A saturation-mutagenesis analysis of the interplay between stability and activation in Ras

Cancer mutations in Ras occur predominantly at three hotspots: Gly 12, Gly 13, and Gln 61. Previously, we reported that deep mutagenesis of H-Ras using a bacterial assay identified many other activating mutations (Bandaru et al., 2017). We now show that the results of saturation mutagenesis of H-Ras in mammalian Ba/F3 cells correlate well with the results of bacterial experiments in which H-Ras or K-Ras are co-expressed with a GTPase-activating protein (GAP). The prominent cancer hotspots are not dominant in the Ba/F3 data. We used the bacterial system to mutagenize Ras constructs of different stabilities and discovered a feature that distinguishes the cancer hotspots. While mutations at the cancer hotspots activate Ras regardless of construct stability, mutations at lower-frequency sites (e.g. at Val 14 or Asp 119) can be activating or deleterious, depending on the stability of the Ras construct. We characterized the dynamics of three non-hotspot activating Ras mutants by using NMR to monitor hydrogen-deuterium exchange (HDX). These mutations result in global increases in HDX rates, consistent with destabilization of Ras. An explanation for these observations is that mutations that destabilize Ras increase nucleotide dissociation rates, enabling activation by spontaneous nucleotide exchange. A further stability decrease can lead to insufficient levels of folded Ras - and subsequent loss of function. In contrast, the cancer hotspot mutations are mechanism-based activators of Ras that interfere directly with the action of GAPs. Our results demonstrate the importance of GAP surveillance and protein stability in determining the sensitivity of Ras to mutational activation.

Association of Radiation Therapy With Risk of Adverse Events in Patients Receiving Immunotherapy: A Pooled Analysis of Trials in the US Food and Drug Administration Database

Importance

Immune checkpoint inhibitors (ICIs) and radiation therapy (RT) are widely used to treat various cancers, but little data are available to guide clinicians on ICI use sequentially with RT.

Objective

To assess whether there is an increased risk of serious adverse events (AEs) associated with RT given within 90 days prior to an ICI.

Design, Setting, and Participants

Individual patient data were pooled from 68 prospective trials of ICIs submitted in initial or supplemental licensing applications in the US Food and Drug Administration (FDA) databases through December 2019. Two cohorts were generated: (1) patients who received RT within the 90 days prior to beginning ICI therapy and (2) those who did not receive RT within the 90 days prior to beginning ICI therapy, and AE frequencies were determined. A 1:1 propensity score-matched analysis was performed.

Interventions

All patients received an ICI (atezolizumab, avelumab, cemiplimab, durvalumab, ipilimumab, nivolumab, or pembrolizumab); 1733 received RT within the 90 days prior to starting ICI therapy, and 13 956 did not.

Main Outcomes and Measures

The primary outcome was frequency and severity of AEs. Incidence of AEs was compared descriptively between participants who did vs did not receive RT in the propensity score-matched set. Because all analyses are exploratory (ie, not preplanned and no alpha allocated), assessment for statistical significance of the differences between groups was not considered appropriate.

Results

A total of 25 469 patients were identified; 8634 were excluded because they lacked comparators who had received RT (n = 976), did not receive an ICI (n = 4949), received RT outside of the target window (n = 2338), or had missing data in 1 or more variables used in the propensity analysis (n = 371), leaving 16 835 patients included in the analysis. The majority were younger than 65 years (9447 [56.1%]), male (10 459 [62.1%]), and White (13 422 [79.7%]). Patients receiving RT had generally similar rates of AEs overall to those patients who did not receive RT. The average absolute difference in rates across the AEs was 1.2%, and the difference ranged from 0% for neurologic AEs to 8% for fatigue. No difference in grade 3 to 4 AEs was observed between the 2 groups (absolute difference ranged from 0.01% to 2%). These findings persisted after propensity score matching.

Conclusions and Relevance

In this pooled analysis, administration of an ICI within 90 days following RT did not appear to be associated with an increased risk of serious AEs. Thus, it would appear to be safe to administer an ICI within 90 days of receiving RT. These findings should be confirmed in future prospective trials.

Impact of radiotherapy on risk of adverse events in patients receiving immunotherapy: A U.S. Food and Drug Administration pooled analysis

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Background: Immune checkpoint inhibitors (ICIs) are widely used in the treatment of multiple advanced malignancies. Radiotherapy (RT) has been used in combination with ICIs to activate tumor-specific T cell responses, and RT also promotes non-specific acute and chronic inflammatory responses both locally and systemically. More than 50% of patients receive RT at some point during their course of cancer therapy, and relatively little information is available pertaining to the impact of RT, if any, on the risk of adverse events (AEs) in patients receiving ICIs. Methods: Pooled data from prospective trials of ICIs submitted to the FDA in initial or supplemental BLAs or NDAs through 12/2019 were included (N=66). Trials from applications that were withdrawn or not approved were not included. Patients were subdivided by whether or not radiotherapy was administered at any time during the course of their cancer treatment. AEs common to both ICI treatment and RT were identified to focus on the following reactions: neutropenia, thrombocytopenia, colitis, hepatitis, pneumonitis, and myocarditis. Descriptive statistics were used to examine AEs associated with the use of radiation and ICIs. Results: A total of 25,836 patients were identified, of which 9087 (35%) received RT and 16,749 (65%) did not. Radiation was associated with similar rates of AEs overall with numerically higher hematologic toxicities and pneumonitis and numerically lower colitis, hepatitis and myocarditis (Table). Patients receiving RT were more likely to experience Grade 3-5 hematologic toxicities compared to those not receiving RT. Conclusions: To our knowledge, this is the largest report of AE risk associated with the use of radiation and ICIs. Our results show that the incidence of hematologic toxicity and pneumonitis in patients receiving RT may be slightly higher. Analysis to determine comparability of baseline demographic characteristics, comprehensive AE profile, and timing of RT is underway. [Table: see text]

Pain medication use in patients with HR+, HER2-neg advanced breast cancer treated with endocrine therapy and a CDK 4/6 inhibitor: A U.S. FDA pooled analysis

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Background: Pain medications (PMs) are commonly used to treat pain in patients (pts) with advanced/metastatic breast cancer (MBC). We examined PM usage patterns in pts receiving CDK 4/6 inhibitor (CDKI) based treatment. Methods: We pooled data from seven phase 3 randomized, controlled trials of CDKI + endocrine therapy in pts with hormone receptor positive, human epidermal growth factor receptor-2 negative MBC. PM were categorized as opioid (includes codeine-containing), NSAID, or other (i.e. bone-directed, antiepileptic, topical PMs). All analyzed pts received at least 1 dose of CDKI/placebo and had concomitant PM with a documented start date. Medications prescribed during hospitalizations were not included. We evaluated percent PM by demographic factors and pts with bone mets, and liver/lung mets. Results: 2416 pts met the inclusion criteria, of which 928 pts started a PM before the study and 1488 pts did not start PM before the study. Of the 1488 pts not on a PM before the study, 739 started a PM after study started, and 749 did not receive any PM at any time. Of the 739 pts who started a PM only after study start, overall, 59% were prescribed only an NSAID, 10% were prescribed only opioid, 17% were prescribed both an NSAID and opioid, and 14% were prescribed other PMs. The PM use by percent in demographic subgroups in the 1488 pts who took none or more PMs only after study start are presented in the table. Conclusions: To our knowledge, this is the first analysis of PM usage patterns in pts with MBC receiving CDKI or placebo with hormonal therapy on clinical trials. NSAID use was higher than opiates in all prespecified subgroups. Future analyses will examine the benefit of different classes of pain medications in treating symptoms of pain and whether there are differences between study treatment arms Percent PM Use by Class (Patients Who Took None or More PM Only After Study Start). [Table: see text]

Evaluation of the correlation between antibiotic use and survival in patients with recurrent or metastatic head and neck squamous cell carcinoma (R/M HNSCC) treated with immune checkpoint inhibitors (ICIs)

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Background: Recent evidence suggests that treatment with systemic antibiotics (Abx) disrupts the intestinal microbiome and may be associated with decreased survival for patients receiving treatment with ICIs for advanced cancers, including R/M HNSCC. However, a potential confounder is that Abx use identifies a subgroup of patients with a worse prognosis. The FDA examined the association between Abx use and survival for ICIs and other drugs used for the treatment of patients with R/M HNSCC. Methods: Data submitted to the FDA from three randomized controlled trials with ICI as a single agent or with chemotherapy (ICI group) compared to chemotherapy and/or cetuximab (Control group) were pooled. The association between systemic Abx use within 30 days of initiating anticancer therapy and survival for the ICI and Control groups was evaluated using Kaplan-Meier (KM) estimates and compared using Cox proportional hazards regression models, controlling for ECOG performance status, line of therapy, HPV status, PD-L1 expression, and other important prognostic factors. Results: In the ICI and Control groups, 36% and 46% of patients received Abx, respectively. For the ICI group, the difference in KM-estimated median overall survival (OS) was 5.6 months based on receipt of Abx (hazard ratio [HR] 1.70). Abx had no impact on OS for the Control group. Similar trends were observed for progression-free survival (PFS). Conclusions: In this exploratory analysis, systemic Abx within 30 days of initiating treatment for R/M HNSCC was associated with decreased survival for patients treated with ICIs compared with patients who did not receive Abx. Use of Abx had no apparent difference in survival in the control group. Further examination of the association between Abx use and clinical outcomes for patients with R/M HNSCC treated with ICIs is needed. [Table: see text]

Impact of timing of antibiotic use on clinical outcomes in patients with urothelial cancer treated with immune checkpoint inhibitors (ICIs)

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Background: Although recent evidence has suggested that patients who receive antibiotics (ABX) during the course of ICI treatment might decrease overall survival (OS) (1), our previous analysis did not support a difference in OS in urothelial cancer patients who did and did not use ABX during the course of ICI treatment without regard to timing (2). This updated analysis aims to addresses the question of timing; specifically, use of ABX in the 30-day window pre- or post- initiation of ICI treatment. Methods: We pooled data from 7 trials that led to drug approval and which included 1747 patients with advanced urothelial cancer treated with an ICI. Five trials enrolled patients who received prior platinum and 2 enrolled cisplatin-ineligible patients. Concomitant medication datasets were searched for systemic ABX use. The association between ABX use and survival was evaluated using Kaplan-Meier estimates and Cox proportional hazards regression models stratified by study. Results: Overall, 56% of patients were exposed to antibiotics (ABX+) and 43% were not exposed (ABX-). In an exploratory analysis, median OS was similar between arms: 9.7 vs. 9.3 months in ABX+ vs. ABX- patients, respectively (HR 0.96). However, OS results differed in the 27% of patients who were exposed to antibiotics in the 30-day window pre- or post- initiation of ICI treatment, for whom median OS was 4.7 months vs. 11.5 months in the ABX+ vs. ABX- patients, respectively (HR 1.8). This remained true after controlling for baseline risk prognostic factors (Bajorin and Bellmunt scores). Similar trends were observed for progression-free survival (PFS). Conclusions: Patients treated with ABX while on therapy with an ICI for urothelial cancer had similar OS outcomes to those not treated with ABX. However, in an exploratory analysis looking at ABX use in the 30-day window pre- or post-initiation of ICI treatment, OS appeared decreased in ABX+ vs ABX- patients. Our exploratory analyses appear to show an association of OS/PFS with timing of antibiotics. References: 1) Routy B, Science (2017) 2) Weinstock C, ASCO 2019, abstract. [Table: see text]

Patient-reported pain and pain medication impact in patients with HR+ Her2-neg advanced breast cancer: A U.S. FDA pooled analysis

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Background: Despite the ubiquitous prescribing of pain medications (PMs) in cancer clinical trials, the impact of such prescribing patterns and reporting on the experience of pain is not often investigated. We examined patient-reported pain before initiation of PM reporting and at the next available pain assessment. Our aim was to understand change in patient-reported pain. Methods: We pooled data from 7 phase 3 randomized, controlled, registration trials of CDKI with endocrine therapy in patients with hormone receptor positive, human epidermal growth factor receptor-2 negative MBC. We restricted our analyses to patients who started therapy with no PM reported and looked at patients who had NSAID or opioid medication documented. We calculated change between 2 assessments in patient-reported pain before and after PM using the pain occurrence item (Q9) on the EORTC Quality of Life questionnaire (QLQ-C30). Results: Of the 4200 patients who received at least 1 dose of CDKI/placebo, 1488 started with no documented PM, with 48% reporting none at all when asked about pain at baseline. Subsequently, 185 patients had documented NSAID and 43 an opioid and had a pain PRO assessment before and after. NSAIDs documentation occurred on average 11 weeks into trial and opioids 5. Before documentation of NSAIDs, 45% of patients reported no pain compared to 23% of patients with an opioid. Patients who had documented NSAIDs, 29% experienced an improvement in their self-reported pain, whereas 32% of patients with documented opioids improved. On average the time between the 2 pain assessments was around 58 days for both PMs. Conclusions: In this analysis in patients who had a pain assessment before and after documentation of a PM, there is a small group whose pain improved. It is important to note that patients’ response to the pain item was not provided to the clinical care team, which may explain why there may have been suboptimal pain control. Further study is needed to examine how pain management can be achieved in patients with advanced breast cancer. Future analysis should be performed with patients whose PRO pain results are communicated with the clinical care team in real-time. [Table: see text]

The Interdependent Activation of Son-of-Sevenless and Ras

The guanine-nucleotide exchange factor (GEF) Son-of-Sevenless (SOS) plays a critical role in metazoan signaling by converting Ras•GDP (guanosine diphosphate) to Ras•GTP (guanosine triphosphate) in response to tyrosine kinase activation. Structural studies have shown that SOS differs from other Ras-specific GEFs in that SOS is itself activated by Ras•GTP binding to an allosteric site, distal to the site of nucleotide exchange. The activation of SOS involves membrane recruitment and conformational changes, triggered by lipid binding, that open the allosteric binding site for Ras•GTP. This is in contrast to other Ras-specific GEFs, which are activated by second messengers that more directly affect the active site. Allosteric Ras•GTP binding stabilizes SOS at the membrane, where it can turn over other Ras molecules processively, leading to an ultrasensitive response that is distinct from that of other Ras-specific GEFs.

Deconstruction of the Ras switching cycle through saturation mutagenesis

Ras proteins are highly conserved signaling molecules that exhibit regulated, nucleotide-dependent switching between active and inactive states. The high conservation of Ras requires mechanistic explanation, especially given the general mutational tolerance of proteins. Here, we use deep mutational scanning, biochemical analysis and molecular simulations to understand constraints on Ras sequence. Ras exhibits global sensitivity to mutation when regulated by a GTPase activating protein and a nucleotide exchange factor. Removing the regulators shifts the distribution of mutational effects to be largely neutral, and reveals hotspots of activating mutations in residues that restrain Ras dynamics and promote the inactive state. Evolutionary analysis, combined with structural and mutational data, argue that Ras has co-evolved with its regulators in the vertebrate lineage. Overall, our results show that sequence conservation in Ras depends strongly on the biochemical network in which it operates, providing a framework for understanding the origin of global selection pressures on proteins.

Identification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition

Human LIN28A and LIN28B are RNA-binding proteins (RBPs) conserved in animals with important roles during development and stem cell reprogramming. We used Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) in HEK293 cells and identified a largely overlapping set of ∼3000 mRNAs at ∼9500 sites located in the 3' UTR and CDS. In vitro and in vivo, LIN28 preferentially bound single-stranded RNA containing a uridine-rich element and one or more flanking guanosines and appeared to be able to disrupt base-pairing to access these elements when embedded in predicted secondary structure. In HEK293 cells, LIN28 protein binding mildly stabilized target mRNAs and increased protein abundance. The top targets were its own mRNAs and those of other RBPs and cell cycle regulators. Alteration of LIN28 protein levels also negatively regulated the abundance of some but not all let-7 miRNA family members, indicating sequence-specific binding of let-7 precursors to LIN28 proteins and competition with cytoplasmic miRNA biogenesis factors.

Mass conservation and inference of metabolic networks from high-throughput mass spectrometry data

We present a step towards the metabolome-wide computational inference of cellular metabolic reaction networks from metabolic profiling data, such as mass spectrometry. The reconstruction is based on identification of irreducible statistical interactions among the metabolite activities using the ARACNE reverse-engineering algorithm and on constraining possible metabolic transformations to satisfy the conservation of mass. The resulting algorithms are validated on synthetic data from an abridged computational model of Escherichia coli metabolism. Precision rates upwards of 50% are routinely observed for identification of full metabolic reactions, and recalls upwards of 20% are also seen.