A whole-slide foundation model for digital pathology from real-world data

Digital pathology poses unique computational challenges, as a standard gigapixel slide may comprise tens of thousands of image tiles1-3. Prior models have often resorted to subsampling a small portion of tiles for each slide, thus missing the important slide-level context4. Here we present Prov-GigaPath, a whole-slide pathology foundation model pretrained on 1.3 billion 256 × 256 pathology image tiles in 171,189 whole slides from Providence, a large US health network comprising 28 cancer centres. The slides originated from more than 30,000 patients covering 31 major tissue types. To pretrain Prov-GigaPath, we propose GigaPath, a novel vision transformer architecture for pretraining gigapixel pathology slides. To scale GigaPath for slide-level learning with tens of thousands of image tiles, GigaPath adapts the newly developed LongNet5 method to digital pathology. To evaluate Prov-GigaPath, we construct a digital pathology benchmark comprising 9 cancer subtyping tasks and 17 pathomics tasks, using both Providence and TCGA data6. With large-scale pretraining and ultra-large-context modelling, Prov-GigaPath attains state-of-the-art performance on 25 out of 26 tasks, with significant improvement over the second-best method on 18 tasks. We further demonstrate the potential of Prov-GigaPath on vision-language pretraining for pathology7,8 by incorporating the pathology reports. In sum, Prov-GigaPath is an open-weight foundation model that achieves state-of-the-art performance on various digital pathology tasks, demonstrating the importance of real-world data and whole-slide modelling.

Integrative multi-omics profiling in human decedents receiving pig heart xenografts

In a previous study, heart xenografts from 10-gene-edited pigs transplanted into two human decedents did not show evidence of acute-onset cellular- or antibody-mediated rejection. Here, to better understand the detailed molecular landscape following xenotransplantation, we carried out bulk and single-cell transcriptomics, lipidomics, proteomics and metabolomics on blood samples obtained from the transplanted decedents every 6 h, as well as histological and transcriptomic tissue profiling. We observed substantial early immune responses in peripheral blood mononuclear cells and xenograft tissue obtained from decedent 1 (male), associated with downstream T cell and natural killer cell activity. Longitudinal analyses indicated the presence of ischemia reperfusion injury, exacerbated by inadequate immunosuppression of T cells, consistent with previous findings of perioperative cardiac xenograft dysfunction in pig-to-nonhuman primate studies. Moreover, at 42 h after transplantation, substantial alterations in cellular metabolism and liver-damage pathways occurred, correlating with profound organ-wide physiological dysfunction. By contrast, relatively minor changes in RNA, protein, lipid and metabolism profiles were observed in decedent 2 (female) as compared to decedent 1. Overall, these multi-omics analyses delineate distinct responses to cardiac xenotransplantation in the two human decedents and reveal new insights into early molecular and immune responses after xenotransplantation. These findings may aid in the development of targeted therapeutic approaches to limit ischemia reperfusion injury-related phenotypes and improve outcomes.

FcγRIIB Is an Immune Checkpoint Limiting the Activity of Treg-Targeting Antibodies in the Tumor Microenvironment

Preclinical murine data indicate that fragment crystallizable (Fc)-dependent depletion of intratumoral regulatory T cells (Treg) is a major mechanism of action of anti-CTLA-4. However, the two main antibodies administered to patients (ipilimumab and tremelimumab) do not recapitulate these effects. Here, we investigate the underlying mechanisms responsible for the limited Treg depletion observed with these therapies. Using an immunocompetent murine model humanized for CTLA-4 and Fcγ receptors (FcγR), we show that ipilimumab and tremelimumab exhibit limited Treg depletion in tumors. Immune profiling of the tumor microenvironment (TME) in both humanized mice and humans revealed high expression of the inhibitory Fc receptor, FcγRIIB, which limits antibody-dependent cellular cytotoxicity/phagocytosis. Blocking FcγRIIB in humanized mice rescued the Treg-depleting capacity and antitumor activity of ipilimumab. Furthermore, Fc engineering of antibodies targeting Treg-associated targets (CTLA-4 or CCR8) to minimize FcγRIIB binding significantly enhanced Treg depletion, resulting in increased antitumor activity across various tumor models. Our results define the inhibitory FcγRIIB as an immune checkpoint limiting antibody-mediated Treg depletion in the TME, and demonstrate Fc engineering as an effective strategy to overcome this limitation and improve the efficacy of Treg-targeting antibodies.

Oral microbiota analyses of paediatric Saudi population reveals signatures of dental caries

BACKGROUND

Oral microbiome sequencing has revealed key links between microbiome dysfunction and dental caries. However, these efforts have largely focused on Western populations, with few studies on the Middle Eastern communities. The current study aimed to identify the composition and abundance of the oral microbiota in saliva samples of children with different caries levels using machine learning approaches.

METHODS

Oral microbiota composition and abundance were identified in 250 Saudi participants with high dental caries and 150 with low dental caries using 16 S rRNA sequencing on a NextSeq 2000 SP flow cell (Illumina, CA) using 250 bp paired-end reads, and attempted to build a classifier using random forest models to assist in the early detection of caries.

RESULTS

The ADONIS test results indicate that there was no significant association between sex and Bray-Curtis dissimilarity (p ~ 0.93), but there was a significant association with dental caries status (p ~ 0.001). Using an alpha level of 0.05, five differentially abundant operational taxonomic units (OTUs) were identified between males and females as the main effect along with four differentially abundant OTUs between high and low dental caries. The mean metrics for the optimal hyperparameter combination using the model with only differentially abundant OTUs were: Accuracy (0.701); Matthew's correlation coefficient (0.0509); AUC (0.517) and F1 score (0.821) while the mean metrics for random forest model using all OTUs were:0.675; 0.054; 0.611 and 0.796 respectively.

CONCLUSION

The assessment of oral microbiota samples in a representative Saudi Arabian population for high and low metrics of dental caries yields signatures of abundances and diversity.

Unsupervised mRNA-seq classification of heart transplant endomyocardial biopsies

BACKGROUND

Endomyocardial biopsy (EMB) is currently considered the gold standard for diagnosing cardiac allograft rejection. However, significant limitations related to histological interpretation variability are well-recognized. We sought to develop a methodology to evaluate EMB solely based on gene expression, without relying on histology interpretation.

METHODS

Sixty-four EMBs were obtained from 47 post-heart transplant recipients, who were evaluated for allograft rejection. EMBs were subjected to mRNA sequencing, in which an unsupervised classification algorithm was used to identify the molecular signatures that best classified the EMBs. Cytokine and natriuretic peptide peripheral blood profiling was also performed. Subsequently, we performed gene network analysis to identify the gene modules and gene ontology to understand their biological relevance. We correlated our findings with the unsupervised and histological classifications.

RESULTS

Our algorithm classifies EMBs into three categories based solely on clusters of gene expression: unsupervised classes 1, 2, and 3. Unsupervised and histological classifications were closely related, with stronger gene module-phenotype correlations for the unsupervised classes. Gene ontology enrichment analysis revealed processes impacting on the regulation of cardiac and mitochondrial function, immune response, and tissue injury response. Significant levels of cytokines and natriuretic peptides were detected following the unsupervised classification.

CONCLUSION

We have developed an unsupervised algorithm that classifies EMBs into three distinct categories, without relying on histology interpretation. These categories were highly correlated with mitochondrial, immune, and tissue injury response. Significant cytokine and natriuretic peptide levels were detected within the unsupervised classification. If further validated, the unsupervised classification could offer a more objective EMB evaluation.

Gut microbiota analyses of inflammatory bowel diseases from a representative Saudi population

BACKGROUND

Crohn's diseases and ulcerative colitis, both of which are chronic immune-mediated disorders of the gastrointestinal tract are major contributors to the overarching Inflammatory bowel diseases. It has become increasingly evident that the pathological processes of IBDs results from interactions between genetic and environmental factors, which can skew immune responses against normal intestinal flora.

METHODS

The aim of this study is to assess and analyze the taxa diversity and relative abundances in CD and UC in the Saudi population. We utilized a sequencing strategy that targets all variable regions in the 16 S rRNA gene using the Swift Amplicon 16 S rRNA Panel on Illumina NovaSeq 6000.

RESULTS

The composition of stool 16 S rRNA was analyzed from 219 patients with inflammatory bowel disease and from 124 healthy controls. We quantified the abundance of microbial communities to examine any significant differences between subpopulations of samples. At the genus level, two genera in particular, Veillonella and Lachnoclostridium showed significant association with CD versus controls. There were significant differences between subjects with CD versus UC, with the top differential genera spanning Akkermansia, Harryflintia, Maegamonas and Phascolarctobacterium. Furthermore, statistically significant taxa diversity in microbiome composition was observed within the UC and CD groups.

CONCLUSIONS

In conclusion we have shown that there are significant differences in gut microbiota between UC, CD and controls in a Saudi Arabian inflammatory bowel disease cohort. This reinforces the need for further studies in large populations that are ethnically and geographically diverse. In addition, our results show the potential to develop classifiers that may have add additional richness of context to clinical diagnosis of UC and CD with larger inflammatory bowel disease cohorts.

Toward structuring real-world data: Deep learning for extracting oncology information from clinical text with patient-level supervision

Most detailed patient information in real-world data (RWD) is only consistently available in free-text clinical documents. Manual curation is expensive and time consuming. Developing natural language processing (NLP) methods for structuring RWD is thus essential for scaling real-world evidence generation. We propose leveraging patient-level supervision from medical registries, which are often readily available and capture key patient information, for general RWD applications. We conduct an extensive study on 135,107 patients from the cancer registry of a large integrated delivery network (IDN) comprising healthcare systems in five western US states. Our deep-learning methods attain test area under the receiver operating characteristic curve (AUROC) values of 94%-99% for key tumor attributes and comparable performance on held-out data from separate health systems and states. Ablation results demonstrate the superiority of these advanced deep-learning methods. Error analysis shows that our NLP system sometimes even corrects errors in registrar labels.

FcyRIIB is a novel immune checkpoint in the tumor microenvironment limiting activity of Treg-targeting antibodies

Despite pre-clinical murine data supporting T regulatory (Treg) cell depletion as a major mechanism by which anti-CTLA-4 antibodies function in vivo, the two main antibodies tested in patients (ipilimumab and tremelimumab) have failed to demonstrate similar effects. We report analogous findings in an immunocompetent murine model humanized for CTLA-4 and Fcy receptors (hCTLA-4/hFcyR mice), where both ipilimumab and tremelimumab fail to show appreciable Treg depletion. Immune profiling of the tumor microenvironment (TME) in both mice and human samples revealed upregulation of the inhibitory Fcy receptor, FcyRIIB, which limits the ability of the antibody Fc fragment of human anti-CTLA-4 antibodies to induce effective antibody dependent cellular cytotoxicty/phagocytosis (ADCC/ADCP). Blocking FcyRIIB in humanized mice rescues Treg depleting capacity and anti-tumor activity of ipilimumab. For another target, CC motif chemokine receptor 8 (CCR8), which is selectively expressed on tumor infiltrating Tregs, we show that Fc engineering to enhance binding to activating Fc receptors, while limiting binding to the inhibitory Fc receptor, leads to consistent Treg depletion and single-agent activity across multiple tumor models, including B16, MC38 and MB49. These data reveal the importance of reducing engagement to the inhibitory Fc receptor to optimize Treg depletion by TME targeting antibodies. Our results define the inhibitory FcyRIIB receptor as a novel immune checkpoint limiting antibody-mediated Treg depletion in tumors, and demonstrate Fc variant engineering as a means to overcome this limitation and augment efficacy for a repertoire of antibodies currently in use or under clinical evaluation in oncology.

A Random Forest Genomic Classifier for Tumor Agnostic Prediction of Response to Anti-PD1 Immunotherapy

Tumor mutational burden (TMB), a surrogate for tumor neoepitope burden, is used as a pan-tumor biomarker to identify patients who may benefit from anti-program cell death 1 (PD1) immunotherapy, but it is an imperfect biomarker. Multiple additional genomic characteristics are associated with anti-PD1 responses, but the combined predictive value of these features and the added informativeness of each respective feature remains unknown. We evaluated whether machine learning (ML) approaches using proposed determinants of anti-PD1 response derived from whole exome sequencing (WES) could improve prediction of anti-PD1 responders over TMB alone. Random forest classifiers were trained on publicly available anti-PD1 data (n = 104), and subsequently tested on an independent anti-PD1 cohort (n = 69). Both the training and test datasets included a range of cancer types such as non-small cell lung cancer (NSCLC), head and neck squamous cell carcinoma (HNSCC), melanoma, and smaller numbers of patients from other tumor types. Features used include summaries such as TMB and number of frameshift mutations, as well as more gene-level features such as counts of mutations associated with immune checkpoint response and resistance. Both ML algorithms demonstrated area under the receiver-operator curves (AUC) that exceeded TMB alone (AUC 0.63 "human-guided," 0.64 "cluster," and 0.58 TMB alone). Mutations within oncogenes disproportionately modulate anti-PD1 responses relative to their overall contribution to tumor neoepitope burden. The use of a ML algorithm evaluating multiple proposed genomic determinants of anti-PD1 responses modestly improves performance over TMB alone, highlighting the need to integrate other biomarkers to further improve model performance.

Genomic analysis of early-stage lung cancer reveals a role for TP53 mutations in distant metastasis

Patients with non-small cell lung cancer (NSCLC) who have distant metastases have a poor prognosis. To determine which genomic factors of the primary tumor are associated with metastasis, we analyzed data from 759 patients originally diagnosed with stage I-III NSCLC as part of the AACR Project GENIE Biopharma Collaborative consortium. We found that TP53 mutations were significantly associated with the development of new distant metastases. TP53 mutations were also more prevalent in patients with a history of smoking, suggesting that these patients may be at increased risk for distant metastasis. Our results suggest that additional investigation of the optimal management of patients with early-stage NSCLC harboring TP53 mutations at diagnosis is warranted in light of their higher likelihood of developing new distant metastases.

Abstract CT502: Preliminary immunological monitoring of first-in-human immunotherapy-trio for advanced head and neck squamous cell carcinoma

Background: Preclinical studies document that complex cancer vaccines, combined with T cell agonists and anti-PD-1, can augment therapeutic efficacy. Here we report preliminary immunological analyses of patients enrolled in a first-in-human immunotherapy-trio study of multivalent autophagosome vaccine (DPV-001), with sequenced checkpoint inhibition (anti-PD-1; retifanlimab), with/without anti-GITR agonist (INCAGN-1949), in recurrent or metastatic HNSCC (NCT04470024).

Methods: Peripheral blood (PB) and sera are collected regularly and PB are evaluated by flow cytometry. Biopsies obtained at baseline, D15 and D45 are analyzed by multiplex IF and 10x Genomics scRNA-Seq. Sera are being analyzed by phage immunoprecipitation (PhIP) sequencing for reactivity against the human proteome.

Results: Preliminary results document increases in activated CD4 and CD8 effector memory T cells (TEM) with vaccine alone. Changes in tumor microenvironment (TEM) were also observed with increased infiltration of immune cells. Evaluation of changes to humoral immunity, T cell function and TCR analyses are ongoing.

Conclusions: We previously reported immunological monitoring of a phase I/II trial of an autophagosome cancer vaccine (DPV-001) containing more than 300 shared cancer antigens, as adjuvant therapy for NSCLC. Vaccination induced or augmented immune responses to more than 50 cancer antigens shared with head and neck squamous cell carcinoma (HNSCC). Preclinical studies combining this cancer vaccine with αGITR agonist and αPD-1 augmented therapeutic efficacy [PMID: 31747946], and provided the rationale for the current study. This is the first clinical trial to perform such a study with αGITR agonist (INCAGN-1949), in humans.

Support: Incyte, Providence Medical Foundation, The Harder Family, Nancy Lematta.

Citation Format: Rom S. Leidner, Matthew H. Taylor, Tarsem L. Moudgil, Tanisha L. Christie, Yoshinobu Koguchi, Alexa Dowdell, William L. Redmond, Shawn M. Jensen, Carmen Ballesteros-Merino, Jake A. Vancampen, Venkatesh Rajamanickam, Brady M. Bernard, Christopher Paustian, Traci L. Hilton, Hong-Ming Hu, Richard B. Bell, Walter J. Urba, Carlo B. Bifulco, Brian Piening, Bernard A. Fox. Preliminary immunological monitoring of first-in-human immunotherapy-trio for advanced head and neck squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr CT502.

Identification of clinically actionable biomarkers via routine comprehensive genomic profiling across a large community health system

e15035

Background: Precision therapies and immunotherapies have revolutionized cancer care, with novel genomic biomarker-associated therapies being introduced into clinical practice rapidly. We assessed the utility of comprehensive genomic profiling (CGP)-based testing for identifying biomarkers associated with approved therapies, and therapies in precision medicine basket clinical trials (CT) across a large cohort of advanced cancer patients in the Providence health system. Methods: Advanced cancer patients were tested utilizing the Providence CGP workflow between 2019-2021. Clinical actionability was assessed for CGP and compared with results from an in silico 50-gene panel based on a previously utilized lab-developed test at Providence. Clinical actionability was assessed based on OncoKB and alterations were assigned as: FDA recognized (Level 1), standard of care (Level 2), FDA approved/investigational drug in another indication or having compelling clinical evidence (Level 3). CT matching was assessed based on enrollment criteria for ASCO-TAPUR, NCI-MATCH and My Pathway CTs at time of testing. Pooled electronic medical record and genomic data were curated and standardized. Results: Of the 3,218 advanced cancer patients tested with CGP, 52% were female, 80% were white, and median age was 67 years. Across 31 tumor types, the most commonly tested were lung (26%), bowel/colon (16%), and breast (9%). Overall, 48% of patients tested with CGP harbored at least one actionable biomarker (OncoKB Levels1/2/3). Clinical actionability was significantly higher in the CGP cohort compared to the in silico cohort based on presence of at least one Level 1 biomarker (45% vs. 19%, p < 0.001). CGP cohort had higher proportion of patients with multiple/co-occurring Level 1 biomarkers compared to in silico cohort (20% vs. 9%, p < 0.001). Of the most prevalent tumor types, 57% lung, 94% bowel/colon, and 37% breast had Level 1 alterations with CGP testing. Notably, 49% of CGP cohort vs. 23% in silico cohort (p < 0.001) harbored a biomarker matching to one or more arms of the three basket CTs. Conclusions: CGP and small panel testing can both identify patients eligible for approved therapies and/or basket CTs with CGP having significantly higher clinical actionability and CT eligibility. We expect value of CGP to increase as biomarker actionability transforms clinical practice.

Pathogenic fusion detection in solid malignancies utilizing RNA-DNA based comprehensive genomic profiling (CGP) testing

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Background: Gene fusions caused by chromosomal rearrangements comprise a key category of oncogenic driver mutations. However, given the diverse array of potentially novel loci where each proto-oncogene can translocate, many assays including DNA-based CGP have technical limitations that disallow the detection of all relevant fusion partners potentially leading to false negatives. Hybrid Capture RNA sequencing renders a more comprehensive evaluation of genes and allows detection of novel and known fusion partners. Here we assessed the impact of utilizing in-house CGP testing with a paired RNA-DNA hybrid assay in the identification of pathogenic fusions and their potential clinical actionability for patients with solid tumors across a large US health system. Methods: Patients in the Providence health system diagnosed with advanced solid tumor malignancies over a two-year period (2019-2021) received reflex CGP testing at the time of diagnosis utilizing an internally validated workflow. DNA/RNA sequencing results as well as histology and staging information were curated from deidentified electronic medical records and in-house databases, and tumor types were mapped to OncoTree tissue categories. Potential clinical actionability was assessed based on OncoKB therapeutic levels 1-3 and clinical trial eligibility matched to the biomarker inclusion criteria for ASCO TAPUR, NCI-MATCH and MyPathway studies (both without time limits and at time of testing). Results: The median patient age at diagnosis was 67 years, 52% of patients were female, and the majority (80%) were white. Across all tested advanced solid tumors, 6.7% (217/3218) were found to harbor a pathogenic fusion. The tumor types most enriched in this set of pathogenic fusions were prostate (30%), lung (27%), CUP (10%) and breast (9%). 29% (n = 64) of the identified pathogenic fusions were identified as actionable based on OncoKB criteria (levels 1-3), and 31% (n = 69) matched to one or more arms in the ASCO TAPUR, NCI-MATCH or MyPathway basket clinical trials. The most frequent actionable fusion driver genes identified were ALK (12%), FGFR 1-3 (12%), RET (7%) NTRK 1-3 (3%), and ROS1 (2%) and a subset of these key drivers were fused with novel gene pairs. A subset of fusions co-occurred with other targetable biomarkers, with the most common comprising tumor mutational burden high (TMB-H) (13%), PIK3CA (7%) and high microsatellite instability (MSI-H) (2%). Conclusions: In-house CGP testing utilizing an RNA-DNA based assay identified actionable fusion targets across tumor types, with many novel fusion partners that may be undetectable by prior generation sequencing assays. While many of these actionable targets are rare individually, the expanding totality of actionable gene alterations supports the growing utility of CGP for identifying patients who are candidates for approved targeted therapies and clinical trials.

Transcriptomic profiles of neoantigen-reactive T cells in human gastrointestinal cancers

Tumor-infiltrating neoantigen-reactive T cells can mediate regression of metastatic gastrointestinal cancers yet remain poorly characterized. We performed immunological screening against personalized neoantigens in combination with single-cell RNA sequencing on tumor-infiltrating lymphocytes from bile duct and pancreatic cancer patients to characterize the transcriptomic landscape of neoantigen-reactive T cells. We found that most neoantigen-reactive CD8⁺ T cells displayed an exhausted state with significant CXCL13 and GZMA co-expression compared with non-neoantigen-reactive bystander cells. Most neoantigen-reactive CD4⁺ T cells from a patient with bile duct cancer also exhibited an exhausted phenotype but with overexpression of HOPX or ADGRG1 while lacking IL7R expression. Thus, neoantigen-reactive T cells infiltrating gastrointestinal cancers harbor distinct transcriptomic signatures, which may provide new opportunities for harnessing these cells for therapy.

Abstract P3-08-05: Multi-omic profiling of simultaneous ductal carcinoma in situ and invasive breast cancer

Background: Simultaneous ductal carcinoma in situ (DCIS) and invasive breast cancer (IBC) is very common. However, it is not clear how often these histologies are clonally related or the mechanism by which DCIS evolves into IBC. In this study we evaluated tissue samples of DCIS and IBC by DNA and RNA sequencing from 39 patients with concurrent disease.Methods: Patients were identified from the Swedish Cancer Institute Breast Cancer Database starting sequentially with 2018 backwards to identify candidates with simultaneous DCIS and IBC. Individual pathologic review was performed from the cohort of patients who had had modified radical mastectomy to select 50 cases for analysis of normal breast, DCIS, and invasive disease. Sequencing was performed using the Tempus xT solid tumor assay (DNA-seq of 648 genes at 500x coverage, full transcriptome RNA-seq). The mutations identified by this assay include germline and/or somatic single nucleotide variants, insertions/deletions, and copy number variations. Results: Thirty-nine cases had adequate tissue for both DCIS and IBC for DNA and 31 for RNA analysis. DCIS and IBC were in the same quadrant of the breast for all cases. All IBC cases were ductal carcinoma. 38/39 IBC were estrogen receptor (ER) positive, 33/39 were progesterone receptor (PR) positive. 5 were HER2/neu amplified (three ER+/PR-, 1 ER+/PR+, 1 ER/PR-). 32/39 had Ki67 of 20% or less (IQR 14(9,19.5)). 35/39 were T1 or T2. Three were T3 and one T4. 21/39 were N0, 4/39 N1mic, 9/39 N1a, 3/33 N2a 2/39 N3a.For DCIS 24/39 had both genomic variants and copy number changes (V+C+), 7/39 were V+C-, 5/39 were V-C+ and 3/39 V-C-. For IBC 25/39 were V+C+, 7/39 were V+C-, 6/39 were V-C+, and 1/39 V-C-. In total, there were 36 unique genomic variants seen in DCIS but not the corresponding invasive sample. In contrast, there were 32 total unique variants seen in invasive but not the corresponding DCIS and 38 variants were seen in both samples. The one BRCA variant seen in both samples of a single patient was BRCA1 p.Q284, a known pathogenic variant but gBRCA normal. There were 86 copy number changes seen in DCIS but not IBC, 75 copy number changes seen in IBC but not DCIS and 47 copy number changes seen in both DCIS and IBC. 24/39 patients shared at least one common variant and 22/39 shared at least one copy number change. 4/39 had no copy changes in either sample but all of these had genomic variants. 5/39 had no variants in either sample but all of these had copy number changes. PIK3CA was seen in 2/39 IBC, 2/39 DCIS and 2/39 in both. TMB IQR was 1.6(1.1, 3.4) for IBC and 2.1 (1.1,3.2) for DCIS. All samples tested for MSI were stable. Only one patient had identical genomic variants and copy changes in both DCIS and IBC. The most frequent changes were:

RNA sequencing revealed 1178 genes with significant gene expression differences between paired DCIS and IBC (q&lt;0.001). RNA-seq data was quantified using Kallisto and differential gene expression was assessed using DESeq2. Pathway enrichment was performed using rank GSEA against the MSigDB C2 collection (filtered to KEGG, Reactome and Biocarta pathways only). Upregulated pathways in DCIS involved more immunogenic pathways while IBC upregulated pathways involved proliferation and cell cycling. Conclusions: The transition from DCIS to IBC is a dynamic process. How much of these differences are the result of tumor heterogeneity and temporal factors as opposed to truly separate clones will require more study. This could have significant implications for the treatment of DCIS.

VariantGain/Loss of FunctionIBC onlyDCIS onlySame in BothTotalTP53Loss53614MAP3K1Loss51511GATA3Gain3249KM2TCLoss0538PTENLoss2237Copy ChangeMCL1 (1q21.2)Gain68822CKS1B (1q21.3)Gain95619ERRB2 (17q12)Gain0459JAK1 (1p31.3)Loss2428IKZF1 (7p12.1)Loss2327

Citation Format: Henry G Kaplan, Anna B Berry, Alexa Dowdell, Brian Piening. Multi-omic profiling of simultaneous ductal carcinoma in situ and invasive breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P3-08-05.

Systematic review of transcriptome and microRNAome associations with gestational diabetes mellitus

PURPOSE

Gestational diabetes (GDM) is associated with increased risk for preterm birth and related complications for both the pregnant person and newborn. Changes in gene expression have the potential to characterize complex interactions between genetic and behavioral/environmental risk factors for GDM. Our goal was to summarize the state of the science about changes in gene expression and GDM.

DESIGN

The systematic review was conducted using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines.

METHODS

PubMed articles about humans, in English, from any date were included if they described mRNA transcriptome or microRNA findings from blood samples in adults with GDM compared with adults without GDM.

RESULTS

Sixteen articles were found representing 1355 adults (n=674 with GDM, n=681 controls) from 12 countries. Three studies reported transcriptome results and thirteen reported microRNA findings. Identified pathways described various aspects of diabetes pathogenesis, including glucose and insulin signaling, regulation, and transport; natural killer cell mediated cytotoxicity; and fatty acid biosynthesis and metabolism. Studies described 135 unique miRNAs that were associated with GDM, of which eight (miR-16-5p, miR-17-5p, miR-20a-5p, miR-29a-3p, miR-195-5p, miR-222-3p, miR-210-3p, and miR-342-3p) were described in 2 or more studies. Findings suggest that miRNA levels vary based on the time in pregnancy when GDM develops, the time point at which they were measured, sex assigned at birth of the offspring, and both the pre-pregnancy and gestational body mass index of the pregnant person.

CONCLUSIONS

The mRNA, miRNA, gene targets, and pathways identified in this review contribute to our understanding of GDM pathogenesis; however, further research is warranted to validate previous findings. In particular, longitudinal repeated-measures designs are needed that control for participant characteristics (e.g., weight), use standardized data collection methods and analysis tools, and are sufficiently powered to detect differences between subgroups. Findings may be used to improve early diagnosis, prevention, medication choice and/or clinical treatment of patients with GDM.

iNetModels 2.0: an interactive visualization and database of multi-omics data

It is essential to reveal the associations between various omics data for a comprehensive understanding of the altered biological process in human wellness and disease. To date, very few studies have focused on collecting and exhibiting multi-omics associations in a single database. Here, we present iNetModels, an interactive database and visualization platform of Multi-Omics Biological Networks (MOBNs). This platform describes the associations between the clinical chemistry, anthropometric parameters, plasma proteomics, plasma metabolomics, as well as metagenomics for oral and gut microbiome obtained from the same individuals. Moreover, iNetModels includes tissue- and cancer-specific Gene Co-expression Networks (GCNs) for exploring the connections between the specific genes. This platform allows the user to interactively explore a single feature's association with other omics data and customize its particular context (e.g. male/female specific). The users can also register their data for sharing and visualization of the MOBNs and GCNs. Moreover, iNetModels allows users who do not have a bioinformatics background to facilitate human wellness and disease research. iNetModels can be accessed freely at https://inetmodels.com without any limitation.

iNetModels 2.0: an interactive visualization and database of multi-omics data

It is essential to reveal the associations between various omics data for a comprehensive understanding of the altered biological process in human wellness and disease. To date, very few studies have focused on collecting and exhibiting multi-omics associations in a single database. Here, we present iNetModels, an interactive database and visualization platform of Multi-Omics Biological Networks (MOBNs). This platform describes the associations between the clinical chemistry, anthropometric parameters, plasma proteomics, plasma metabolomics, as well as metagenomics for oral and gut microbiome obtained from the same individuals. Moreover, iNetModels includes tissue- and cancer-specific Gene Co-expression Networks (GCNs) for exploring the connections between the specific genes. This platform allows the user to interactively explore a single feature's association with other omics data and customize its particular context (e.g. male/female specific). The users can also register their data for sharing and visualization of the MOBNs and GCNs. Moreover, iNetModels allows users who do not have a bioinformatics background to facilitate human wellness and disease research. iNetModels can be accessed freely at https://inetmodels.com without any limitation.

Cancer microenvironment and genomics: evolution in process

Cancer heterogeneity is a result of genetic mutations within the cancer cells. Their proliferation is not only driven by autocrine functions but also under the influence of cancer microenvironment, which consists of normal stromal cells such as infiltrating immune cells, cancer-associated fibroblasts, endothelial cells, pericytes, vascular and lymphatic channels. The relationship between cancer cells and cancer microenvironment is a critical one and we are just on the verge to understand it on a molecular level. Cancer microenvironment may serve as a selective force to modulate cancer cells to allow them to evolve into more aggressive clones with ability to invade the lymphatic or vascular channels to spread to regional lymph nodes and distant sites. It is important to understand these steps of cancer evolution within the cancer microenvironment towards invasion so that therapeutic strategies can be developed to control or stop these processes.

Germinal center reactions in tertiary lymphoid structures associate with neoantigen burden, humoral immunity and long-term survivorship in pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) has traditionally been thought of as an immunologically quiescent tumor type presumably because of a relatively low tumor mutational burden (TMB) and poor responses to checkpoint blockade therapy. However, many PDAC tumors exhibit T cell inflamed phenotypes. The presence of tertiary lymphoid structures (TLS) has recently been shown to be predictive of checkpoint blockade response in melanomas and sarcomas, and are prognostic for survival in PDAC. In order to more comprehensively understand tumor immunity in PDAC patients with TLS, we performed RNA-seq, single and multiplex IHC, flow cytometry and predictive genomic analysis on treatment naïve, PDAC surgical specimens. Forty-six percent of tumors contained distinct T and B cell aggregates reflective of “early-stage TLS” (ES-TLS), which correlated with longer overall and progression-free survival. These tumors had greater CD8⁺ T cell infiltration but were not defined by previously published TLS gene-expression signatures. ES-TLS⁺ tumors were enriched for IgG1 class-switched memory B cells and memory CD4⁺ T cells, suggesting durable immunological memory persisted in these patients. We also observed the presence of active germinal centers (mature-TLS) in 31% of tumors with lymphocyte clusters, whose patients had long-term survival (median 56 months). M-TLS-positive tumors had equivalent overall T cell infiltration to ES-TLS, but were enriched for activated CD4⁺ memory cells, naive B cells and NK cells. Finally, using a TCGA-PDAC dataset, ES-TLS⁺ tumors harbored a decreased TMB, but M-TLS with germinal centers expressed significantly more MHCI-restricted neoantigens as determined by an in silico neoantigen prediction method. Interestingly, M-TLS⁺ tumors also had evidence of increased rates of B cell somatic hypermutation, suggesting that germinal centers form in the presence of high-quality tumor neoantigens leading to increased humoral immunity that confers improved survival for PDAC patients.

AbbreviationsTLS: tertiary lymphoid structures; GC: germinal center(s); PDAC: pancreatic ductal adenocarcinoma; RNA-seq: RNA sequencing; BCRseq: B cell receptor sequencing; HEV: high endothelial venule; PNAd: peripheral node addressin; TMB: tumor mutational burden; TCGA: the cancer genome atlas; PAAD: pancreatic adenocarcinoma; FFPE: formalin fixed paraffin embedded; TIME: tumor immune microenvironment.

Metabolic Dynamics and Prediction of Gestational Age and Time to Delivery in Pregnant Women

Metabolism during pregnancy is a dynamic and precisely programmed process, the failure of which can bring devastating consequences to the mother and fetus. To define a high-resolution temporal profile of metabolites during healthy pregnancy, we analyzed the untargeted metabolome of 784 weekly blood samples from 30 pregnant women. Broad changes and a highly choreographed profile were revealed: 4,995 metabolic features (of 9,651 total), 460 annotated compounds (of 687 total), and 34 human metabolic pathways (of 48 total) were significantly changed during pregnancy. Using linear models, we built a metabolic clock with five metabolites that time gestational age in high accordance with ultrasound (R = 0.92). Furthermore, two to three metabolites can identify when labor occurs (time to delivery within two, four, and eight weeks, AUROC ≥ 0.85). Our study represents a weekly characterization of the human pregnancy metabolome, providing a high-resolution landscape for understanding pregnancy with potential clinical utilities.

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Weekly metabolome of maternal blood changes dynamically through healthy pregnancy

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A metabolic clock of five blood metabolites accurately predicts gestational age

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Two to three metabolites identify labor onset within two, four, and eight weeks

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Women with metabolic clocks that outpaced ultrasound evaluation tend to deliver earlier

480 Preliminary evaluation of a novel coronavirus vaccine (CORVax) using electroporation of plasmid DNA encoding a stabilized prefusion SARS-CoV-2 spike protein alone or with transfection of plasmid IL-12

Background

SARS-CoV-2 (CoV2) has precipitated a global pandemic and the effectiveness of standard vaccine strategies to induce potent and persistent immunity to CoV2 is in question, particularly for the elderly. This problem is not dissimilar to what we have struggled with in our quest to induce immunity to cancer antigens, where vaccine-induced anti-cancer immune responses can be weak. Here, we describe a novel vaccine approach which leverages electroporation (EP) of a plasmid encoding a prefusion stabilized CoV2 spike protein (CORVax). As IL-12 has been shown to augment the efficacy of immunotherapy in aged mice,1 we have initiated studies to evaluate if plasmid IL-12 (TAVO™) can similarly augment anti-CoV2 immune responses in young mice and have planned studies in aged animals.

Methods

A prefusion stabilized CoV2 spike plasmid expression vector was constructed, a master cell bank generated and clinical-grade plasmid manufactured. C57BL/6 and BALB/c were vaccinated via intramuscular (IM) and/or intradermal (ID) injection followed immediately by EP of plasmids encoding the CoV2 spike protein with or without plasmid-encoded murine IL-12 on days 1 and 14 or 21. Mice were followed for >120 days to assess safety. Splenocytes and serum were harvested at different time points to interrogate virus-specific cellular responses as well anti-spike IgG1/IgG2 antibody titers. A surrogate viral neutralization test (sVNT) assessed serum blockade of soluble hACE2R binding to immobilized CoV2 spike.

Results

Preliminary data shows that EP of CORVax alone or combined with IL-12 was safe. EP of CORVax was able to elicit anti-Spike IgG antibodies (IC50 = 1/2112), as well as IgG antibodies targeting the receptor binding domain of the Spike protein (IC50 = 1/965) approximately 40 days after the booster vaccination. In 2 of 2 experiments, CORVax combined with IL-12 significantly (P<0.0001) increased the sVNT titers at 2 months, but this benefit was lost by 3 months.

Conclusions

Early preclinical data shows that EP of CORVax can induce IgG responses to CoV2 Spike and the receptor binding domain (RBD) as well as apparent viral neutralizing activity. The addition of IL-12, at least transiently, increased sVNT titer. We plan to investigate alternate vaccine boosting strategies while extending these studies into aged animals and initiate a clinical trial in the near future.

References

Ruby CE, Weinberg AD. OX40-Enhanced tumor rejection and effector T cell differentiation decreases with age. J Immunol2009;182:1481–9. https://doi.org/10.4049/jimmunol.182.3.1481.

Abstract B01: Surgical outcomes following neoadjuvant hypofractionated radiation in combination with nivolumab: High rate of pathologic complete response in patients with p16+ head and neck squamous cell carcinoma

Hypothesis: Hypofractionated radiation therapy (HFRT) in combination with checkpoint blockade may modulate the tumor microenvironment to induce favorable antitumor immune responses and enhance surgical resection.

Purpose: The purpose of this first-in-human phase Ib clinical trial was to test the safety and immunologic effects of neoadjuvant immunoradiotherapy prior to surgery in patients with head and neck squamous cell carcinoma (HNSCC) (NCT03247712).

Methods: Patients with previously untreated stage I-III (AJCC 8th Ed) p16 positive squamous cell carcinoma of the oropharynx (OPSCC) or cervical lymph nodes from an unknown primary (SCCUP) were eligible to enroll. Neoadjuvant treatment consisted of sandwich nivolumab in combination with HFRT to gross tumor volume in one of two dose-finding cohorts of 8Gy x5 (Monday-Friday) or 8Gy x3 (Monday-Wednesday-Friday), followed five weeks later by definitive surgical resection. The primary endpoint was &lt; 33% unplanned surgical delay; secondary endpoint was pathologic response. Surgical complications were assessed using the Clavien-Dindo scale, a validated scoring tool for surgical complications, applied for 90 days postoperatively. Serial blood and tissue specimens were obtained longitudinally for immunogenomic changes over time.

Results: 10 patients (stage: T0N1M0, N=3; T1N1M0, N=1; T2N1M0, N=6) enrolled and underwent neoadjuvant immunoradiotherapy prior to surgery with curative intent, which consisted of selective neck dissection (level II-IV) and transoral robotic assisted oropharyngectomy for patients with mucosal disease. Surgery was safely performed in all patients without delay, thus meeting the primary endpoint. 7 patients demonstrated a partial radiologic response (PR) by RECIST criteria prior to surgery and 3 patients had stable disease (SD). The pathologic complete response rate (pCR) was 90% (8GyX5 cohort=5/5; 8GyX3 cohort=4/5) with the remaining patient achieving a major pathologic response (MPR; &lt;10% viable tumor cells). All patients were successfully downstaged prior to surgery (ypT0N0M0=9; ypT0N1M0=1) and no patient required adjuvant radiation or chemoradiation. Grade 3 surgical complications as assessed by Clavien-Dindo occurred in 3/5 patients in the 8Gy X5 cohort, but there were no grade 3 or 4 complications in in the 8Gy X3 cohort. All patients are alive without evidence of disease (median follow-up &lt;1 year).

Conclusions: Neoadjuvant HFRT in combination with nivolumab is safe, does not delay definitive surgical resection, and results in significant downstaging with major pathologic response. A lower toxicity profile favors a radiation dose of 8Gy x3 for future development in both human papilloma virus (HPV)-related and HPV-unrelated HNSCC.

Citation Format: R. Bryan Bell, Rom Leidner, Marcus Couey, Ashish Patel, Amber Watters, Hong Ziao, Carlo Bifulco, Brian Piening, George Morris, Lessli Rushforth, Dawn Brucker, Shoren Nemeth, Kristina Young, Michael Gough, Marka Crittenden. Surgical outcomes following neoadjuvant hypofractionated radiation in combination with nivolumab: High rate of pathologic complete response in patients with p16+ head and neck squamous cell carcinoma [abstract]. In: Proceedings of the AACR-AHNS Head and Neck Cancer Conference: Optimizing Survival and Quality of Life through Basic, Clinical, and Translational Research; 2019 Apr 29-30; Austin, TX. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(12_Suppl_2):Abstract nr B01.

Tumor antigen expression and survival of patients with previously treated advanced non-small cell lung cancer (NSCLC) receiving viagenpumatucel-L (HS-110) plus nivolumab

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Background: Viagenpumatucel-L (HS-110) is an allogeneic cellular vaccine derived from a human lung adenocarcinoma cell line transfected with gp96-Ig fusion protein. Gp96-Ig functions as an antigen chaperone for dendritic cell activation and direct CD8+T cell expansion via cross presentation. DURGA is a multi-cohort study evaluating HS-110 plus anti-PD-1 mAbs in patients (pts) with advanced NSCLC. We report on Cohort A, which enrolled previously-treated pts who had not received an anti-PD(L)1 prior to study entry. Methods: Primary objectives were safety and objective response rate (ORR). Overall Survival (OS) was a secondary endpoint. Pts received 1 X 107 HS-110 cells intradermally every week for 18 wks and nivolumab until tumor progression. To determine cancer testis antigen (CTA) overexpression from baseline pt tumor samples, hybrid-capture RNA-seq libraries were prepared from macrodissected formalin fixed paraffin embedded tumor tissue and sequenced on an Illumina NovaSeq 6000. Gene-level transcripts were quantified using the Salmon software package. Results: 47 pts were enrolled into Cohort A. ORR and clinical benefit rate (CR + PR + SD) were 21% and 43%, respectively, with a 17.2 month median duration of response. Median OS was 28.7 months (mos), with a median follow up of 15.7 mos. One and 2-year survival were 57% and 36%, respectively. A prespecified exploratory analysis of CTA expression level in baseline pt tumor tissue was performed. 50% of pts shared at least 8 of the 39 total antigens overexpressed by HS110. Although there was no difference in ORR between these groups, mOS was higher in pts with tumors that shared ≥ 8 antigens with HS-110 (not reached (NR) [95%CI: 10.3 mos, NR] vs 6.7 mos [95%CI: 1.4 mos, NR]), p = 0.028. Pts whose tumors expressed the ZNF492 antigen also had improved OS (NR [95%CI: 11.6 mos, NR] vs 7.2 mos [95%CI: 1.6 mos, NR]), p = 0.03. All pts experienced at least one adverse event (AE), and the most common AEs were fatigue (28%), arthralgia (19%) and cough (17%). There were 2 grade 5 AEs not related to treatment. Conclusions: The combination of HS-110 and nivolumab appears safe and well tolerated. OS was improved in pts whose tumors express ≥ 8 shared antigens with HS110, as well as in those who specifically expressed ZNF492. Further exploration of antigen expression as a predictor for treatment outcome with HS110 plus nivolumab is ongoing. Clinical trial information: NCT02439450 .

Abstract CT182: Neoadjuvant immuno-radiotherapy (NIRT) in head and neck cancer: Phase I/Ib study of combined PD-1/SBRT prior to surgical resection

Background: Standard treatment of locally advanced HPV-associated oropharyngeal HNSCC includes definitive chemoRT or surgery followed by risk-adapted adjuvant RT +/- chemo. These approaches provide high rates of long term survival, but are associated with significant subacute as well as long term morbidity. Therefore, increasing efforts have been directed at exploring alternative approaches. Combined SBRT and PD-1 blockade may have particularly favorable properties for anti-tumor immune response in HNSCC (Gough 2009). We present phase I safety & efficacy data from the NIRT trial of neoadjuvant nivolumab/SBRT in oropharyngeal p16+ HNSCC (NCT03247712).

Methods: Patients with p16+ oropharyngeal or unknown primary HNSCC, with clinical indications for adjuvant RT, or upfront TORS ineligible due to tumor size, could enroll. Patients received Nivo 240mg IV q2wks x3 prior to surgery, with SBRT to GTV+3mm delivered between Nivo doses 1 & 2, in two dose finding cohorts (n=5 each): 8Gy x5 daily (M-F) and de-escalated 8Gy x3 (M,W,F). Surgery was performed 5 weeks post-SBRT followed by adjuvant Nivo 480mg IV q4wks x3, starting 4 weeks post-op. The primary endpoint was &lt; 33% unplanned surgical delay; the secondary endpoint was pathologic response by irPRC (Cottrell 2018).

Results: There were no unplanned surgical delays. All patients had radiologic evidence of decreased tumor size prior to surgery, but none showed a CR by RECIST. Remarkably, the pathologic CR rate was 100% in the 8Gy x 5 cohort (5/5) and 80% In the 8 Gy x 3 cohort (4/5), with the remaining patient achieving MPR (major pathologic response; &lt;10% residual viable tumor). G3 toxicity was observed after surgery in both cohorts but was higher in the 8 Gy x 5 cohort. No G4 or higher toxicity was observed. Interestingly, G2 adrenal insufficiency was observed in 50% (5/10), a higher rate than previously reported with PD-1 blockade for recurrent/metastatic HNSCC. Notably, patients did not experience xerostomia or ageusia rates associated with standard adjuvant radiation in HNSCC. Tissue responses were characterized by robust inflammatory infiltrates into the regression bed and cholesterol clefts, as previously described. Circulating immune cells, baseline tissue, end of RT biopsy and surgical specimen were analyzed using flow cytometry and RNAseq to characterize of immunologic changes over time. There have been no local or distant failures, but median follow up remains &lt; 1 year.

Conclusions: Neoadjuvant combined PD-1/SBRT to GTV+3mm dosed at either 8Gy x5 (M-F) or 8Gy x3 (M,W,F) did not delay HNSCC surgery in this Phase I trial (n=10; five per dose). Potent anti-tumor response was observed in all cases (CR=9 + MPR=1). A high response rate and lower toxicity profile favors the 8Gy x3 cohort for development. This study represents a major paradigm shift in the approach to treatment of locally advanced p16+ oropharyngeal cancers.

Citation Format: Rom Leidner, R. Bryan Bell, Kristina Young, Brendan Curti, Marcus Couey, Ashish Patel, Amber Watters, Hong Xiao, Carlo Bifulco, Brian Piening, George Morris, Lessli Rushforth, Dawn Brucker, Shorin Nemeth, Michael Gough, Marka Crittenden. Neoadjuvant immuno-radiotherapy (NIRT) in head and neck cancer: Phase I/Ib study of combined PD-1/SBRT prior to surgical resection [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr CT182.

Responses of metastatic basal cell and cutaneous squamous cell carcinomas to anti-PD1 monoclonal antibody REGN2810

Background

Basal cell carcinoma (BCC) and cutaneous squamous cell carcinoma (CSCC) share exposure to UV light as the dominant risk factor, and these tumors therefore harbor high mutation burdens. In other malignancies, high mutation burden has been associated with clinical benefit from therapy with antibodies directed against the Programmed Death 1 (PD-1) immune checkpoint receptor. Highly mutated tumors are more likely to express immunogenic tumor neoantigens that attract effector T cells, which can be unleashed by blockade of the PD-1 immune checkpoint.

Case presentations

This report describes a patient with metastatic BCC and a patient with metastatic CSCC who were treated with REGN2810, a fully human anti-PD-1 monoclonal antibody, in an ongoing phase 1 trial (NCT02383212). The CSCC patient has experienced an ongoing complete response (16+ months), and the BCC patient has experienced an ongoing partial response (12+ months).

Conclusions

These case reports suggest that UV-associated skin cancers, beyond melanoma, are sensitive to PD-1 blockade.

Trial registration

Clinicaltrials.gov NCT02383212. Registered 2 February 2015.

Epidemiology of healthcare associated infections in Germany: Nearly 20 years of surveillance

OBJECTIVE

To describe the epidemiology of healthcare-associated infections (HAI) in hospitals participating in the German national nosocomial infections surveillance system (KISS).

METHOD

The epidemiology of HAI was described for the surveillance components for intensive care units (ITS-KISS), non-ICUs (STATIONS-KISS), very low birth weight infants (NEO-KISS) and surgical site infections (OP-KISS) in the period from 2006 to 2013. In addition, risk factor analyses were performed for the most important infections of ICU-KISS, NEO-KISS and OP-KISS.

RESULTS

Data from a total of 3,454,778 ICU patients from 913 ICUs, 618,816 non-ICU patients from 142 non-ICU wards, 53,676 VLBW from 241 neonatal intensive care units (NICU) and 1,005,064 surgical patients from operative departments from 550 hospitals were used for analysis. Compared with baseline data, a significant reduction of primary bloodstream infections (PBSI) and lower respiratory tract infections (LRTI) was observed in ICUs with the maximum effect in year 5 (or longer participation) (incidence rate ratio 0.60 (CI95 0.50-0.72) and 0.61 (CI95 0.52-0.71) respectively). A significant reduction of PBSI and LRTI was also observed in NEO-KISS when comparing the baseline situation with the 5th year of participation (hazard ratio 0.70 (CI95 0.64-0.76) and 0.43 (CI95 0.35-0.52)). The effect was smaller in operative departments after the introduction of OP-KISS (OR 0.80; CI95 0.64-1.02 in year 5 or later for all procedure types combined). Due to the large database, it has not only been possible to confirm well-known risk factors for HAI, but also to identify some new interesting risk factors like seasonal and volume effects.

CONCLUSIONS

Participating in a national surveillance system and using surveillance data for internal quality management leads to substantial reduction of HAI. In addition, a surveillance system can identify otherwise not recognized risk factors which should - if possible - be considered for infection control management and for risk adjustment in the benchmarking process.

Stereochemistry of 2,6-Dipyridine Substituted N-Benzyl-4-piperidone Mono- and Dicarboxylates and of the Corresponding Reduction Products

The alkyl N-benzyl-4-piperidone-3-carboxylate (1) is synthesized by a Mannich procedure from pyridine aldehyde, benzylamine and the monoester of acetonedicarboxylate; the corresponding diester 2 is formed by condensation of pyridine aldehyde, benzylamine and dimethyl 3-oxoglutarate. Isomerism is observed with respect to keto-enol tautomerism and cis or trans substitution of the pyridines. The structure of the enol lb (C24H23N3O3) is determined by X-ray analysis: it crystallizes in the triclinic space group P 1̄ with a = 9.965(2), b = 10.476(2), c = 10.838(2) Å, α = 69.48(1), β/3 = 81.56(1), γ = 79.09(1)°, Ζ = 2 and Dx = 1.29 g cm-3. It is refined to R(unweighted) = 0.047 and R(weighted) = 0.045 using 1459 non-equivalent reflections. The structures of la/b and 2a/b were determined by 1H and 13C NMR data. MNDO calculations of 1a/b are discussed. The enols 1/2b are reduced by sodium borohydride. The configuration of the obtained alcohols is determined by NMR data.

[Healthcare-associated infection rates: measuring and comparing. Experiences from the German National Nosocomial Infection Surveillance System (KISS) and from other surveillance systems]

Surveillance of nosocomial infections is meanwhile a cornerstone of infection prevention activities in hospitals. The objective of this article is to compare healthcare-associated infection rates in intensive care patients, neonatal intensive care patients and operated patients (ICU-KISS, OP-KISS, NEO-KISS) of the German nosocomial infection surveillance system (KISS) with the corresponding data of the US American National Healthcare Safety Network (NHSN) and the European Centre for Disease Prevention and Control (ECDC). In general, the methodological differences among the three surveillance systems are minor but there are some exceptions. Therefore, differences between countries have to be interpreted very carefully as they may be due to differences in diagnostics, patient mix, types of interventions, length of stay, selection of participating hospitals, post-discharge surveillance activities and interpretation of case definitions. Organizational aspects, such as mandatory participation with public disclosure on infection rates may also have an impact.

How many outbreaks of nosocomial infections occur in German neonatal intensive care units annually?

BACKGROUND

Outbreaks on neonatal intensive care units (NICUs) achieve huge media interest, but the real number of neonatal outbreaks within a country is unknown.

METHOD

This calculation is based on the data of the component for nosocomial infections in very low birth weight (VLBW) infants of the German national nosocomial infection surveillance system (NEO-KISS) from 2006 to 2011. Almost all German NICUs caring for VLBW infants participated in this surveillance system. A cluster was defined and an outbreak was assumed when at least two cases of severe neonatal infection (bloodstream infection, pneumonia) occurred within a defined time interval in one center with the same pathogen species in different patients. Four different intervals were used for calculation: 14, 30, 60, and 90 days. Infections with coagulase-negative staphylococci (CoNS) were excluded.

RESULTS

A total of 228 NICUs provided data in the six-year study period. A total of 37,038 VLBW infants and 1,361,950 patient days were used for the calculation. 7,405 severe neonatal infections occurred, and a microbiological detection of the pathogen was successful in 2,084 cases. Altogether, between 121 and 280 outbreaks were calculated according to the different time intervals used. Most outbreaks were due to Staphylococcus aureus, followed by Enterococcus spp. and Enterobacter spp.

CONCLUSION

It can be assumed that at least between 26 and 61 neonatal outbreaks with at least two severe infections take place in German NICUs per year. The actual number seems to be higher because only laboratory-confirmed infections in a subgroup of patients were used for the analysis.

Nosocomial infections in very low birthweight infants in Germany: current data from the National Surveillance System NEO-KISS

BACKGROUND

Infants with very low birthweight (< 1 500 g, VLBW) are at increased risk for nosocomial infections (NI). In 2 000, we implemented a surveillance system for VLBW infants in Germany: NEO-KISS. In 2005, a joint committee of healthcare providers and insurance companies required German neonatology departments to participate. As a result, NEO-KISS is now a nationwide surveillance system for NI in VLBW infants.

PATIENTS AND METHODS

We present NEO-KISS data collected between 2007 and 2011 by 228 neonatology departments. Rates of sepsis, pneumonia and necrotising enterocolitis (NEC) were calculated. In order to evaluate the department-specific infection rate we introduced a new indicator: the Standardised Infection Rate (SIR). The SIR considers the department-specific patient distribution (based on the patients' birthweight) and describes the ratio of observed and expected infections (calculated from the reference data for this individual patient distribution). The data presented comprise 33 048 VLBW infants.The incidence density of CVC-associated sepsis 8.6 per 1 000 CVC-days.

RESULTS AND CONCLUSION

The incidence of pneumonia among mechanically ventilated patients was 2.7/1 000 ventilator days. The incidence of NEC was 0.8. The SIR showed strong variation among the participating departments. It is an excellent tool for identifying outliers in nosocomial infection rates and for stimulating activities to decrease the risk of nosocomial infections.

Assessing bias in experiment design for large scale mass spectrometry-based quantitative proteomics

Mass spectrometry-based proteomics holds great promise as a discovery tool for biomarker candidates in the early detection of diseases. Recently much emphasis has been placed upon producing highly reliable data for quantitative profiling for which highly reproducible methodologies are indispensable. The main problems that affect experimental reproducibility stem from variations introduced by sample collection, preparation, and storage protocols and LC-MS settings and conditions. On the basis of a formally precise and quantitative definition of similarity between LC-MS experiments, we have developed Chaorder, a fully automatic software tool that can assess experimental reproducibility of sets of large scale LC-MS experiments. By visualizing the similarity relationships within a set of experiments, this tool can form the basis of systematic quality control and thus help assess the comparability of mass spectrometry data over time, across different laboratories, and between instruments. Applying Chaorder to data from multiple laboratories and a range of instruments, experimental protocols, and sample complexities revealed biases introduced by the sample processing steps, experimental protocols, and instrument choices. Moreover we show that reducing bias by correcting for just a few steps, for example randomizing the run order, does not provide much gain in statistical power for biomarker discovery.