Hidden Decomposers: the Role of Bacteria and Fungi in Recently Intermittent Alpine Streams Heterotrophic Pathways

The frequency of flow intermittency and drying events in Alpine rivers is expected to increase due to climate change. These events can have significant consequences for stream ecological communities, though the effects of reduced flow conditions on microbial communities of decomposing allochthonous leaf material require additional research. In this study, we investigated the bacterial and fungal communities associated with the decomposition of two common species of leaf litter, chestnut (Castanea sativa), and oak (Quercus robur). A sampling of experimentally placed leaf bags occurred over six collection dates (up to 126 days after placement) at seven stream sites in the Western Italian Alps with historically different flow conditions. Leaf-associated bacterial and fungal communities were identified using amplicon-based, high-throughput sequencing. Chestnut and oak leaf material harbored distinct bacterial and fungal communities, with a number of taxonomic groups differing in abundance, though bacterial community structure converged later in decomposition. Historical flow conditions (intermittent vs perennial rivers) and observed conditions (normal flow, low flow, ongoing drying event) had weaker effects on bacterial and fungal communities compared to leaf type and collection date (i.e., length of decomposition). Our findings highlight the importance of leaf characteristics (e.g., C:N ratios, recalcitrance) to the in-stream conditioning of leaf litter and a need for additional investigations of drying events in Alpine streams. This study provides new information on the microbial role in leaf litter decomposition with expected flow changes associated with a global change scenario.

Abstract 1224: UMIBB: A novel nonparametric Bayesian method improves robustness and sensitivity of analysis in pooled CRISPR-Cas9 screens leveraging unique molecular identifiers

CRISPR-based functional genomics screens are a powerful tool for identifying synthetically lethal cancer drug targets. Current strategies for analyzing pooled CRISPR screens usually rely on signals from single guide RNAs (sgRNA) with differential relative abundance between two experimental conditions. However, conventional approaches are susceptible to false positives and false negatives driven by outlier cell clones, since the sgRNA abundance does not account for the heterogeneous phenotypes resulting from different editing outcomes of the same sgRNA. To overcome this, we added DNA barcodes to each sgRNA to create unique molecular identifiers (UMIs) for CRISPR libraries and developed a companion analytical platform that enables robust, industry-scale CRISPR screens. Here, we present UMIBB, a novel nonparametric Bayesian approach for analyzing UMI-CRISPR data. The number of UMIs with normalized count depletion or enrichment compared to the control experimental condition for each sgRNA is modeled by a beta-binomial distribution. The gene level statistics are derived by combining z-scores of the sgRNAs level posterior probabilities weighted by the number of UMIs in each sgRNA. This approach minimizes the impact of outlier cell clones on statistics and prioritizes genes with consistent count differentials across multiple UMIs in each gene. To assess the power of UMIBB, we benchmarked it on a low coverage (200X) genome-scale negative-selection screen, comparing with results from a high coverage (1000X) screen. These screens were conducted on KRAS mutant cancer celllines (A549) treated with trametinib or vehicle control. Despite the high noise level usually observed in lower coverage screens, our method was able to uncover most of the validated sensitizer genes for trametinib and achieved the highest sensitivity compared to conventional methods. Furthermore, we applied UMIBB on a genome-scale positive-selection screen and successfully identified novel genes (RAD18 and UBE2K) as key mediators of USP1 dependency in BRCA1 mutant cell lines. Our studies demonstrate that UMIBB is highly robust against false positives due to clonal heterogeneity and is more likely to identify true genetic interactions.

Citation Format: Ashley Choi, Samuel Meier, Silvia Fenoglio, Tianshu Feng, Justin Engel, Binzhang Shen, Shangtao Liu, Teng Teng, Tenzing Khendu, Alan Huang, Jannik Andersen, Xuewen Pan, Yi Yu. UMIBB: A novel nonparametric Bayesian method improves robustness and sensitivity of analysis in pooled CRISPR-Cas9 screens leveraging unique molecular identifiers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1224.

Abstract P183: CRISPR screens identify sensitizers to trametinib in KRAS mutant cancer cell lines

KRAS is the most frequently mutated oncogene in human tumors and drives tumorigenesis across multiple lineages. Specifically, KRAS is mutated in about 30% of lung cancer and over 90% of pancreatic cancer. Despite recent progress in developing mutant selective KRASG12C inhibitors, patient treatment options for RAS activated cancers remain very limited. Targeting the MAPK pathway by means of MEK and ERK inhibitors has been explored as an alternative strategy for KRAS mutant cancer. However, the clinical benefit is modest due to drug resistance caused by reactivation of the MAPK pathway and potentially other pathways and/or bypass mechanisms. Here we used CRISPR-based screens to identify potential combination therapy targets to enhance trametinib response in KRAS mutant cancers. We screened in five KRAS mutant cell lines of lung and pancreatic lineages and identified both known as well as novel modulators of MEK inhibitor response. Consistent with previous reports, gene knockouts that impair the reactivation of ERK downstream of MEK inhibition scored as top hits in our drop-out screens. Knocking out MAPK1, RAF1, BRAF and PTPN11 sensitized all five cell lines to trametinib treatment supporting these as candidate drug combination targets for MAPK pathway inhibition. Our screens also identified multiple genes within the heparan sulfate pathway (EXT1, EXT2, EXTL3, XYLT2, ALG6, B3GAT3, B4GALT7 and HS2ST1) and the MAPK7 pathway (MAPK7 and MAP2K5) that sensitize multiple but not all cell lines to trametinib. As part of our target discovery platform, we further validated these screening results using various phenotypic assays. Altogether, our results suggest that resistance to MEK inhibitors is driven by reactivation of the MAPK pathway as previously demonstrated and that impairing such reactivation restores the sensitivity of KRAS mutant cancer cells to trametinib. The genetic mechanisms driving the MAPK pathway rebound are likely different in different cancers and understanding such mechanisms will be key for achieving clinical success.

Citation Format: Silvia Fenoglio, Aileen M. Cristo, James Tepper, Teng Teng, Samuel R. Meier, Ashley Choi, Hongxiang Zhang, Shan-chuan Zhao, Shangtao Liu, Leanne G. Ahronian, Daniel Aird, Nikitha M. Das, Yi Yu, Robert Tjin Tham Sjin, Jannik N. Andersen, Alan Huang, Fang Li, Xuewen Pan. CRISPR screens identify sensitizers to trametinib in KRAS mutant cancer cell lines [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P183.

Abstract P146: Loss of HS2ST1 cooperates with MAPK inhibition to impair growth of mesenchymal KRAS mutant NSCLC

Activating mutations in the KRAS oncogene occur in approximately 30% of non-small cell lung cancers (NSCLC). Hence, multiple therapeutic strategies have been explored to block RAS including inhibition of downstream effector molecules in the MAPK pathway and direct pharmacological inhibition of the KRAS G12C mutant protein. However, inhibition of the RAS-RAF-MEK-ERK cascade with MEK inhibitor monotherapy has been insufficient to induce robust clinical responses. To identify novel drug targets that are synthetic lethal with MEK inhibition, CRISPR screens were conducted in multiple KRAS mutant NSCLC cell lines with or without trametinib treatment. Consistent with previous reports, several known MAPK-pathway genes, including KRAS, MEK, ERK, and FGFR1, were identified as top sensitizers validating our functional genomics approach. Interestingly, several novel targets were ranked among these top hits, including several members of the heparan sulfate biosynthesis pathway, such as the heparan sulfate 2-O-sulfotransferase (HS2ST1). In cells, HS2ST1 is responsible for transferring a sulfate from PAPS (3-phosphoadenosine-5’-phosphosulfate) to the 2-O position of a growing heparan sulfate chain. These chains partner with receptor tyrosine kinases at the cell surface to facilitate their interactions with growth factors. In this case, the interaction of FGF2 and FGFR1 has been shown to require HS2ST1-mediated 2-O sulfation, making HS2ST1 a novel druggable target in a well-validated FGFR-MAPK adaptive signaling axis. Here, we report that HS2ST1 is required for the feedback activation of the MAPK pathway that occurs downstream and in response to MEK or KRAS G12C inhibition via genetic validations studies. Knockout of HS2ST1 results in reduced feedback activation via FGFR1 and reduced MAPK pathway signaling. This reduced signaling leads to a reduction in cell growth in the presence of a MEK inhibitor, such as trametinib or selumetinib, or a KRAS G12C inhibitor like sotorasib. Our screen results reiterate the findings of others which indicate that effective MAPK suppression is key to inhibiting KRAS-mutant NSCLC cell growth. We find that HS2ST1 blockade would aid in maintaining the suppression of MAPK pathway signaling in KRAS-mutant NSCLC, leading to reduced cell viability and growth suppression. While others have described pairing receptor tyrosine kinase inhibitors with MAPK pathway inhibitors, this would be a novel approach to reducing upstream MAPK pathway feedback that may lead to reduced toxicity in patients.

Citation Format: Leanne G. Ahronian, Silvia Fenoglio, Nikitha Das, Daniel Aird, David Guerin, Douglas Whittington, Haris Jahic, Erin Brophy, Patrick McCarren, Brian McMillan, James Tepper, Michaela Mentzer, Fang Li, Hongxiang Zhang, Xuewen Pan, John Maxwell, Jannik Andersen, Alan Huang, Robert Tjin Tham Sjin. Loss of HS2ST1 cooperates with MAPK inhibition to impair growth of mesenchymal KRAS mutant NSCLC [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P146.

Deoxycytidine Release from Pancreatic Stellate Cells Promotes Gemcitabine Resistance

Pancreatic ductal adenocarcinoma (PDAC) is a leading cause of cancer deaths in the United States. The deoxynucleoside analogue gemcitabine is among the most effective therapies to treat PDAC, however, nearly all patients treated with gemcitabine either fail to respond or rapidly develop resistance. One hallmark of PDAC is a striking accumulation of stromal tissue surrounding the tumor, and this accumulation of stroma can contribute to therapy resistance. To better understand how stroma limits response to therapy, we investigated cell-extrinsic mechanisms of resistance to gemcitabine. Conditioned media from pancreatic stellate cells (PSC), as well as from other fibroblasts, protected PDAC cells from gemcitabine toxicity. The protective effect of PSC-conditioned media was mediated by secretion of deoxycytidine, but not other deoxynucleosides, through equilibrative nucleoside transporters. Deoxycytidine inhibited the processing of gemcitabine in PDAC cells, thus reducing the effect of gemcitabine and other nucleoside analogues on cancer cells. These results suggest that reducing deoxycytidine production in PSCs may increase the efficacy of nucleoside analog therapies. SIGNIFICANCE: This study provides important new insight into mechanisms that contribute to gemcitabine resistance in PDAC and suggests new avenues for improving gemcitabine efficacy.

Coordinated Splicing of Regulatory Detained Introns within Oncogenic Transcripts Creates an Exploitable Vulnerability in Malignant Glioma

Glioblastoma (GBM) is a devastating malignancy with few therapeutic options. We identify PRMT5 in an in vivo GBM shRNA screen and show that PRMT5 knockdown or inhibition potently suppresses in vivo GBM tumors, including patient-derived xenografts. Pathway analysis implicates splicing in cellular PRMT5 dependency, and we identify a biomarker that predicts sensitivity to PRMT5 inhibition. We find that PRMT5 deficiency primarily disrupts the removal of detained introns (DIs). This impaired DI splicing affects proliferation genes, whose downregulation coincides with cell cycle defects, senescence and/or apoptosis. We further show that DI programs are evolutionarily conserved and operate during neurogenesis, suggesting that they represent a physiological regulatory mechanism. Collectively, these findings reveal a PRMT5-regulated DI-splicing program as an exploitable cancer vulnerability.

Ab-induced ectodomain shedding mediates hepatocyte growth factor receptor down-regulation and hampers biological activity

Targeting tyrosine kinase receptors (RTKs) with specific Abs is a promising therapeutic approach for cancer treatment, although the molecular mechanism(s) responsible for the Abs' biological activity are not completely known. We targeted the transmembrane RTK for hepatocyte growth factor (HGF) with a monoclonal Ab (DN30). In vitro, chronic treatment of carcinoma cell lines resulted in impairment of HGF-induced signal transduction, anchorage-independent growth, and invasiveness. In vivo, administration of DN30 inhibited growth and metastatic spread to the lung of neoplastic cells s.c. transplanted into immunodeficient nu/nu mice. This Ab efficiently down-regulates HGF receptor through a molecular mechanism involving a double proteolytic cleavage: (i) cleavage of the extracellular portion, resulting in "shedding" of the ectodomain, and (ii) cleavage of the intracellular domain, which is rapidly degraded by the proteasome. Interestingly, the "decoy effect" generated by the shed ectodomain, acting as a dominant negative molecule, enhanced the inhibitory effect of the Ab.

Prevalence of HCV antibodies in a uraemic population undergoing maintenance dialysis therapy and in the staff members of the dialysis unit

We studied, by both 1st and 2nd generation assay, the prevalence rate of HCVAb in a population of 141 dialysis patients, 37 transplanted patients and 55 staff members. From this study emerges a higher sensitivity of the 2nd generation HCVAb test (15.38 versus 36.79% of positive responses, respectively), and a significant positive correlation between lengths of dialysis period. We have not found a significant difference between HCVAb-positive and -negative patients in relation to the blood transfusions. None of the 21 CAPD patients (home dialysis) resulted positive, even if transfused. Two nurses were positive. In our experience, the environmental factor seems more important. Since the isolation of the positive patients is an effective but not feasible measure, it is necessary to improve the operating management of the hemodialysis sessions, avoiding any contact between patients via material (instrumentation, monitors) and teaching the staff members to use severe preventive standards with all hemodialysis patients.