Novel autoantibodies help diagnose anti-SSA antibody negative Sjögren disease and predict abnormal labial salivary gland pathology

OBJECTIVES

Sjögren disease (SjD) diagnosis often requires either positive anti-SSA antibodies or a labial salivary gland biopsy with a positive focus score (FS). One-third of patients with SjD lack anti-SSA antibodies (SSA-), requiring a positive FS for diagnosis. Our objective was to identify novel autoantibodies to diagnose 'seronegative' SjD.

METHODS

IgG binding to a high-density whole human peptidome array was quantified using sera from SSA- SjD cases and matched non-autoimmune controls. We identified the highest bound peptides using empirical Bayesian statistical filters, which we confirmed in an independent cohort comprising SSA- SjD (n=76), sicca-controls without autoimmunity (n=75) and autoimmune-feature controls (SjD features but not meeting SjD criteria; n=41). In this external validation, we used non-parametric methods for binding abundance and controlled false discovery rate in group comparisons. For predictive modelling, we used logistic regression, model selection methods and cross-validation to identify clinical and peptide variables that predict SSA- SjD and FS positivity.

RESULTS

IgG against a peptide from D-aminoacyl-tRNA deacylase (DTD2) bound more in SSA- SjD than sicca-controls (p=0.004) and combined controls (sicca-controls and autoimmune-feature controls combined; p=0.003). IgG against peptides from retroelement silencing factor-1 and DTD2 were bound more in FS-positive than FS-negative participants (p=0.010; p=0.012). A predictive model incorporating clinical variables showed good discrimination between SjD versus control (area under the curve (AUC) 74%) and between FS-positive versus FS-negative (AUC 72%).

CONCLUSION

We present novel autoantibodies in SSA- SjD that have good predictive value for SSA- SjD and FS positivity.

Development of a next-generation sequencing protocol for the canine T cell receptor beta chain repertoire

Profiling the T cell receptor (TCR) repertoire using next-generation sequencing has become common in both human and translational research. Companion dogs with spontaneous tumors, including canine melanoma, share several features, e.g., natural occurrence, shared environmental exposures, natural outbred population, and immunocompetence. T cells play an important role in the adaptive immune system by recognizing specific antigens via a surface TCR. As such, understanding the canine T cell response to vaccines, cancer, immunotherapies, and infectious diseases is critically important for both dog and human health. Off-the-shelf commercial reagents, kits and services are readily available for human, non-human primate, and mouse in this context. However, these resources are limited for the canine. In this study, we present a cost-effective protocol for analysis of canine TCR beta chain genes. Workflow can be accomplished in 1-2 days starting with total RNA and resulting in libraries ready for sequencing on Illumina platforms.

Natural History of Colorectal Polyps Undergoing Longitudinal in Vivo CT Colonography Surveillance

Background The natural history of colorectal polyps is not well characterized due to clinical standards of care and other practical constraints limiting in vivo longitudinal surveillance. Established CT colonography (CTC) clinical screening protocols allow surveillance of small (6-9 mm) polyps. Purpose To assess the natural history of colorectal polyps followed with CTC in a clinical screening program, with histopathologic correlation for resected polyps. Materials and Methods In this retrospective study, CTC was used to longitudinally monitor small colorectal polyps in asymptomatic adult patients from April 1, 2004, to August 31, 2020. All patients underwent at least two CTC examinations. Polyp growth patterns across multiple time points were analyzed, with histopathologic context for resected polyps. Regression analysis was performed to evaluate predictors of advanced histopathology. Results In this study of 475 asymptomatic adult patients (mean age, 56.9 years ± 6.7 [SD]; 263 men), 639 unique polyps (mean initial diameter, 6.3 mm; volume, 50.2 mm3) were followed for a mean of 5.1 years ± 2.9. Of these 639 polyps, 398 (62.3%) underwent resection and histopathologic evaluation, and 41 (6.4%) proved to be histopathologically advanced (adenocarcinoma, high-grade dysplasia, or villous content), including two cancers and 38 tubulovillous adenomas. Advanced polyps showed mean volume growth of +178% per year (752% per year for adenocarcinomas) compared with +33% per year for nonadvanced polyps and -3% per year for unresected, unretrieved, or resolved polyps (P < .001). In addition, 90% of histologically advanced polyps achieved a volume of 100 mm3 and/or volume growth rate of 100% per year, compared with 29% of nonadvanced and 16% of unresected or resolved polyps (P < .001). Polyp volume-to-diameter ratio was also significantly greater for advanced polyps. For polyps observed at three or more time points, most advanced polyps demonstrated an initial slower growth interval, followed by a period of more rapid growth. Conclusion Small colorectal polyps ultimately proving to be histopathologically advanced neoplasms demonstrated substantially faster growth and attained greater overall size compared with nonadvanced polyps. Clinical trial registration no. NCT00204867 © RSNA, 2024 Supplemental material is available for this article. See also the editorial by Dachman in this issue.

NK cells propagate T cell immunity following in situ tumor vaccination

We report an in situ vaccination, adaptable to nearly any type of cancer, that combines radiotherapy targeting one tumor and intratumoral injection of this site with tumor-specific antibody and interleukin-2 (IL-2; 3xTx). In a phase I clinical trial, administration of 3xTx (with an immunocytokine fusion of tumor-specific antibody and IL-2, hu14.18-IL2) to subjects with metastatic melanoma increases peripheral CD8+ T cell effector polyfunctionality. This suggests the potential for 3xTx to promote antitumor immunity against metastatic tumors. In poorly immunogenic syngeneic murine melanoma or head and neck carcinoma models, 3xTx stimulates CD8+ T cell-mediated antitumor responses at targeted and non-targeted tumors. During 3xTx treatment, natural killer (NK) cells promote CTLA4+ regulatory T cell (Treg) apoptosis in non-targeted tumors. This is dependent on NK cell expression of CD86, which is upregulated downstream of KLRK1. NK cell depletion increases Treg infiltration, diminishing CD8+ T cell-dependent antitumor response. These findings demonstrate that NK cells sustain and propagate CD8+ T cell immunity following 3xTx.

Growth rates and histopathological outcomes of small (6-9 mm) colorectal polyps based on CT colonography surveillance and endoscopic removal

BACKGROUND AND AIMS

The natural history of small polyps is not well established and rests on limited evidence from barium enema studies decades ago. Patients with one or two small polyps (6-9 mm) at screening CT colonography (CTC) are offered CTC surveillance at 3 years but may elect immediate colonoscopy. This practice allows direct observation of the growth of subcentimetre polyps, with histopathological correlation in patients undergoing subsequent polypectomy.

DESIGN

Of 11 165 asymptomatic patients screened by CTC over a period of 16.4 years, 1067 had one or two 6-9 mm polyps detected (with no polyps ≥10 mm). Of these, 314 (mean age, 57.4 years; M:F, 141:173; 375 total polyps) elected immediate colonoscopic polypectomy, and 382 (mean age 57.0 years; M:F, 217:165; 481 total polyps) elected CTC surveillance over a mean of 4.7 years. Volumetric polyp growth was analysed, with histopathological correlation for resected polyps. Polyp growth and regression were defined as volume change of ±20% per year, with rapid growth defined as +100% per year (annual volume doubling). Regression analysis was performed to evaluate predictors of advanced histology, defined as the presence of cancer, high-grade dysplasia (HGD) or villous components.

RESULTS

Of the 314 patients who underwent immediate polypectomy, 67.8% (213/314) harboured adenomas, 2.2% (7/314) with advanced histology; no polyps contained cancer or HGD. Of 382 patients who underwent CTC surveillance, 24.9% (95/382) had polyps that grew, while 62.0% (237/382) remained stable and 13.1% (50/382) regressed in size. Of the 58.6% (224/382) CTC surveillance patients who ultimately underwent colonoscopic resection, 87.1% (195/224) harboured adenomas, 12.9% (29/224) with advanced histology. Of CTC surveillance patients with growing polyps who underwent resection, 23.2% (19/82) harboured advanced histology vs 7.0% (10/142) with stable or regressing polyps (OR: 4.0; p<0.001), with even greater risk of advanced histology in those with rapid growth (63.6%, 14/22, OR: 25.4; p<0.001). Polyp growth, but not patient age/sex or polyp morphology/location were significant predictors of advanced histology.

CONCLUSION

Small 6-9 mm polyps present overall low risk to patients, with polyp growth strongly associated with higher risk lesions. Most patients (75%) with small 6-9 mm polyps will see polyp stability or regression, with advanced histology seen in only 7%. The minority of patients (25%) with small polyps that do grow have a 3-fold increased risk of advanced histology.

Novel autoantibodies help diagnose anti-SSA antibody negative Sjögren's disease and predict abnormal labial salivary gland pathology

Objectives

Sj□gren's disease (SjD) diagnosis requires either positive anti-SSA antibodies or a labial salivary gland biopsy with a positive focus score (FS). One-third of SjD patients lack anti-SSA antibodies (SSA-), requiring a positive FS for diagnosis. Our objective was to identify novel autoantibodies to diagnose 'seronegative' SjD.

Methods

IgG binding to a high density whole human peptidome array was quantified using sera from SSA- SjD cases and matched non-autoimmune controls. We identified the highest bound peptides using empirical Bayesian statistical filters, which we confirmed in an independent cohort comprising SSA- SjD (n=76), sicca controls without autoimmunity (n=75), and autoimmune controls (SjD features but not meeting SjD criteria; n=41). In this external validation, we used non-parametric methods for peptide abundance and controlled false discovery rate in group comparisons. For predictive modeling, we used logistic regression, model selection methods, and cross-validation to identify clinical and peptide variables that predict SSA- SjD and FS positivity.

Results

IgG against a peptide from D-aminoacyl-tRNA deacylase (DTD2) was bound more in SSA- SjD than sicca controls (p=.004) and more than combined controls (sicca and autoimmune controls combined; p=0.003). IgG against peptides from retroelement silencing factor-1 (RESF1) and DTD2, were bound more in FS-positive than FS-negative participants (p=.010; p=0.012). A predictive model incorporating clinical variables showed good discrimination between SjD versus control (AUC 74%) and between FS-positive versus FS-negative (AUC 72%).

Conclusion

We present novel autoantibodies in SSA- SjD that have good predictive value for SSA- SjD and FS-positivity.

KEY MESSAGES

What is already known on this topic - Seronegative (anti-SSA antibody negative [SSA-]) Sjögren's disease (SjD) requires a labial salivary gland biopsy for diagnosis, which is challenging to obtain and interpret. What this study adds - We identified novel autoantibodies in SSA- SjD that, when combined with readily available clinical variables, provide good predictive ability to discriminate 1) SSA- SjD from control participants and 2) abnormal salivary gland biopsies from normal salivary gland biopsies. How this study might affect research, practice or policy - This study provides novel diagnostic antibodies addressing the critical need for improvement of SSA- SjD diagnostic tools.

SURROGATE SELECTION OVERSAMPLES EXPANDED T CELL CLONOTYPES

Inference from immunological data on cells in the adaptive immune system may benefit from modeling specifications that describe variation in the sizes of various clonal sub-populations. We develop one such specification in order to quantify the effects of surrogate selection assays, which we confirm may lead to an enrichment for amplified, potentially disease-relevant T cell clones. Our specification couples within-clonotype birth-death processes with an exchangeable model across clonotypes. Beyond enrichment questions about the surrogate selection design, our framework enables a study of sampling properties of elementary sample diversity statistics; it also points to new statistics that may usefully measure the burden of somatic genomic alterations associated with clonal expansion. We examine statistical properties of immunological samples governed by the coupled model specification, and we illustrate calculations in surrogate selection studies of melanoma and in single-cell genomic studies of T cell repertoires.

Notch Signaling Suppresses Melanoma Tumor Development in BRAF/Pten Mice

Both oncogenic and tumor suppressor roles have been assigned to Notch signaling in melanoma. In clinical trials, Notch inhibitors proved to be ineffective for melanoma treatment. Notch signaling has also been implicated in melanoma transdifferentiation, a prognostic feature in primary melanoma. In this study, we investigated the role of Notch signaling in melanoma tumor development and growth using the genetic model of mouse melanoma by crossing BRAFCA/+/Pten+/+/Tyr-CreER+ (B) and BRAFCA/+/Pten-/-/Tyr-CreER + (BP) mice with Notch1 or Notch2 floxed allele mice. The topical application of tamoxifen induced tumors in BP mice but not in B mice with or without the deletion of either Notch1 or Notch2. These data show that the loss of either Notch1 nor Notch2 can substitute the tumor suppressor function of Pten in BRAFV600E-induced melanomagenesis. However, in Pten-null background, the loss of either Notch1 or Notch2 appeared to accelerate BRAFV600E-induced tumor development, suggesting a tumor suppressor role for Notch1 and Notch2 in BRAFV600E/Pten-null driven melanomagenesis. Quantitative immunochemical analysis of a human cutaneous melanoma tissue microarray that consists of >100 primary tumors with complete clinical history showed a weak to moderate correlation between NOTCH protein levels and clinical and pathological parameters. Our data show that Notch signaling is involved during melanomagenesis and suggest that the identification of genes and signaling pathways downstream of Notch could help devise strategies for melanoma prevention.

SpatialCorr identifies gene sets with spatially varying correlation structure

Recent advances in spatially resolved transcriptomics technologies enable both the measurement of genome-wide gene expression profiles and their mapping to spatial locations within a tissue. A first step in spatial transcriptomics data analysis is identifying genes with expression that varies spatially, and robust statistical methods exist to address this challenge. While useful, these methods do not detect spatial changes in the coordinated expression within a group of genes. To this end, we present SpatialCorr, a method for identifying sets of genes with spatially varying correlation structure. Given a collection of gene sets pre-defined by a user, SpatialCorr tests for spatially induced differences in the correlation of each gene set within tissue regions, as well as between and among regions. An application to cutaneous squamous cell carcinoma demonstrates the power of the approach for revealing biological insights not identified using existing methods.

GM-CSF elicits antibodies to tumor-associated proteins when used as a prostate cancer vaccine adjuvant

Antibody responses to off-target cancer-associated proteins have been detected following immunotherapies for cancer, suggesting these may be the result of antigen spread. We have previously reported that serum antibodies to prostate cancer-associated proteins were detectable using a high-throughput peptide array. We hypothesized that the breadth of antibody responses elicited by a vaccine could serve as a measure of the magnitude of its induced antigen spread. Consequently, sera from patients with prostate cancer, treated prior to or after vaccination in one of four separate clinical trials, were evaluated for antibody responses to an array of 177,604 peptides derived from over 1600 prostate cancer-associated gene products. Antibody responses to the same group of 5680 peptides previously reported were identified following vaccinations in which patients were administered GM-CSF as an adjuvant, but not with vaccine in the absence of GM-CSF. Hence, antibody responses to off-target proteins following vaccination may not necessarily serve as evidence of antigen spread and must be interpreted with particular caution following vaccine strategies that use GM-CSF, as GM-CSF appears to have direct effects on the production of antibodies. The evaluation of T cell responses to non-target antigens is likely a preferred approach for detection of immune-mediated antigen spread.

Role of dual specificity phosphatases (DUSPs) in melanoma cellular plasticity and drug resistance

Melanoma cells exhibit phenotypic plasticity that allows transition from a proliferative and differentiated phenotype to a more invasive and undifferentiated or transdifferentiated phenotype often associated with drug resistance. The mechanisms that control melanoma phenotype plasticity and its role in drug resistance are not fully understood. We previously demonstrated that emergence of MAPK inhibitor (MAPKi)-resistance phenotype is associated with decreased expression of stem cell proliferation genes and increased expression of MAPK inactivation genes, including dual specificity phosphatases (DUSPs). Several members of the DUSP family genes, specifically DUSP1, -3, -8 and -9, are expressed in primary and metastatic melanoma cell lines and pre-and post BRAFi treated melanoma cells. Here, we show that knockdown of DUSP1 or DUSP8 or treatment with BCI, a pharmacological inhibitor of DUSP1/6 decrease the survival of MAPKi-resistant cells and sensitizes them to BRAFi and MEKi. Pharmacological inhibition of DUSP1/6 upregulated nestin, a neural crest stem cell marker, in both MAPKi-sensitive cells and cells with acquired MAPKi-resistance. In contrast, treatment with BCI resulted in upregulation of MAP2, a neuronal differentiation marker, only in MAPKi-sensitive cells but caused downregulation of both MAP2 and GFAP, a glial marker, in all MAPKi-resistant cell lines. These data suggest that DUSP proteins are involved in the regulation of cellular plasticity cells and melanoma drug resistance and are potential targets for treatment of MAPKi-resistant melanoma.

SpotClean adjusts for spot swapping in spatial transcriptomics data

Spatial transcriptomics is a powerful and widely used approach for profiling the gene expression landscape across a tissue with emerging applications in molecular medicine and tumor diagnostics. Recent spatial transcriptomics experiments utilize slides containing thousands of spots with spot-specific barcodes that bind RNA. Ideally, unique molecular identifiers (UMIs) at a spot measure spot-specific expression, but this is often not the case in practice due to bleed from nearby spots, an artifact we refer to as spot swapping. To improve the power and precision of downstream analyses in spatial transcriptomics experiments, we propose SpotClean, a probabilistic model that adjusts for spot swapping to provide more accurate estimates of gene-specific UMI counts. SpotClean provides substantial improvements in marker gene analyses and in clustering, especially when tissue regions are not easily separated. As demonstrated in multiple studies of cancer, SpotClean improves tumor versus normal tissue delineation and improves tumor burden estimation thus increasing the potential for clinical and diagnostic applications of spatial transcriptomics technologies.

Bayes optimal informer sets for early-stage drug discovery

An important experimental design problem in early-stage drug discovery is how to prioritize available compounds for testing when very little is known about the target protein. Informer based ranking (IBR) methods address the prioritization problem when the compounds have provided bioactivity data on other potentially relevant targets. An IBR method selects an informer set of compounds, and then prioritizes the remaining compounds on the basis of new bioactivity experiments performed with the informer set on the target. We formalize the problem as a two-stage decision problem and introduce the Bayes Optimal Informer SEt (BOISE) method for its solution. BOISE leverages a flexible model of the initial bioactivity data, a relevant loss function, and effective computational schemes to resolve the two-step design problem. We evaluate BOISE and compare it to other IBR strategies in two retrospective studies, one on protein-kinase inhibition and the other on anti-cancer drug sensitivity. In both empirical settings BOISE exhibits better predictive performance than available methods. It also behaves well with missing data, where methods that use matrix completion show worse predictive performance. This article is protected by copyright. All rights reserved.

Rheumatoid factor and anti-modified protein antibody reactivities converge on IgG epitopes

OBJECTIVE

Rheumatoid arthritis (RA) patients often develop rheumatoid factors (RFs), antibodies that bind IgG Fc, and anti-modified protein antibodies (AMPAs), multi-reactive autoantibodies that commonly bind citrullinated, homocitrullinated, and acetylated antigens. Recently, antibodies that bind citrulline-containing IgG epitopes were discovered in RA, suggesting that additional undiscovered IgG epitopes could exist and that IgG could be a shared antigen for RFs and AMPAs. The objective of this study was to reveal new IgG epitopes in rheumatic disease and to determine if multi-reactive AMPAs bind IgG.

METHODS

Using RA, systemic lupus erythematosus, Sjögren's disease, and spondyloarthropathy sera, IgG binding to native, citrulline-containing, and homocitrulline-containing linear epitopes of the IgG constant region were evaluated by peptide array with highly bound epitopes further evaluated by ELISA. Monoclonal AMPA binding to IgG-derived peptides and IgG Fc was evaluated by ELISA.

RESULTS

Seropositive RA sera had high IgG binding to multiple citrulline- and homocitrulline-containing IgG-derived peptides, whereas anti-SSA+ Sjögren's disease sera had consistent binding to a single linear native epitope of IgG in the hinge region. Monoclonal AMPAs bound citrulline- and homocitrulline-containing IgG peptides and modified IgG Fc.

CONCLUSION

The repertoire of epitopes bound by AMPAs includes modified IgG epitopes, positioning IgG as a common antigen that connects the otherwise divergent reactivities of RFs and AMPAs.

Validation of genetic classifiers derived from mouse and human tumors to identify molecular subtypes of colorectal cancer

Colorectal cancer (CRC) is a leading cause of cancer death in the United States. Standard treatment for advanced-stage CRC for decades has included 5-fluorouracil-based chemotherapy. More recently, targeted therapies for metastatic CRC are being used based on the individual cancer's molecular profile. In the past few years, several different molecular subtype schemes for human CRC have been developed. The molecular subtypes can be distinguished by gene expression signatures and have the potential to be used to guide treatment decisions. However, many subtyping classification methods were developed using mRNA expression levels of hundreds to thousands of genes, making them impractical for clinical use. In this study, we assessed whether an immunohistochemical approach could be used for molecular subtyping of CRCs. We validated two previously published, independent sets of immunohistochemistry classifiers and modified the published methods to improve the accuracy of the scoring methods. In addition, we evaluated whether protein and genetic signatures identified originally in the mouse were linked to clinical outcomes of patients with CRC. We found that low DDAH1 or low GAL3ST2 protein levels in human CRCs correlate with poor patient outcomes. The results of this study have the potential to impact methods for determining the prognosis and therapy selection for patients with CRC.

MixTwice: large-scale hypothesis testing for peptide arrays by variance mixing

SUMMARY

Peptide microarrays have emerged as a powerful technology in immunoproteomics as they provide a tool to measure the abundance of different antibodies in patient serum samples. The high dimensionality and small sample size of many experiments challenge conventional statistical approaches, including those aiming to control the false discovery rate (FDR). Motivated by limitations in reproducibility and power of current methods, we advance an empirical Bayesian tool that computes local FDR statistics and local false sign rate statistics when provided with data on estimated effects and estimated standard errors from all the measured peptides. As the name suggests, the MixTwice tool involves the estimation of two mixing distributions, one on underlying effects and one on underlying variance parameters. Constrained optimization techniques provide for model fitting of mixing distributions under weak shape constraints (unimodality of the effect distribution). Numerical experiments show that MixTwice can accurately estimate generative parameters and powerfully identify non-null peptides. In a peptide array study of rheumatoid arthritis, MixTwice recovers meaningful peptide markers in one case where the signal is weak, and has strong reproducibility properties in one case where the signal is strong.

AVAILABILITYAND IMPLEMENTATION

MixTwice is available as an R software package https://cran.r-project.org/web/packages/MixTwice/.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Multi-ancestral origin of intestinal tumors: Impact on growth, progression, and drug efficacy

Background

Data are steadily accruing that demonstrate that intestinal tumors are frequently derived from multiple founding cells, resulting in tumors comprised of distinct ancestral clones that might cooperate or alternatively compete, thereby potentially impacting different phases of the disease process.

Aim

We sought to determine whether tumors with a multi‐ancestral architecture involving at least two distinct clones show increased tumor number, growth, progression, or resistance to drug intervention.

Methods

Mice carrying the Min allele of Apc were generated that were mosaic with only a subset of cells in the intestinal epithelium expressing an activated form of PI3K, a key regulatory kinase affecting several important cellular processes. These cells were identifiable as they fluoresced green, whereas all other cells fluoresced red.

Results

Cell lineage tracing revealed that many intestinal tumors from our mouse model were derived from at least two founding cells, those expressing the activated PI3K (green) and those which did not (red). Heterotypic tumors with a multi‐ancestral architecture as evidenced by a mixture of green and red cells exhibited increased tumor growth and invasiveness. Clonal architecture also had an impact on tumor response to low‐dose aspirin. Aspirin treatment resulted in a greater reduction of heterotypic tumors derived from multiple founding cells as compared to tumors derived from a single founding cell.

Conclusion

These data indicate that genetically distinct tumor‐founding cells can contribute to early intratumoral heterogeneity. The coevolution of the founding cells and their progeny enhances colon tumor progression and impacts the response to aspirin. These findings are important to a more complete understanding of tumorigenesis with consequences for several distinct models of tumor evolution. They also have practical implications to the clinic. Mouse models with heterogenous tumors are likely better for predicting drug efficacy as compared to models in which the tumors are highly homogeneous. Moreover, understanding how interactions among different populations in a single heterotypic tumor with a multi‐ancestral architecture impact response to a single agent and combination therapies are necessary to fully develop personalized medicine.

Dimension constraints improve hypothesis testing for large-scale, graph-associated, brain-image data

For large-scale testing with graph-associated data, we present an empirical Bayes mixture technique to score local false-discovery rates (FDRs). Compared to procedures that ignore the graph, the proposed Graph-based Mixture Model (GraphMM) method gains power in settings where non-null cases form connected subgraphs, and it does so by regularizing parameter contrasts between testing units. Simulations show that GraphMM controls the FDR in a variety of settings, though it may lose control with excessive regularization. On magnetic resonance imaging data from a study of brain changes associated with the onset of Alzheimer’s disease, GraphMM produces greater yield than conventional large-scale testing procedures.

Antibody profiling of patients with prostate cancer reveals differences in antibody signatures among disease stages

BACKGROUND

Previous studies of prostate cancer autoantibodies have largely focused on diagnostic applications. So far, there have been no reports attempting to more comprehensively profile the landscape of prostate cancer-associated antibodies. Specifically, it is unknown whether the quantity of antibodies or the types of proteins recognized change with disease progression.

METHODS

A peptide microarray spanning the amino acid sequences of the gene products of 1611 prostate cancer-associated genes was synthesized. Serum samples from healthy male volunteers (n=15) and patients with prostate cancer (n=85) were used to probe the array. These samples included patients with various clinical stages of disease: newly diagnosed localized prostate cancer (n=15), castration-sensitive non-metastatic prostate cancer (nmCSPC, n=40), castration-resistant non-metastatic prostate cancer (n=15) and castration-resistant metastatic disease (n=15). The patients with nmCSPC received treatment with either standard androgen deprivation therapy (ADT) or an antitumor DNA vaccine encoding prostatic acid phosphatase. Serial sera samples from these individuals were also used to probe the array, to secondarily determine whether this approach could be used to detect treatment-related changes.

RESULTS

We demonstrated that this peptide array yielded highly reproducible measurements of serum IgG levels. We found that the overall number of antibody responses did not increase with disease burden. However, the composition of recognized proteins shifted with clinical stage of disease. Our analysis revealed that the largest difference was between patients with castration-sensitive and castration-resistant disease. Patients with castration-resistant disease recognized more proteins associated with nucleic acid binding and gene regulation compared with men in other groups. Our longitudinal data showed that treatments can elicit antibodies detectable by this array, and notably vaccine-treated patients developed increased responses to more proteins over the course of treatment than did ADT-treated patients.

CONCLUSIONS

This study represents the largest survey of prostate cancer-associated antibodies to date. We have been able to characterize the classes of proteins recognized by patients and determine how they change with disease burden. Our findings further demonstrate the potential of this platform for measuring antigen spread and studying responses to immunomodulatory therapies.

Abstract B27: MTORC1/2 inhibition as a treatment strategy for PIK3CA mutant colorectal cancer

Colorectal cancer (CRC) is a leading cause of cancer-related death. PIK3CA mutations are common, leading to a constitutively active phosphoinositide-3 kinase (PI3K). An effective means to target this pathway has yet to be identified. We investigated the use of a panel of inhibitors targeting the PI3K pathway including copanlisib (dual PI3K/mTOR), BYL-719 (alpha isomer specific PI3K), GDC-0941 (pan PI3K), and TAK-228 (MTORC1/2). To test the efficacy of these inhibitors in CRC, murine organotypic cancer spheroids (MDOCS) were generated from the invasive adenocarcinomas of Apc and Pik3ca transgenic mice. These inhibitors were investigated at clinically relevant doses (100-400nM). Copanlisib and TAK-228 were the only inhibitors to result in a significant reduction in the size of the MDOCS (200nM; 27% p-value&lt;0.001, 18% p-value&lt;0.001, respectively). This result correlated with a decrease in the phosphorylation of AKT (ser473), RPS6, and 4EBP1. Minimal induction of apoptosis was observed using these inhibitors alone as measured by cleaved PARP and cleaved caspase 3. These results were confirmed in vivo using transgenic mice with TAK-228 (1mg/kg/day) and copanlisib (10mg/kg q2d x5) resulting in a reduction in lumen occlusion of the colon tumors. Persistent BCL-2 and BCL-xL signaling was hypothesized to be preventing the induction of apoptosis. To determine if inhibition of these BCL-2 family members would further sensitize these MDOCS to copanlisib and TAK-228, these inhibitors were tested in combination with navitoclax (ABT-263; BCL-2 family inhibitor). A dramatic enhanced sensitivity was observed in MDOCS (30% p-value&lt;0.001, 23% p-value&lt;0.001, respectively). This correlated with an induction of apoptosis as measured by cleaved caspase 3. Next a panel of eight CRC patient-derived organotypic cancer spheroids (PDOCS) were treated with the combination of TAK-228 and navitoclax. Differential sensitivity was observed across the panel (25% resistant, 37.5% intermediate, and 37.5% highly sensitive) owing to the importance of mutational profile with targeted therapies. These studies indicate the benefit of MTORC1/2 for the treatment of PIK3CA mutant CRC and with enhanced activity of the combination of MTORC1/2 inhibition in combination with BCL-2 family inhibition. These therapies deserve further investigation for the treatment of patients with PIK3CA mutant CRC.

Citation Format: Rebecca A. DeStefanis, Susan N. Payne, Devon Miller, Cheri A. Pasch, Christopher Babiarz, Alyssa DeZeeuw, Stephanie L. Fricke, Carley Sprackling, Alexander E. Yueh, Demetra P. Korkos, Dana R. Van De Hey, Gioia Sha, Aurora Greane, Jeremy D. Kratz, Linda Clipson, Kristina A. Matkowskyj, Michael A. Newton, Dustin A. Deming. MTORC1/2 inhibition as a treatment strategy for PIK3CA mutant colorectal cancer [abstract]. In: Proceedings of the AACR Special Conference on Targeting PI3K/mTOR Signaling; 2018 Nov 30-Dec 8; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(10_Suppl):Abstract nr B27.

Correction to: Ancestral Folate Promotes Neuronal Regeneration in Serial Generations of Progeny

The original version of this article unfortunately contained error in Figure 4a to where some of the text was overlapping.

Disordered Antigens and Epitope Overlap Between Anti-Citrullinated Protein Antibodies and Rheumatoid Factor in Rheumatoid Arthritis

OBJECTIVE

Anti-citrullinated protein antibodies (ACPAs) and rheumatoid factor (RF) are commonly present in rheumatoid arthritis (RA) without a clear rationale for their coexistence. Moreover, autoantibodies develop against proteins with different posttranslational modifications and native proteins without obvious unifying characteristics of the antigens. We undertook this study to broadly evaluate autoantibody binding in seronegative and seropositive RA to identify novel features of reactivity.

METHODS

An array was created using a total of 172,828 native peptides, citrulline-containing peptides, and homocitrulline-containing peptides derived primarily from proteins citrullinated in the rheumatoid joint. IgG and IgM binding to peptides were compared between cyclic citrullinated peptide (CCP)-positive RF+, CCP+RF-, CCP-RF+, and CCP-RF- serum from RA patients (n = 48) and controls (n = 12). IgG-bound and endogenously citrullinated peptides were analyzed for amino acid patterns and predictors of intrinsic disorder, i.e., unstable 3-dimensional structure. Binding to IgG-derived peptides was specifically evaluated. Enzyme-linked immunosorbent assay confirmed key results.

RESULTS

Broadly, CCP+RF+ patients had high citrulline-specific IgG binding to array peptides and CCP+RF- and CCP-RF+ patients had modest citrulline-specific IgG binding (median Z scores 3.02, 1.42, and 0.75, respectively; P < 0.0001). All RA groups had low homocitrulline-specific binding. CCP+RF+ patients had moderate IgG binding to native peptides (median Z score 2.38; P < 0.0001). The highest IgG binding was to citrulline-containing peptides, irrespective of protein identity, especially if citrulline was adjacent to glycine or serine, motifs also seen in endogenous citrullination in the rheumatoid joint. Highly bound peptides had multiple features predictive of disorder. IgG from CCP+RF+ patients targeted citrulline-containing IgG-derived peptides.

CONCLUSION

Disordered antigens, which are frequently citrullinated, and common epitopes for ACPAs and RF are potentially unifying features for RA autoantibodies.

Melanoma Progression Inhibits Pluripotency and Differentiation of Melanoma-Derived iPSCs Produces Cells with Neural-like Mixed Dysplastic Phenotype

Melanomas are known to exhibit phenotypic plasticity. However, the role cellular plasticity plays in melanoma tumor progression and drug resistance is not fully understood. Here, we used reprogramming of melanocytes and melanoma cells to induced pluripotent stem cell (iPSCs) to investigate the relationship between cellular plasticity and melanoma progression and mitogen-activated protein kinase (MAPK) inhibitor resistance. We found that melanocyte reprogramming is prevented by the expression of oncogenic BRAF, and in melanoma cells harboring oncogenic BRAF and sensitive to MAPK inhibitors, reprogramming can be restored by inhibition of the activated oncogenic pathway. Our data also suggest that melanoma tumor progression acts as a barrier to reprogramming. Under conditions that promote melanocytic differentiation of fibroblast- and melanocyte-derived iPSCs, melanoma-derived iPSCs exhibited neural cell-like dysplasia and increased MAPK inhibitor resistance. These data suggest that iPSC-like reprogramming and drug resistance of differentiated cells can serve as a model to understand melanoma cell plasticity-dependent mechanisms in recurrence of aggressive drug-resistant melanoma.

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Metastatic melanoma exhibits less plasticity to reprogramming than primary melanoma

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Oncogenic BRAF^V600E and resistance to MAPKi inhibit reprogramming of melanoma

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Differentiation of melanoma-iPSCs produces cells with mixed dysplastic phenotype

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Melanoma-iPSC-differentiated cells exhibit acquired resistance to MAPKi

Patient-Derived Cancer Organoid Cultures to Predict Sensitivity to Chemotherapy and Radiation

PURPOSE

Cancer treatment is limited by inaccurate predictors of patient-specific therapeutic response. Therefore, some patients are exposed to unnecessary side effects and delays in starting effective therapy. A clinical tool that predicts treatment sensitivity for individual patients is needed.

EXPERIMENTAL DESIGN

Patient-derived cancer organoids were derived across multiple histologies. The histologic characteristics, mutation profile, clonal structure, and response to chemotherapy and radiation were assessed using bright-field and optical metabolic imaging on spheroid and single-cell levels, respectively.

RESULTS

We demonstrate that patient-derived cancer organoids represent the cancers from which they were derived, including key histologic and molecular features. These cultures were generated from numerous cancers, various biopsy sample types, and in different clinical settings. Next-generation sequencing reveals the presence of subclonal populations within the organoid cultures. These cultures allow for the detection of clonal heterogeneity with a greater sensitivity than bulk tumor sequencing. Optical metabolic imaging of these organoids provides cell-level quantification of treatment response and tumor heterogeneity allowing for resolution of therapeutic differences between patient samples. Using this technology, we prospectively predict treatment response for a patient with metastatic colorectal cancer.

CONCLUSIONS

These studies add to the literature demonstrating feasibility to grow clinical patient-derived organotypic cultures for treatment effectiveness testing. Together, these culture methods and response assessment techniques hold great promise to predict treatment sensitivity for patients with cancer undergoing chemotherapy and/or radiation.

Notch signaling activation induces cell death in MAPKi-resistant melanoma cells

The role of Notch signaling in melanoma drug resistance is not well understood. In this study, we show that although NOTCH proteins are upregulated in metastatic melanoma cell lines, Notch signaling inhibition had no effect on cell survival, growth, migration or the sensitivity of BRAFV600E-melanoma cells to MAPK inhibition (MAPKi). We found that NOTCH1 is downregulated in melanoma cell lines with intrinsic and acquired resistance to MAPKi. Forced expression of NICD1, the active form of Notch1, caused apoptosis of the NOTCH^lo , MAPKi-resistant cells, but not the NOTCH^hi , MAPKi-sensitive melanoma cell lines. Whole transcriptome-sequencing analyses of NICD1-transduced MAPKi-sensitive and MAPKi-resistant cells revealed differential regulation of endothelin 1 (EDN1) by NICD1, that is, downregulation in MAPKi-resistant cells and upregulation in MAPKi-sensitive cells. Knockdown of EDN1 partially mimicked the effect of NICD1 on the survival of MAPKi-resistant cells. We show that the opposite regulation of EDN1 by Notch signaling is mediated by the differential regulation of c-JUN by NICD1. Our data show that MAPKi-resistant melanoma cells acquire vulnerability to Notch signaling activation and suggest that Notch-c-JUN-EDN1 axis is a potential therapeutic target in MAPKi-resistant melanoma.

MTORC1/2 Inhibition as a Therapeutic Strategy for PIK3CA Mutant Cancers

PIK3CA mutations are common in clinical molecular profiling, yet an effective means to target these cancers has yet to be developed. MTORC1 inhibitors are often used off-label for patients with PIK3CA mutant cancers with only limited data to support this approach. Here we describe a cohort of patients treated with cancers possessing mutations activating the PI3K signaling cascade with minimal benefit to treatment with the MTORC1 inhibitor everolimus. Previously, we demonstrated that dual PI3K/mTOR inhibition could decrease proliferation, induce differentiation, and result in a treatment response in APC and PIK3CA mutant colorectal cancer. However, reactivation of AKT was identified, indicating that the majority of the benefit may be secondary to MTORC1/2 inhibition. TAK-228, an MTORC1/2 inhibitor, was compared with dual PI3K/mTOR inhibition using BEZ235 in murine colorectal cancer spheroids. A reduction in spheroid size was observed with TAK-228 and BEZ235 (-13% and -14%, respectively) compared with an increase of >200% in control (P < 0.001). These spheroids were resistant to MTORC1 inhibition. In transgenic mice possessing Pik3ca and Apc mutations, BEZ235 and TAK-228 resulted in a median reduction in colon tumor size of 19% and 20%, respectively, with control tumors having a median increase of 18% (P = 0.02 and 0.004, respectively). This response correlated with a decrease in the phosphorylation of 4EBP1 and RPS6. MTORC1/2 inhibition is sufficient to overcome resistance to everolimus and induce a treatment response in PIK3CA mutant colorectal cancers and deserves investigation in clinical trials and in future combination regimens.

The conserved protective cyclic AMP-phosphodiesterase function PDE4B is expressed in the adenoma and adjacent normal colonic epithelium of mammals and silenced in colorectal cancer

Conservation over three mammalian genera-the mouse, rat, and human-has been found for a subset of the transcripts whose level differs between the adenoma and normal epithelium of the colon. Pde4b is one of the triply conserved transcripts whose level is enhanced both in the colonic adenoma and in the normal colonic epithelium, especially adjacent to adenomas. It encodes the phosphodiesterase PDE4B, specific for cAMP. Loss of PDE4B function in the ApcMin/+ mouse leads to a significant increase in the number of colonic adenomas. Similarly, Pde4b-deficient ApcMin/+ mice are hypersensitive to treatment by the inflammatory agent DSS, becoming moribund soon after treatment. These observations imply that the PDE4B function protects against ApcMin-induced adenomagenesis and inflammatory lethality. The paradoxical enhancement of the Pde4b transcript in the adenoma versus this inferred protective function of PDE4B can be rationalized by a feedback model in which PDE4B is first activated by early oncogenic stress involving cAMP and then, as reported for frank human colon cancer, inactivated by epigenetic silencing.

Abstract 2936: MTORC1/2 inhibition in combination with BCL-2/BCL-xL inhibition in APC and PIK3CA mutant colorectal cancer

Background: Intrinsic resistance to agents targeting the PI3K/AKT/mTOR pathway has been commonly encountered in clinical trials of patients with PIK3CA mutant colorectal cancer (CRC). Upregulation of antiapoptotic signaling has been proposed as a mechanism of resistance to these therapies, including upregulation of BCL-2 and BCL-xL. To investigate if inhibition of BCL-2 family members would sensitize Pik3ca mutant cancers to MTORC1/2 inhibition, treatment studies were performed with TAK-228 (MTORC1/2 inhibitor), BEZ235 (dual PI3K/mTOR inhibitor), navitoclax (ABT-263; BCL-2, BCL-xL and BCL-w inhibitor) and the combination of navitoclax with either TAK-228 or BEZ235.

Methods: Therapeutic investigations with 200 nM TAK-228 or 200 nM BEZ235 and 250 nM navitoclax were performed in murine CRC spheroids with loss of APC and a constitutively active PI3K. Images were taken both pre- and post-treatment and changes in spheroid diameter were measured. Parallel treatment studies were performed on patient-derived organotypic CRC spheroids. Additionally, treatment studies were performed in vivo using a novel transgenic mouse model carrying Apc and Pik3ca mutations. The mice were treated with the combination of BEZ235 and navitoclax or with a single agent alone for 7 consecutive days.

Results: Treatment of CRC spheroids with TAK-228 resulted in a reduction of sphere size by 16% while control treated spheres increased by 77% of their size at day 0. No response was seen with navitoclax treatment alone. A profound synergistic treatment response was observed with the combination of TAK-228 and navitoclax (reduction of 26%, p&lt;0.001), with most spheroids undergoing complete collapse. A similar treatment response was observed with BEZ235 and navitoclax. Human CRC spheroids treated with TAK-228 and/or navitoclax demonstrated a variable response with 3 of 5 lines having a greater than 15% reduction in sphere size when treated with the combination of TAK-228 and navitoclax (p&lt;0.001). This enhanced treatment response correlated with an increase in apoptosis as measured by cleaved caspase 3. No enhanced activity was observed with the combination of BEZ235 and ABT-199 (selective BCL-2 inhibitor). In transgenic mice with Apc and Pik3ca mutant cancers, a median change in lumen occlusion of -42% was observed with the combination of BEZ235 and navitoclax compared to -15% with BEZ235 alone (one-sided p&lt;0.03, n=34 mice).

Conclusion: Synergistic activity was seen with the combination of TAK-228 or BEZ235 and navitoclax. This combination deserves further study in future clinical trials.

Citation Format: Stephanie L. Fricke, Susan N. Payne, Cheri A. Pasch, Demetra P. Korkos, Gioia Sha, Alex E. Yueh, Christopher Babiarz, Linda Clipson, Kristina A. Matkowskyj, Michael A. Newton, Dustin A. Deming. MTORC1/2 inhibition in combination with BCL-2/BCL-xL inhibition in APC and PIK3CA mutant colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2936.

Abstract 5011: Patient-derived organotypic cancer spheroids (PDOCS) as predictive models for the treatment of cancer in a clinically meaningful time frame

Background: Standard two-dimensional cell cultures do not retain the key characteristics of the human cancers from which they are derived and treatment effects are not always able to be replicated in vivo, making the development of alternative culturing systems paramount. Specifically, commercially available cell lines do not fully represent the mutation profiles seen in human cancers. Here we investigate the feasibility of three-dimensional PDOCS to more accurately represent the cancers from which they are derived and to predict treatment sensitivity in a clinically meaningful time frame.

Methods: Surgical resection, core needle biopsies, paracentesis or thoracentesis samples from patients with various types of cancer were obtained under an approved IRB protocol, digested and spheroid cultures grown suspended in Matrigel. PDOCS were grown for up to two weeks and passaged at least once prior to treatment. PDOCS were imaged using brightfield imaging (4X) prior to treatment with vehicle or 5-fluorouracil (5-FU; 1, 10, or 100 µM) and/or radiation (2 or 5 Gy). After 2 days of treatment, the 5-FU was removed and the cultures were allowed to grow for an additional 2 days. PDOCS were re-imaged and the relative change in diameter was calculated using ImageJ software and compared to untreated controls. Optical metabolic imaging (OMI) was performed with a multiphoton microscope to probe the fluorescence lifetime and optical redox ratio of metabolic co-enzymes NAD(P)H and FAD. Single-cell analysis of each image was completed using Cell Profiler software to parse resistant cell populations in each PDOCS sample tested. DNA for mutation profile analysis was isolated and sequenced using a QIAseq targeted panel.

Results: PDOCS were successfully isolated from a variety of cancers including colorectal (CRC), pancreas, lung, neuroendocrine, liver, breast, and ovarian. Key phenotypic characteristics of the tumors were retained in PDOCS cultured including crypt-like structures, mucin production and Ki67 proliferation rates. Cancer hot spot sequencing was performed comparing PDOCS and the tumors from which they were derived. Over 90% of the nonsynonymous mutations were identical, except in the setting of microsatellite instability. All driver mutations were identical (i.e., APC, KRAS, PIK3CA, TP53). Differential sensitivity to chemoradiation was observed among 4 different colorectal PDOCS treated with 5-FU and radiation (Median % PDOCS diameter change vs control: Patient A 17.1, p=0.64; Patient B -3.05, p=0.02; Patient C -19.4, p=2x10-5; Patient D -31.3, p=0.002). Similar response data were determined using OMI; however, single-cell analyses identified potentially resistant cell populations.

Conclusions: PDOCS retain key characteristics of the cancers from which they are derived and can be utilized for treatment sensitivity testing in a clinically meaningful time frame.

Citation Format: Cheri A. Pasch, Peter F. Favreau, Alex E. Yueh, Kwang P. Nickel, Christopher P. Babiarz, Philip B. Emmerich, Rosabella T. Pitera, Susan N. Payne, Demetra P. Korkos, Joseph T. Sharick, Carley M. Sprackling, Linda Clipson, Kristina A. Matkowskyj, Michael A. Newton, Melissa C. Skala, Michael F. Bassetti, Randall J. Kimple, Dustin A. Deming. Patient-derived organotypic cancer spheroids (PDOCS) as predictive models for the treatment of cancer in a clinically meaningful time frame [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5011.

RNA expression profiling in sulfamethoxazole-treated patients with a range of in vitro lymphocyte cytotoxicity phenotypes

The lymphocyte toxicity assay (LTA) is a proposed surrogate marker of sulfonamide antibiotic hypersensitivity. In the LTA, peripheral blood mononuclear cells (PBMCs) undergo apoptosis more readily in hypersensitive versus tolerant patients when exposed to drug-hydroxylamine metabolites in vitro. The purpose of this study was to identify key gene transcripts associated with increased cytotoxicity from sulfamethoxazole-hydroxylamine in human PBMCs in the LTA. The LTA was performed on PBMCs of 10 patients hypersensitive to trimethoprim-sulfamethoxazole (HS) and 10 drug-tolerant controls (TOL), using two cytotoxicity assays: YO-PRO (n = 20) and MTT (n = 12). mRNA expression profiles of PBMCs, enriched for CD8+ T cells, were compared between HS and TOL patients. Transcript expression was interrogated for correlation with % cytotoxicity from YO-PRO and MTT assays. Correlated transcripts of interest were validated by qPCR. LTA results were not significantly different between HS and TOL patients, and no transcripts were found to be differentially expressed between the two groups. 96 transcripts were correlated with cytotoxicity by YO-PRO (r = ±.63-.75, FDR 0.188). Transcripts were selected for validation based on mechanistic plausibility and three were significantly over-expressed by qPCR in high cytotoxicity patients: multi-specific organic anion transporter C (ABCC5), mitoferrin-1 (SLC25A37), and Porimin (TMEM123). These data identify novel transcripts that could contribute to sulfonamide-hydroxylamine induced cytotoxicity. These include SLC25A37, encoding a mitochondrial iron transporter, ABCC5, encoding an arylamine drug transporter, and TMEM123, encoding a transmembrane protein that mediates cell death.

Subclonal diversity arises early even in small colorectal tumours and contributes to differential growth fates

OBJECTIVE AND DESIGN

The goal of the study was to determine whether the mutational profile of early colorectal polyps correlated with growth behaviour. The growth of small polyps (6-9 mm) that were first identified during routine screening of patients was monitored over time by interval imaging with CT colonography. Mutations in these lesions with known growth rates were identified by targeted next-generation sequencing. The timing of mutational events was estimated using computer modelling and statistical inference considering several parameters including allele frequency and fitness.

RESULTS

The mutational landscape of small polyps is varied both within individual polyps and among the group as a whole but no single alteration was correlated with growth behaviour. Polyps carried 0-3 pathogenic mutations with the most frequent being in APC, KRAS/NRAS, BRAF, FBXW7 and TP53. In polyps with two or more pathogenic mutations, allele frequencies were often variable, indicating the presence of multiple populations within a single tumour. Based on computer modelling, detectable mutations occurred at a mean polyp size of 30±35 crypts, well before the tumour is of a clinically detectable size.

CONCLUSIONS

These data indicate that small colon polyps can have multiple pathogenic mutations in crucial driver genes that arise early in the existence of a tumour. Understanding the molecular pathway of tumourigenesis and clonal evolution in polyps that are at risk for progressing to invasive cancers will allow us to begin to better predict which polyps are more likely to progress into adenocarcinomas and which patients are at greater risk of developing advanced disease.

Pilot study of safety and feasibility of DNA microseeding for treatment of spontaneous canine melanoma

Spontaneous canine malignant melanoma provides an excellent pre-clinical model to study DNA vaccines for melanoma immunotherapy. A USDA-approved xenogeneic human tyrosinase (huTYR) plasmid DNA vaccine delivered intramuscularly induces detectable immune responses and has clinical activity in some dogs with melanoma. The objective of this pilot study was to evaluate the feasibility, safety and immunogenicity of huTYR plasmid DNA administered to the skin via microseeding in dogs with spontaneous melanoma. DNA microseeding utilizes a modified tattooing device as an alternate and potentially more potent delivery method for DNA immunization. DNA was delivered to shaved inner thigh skin of six companion dogs with melanoma approximately every 14 days for a planned total of four vaccination time points. An anti-huTYR ELISA was used to test pre- and post-treatment sera. Biopsies of treated skin were obtained for detection of huTYR transgene expression. DNA microseeding was well tolerated with no significant toxicity detected beyond local site irritation, and there were no signs of autoimmunity. huTYR-expressing cells were observed in biopsies of huTYR DNA microseeding sites. Increased humoral anti-huTYR antibodies were seen in two of five evaluable dogs following microseeding compared to baseline. DNA microseeding is well tolerated in companion dogs with melanoma. Further investigation is needed to determine if combining DNA microseeding with other immunotherapy regimens potentiates this delivery platform for cancer immunotherapy.

Identification of tissue-specific transcriptional markers of caloric restriction in the mouse and their use to evaluate caloric restriction mimetics

Caloric restriction (CR) without malnutrition has been shown to retard several aspects of the aging process and to extend lifespan in different species. There is strong interest in the identification of CR mimetics (CRMs), compounds that mimic the beneficial effects of CR on lifespan and healthspan without restriction of energy intake. Identification of CRMs in mammals is currently inefficient due to the lack of screening tools. We have performed whole‐genome transcriptional profiling of CR in seven mouse strains (C3H/HeJ, CBA/J, DBA/2J, B6C3F1/J, 129S1/SvImJ, C57BL/6J, and BALB/cJ) in white adipose tissue (WAT), gastrocnemius muscle, heart, and brain neocortex. This analysis has identified tissue‐specific panels of genes that change in expression in multiple mouse strains with CR. We validated a subset of genes with qPCR and used these to evaluate the potential CRMs bezafibrate, pioglitazone, metformin, resveratrol, quercetin, 2,4‐dinitrophenol, and L‐carnitine when fed to C57BL/6J 2‐month‐old mice for 3 months. Compounds were also evaluated for their ability to modulate previously characterized biomarkers of CR, including mitochondrial enzymes citrate synthase and SIRT3, plasma inflammatory cytokines TNF‐α and IFN‐γ, glycated hemoglobin (HbA1c) levels and adipocyte size. Pioglitazone, a PPAR‐γ agonist, and L‐carnitine, an amino acid involved in lipid metabolism, displayed the strongest effects on both the novel transcriptional markers of CR and the additional CR biomarkers tested. Our findings provide panels of tissue‐specific transcriptional markers of CR that can be used to identify novel CRMs, and also represent the first comparative molecular analysis of several potential CRMs in multiple tissues in mammals.

Machine Learning Consensus Scoring Improves Performance Across Targets in Structure-Based Virtual Screening

In structure-based virtual screening, compound ranking through a consensus of scores from a variety of docking programs or scoring functions, rather than ranking by scores from a single program, provides better predictive performance and reduces target performance variability. Here we compare traditional consensus scoring methods with a novel, unsupervised gradient boosting approach. We also observed increased score variation among active ligands and developed a statistical mixture model consensus score based on combining score means and variances. To evaluate performance, we used the common performance metrics ROCAUC and EF1 on 21 benchmark targets from DUD-E. Traditional consensus methods, such as taking the mean of quantile normalized docking scores, outperformed individual docking methods and are more robust to target variation. The mixture model and gradient boosting provided further improvements over the traditional consensus methods. These methods are readily applicable to new targets in academic research and overcome the potentially poor performance of using a single docking method on a new target.

Riemannian Variance Filtering: An Independent Filtering Scheme for Statistical Tests on Manifold-valued Data

Performing large scale hypothesis testing on brain imaging data to identify group-wise differences (e.g., between healthy and diseased subjects) typically leads to a large number of tests (one per voxel). Multiple testing adjustment (or correction) is necessary to control false positives, which may lead to lower detection power in detecting true positives. Motivated by the use of so-called "independent filtering" techniques in statistics (for genomics applications), this paper investigates the use of independent filtering for manifold-valued data (e.g., Diffusion Tensor Imaging, Cauchy Deformation Tensors) which are broadly used in neuroimaging studies. Inspired by the concept of variance of a Riemannian Gaussian distribution, a type of non-specific data-dependent Riemannian variance filter is proposed. In practice, the filter will select a subset of the full set of voxels for performing the statistical test, leading to a more appropriate multiple testing correction. Our experiments on synthetic/simulated manifold-valued data show that the detection power is improved when the statistical tests are performed on the voxel locations that "pass" the filter. Given the broadening scope of applications where manifold-valued data are utilized, the scheme can serve as a general feature selection scheme.

Abstract 2915: The timing of mutational burst events impact the growth of tumors in the colon

Basic and clinical scientists believe that benign polyps in the colon progress to cancers through the slow, stepwise accumulation of mutations. Interestingly, only a small percentage of all tumors progress, whereas a significant number remain static in size, regress, or resolve completely. The mechanisms underlying these differential fates are unknown, and mechanisms of tumor evolution during this premalignant phase are still under investigation and continued debate. We previously reported that sub-clonal diversity arises early in small human adenomas and contributes to the growth of tumors in the colon. An emerging hypothesis is that colorectal tumors form and progress via a process of punctuated equilibrium, where multiple copy number alterations and mutational events happen simultaneously in a burst-like fashion. In this study, we prospectively test this concept using a mouse model in which tumor induction is spatially and temporally controlled via a non-surgical delivery of adenovirus expressing CRE recombinase and a temporally controlled mutational burst via administration of the carcinogen Azoxymethane. Tumors are induced at a similar rate regardless the timing of the burst relative to tumor induction with a mean tumor incidence of 62% at three weeks post induction. However, tumor growth may be affected by the timing of the burst. Animals that had a mutational burst event prior to tumor induction or those that had a late mutational burst event had a lower average in vivo growth rate compared to controls and those with an early burst event, but the average in vivo tumor size was comparable across all groups. Taken together, these preliminary data provide evidence that the timing of a mutational burst event contributes to tumor growth. This prospective experiment is being extended through computer modeling and statistical inference to compare in silico mutational landscapes to a cohort of colon polyps removed from patients at normal screening. The findings will provide new insights into the earliest stages of tumorigenesis.

Citation Format: Chelsie K. Sievers, Tien N. Vo, Perry J. Pickhardt, Bryan D. Pooler, Kristina A. Matkowskyj, Dawn M. Albrecht, Quincy Rosemarie, Michael A. Newton, Richard B. Halberg. The timing of mutational burst events impact the growth of tumors in the colon [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2915. doi:10.1158/1538-7445.AM2017-2915

Dual PI3K/mTOR Inhibition in Colorectal Cancers with APC and PIK3CA Mutations

Therapeutic targeting of the PI3K pathway is an active area of research in multiple cancer types, including breast and endometrial cancers. This pathway is commonly altered in cancer and plays an integral role in numerous vital cellular functions. Mutations in the PIK3CA gene, resulting in a constitutively active form of PI3K, often occur in colorectal cancer, though the population of patients who would benefit from targeting this pathway has yet to be identified. In human colorectal cancers, PIK3CA mutations most commonly occur concomitantly with loss of adenomatous polyposis coli (APC). Here, treatment strategies are investigated that target the PI3K pathway in colon cancers with mutations in APC and PIK3CA Colorectal cancer spheroids with Apc and Pik3ca mutations were generated and characterized confirming that these cultures represent the tumors from which they were derived. Pan and alpha isomer-specific PI3K inhibitors did not induce a significant treatment response, whereas the dual PI3K/mTOR inhibitors BEZ235 and LY3023414 induced a dramatic treatment response through decreased cellular proliferation and increased differentiation. The significant treatment responses were confirmed in mice with Apc and Pik3ca-mutant colon cancers as measured using endoscopy with a reduction in median lumen occlusion of 53% with BEZ235 and a 24% reduction with LY3023414 compared with an increase of 53% in controls (P < 0.001 and P = 0.03, respectively). This response was also confirmed with 18F-FDG microPET/CT imaging.Implications: Spheroid models and transgenic mice suggest that dual PI3K/mTOR inhibition is a potential treatment strategy for APC and PIK3CA-mutant colorectal cancers. Thus, further clinical studies of dual PI3K/mTOR inhibitors are warranted in colorectal cancers with these mutations. Mol Cancer Res; 15(3); 1-11. ©2016 AACR.

A statistical approach for identifying differential distributions in single-cell RNA-seq experiments

The ability to quantify cellular heterogeneity is a major advantage of single-cell technologies. However, statistical methods often treat cellular heterogeneity as a nuisance. We present a novel method to characterize differences in expression in the presence of distinct expression states within and among biological conditions. We demonstrate that this framework can detect differential expression patterns under a wide range of settings. Compared to existing approaches, this method has higher power to detect subtle differences in gene expression distributions that are more complex than a mean shift, and can characterize those differences. The freely available R package scDD implements the approach.

Making the cut: improved ranking and selection for large-scale inference

Identifying leading measurement units from a large collection is a common inference task in various domains of large-scale inference. Testing approaches, which measure evidence against a null hypothesis rather than effect magnitude, tend to overpopulate lists of leading units with those associated with low measurement error. By contrast, local maximum likelihood (ML) approaches tend to favor units with high measurement error. Available Bayesian and empirical Bayesian approaches rely on specialized loss functions that result in similar deficiencies. We describe and evaluate a generic empirical Bayesian ranking procedure that populates the list of top units in a way that maximizes the expected overlap between the true and reported top lists for all list sizes. The procedure relates unit-specific posterior upper tail probabilities with their empirical distribution to yield a ranking variable. It discounts high-variance units less than popular non-ML methods and thus achieves improved operating characteristics in the models considered.

Abstract 151: Modeling the rise of intratumoral heterogeneity in growing, static, and regressing human colorectal polyps

Benign adenomatous colon polyps are thought to be transformed into cancers through the stepwise accumulation of mutations. However, not all polyps progress. A significant number remain static in size, regress, or resolve completely. The mechanisms underlying these differential fates are unknown, and currently there are no biological characteristics that can reliably predict which polyps will grow or progress into invasive cancer. To determine the mutational landscape, targeted next generation sequencing was performed on a unique collection of small (6-9mm) colorectal polyps with known growth rates based on interval imaging with CT colonography. To determine spatial location of identified mutations within a polyp, micro-dissection was performed followed by quantitative PCR to validate low frequency mutations. The mutational landscape of small polyps is varied both within and among individual polyps. Polyps carried 0-3 pathogenic mutations with the most frequent being in APC (67%, 32/48), KRAS/NRAS (17%, 8/48), BRAF (17%, 8/48), FBXW7 (10%, 5/48), and TP53 (8%, 4/48). Additionally, 13% (6/48) contained driver mutations at varied mutant allele frequencies, indicating the presence of subclonal populations. In silico modeling of tumor growth was used to determine the likely size at which additional driver mutations arose in order to observe those varied frequencies. This model of colon tumor growth was adapted so that mutations occur with a given probability of 10−5, which may change the fitness positively or negatively, and the lineage from these mutant subpopulations was tracked during tumor growth. In silico polyps were sectioned and mutant allele frequency was recorded and compared to the frequencies observed from the targeted sequencing of human polyps. Contrary to the slow step-wise accumulation of mutations theory, these data indicate small colonic polyps can have multiple pathogenic mutations in crucial driver genes that arise early in a tumor's existence. Understanding the molecular pathway of tumorigenesis and clonal evolution in polyps that are at risk for progressing to invasive cancers will allow us to begin to better predict which polyps may be more likely to progress into adenocarcinomas and which patients are predisposed to developing advanced disease.

Citation Format: Chelsie K. Sievers, Luli Zou, Perry J. Pickhardt, Kristina A. Matkowskyj, Dawn Albrecht, David H. Kim, Fouad J. Moawad, Brooks D. Cash, Mark Reichelderfer, Michael A. Newton, Richard B. Halberg. Modeling the rise of intratumoral heterogeneity in growing, static, and regressing human colorectal polyps. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 151.

Abstract 2366: Pilot study of DNA microseeding to activate immune rejection of canine melanoma

Background: Canine malignant melanoma provides a model to study DNA vaccine delivery systems. A xenogeneic human tyrosinase (huTYR) DNA vaccine delivered by Biojector2000 received United States Department of Agriculture licensure when it appeared to prolong survival of dogs with melanoma compared to historical, stage-matched controls and to stimulate immune responses in some dogs. The current study evaluates toxicity, transgene expression, and antibody responses to huTYR in companion dogs with spontaneously developing melanoma following delivery of huTYR DNA to the skin via a modified tattoo device, a method termed DNA microseeding.

Methods: Five companion dogs with melanoma were scheduled to receive huTYR DNA at two sites (Site A and Site B) on the inner thigh by DNA microseeding every 2 weeks for 4 administrations at a range of huTYR DNA doses; 2 dogs (50 μg [Site A] and 100 μg [Site B]); 2 dogs (200 μg [Site A] and 400 μg [Site B]); and 1 dog (83 μg [Site A] and 83 μg commercial huTYR plasmid [Site B]). Vaccine site biopsies were obtained to determine transgene expression 24 hours after the 1st and 3rd vaccination time-points, and 48 hours after the 2nd and 4th vaccination time-points. Blood samples were obtained at baseline and 2 weeks after the 2nd, 3rd, and 4th vaccinations to quantify TYR-specific antibodies via indirect ELISA.

Results: No toxicity, beyond local site irritation, related to the vaccine administration was observed. The 3 dogs with known disease at study entry received 3, 1 and 4 treatments before discontinuation of treatment due to progressive disease. The 2 dogs without evidence of disease at study entry received all 4 planned treatments and remained without evidence for recurrence after treatment for the duration of the study (6 weeks). Only rare huTYR+ cells with macrophage-like morphology were observed in some vaccine site biopsies. A significant increase in anti-huTYR IgG was detected at Day 57 compared to pre-treatment in 2 of the 4 evaluable dogs (p = 0.03 Wilcoxon Mann Whitney), and these were the 2 dogs without evidence of disease at study entry. Baseline anti-huTYR IgG levels were also greater compared to IgG levels against an irrelevant control antigen.

Conclusions: While microseeding of huTYR plasmid DNA resulted in only rare transgene expression at DNA doses up to 400 μg, humoral responses against huTYR were substantially boosted in 2 of 4 evaluable dogs. Additional testing is needed to determine if DNA microseeding enhances huTYR DNA vaccine immunogenicity compared to Biojector delivery.

Citation Format: Cindy L. Zuleger, Chulhi Kang, Erik A. Ranheim, Ilene Kurzman, Michael D. Macklin, Michael A. Newton, David M. Vail, Jedd D. Wolchok, Elof Eriksson, Mark R. Albertini. Pilot study of DNA microseeding to activate immune rejection of canine melanoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2366.

Phase I study to evaluate toxicity and feasibility of intratumoral injection of α-gal glycolipids in patients with advanced melanoma

Effective uptake of tumor cell-derived antigens by antigen-presenting cells is achieved pre-clinically by in situ labeling of tumor with α-gal glycolipids that bind the naturally occurring anti-Gal antibody. We evaluated toxicity and feasibility of intratumoral injections of α-gal glycolipids as an autologous tumor antigen-targeted immunotherapy in melanoma patients (pts). Pts with unresectable metastatic melanoma, at least one cutaneous, subcutaneous, or palpable lymph node metastasis, and serum anti-Gal titer ≥1:50 were eligible for two intratumoral α-gal glycolipid injections given 4 weeks apart (cohort I: 0.1 mg/injection; cohort II: 1.0 mg/injection; cohort III: 10 mg/injection). Monitoring included blood for clinical, autoimmune, and immunological analyses and core tumor biopsies. Treatment outcome was determined 8 weeks after the first α-gal glycolipid injection. Nine pts received two intratumoral injections of α-gal glycolipids (3 pts/cohort). Injection-site toxicity was mild, and no systemic toxicity or autoimmunity could be attributed to the therapy. Two pts had stable disease by RECIST lasting 8 and 7 months. Tumor nodule biopsies revealed minimal to no change in inflammatory infiltrate between pre- and post-treatment biopsies except for 1 pt (cohort III) with a post-treatment inflammatory infiltrate. Two and four weeks post-injection, treated nodules in 5 of 9 pts exhibited tumor cell necrosis without neutrophilic or lymphocytic inflammatory response. Non-treated tumor nodules in 2 of 4 evaluable pts also showed necrosis. Repeated intratumoral injections of α-gal glycolipids are well tolerated, and tumor necrosis was seen in some tumor nodule biopsies after tumor injection with α-gal glycolipids.

Further support for aneuploidy tolerance in wild yeast and effects of dosage compensation on gene copy-number evolution

In our prior work by Hose et al., we performed a genome-sequencing survey and reported that aneuploidy was frequently observed in wild strains of S. cerevisiae. We also profiled transcriptome abundance in naturally aneuploid isolates compared to isogenic euploid controls and found that 10–30% of amplified genes, depending on the strain and affected chromosome, show lower-than-expected expression compared to gene copy number. In Hose et al., we argued that this gene group is enriched for genes subject to one or more modes of dosage compensation, where mRNA abundance is decreased in response to higher dosage of that gene. A recent manuscript by Torres et al. refutes our prior work. Here, we provide a response to Torres et al., along with additional analysis and controls to support our original conclusions. We maintain that aneuploidy is well tolerated in the wild strains of S. cerevisiae that we studied and that the group of genes enriched for those subject to dosage compensation show unique evolutionary signatures.

DOI:http://dx.doi.org/10.7554/eLife.14409.001

Cells package their DNA into structures called chromosomes. Sometimes when a cell divides, it fails to allocate the right number of chromosomes to each new cell and so they end up with too many or too few chromosomes. The extra copies of the genes on an additional chromosome can be harmful to the cells, because the levels of the proteins encoded by those genes may rise abnormally.

Some organisms counteract the harmful effect of having additional chromosomes through a process called dosage compensation. Proteins are produced using genetic information via two steps: first a gene’s DNA sequence is copied into a molecule of RNA, which is then translated into a protein. Dosage compensation can inactivate single genes or whole chromosomes via various means to ensure that the levels of RNA expressed remain normal, even in the presence of extra genes.

In 2015, researchers from the University of Wisconsin-Madison reported that dosage compensation occurs in wild strains of budding yeast and effectively protects against the harmful effects of having extra chromosomes. However, these findings conflicted with earlier studies of laboratory strains of this yeast, and earlier in 2016, other researchers re-analysed the previous study’s data and challenged its findings.

Now, Gasch et al. – who conducted the work reported in 2015 – provide additional controls and computational experiments that support their original analysis. The latest analysis confirmed that the genes identified in the first study are indeed commonly duplicated in wild yeast populations, yet the expression of these genes remains controlled. This is consistent with a model of dosage compensation, for at least some of duplicated genes.

Gasch et al. believe that part of the difference in interpretation of the data relates to perspective. The challenging researchers tested to see if there was a mechanism of dosage compensation that acted across entire chromosomes, which is known to occur in the case of sex chromosomes in mammals. Gasch et al. on the other hand took a different approach and looked to identify effects at the level of individual genes.

Together, the analyses show that, while there is no evidence for a widespread mechanism, the expression of a select set of genes in wild yeast is consistent with gene-specific dosage compensation. Future work will now undoubtedly test the mechanisms behind the gene-specific effects, and explore why wild yeast strains are more tolerant to extra chromosomes than laboratory strains.

DOI:http://dx.doi.org/10.7554/eLife.14409.002