Condensation of LINE-1 is critical for retrotransposition

LINE-1 (L1) is the only autonomously active retrotransposon in the human genome, and accounts for 17% of the human genome. The L1 mRNA encodes two proteins, ORF1p and ORF2p, both essential for retrotransposition. ORF2p has reverse transcriptase and endonuclease activities, while ORF1p is a homotrimeric RNA-binding protein with poorly understood function. Here we show that condensation of ORF1p is critical for L1 retrotransposition. Using a combination of biochemical reconstitution and live-cell imaging, we demonstrate that electrostatic interactions and trimer conformational dynamics together tune the properties of ORF1p assemblies to allow for efficient L1 ribonucleoprotein (RNP) complex formation in cells. Furthermore, we relate the dynamics of ORF1p assembly and RNP condensate material properties to the ability to complete the entire retrotransposon life-cycle. Mutations that prevented ORF1p condensation led to loss of retrotransposition activity, while orthogonal restoration of coiled-coil conformational flexibility rescued both condensation and retrotransposition. Based on these observations, we propose that dynamic ORF1p oligomerization on L1 RNA drives the formation of an L1 RNP condensate that is essential for retrotransposition.

Glioblastoma hijacks microglial gene expression to support tumor growth

BACKGROUND

Glioblastomas are the most common and lethal primary brain tumors. Microglia, the resident immune cells of the brain, survey their environment and respond to pathogens, toxins, and tumors. Glioblastoma cells communicate with microglia, in part by releasing extracellular vesicles (EVs). Despite the presence of large numbers of microglia in glioblastoma, the tumors continue to grow, and these neuroimmune cells appear incapable of keeping the tumor in check. To understand this process, we analyzed gene expression in microglia interacting with glioblastoma cells.

METHODS

We used RNASeq of isolated microglia to analyze the expression patterns of genes involved in key microglial functions in mice with glioblastoma. We focused on microglia that had taken up tumor-derived EVs and therefore were within and immediately adjacent to the tumor.

RESULTS

We show that these microglia have downregulated expression of genes involved in sensing tumor cells and tumor-derived danger signals, as well as genes used for tumor killing. In contrast, expression of genes involved in facilitating tumor spread was upregulated. These changes appear to be in part EV-mediated, since intracranial injection of EVs in normal mice led to similar transcriptional changes in microglia. We observed a similar microglial transcriptomic signature when we analyzed datasets from human patients with glioblastoma.

CONCLUSION

Our data define a microglia_Glioblastoma specific phenotype, whereby glioblastomas have hijacked gene expression in the neuroimmune system to favor avoiding tumor sensing, suppressing the immune response, clearing a path for invasion, and enhancing tumor propagation. For further exploration, we developed an interactive online tool at http://www.glioma-microglia.com with all expression data and additional functional and pathway information for each gene.

Comprehensive Scanning Mutagenesis of Human Retrotransposon LINE-1 Identifies Motifs Essential for Function

Long Interspersed Nuclear Element-1 (LINE-1, L1) is the only autonomous active transposable element in the human genome. The L1-encoded proteins ORF1p and ORF2p enable the element to jump from one locus to another via a "copy-and-paste" mechanism. ORF1p is an RNA-binding protein, and ORF2p has endonuclease and reverse transcriptase activities. The huge number of truncated L1 remnants in the human genome suggests that the host has likely evolved mechanisms to prevent full L1 replication, and thereby decrease the proliferation of active elements and reduce the mutagenic potential of L1. In turn, L1 appears to have a minimized length to increase the probability of successful full-length replication. This streamlining would be expected to lead to high information density. Here, we describe the construction and initial characterization of a library of 538 consecutive trialanine substitutions that scan along ORF1p and ORF2p to identify functionally important regions. In accordance with the streamlining hypothesis, retrotransposition was overall very sensitive to mutations in ORF1p and ORF2p; only 16% of trialanine mutants retained near-wild-type (WT) activity. All ORF1p mutants formed near-WT levels of mRNA transcripts and 75% formed near-WT levels of protein. Two ORF1p mutants presented a unique nucleolar-relocalization phenotype. Regions of ORF2p that are sensitive to mutagenesis but lack phylogenetic conservation were also identified. We provide comprehensive information on the regions most critical to retrotransposition. This resource will guide future studies of intermolecular interactions that form with RNA, proteins, and target DNA throughout the L1 life cycle.

Stromal Microenvironment Shapes the Intratumoral Architecture of Pancreatic Cancer

Single-cell technologies have described heterogeneity across tissues, but the spatial distribution and forces that drive single-cell phenotypes have not been well defined. Combining single-cell RNA and protein analytics in studying the role of stromal cancer-associated fibroblasts (CAFs) in modulating heterogeneity in pancreatic cancer (pancreatic ductal adenocarcinoma [PDAC]) model systems, we have identified significant single-cell population shifts toward invasive epithelial-to-mesenchymal transition (EMT) and proliferative (PRO) phenotypes linked with mitogen-activated protein kinase (MAPK) and signal transducer and activator of transcription 3 (STAT3) signaling. Using high-content digital imaging of RNA in situ hybridization in 195 PDAC tumors, we quantified these EMT and PRO subpopulations in 319,626 individual cancer cells that can be classified within the context of distinct tumor gland "units." Tumor gland typing provided an additional layer of intratumoral heterogeneity that was associated with differences in stromal abundance and clinical outcomes. This demonstrates the impact of the stroma in shaping tumor architecture by altering inherent patterns of tumor glands in human PDAC.

Abstract 210: Uncovering a novel layer of complexity in the architecture of pancreatic cancer

Single cell technologies have described heterogeneity across tissues, but the spatial distribution and forces that drive single cell phenotypes has not been well defined. We integrated single cell RNA-seq (scRNA-Seq) and phospho mass cytometry (CyTOF) with high-content digital imaging to investigate tumor heterogeneity of human pancreatic cancer (PDAC) using a novel tumor-architecture approach.

Patient-derived PDAC cells co-cultured at different ratios with cancer associated fibroblasts (CAFs) were found to heterogeneously acquire proliferative (PRO) and invasive (EMT) phenotypes. scRNA-Seq enabled the identification of a novel cell phenotype with upregulation of both PRO and EMT programs, which we named the double positive (DP) phenotype. Functional studies confirmed the heterogeneous activation of PRO and EMT programs with different patterns of tumor growth and metastasis in mice orthotopically xenografted with distinct PDAC:CAF ratios.

In a time-course experiment of PDAC cells with CAF conditioned media (CM), mass spectrometry-based phosphoproteomics demonstrated selective enrichment of MAPK and STAT3 pathways. This was validated with mass cytometry (CyTOF) at the single cell level in our cell line model as well as from primary PDAC tumors, which identified the dual enrichment of MAPK and STAT3 signaling in the DP cell population. Functional validation of MAPK and STAT3 signaling was performed with small molecule inhibitors of MAPK (Trametinib) and STAT3 (pyrimethamine) in our cell line models.

To evaluate the generalizability of these cell subpopulations, we performed RNA-ISH for EMT (FN1) and PRO (MKI67) across 195 human PDAC primary tumors and scored 319,626 cancer cells revealing significant heterogeneity of PRO, EMT, and DP cells among patients. Single-cell analysis within the context of tissue architecture

revealed these cells were grouped together in discrete tumor glands. Using each of the 3 cell types (PRO, EMT, and DP), we classified 8 distinct types of tumor glands in these primary tumors. This provided the ability to define inter and intra-tumor heterogeneity at the tumor gland level, which provides an extra layer of tumor cell organization not appreciable with single cell analysis alone. We showed that tumor glands are independent functional units in human PDACs carrying distinct prognostic information. In fact, by comparing their prognostic power we noticed that some tumor glands are positively linked with worsened survival (Type I p=0.003, Type II p=0.04, Type II p=0.001 and Type VII p=0.02), while Type III glands are associated with a favorable patient prognosis (p=0.01, log-rank test).

In conclusion, our study showed for the first time at this scale level that integrating single-cell technologies with tissue architectural information provides a more comprehensive landscape of intra-tumoral cancer cell heterogeneity that has implications on PDAC cell behavior and patient outcomes.

Citation Format: Matteo Ligorio, Srinjoy Sil, Jose Malagon-Lopez, Sandra Misale, Murat Karabacak, Linda Nieman, Shyamala Maheswaran, Daniel A. Haber, Andrew L. Warshaw, Carlos Fernandez-Del Castillo, Cristina R. Ferrone, Wilhelm Haas, Martin Aryee, David T. Ting. Uncovering a novel layer of complexity in the architecture of pancreatic 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 210.

Detection and classification of Bacteria using Raman Spectroscopy Combined with Multivariate Analysis

<p class="p1">Vibrational spectroscopic techniques have advantages over conventional microbiological approaches towards identification &amp; detection of pathogens. Since unique spectral fingerprint is obtained, one can identify very closely related bacteria using such methods. In this study Raman microspectroscopy in combination with chemometric method has been used to classify four strains of <em>E</em>. <em>coli </em>(two pathogenic &amp; two non-pathogenic). Different multivariate approaches such as hierarchical cluster analysis, principal component analysis &amp; linear discriminant analysis were explored to obtain efficient classification of the Raman signals obtained from the four strains of <em>E.coli</em>. It was observed that multivariate analysis was able to classify the bacteria at strain level. Linear discrimination analysis using PC scores (PC-LDA) was found to give very good result with as high as 100% accuracy. This hybrid technique (Raman spectroscopy &amp; multivariate analysis) has tremendous potential to be developed as a tool for bacterial identification.<span class="Apple-converted-space"> </span></p>

Abstract 1734: Absolute quantification of circulating tumor cell RNA enables high specificity detection of hepatocellular carcinoma

Background: Although liver cancer has the second-highest mortality rate among cancers internationally, accurate and scalable assays for the early detection and longitudinal monitoring of hepatocellular carcinoma are lacking. Circulating tumor cells are released from invasive cancers into the blood stream, but the difficulty inherent in isolating, identifying, and characterizing these ultra-rare cells has precluded their widespread implementation as a biomarker. By combining a high-throughput microfluidic negative depletion CTC isolation strategy with the absolute quantification of lineage-specific RNAs, we report the highly specific detection of hepatocellular carcinoma CTCs from patient blood draws.

Methods: Blood draws from 48 hepatocellular carcinoma patients, 31 chronic liver disease patients, 25 healthy donors, and 44 patients with primary cancers other than hepatocellular carcinoma were processed through the microfluidic device (CTC-iChip). RNA was extracted, whole-transcriptome amplified, and quantified using droplet digital PCR. Transcript counts were used to fit a logistic regression model to integrate distinct transcript levels into a single CTC-score. The technical feasibility of utilizing RNA sequencing for identification of novel CTC transcripts of interest was also demonstrated with a liver cancer cell line spike-in study.

Results: 9 of the 16 untreated HCC patients were successfully detected, while only 1/31 chronic liver disease patients were incorrectly classified. HCC patients undergoing treatment showed a significant decrease in their CTC-score; only 9/32 patients actively receiving treatment were positive. The CTC-score was not correlated with the HCC serum biomarker alpha-fetoprotein, and combining these two orthogonal measures led to estimated positive and negative predictive values of 80% and 86%, respectively, in a high-risk cohort. RNAseq analysis of cell line spike-in data revealed the potential of RNA sequencing for uncovering novel transcripts of interest.

Conclusion: Coupling microfluidic depletion with droplet digital PCR allows for the highly specific detection of hepatocellular carcinoma. The CTC-score generated from these data tracks with clinical intervention and is orthogonal to the existing biomarker AFP; combining these two assays has the potential to provide superior detection compared to either individual approach.

Citation Format: Mark Kalinich, Irun Bhan, Tanya T. Kwan, David T. Miyamoto, Sarah Javaid, Joseph A. LiCausi, John D. Milner, Xin Hong, Lipika Goyal, Srinjoy Sil, Melissa Choz, Ravi Kapur, Alona Muzikansky, Huidan Zhang, David A. Weitz, Lecia V. Sequist, David P. Ryan, Raymond Chung, Andrew X. Zhu, Kurt J. Isselbacher, David T. Ting, Mehmet Toner, Shyamala Maheswaran, Daniel A. Haber. Absolute quantification of circulating tumor cell RNA enables high specificity detection of hepatocellular carcinoma [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 1734. doi:10.1158/1538-7445.AM2017-1734

Diverse repetitive element RNA expression defines epigenetic and immunologic features of colon cancer

There is tremendous excitement for the potential of epigenetic therapies in cancer, but the ability to predict and monitor response to these drugs remains elusive. This is in part due to the inability to differentiate the direct cytotoxic and the immunomodulatory effects of these drugs. The DNA-hypomethylating agent 5-azacitidine (AZA) has shown these distinct effects in colon cancer and appears to be linked to the derepression of repeat RNAs. LINE and HERV are two of the largest classes of repeats in the genome, and despite many commonalities, we found that there is heterogeneity in behavior among repeat subtypes. Specifically, the LINE-1 and HERV-H subtypes detected by RNA sequencing and RNA in situ hybridization in colon cancers had distinct expression patterns, which suggested that these repeats are correlated to transcriptional programs marking different biological states. We found that low LINE-1 expression correlates with global DNA hypermethylation, wild-type TP53 status, and responsiveness to AZA. HERV-H repeats were not concordant with LINE-1 expression but were found to be linked with differences in FOXP3⁺ Treg tumor infiltrates. Together, distinct repeat RNA expression patterns define new molecular classifications of colon cancer and provide biomarkers that better distinguish cytotoxic from immunomodulatory effects by epigenetic drugs.

Genomic Instability Is Induced by Persistent Proliferation of Cells Undergoing Epithelial-to-Mesenchymal Transition

TGF-β secreted by tumor stroma induces epithelial-to-mesenchymal transition (EMT) in cancer cells, a reversible phenotype linked to cancer progression and drug resistance. However, exposure to stromal signals may also lead to heritable changes in cancer cells, which are poorly understood. We show that epithelial cells failing to undergo proliferation arrest during TGF-β-induced EMT sustain mitotic abnormalities due to failed cytokinesis, resulting in aneuploidy. This genomic instability is associated with the suppression of multiple nuclear envelope proteins implicated in mitotic regulation and is phenocopied by modulating the expression of LaminB1. While TGF-β-induced mitotic defects in proliferating cells are reversible upon its withdrawal, the acquired genomic abnormalities persist, leading to increased tumorigenic phenotypes. In metastatic breast cancer patients, increased mesenchymal marker expression within single circulating tumor cells is correlated with genomic instability. These observations identify a mechanism whereby microenvironment-derived signals trigger heritable genetic changes within cancer cells, contributing to tumor evolution.

Abstract 609: Molecular subtyping of pancreatic adenocarcinoma identifies SV2 positive subpopulation in classical PDAC

Pancreatic adenocarcinoma (PDAC) is a lethal disease with a rising incidence, expected to become the second cause of cancer death in the next 5 years. Despite advances in novel therapies for other malignancies, PDAC has remained a highly chemorefractory disease leading to inevitable disease recurrence in the vast majority of patients. The identification of the cellular mechanisms of chemoresistance unique to PDAC is of particular importance. Our prior work using single cell RNA-sequencing in pancreatic circulating tumor cells (CTCs) identified 878 genes enriched in CTCs compared to matched primary tumor cells. CTCs are thought to be enriched for cells with high metastatic potential, which we predict to have intrinsic chemoresistant behavior. We hypothesized that CTC enriched genes may identify a subpopulation of cells resistant to chemotherapy that could be used as a biomarker and novel therapeutic target. The neuroendocrine marker SV2 was found in both mouse and human pancreatic CTCs and was selected given its presence on cell membranes, providing a potential therapeutic target. We evaluated a panel of patient derived cell lines and identified an SV2 positive subpopulation comprising ∼1% of cells in 3 of 5 cell lines. Notably, only differentiated epithelioid PDAC cell lines contained an SV2 subpopulation, while this population is not present in poorly differentiated quasi-mesenchymal cell lines. We performed RNA-ISH for SV2 isoforms in an annotated PDAC tissue microarray demonstrating positive staining in 77% of samples (245/317). Interestingly, SV2 positivity was often focally positive in a subpopulation of cells at the basolateral region of ductal adenocarcinoma and was found in more differentiated morphology (69% well/moderate vs 31% poor/undifferentiated; p = 0.047). The presence of SV2 cells was associated with an improved disease free survival (HR: 0.49 p = 0.009) and overall survival (HR: 0.54 p = 0.018) even after correction in multivariate analysis.

Analysis in both cell lines and tissue revealed SV2 positive cells were also found to have higher levels of the ALDH1 stem cell marker (Pearson coefficient = 0.92 in tissue). Initial in vivo treatment of human orthotopic xenografts with gemcitabine, reveal an enrichment of SV2 positive cells pointing to their potential role as the recalcitrant cancer cells treated with cytotoxic chemotherapy population.

Together, this is consistent with prior work demonstrating classical epithelial PDAC has improved survival compared to quasi-mesenchymal tumors. However, almost all patients with classical epithelial PDAC will die from recurrent disease, and we have now shown SV2 as a potential marker that identifies the chemoresistant pancreatic cancer cells in this patient population. Ultimately, a more detailed characterization of the SV2 subpopulation in classical PDAC will help us develop novel targeted therapies to overcome chemoresistance.

Citation Format: Daniela Dias-Santos, Matteo Ligorio, Kshitij Arora, Vishal Thapar, Olivia C. MacKenzie, Srinjoy Sil, Niyati Desai, Vikram Deshpande, Miguel N. Rivera, Cristina R. Ferrone, David T. Ting. Molecular subtyping of pancreatic adenocarcinoma identifies SV2 positive subpopulation in classical PDAC. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 609. doi:10.1158/1538-7445.AM2015-609

Protoporphyrin IX potentiates horseradish peroxidase-catalyzed oxidation of NADH:Involvement of enzyme-porphyrin interaction

Protoporphyrin IX potentiates horseradish peroxidase-catalyzed hydrogen peroxide-mediated NADH oxidation, but the porphyrin cannot change the enzyme-catalyzed o-dianisidine oxidation. Spectrofluorimetric studies reveal that an interaction occurs between horseradish peroxidase and protoporphyrin IX. The interaction is predominantly hydrophobic and entropy-driven endothermic process. This interaction may influence the potentiation effect of the protoporphyrin IX on horseradish peroxidase-catalyzed NADH oxidation because the latter has a positive correlation with the extent of binding of the protein with the porphyrin.

Prevalence and significance of antiphospholipid antibodies in selected at-risk obstetrics cases: a comparative prospective study

In a prospective comparative study we screened 112 women with a past history either of pre-eclampsia, eclampsia, recurrent abortion, IUGR, IUFD or abruptio placentae, with no apparent aetiology and a demographically matched cohort of 106 women having a past history of uncomplicated pregnancy outcome for the presence of antiphospholipid antibodies (aPL) and their significance. In the former group, the prevalence of aPL ranged from 10-46.87% compared with 8.49% in the later group. In women with the presence of aPL, the incidence of pre-eclampsia, early onset pre-eclampsia and abruptio placentae were 25%, 14.58% and 18.75%, respectively. In the same group, the abortion rate was 25% and live-birth rate was 64.58% with IUFD rate of 10.42%. Fetal morbidity rates were also higher in the mothers with aPL positivity, the incidence of IUGR was 27.08% and oligohydramnios was 33.33% in them. All these complications were statistically significant when compared with those of aPL negative mothers.

Studies on the interaction of hematoporphyrin with hemoglobin

Spectrophotometric and spectrofluorimetric studies reveal that an interaction occurs between hemoglobin and hematoporphyrin, a photosensitizing drug used in photodynamic therapy. Two concentration ranges of hematoporphyrin, 0.4-0.9 microM and 1.8-3.6 microM, representing significantly monomeric and aggregated (dimeric) state, respectively, have been used in the binding studies. The binding affinity constant (K) decreases, while the possible number of binding sites (p) increases as the concentration range of the porphyrin is increased. The nature of interaction has been studied by fluorescence quenching titration method under different ionic strengths and temperature conditions. It appears to be predominantly electrostatic and enthalpy-driven in the lower range of porphyrin concentration. However, the interaction follows mostly hydrophobic and entropy-driven modality in the higher concentration range of the ligand. The porphyrin-hemoglobin interaction results in release of oxygen from the protein. The extent of oxygen release depends on the stoichiometric ratio of hematoporphyrin:hemoglobin.

Arsenate resistance as a possible marker in the differentiation of environmental and clinical isolates of Vibrio parahaemolyticus

Strains of Vibrio parahaemolyticus were isolated from clinical, marine and freshwater fish of Calcutta, West Bengal, India. Drug and metal resistance characteristics were compared for differentiation of clinical and environmental strains. Eighteen out of the twenty environmental isolates were resistant to arsenate, unlike the clinical isolates which were all susceptible. All the thirty-five isolates of V. parahaemolyticus were resistant to ampicillin and streptomycin.

Comparative studies on the interaction of protoporphyrin with hemoglobin and myoglobin

The binding parameters of protoporphyrin IX (PPIX) with hemoglobin (Hb) were studied spectrofluorimetrically and the results were compared with those of PPIX interacting with myoglobin (Mb). Two concentration ranges of PPIX (0.3 microM-1.5 microM and 1.5 microM-3.0 microM) were used. For both hemoglobin and myoglobin, the binding affinity constant (K) decreased while the number of binding sites (p) increased as the concentration range of PPIX increased. The interactions occurred in non-cooperative mode. Over a particular PPIX range, the interaction of PPIX with hemoglobin decreased significantly with increasing NaCl molarity indicating a trend in electrostatic interaction, whereas PPIX binding with myoglobin did not change significantly indicating mostly non-electrostatic mode of interaction. Total bound charge (z psi) decreased significantly with increased PPIX concentration range in case of hemoglobin-PPIX interaction, but remained almost same in case of myoglobin-PPIX interactions. Thermodynamic analysis revealed that binding of PPIX to hemoglobin was mostly electrostatic at lower concentration range of PPIX but became less electrostatic at higher concentration range and myoglobin-PPIX interaction, predominantly hydrophobic in nature, became more hydrophobic with increased range of PPIX concentration. The difference in binding modality between PPIX-Hb and PPIX-Mb has been discussed in relation to the state of aggregation of porphyrin as well as the subunit interaction property present and absent in hemoglobin and myoglobin, respectively.