estimation of RS according to the online tool resulted in classification of 61% (121) of the samples as low risk (RS ≤25). Of these 74% and 98% of samples had observed RS values below 18 and between 18 and 25 respectively. 2 and 1 samples called as low risk by the online tool had an RS of 26-30 and &gt;30 and, respectively.

In linear regression analysis of IHC against RS only PR and Ki67 were significant predictors (p-values &lt;0.0001 and 0.0128) while when using mRNA values ESR1, PGR and MKI67 were found as predictors of RS in the multivariate model (all p-values &lt;0.0001). On a training set (67% of samples) the IHC based prediction model was correlated to the observed RS with an R2 of 0.305 whereas the mRNA based model achieved an R2 of 0.489. When the models were applied to training and validation dataset (33% of samples) for prediction of an RS &gt;25 result, the IHC based model had AUCs of 0.887 and 0.836, respectively, while the mRNA based model achieved AUCs of 0.909 and 0.899, respectively.

Conclusion: mRNA based prediction of RS was considerably better than prediction based on IHC. As Ki67 IHC standardization is reaching its limits, local gene expression measurements with their high degree of standardization could serve as a safer way for prediction of Oncotype low risk results.

Citation Format: Lehr H-A, Aulmann S, Laible M, Etzrodt A, Hartmann K, Gürtler C, Sahin U, Varga Z. Prediction of oncotype DX® results based on local gene expression measurements by MammaTyper® [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P1-06-11.

Abstract P3-08-14: Prediction of distant recurrence in low risk early breast cancer by RT-qPCR based subtyping using MammaTyper®

Background:

Estrogen receptor (ER/ESR1), progesterone receptor (PR/PGR) and epidermal growth factor receptor 2 (HER2/ERBB2) are routinely assessed by immunohistochemistry (IHC) during workup of breast cancer samples. The routine use of Ki67 (MKI67) IHC assessment in the context of breast cancer subtyping, however, remains controversial, due to poor reproducibility and lack of standardization.

The MammaTyper® test is an in-vitro diagnostic (IVD) test which measures the expression status of the four breast cancer biomarkers ERBB2, ESR1, PGR and MKI67 on the mRNA level via reverse transcription-quantitative PCR (RT-qPCR) and has demonstrated a high degree of reproducibility in the assessment of the four markers.

In this retrospective analysis we assessed the prognostic power of molecular subtyping by MammaTyper® in archived samples from low risk early breast cancers treated with adjuvant endocrine therapy only.

Methods:

ER+/HER2- (according to initial diagnosis) FFPE breast cancer samples from patients treated with adjuvant endocrine therapy only were obtained from 6 different centers. Tumor cellularity was assessed by H&E staining and RNA was extracted from samples with a tumor cell content of ≥20% using a bead-based RNA purification kit (RNXtract®). Total RNA was then used as input for MammaTyper® RT-qPCR. Expression values were classified as positive or negative for each marker based on predefined cutoff values. Tumor subtypes were assigned to each sample based on the combination of binary (pos/neg) single marker expression status according the St Gallen surrogate subtype definition. Distant disease free survival of Luminal A-like samples vs. samples with other subtypes was assessed by Kaplan Meier analysis and Cox regression using SAS version 9.4.

Results:

The final analysis included 319 samples with sufficient tumor cellularity and RNA content for reliable analysis. The rate of distant recurrence in the analyzed set was 8.5%. Median follow up was 7.8 years. The MammaTyper® test called 60% (192) of samples as Luminal-A-like (4.7% (9) distant events), 37% (119) as Luminal B-like (HER2 negative) (13.4% (16) distant events), 1.3% (4) as Triple negative (ductal) (25% (1) distant events), 0.6% (2) as “not defined according to St Gallen” (ESR1-/PGR+) (50% (1) distant events) and 0.6% (2) as Luminal B-like (HER2 positive) (no distant events).

When comparing Luminal A-like samples with the samples of the other subtypes in survival analysis, Luminal A-like samples had a significantly better distant disease free survival when assessing samples from patients with pN0 status (278) (p=0.0177, HR=0.344 (95% CI 0.137-0.866), pN1 status (0-3 affected nodes) (314) (p=0.0153, HR=0.374 (95% CI 0.163-0.855) as well as for all samples (p=0.0032, HR=0.319 (95% CI 0.143-0.711).

Conclusion:

Determination of HER2, ER, PR and Ki67 mRNA levels allows molecular subtyping according to the St Gallen surrogate subtype definition. Low risk of distant recurrence could be confirmed for the MammaTyper® Luminal A-like samples suggesting that for this patient group endocrine treatment alone may be sufficient. The high degree of standardization of mRNA measurement may drive the use of the Ki67/MKI67 biomarker in routine breast cancer pathology.

Citation Format: Laible M, Hartmann K, Gürtler C, Anzeneder T, Weber S, Keller T, Sahin U. Prediction of distant recurrence in low risk early breast cancer by RT-qPCR based subtyping using MammaTyper® [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P3-08-14.

Actively personalized cancer vaccines--the step into clinical application

Cancer vaccine development enters a new phase of innovation based on the development of modern sequencing technologies and novel RNA-based synthetic drug formats which enable the analysis and therapeutic targeting of every patient's tumor genome. By applying and combining these innovations, we have brought the concept of "actively personalized cancer vaccines" to clinical testing. Synthetic RNA is used as the drug format, allowing affordable, individual "on demand" manufacturing of tumor-optimized vaccines.

Detection of Protein SUMOylation In Situ by Proximity Ligation Assays

Sumoylation is a posttranslational process essential for life and concerns a growing number of crucial proteins. Understanding the influence of this phenomenon on individual proteins or on cellular pathways in which they function has become an intense area of research. A critical step in studying protein sumoylation is to detect sumoylated forms of a particular protein. This has proven to be a challenging task for a number of reasons, especially in the case of endogenous proteins and in vivo studies or when studying rare cells such as stem cells. Proximity ligation assays that allow detection of closely interacting protein partners can be adapted for initial detection of endogenous sumoylation or ubiquitination in a rapid, ultrasensitive, and cheap manner. In addition, modified forms of a given protein can be detected in situ in various cellular compartments. Finally, the flexibility of this technique may allow rapid screening of drugs and stress signals that may modulate protein sumoylation.

PML nuclear bodies: assembly and oxidative stress-sensitive sumoylation

PML Nuclear Bodies (NBs) have fascinated cell biologists due to their exquisitely dynamic nature and their involvement in human diseases, notably acute promyelocytic leukemia. NBs, as well as their master organizer--the PML protein--exhibit multiple connections with stress responses. Initially viewed as a tumor suppressor, PML recently re-emerged as a multifaceted protein, capable of controlling numerous aspects of cellular homeostasis. NBs recruit many functionally diverse proteins and function as stress-regulated sumoylation factories. SUMO-initiated partner retention can subsequently facilitate a variety of other post-translational modifications, as well as partner degradation. With this newly elucidated central role of stress-enhanced sumoylation, it should now be possible to build a working model for the different NB-regulated cellular activities. Moreover, pharmacological manipulation of NB formation by interferons or oxidants holds the promise of clearing many undesirable proteins for clinical management of malignant, viral or neurodegenerative diseases.

Translation of genomics-guided RNA-based personalised cancer vaccines: towards the bedside

Cancer is a disease caused by DNA mutations. Cancer therapies targeting defined functional mutations have shown clinical benefit. However, as 95% of the mutations in a tumour are unique to that single patient and only a small number of mutations are shared between patients, the addressed medical need is modest. A rapidly determined patient-specific tumour mutation pattern combined with a flexible mutation-targeting drug platform could generate a mutation-targeting individualised therapy, which would benefit each single patient. Next-generation sequencing enables the rapid identification of somatic mutations in individual tumours (the mutanome). Immunoinformatics enables predictions of mutation immunogenicity. Mutation-targeting RNA-based vaccines can be rapidly and affordably synthesised as custom GMP drug products. Integration of these cutting-edge technologies into a clinically applicable process holds the promise of a disruptive innovation benefiting cancer patients. Here, we describe our translation of the individualised RNA-based cancer vaccine concept into clinic trials.

PML nuclear bodies: regulation, function and therapeutic perspectives

PML nuclear bodies (NBs) were first described by electron microscopy and rediscovered through their treatment-reversible disruption in a rare leukaemia. They recruit multiple partner proteins and now emerge as interferon- and oxidative stress-responsive sumoylation factories. NBs mediate interferon-induced viral restriction, enhance proteolysis, finely tune metabolism and enforce stress-induced senescence. Apart from being markers of cellular stress, PML NBs could be harnessed pharmacologically in a number of conditions, including cancer, viral infection or neurodegenerative diseases.

Sumoylation of human argonaute 2 at lysine-402 regulates its stability

Gene silencing by small RNAs has emerged as a powerful post-transcriptional regulator of gene expression, however processes underlying regulation of the small RNA pathway in vivo are still largely elusive. Here, we identified sumoylation as a novel post-translational modification acting on Ago2, the main effector of small RNA-mediated gene silencing. We demonstrate that Ago2 can be modified by SUMO1 and SUMO2/3 and identified Lys402 as the major Ago2 sumoylation site in vivo. Ago2 physically interacts with the SUMO E2 conjugating enzyme Ubc9 and the E3 ligase RanBP2 facilitates Ago2 sumoylation in vitro. Mutation of Lys402 enhances the stability of Ago2 protein and impairment of cellular sumoylation by siRNA- or shRNA-mediated extinction of Ubc9 or in Ubc9 knockout mouse tissues results in increased steady-state levels and enhanced stability of Ago2. Similarly, knockdown of RanBP2 or of the SAE2 E1 enzyme enhances Ago2 protein levels. Lys402 is located in the L2g1 loop linking the PAZ and PIWI domains of Ago2, in the immediate vicinity of Tyr393 which can be phosphorylated, implying that the L2g1 linker represents an easily accessible hot spot for post-translational modifications. Altogether, our results show that sumoylation of Ago2 at Lys402 negatively regulates its stability, thereby establishing a first link between SUMO and the small RNA machinery.