Integrative systems biology reveals NKG2A-biased immune responses correlate with protection in infectious disease, autoimmune disease, and cancer

Infection, autoimmunity, and cancer are principal human health challenges of the 21st century. Often regarded as distinct ends of the immunological spectrum, recent studies hint at potential overlap between these diseases. For example, inflammation can be pathogenic in infection and autoimmunity. T resident memory (TRM) cells can be beneficial in infection and cancer. However, these findings are limited by size and scope; exact immunological factors shared across diseases remain elusive. Here, we integrate large-scale deeply clinically and biologically phenotyped human cohorts of 526 patients with infection, 162 with lupus, and 11,180 with cancer. We identify an NKG2A+ immune bias as associative with protection against disease severity, mortality, and autoimmune/post-acute chronic disease. We reveal that NKG2A+ CD8+ T cells correlate with reduced inflammation and increased humoral immunity and that they resemble TRM cells. Our results suggest NKG2A+ biases as a cross-disease factor of protection, supporting suggestions of immunological overlap between infection, autoimmunity, and cancer.

Antitumor Immune Responses in B2M-Deficient Cancers

β2-microglobulin (B2M) is a critical component of the MHC class I molecule and is required to present tumor antigens to T cells. Its loss results in acquired resistance to immune checkpoint blockade (ICB) therapies. However, there have been well-documented cases of B2M-inactivated tumors responding to ICB, justifying investigation of how an antitumor immune response can be generated to tumors without surface MHC class I. We knocked out B2M in three murine models with varying baseline MHC class I expression and sensitivity to anti-programmed death receptor (PD-1) therapy and analyzed the immune responses. MC38 and YUMMER2.1 without B2M responded to anti-PD-1 alone or with an IL2 agonist, and this was mediated by CD4+ T cells and natural killer (NK) cells. The more aggressive B16 without B2M expression only partially responded to the IL2 agonist, and this was dependent on NK cells. When analyzing nearly 300 pretreatment biopsies from patients with melanoma receiving PD-1 blockade-based therapies, we found infrequent B2M mutations or homozygous loss but more frequent LOH or copy-number gains. B2M LOH was enriched in biopsies from patients without response to therapy, and these biopsies were more frequently infiltrated by activated NK cells. We conclude that in the absence of B2M, activation of CD4+ T cells and NK cells can mediate responses to murine models of PD-1 blockade therapy. In addition, in human melanoma, the intratumoral presence of activated NK cells upon partial B2M loss likely selects against tumor escape through low surface MHC class I expression.

An NKG2A biased immune response confers protection for infection, autoimmune disease, and cancer

Infection, autoimmunity, and cancer are the principal human health challenges of the 21st century and major contributors to human death and disease. Often regarded as distinct ends of the immunological spectrum, recent studies have hinted there may be more overlap between these diseases than appears. For example, pathogenic inflammation has been demonstrated as conserved between infection and autoimmune settings. T resident memory (TRM) cells have been highlighted as beneficial for infection and cancer. However, these findings are limited by patient number and disease scope; exact immunological factors shared across disease remain elusive. Here, we integrate large-scale deeply clinically and biologically phenotyped human cohorts of 526 patients with infection, 162 with lupus, and 11,180 with cancer. We identify an NKG2A+ immune bias as associative with protection against disease severity, mortality, and autoimmune and post-acute chronic disease. We reveal that NKG2A+ CD8+ T cells correlate with reduced inflammation, increased humoral immunity, and resemble TRM cells. Our results suggest that an NKG2A+ bias is a pan-disease immunological factor of protection and thus supports recent suggestions that there is immunological overlap between infection, autoimmunity, and cancer. Our findings underscore the promotion of an NKG2A+ biased response as a putative therapeutic strategy.

ERK mediates interferon gamma-induced melanoma cell death

BACKGROUND

Interferon-gamma (IFNγ) exerts potent growth inhibitory effects on a wide range of cancer cells through unknown signaling pathways. We pursued complementary screening approaches to characterize the growth inhibition pathway.

METHODS

We performed chemical genomics and whole genome targeting CRISPR/Cas9 screens using patient-derived melanoma lines to uncover essential nodes in the IFNγ-mediated growth inhibition pathway. We used transcriptomic profiling to identify cell death pathways activated upon IFNγ exposure. Live imaging experiments coupled with apoptosis assays confirmed the involvement of these pathways in IFNγ-mediated cell death.

RESULTS

We show that IFNγ signaling activated ERK. Blocking ERK activation rescued IFNγ-mediated apoptosis in 17 of 23 (~ 74%) cell lines representing BRAF, NRAS, NF1 mutant, and triple wild type subtypes of cutaneous melanoma. ERK signaling induced a stress response, ultimately leading to apoptosis through the activity of DR5 and NOXA proteins.

CONCLUSIONS

Our results provide a new understanding of the IFNγ growth inhibition pathway, which will be crucial in defining mechanisms of immunotherapy response and resistance.

Ipilimumab with or without nivolumab in PD-1 or PD-L1 blockade refractory metastatic melanoma: a randomized phase 2 trial

In this randomized phase 2 trial, blockade of cytotoxic T-lymphocyte protein 4 (CTLA-4) with continuation of programmed death protein 1 (PD-1) blockade in patients with metastatic melanoma who had received front-line anti-PD-1 or therapy against programmed cell death 1 ligand 1 and whose tumors progressed was tested in comparison with CTLA-4 blockade alone. Ninety-two eligible patients were randomly assigned in a 3:1 ratio to receive the combination of ipilimumab and nivolumab, or ipilimumab alone. The primary endpoint was progression-free survival. Secondary endpoints included the difference in CD8 T cell infiltrate among responding and nonresponding tumors, objective response rate, overall survival and toxicity. The combination of nivolumab and ipilimumab resulted in a statistically significant improvement in progression-free survival over ipilimumab (hazard ratio = 0.63, 90% confidence interval (CI) = 0.41-0.97, one-sided P = 0.04). Objective response rates were 28% (90% CI = 19-38%) and 9% (90% CI = 2-25%), respectively (one-sided P = 0.05). Grade 3 or higher treatment-related adverse events occurred in 57% and 35% of patients, respectively, which is consistent with the known toxicity profile of these regimens. The change in intratumoral CD8 T cell density observed in the present analysis did not reach statistical significance to support the formal hypothesis tested as a secondary endpoint. In conclusion, primary resistance to PD-1 blockade therapy can be reversed in some patients with the combination of CTLA-4 and PD-1 blockade. Clinicaltrials.gov identifier: NCT03033576 .

A Pilot Study of Neoadjuvant Nivolumab, Ipilimumab, and Intralesional Oncolytic Virotherapy for HER2-negative Breast Cancer

Purpose

Neoadjuvant combination immune checkpoint blockade and intralesional oncolytic virotherapy have the potential to activate antitumor responses in patients with breast cancer.

Experimental Design

Eligibility for this pilot phase I trial included patients with localized HER2-negative breast cancer who received systemic nivolumab and ipilimumab and intratumor talimogene laherparepvec (T-VEC; NCT04185311). The primary objective was to evaluate the safety and adverse event profile of immunotherapy combined with T-VEC in patients with localized, HER2-negative breast cancer.

Results

Six patients were enrolled, 4 having relapses after prior neoadjuvant chemotherapy and 2 who were previously untreated. Toxicities included 1 patient having grade 3 hypotension and type 1 diabetes mellitus, 3 patients with hypothyroidism, and all patients having constitutional symptoms known to be associated with the administration of T-VEC. One patient had a pathologic complete response, 3 patients had pathologic partial responses, 1 showed no significant response, and 1 had disease progression. Biopsies demonstrated increased immune cell infiltration in samples from patients who responded to therapy.

Conclusions

This triple immunotherapy regimen provided responses in patients with advanced or relapsed HER2-negative breast cancer, at the expense of long-term toxicities.

Significance

Systemic immune checkpoint blockade with a programmed death receptor 1 and a CTL antigen-4 blocking antibody, combined with intralesional oncolytic virotherapy, is a chemotherapy-free combination aimed at inducing an antitumor immune response locally and systemic immunity.

Highly Parallelized Screening of Functionally Enhanced XNA Aptamers in Uniform Hydrogel Particles

Xeno-nucleic acid (XNA) aptamers based on evolvable non-natural genetic polymers hold enormous potential as future diagnostic and therapeutic agents. However, time-consuming and costly procedures requiring the purification of individual XNA sequences produced by large-scale polymerase-mediated primer extension reactions pose a major bottleneck to the discovery of highly active XNA motifs for biomedical applications. Here, we describe a straightforward approach for rapidly surveying the binding properties of XNA aptamers identified by in vitro selection. Our strategy involves preparing XNA aptamer particles in which many copies of the same aptamer sequence are distributed throughout the gel matrix of a polyacrylamide-encapsulated magnetic particle. Aptamer particles are then screened by flow cytometry to assess target binding affinity and deduce structure-activity relationships. This generalizable and highly parallel assay dramatically accelerates the pace of secondary screening by allowing a single researcher to evaluate 48-96 sequences per day.

Prior anti-CTLA-4 therapy impacts molecular characteristics associated with anti-PD-1 response in advanced melanoma

Immune checkpoint inhibitors (ICIs), including CTLA-4- and PD-1-blocking antibodies, can have profound effects on tumor immune cell infiltration that have not been consistent in biopsy series reported to date. Here, we analyze seven molecular datasets of samples from patients with advanced melanoma (N = 514) treated with ICI agents to investigate clinical, genomic, and transcriptomic features of anti-PD-1 response in cutaneous melanoma. We find that prior anti-CTLA-4 therapy is associated with differences in genomic, individual gene, and gene signatures in anti-PD-1 responders. Anti-CTLA-4-experienced melanoma tumors that respond to PD-1 blockade exhibit increased tumor mutational burden, inflammatory signatures, and altered cell cycle processes compared with anti-CTLA-4-naive tumors or anti-CTLA-4-experienced, anti-PD-1-nonresponsive melanoma tumors. We report a harmonized, aggregate resource and suggest that prior CTLA-4 blockade therapy is associated with marked differences in the tumor microenvironment that impact the predictive features of PD-1 blockade therapy response.

Abstract 4532: Spatial profiling delineates tumor-T-cell dynamics in anti-PD-1-refractory melanoma treated with ipilimumab or ipilimumab plus nivolumab

Background: Immune checkpoint blockade (ICB) therapies promote anti-tumor activity by facilitating CD8 T-cell activation at the tumor site (e.g., anti-PD-1), or in the lymph node, promoting T-cells trafficking to the tumor site (e.g., anti-CTLA-4). Focusing on patients with metastatic melanoma refractory to anti-PD-1 therapy who received ipilimumab ± nivolumab (ipi±nivo), we hypothesize that combination therapy could overcome anti-PD-1 primary resistance in some patients, by facilitating T-cell trafficking and infiltration into the tumor.

Methods: Visium spatial transcriptomics using 18,000 RNA plex (n=10), multiplexed ion beam imaging (MIBI) using 32 protein plex (n=4), and CosMx single cell imaging using 1000 RNA plex (n=2) were performed on paired baseline (n=5) and on-therapy biopsy samples (n=5). Paired samples were derived from patients with complete response to ipi+nivo (n=3), partial response to ipi+nivo (n=1), and no response to ipi monotherapy (n=1).

Results: Visium spatial transcriptomics revealed a decrease in melanoma gene expression clusters and an increase in expression of immune clusters. Further characterization of the immune clusters revealed signatures of CD4+ and CD8+ T cells displaying stronger activation markers, in particular cytotoxic markers and interferon gamma clusters, along with M1 macrophage transcripts. However, further analysis of the paired biopsies in the ipi monotherapy non-responder revealed a concomitant increase in the immune-suppressive M2 macrophages, tolerogenic DCs, regulatory T cells, and exhausted T cells, which was not observed in the ipi+nivo responders. Confirmatory studies performed in two patients (ipi+nivo responder vs ipi non-responder) using MIBI confirmed a decrease in the tumor burden, and large increases in CD8 (199X in ipi+nivo vs 1.52X in ipi), CD4 (22.3X in ipi+nivo vs 8.56X in ipi), and T cells (26.1X in ipi+nivo vs 2.13X in ipi). Focusing on the non-responder (ipi) paired biopsies, CosMx revealed heterogeneous tumor clusters, with little to no immune infiltration in the baseline biopsy, and a decrease in tumor burden with increased markers of immune response and immune suppression in the on-therapy biopsy.

Conclusion: Integrated single cell spatial analyses, on the RNA and protein levels, revealed increased immune cell recruitment to the tumor site in responders to anti-CTLA-4 + anti-PD-1 therapy compared to a non-responder to anti-CTLA-4 monotherapy, and may provide clues to cancer-immune cell interactions in response to ICB. The presence of immune suppressive clusters at the tumor site in the on-therapy biopsy in the anti-CTLA-4 monotherapy would support our hypothesis that while anti-CTLA-4 facilitates T-cell trafficking and infiltration into the tumor site, anti-CTLA-4 alone without anti-PD-1 may not be sufficient to overcome anti-PD-1 primary resistance in some patients.

Citation Format: Nataly Naser Al Deen, Katie M. Campbell, Egmidio Medina, Cynthia R. Gonzalez, Philip O. Scumpia, Antoni Ribas. Spatial profiling delineates tumor-T-cell dynamics in anti-PD-1-refractory melanoma treated with ipilimumab or ipilimumab plus nivolumab. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4532.

Abstract 5965: B2M loss of heterozygosity in melanoma is associated with increased numbers of activated NK cells and higher expression of the NK cell inhibitory ligand, HLA-G

β2-microglobulin (B2M) is a critical subunit of antigen presenting major histocompatibility complex (MHC) class I molecules. Its genetic inactivation in tumor cells has been implicated in tumor-intrinsic immune escape and immunotherapy resistance. Currently, the impact of B2M dysregulation on tumor-immune dynamics requires furthers characterization. Using a clinical dataset of patients with melanoma treated with immune checkpoint blockade (ICB), whole-exome sequencing and bulk RNA-sequencing data from baseline tumor biopsies (n=295) were analyzed to identify somatic B2M alterations and evaluate correlative clinical outcomes, infiltrating immune cells, and gene expression patterns. No loss-of-function mutations in B2M were found; however, 50% of tumors had B2M alterations in the form of homozygous loss (n=2), loss of heterozygosity (LOH; n=56), or copy number gains (n=88). B2M LOH events were overrepresented in tumors from patients who progressed during ICB therapy compared to those who responded (34% versus 19%; Pearson chi-square test, p=0.035). Additionally, tumors with B2M LOH had lower B2M expression compared to B2M-unaltered tumors (Wilcoxon test, p=0.05). Gene set enrichment analysis revealed reduced expression of immune and inflammatory signatures in B2M-LOH tumors. Furthermore, immune cell deconvolution showed that B2M-LOH tumors had lower total immune cell counts, but greater numbers and proportions of activated natural killer (NK) cells (Wilcoxon test, numbers p=0.021, proportions p=0.032). Differential gene expression analysis revealed concordant higher expression of human leukocyte antigen G (HLA-G), an NK cell inhibitory ligand, in B2M-LOH tumors (Wilcoxon test, p=0.0035). Moreover, B2M-LOH progressive tumors had the highest median HLA-G expression and trended toward a positive correlation between increasing HLA-G expression and increasing numbers of activated NK cells (Pearson correlation, r=0.55, p=0.015). In conclusion, melanoma biopsies with B2M LOH were associated with non-response to ICB, had increased presence of activated NK cells, and demonstrated a compensatory increase in HLA-G. These results suggest that in melanoma B2M alterations may be implicated in modulating NK cell interactions and point toward HLA-G potentially playing a role in inhibiting NK cell anti-tumor activity.

Citation Format: Mildred Galvez, Katie M. Campbell, Egmidio Medina, Antoni Ribas. B2M loss of heterozygosity in melanoma is associated with increased numbers of activated NK cells and higher expression of the NK cell inhibitory ligand, HLA-G [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5965.

Abstract 4527: CD8 T cell-melanoma cell interactions in response and resistance to ipilimumab plus nivolumab: Biopsy analysis of SWOG S1616

Background: In the randomized S1616 trial (NCT03033576), patients with metastatic melanoma refractory to anti-PD-1-based therapy had improved progression free survival (PFS, HR = 0.63, p = 0.037) and objective response to ipilimumab plus nivolumab (ipi/nivo, RR 28%) compared to ipilimumab alone (ipi, RR = 9%). We hypothesized that reversal of resistance to PD-1 blockade with CTLA-4 blockade would result in increased CD8 T-cell infiltration in patient biopsies.

Methods: Multiplex ion beam imaging (MIBI) for 32 protein markers, spanning tumor, immune, and stromal cell types, was used to evaluate the tumor microenvironment in melanoma tumor biopsies collected at baseline (N=21 samples) and one month on-treatment (N=22; N=16 paired timepoints). Tumor-immune cell dynamics were determined by comparing baseline and on-treatment biopsies within clinical groups (ipi/nivo response, N=10; ipi/nivo no-response, N=9; ipi no-response, N=8).

Results: Multiplex analysis in ipi/nivo responsive patients demonstrated increased proportions of CD8 (median 1.6X increase), CD4 (2.1X), regulatory T cells (1.6X), and monocytes (1.4X), with a paralleled 8.1X decrease in melanoma cells over the course of treatment. This was confirmed by histopathologic evidence of tumor regression, necrosis, and immune infiltrate in on-treatment, responding tumor biopsies, as determined by dermatopathologists. Melanoma cells had direct, cell-membrane interactions with CD8 T cells in ipi/nivo responsive patients, both at baseline (median 26%) and on-treatment (median 86%). The shared interface between melanoma and CD8 T-cells had polarized expression of CD3, CD8, and CD45RO. There was no change in T-cell infiltration nor tumor cell content over the course of treatment in ipi/nivo non-responders nor ipi non-responders; similar proportions of melanoma cells were interacting with CD8 T-cells at baseline (median 24%) and on-treatment (27%).

Conclusion: Reversal of resistance to PD-1 blockade is associated with increased frequency of CD8 T-melanoma cell interactions and pathological response, reflective of different stages of antitumor immune responses. Response to ipi/nivo in the anti-PD-1 refractory setting was further associated with increased tumor-polarized and activated CD8 T cells interacting with melanoma cells, demonstrated by the colocalized expression of immune synapse proteins at tumor-CD8-T-cell membrane interfaces.

Citation Format: Katie M. Campbell, Lawrence Kuklinski, Zaid Bustami, Jessica Maxey, Egmidio Medina, Sandra Santulli-Marotto, Cynthia R. Gonzalez, Nataly Naser Aldeen, Kari Kendra, Sapna Patel, Siwen Hu-Lieskovan, James Moon, Shay Bellasea, Christine N. Spencer, Marshall A. Thompson, Michael Wu, Ari Vanderwalde, Philip O. Scumpia, Antoni Ribas. CD8 T cell-melanoma cell interactions in response and resistance to ipilimumab plus nivolumab: Biopsy analysis of SWOG S1616. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4527.

Neoantigen-targeted CD8+ T cell responses with PD-1 blockade therapy

Neoantigens are peptides derived from non-synonymous mutations presented by human leukocyte antigens (HLAs), which are recognized by antitumour T cells1-14. The large HLA allele diversity and limiting clinical samples have restricted the study of the landscape of neoantigen-targeted T cell responses in patients over their treatment course. Here we applied recently developed technologies15-17 to capture neoantigen-specific T cells from blood and tumours from patients with metastatic melanoma with or without response to anti-programmed death receptor 1 (PD-1) immunotherapy. We generated personalized libraries of neoantigen-HLA capture reagents to single-cell isolate the T cells and clone their T cell receptors (neoTCRs). Multiple T cells with different neoTCR sequences (T cell clonotypes) recognized a limited number of mutations in samples from seven patients with long-lasting clinical responses. These neoTCR clonotypes were recurrently detected over time in the blood and tumour. Samples from four patients with no response to anti-PD-1 also demonstrated neoantigen-specific T cell responses in the blood and tumour to a restricted number of mutations with lower TCR polyclonality and were not recurrently detected in sequential samples. Reconstitution of the neoTCRs in donor T cells using non-viral CRISPR-Cas9 gene editing demonstrated specific recognition and cytotoxicity to patient-matched melanoma cell lines. Thus, effective anti-PD-1 immunotherapy is associated with the presence of polyclonal CD8+ T cells in the tumour and blood specific for a limited number of immunodominant mutations, which are recurrently recognized over time.

Remodeling of the tumor microenvironment through PAK4 inhibition sensitizes tumors to immune checkpoint blockade

PAK4 inhibition can sensitize tumors to immune checkpoint blockade (ICB) therapy, however, the underlying mechanisms remain unclear. We report that PAK4 inhibition reverses immune cell exclusion by increasing the infiltration of CD8 T cells and CD103+ dendritic cells (DCs), a specific type of DCs that excel at cross-presenting tumor antigens and constitute a source of CXCL10. Interestingly, in melanoma clinical datasets, PAK4 expression levels negatively correlate with the presence of CCL21, the ligand for CCR7 expressed in CD103+ DCs. Furthermore, we extensively characterized the transcriptome of PAK4 knock out (KO) tumors, in vitro and in vivo, and established the importance of PAK4 expression in the regulation of the extracellular matrix, which can facilitate immune cell infiltration. Comparison between PAK4 wild type (WT) and KO anti-PD-1 treated tumors revealed how PAK4 deletion sensitizes tumors to ICB from a transcriptomic perspective. In addition, we validated genetically and pharmacologically that inhibition of PAK4 kinase activity is sufficient to improve anti-tumor efficacy of anti-PD-1 blockade in multiple melanoma mouse models. Therefore, this study provides novel insights into the mechanism of action of PAK4 inhibition and provides the foundation for a new treatment strategy that aims to overcome resistance to PD-1 blockade by combining anti-PD-1 with a small molecule PAK4 kinase inhibitor.

Abstract 1388: Mutations in transcriptional activators of MHC I antigen presentation, NLRC5 and CIITA, are mutually exclusive and have different effects on melanoma gene transcripts

Response to many immunotherapies depends on effective recognition and eradication of tumor cells by the immune system. This is mediated by the successful presentation of tumor-specific antigens on major histocompatibility complex class I (MHC I) molecules on the surface of tumor cells. Studies have focused on alterations in MHC I complex proteins (e.g. HLA, B2M) and gene regulatory elements (e.g. NLRC5). However, the impact on tumor response of individual defects in components regulating and composing the MHC I antigen processing and presentation machinery (APM) have not been extensively studied. Using a harmonized dataset of six clinical trials of patients with melanoma treated with ICB, whole-exome sequencing (WES, n= 244) and RNA sequencing (RNAseq, n= 426) data from untreated tumor samples were assessed to identify mutations in genes associated with MHC I APM and their regulation. Somatic alterations were correlated with clinical response to ICB and with gene expression profiles in tumor-matched RNAseq data. Mutations in MHC I and MHC I-related genes were found in 63% of patients (n= 154/244). The most recurrently mutated genes were NCAM1 (11%, n=28), TRIM48 (7%, n=17), and CAMK2B (6.6%, n=16), and the transcriptional regulators NLRC5 (9.4%, n=23) and CIITA (9.4%, n=23). Mutations in NLRC5 and CIITA trended toward being mutually exclusive from one another (Fisher’s exact test, p= 0.157) and mutations were overrepresented in tumors with stable or progressive disease following ICB therapy. In addition, lower expression of NLRC5 and CIITA were associated with stable or progressive disease status. NLRC5-mutant tumors that progressed following ICB therapy trended towards lower expression of transcriptional target HLA-A (Kruskal-Wallis, p=0.27); however, there was no difference in HLA-A expression across NLRC5-wildtype tumors. For class II transactivating factor, CIITA, which can induce MHC I expression, mutational status was not associated with HLA-A expression across all clinical response groups. There are genetic alterations spanning MHC I and MHCI-associated genes that may be responsible for inactivating class I antigen presentation by melanoma cells. The impact of these alterations may result in varied clinical responses to ICB therapies. The landscape of these alterations needs to be further delineated to understand how tumors are directly evading class I-mediated recognition and elimination.

Citation Format: Mildred Galvez, Katie M. Campbell, Egmidio Medina, Antoni Ribas. Mutations in transcriptional activators of MHC I antigen presentation, NLRC5 and CIITA, are mutually exclusive and have different effects on melanoma gene transcripts [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 1388.

Abstract 3818: Infrequent chromosomal loss and recurrent gains lead to imbalanced expression of HLA genes in melanoma

Introduction: Loss-of-heterozygosity (LOH) events in chromosome 6p, comprising the human leukocyte antigen (HLA) genes, have been reported in about 10% of cutaneous melanoma (compared to 20-40% of squamous cell carcinomas), while copy number gains in this region have been observed in over 50% of melanoma. Recent studies focused in HLA allelic loss have been restricted to DNA-based approaches, and have not been validated orthogonally at the RNA or protein levels. Here, using clinical melanoma biopsies and patient-derived melanoma cell lines, we show that genetic alterations in HLA genes results in imbalanced allele expression, subsequently skewing antigen presentation by melanoma cells.

Methods: Whole exome and RNA sequencing (WES, RNAseq) analyses were performed on 760 melanoma biopsies and 60 patient-derived melanoma cell lines. Patient-matched normal WES was used to perform HLA haplotyping across Class I and II HLA genes. Tumor WES was analyzed for copy number alterations in chromosome 6, identifying which alleles were lost or gained. Differential expression of HLA alleles was quantified in tumor RNAseq, correlating the allelic imbalance at the DNA and RNA levels. Melanoma cell lines heterozygous for HLA-A*02, A*03, and A*24 were analyzed by flow cytometry for surface-level HLA protein expression using allele-specific antibodies to quantify allelic densities and compare the imbalance of HLA-A alleles at the DNA, RNA, and protein levels.

Results: Across 760 melanoma biopsies, copy number alterations in chromosome 6p were identified in 76% of tumors; 12% had LOH, and 54% had copy number gains that resulted in imbalanced copies of alleles. In paired tumor WES and RNAseq (N=682), genetic imbalance was correlated with imbalanced expression of HLA alleles in the classical Class I HLA genes (Spearman rho=0.64-0.7; p=2.2e-16); this association was strengthened in tumors with high tumor cellularity, and was not associated with the total expression of the HLA genes.These patterns were explored in a 60 patient-derived melanoma cell lines with matched tumor WES and RNAseq, confirming that alleles gained at the genetic level were also expressed at higher levels than alleles that were not gained or lost. In 10 cell lines heterozygous for either HLA-A*02, A*03, or A*24, allelic imbalance at the DNA and RNA level resulted in correlative imbalanced surface presentation of alleles at the protein level.

Conclusions: Evaluation of paired tumor WES and RNAseq revealed orthogonal validation of HLA allelic imbalance, and analysis in cell lines suggested that these patterns were likely tumor intrinsic. Experimental validation of these findings at the protein level suggests that antigen presentation density can be modulated by chromosomal gains, and not just allelic loss, in HLA genes. This knowledge is important for the design of cancer vaccines or T cell therapies targeting neoantigens presented by HLA class I complexes.

Citation Format: Katie M. Campbell, Justin Saco, Egmidio Medina, Meelad Amouzgar, Shannon M. Pfeiffer, Cynthia R. Gonzalez, Gabriela Steiner, Ameya Champhekar, Cristina Puig Saus, Jesse Zaretsky, Gabriel Abril Rodriguez, Agustin Vega-Crespo, Ignacio Baselga Carretero, Mito Tariveranmoshabad, Anusha Kalbasi, Christine Spencer, Zachary L. Skidmore, Malachi Griffith, Obi L. Griffith, Daniel K. Wells, Antoni Ribas. Infrequent chromosomal loss and recurrent gains lead to imbalanced expression of HLA genes in melanoma [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 3818.

Abstract 765: Hybridized-capture sequencing methods bias analysis of antigen presentation genes

Introduction: Tumor-immune dynamics are often interrogated using hybridized capture-based sequencing approaches which require the use of baits that target the protein-coding regions of the genome. However, the genes encoding the antigen presentation machinery, including human leukocyte antigen (HLA) proteins, are very polymorphic, resulting in thousands of unique genotypes across patient cohorts. Here, using whole exome sequencing (WES) and hybridized capture-based RNA sequencing (RNAseq) from melanoma patients, we show that these genes are not uniformly assessed by common sequencing methods, and require careful analysis for accurate detection of copy number and somatic alterations.

Methods: WES and RNAseq data was analyzed from 760 melanoma tumor biopsies, with WES derived from patient-matched normal blood samples. Coverage metrics for 26 antigen presentation genes, including classical and non-classical HLA genes, were evaluated, and the difference in coverage was calculated for heterozygous alleles. Each individual was assessed for heterozygous single nucleotide polymorphisms (SNPs) within each allele, and with respect to the haplotype of the human reference genome.

Results: Focusing on the 26 genes assessed, HLA-A, HLA-B, HLA-C, and HLA-DRB1 were the most diverse across our patient cohort; there was an average of 134 unique pairs of HLA alleles in these genes. We compared the SNP profiles of allele combinations to the haplotype of the human reference genome, and observed four patterns: heterozygous alleles are similar to each other and the reference haplotype, heterozygous alleles are different from each other and different to the reference, alleles are very similar to each other and greatly differ from the reference, or one allele is more similar to the reference haplotype. The fourth pattern showed the greatest bias in sequencing, where the allele more similar to the human reference genome had a median 4-fold increase in coverage in normal WES data.

Conclusions: Capture-based sequencing shows selection bias, as exome probes have been designed based upon the reported human reference genome, but results in selection bias in hybridized capture sequencing approaches. Alleles that have higher polymorphic differences with respect to the reference are not equally captured, resulting in nonuniform sequencing of heterozygous alleles.

Citation Format: Egmidio Medina, Katie Campbell, Antoni Ribas. Hybridized-capture sequencing methods bias analysis of antigen presentation genes [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 765.

Spatial profiling reveals association between WNT pathway activation and T-cell exclusion in acquired resistance of synovial sarcoma to NY-ESO-1 transgenic T-cell therapy

BACKGROUND

Genetically engineered T-cell immunotherapies for adoptive cell transfer (ACT) have emerged as a promising form of cancer treatment, but many of these patients develop recurrent disease. Furthermore, delineating mechanisms of resistance may be challenging since the analysis of bulk tumor profiling can be complicated by spatial heterogeneity.

METHODS

Tumor samples were collected from a patient with synovial sarcoma who developed acquired resistance to ACT targeting NY-ESO-1. Biopsies (primary, progressive metastasis, and recurrence) were subjected to bulk tumor DNA and RNA sequencing, as well as high-dimensional spatial profiling of RNA and protein targets. Untreated and progressive lesions were compared with identified patterns associated with acquired resistance to ACT.

RESULTS

Gene expression patterns due to immune activity and infiltration were diluted in bulk tumor sequencing. The metastasis was enriched for tumor regions with increased CTNNB1 (encoding beta-catenin), which were negatively associated with the expression of T-cell surface proteins and antigen presentation machinery. Spatial profiling was most highly concordant with bulk sequencing in the lesions with decreased spatial heterogeneity.

CONCLUSIONS

Complementary use of bulk and spatial profiling enables more accurate interrogation of tumor specimens, particularly to address complex questions regarding immunotherapeutic mechanisms. Our study uses this approach to demonstrate a mechanism of T-cell exclusion and resistance to cellular immunotherapy in synovial sarcoma.

Chemical parameters and antioxidant activity of turning color natural-style table olives of the Sigoise cultivar

A chemical characterization of turning color table olives of the Sigoise variety was made through their processing as natural-style. Polyphenols, sugars, tocopherols, fatty acids, and antioxidant activity in the olives were monitored throughout the elaboration process. Oleuropein, salidroside, hydroxytyrosol 4-glucoside, rutin, ligustroside and verbascoside showed a decrease of 16.90-83.34%, while hydroxytyrosol increased during the first months of brining. Glucose was consumed by 90% due to the metabolism of the fermentative microbiota. The tocopherol content remained stable during the process and only the α-tocopherol decreased. The fatty acids were not affected. The loss in antioxidant compounds resulted in a decrease in the percentage of DPPH radical inhibition from 75.91% in the raw fruit to 44.20% after 150 days of brining. Therefore, the turning color natural table olives of the Sigoise variety are a good source of bioactive compounds.

Reducing Skin Toxicities from EGFR Inhibitors with Topical BRAF Inhibitor Therapy

Treatment of cancer with EGFR inhibitors is limited by on-target skin toxicities induced by inhibition of the MAPK pathway. BRAF inhibitors are known to paradoxically activate the MAPK downstream of EGFR, which we confirmed using human skin keratinocytes. We then conducted a phase I clinical trial testing the hypothesis that topical therapy with the BRAF inhibitor LUT014 could improve skin toxicities induced by EGFR inhibitors. Ten patients with metastatic colorectal cancer who had developed acneiform rash while being treated with cetuximab or panitumumab were enrolled in three cohorts. LUT014 was well tolerated, and there were no dose-limiting toxicities. The acneiform rash improved in the 6 patients who started with grade 2 rash in the low and intermediate cohorts. We conclude that topical LUT014 is safe and efficacious in improving rash from EGFR inhibitors, consistent with the mechanism of action inducting paradoxical MAPK activation. SIGNIFICANCE: BRAF inhibitor topical therapy could avoid dose reductions of EGFR inhibitors, locally treating the main dose-limiting skin toxicity of this class of agents.This article is highlighted in the In This Issue feature, p. 2113.

Abstract 1893: The dynamics of T cell clonal repertoire under targeted therapy vs. immunotherapy in melanoma

Introduction. The current standard of care for metastatic melanoma patients utilizes either MAPK pathway inhibitors (MAPKi)-based targeted therapies or immune checkpoint inhibitors (ICI)-based immunotherapies. Almost every melanoma patient treated with MAPKi will relapse in a median of one year, whereas a small subset of ICI-treated melanoma patients experienced prolonged tumor control. Multiple reports have shown that both MAPKi and ICI treatment will induce increased T cell infiltration into the tumor. However, the T-cell receptor (TCR) clonotype dynamics across different therapies (MAPKi vs. ICI) and/or clinical response (responding vs. resistant) is still unknown. This study aims to compare the TCR repertoire dynamics and their associated tumor microenvironment (TME) phenotypes in melanoma pre- vs. post-ICI or MAPKi to see if there are unique patterns associated with better tumor control.

Methods. Publicly available bulk RNA-seq data of 345 melanoma samples pre- and post- treatment were downloaded, including two MAPKi (n=116 tumors) and two ICI data sets (n = 229 tumors). All samples were classified into three groups: pre-treatment (PT), on-treatment responding (OT-R), and on-treatment non-responding (OT-NR). T cell clonotype and gene expression were quantified from the RNA-seq data using trust4 and HISAT2/htseq-count, respectively. Although the transcripts of T cells are mixed with tumor cells in the bulk RNA-seq data, the TCR clonotype abundance showed significant correlation with T cell marker expression, offering a measure of robustness in the identification of TCR from bulk tumor derived RNA-seq data.

Results. Both MAPKi and ICI therapies significantly increase the TCR count, abundance, diversity, and clonality in OT-R samples compared to PT and OT-NR samples. Intriguingly, we observed significantly higher clonal replacement of PT samples' T cell clonotypes with novel, OT-specific clonotypes under both therapies. Of note, in the tumor subset that responded to the ICI, the increase of these novel TCR were significantly associated with the enrichment of naïve/memory CD4 and CD8 T cell signatures.

Conclusions. In melanoma, intratumoral TCR dynamics patterns in response to MAPKi and ICI are mostly similar, except for the upregulation of naïve/memory T cell signatures in the subset of ICI-responder tumors. These insights may eventually lead to better markers for therapy-induced, productive anti-tumor immunity in melanoma.

Citation Format: Lizhong Ding, Katie M. Campbell, Egmidio Medina, Kevin Chen, Willy Hugo. The dynamics of T cell clonal repertoire under targeted therapy vs. immunotherapy in melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1893.

Abstract 3006: Melanoma cell lines derived from patient derived xenografts (PDX) can contain murine chromosomes resultant from cell fusions

Introduction: Patient Derived Xenografts (PDX) provide a distinct platform to generate in vivo and ex vivo cell lines to investigate novel therapies. However, human-murine cell fusions may skew the models and is a poorly characterized phenomenon.

Methods: Malignant melanoma IRB-consented biopsies [IRBs: 17-000548; 17-001685; 17-001351; 11-003254] were excised from various sites and implanted into gender-matched 4-6 weeks old NOD-scid IL2Rgammanull mice. Tumor-bearing mice were humanely euthanized and adherent cell lines were generated after Miltenyi gentleMACS™ dissociation of the PDXs. Briefly, adherent cells are allowed to proliferate and passaged when 70% confluent for approximately 4-8 weeks. PDX-derived cell products were processed for long term-cryostorage and an aliquot was sent for GenePrint 10 System-Promega®-LaragenTM cell line authentication paired with patient-matched peripheral blood mononuclear cells (PBMC) for specimen congruency. Mouse-genome contaminant resulting cultures were prepared and sent for cell line characterization by G-banded metaphase karyotyping-Cell Line GeneticsTM. Cultures containing murine karyotypes were processed according to manufacturer recommendations by Miltenyi Mouse Cell Depletion KitTM where the flow through (negative fraction) represents the human-cell fraction.

Results: We implanted 86 patient-derived biopsies into mice over 3years, from which 39 [45%] resulted in progressively growing PDXs. From these PDXs we have generated 26 [37%]-patient-specific PDX-derived cell lines. G-banded metaphase karyotyping demonstrated that 6 [24%]- cell lines presented murine chromosome contamination. The immunoprofile of these 6 cellular materials appear to be murine as the totality of the cultures were sequestered in the column by mouse depletion cell cocktail. Separation assay was validated by bonafide human cell lines, utilized as human positive controls, M257 and MX210 both with human karyotypes and matched Cell ID profiling. The murine colon carcinoma cell line MC38, was utilized as a positive murine control, and performed identically as the 6 PDX-derived cellular materials with abnormal mouse genomes.

Conclusion: Detection of murine-human fusion cells in cell lines derived from PDXs may limit the utility of these models.

Citation Format: Agustin Vega-Crespo, Ignacio Baselga-Carretero, Ivan Perez-Garcilaso, Sameeha Jilani, Kevin Chen, Vaneet Khullar, Egmidio Medina, Yaroslav Teper, Antoni Ribas, Begoña Comin-Anduix. Melanoma cell lines derived from patient derived xenografts (PDX) can contain murine chromosomes resultant from cell fusions [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 3006.

Melanoma dedifferentiation induced by IFN-γ epigenetic remodeling in response to anti-PD-1 therapy

Melanoma dedifferentiation has been reported to be a state of cellular resistance to targeted therapies and immunotherapies as cancer cells revert to a more primitive cellular phenotype. Here, we show that, counterintuitively, the biopsies of patient tumors that responded to anti-programmed cell death 1 (anti-PD-1) therapy had decreased expression of melanocytic markers and increased neural crest markers, suggesting treatment-induced dedifferentiation. When modeling the effects in vitro, we documented that melanoma cell lines that were originally differentiated underwent a process of neural crest dedifferentiation when continuously exposed to IFN-γ, through global chromatin landscape changes that led to enrichment in specific hyperaccessible chromatin regions. The IFN-γ-induced dedifferentiation signature corresponded with improved outcomes in patients with melanoma, challenging the notion that neural crest dedifferentiation is entirely an adverse phenotype.

Conserved Interferon-γ Signaling Drives Clinical Response to Immune Checkpoint Blockade Therapy in Melanoma

We analyze the transcriptome of baseline and on-therapy tumor biopsies from 101 patients with advanced melanoma treated with nivolumab (anti-PD-1) alone or combined with ipilimumab (anti-CTLA-4). We find that T cell infiltration and interferon-γ (IFN-γ) signaling signatures correspond most highly with clinical response to therapy, with a reciprocal decrease in cell-cycle and WNT signaling pathways in responding biopsies. We model the interaction in 58 human cell lines, where IFN-γ in vitro exposure leads to a conserved transcriptome response unless cells have IFN-γ receptor alterations. This conserved IFN-γ transcriptome response in melanoma cells serves to amplify the antitumor immune response. Therefore, the magnitude of the antitumor T cell response and the corresponding downstream IFN-γ signaling are the main drivers of clinical response or resistance to immune checkpoint blockade therapy.

Abstract 3166: The degree of conserved interferon gamma signaling guides response to immune checkpoint blockade therapy

The long-lasting responses to immune blockade therapy in a subset of patients with melanoma remain largely unexplained. We assessed baseline and on-therapy biopsies from 118 patients with advanced melanoma treated with the anti-PD-1 antibody nivolumab alone (N = 82) or in combination with the anti-CTLA-4 antibody ipilimumab (N = 36) (CheckMate 038 study). There were 46 progressive disease (PD) cases, 26 stable disease (SD) cases, and 46 complete or partial response (CRPR) cases. Tumors were analyzed by RNA sequencing. RNAseq bulk immune cell deconvolution revealed that the largest immune cell change on-treatment was an increase in CD8+ T cell infiltration for patients regardless of treatment or clinical response (P < 0.04, 0.02, 2e-4 for PD, SD, CRPR). In CRPR, there was a corresponding increase in CD4+ T cells (P < 2e-4), Tregs (P < 9e-4), NK cells (P < 3e-5) and macrophages (P < 3e-5). Principal component analysis showed that T cell infiltration was the best organizer of the RNAseq biopsies; 3694 genes were correlated or negatively correlated with T cell infiltration.

Analysis of 58 human melanoma cell lines exposed in vitro to interferon-gamma (IFNγ) for 6 hours showed a conserved response to this cytokine in all cell lines able to signal through the IFNγ receptor (N = 46), including an increase in antigen presentation machinery, an increase in expression of IFNγ signaling molecules representing a signal amplification, and production of chemokines that attract other immune cells, while there was a decrease in cell cycle and WNT signaling pathways. These same gene sets are present in the list of genes correlated and negatively correlated with T cell infiltration in the patient data, as well as the list of genes significantly up- or down-regulated in CRPR cases. Only cell lines with JAK1 or JAK2 mutations (N = 12) did not exhibit this conserved response; in fact, these mutants had no genes with at least a 2-fold change.

Analysis of the patient biopsies using the IFNγ regulated gene sets revealed that in CRPR cases there was a large increase in HLA expression (P < 0.04, 4e-3, 8e-4 for HLA-A, HLA-B, HLA-C), along with a corresponding large decrease in WNT signaling (P < 3e-4), a driver of immune exclusion. We did not find genomic alterations (in the subset of cases that we exome sequenced) or gene expression differences pre-treatment to explain the greater response in the CRPR cases, including no JAK1/2 mutations. The lack of naturally occurring mutations disabling IFNγ signaling in our baseline biopsies is likely selected for by the role IFNγ plays in up-regulating PD-L1 expression necessary for establishing the anti-PD1 immune blockade. Using RNAseq immune cell deconvolution, the 36 CRPR cases (16 monotherapy, 20 combination) had significantly larger CD8+ T cell infiltration pre-treatment (P < 8e-4 compared to PD cases). Therefore, our data showed that the strength of the antitumor T cell response and corresponding downstream IFNγ signaling is the main driver of response or resistance to immune checkpoint blockade therapy.

Citation Format: Catherine Grasso, Jennifer Tsoi, Mykola Onyshchenko, Gabriel Abril-Rodriguez, Ameya Champhekar, Egmidio Medina, Davis Torrejon, Daniel Shin, Michael Quist, Petra Ross-Mcdonald, Megan Wind-Rotolo, Daniel Speiser, Anusha Kalbasi, Anthony Ribas. The degree of conserved interferon gamma signaling guides response to immune checkpoint blockade therapy [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3166.

Role of lactic acid bacteria in fermented vegetables

The consumption of fermented vegetables is widespread throughout the world and represents an important component of the human diet with considerable contribution to the food supply for a world popula­tion in continuous growth. Many of the fermented vegetables share a general process which requires salting and acidification steps. Among the microorganisms responsible for fermentation, lactic acid bacteria are the most relevant with important organoleptic, quality and safety benefits. This review deals with the microbial ecology of fermented vegetables focusing on the biodiversity of lactic acid bacteria, the most important molecular tech­niques used for their identification and genotyping, their importance for the formation of biofilms as well as their use as starter cultures for obtaining high-quality and safe vegetable products.

Intrinsic Rashba coupling due to hydrogen bonding in DNA

We present an analytical model for the role of hydrogen bonding on the spin-orbit coupling of a model DNA molecule. Here, we analyze in detail the electric fields due to the polarization of the hydrogen bond on the DNA base pairs and derive, within a tight binding analytical band folding approach, an intrinsic Rashba coupling which should dictate the order of the spin active effects in the chiral-induced spin selectivity effect. The coupling found is ten times larger than the intrinsic coupling estimated previously and points out to the predominant role of hydrogen bonding in addition to chirality in the case of biological molecules. We expect similar dominant effects in oligopeptides, where the chiral structure is supported by hydrogen-bonding and bears on orbital carrying transport electrons.

Assessment of the bacterial community in directly brined Aloreña de Málaga table olive fermentations by metagenetic analysis

This study uses an "omics" approach to evaluate the bacterial biodiversity changes during fermentation process of natural green cracked Aloreña de Málaga table olives, from raw material to fermented fruit. For this purpose, two industries separated by almost 20km in Guadalhorce Valley (Málaga, Spain) were analysed for obtaining both brines and fruit samples at different moments of fermentation (0, 7, 30 and 120days). Physicochemical and microbial counts during fermentation showed the typical evolution of this type of processes, apparently dominated by yeasts. However, high-throughput barcoded pyrosequencing analysis of V2-V3 hypervariable region of the bacterial 16S rRNA gene showed at 97% identity the presence of 131 bacterial genera included in 357 operational taxonomic units, not detected by the conventional approach. The bacterial biodiversity was clearly higher in the olives at the moment of reception in the industry and during the first days of fermentation, while decreased considerably as elapse the fermentation process. The presence of Enterobacteriaceae and Lactobacillaceae species was scarce during the four months of study. On the contrary, the most important genus at the end of fermentation was Celerinatantimonas in both brine (95.3% of frequency) and fruit (89.4%) samples, while the presence of well-known spoilage microorganisms (Pseudomonas and Propionibacterium) and halophilic bacteria (Modestobacter, Rhodovibrio, Salinibacter) was also common during the course of fermentation. Among the most important bacterial pathogens related to food, only Staphylococcus genus was found at low frequencies (<0.02% of total sequences). Results show the need of this type of studies to enhance our knowledge of the microbiology of table olive fermentations. It is also necessary to determine the role played by these species not previously detected in table olives on the quality and safety of this fermented vegetable.

Heterogeneity of elemental composition and natural abundance of stables isotopes of C and N in soils and leaves of mangroves at their southernmost West Atlantic range

Mangrove communities were selected in the state of Santa Catarina, Brazil, near their southernmost limit of distribution, to study mineral nutrient relation in soils and plants. Communities included three true mangrove species, Rhizophora mangle, Laguncularia racemosa and Avicennia germinans, and two associated species, the fern Acrostichum danaeifolium, and the grass Spartina densiflora. The sites included communities in the lower Río Tavares near Florianopolis city, Sonho beach near Palhoça city, and the Santo Antonio lagoon. These sites included a full range of mangroves under humid climate where winter temperatures, instead of salinity, may be the main factor regulating their productive capacity and species composition. Soil salinity was determined by the concentration of soluble Na, and soil C and N were linearly correlated indicating their association in organic matter. Tavares site showed higher specific conductivity, and concentrations of Na and Mg in the soil layer below 40 cm depth, indicating larger influence of marine water. Isotopic signature of C increased with soil depth suggesting that microorganisms decomposing organic matter are releasing 13C depleted CO2. Nitrogen isotopic signature decreased with soil depth, indicating enrichment in 15N possibly as a result of denitrification in the upper soil layers. Mineral elements in leaf tissues showed A. schaueriana with higher concentrations of N, P, Na, K, Cu, Zn, and Na/Ca ratio. Spartina densiflora was characterized by the lowest N and K concentrations, and the highest concentrations of Al and Fe. Rhizophora mangle and L. racemosa had the highest Ca concentrations. Carbon isotopic signatures identified S. densiflora as a C4 plant, and A. schaueriana as the mangrove species occupying comparatively more water stressed microsites than the rest. Leaf nitrogen isotopic signatures were positive, in correspondence with the soil values. The results support the hypothesis that sites sampled were comparatively fertile, because sediment transport through fresh water run-off is predominant in humid coasts, and therefore plants were not limited by nutrient supply, nor particularly stressed by soil salinity.

Staphylococcus aureus develops increased resistance to antibiotics by forming dynamic small colony variants during chronic osteomyelitis

OBJECTIVES

Staphylococcus aureus osteomyelitis often develops to chronicity despite antimicrobial treatments that have been found to be susceptible in in vitro tests. The complex infection strategies of S. aureus, including host cell invasion and intracellular persistence via the formation of dynamic small colony variant (SCV) phenotypes, could be responsible for therapy-refractory infection courses.

METHODS

To analyse the efficacy of antibiotics in the acute and chronic stage of bone infections, we established long-term in vitro and in vivo osteomyelitis models. Antibiotics that were tested include β-lactams, fluoroquinolones, vancomycin, linezolid, daptomycin, fosfomycin, gentamicin, rifampicin and clindamycin.

RESULTS

Cell culture infection experiments revealed that all tested antibiotics reduced bacterial numbers within infected osteoblasts when treatment was started immediately, whereas some antibiotics lost their activity against intracellular persisting bacteria. Only rifampicin almost cleared infected osteoblasts in the acute and chronic stages. Furthermore, we detected that low concentrations of gentamicin, moxifloxacin and clindamycin enhanced the formation of SCVs, and these could promote chronic infections. Next, we treated a murine osteomyelitis model in the acute and chronic stages. Only rifampicin significantly reduced the bacterial load of bones in the acute phase, whereas cefuroxime and gentamicin were less effective and gentamicin strongly induced SCV formation. During chronicity none of the antimicrobial compounds tested showed a beneficial effect on bone deformation or reduced the numbers of persisting bacteria.

CONCLUSIONS

In all infection models rifampicin was most effective at reducing bacterial loads. In the chronic stage, particularly in the in vivo model, many tested compounds lost activity against persisting bacteria and some antibiotics even induced SCV formation.

Characterization of the microbial diversity in yacon spontaneous fermentation at 20 °C

The prebiotic fructooligosaccharide content of yacon makes this root an attractive alternative for the supplementation of a variety of food products. The preservation of yacon by fermentation has been proposed as an alternative to increase the probiotic content of the root concomitantly with its shelf life. Thus the fermented yacon could have significant functional content. The objective of this research was to characterize the biochemistry and microbiology of spontaneous yacon fermentation with 2% NaCl and define the viability of the proposed process. The biochemical analysis of spontaneous heterolactic fermentation of yacon showed a progressive drop in pH with increased lactic and acetic acids, and the production of mannitol during fermentation. The microbial ecology of yacon fermentation was investigated using culture-dependent and culture-independent methods. Bacterial cell counts revealed a dominance of lactic acid bacteria (LAB) over yeasts, which were also present during the first 2 days of the fermentation. Results showed that the heterofermentative LAB were primarily Leuconostoc species, thus it presents a viable method to achieve long term preservation of this root.

The complete picture of changing pediatric inflammatory bowel disease incidence in Spain in 25 years (1985-2009): the EXPERIENCE registry

OBJECTIVES

A growing incidence of pediatric IBD (PIBD) in southern Europe has been recently reported. The SPIRIT registry (1996-2009) confirmed these tendencies in Spain. Our aim is to obtain data from 1985 to 1995 and describe the complete picture of PIBD presentation changes in Spain in the last 25years.

METHODS

A retrospective survey of incident PIBD in the period 1985-1995 was performed. Patients' data were obtained from the hospitals' databases and compared with the published data from the 1996 to 2009 period. Seventy-eight IBD reference centers took part in this survey.

RESULTS

Data from 495 patients were obtained: 278 CD (56.2%), 198 UC (40%), and 19 IBDU (3.8%); 51.7% were female, with higher predominance both in UC (58.6%) and in IBDU (57.9%), but not in CD (46.4%). Median (IQR) age at diagnosis was 12.9 (10.0-15.7) years, with significant differences among IBD subtypes: CD: 13.1 (10.8-16.0) vs UC: 12.4 (9.4-15.1) vs IBDU: 7.5 (3.0-13.0) (p≤0.001). These results are significantly different to the ones in the SPIRIT registry, with a higher proportion of IBDU, younger age and male predominance. The data from both periods taken together give a complete picture of a 25-year period. An annual increase of incident patients was observed, with a ten-fold increase over this period.

CONCLUSION

These data extend the epidemiological trends to a full 25-year period (1985-2009). PIBD incidence in Spain has experienced a sixteen-fold increase. The IBD subtype, localization of the affected segment, age- and sex distribution observed are in accordance with our previously published ones of 1996-2009.

First Report of Phytophthora infestans Causing Late Blight on Solanum viarum in Colombia

Solanum viarum Dunal (tropical soda apple) belongs to the section Acanthophora in the genus Solanum, which includes nearly 20 neotropical species of herbs and small shrubs (2). The species in this section are sometimes called the 'spiny Solanums' (2) and are adapted mainly to highly disturbed habitats and open secondary forests. The center of diversity is eastern Brazil (3). Since the early 1990s, S. viarum has been a problematic weed in Florida where it was listed as a noxious weed in 1993, followed in 1994 by its addition to the Federal Noxious Weed List of the USDA. On 17 April 2010, 12 plants of S. viarum located close to a S. betaceum crop (tree tomato) in the province of Caldas (Department of Antioquia, central northwestern Colombia) were found with symptoms similar to late blight caused by Phytophthora infestans on S. tuberosum (potato). Fifteen leaves from 12 plants with blackish, water-soaked lesions showing a white sporulation on the abaxial side were collected and processed within 3 days. The leaves were placed in a humid chamber and incubated in darkness at room temperature (18°C mean temperature) until sporulation was observed. Microscopic characteristics were consistent with Phytophthora spp. Only one axenic culture was obtained by successive subcultures in rye B agar plates. After an incubation period of 8 days, plates were washed with distilled water and ovoid, semipapillate caduceus sporangia ranging from 38 to 41 μm long (average 39; N = 86) and 23 to 29 μm wide (average 26; N = 86) were observed. To fulfill Koch's postulates and test the isolate for the ability to infect potato as well as Solanum spp. associated with potato crops in Colombia, triplicate pathogenicity tests were carried out on three detached leaves of S. viarum, S. tuberosum, and S. americanum (American nightshade). A 1 × 10⁴ sporangia/ml suspension of the Phytophthora isolate, estimated using a haemocytometer, was obtained from 8-day-old cultures grown on rye B agar. The suspension was incubated at 4°C for 2 h to induce zoospore release. The leaves were then inoculated by spraying them until runoff. After an incubation period of 5 days at 18°C in a humidity chamber, mycelia, sporangia, and brownish lesions, similar to those described above, were observed in the leaves of all three hosts, indicating pathogenicity. DNA extraction was performed from the P. infestans isolate (4). Four nuclear loci, ITS, β-tubulin, Ras, and Avr3a, as well as one mitochondrial gene, cytochrome c oxidase 1 (Cox1), were amplified and sequenced. Sequences were compared with GenBank databases using Blastn. In all cases, the best hits corresponded to P. infestans (GenBank Accession No. HQ639930 for Avr3A, HQ639931 for β-tubulin, HQ639932 for Cox1, HQ639933 for iRas, HQ639934 for Ras, and JF419363 for ITS). Reports of P. infestans causing typical late blight symptoms on wild solanaceous plants are becoming more frequent and have been made from other countries such as Peru (1). To our knowledge, this is the first time that P. infestans has been observed and isolated from S. viarum in Colombia, introducing the possibility of this wild solanaceous weed as another late blight host. References: (1) G. Garry et al. Eur. J. Plant Pathol. 113:71, 2005. (2) R. Levin et al. Am. J. Bot. 92:603, 2005. (3) M. Nee. A Revision of Solanum Section Acanthophora. Ph.D. diss. University of Wisconsin, Madison, 1979. (4) A. M. Vargas et al. Phytopathology 99:82, 2009.

Bipolar disorder therapy in daily clinical practice: Analysis of retrospective data from a large multinational longitudinal study (WAVE-BD)

Introduction

The Wide AmbispectiVE study of clinical management and burden of bipolar disorder (BD) (WAVE-bd; NCT01062607) is ongoing to address limitations of longitudinal BD studies to-date focused on single disease phases or treatment.

Aim/Objective

To understand current treatment approaches for patients with BD in daily clinical practice.

Methods

Multinational, multicentre, non-interventional, longitudinal study of patients diagnosed with BD-I or BD-II with ≥1 mood event in the preceding 12 months, followed-up for 12-27 months (including retrospective and prospective phases). Site and patient selection provided a sample representative of bipolar populations. The study includes descriptive analyses of demographics, diagnosis, medical history and clinical management. Medication use during the retrospective phase will be presented.

Results

Preliminary results (based on data availability at time of submission) are presented from 2829 patients recruited March-September 2010. During the retrospective period, 94.3% (94.2% BD-I, 94.6% BD-II) of patients received BD therapy. Among BD-I and BD-II patients, respectively, the most common number of prescribed drugs was two (29.5%, 31.5%); 17.6% and 18.1% were prescribed one drug, and 11.5% and 9.8% were prescribed five or more. Drug classes most commonly used (BD-I, BD-II, respectively) were atypical antipsychotics (64.5%, 48.9%) anticonvulsants (58.0%, 54.3%), antidepressants (39.6%, 66.7%) and lithium (31.2%, 17.3%). Electroconvulsive therapy was used in 12 (0.4%) patients (9 BD-I, 3 BD-II). Average treatment duration with atypical antipsychotics, anticonvulsants and antidepressants was 165.0, 199.7 and 169.7 days, respectively.

Conclusions

This ongoing study provides a multinational perspective on BD patient management practices in a large sample population. Financial support: AstraZeneca

Patterns of disease and severity in bipolar disorder: Retrospective data from a large multinational longitudinal study (WAVE-bd)

Introduction

The Wide AmbispectiVE study of the clinical management and burden of bipolar disorder (BD) (WAVE-bd; NCT01062607) is ongoing to address limitations of longitudinal BD studies to-date focused on single disease phases or treatment.

Aim/Objective

To describe baseline bipolar mood state and severity in a cohort of patients with BD.

Methods

Multinational, multicentre, non-interventional, longitudinal study of patients diagnosed with BD-I or BD-II with ≥1 mood event in the preceding 12 months (retrospective data collection from index mood event to enrolment, followed by 9-14 months’ prospective follow-up). Site and patient selection provided a sample representative of bipolar populations. The study includes descriptive analyses of demographics, diagnosis and medical history.

Results

2880 patients (mean age 46.5 years [SD: 13.3]; 62.0% female) were recruited March to September 2010: 1989 (69.1%) BD-I and 891 (30.9%) BD-II. Time (years) from first symptoms to diagnosis was 2.9 [SD: 6.6] (BD-I) and 4.4 [SD: 8.0] (BD-II). Of the total population, 20.8% lived alone (13.9% BD-I, 6.9% BD-II), 36.7% were employed (24.0% BD-I, 12.7% BD-II) and 13.3% unemployed (9.5% BD-I, 3.8% BD-II). Disease status at inclusion (BD-I, BD-II, respectively [mild, moderate, severe]) included hypomania (7.9% [67.7%, 31.0%, 1.3%], 6.5% [70.7%, 29.3%, 0%]), mania (7.1% [26.1%, 47.2%, 26.8%], 0%), euthymia (58.6%, 60.3%), depression (19.7% [38.8%, 47.7%, 13.5%], 31.1% [41.2%, 46.9%, 11.9%]) and mixed (5.7% [30.1%, 46.9%, 23.0%], 0%).

Conclusions

This ongoing study provides detailed insight into a large BD population, showing the majority with euthymia and an important proportion with depression both in BD-I and BD-II patients.