Neoadjuvant Durvalumab Alone or Combined with Novel Immuno-Oncology Agents in Resectable Lung Cancer: The Phase II NeoCOAST Platform Trial

Neoadjuvant chemoimmunotherapy improves pathologic complete response rate and event-free survival in patients with resectable non-small cell lung cancer (NSCLC) versus chemotherapy alone. NeoCOAST was the first randomized, multidrug platform trial to examine novel neoadjuvant immuno-oncology combinations for patients with resectable NSCLC, using major pathologic response (MPR) rate as the primary endpoint. Eighty-three patients received a single cycle of treatment: 26 received durvalumab (anti-PD-L1) monotherapy, 21 received durvalumab plus oleclumab (anti-CD73), 20 received durvalumab plus monalizumab (anti-NKG2A), and 16 received durvalumab plus danvatirsen (anti-STAT3 antisense oligonucleotide). MPR rates were higher for patients in the combination arms versus durvalumab alone. Safety profiles for the combinations were similar to those of durvalumab alone. Multiplatform immune profiling suggested that improved MPR rates in the durvalumab plus oleclumab and durvalumab plus monalizumab arms were associated with enhanced effector immune infiltration of tumors, interferon responses and markers of tertiary lymphoid structure formation, and systemic functional immune cell activation.

SIGNIFICANCE

A neoadjuvant platform trial can rapidly generate clinical and translational data using candidate surrogate endpoints like MPR. In NeoCOAST, patients with resectable NSCLC had improved MPR rates after durvalumab plus oleclumab or monalizumab versus durvalumab alone and tumoral transcriptomic signatures indicative of augmented immune cell activation and function. See related commentary by Cooper and Yu, p. 2306. This article is featured in Selected Articles from This Issue, p. 2293.

Abstract 3404: Detection of circulating tumor DNA using CRISPR-Cas13a in non-small cell lung cancer

Background: Lung cancer remains the leading cause of cancer-related death and despite advances in low-dose CT screening, most lung cancer patients still present with advanced disease. The development of assays that are sensitive, specific, economical, and non-invasive may lead to the development of further effective screening strategies. Non-invasive liquid biopsy by detection in plasma of circulating tumor DNA (ctDNA) carrying somatic lung cancer mutations is now routinely used for identifying targeted therapy options in advanced non-small cell lung cancer (NSCLC) patients. Recent adaptation of bacterial CRISPR-Cas13a systems with promiscuous ribonuclease activity into reporter assays for the sensitive and economical detection of specific nucleic acid sequences makes an attractive system for ctDNA detection without needing more costly next-generation sequencing (NGS) techniques.

Methods: We adapted the CRISPR-Cas13a system used in the SHERLOCK detection assay for the detection of common driver mutations (KRAS G12C/V, EGFR Exon 19 deletion, and EGFR L858R) in NSCLC and tested the assay on a retrospective cohort of 52 NSCLC patients with known mutations (based on tissue NGS) and with plasma obtained prior to or at the time of any surgical resection and a prospective cohort of 71 patients who underwent lung resection with plasma collected at the time of surgical resection.

Results: We designed several CRISPR guide RNAs targeting common EGFR and KRAS oncogenic mutations in NSCLC and were able to generate sensitive CRISPR-Cas13a detection assays against KRAS G12C and G12V, EGFR L858R, and EGFR E746_A750 exon 19 deletion mutations that could identify allele fractions below 1% in reference standards. We then tested plasma of a 52 patient (33 advanced stage IIIB and IV, 19 resectable stage I-IIIA) retrospective cohort with known KRAS and EGFR mutations and matching non-cancer controls using the CRISPR-Cas13a assay as well as with NGS panels (ArcherDx). Using NGS, we were able to confirm ctDNA in 15 samples which we were also able to detect using the CRISPR-Cas13a assay with similar allele frequencies. The CRISPR-Cas13a assay was able to identify ctDNA in 42 out of the 52 retrospective NSCLC samples including 13 out of 19 samples from resectable-stage patients, although the detection rate decreased with earlier stage I and II patients who have a much lower ctDNA level in plasma. We then prospectively collected a cohort of 71 subjects who underwent surgical resection with 38 subjects with lung adenocarcinoma (mostly stage I and II), 11 subjects with benign nodules, and 22 subjects with a different histology malignancy. Our CRISPR-Cas13a assay was able to detect 9 out of 38 lung adenocarcinomas with no false positives in subjects with benign nodules.

Conclusion: We adapted a CRISPR-Cas13a assay for the detection of ctDNA in NSCLC and evaluated this assay on plasma from NSCLC subjects.

Citation Format: Edwin H. Yau, Bojidar Kandar, Catrina Ting, Sai Yendamuri, Mary Reid. Detection of circulating tumor DNA using CRISPR-Cas13a in non-small cell lung cancer [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 3404.

Integrin αvβ5 Internalizes Zika Virus during Neural Stem Cells Infection and Provides a Promising Target for Antiviral Therapy

We perform a CRISPR-Cas9 genome-wide screen in glioblastoma stem cells and identify integrin αvβ5 as an internalization factor for Zika virus (ZIKV). Expression of αvβ5 is correlated with ZIKV susceptibility in various cells and tropism in developing human cerebral cortex. A blocking antibody against integrin αvβ5, but not αvβ3, efficiently inhibits ZIKV infection. ZIKV binds to cells but fails to internalize when treated with integrin αvβ5-blocking antibody. αvβ5 directly binds to ZIKV virions and activates focal adhesion kinase, which is required for ZIKV infection. Finally, αvβ5 blocking antibody or two inhibitors, SB273005 and cilengitide, reduces ZIKV infection and alleviates ZIKV-induced pathology in human neural stem cells and in mouse brain. Altogether, our findings identify integrin αvβ5 as an internalization factor for ZIKV, providing a promising therapeutic target, as well as two drug candidates for prophylactic use or treatments for ZIKV infections.

Wang et al. show that Zika virus (ZIKV) uses integrin αvβ5 to infect neural stem cells. ZIKV infection can be inhibited by αvβ5 blocking antibody or inhibitors, SB273005 and cilengitide, in human neural stem cells and in mouse brain, providing drug candidates for prophylactic use or treatments for ZIKV infections.

Systematic Screening, Rational Development, and Initial Optimization of Efficacious RNA Silencing Agents for Human Rod Opsin Therapeutics

Purpose

To systematically evaluate human rod opsin (hRHO) mRNA for potential target sites sensitive to posttranscriptional gene silencing (PTGS) by hammerhead ribozyme (hhRz) or RNA interference (RNAi) in human cells. To develop a comprehensive strategy to identify and optimize lead candidate agents for PTGS gene therapeutics.

Methods

In multidisciplinary RNA drug discovery, computational mRNA accessibility and in vitro experimental methods using reverse transcription–polymerase chain reaction (RT-PCR) were used to map accessibility in full-length hRHO transcripts. HhRzs targeted predicted accessible and inaccessible sites and were screened for cellular knockdown using a bicistronic reporter construct. Lead hhRz and RNAi PTGS agents were rationally optimized for target knockdown in human cells.

Results

Systematic screening of hRHO mRNA targeting agents resulted in lead candidate identification of a novel hhRz embedded in an RNA scaffold. Rational optimization strategies identified a minimal 725 hhRz as the most active agent. Recently identified tertiary accessory elements did not enhance activity. A 725-short-hairpin RNA (shRNA) agent exerts log-order knockdown. Silent modulation of the 725-hhRz target site in hRHO mRNA resulted in resistance to knockdown.

Conclusions

Combining rational RNA drug design with cell-based screening allowed rapid identification of lead agents targeting hRHO. Optimization strategies identified the agent with highest intracellular activity. These agents have therapeutic potential in a mutation-independent strategy for adRP, or other degenerations where hRHO is a target. This approach can be broadly applied to any validated target mRNA, regardless of the disease.

Translational Relevance

This work establishes a platform approach to develop RNA biologicals for the treatment of human disease.

Abstract PR12: Genome-wide in-vivo tumor xenograft CRISPR knockout screening for identifying KRAS mutant synthetic lethal interactions

The KRAS oncogene is frequently mutated in many of the most lethal human cancers and has been resistant to targeted therapies, leading to efforts to identify synthetic lethal genetic interactions in large-scale screens. These screens have been carried out largely in in-vitro cell culture systems using RNA interference (RNAi). Functional genomic screening using the bacterial type II clustered regularly interspaced short palindrome repeats and their associated proteins (CRISPR-Cas9) system has proven to be more powerful than RNAi for systematic genomic perturbation due to its simplicity, decreased off-target effects, and the ability to create knockout rather than knockdown phenotypes.

We have conducted a genome-wide CRISPR-Cas9 loss-of-function screen with the human GeCKO v2 library directly in-vivo utilizing a paired isogenic human colorectal cell line (HCT116) with and without a KRAS oncogenic mutation (G13D) to identify genes whose knockout results in synthetic lethal interactions in tumor xenografts with mutated KRAS. Compared to cell culture models, tumor xenografts better recapitulate obstacles tumor cells must overcome for continued proliferation including limited accessibility to nutrients and oxygen. Many recent studies have also highlighted the effect of KRAS oncogenic mutations on the rewiring of metabolic pathways to fuel increased tumor growth. Tumor xenografts offer a better screening platform in identifying factors that might exploit these metabolic pathways.

Pathway analysis of our genome-wide CRISPR screen indeed revealed candidate synthetic lethal genes involved in metabolic and nucleic acid synthesis pathways in KRAS mutant tumor xenografts. We individually validated some of the candidate genes in these metabolic pathways (including the TCA cycle, pentose phosphate pathway, and fructose metabolism) with individual CRISPR-Cas9 knockouts and confirmed that knockout of these genes resulted in decreased tumor xenograft growth in KRAS mutant tumors. One of the KRAS synthetic lethal genes that we identified was the gene NADK, which encodes NAD+ kinase that converts NAD+ into NADP+. Low-frequency activating mutations in NADK were also recently discovered by another group to harbor oncogenic potential in pancreatic adenocarcinoma. Given the high frequency of KRAS mutations in pancreatic adenocarcinoma, NADK may represent a therapeutic target in KRAS mutant tumors in general.

While more sensitive than RNAi screens, there was still significant noise in our CRISPR-Cas9 genome-wide screen as expected in an in-vivo dropout screen. To overcome this noise, we generated a smaller pooled lentiviral CRISPR library (targeting ~250 genes) based on candidate hits in the genome-wide screen and again directly screened this smaller but deeper pooled library in tumor xenografts with higher coverage and more replicates. This strategy allowed for better discrimination of novel KRAS dependent synthetic lethal genes.

Citation Format: Edwin H. Yau, Tariq Rana. Genome-wide in-vivo tumor xenograft CRISPR knockout screening for identifying KRAS mutant synthetic lethal interactions [abstract]. In: Proceedings of the AACR Precision Medicine Series: Opportunities and Challenges of Exploiting Synthetic Lethality in Cancer; Jan 4-7, 2017; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2017;16(10 Suppl):Abstract nr PR12.

Genome-Wide CRISPR Screen for Essential Cell Growth Mediators in Mutant KRAS Colorectal Cancers

Targeting mutant KRAS signaling pathways continues to attract attention as a therapeutic strategy for KRAS-driven tumors. In this study, we exploited the power of the CRISPR-Cas9 system to identify genes affecting the tumor xenograft growth of human mutant KRAS (KRAS^MUT) colorectal cancers. Using pooled lentiviral single-guide RNA libraries, we conducted a genome-wide loss-of-function genetic screen in an isogenic pair of human colorectal cancer cell lines harboring mutant or wild-type KRAS. The screen identified novel and established synthetic enhancers or synthetic lethals for KRAS^MUT colorectal cancer, including targetable metabolic genes. Notably, genetic disruption or pharmacologic inhibition of the metabolic enzymes NAD kinase or ketohexokinase was growth inhibitory in vivo In addition, the chromatin remodeling protein INO80C was identified as a novel tumor suppressor in KRAS^MUT colorectal and pancreatic tumor xenografts. Our findings define a novel targetable set of therapeutic targets for KRAS^MUT tumors. Cancer Res; 77(22); 6330-9. ©2017 AACR.

A cellular high-throughput screening approach for therapeutic trans-cleaving ribozymes and RNAi against arbitrary mRNA disease targets

Major bottlenecks in development of therapeutic post transcriptional gene silencing (PTGS) agents (e.g. ribozymes, RNA interference, antisense) include the challenge of mapping rare accessible regions of the mRNA target that are open for annealing and cleavage, testing and optimization of agents in human cells to identify lead agents, testing for cellular toxicity, and preclinical evaluation in appropriate animal models of disease. Methods for rapid and reliable cellular testing of PTGS agents are needed to identify potent lead candidates for optimization. Our goal was to develop a means of rapid assessment of many RNA agents to identify a lead candidate for a given mRNA associated with a disease state. We developed a rapid human cell-based screening platform to test efficacy of hammerhead ribozyme (hhRz) or RNA interference (RNAi) constructs, using a model retinal degeneration target, human rod opsin (RHO) mRNA. The focus is on RNA Drug Discovery for diverse retinal degeneration targets. To validate the approach, candidate hhRzs were tested against NUH↓ cleavage sites (N = G,C,A,U; H = C,A,U) within the target mRNA of secreted alkaline phosphatase (SEAP), a model gene expression reporter, based upon in silico predictions of mRNA accessibility. HhRzs were embedded in a larger stable adenoviral VAI RNA scaffold for high cellular expression, cytoplasmic trafficking, and stability. Most hhRz expression plasmids exerted statistically significant knockdown of extracellular SEAP enzyme activity when readily assayed by a fluorescence enzyme assay intended for high throughput screening (HTS). Kinetics of PTGS knockdown of cellular targets is measureable in live cells with the SEAP reporter. The validated SEAP HTS platform was transposed to identify lead PTGS agents against a model hereditary retinal degeneration target, RHO mRNA. Two approaches were used to physically fuse the model retinal gene target mRNA to the SEAP reporter mRNA. The most expedient way to evaluate a large set of potential VAI-hhRz expression plasmids against diverse NUH↓ cleavage sites uses cultured human HEK293S cells stably expressing a dicistronic Target-IRES-SEAP target fusion mRNA. Broad utility of this rational RNA drug discovery approach is feasible for any ophthalmological disease-relevant mRNA targets and any disease mRNA targets in general. The approach will permit rank ordering of PTGS agents based on potency to identify a lead therapeutic compound for further optimization.

Variables and strategies in development of therapeutic post-transcriptional gene silencing agents

Post-transcriptional gene silencing (PTGS) agents such as ribozymes, RNAi and antisense have substantial potential for gene therapy of human retinal degenerations. These technologies are used to knockdown a specific target RNA and its cognate protein. The disease target mRNA may be a mutant mRNA causing an autosomal dominant retinal degeneration or a normal mRNA that is overexpressed in certain diseases. All PTGS technologies depend upon the initial critical annealing event of the PTGS ligand to the target RNA. This event requires that the PTGS agent is in a conformational state able to support hybridization and that the target have a large and accessible single-stranded platform to allow rapid annealing, although such platforms are rare. We address the biocomplexity that currently limits PTGS therapeutic development with particular emphasis on biophysical variables that influence cellular performance. We address the different strategies that can be used for development of PTGS agents intended for therapeutic translation. These issues apply generally to the development of PTGS agents for retinal, ocular, or systemic diseases. This review should assist the interested reader to rapidly appreciate critical variables in PTGS development and facilitate initial design and testing of such agents against new targets of clinical interest.

Bottlenecks in development of retinal therapeutic post-transcriptional gene silencing agents

Development of post-transcriptional gene silencing (PTGS) agents for therapeutic purposes is an immense challenge in modern biology. Established technologies used to knockdown a specific target RNA and its cognate protein: antisense, ribozyme, RNAi, all conditionally depend upon an initial, critical annealing event of the PTGS ligand to a target RNA. In this review we address the nature of the bottlenecks, emphasizing the biocomplexity of target RNA structure, that currently limit PTGS therapeutic development. We briefly review existing and emerging technologies designed to release these constraints to realize the potential of PTGS agents in gene based therapies.

Oxygen transport patterns in patients with sepsis syndrome or septic shock: influence of treatment and relationship to outcome

OBJECTIVE

To investigate the relationship between oxygen transport patterns and outcome in patients with sepsis syndrome or septic shock managed according to two different treatment regimens.

DESIGN

Retrospective study of a subgroup of patients with sepsis syndrome or septic shock taken from a randomized, prospective, controlled trial.

SETTING

General intensive care units in a teaching and a district general hospital.

PATIENTS

Seventy-eight patients classified according to predetermined criteria as having sepsis syndrome or septic shock were drawn retrospectively from a larger study group of 109 consecutive patients considered to be at risk for developing multiple organ failure.

INTERVENTIONS

All patients received volume expansion to an optimal pulmonary artery occlusion pressure. If the therapeutic goals (cardiac index of > 4.5 L/min/m2, oxygen delivery [DO2] of > 600 mL/min/m2, and oxygen consumption [VO2] of > 170 mL/min/m2) were not achieved with fluids alone, patients were randomized to either a control group or a treatment group. In the treatment group, dobutamine (5 to 200 micrograms/kg/min) was administered to increase cardiac index and DO2 until all three goals were simultaneously achieved. In the control group, dobutamine was administered only if the cardiac index was < 2.8 L/min/m2. In both groups, norepinephrine was infused to maintain mean arterial pressure at 80 mm Hg.

MEASUREMENTS AND MAIN RESULTS

Hemodynamic, oxygen transport, and lactate measurements were made at the time of admission to the study, at the time of optimal volume administration, at 1, 2, 4, 8, 12, 16, 20, and 24 hrs, then every 6 hrs for the next 24 hrs, and at least every 8 hrs thereafter. The time at which all therapeutic goals were first achieved simultaneously or the time of maximal DO2 was identified and termed "tmax." Survivors from both the control and treatment groups significantly (p < .001) increased cardiac index and DO2 in response to maximal resuscitation, and despite an associated decrease in oxygen extraction (p < .01), there was a significant (p < .01) increase in VO2. In nonsurvivors from both groups, despite significant increases in cardiac index (p < .05) and DO2 (p < .01) at tmax, oxygen extraction decreased (p < .01) and VO2 remained unchanged. DO2 and VO2 were significantly lower (p < .05) at tmax in nonsurvivors than in survivors from both groups. Persistently high lactate concentrations were characteristic of nonsurvivors.

CONCLUSIONS

Survivors of sepsis syndrome or septic shock are characterized by an ability to increase both DO2 and VO2. In contrast, nonsurvivors typically have reduced cardiac reserve, they fail to increase VO2 following resuscitation, and when delivery is enhanced with aggressive inotropic support, oxygen extraction falls. These patterns of response were similar in both treatment and control groups, although the magnitude of the changes was exaggerated in the treatment group. These observations may help to explain the findings by some investigators that treatment aimed at achieving survivor values of cardiac index, DO2, and VO2 fails to improve outcome when instituted following admission to intensive care.

Elevation of systemic oxygen delivery in the treatment of critically ill patients

BACKGROUND

Elevation of systemic oxygen delivery and consumption has been associated with an improved outcome in critically ill patients. We conducted a randomized trial to determine whether boosting oxygen delivery by infusing the inotropic agent dobutamine would improve the outcome in a diverse group of such patients.

METHODS

On the basis of previously published recommendations, we established the following goals: a cardiac index above 4.5 liters per minute per square meter of body-surface area, oxygen delivery above 600 ml per minute per square meter, and oxygen consumption above 170 ml per minute per square meter. If these goals were not achieved with volume expansion alone, patients were randomly assigned to a treatment or control group. The treatment group received intravenous dobutamine (5 to 200 micrograms per kilogram of body weight per minute) until all three goals had been achieved. Dobutamine was administered to the control group only if the cardiac index was below 2.8 liters per minute per square meter.

RESULTS

A total of 109 patients were studied. In nine patients the therapeutic goals were achieved with volume expansion alone; all nine patients survived to leave the hospital. Fifty patients were randomly assigned to the treatment group, and 50 to the control group. During treatment, there were no differences between the two groups in mean arterial pressure or oxygen consumption, despite a significantly higher cardiac index and level of oxygen delivery in the treatment group (P < 0.05). Although the predicted risk of death during hospitalization was 34 percent for both groups, the in-hospital mortality was lower in the control group (34 percent) than in the treatment group (54 percent) (P = 0.04; 95 percent confidence interval, 0.9 to 39.1 percent).

CONCLUSIONS

The use of dobutamine to boost the cardiac index and systemic oxygen delivery failed to improve the outcome in this heterogeneous group of critically ill patients. Contrary to what might have been expected, our results suggest that in some cases aggressive efforts to increase oxygen consumption may have been detrimental.

Response of critically ill patients to treatment aimed at achieving supranormal oxygen delivery and consumption. Relationship to outcome

STUDY OBJECTIVE

To evaluate the response to therapy aimed at achieving supranormal cardiac and oxygen transport variables (cardiac index [CI] > 4.5 L/min/m2, oxygen delivery [DO2] > 600 ml/min/m2, and oxygen consumption [VO2] > 170 ml/min/m2) in a heterogenous group of critically ill patients and to assess its relationship to outcome.

DESIGN

Patients were divided retrospectively into two groups. Group 1 (n = 15) achieved supranormal values for CI, DO2 and VO2 simultaneously during the first 24 h. Group 2 (n = 17) failed to achieve these goals simultaneously at any time point.

SETTING

General intensive care units in a teaching and a district general hospital.

PATIENTS

Thirty-two patients at risk of developing multiple organ failure were studied prospectively.

INTERVENTIONS

Patients received volume expansion and then, if necessary, dobutamine (5 to 200 micrograms/kg/min) to increase CI and DO2 until all three goals were achieved simultaneously.

RESULTS

In group 2, target VO2 could never be reached despite the fact that 11 (65 percent) patients achieved target CI and DO2 simultaneously. In this group, lactate levels did not fall and 16 patients died. In contrast, in group 1, attainment of all goals was associated with a significant reduction (p < 0.05) in blood lactate levels, and all but one of these patients survived. The persistently raised lactate levels in group 2 were associated with significantly higher venous oxygen saturation (SvO2) and lower oxygen extraction ratio (OER); in these patients, SvO2 rose and OER fell in response to increases in DO2.

CONCLUSION

These results suggest that failure to increase VO2 was related predominantly to an inability of the tissues to extract or utilize oxygen rather than a failure to increase DO2. These findings support the hypothesis that in order to survive a critical illness, patients must achieve a high level of VO2. An inability to do so is reflected in persistently elevated blood lactate levels and an extremely poor prognosis.

Symmetrical peripheral gangrene: association with noradrenaline administration

The syndrome of symmetrical peripheral gangrene is characterised by distal ischaemic damage in two or more extremities, without large vessel obstruction. Four patients with bilateral pedal ischaemia are described and their haemodynamic profiles presented. In all four cases the syndrome developed in association with noradrenaline administration, sepsis and DIC, despite a high cardiac output and a low calculated systemic vascular resistance index. Early treatment with epoprostenol was instituted in the final case and was successful.