The risk of diarrhea and colitis in patients with lung cancer treated with immune checkpoint inhibitors: a systematic review and meta-analysis

Background

Immune checkpoint inhibitors (icis), including inhibitors of PD-1, PD-L1, and ctla-4, are relatively novel therapies for lung cancer, although their use might be limited by gastrointestinal toxicity. The aim of the present study was to determine the risk of diarrhea and colitis associated with icis in lung cancer and the rates of discontinuation because of those toxicities.

Methods

Electronic databases were searched for prospective trials reporting the risk of diarrhea and colitis in patients with lung cancer treated with PD-1, PD-L1, and ctla-4 inhibitors. The incidences of diarrhea and colitis and their grades were assessed clinically using standardized reporting criteria. Pooled incidence and weighted relative risk estimates for diarrhea and colitis with 95% confidence intervals (cis) were estimated using a random effects model. The incidence of discontinuations for gi toxicity was also calculated.

Results

Twenty-seven studies were included: sixteen studies with PD-1 inhibitors, nine studies with PD-L1 inhibitors, and four studies combining PD-based strategies with ctla-4 inhibitors. The incidence of all-grade diarrhea was 9.1% (95% ci: 7.8% to 10.5%) for anti-PD-1 therapy and 11.0% (95% ci: 7.5% to 14.5%) for anti-PD-L1 therapy. The incidence of all-grade colitis was 0.9% (95% ci: 0.4% to 1.3%) for anti-PD-1 therapy and 0.4% (95% ci: 0.0% to 0.8%) for anti-PD-L1 therapy. The relative risk for all-grade diarrhea was higher with combination anti-PD-1 and anti-ctla-4 than with anti-PD-1 monotherapy (relative risk: 1.61; 95% ci: 1.14 to 2.29). Anti-PD-1 therapy was discontinued in 4.1% of patients with diarrhea (95% ci: 0.7% to 7.4%) and in 35.7% of those with colitis (95% ci: 0.0% to 81.1%); combination therapy was discontinued in 10.1% of patients with diarrhea (95% ci: 4.8% to 15.4%) and in 39.9% of those with colitis (95% ci: 3.9% to 75.9%).

Conclusions

Diarrhea is a relatively frequently encountered gi toxicity when ici therapy is used in lung cancer treatment. Colitis is less frequently encountered, although when it does occur, it often results in therapy discontinuation.

Abstract 1334: A diagnostic platform for precision cancer therapy enabling composite biomarkers by combining tumor and immune features from an enhanced exome and transcriptome

There is an increasing need for more advanced, composite biomarkers that can model the complex systems biology driving response and resistance to cancer therapy. However, many cancer diagnostic platforms to date, with their focus on mutational changes in a relatively small panel of genes, provide limited data to support integrative, multidimensional biomarkers that can better predict immunotherapy response.

To enable the identification of composite biomarkers that combine tumor- and immune-related information from both DNA and RNA, we have developed ImmunoID NeXT, an enhanced exome/transcriptome-based diagnostic platform that can simultaneously profile the tumor and immune system from a single FFPE sample, across all of the approximately 20,000 genes. By co-optimizing assay and analytics design, we enable sensitive evaluation of clinically-relevant cancer biomarkers from >=25ng of co-extracted DNA/RNA, while also providing a broader evaluation of neoantigens, HLA typing and LOH, antigen processing machinery (APM), TCR/BCR repertoire, immune expression signatures, tumor-infiltrating lymphocytes (TILs), oncoviruses, and germline variants. Leveraging this expansive feature set, we developed methods that combine individual analytes to construct composite biomarker scores that correlate with immunotherapy response.

Validation of ImmunoID NeXT demonstrated high sensitivity and specificity to somatic and structural variants across ~20,000 genes at allelic fractions as low as 5%, with clinical diagnostic reporting on actionable mutations (SNVs, indels, CNAs, fusions) in 248 cancer-driver genes that have been boosted further for higher sensitivity, as well as reporting on TMB and MSI status. For neoantigen prediction, immuno-peptidomic data from monoallelic HLA-transfected cell lines were used to train neural networks to predict pMHC binding with higher precision than public tools. For TCRα/β analysis in FFPE tumor samples, strong correlation with targeted TCR kit results was shown (R^2>0.9 and >0.94). For TILs, we developed signatures for eight immune cell types, demonstrating concordance with orthogonal immunofluorescence methods. We achieved genotyping accuracy of 99.1% for HLA Class I, and 95% for HLA Class II, and have developed and verified the performance of a tool for HLA LOH detection. In a cohort of 55 late-stage melanoma patients, the integration of neoantigen burden, HLA LOH, and APM mutational data formed a composite neoantigen score that more accurately predicted response to checkpoint blockade than other markers such as TMB.

With ImmunoID NeXT, we have developed a broad diagnostic platform that can be leveraged for the development of advanced composite biomarkers (and novel resistance mechanisms) that combine both tumor and immune features from DNA and RNA; enabling more accurate stratification of patient response to immunotherapy. The platform has been validated and optimized for use with limited FFPE tissue samples, making it ideal for both research and clinical applications.

Citation Format: Robert Peter Power, Gabor Bartha, Jason Harris, Sean M. Boyle, Eric Levy, Pamela Milani, Prateek Tandon, Paul McNitt, Mandy Lee, Massimo Morra, Sejal Desai, Sebastian Salvidar, Michael J. Clark, Christian Haudenschild, Sekwon Jang, John West, Richard Chen. A diagnostic platform for precision cancer therapy enabling composite biomarkers by combining tumor and immune features from an enhanced exome and transcriptome [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1334.

Validation of an exome and transcriptome based diagnostic platform enabling clinical cancer therapy selection and emerging composite biomarkers for immunotherapy

e15583

Background: While immunotherapy has become a pillar of cancer treatment, diagnostic biomarkers that consistently predict patient response to these therapies have remained elusive. There is an increasing need for the development of integrative, composite biomarkers that can model the complex biology driving response and/or resistance to immunotherapy more effectively than existing single-analyte approaches. However, the majority of current cancer diagnostic panels, with their focus on a small set of genes, provide limited ability to support these emerging advanced biomarkers. Methods: To address these limitations, we developed and validated NeXT Dx, a comprehensive enhanced exome and transcriptome based diagnostic platform designed to simultaneously characterize tumor and immune genomics from a single limited FFPE sample. To achieve higher accuracy and sensitivity for an exome scale diagnostic platform, we developed an augmented exome assay that improves uniformity of coverage across all ~20,000 genes, including boosted coverage of 248 clinically-relevant cancer genes. We validated this assay using genomic DNA and RNA extracted from tumor-derived cell-lines, constructs, clinical FFPE samples, and proficiency testing samples. The assay utilizes > = 25ng of co-extracted DNA and RNA which were sequenced using Illumina NovaSeq instruments at our CAP-accredited, CLIA-certified laboratory. Additional assay enhancements for HLA, immune repertoire, and oncoviruses were designed to further optimize the platform for immunotherapy biomarker discovery applications. Results: Validation of NeXT Dx demonstrated a performance of 99.5% sensitivity and 99.8% positive predictive value (PPV) for SNVs with > = 5% AF; 98.7% sensitivity and 97.4% PPV for indels with > = 10% AF; 97.2% sensitivity and 94.6% PPV for CNAs in samples with > = 30% tumor content; 94.9% sensitivity and 94.9% PPV for fusions; and a 2.1% error rate for MSI classification. TMB was calculated using gold-standard whole exome data from SNVs and indels. Typical median coverage depth was > 1,000X for 248 clinically-relevant genes, ~300X for the remaining (whole exome) footprint. Conclusions: With NeXT Dx, we demonstrate a exome/transcriptome scale diagnostic platform that can detect current clinical biomarkers with high sensitivity as well as support emerging, advanced biomarkers that integrate across both tumor and immune features.

A245 IMPROVING KNOWLEDGE TRANSFER OF PREVENTATIVE CARE IN INFLAMMATORY BOWEL DISEASE USING ELECTRONIC LEARNING

Background

Inflammatory bowel disease (IBD) is a complex chronic disease and it is imperative that gastroenterologists are familiar with the unique needs of the IBD patient. An important part of management involves education surrounding the general health maintenance needs of this patient population, especially those on immunomodulator and biologic therapy or those being considered for such treatment. A recent study showed that Canadian GI trainees are uncomfortable managing preventative care in IBD including vaccinations and bone protection. Using educational videos for trainees to improve core knowledge of these concepts remains unclear.

Aims

Assess educational efficacy of a core training module on trainee confidence and knowledge on preventative care in IBD.

Methods

This study assessed a preventative care in IBD video used as an educational tool in the University of Toronto GI trainee program as part of the annual GI in-training objective structured clinical examination (OSCE). Prior to the OSCE, a randomly selected cohort of trainees were provided the preventative care video. The remaining trainees prepared for the OSCE as standard. At the OSCE, one station asked all trainees to address preventative care in IBD with a standardized patient. Following the OSCE, a standardized evaluation of trainee confidence and degree of knowledge on vaccination, cancer screening, bone health, and mental health in IBD patients was performed. These evaluations and OSCE score were then compared between both cohorts. Data was analyzed using a t-test and p<0.05 was considered significant.

Results

A total of 10 subjects took part in the study. 5 subjects were exposed to the video prior to the OSCE and 5 were not exposed. Overall total score for trainees who had seen the video prior to the OSCE had a mean score of 85.3% (38.4/45) compared to those who had not seen the video prior had a mean score of 65.3% (29.4/45) with a p = 0.03. Global score in those exposed to the video was 70% (3.5/5) compared to 48% (2.4/5) in the unexposed group with a p= 0.006. Upon assessment of individuals topics, there was a trend in improved knowledge of vaccination and mental health screening in those exposed vs. unexposed to the educational video (52.6% vs. 32.6%, and 80% vs. 20%, respectively). No significant difference was identified between groups with respect to cancer screening and bone health.

Conclusions

Our study shows evidence that use of educational videos was efficacious with respect to GI trainee confidence and knowledge surrounding key concepts in preventative care of IBD patients. This exposure allows for improved patient education and management and lead to better-quality patient care. Overall, this study identifies a knowledge gap in trainee education and highlights the need for development of training tools to improve overall management of this complex and dynamic disease.

Funding Agencies

CAGVideo was a CAG accredited educational material, and supported by an educational grant from the Canadian Association of Gastroenterology and Abbvie Canada

A220 A COMPREHENSIVE SYSTEMATIC REVIEW AND META-ANALYSIS OF THE RISK OF ADVERSE NEONATAL OUTCOME IN INFLAMMATORY BOWEL DISEASE AND PREGNANCY

Background

Inflammatory bowel disease (IBD) often affects women in their child-bearing years. These women may be at an increased risk of adverse neonatal outcomes.

Aims

The aim of this study was to evaluate the risk of these outcomes in this population of patients, with an emphasis of determining risk factors for development of these conditions.

Methods

Medline, Embase, and Cochrane library were searched through to May 2019 for studies reporting adverse neonatal outcomes in IBD patients. Weighted odds ratios (OR) with 95% confidence intervals (CI) were calculated to assess the risk of these outcomes in patients with IBD compared to healthy controls, with risk factors such as disease activity and medication exposure also being assessed.

Results

Sixty studies were included (8194 pregnancies with inflammatory bowel disease and 3253 healthy pregnancies). Compared to healthy controls, patients with inflammatory bowel disease were more likely to deliver infants with low birth weight (LBW) (OR 2.78, 95% CI 1.16–6.66) and infants who were admitted to the neonatal intensive care unit (NICU) (OR 3.33, 95% CI 1.83–6.05). Patients with Crohn’s disease had an increased risk of infants born with congenital anomalies (OR 3.03, 95% CI, 1.43–6.42), whereas patients with ulcerative colitis had an increased risk of preterm delivery (OR 2.68, 95% CI, 1.12–6.43). Active disease increased the risk of preterm birth (OR 2.06, 95% CI 1.21–3.51), LBW (OR 2.96, 95% CI 1.54–5.70), and small for gestation age (OR 2.62, 95% CI 1.18–5.83) compared to disease in remission. Tumor necrosis factor antagonists was associated with increased risk of NICU admission (OR 2.42, 95% CI 1.31–4.45) and LBW (OR 1.54, 95% CI, 1.01–2.35).

Conclusions

Patients with inflammatory bowel disease are at an increased risk of developing adverse neonatal outcomes such as preterm birth, LBW, congenital anomalies, and NICU admissions. Patients with clinically active disease and those exposed to anti-TNF therapy may be at higher risk of developing these adverse outcomes. The findings of this study are important to communicate to patients and healthcare providers alike. Furthermore, this information may help to mitigate these risks through collaborative specialized care during pregnancy in order to reduce the overall morbidity and mortality for both mother and baby.

Funding Agencies

None

A244 MATERNAL THIOPURINE AND ANTI-TUMOR NECROSIS FACTOR THERAPY DURING PREGNANCY IS ASSOCIATED WITH AN INCREASED RISK OF PLACENTAL-RELATED DISEASES

Background

Though previous studies have suggested that most therapies for inflammatory bowel disease (IBD) are safe during pregnancy, the effect of these medications on placental-related diseases remain unknown.

Aims

To determine the effect of gestational medication exposure on pregnancy-related outcomes in patients with IBD.

Methods

We retrospectively reviewed the University of Alberta and University of Toronto pregnancy databases to identify patients (age > 18) who underwent routine assessment by a gastroenterologist at least once during pregnancy (first trimester (T1), second trimester (T2), and third trimester (T3). Pregnancy-related outcomes (maternal, obstetrical, and neonatal) were recorded from obstetrical records. Low-birth weight (LBW) was defined as an infant weight < 2500g at birth. Pre-term delivery was defined as birth < 37 weeks gestation. Medication exposure, such as 5-aminosalicylates (5-ASA), thiopurines, steroids, and anti-tumor necrosis factor (TNF) therapy was recorded for each trimester. Categorical variables were statistically compared using the Chi-square (x2) test through the SPSS software.

Results

A total of 84 patients were included. Compared to those not exposed to thiopurines, patients exposed to thiopurine therapy during T2 had an increased risk of pre-term birth (26.7% vs. 7.7%, p=0.046) and pre-eclampsia (13.3% vs. 0%, p=0.008) and a trend towards an increased risk of placental abruption (6.7% vs, 0%, p=0.061). Furthermore, compared to those not treated with corticosteroids, those prescribed corticosteroid therapy during any trimester had an increased risk of pre-term birth (T1 exposure: 50% vs. 10.2%, p=0.024; T2 exposure: 37.5% vs. 8.5%. p=0.018; T3 exposure: 42.9% vs. 8.8%, p=0.008) and infants born with LBW (T1 exposure: 50.0% vs. 7.8%, p=0.009; T2 exposure: 37.5% vs. 8.2%, p=0.015; T3 exposure: 57.1% vs. 8.6%, p=0.0005). Those exposed to corticosteroids in T3 only had an increased risk of PPROM (60.0% vs. 7.5%, p=0.0003) and chorioamnionitis (14.3% vs. 0%, p=0.002). Finally, anti-TNF therapy in T2 was associated with an increased risk of pre-eclampsia (9.1% vs. 0%, p=0.040. 5-ASA therapy was not associated with an increased risk of any adverse pregnancy-related outcome. No medication increased the risk of other maternal (i.e. gestational diabetes, emergency Cesarean-section delivery) and neonatal (intensive care unit admission, congenital anomalies) outcomes.

Conclusions

Placental related diseases, such as pre-eclampsia, appear to be increased with maternal exposure to thiopurine and anti-TNF therapy during pregnancy. Larger studies are required to confirm these associations.

Funding Agencies

None

A250 SYSTEMATIC REVIEW WITH META-ANALYSIS: ADVERSE PREGNANCY-RELATED OUTCOMES WITH INFLAMMATORY BOWEL DISEASE

Background

Inflammatory bowel disease (IBD) is a chronic inflammatory condition. While it is reported that IBD may result in adverse pregnancy-related outcomes, its effects on placental related diseases are relatively not known.

Aims

The aim of our work was to determine the risk of adverse pregnancy outcomes in patients with IBD.

Methods

Medline, Embase, and Cochrane library were searched for studies that reported adverse maternal and obstetrical outcomes in patients with IBD. Weighted odds ratios (OR) with 95% confidence intervals (CI) were calculated for the risk of these outcomes in patients with IBD compared to healthy controls.

Results

Fifty-three studies were included (7917 patients with IBD and 3253 healthy controls). Cesarean delivery was more common in patients with IBD compared to healthy controls (OR 1.79, 95% CI, 1.16–2.77). This remained significant for UC (OR 1.80, 95% CI, 1.21–2.90) but not CD (OR 1.48, 95% CI, 0.94–2.34). Similarly, gestational diabetes occurred more commonly in IBD (OR 2.96, 95% CI, 1.47–5.98). Furthermore, the incidences of placental diseases were low, 2.0% (95% CI, 0.9–3.1%) for pre-eclampsia, 3.3% (95% CI, 0–7.2%) for placental abruption, 0.5% (95% CI, 0.2–0.9%) for placenta previa, and 0.3% (95% CI, 0–0.5%) for chorioamnionitis. Finally, patients with IBD were more likely to experience preterm premature rupture of membranes (PPROM, OR 12.10, 95% CI, 2.15–67.98), but not an early pregnancy loss (OR 1.63, 95% CI 0.49–5.43). Anti-tumour necrosis factor therapy was not associated with chorioamnionitis (OR 1.12, 95% CI, 0.16–7.67), early pregnancy loss (OR 1.49, 95% CI, 0.83- 2.64), and placenta previa (OR 1.58, 95% CI, 0.30–8.47).

Conclusions

Patients with IBD are more likely to develop adverse pregnancy-related outcomes such as Gestational Diabetes and PPROM. Pregnancy in patients with IBD should be considered a high-risk period and as such, a multi-disciplinary team, including gastroenterologists, obstetricians and maternal-fetal medicine specialists, is necessary to recognize and effectively manage adverse obstetrical outcomes in order to reduce overall morbidity and mortality.

Funding Agencies

None

A162 THE UTILITY OF FECAL CALPROTECTIN IN PREDICTING SEVERITY OF CLOSTRIDIUM DIFFICILE INFECTION: A SYSTEMATIC REVIEW

Background

Clostridium difficile is an anaerobic, spore-forming, gram-positive bacillus, and a leading cause of infectious diarrhea in hospitalized patients. It is associated with high mortality and morbidity, and places an enormous burden on the healthcare system. Symptoms and severity of CDI vary widely, from illness that resolves with antibiotics, to toxic megacolon, colectomy, and death. The ability to risk-stratify patients to predict severe versus non-severe outcomes at baseline would be clinically useful. The role of fecal calprotectin in predicting severity of CDI has not been well established.

Aims

To perform a systematic review of the literature on the ability of fecal calprotectin to predict disease severity in patients with CDI.

Methods

PubMed, OVID (EMBASE/MedLine) and Cochrane Library databases were searched up until October 2, 2019. Publications of pediatric populations, Inflammatory Bowel diseases, and those only published as abstracts were excluded.

Results

130 non-duplicate citations were screened; after title/abstract screening, and full-text review, 7 articles were included for analysis. Articles were from 2014 onwards, and varied from 29 to 232 patients/samples analyzed; 832 patients in total were analyzed. Three studies were conducted in the USA, two in Europe, one in Israel and in South Korea. Four studies were prospective, and the remaining three were retrospective cohort studies. There was significant heterogeneity between studies with respect to population size, age (when reported), fecal calprotectin assay and cutoff used, method of diagnosis of CDI, and criteria for defining disease severity. There was wide variation in median fecal calprotectin levels between studies. Four studies demonstrated a statistically significant difference of fecal calprotectin according to disease severity, and three did not, of which two of these demonstrated an overall predictive trend with fecal calprotectin.

Conclusions

It is unclear whether fecal calprotectin is predictive of severity of CDI in adult patients without IBD. In the existing literature, there seems to be a statistically significant association or trend towards association in most studies, but due to heterogeneity of methods, assays, cutoffs and populations, the data within these studies cannot be pooled in meta-analysis. Further high-powered, well-designed studies are required to clarify this important clinical question.

Funding Agencies

None

Abstract A051: A comprehensive, highly accurate genomics platform for precision immunotherapy: Simultaneously characterize tumors and the TME from a single FFPE sample

Immunogenomic profiling of the tumor and the tumor microenvironment (TME) is critical for identifying new biomarkers of immunotherapy response, understanding resistance, and enabling the development of personalized immunotherapies. However, running a comprehensive array of biomarker assays for each patient sample is often impractical given limited sample quantity, processing complexity, and prohibitive cost. To address these challenges, we developed a novel, augmented exome and transcriptome-based platform that simultaneously characterizes the tumor and TME from a single FFPE sample. We co-optimized the design of our sequencing assays and analytics to increase performance for the detection of somatic SNVs, indels, CNAs, and fusions across ~20,000 genes, as well as the evaluation of neoantigens, expression signatures, HLA typing and LOH, TCR/BCR repertoires, oncoviruses, tumor-infiltrating lymphocytes (TILs), clinically-actionable mutations, tumor mutational burden (TMB), and MSI status. We developed novel methods to sequence difficult regions of the exome and to extend coverage to key immunogenomic biomarkers. Analytic pipelines were designed to utilize assay optimizations to achieve higher accuracy than with other platforms. We then validated the platform for diagnostic and therapeutic use. With as little as 50ng of DNA per FFPE sample and co-extracted RNA, this platform completely covers between 17% to 40% more genes compared to a non-augmented exome, thus increasing sensitivity to somatic mutations and putative neoantigens. For neoantigen performance, we generated immune-peptidomic data from mono-allelic HLA transfected cell-lines and trained neural networks to predict neoepitope binding to MHC, demonstrating a higher precision (0.88) across alleles than publicly available tools (<0.7). For TCR alpha and beta clonotype profiling in tumor samples, we demonstrate strong correlation with the results from a targeted TCR kit (R2>0.9 and >0.94, respectively). For TILs, we developed signatures for CD4, CD8 T-cells, and other immune cells, demonstrating concordance with synthetic and CyTOF-derived validation sets. For HLA typing, we achieve an accuracy of 99.1% for HLA Class I, and 95% for HLA Class II typing calls, and have developed a novel tool for HLA LOH detection. We demonstrate sensitive detection of HPV, EBV, HCV, HTLV, and KSHV in known samples, and accurate MSI and TMB assessment. Finally, for diagnostic reporting, we achieve high sensitivity and specificity for clinically-reportable mutations comparable with diagnostic cancer panels. With this platform, we have developed a novel immunogenomics platform that can characterize both the tumor and TME from a single sample. By co-optimizing our assay and analytics for immuno-oncology, we enhance biomarker sensitivity compared to non-optimized genomics assays. Validation of the platform extends its use to diagnostics and personalized immunotherapy development.

Citation Format: Robert Power, Gabor Bartha, Jason Harris, Sean Michael Boyle, Eric Levy, Pamela Milani, Prateek Tandon, Robin Li, Manjula Chinnappa, Paul McNitt, Rena McClory, Massimo Morra, Sebastian Saldivar, Michael Clark, Christian Haudenschild, Erin Newburn, Christelle Johnson, John West. A comprehensive, highly accurate genomics platform for precision immunotherapy: Simultaneously characterize tumors and the TME from a single FFPE sample [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr A051. doi:10.1158/1535-7163.TARG-19-A051

Paternally inherited cis-regulatory structural variants are associated with autism

The genetic basis of autism spectrum disorder (ASD) is known to consist of contributions from de novo mutations in variant-intolerant genes. We hypothesize that rare inherited structural variants in cis-regulatory elements (CRE-SVs) of these genes also contribute to ASD. We investigated this by assessing the evidence for natural selection and transmission distortion of CRE-SVs in whole genomes of 9274 subjects from 2600 families affected by ASD. In a discovery cohort of 829 families, structural variants were depleted within promoters and untranslated regions, and paternally inherited CRE-SVs were preferentially transmitted to affected offspring and not to their unaffected siblings. The association of paternal CRE-SVs was replicated in an independent sample of 1771 families. Our results suggest that rare inherited noncoding variants predispose children to ASD, with differing contributions from each parent.