Evidence blocks for effective presentation of genomic findings at molecular tumor boards: Single institution experience

Genomic profiling, or molecular profiling of the tumor, is becoming a key component of therapeutic decision making in clinical oncology, and is typically carried out via next generation sequencing. However, the interpretation of the results and evaluation of rationale for targeting the uncovered alterations is challenging and requires a deep understanding of cancer biology, genetics, genomics and oncology. Multidisciplinary molecular tumor boards represent a promising strategy in the facilitation of molecularly-informed therapeutic decisions, and usually consist of specialists with various fields of expertise. To effectively communicate the biological and clinical significance of genomic findings, as well as to make molecular tumor board discussions more productive, we developed and implemented evidence blocks into case discussions in our center. We found that this approach facilitated clinicians' understanding of the results of genomic profiling, and resulted in shorter yet more efficient case discussions within the molecular tumor board. Here, we discuss our experience with evidence blocks and how their implementation influenced the molecular tumor board practice.

Impact of the STK11/KRAS co-mutation on the response to immunotherapy in a real-world pan-cancer cohort

INTRODUCTION

Immune checkpoint inhibitors are highly effective in treating various cancers. We analyzed the significance of the KRAS/STK11 co-mutation in relation to the efficacy of immune checkpoint inhibitors in pan-cancer patient cohort.

METHODS

We analyzed data from open-access research: MSK-IMPACT (molecular profiling data from patients receiving systemic antitumor therapy) and MSK-TMB (molecular profiling data from patients receiving immune checkpoint inhibitors). In both studies, high throughput sequencing was used for molecular profiling.

RESULTS

A total of 10,336 patients receiving antitumor therapy (MSK-IMPACT study) and 1661 patients receiving immune checkpoint inhibitors (MSK-TMB study) were included in the analysis. Co-mutation STK11/KRAS was found in 156 (1.5%) and 46 (2.8%) patients in the two studies, respectively. Most patients with the STK11/KRAS co-mutation had non-small cell lung cancer (83% and 85% in the two studies, respectively). Among non-small cell lung cancer patients, the STK11 mutation was associated with a worse outcome for patients receiving systemic antitumor therapy, but not immune checkpoint inhibition therapy (HR for OS 1.90 [95% CI 1.36-2.65] and 1.44 [95% CI 0.88-2.37]). Co-mutation STK11/KRAS was also not associated with patient outcome in any of the studies (HR for OS 0.93 [95% CI 0.56-1.52] and 1.09 [95% CI 0.54-2.19]). High tumor mutational burden was associated with better outcome in the cohort of patients receiving immune checkpoint inhibitors. An analogous analysis among patients in the pan-cancer cohort (excluding patients with non-small cell lung cancer) showed STK11 mutations and high tumor mutational burden have a predictive role for the efficacy of immune checkpoint inhibitors, but not STK11/KRAS co-mutation.

CONCLUSIONS

Co-mutation STK11/KRAS is common among patients with non-small cell lung cancer and is not an independent predictive marker for the efficacy of immune checkpoint inhibitors. Further studies are required to clarify the role of STK11 mutations in immune checkpoint inhibitor treatment response.

Prognostic and predictive role of immune microenvironment in colorectal cancer

Colorectal cancer (CRC) represents a molecularly heterogeneous disease and one of the most frequent causes of cancer-related death worldwide. The traditional classification of CRC is based on pathomorphological and molecular characteristics of tumor cells (mucinous, ring-cell carcinomas, etc.), analysis of mechanisms of carcinogenesis involved (chromosomal instability, microsatellite instability, CpG island methylator phenotype) and mutational statuses of commonly altered genes (KRAS, NRAS, BRAF, APC, etc.), as well as expression signatures (CMS 1-4). It is also suggested that the tumor microenvironment is a key player in tumor progression and metastasis in CRC. According to the latest data, the immune microenvironment can also be predictive of the response to immune checkpoint inhibitors. In this review, we highlight how the immune environment influences CRC prognosis and sensitivity to systemic therapy.

Case Report: Progressive disease of BRCA2-mutant colon adenocarcinoma following talazoparib therapy

Colorectal cancer (CRC) is currently one of the most common tumor types diagnosed worldwide. In the early stages, the disease responds well to surgical and chemotherapeutic treatment, but in the later stages when therapeutic options are exhausted, comprehensive genomic profiling can guide further treatment decisions. We present the case of a 46-year-old man of Ashkenazi Jewish ancestry who was diagnosed with KRAS-mutated metastatic colorectal cancer. After surgery and progression on standard FOLFOX/FOLFIRI + bevacizumab therapy, as well as on Trifluridine/Tipiracil, comprehensive genomic profiling was performed with the hope of expanding therapeutic options. Following comprehensive tumor molecular profiling via NGS, a discussion of the case was discussed at the local molecular tumor board in order to determine further treatment strategy. An activating variant of KRAS and PIK3CA, FLT3 and SRC amplification and damaging TP53 and APC variants were discarded by MTB as potential targetable biomarkers. The BRCA2 p.S1415fs*4 founder frameshift variant was of interest and the patient was included in the clinical trial investigating the efficacy of a PARP inhibitor talazoparib. Unfortunately, the disease progression was detected within one month of talazoparib treatment and the patient died during the 8th cycle of FOLFIRI + bevacizumab therapy rechallenge.

Utility of public knowledge bases for the interpretation of comprehensive tumor molecular profiling results

With the growing use of comprehensive tumor molecular profiling (CTMP), the therapeutic landscape of cancer is rapidly evolving. NGS produces large amounts of genomic data requiring complex analysis and subsequent interpretation. We sought to determine the utility of publicly available knowledge bases (KB) for the interpretation of the cancer mutational profile in clinical practice. Analysis was performed across patients who previously underwent CTMP. Independent interpretation of the CTMP was performed manually, and then, the recommendations were compared to ones present in KBs (OncoKB, CIViC, CGI, CGA, VICC, MolecularMatch). A total of 222 CTMP reports from 222 patients with 932 genomic alterations (GA) were identified. For 368 targetable GA identified in 171 (77%) of the patients, 1381 therapy recommendations were compiled. Except for CGA, therapy ESCAT LOE I, II, IIIA and IIIB therapy options were equally represented in the majority of KB. Personalized treatment options with ESCAT LOE I-II were provided for 35 patients (16%); MolecularMatch/CIViC allowed to collect ESCAT I-II treatment options for 34 of them (97%), OncoKB/CGI-for 33 of them (94%). Employing VICC and CGA 6 (17%) and 20 (57%) of patients were left without ESCAT I or II treatment options. For 88 patients with ESCAT level III-B therapy recommendations: only 2 (2%), 3 (3%), 4 (5%) and 6 (7%) of patients were left without options with CIViC, MolecularMatch, CGI and OncoKB, and with VICC-12 (14%). Highest overlap ratio was observed for IIIA (0.81) biomarkers, with the comparable results for LOE I-II. Meanwhile, overlap ratio for ESCAT LOE IV was 0.22. Public KBs provide substantial information on ESCAT-I/R1 biomarkers, but the information on ESCAT II-IV and resistance biomarkers is underrepresented. Manual curation should be considered the gold standard for the CTMP interpretation.

Precision oncology strategy in cetuximab-resistant ERRFI1-mutant colon cancer: case report of disease progression on afatinib

Despite the existence of effective first and second line therapy options for patients with colorectal cancer, heavily treated patients have limited additional therapies. Genomic profiling is a promising tool for guiding subsequent treatment selection. Here, we describe the results of treating a colorectal cancer patient with molecularly-matched therapy based on the results of genomic profiling. The patient received a combination of afatinib and bevacizumab due to the presence of ERRFI1 variant. To our knowledge, this is the first report on the effect of EGFR inhibitors in patients with ERRFI1-altered RAS/BRAF wild-type colorectal adenocarcinoma.

Microsatellite Instability: A Review of Molecular Epidemiology and Implications for Immune Checkpoint Inhibitor Therapy

Microsatellite instability (MSI) is one of the most important molecular characteristics of a tumor, which occurs among various tumor types. In this review article, we examine the molecular characteristics of MSI tumors, both sporadic and Lynch-associated. We also overview the risks of developing hereditary forms of cancer and potential mechanisms of tumor development in patients with Lynch syndrome. Additionally, we summarize the results of major clinical studies on the efficacy of immune checkpoint inhibitors for MSI tumors and discuss the predictive role of MSI in the context of chemotherapy and checkpoint inhibitors. Finally, we briefly discuss some of the underlying mechanisms causing therapy resistance in patients treated with immune checkpoint inhibitors.

Importance of critical evaluation of genomic findings reported following comprehensive tumor molecular profiling (CTMP) for discussion within molecular tumor boards (MTB)

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Background: As precision oncology evolves, a growing number of physicians refer cancer patients for CTMP. Oftentimes, CTMP cannot be performed at local centers and patients turn to third-party facilities or commercial solutions. CTMP findings summarized in molecular profiling reports are used by physicians as a basis for MTB. Methods: A molecular tumor board was developed at our cancer center for patients who had undergone CTMP via NGS. Before each MTB, experts in cancer biology and bioinformatics performed reported alteration annotation, interpretation and critical evidence evaluation for each patient, not taking into account the recommendations provided in the original CTMP reports. Results: In total, 29 patients with various tumor types (31% CRC, 25% NSCLC, 10% SOC, 8% Breast; 26% other) who had undergone CTMP in a third-party for-profit organization (2 international, 4 Russian based organizations) were evaluated for discussion at MTB. In 4 CTMP reports therapy recommendations were compiled at odds with principles of evidence-based medicine and did not contain information on detected molecular alteration and, thus, these patients were not discussed within MTB. In 48% (12/25) of reports discussed within MTB, ranking of genomic findings based on potential clinical evidence and actionability was not provided. 24% (6/25) of the reports did not comply with the ASCO recommendations on genomic findings reporting in oncology. In 8 (32%) reports, only drug classes and not specific drugs were recommended. A total of 362 alterations were identified in 25 CTMP reports. Of those, 93 (26%) were not annotated according to the well-established HGVS nomenclature of sequence variants. Out of these 93, 32 (34%) could not be further identified using various genomic tools. Following our interpretation of the reported variants, 16 (4.4%) of the reported variants were found to be benign and, in fact, well-established population polymorphisms (gnomAD MAF > 1%). Only in 40% (10/25) of the reports, genomic alterations were classified based on their origin (somatic/likely germline). For 10 patients, 18 additional therapy options were recommended. Finally, 3-4 hours of preparatory work was required in order to reevaluate the reported findings following CTMP. Conclusions: As tumor molecular profiling becomes a more available tool for precision oncology, the number of patients requiring treatment strategy correction increases. Specific treatment plans can be set up following a discussion within a multidisciplinary team at MTB. Due to the lack of standardization of molecular profiling reporting, thorough preparatory work by experts trained in cancer biology is required before each MTB. Such preliminary work ensures time efficient discussion at MTB, requiring no more than 15 minutes of the physician’s time.

Utility of public Knowledge Bases (KB) for comprehensive tumor molecular profiling (CTMP) result interpretation

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Background: With the spread of CTMP in cancer patient management and expansion of molecular-targeted treatment opportunities, resources for quick and efficient molecular profile interpretation are in high demand. Number of public KBs have been introduced. We analysed their utility to compile per patient treatment recommendations. Methods: Analysis was performed across patients, who underwent CTMP. Based on the reported molecular alterations, interpretation and critical evidence evaluation was performed not taking into account the recommendations provided in the original CTMP reports. Therapy recommendations were ranked according to ESCAT. Resistance biomarkers were ranked according to OncoKB V2 level of evidence system. OncoKB, CIViC, CGI, CGA, VICC and MolecularMatch were assessed. KBs were assessed through API or local copy of KB. Results: A total of 222 CTMP reports from 222 patients (35% - NSCLC; 24% - CRC; 8% - pancreas; 7% - breast; 4% - gastric; 22% - other) were analysed. CTMP was performed in Foundation Medicine (82%) or Atlas Oncology Diagnostics (18%). Across 222 patients 932 molecular alterations were identified. A total of 1394 therapy recommendations were compiled associated with 368 molecular alteration across 171 (77%) patients (112 recommendations ESCAT level I; 908 - ESCAT III-IV; 70 - OncoKB R1). Across 181 ESCAT-I/R1 therapy recommendations 172 (95%) were present in at least 1 KB (92% for ESCAT-I recommendations, 100% - R1) with the VICC providing the highest rate of retrieval (80%), followed by OncoKB (78%), MolecularMatch (70%), CIViC - (69%) and CGI (69%). Only 92 (53%) of ESCAT-I/R1 therapy recommendations were present in all KBs. Across 27 patients with ESCAT-I recommendations, at least 1 therapy recommendation was retrieved in any KB for all patients. ESCAT II-IV therapy recommendations were provided for 161 patients and grouped by drug class, resulting in 457 [biomarker]-[drug class] associations. Of them 346 (75%) were present in at least 1 KB with the VICC providing the highest rate of retrieval (69%), followed by CGI (61%), CGA (56%), OncoKB (48%), CIViC (48%) and MolecularMatch (45%). Of 161 patients, for 24 (15%) no recommendations were retrieved in any KB for any biomarker identified. For random 15 (a total of 68 molecular alterations) patients KBs were assessed manually in order to estimate the average time in use. CGI was the most easily accessible (3.2 min per patient in average), following by CGA (5.6 min), OncoKB (7.2 min), CIViC (26.2 min), and VICC (35.9 min). Conclusions: Public KBs provide substantial information on ESCAT-I/R1 biomarkers and decent information on ESCAT II-IV biomarkers, reasoning manual curation. VICC provided the most complete information, though was thorough for manual use. The use of multiple KBs may significantly improve retrieval results, though is time-consuming and results in excess of misleading/outdated recommendations.

Incidental germline findings during molecular profiling of tumor tissues for precision oncology: molecular survey and methodological obstacles

Background

A fraction of patients referred for complex molecular profiling of biopsied tumors may harbor germline variants in genes associated with the development of hereditary cancer syndromes (HCS). Neither the bioinformatic analysis nor the reporting of such incidental germline findings are standardized.

Methods

Data from Next-Generation Sequencing (NGS) of biopsied tumor samples referred for complex molecular profiling were analyzed for germline variants in HCS-associated genes. Analysis of variant origin was performed employing bioinformatic algorithms followed by manual curation. When possible, the origin of the variant was validated by Sanger sequencing of the sample of normal tissue. The variants’ pathogenicity was assessed according to ACMG/AMP.

Results

Tumors were sampled from 183 patients (Males: 75 [41.0%]; Females: 108 [59.0%]; mean [SD] age, 57.7 [13.3] years) and analysed by targeted NGS. The most common tumor types were colorectal (19%), pancreatic (13%), and lung cancer (10%). A total of 56 sequence variants in genes associated with HCS were detected in 40 patients. Of them, 17 variants found in 14 patients were predicted to be of germline origin, with 6 variants interpreted as pathogenic (PV) or likely pathogenic (LPV), and 9 as variants of uncertain significance (VUS). For the 41 out of 42 (97%) missense variants in HCS-associated genes, the results of computational prediction of variant origin were concordant with that of experimental examination. We estimate that Sanger sequencing of a sample of normal tissue would be required for ~ 1–7% of the total assessed cases with PV or LPV, when necessity to follow with genetic counselling referral in ~ 2–15% of total assessed cases (PV, LPV or VUS found in HCS genes).

Conclusion

Incidental findings of pathogenic germline variants are common in data from cancer patients referred for complex molecular profiling. We propose an algorithm for the management of patients with newly detected variants in genes associated with HCS.

Long-term post-discharge coagulation abnormalities in patients with moderate to severe COVID-19

Introduction

Coagulopathy plays a significant role in COVID-19 pathogenesis. Benefit from anticoagulation is well established in hospitalized patients. But since there is a lack of data on coagulopathy resolution: there is no consensus in guidelines if extended anticoagulation is required.

Purpose

The purpose of our work was to analyze coagulation abnormalities at 2 to 5 months after moderate to severe COVID-19.

Methods

COVID-19 reconvalescents (CR), discharged from our hospital, were called for follow-up at 2–3 (CR1 group, 21 patients) or 5–6 (CR2 group, 26 patients) months after discharge. All CR were not on the anticoagulation therapy by that time. In addition to clinical examination and standard lab tests, we performed an FMD-test to analyze endothelial function, impedance aggregometry to analyze platelet aggregation, and a thrombodynamics test to assess thrombogenesis and fibrinolysis. The control group was recruited before the pandemic started.

Results

All CR were free from thrombotic complications after discharge from the hospital.

Endothelial function was not significantly impaired in CR compared with control, and was still in the normal range (7,07, IQR (3,36; 11,56) vs. 7,87 (5,42; 13,45)).

Platelet aggregation was significantly lower in CR1 than in the control group in ADP-induced mode (37, IQR (19; 47) vs. 46, IQR (41; 50), p=0,02) and didn't differ in other groups and other modes (Asa, TRAP-induced).

Thrombodynamics tests revealed suppression of the clot formation process in both CR1 and CR2 compared with control. There were decreased clot growth rates (μm/min) (CR1/CR2: 27,1, IQR (26,1; 29,2)/27,6, IQR (26,4; 30,0) vs. 32,2, IQR (30,0; 35,1), both p<0,001); decreased clot size (μm) (CR1/CR2: 1099, IQR (1069; 1194)/1199, IQR (1058; 1221) vs. 1304, IQR (1164; 1380), both p<0,001), and decreased optical density (arb units) (CR1/CR2: 21'607, IQR (20'363; 24'545)/22'741, IQR (21'344; 25'961) vs. 26'556, IQR (24'672; 29'387, p<0,001 and p=0,09 respectively.

Fibrinolysis was enhanced in CR groups compared with control (lysis progression was significantly higher for CR2 only, CR1/CR2: 2,9, IQR (2,5; 3,8)/3,8, IQR (2,6; 5,4) vs. 2,5, IQR (1,1; 3,4) %/min, p=0,087 and p=0,007 respectively; expected clot lysis time was shorter in both CR1 and CR2: 36,5, IQR (29,8; 44,2)/31,7, IQR (24,3; 42,7) vs. 65,9. IQR (36,3; 95,5) min, p=0,019 and p=0,016 respectively).

There was no statistical difference in clot formation and in fibrinolysis between CR1 and CR2.

Conclusion

In the deferred period (2–5 months) of COVID-19 the fibrinolysis process remains still active whereas the process of clot formation is mostly suppressed. Endothelial function assessed via the FMD test is within the normal range in the post COVID period.

FUNDunding Acknowledgement

Type of funding sources: None.

Impact of hypoxia on immune cells in human atherosclerotic plaques

Background

Inflammation plays a major role in atherosclerotic plaques' progression and was shown to be associated with the formation of hypoxic areas within the plaques. However, the data about the impact of hypoxia on atherosclerosis are contradictory, in part due to inadequacy of in vitro and animal models to reproduce faithfully the complexity of human atherosclerotic plaques.

Purpose

The aim of this study was to investigate the effect of hypoxia on immune status in the ex vivo system of human atherosclerotic plaques.

Methods

We collected 25 atherosclerotic plaques from patients undergoing carotid endarterectomy, cut plaques into ring-shaped slices and cultured them for 24 hours at the liquid/air interface on collagen sponges under hypoxic (2% O2) and normoxic (12% O2) conditions. After 24 hours we evaluated T-cell activation status within plaques according to the presence of membrane activation markers by means of multiparametric flow cytometry and the activity of cytokine production using xMAP technology.

Results

We found that CD8 T cells from human atherosclerotic plaques cultured under hypoxic conditions compared to normoxic conditions have a decreased expression of CD69 activation marker (42.7 [34.3; 50.9]% vs 53.8 [33.3; 63.3]%, n=10, p=0.047) and lower level of CD69 and HLA-DR coexpression (16.0 [10.5; 22.3] vs 22.6 [11.3; 28.2], n=10, p=0.02). CD4 T cells did not show any significant changes in expression of activation markers under hypoxia. Hypoxic conditions also resulted in a reduced IL-10 production (104.2 [53.8; 170.9] vs 235.2 [158.5; 335.3] pg/100 mg of tissue, n=20, p=0.0001) and increased VEGF production (116.1 [79.8; 253.5] vs 89.9 [71.1; 148.8] pg/100 mg of tissue, n=20, p=0.033).

Conclusions

Our results indicate that hypoxia causes a decrease in the activity of cytotoxic T cells and increases stimuli for angiogenesis within the human atherosclerotic plaques. The established ex vivo model of human atherosclerotic plaques culture under hypoxia enables further studies of the hypoxia impact on atherosclerosis.

Funding Acknowledgement

Type of funding source: Foundation. Main funding source(s): Russian Science Foundation grant

Longitudinal relationships among depressive symptoms, cortisol, and brain atrophy in the neocortex and the hippocampus

OBJECTIVE

Depression is associated with accelerated aging and age-related diseases. However, mechanisms underlying this relationship remain unclear. The aim of this study was to longitudinally assess the link between depressive symptoms, brain atrophy, and cortisol levels.

METHOD

Participants from the Betula prospective cohort study (mean age = 59 years, SD = 13.4 years) underwent clinical, neuropsychological and brain 3T MRI assessments at baseline and a 4-year follow-up. Cortisol levels were measured at baseline in four saliva samples. Cortical and hippocampal atrophy rates were estimated and compared between participants with and without depressive symptoms (n = 81) and correlated with cortisol levels (n = 49).

RESULTS

Atrophy in the left superior frontal gyrus and right lingual gyrus developed in parallel with depressive symptoms, and in the left temporal pole, superior temporal cortex, and supramarginal cortex after the onset of depressive symptom. Depression-related atrophy was significantly associated with elevated cortisol levels. Elevated cortisol levels were also associated with widespread prefrontal, parietal, lateral, and medial temporal atrophy.

CONCLUSION

Depressive symptoms and elevated cortisol levels are associated with atrophy of the prefrontal and limbic areas of the brain.