Cas13d-mediated isoform-specific RNA knockdown with a unified computational and experimental toolbox

Alternative splicing is an essential mechanism for diversifying proteins, in which mature RNA isoforms produce proteins with potentially distinct functions. Two major challenges in characterizing the cellular function of isoforms are the lack of experimental methods to specifically and efficiently modulate isoform expression and computational tools for complex experimental design. To address these gaps, we developed and methodically tested a strategy which pairs the RNA-targeting CRISPR/Cas13d system with guide RNAs that span exon-exon junctions in the mature RNA. We performed a high-throughput essentiality screen, quantitative RT-PCR assays, and PacBio long read sequencing to affirm our ability to specifically target and robustly knockdown individual RNA isoforms. In parallel, we provide computational tools for experimental design and screen analysis. Considering all possible splice junctions annotated in GENCODE for multi-isoform genes and our gRNA efficacy predictions, we estimate that our junction-centric strategy can uniquely target up to 89% of human RNA isoforms, including 50,066 protein-coding and 11,415 lncRNA isoforms. Importantly, this specificity spans all splicing and transcriptional events, including exon skipping and inclusion, alternative 5' and 3' splice sites, and alternative starts and ends.

Establishing a complementary diagnostic for anti-PD-1 immune checkpoint inhibitor therapy

The role of tumor PD-L1 expression was investigated across the nivolumab clinical development program. Phase III nivolumab trials have shown that patients with tumors not expressing PD-L1 may benefit; therefore, testing is not required to select patients for therapy. The Dako PD-L1 IHC 28-8 pharmDx assay may be used to determine tumor PD-L1 expression as a complementary and informative test.

Meeting report: Emerging respiratory viral infections and nonhuman primate case reports

A workshop on Emerging Respiratory Viral Infections and Spontaneous Diseases in nonhuman primates was sponsored by the concurrent Annual Meetings of the American College of Veterinary Pathologists and the American Society for Veterinary Clinical Pathology, held December 1-5, 2012, in Seattle, Washington. The session had platform presentations from Drs Karen Terio, Thijs Kuiken, Guy Boivin, and Robert Palermo that focused on naturally occurring influenza, human respiratory syncytial virus, and metapneumovirus in wild and zoo-housed great apes; the molecular biology and pathology of these viral respiratory diseases in nonhuman primate (NHP) models; and the therapeutic and vaccine approaches to prevention and control of these emerging respiratory viral infections. These formal presentations were followed by presentations of 14 unique case studies of rare or newly observed spontaneous lesions in NHPs (see online files for access to digital whole-slide images corresponding to each case report at http://scanscope.com/ACVP%20Slide%20Seminars/2012/Primate%20Pathology/view.apml). The session was attended by meeting participants that included students, pathology trainees, and experienced pathologists from academia and industry with an interest in respiratory and spontaneous diseases of NHPs.

Meeting report: Spontaneous lesions and diseases in wild, captive-bred, and zoo-housed nonhuman primates and in nonhuman primate species used in drug safety studies

The combination of loss of habitat, human population encroachment, and increased demand of select nonhuman primates for biomedical research has significantly affected populations. There remains a need for knowledge and expertise in understanding background findings as related to the age, source, strain, and disease status of nonhuman primates. In particular, for safety/biomedical studies, a broader understanding and documentation of lesions would help clarify background from drug-related findings. A workshop and a minisymposium on spontaneous lesions and diseases in nonhuman primates were sponsored by the concurrent Annual Meetings of the American College of Veterinary Pathologists and the American Society for Veterinary Clinical Pathology held December 3-4, 2011, in Nashville, Tennessee. The first session had presentations from Drs Lowenstine and Montali, pathologists with extensive experience in wild and zoo populations of nonhuman primates, which was followed by presentations of 20 unique case reports of rare or newly observed spontaneous lesions in nonhuman primates (see online files for access to digital whole-slide images corresponding to each case report at http://www.scanscope.com/ACVP%20Slide%20Seminars/2011/Primate%20Pathology/view.apml). The minisymposium was composed of 5 nonhuman-primate researchers (Drs Bradley, Cline, Sasseville, Miller, Hutto) who concentrated on background and spontaneous lesions in nonhuman primates used in drug safety studies. Cynomolgus and rhesus macaques were emphasized, with some material presented on common marmosets. Congenital, acquired, inflammatory, and neoplastic changes were highlighed with a focus on clinical, macroscopic, and histopathologic findings that could confound the interpretation of drug safety studies.

Biomarker Analyses in Phase 2 Single-Agent Trials of Dasatinib for Breast Cancer

Background: Dasatinib (BMS-354825) is a potent SRC inhibitor being studied in several solid tumors including breast cancer. Expression profiling of breast cancer cell lines led to the identification of genes putatively correlated with dasatinib sensitivity.1,2 Inhibition of Src-family kinases may have complex effects on angiogenesis; circulating levels of VEGFR2 and collagen type IV (CollIV) are related to changes in VEGF signaling. Two Phase 2 single-agent trials of dasatinib3,4 have been performed in patients with locally-advanced or metastatic advanced breast cancers. Tumor markers may be used to predict clinical benefit and circulating biomarkers may reveal key mechanisms of action.Methods: Biomarker data from two Phase 2 trials including 114 patients were aggregated for this analysis. Archival tumor tissue from most recent prior surgery was collected in both trials; tumor samples were submitted for 38 of 44 patients with triple-negative, 39 of 46 patients with ER/PR+, and 20 of 24 patients with Her2/neu-amplified breast cancer. The initial dasatinib dose of 100 mg BID (n=46) was reduced to 70 mg BID (n=68) to improve tolerability. Based on mRNA results, immunohistochemical (IHC) procedures were developed for caveolin (Cav), phospho-Cav (p-Cav; scored as membrane vs cytoplasmic), EphA2 and IGFBP-2. Staining intensity was expressed on a scale of 0–3. Plasma was collected at baseline and after 2 and 4 weeks of dasatinib treatment and analyzed for VEGFR2 and CollIV by enzyme-linked immunosorbent assay (ELISA). Quantitative biomarker values pre-treatment and at ≥1 on-study time point for 71 of 114 patients were expressed as percent change from baseline. Tumor mRNA expression is being analyzed in all available tissue.Results: Protocol-defined clinical benefit was observed in 13 patients: 4 with triple-negative, 7 with ER/PR+, and 2 with Her2+ (which were also ER+) malignancies. Tumor tissue was prioritized and adequate for analysis in 89 tumors for Cav, 80 for p-Cav, 88 for EphA2 and 84 for IGFBP-2. Positive IHC (2-3+ intensity) was recorded for Cav in 35% of patients, with 11% and 25% positive for p-Cav in cytoplasm and membrane, respectively, and in 27% for EphA2 and 23% for IGFBP-2. No association was detected between clinical benefit and IHC results. Consistent increases in plasma biomarkers were observed in >90% of subjects. Median percent change (at Days 15 & 29, respectively) was 22% & 27% in VEGFR2 and 32% & 46% in CollIV; the mechanism of this change is being further investigated. Increased CollIV on treatment was associated with drug-related Grade 3-4 adverse events in first 4 weeks and with clinical benefit, but not with tumor subtype. Data on mRNA expression will be presented.Conclusions: The selected IHC analytes did not predict clinical benefit in these trials. Consistent early increases in VEGFR2 and CollIV suggest an effect of dasatinib on vascular endothelium which appears related to both safety and efficacy.1. Huang et al. Cancer Res. 2007;67(5):2226-38.2. Finn et al. Breast Cancer Res Treat. 2007;105(3):319-26.3. Finn et al. SABCS 2008;abstract 3118.4. Mayer et al. ASCO 2009;abstract 1011.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 2034.

High epiregulin (EREG) gene expression plus K-ras wild-type (WT) status as predictors of cetuximab benefit in the treatment of advanced colorectal cancer (ACRC): Results from NCIC CTG CO.17—A phase III trial of cetuximab versus best supportive care (BSC)

4016

Background: Cetuximab, a monoclonal antibody targeting the epidermal growth factor receptor (EGFR), improves overall survival (OS) and progression free survival (PFS) in patients with K-ras WT chemotherapy refractory ACRC. Gene expression of the EGFR ligand epiregulin (EREG) may further predict benefit from cetuximab. Methods: CRC tumour samples were analyzed from a phase III clinical trial of cetuximab plus BSC vs BSC alone (NEJM 2007; 357(20)). EREG gene expression was detected in tumour-derived genomic RNA blinded to clinical outcome by quantitative real time-PCR. Using a pre-specified threshold for “high” EREG derived from a prior study (CA225–045), the predictive effect of (1) high vs low EREG among K-ras WT and (2) high EREG/K-ras WT status (“Combimarker”) versus all other patients on OS and PFS was examined using a Cox model with tests for treatment-biomarker interaction. Results: Both EREG gene expression levels and K-ras mutation status were ascertained in 385 (67%) of the total study population (193 cetuximab, 192 BSC). In the K-ras WT subset, OS was better for cetuximab than BSC among patients with high EREG (HR 0.43; p<0.0001) but not for low EREG patients (HR 0.77, p=0.28). The test for interaction showed a non-significantly larger treatment effect in the high EREG group (HR 0.62, p=0.13). High EREG AND K-ras WT status (“Combimarker”) was present in 139 (36%). Within the Combimarker positive group the median PFS was 5.4 vs 1.9 months (HR, 0.31; p<0.0001), and median OS 9.8 vs 5.1 months (HR, 0.43; p<0.001) in the cetuximab vs BSC arms, respectively. In the rest (n=246, 64%) cetuximab was not associated with improved PFS (HR, 0.82; p=0.12) or OS (HR, 0.90; p=0.45). The test for treatment-Combimarker interaction showed a larger cetuximab effect on OS (HR 0.52; p=0.007) and PFS (HR 0.49; p=0.001) in the Combimarker positive group. Conclusions: In the setting of pre-treated ACRC, patients with both high EREG gene expression and K-ras wild- type status may benefit from cetuximab therapy. Determination of EREG gene expression levels should be prospectively evaluated in patient selection for EGFR targeted therapy.

[Table: see text]

K-Ras mutation (mut), EGFR-related, and exploratory markers as response predictors of cetuximab in first-line advanced NSCLC: Retrospective analyses of the BMS099 trial

8021

Background: This phase III study investigated cetuximab (C) plus taxane/carboplatin (TC) in 1st-line advanced NSCLC. Progression-free survival (PFS) was not significantly different with the addition of C to TC; response rate (RR) was significantly higher; median overall survival (OS) was longer, with a difference (not statistically significant) similar in magnitude to the significant OS improvement from FLEX (cisplat/vinorelb±C). Potential patient-selection markers were analyzed, including mut in K-Ras, EGFR mut and gene copy number (GCN), EGFR protein expression, and gene expression profiles. Methods: Chemonaïve patients (pts) with stage IIIB/IV NSCLC (any histology or EGFR expression status) were randomized to TC±C. K-Ras gene exon 2, and EGFR exons 18–21 were sequenced bidirectionally using formalin-fixed paraffin embedded tissue-derived genomic DNA. EGFR GCN was measured by fluorescence in situ hybridization (FISH) and EGFR protein expression by immunohistochemistry (IHC). Exploratory expression profiling studies using Affymetrix GeneChip are ongoing. Analyses were blinded to clinical outcome. The relationships between biomarker status and efficacy were assessed with log-rank tests per study arm for treatment-specific effects, and across the total evaluable population. Results: Samples from 225/676 randomized pts were available; 35/202 (17%) had K-Ras mut, 17/167 (10%) had EGFR mut, 54/104 (52%) were EGFR FISH+, 131/148 (89%) were EGFR IHC+. There were no significant treatment-specific correlations between any biomarker assessed and PFS, OS or RR, except superior OS with TC for the EGFR FISH+ group (P=0.03). With all pts combined, OS was longer in the EGFR mut subset vs wt (P=0.09); PFS was longer in EGFR IHC- pts vs IHC+ (P=0.048). Results from gene expression profiling studies, including EGFR ligands, will be presented. Conclusions: There was no significant correlation between patient response to C and any molecular marker evaluated to date (K-RAS mut, EGFR mut, EGFR IHC, EGFR FISH), exploratory analyses are ongoing. Additional predictive-marker studies are needed to optimize cetuximab therapeutic use in NSCLC.

[Table: see text]

Tumor regression and pharmacodynamic (PD) biomarker validation in non-small cell lung cancer (NSCLC) patients treated with the ErbB/VEGFR inhibitor BMS-690514

8098

Background: BMS-690514 is an oral selective inhibitor of EGFR, HER2, and VEGFR1–3. Previous results from the phase I portion of this phase I/II study established 200 mg/day as safe and tolerable (ASCO 2008; abstr 2564). Methods: Erlotinib-naïve and erlotinib-resistant adult patients with advanced/metastatic, measurable NSCLC received BMS-690514 200 mg/d. Eligible patients had an ECOG PS ≤1 and adequate organ function. Objectives were to assess disease control rate (DCR; CR, PR, SD ≥4 months), safety, PK and potential predictive and PD biomarkers of BMS-690514. Response was assessed every 8 weeks (modified WHO criteria). Predictive biomarkers included EGFR copy number, and EGFR and KRAS mutations. PD biomarkers included immunohistochemistry of EGFR signaling proteins in skin biopsies, circulating sVEGFR2, blood pressure, skin rash and diarrhea. Results: For 60 patients treated, DCR were 11/28 (39%) and 7/32 (22%) for erlotinib-naive and -resistant patients, respectively. DCR was significantly higher among patients harboring an EGFR mutation (6/8) than those with WT EGFR (5/18). One erlotinib-naive patient had PR (57 wks) and subsequent surgical removal of remaining tumor. Regression (48%) was seen in one erlotinib-naive patient harboring a KRAS G13D mutation. One erlotinib-resistant patient had PR (66%, 31 wks). Two erlotinib-resistant patients with EGFR T790M mutations had SD with 6% and 31% decrease in tumor burden. Most frequent treatment-related AES were diarrhea (90%), skin rash (31%), asthenia (29%), anorexia (27%), hypertension (26%), and reversible acute renal insufficiency (11%). sVEGFR2 (14% decrease from baseline, n=14) and decreased pMAPK levels from skin biopsies (14 of 18 pts) were consistent with EGFR and VEGFR2 inhibition. Conclusions: BMS-690514 200 mg/d showed evidence of anti-tumor activity and disease control in patients with NSCLC, including erlotinib-resistant and those with WT EGFR, EGFR T790M or KRAS mutations. Predictive and PD clinical biomarkers confirmed inhibition of both EGFR and VEGFR signaling pathways by BMS-690514. A randomized phase II trial versus erlotinib in NSCLC is underway.

[Table: see text]

A multidimensional measure of religious involvement for cancer patients: the Duke Religious Index

Despite increasing interest in the relationship between religious involvement and health outcomes for cancer patients, research has been limited by the lack of appropriate measures. Few of the many instruments available are well suited to cancer patients. The current study examined the psychometric properties of one recently developed measure, the Duke Religious Index (DRI), which assesses several aspects of religious involvement. The DRI was evaluated in two distinct samples: 104 cancer patients receiving treatment at a bone marrow transplantation program and 175 gynecology clinic patients. The instrument demonstrated good internal consistency (coefficient alphas 0.87-0.94). Moderate to high correlations with other measures of religiosity provided support for convergent validity. Modest relationships with other measures commonly used in psychosocial oncology (e.g., optimism, social support, purpose in life) indicated that the instrument provides unique information (all rs's < 0. 42). Small relationships with social desirability response bias, negative affect, and relationship cohesion further supported the divergent validity of the instrument (all rs's < 0.22). The DRI was significantly associated with demographic characteristics but not with medical variables. Findings support the value of the DRI for use in oncology settings.

Diversity and heterogeneity of epibiotic bacterial communities on the marine nematode Eubostrichus dianae

The diversity of a microbial community covering the surface of a marine nematode was analyzed by performing a 16S ribosomal DNA (rDNA) restriction cutting and sequencing analysis. In two clone libraries constructed by using individual nematodes, 54 and 85 restriction patterns were identified, and only 13 of these patterns were common to both libraries. Sequence analysis indicated that the common patterns belonged to four groups related to sequences of cytophagas, sulfate-reducing bacteria, members of the gamma subclass of the class Proteobacteria, and caulobacters. At least two groups appeared to be permanent members of the community as they were also detected in a 16S rDNA library constructed 3 years previously by using 100 pooled nematode specimens. A surprising outcome was that very dominant filamentous bacteria were apparently not represented in the clone libraries, as quantitative probing showed that none of the common operational taxonomic unit groups displayed the expected overwhelming dominance. Nevertheless, our analysis revealed both an unexpectedly high level of bacterial diversity and heterogeneity in samples representing presumably very similar microenvironments.