Gene Fusions In Patients Research Articles

Detection of rare and novel gene fusions in patients with diffuse glioma: An institutional retrospective study.

Detection of rare and novel gene fusions in patients with diffuse glioma: An institutional retrospective study.

Frequency of EGFR mutation and EML4-ALK fusion genes in patients with non-small cell lung carcinoma

Lung cancer ranks among the top causes of mortality worldwide. Non-small cell lung cancer (NSCLC) accounts for the majority of cases. Advances in genomics have identified potential biomarkers to predict therapeutic strategies in lung cancer. Despite the availability of targeted drugs such as tyrosine kinase inhibitors, a substantial proportion of patients still experience problems such as drug resistance. Mutations in genes like epidermal growth factor receptor (EGFR) and EML4ALK have already been established with altered clinical outcomes in NSCLC patients. With a focus on non-small cell lung cancer (NSCLC),the study was conducted at indraprastha apollo hospital in new delhi. With their informed agreement, 90 patients who were admitted between january 2012 and december 2015 and who had been diagnosed with fine-needle aspiration cytology (FNAC)/biopsy utilizing computed tomography (CT) guidance were included in the study. Excluded from the study were those receiving radiation therapy or chemotherapy concurrently. Information on age, gender, a thorough medical history, a history of smoking, and any additional co-morbidities were taken from medical records. Investigation of EGFR mutation and EML4-ALK gene fusion in NSCLC patients was done. Eleven (11% ) were positive and (89%) were negative for EGFR mutations. The positive cases were analyzed for exon 19 deletion and exon 21 (L858R) substitution and found positive for (60%) and (40%) of cases, respectively. Amongst 90 EGFR-negative patients, 4 (4.4%) had the EML4-ALK fusion gene, while 86 (95.5%) were negative for EML4-ALK. This study’s EML4-ALK fusion gene incidence was only (4%). Females have a higher occurrence of EGFR mutations than males (p=0.003) and the frequency of EGFR mutation was higher in non-smokers. The overall incidence of the EML4-ALK fusion gene was (4.44%) and was higher in patients below 60 years of age.

The landscape of cancer-associated transcript fusions in adult brain tumors: a longitudinal assessment in 140 patients with cerebral gliomas and brain metastases.

Oncogenic fusions of neurotrophic receptor tyrosine kinase NTRK1, NTRK2, or NTRK3 genes have been found in different types of solid tumors. The treatment of patients with TRK fusion cancer with a first-generation TRK inhibitor (such as larotrectinib or entrectinib) is associated with high response rates (>75%), regardless of tumor histology and presence of metastases. Due to the efficacy of TRK inhibitor therapy of larotrectinib and entrectinib, it is clinically important to identify patients accurately and efficiently with TRK fusion cancer. In this retrospective study, we provide unique data on the incidence of oncogenic NTRK gene fusions in patients with brain metastases (BM) and gliomas. 140 samples fixed and paraffin-embedded tissue (FFPE) of adult patients (59 of gliomas [17 of WHO grade II, 20 of WHO grade III and 22 glioblastomas] and 81 of brain metastasis (BM) of different primary tumors) are analyzed. Identification of NTRK gene fusions is performed using next-generation sequencing (NGS) technology using Focus RNA assay kit (Thermo Fisher Scientific). We identified an ETV6 (5)::NTRK3 (15) fusion event using targeted next-generation sequencing (NGS) in one of 59 glioma patient with oligodendroglioma-grade II, IDH-mutated and 1p19q co-deleted at incidence of 1.69%. Five additional patients harboring TMPRSS (2)::ERG (4) were identified in pancreatic carcinoma brain metastasis (BM), prostatic carcinoma BM, endometrium BM and oligodendroglioma (grade II), IDH-mutated and 1p19q co-deleted. A FGFR3 (17)::TACC3 (11) fusion was identified in one carcinoma breast BM. Aberrant splicing to produce EGFR exons 2-7 skipping mRNA, and MET exon 14 skipping mRNA were identified in glioblastoma and pancreas carcinoma BM, respectively. This study provides data on the incidence of NTRK gene fusions in brain tumors, which could strongly support the relevance of innovative clinical trials with specific targeted therapies (larotrectinib, entrectinib) in this population of patients. FGFR3 (17)::TACC3 (11) rearrangement was detected in breast carcinoma BM with the possibility of using some specific targeted therapies and TMPRSS (2)::ERG (4) rearrangements occur in a subset of patients with, prostatic carcinoma BM, endometrium BM, and oligodendroglioma (grade II), IDH-mutated and 1p19q co-deleted, where there are yet no approved ERG-directed therapies.

Novel gene fusions in human oropharyngeal carcinoma

Few reports have analyzed the fusion genes involved in carcinogenesis in the oropharynx, where the incidence of human papillomavirus-associated tumors is relatively low. The aim of this study was to identify novel driver fusion genes in patients with oropharyngeal cancer. The study enrolled fifty-seven patients who were diagnosed with oropharyngeal carcinoma. RNA sequencing data from fresh-frozen specimens were used to identify candidate fusion genes via the JAFFA, arriba, and STAR-Fusion pipelines. Candidate fusion genes were confirmed by direct sequencing. The expression level of a candidate fusion gene was compared to that of tumors without fusion genes. Finally, filtering was performed for driver genes using the annoFuse pipeline. In addition, the VIRTUS pipeline was used to analyze the presence of human papillomavirus in the tumors. We identified 5 (8.8 %) novel potential driver in-frame fusion genes, MKNK2::MOB3A, ICMT::RPS6KA3, ATP1B3::GRK7, CSNK2A1::KIF16B, and FGFR3::MAEA, and 1 (1.8 %) known in-frame fusion gene, FGFR3::TACC3, in 57 patients with pharyngeal carcinoma. Our results suggest that sporadic fusion genes may contribute to tumorigenesis in oropharyngeal carcinomas.

Rare FGFR fusion genes in cervical cancer and transcriptome-based subgrouping of patients with a poor prognosis.

Although cervical cancer is often characterized as preventable, its incidence continues to increase in low- and middle-income countries, underscoring the need to develop novel therapeutics for this disease.This study assessed the distribution of fusion genes across cancer types and used an RNA-based classification to divide cervical cancer patients with a poor prognosis into subgroups. RNA sequencing of 116 patients with cervical cancer was conducted. Fusion genes were extracted using StarFusion program. To identify a high-risk group for recurrence, 65 patients who received postoperative adjuvant therapy were subjected to non-negative matrix factorization to identify differentially expressed genes between recurrent and nonrecurrent groups. We identified three cases with FGFR3-TACC3 and one with GOPC-ROS1 fusion genes as potential targets. A search of publicly available data from cBioPortal (21,789 cases) and the Center for Cancer Genomics and Advanced Therapeutics (32,608 cases) showed that the FGFR3 fusion is present in 1.5% and 0.6% of patients with cervical cancer, respectively. The frequency of the FGFR3 fusion gene was higher in cervical cancer than in other cancers, regardless of ethnicity. Non-negative matrix factorization identified that the patients were classified into four Basis groups. Pathway enrichment analysis identified more extracellular matrix kinetics dysregulation in Basis 3 and more immune system dysregulation in Basis 4 than in the good prognosis group. CIBERSORT analysis showed that the fraction of M1 macrophages was lower in the poor prognosis group than in the good prognosis group. The distribution of FGFR fusion genes in patients with cervical cancer was determined by RNA-based analysis and used to classify patients into clinically relevant subgroups.

A Two-Step Diagnostic Approach for NTRK Gene Fusion Detection in Biliary Tract and Pancreatic Adenocarcinomas.

It is of interest to determine the incidence and molecular characteristics of NTRK gene fusions in patients with bilio-pancreatic cancers, because of possible treatment with TRK inhibitors for advanced tumors. The aim of the present study was to apply the guidelines for NTRK testing algorithm to a series of patients with bilio-pancreatic cancers. Immunohistochemistry screening was applied on formalin-fixed paraffin-embedded archival blocks from surgical resections, biopsies, or cytological samples of biliary tract and pancreatic adenocarcinomas. The presence of at least a weak staining in rare tumor cells led to testing by 2 RNA-based NGS panels. For biliary tract tumors, 153 samples have been selected. A total of 140 samples were suitable to perform IHC, and 17 samples were IHC positive. RNA NGS testing of the 17 IHC-positive samples revealed a single NTRK3 gene fusion (ETV6(4)-NTRK3(14)) that was detected by both NGS panels. In this perihilar cholangiocarcinoma, IHC performed on a biopsy showed a weak focal cytoplasmic and nuclear staining. No other NTRK fusion was detected on the 16 other samples with both panels. Overall in the patients screened by IHC and confirmed by NGS, the percentage of NTRK fusions was 0.7%. For pancreatic cancers, 319 samples have been selected and 297 were suitable to perform IHC. Nineteen samples were IHC positive. No fusion was detected by NGS. NTRK gene fusions are rare in bilio-pancreatic cancers but testing is of high interest due to possible treatment with specific TRK inhibitors.

Differences In Hematology And Bcr-Abl Molecular Profiles In Patients With Chronic Myeloid Leukemia Undergoing Tyrosine Kinase Inhibitor Therapy

Chronic myeloid leukemia (CML) is a myeloproliferative malignancy due to the formation of the BCR-ABL fusion gene in chronic myeloid leukemia. This condition causes excessive cell proliferation, resulting in an increase in the number of leukocytes. Tyrosine Kinase Inhibitor (TKI) is a first-line therapy that helps reduce the percentage of the BCR-ABL fusion gene in patients with chronic myeloid leukemia. This study was conducted to determine differences in the hematological profiles (hemoglobin levels, leukocyte counts, platelet counts) and molecular BCR-ABL in patients with chronic myeloid leukemia before and after 12 months of tyrosine kinase inhibitors therapy. This analytic observational study was administered using a cross-sectional design to in analyzing the medical records of CML patients who underwent TKI therapy at the Sub Specialist Polyclinic of Internal Medicine Hematology Oncology Ulin Banjarmasin Regional Hospital from March 2021-April 2022. Dependent T-test and McNemar's test were performed in data analysis which results showed that 12 month tyrosine kinase inhibitor therapy could increase the hemoglobin levels, decrease leukocyte counts, platelet counts as well as decreasing the percentage of BCR-ABL gene fusion in patients with chronic myeloid leukemia. In conclusion, significant differences were found in the hematological profiles (p<0.001) and the molecular BCR-ABL (p<0.001) before and after 12 months of tyrosine kinase inhibitor therapy

HTA261 Comparison of Molecular Tests for Detection of NTRK Gene Fusions in Patients With Advanced Solid Tumours- A Systematic Review and Economic Evaluation

To summarise available evidence on the accuracy and the clinical utility, as well as assess the economic aspect of molecular testing (immunohistochemistry (IHC), fluorescence in situ hybridization (FISH), reverse transcription-polymerase chain reaction (RT-PCR) and next-generation sequencing (NGS)) for the identification of NTRK neurotrophic tyrosine receptor kinase (NTRK) gene fusions in patients with locally advanced or metastatic solid tumours.

NTRK Gene Fusions in Solid Tumors and TRK Inhibitors: A Systematic Review of Case Reports and Case Series

The approval of larotrectinib and entrectinib for cancer patients harboring an NTRK gene fusion has represented a milestone in the era of "histology-agnostic" drugs. Among the clinical trials that led to the approval of these two drugs, most of the enrolled patients were affected by soft tissue sarcomas, lung, and salivary gland cancer. However, as next-generation sequencing assays are increasingly available in the clinical setting, health care professionals may be able to detect NTRK gene fusions in patients affected by tumor types under or not represented in the clinical trials. To this aim, we systematically reviewed MEDLINE from its inception to 31 August 2022 for case reports and case series on patients with NTRK gene fusion-positive tumors treated with TRK inhibitors. A virtual cohort of 43 patients was created, excluding those enrolled in the above-mentioned clinical trials. Although our results align with those existing in the literature, various cases of central nervous system tumors were registered in our cohort, confirming the benefit of these agents in this subgroup of patients. Large, multi-institutional registries are needed to provide more information about the efficacy of TRK inhibitors in cancer patients affected by tumor types under or not represented in the clinical trials.

Unraveling the Biology of Epithelioid Hemangioendothelioma, a TAZ-CAMTA1 Fusion Driven Sarcoma.

Simple SummaryEpithelioid hemangioendothelioma (EHE) is a rare vascular cancer that involves a gain-of-function gene fusion involving TAZ, a transcriptional coactivator, and one of two end effectors of the Hippo pathway. Although the activity of TAZ and/or YAP, a paralog of TAZ, is consistently altered in many cancers, genetic alterations involving YAP/TAZ are rare, and the precise mechanisms by which YAP/TAZ are activated are not well understood in most cancers. Because WWTR1(TAZ)–CAMTA1 is the only genetic alteration in approximately half of EHE, EHE is a genetically clean and homogenous system for understanding how the dysregulation of TAZ promotes tumorigenesis. Therefore, by using EHE as a model system, we hope to elucidate the essential biological pathways mediated by TAZ and identify mechanisms to target them. The findings of EHE research can be applied to other cancers that are addicted to high YAP/TAZ activity.The activities of YAP and TAZ, the end effectors of the Hippo pathway, are consistently altered in cancer, and this dysregulation drives aggressive tumor phenotypes. While the actions of these two proteins aid in tumorigenesis in the majority of cancers, the dysregulation of these proteins is rarely sufficient for initial tumor development. Herein, we present a unique TAZ-driven cancer, epithelioid hemangioendothelioma (EHE), which harbors a WWTR1(TAZ)–CAMTA1 gene fusion in at least 90% of cases. Recent investigations have elucidated the mechanisms by which YAP/TAP-fusion oncoproteins function and drive tumorigenesis. This review presents a critical evaluation of this recent work, with a particular focus on how the oncoproteins alter the normal activity of TAZ and YAP, and, concurrently, we generate a framework for how we can target the gene fusions in patients. Since EHE represents a paradigm of YAP/TAZ dysregulation in cancer, targeted therapies for EHE may also be effective against other YAP/TAZ-dependent cancers.

A cell-free RNA-based next-generation sequencing (NGS) assay for the detection of actionable gene fusions in patients with non–small cell lung cancer (NSCLC).

3040 Background: Gene fusions and alternate RNA splice forms represent clinically actionable driver and resistance-conferring alterations in NSCLC and other cancers. Where tissue samples are inadequate for molecular testing, liquid biopsies could address the gap in detection of clinically relevant gene fusions. Targeted cell-free (cf) DNA-based NGS methods are typically used for non-invasive blood-based testing of gene fusions, but have limited sensitivity if fusion breakpoints involve long intronic regions or repetitive sequences (e.g. NTRKs and NRG1). RNA-based approaches are not affected by introns, can identify expressed fusion genes and can discriminate splicing. We developed an NGS assay optimized for cfRNA analyte for the detection of actionable gene fusions and exon deletion/skipping events in liquid biopsies. Methods: A highly multiplexed molecular-barcoded primer panel was designed for cfRNA-based detection of actionable fusion genes in NSCLC ( ALK, BRAF, FGFR2, FGFR3, MET (including exon 14 skipping), NRG1, NTRK1/2/3, RET and ROS1) covering > 90% of reported driver and partner gene exons in COSMIC database. The panel also targets housekeeping genes as endogenous sample controls. We developed a custom bioinformatics pipeline to call fusions and exon skipping based on split and spanning reads. Results: In initial analytical validation using fragmented RNA from pre-characterized reference material (representing 32 unique fusions at known copy numbers), the assay could detect as low as 10 fusion copies with a sensitivity of 97.6% and a specificity of 100%. For clinical testing, cfRNA co-eluted with cfDNA in nucleic acid extracts from plasma was used. In plasma samples (n = 103) from advanced NSCLC, 76% (15/21) of fusions (5 ALK, 3 RET, 2 ROS1, 5 MET ex14 skipping, 1 FGFR3-TACC3) detected in a clinically validated cfDNA assay (LiquidHALLMARK) were also detected in corresponding cfRNA. In a subset of samples that were driver-negative untreated or tyrosine kinase-inhibitor treated, the cfRNA assay yielded 9 gene fusions or breakpoints (1 CD74-NRG1, 4 BRAF, 2 MET, 2 FGFR3-TACC3 fusions) that could not be detected by the cfDNA assay. This represents an increase of 8.7% (9/103) of actionable alterations (driver or resistance) identified using cfRNA. Together cfRNA and cfDNA resulted in 30 fusion events to be detected compared to 21 by the cfDNA assay alone, representing a 42.8% (9/21) increase in fusion-specific detection of the combined assay. Conclusions: This novel cfRNA assay can detect actionable gene fusions and exon skipping events in liquid biopsies with high sensitivity. Combining cfRNA with more routine cfDNA testing can increase the total actionable diagnostic information from non-invasive testing in NSCLC patients where tissue samples are lacking, especially for gene fusions not amenable to detection in cfDNA.

SO-31 Long-term efficacy and safety of larotrectinib in patients with tropomyosin receptor kinase (TRK) fusion gastrointestinal (GI) cancer: An expanded dataset

Neurotrophic tyrosine receptor kinase ( NTRK ) gene fusions are oncogenic drivers in various tumour types. Larotrectinib is a first-in-class, highly selective tropomyosin receptor kinase (TRK) inhibitor approved for use in adult and paediatric patients with TRK fusion cancer, demonstrating an objective response rate (ORR) of 41% across 18 patients with gastrointestinal (GI) cancer (Boni et al, WCGI 2021). We report an updated analysis from an expanded dataset of patients with TRK fusion GI cancer with longer follow-up. Patients with TRK fusion GI cancer treated with larotrectinib in the phase II clinical trial NAVIGATE (NCT02576431) were included in this analysis. Responses were investigator-assessed using RECIST v1.1. Data cut-off was 20 July 2021. As of data cut-off, 34 patients with metastatic TRK fusion GI cancer were enrolled. Median age was 63.5 years (range 32–90). The tumour types included were colorectal (CRC; n=19), pancreatic (n=6), cholangiocarcinoma (n=4), appendiceal (n=1), duodenal (n=1), gastric (n=1), hepatocellular carcinoma (n=1) and oesophageal (n=1). Among the patients with CRC, 10 were microsatellite instability high (MSI-H), seven were MSI-H not detected (including stable) and two were unknown. Overall, 32%, 35% and 18% of patients had received 1, 2, or ≥3 prior lines of systemic therapy, respectively. ORR in the 33 evaluable patients was 33% (95% confidence interval [CI] 18–52): one complete response (CR; 3%), 10 partial responses (PR; three pending confirmation [30%]), 15 stable disease (SD; 45%), four progressive disease (PD; 12%) and three not determined (ND; 9%). Median time to response was 1.9 months (range 1.7–5.0). Median duration of response (DoR) was 7.3 months (95% CI 3.5–27.3); median follow-up was 26.4 months. Median progression-free survival (PFS) was 5.4 months (95% CI 2.7–9.0); median follow-up was 5.4 months. Median overall survival (OS) was 12.5 months (95% CI 6.1–33.4); median follow-up was 7.7 months. In the 19 patients with CRC, ORR was 47% (95% CI 24–71): one CR (5%), eight PR (three pending confirmation [42%]), eight SD (42%), one PD (5%) and one ND (5%). Of the nine responders, six were MSI-H. The median DoR was not reliably estimable, but the 12-month rate was 67% (95% CI 29–100); median follow-up was 17.8 months. Median PFS was 5.5 months (95% CI 2.7–not estimable); median follow-up was 5.6 months. Median OS was 12.5 months (95% CI 6.1–36.5); median follow-up was 7.8 months. Treatment duration for all GI patients ranged from 0.2+ to 32.2+ months. At data cut-off, 14 patients had progressed; four continued treatment post-progression for ≥4 weeks. Treatment-related adverse events (TRAEs) occurred in 65% of patients (27% were Grade [G]1, 21% G2, 12% G3 and 6% G4). No patients discontinued treatment due to TRAEs. In this expanded dataset with longer follow-up, larotrectinib continues to demonstrate rapid, durable responses, extended survival and a favourable safety profile in patients with TRK fusion GI cancer, particularly in those with CRC. These results highlight the importance of identifying NTRK gene fusions in patients with GI cancer, particularly in those with MSI-H CRC.

Clinical and molecular characterization of fusion genes in colorectal cancer.

e15568 Background: Next-generation sequencing (NGS) based molecular profiling technologies have revealed several oncogenic fusion genes that are actionable with small molecule inhibitors leading to practice change, particularly in lung cancer. The molecular and clinical characteristics of these gene fusions are not well defined in colorectal cancer patients (CRC). In this study, we aimed to define clinical and molecular characteristics of fusion genes in patients with CRC who underwent molecular profiling. Methods: Molecular characteristics of tissue confirmed 917 CRC patients were retrieved from the Moffit Cancer Center Clinical Genomics Action Committee database. Patients’ demographic and clinicopathological features and treatment history were collected from the database. All fusion genes were shown by hybridization-based NGS computational algorithms that determined cancer‐related genes, including single‐nucleotide variations, indels, microsatellite instability (MSI) status. Results: Among a total of 917 patients, 24 patients with CRC (2.6%) were found to have at least one fusion gene with a total number of 26 pathogenic fusions. The gene fusions are shown in Table. The most common, potentially targetable, fusion genes in our cohort were (1) RET fusions 0.5% (5/917), (2) ALK fusions 0.4% (4/917), (3) ROS1 fusions 0.2% (2/917), (4) NTRK1 fusion 0.1% (1/917), (5) NRG1 fusion 0.1% (1/917). Fusion genes were more common in MSI-H CRC (N = 27), and 3 (11.1%) patients with MSI-H CRC were found to have fusion genes [(RET (2) and NTRK(1)]. Fusion genes were present in both RAS wild-type (54%; 13/24) and RAS mutant (46%; 11/24) tumors. Most patients were older than 50 years (75%, 18/24) and had left-sided tumor (61.1%) tumor. Conclusions: Fusion genes are rare events in CRC. While fusion genes seem to be more prevalent in MSI-H CRC, RAS status does not correlate with the frequency of fusion genes. Actionable RET and ALK/ROS gene fusion are more common than NTRK fusion genes in this cohort of CRC patients.[Table: see text]

Long-term control and safety of larotrectinib in a cohort of adult and pediatric patients with tropomyosin receptor kinase (TRK) fusion primary central nervous system (CNS) tumors.

2010 Background: Neurotrophic tyrosine receptor kinase ( NTRK) gene fusions are known oncogenic drivers in a variety of tumor types. Larotrectinib is a highly selective, CNS-active TRK inhibitor that demonstrated an objective response rate (ORR) of 30% and a 24-week disease control rate (DCR) of 73% across 33 evaluable adult and pediatric patients with TRK fusion primary CNS tumors, as of July 2020 (Doz et al, Neuro Oncol 2021). We report updated data on an expanded dataset of patients. Methods: Patients with TRK fusion primary CNS tumors in two clinical trials (NCT02637687, NCT02576431) were included. Larotrectinib was administered at 100 mg twice daily (BID) in adults and 100 mg/m2 (max 100 mg) BID in pediatric patients. Response was investigator-assessed. Results: As of July 2021, 38 adult and pediatric patients with TRK fusion primary CNS tumors were identified: high-grade glioma (HGG; n =23), low-grade glioma (LGG; n =9), and other (n =6; includes glioneuronal, neuroepithelial, diffuse leptomeningeal, neuroblastoma, recurrent small round blue cell, and not otherwise specified). Median age at enrollment was 10.8 years (range 1.3–79.0; 28 [74%] patients < 18 years old). The gene fusions involved NTRK2 (n = 28), NTRK1 (n = 6), and NTRK3 (n = 4). Sixteen (42%) patients received one prior line of systemic therapy and 16 (42%) received ≥2 prior lines. The ORR for 37 evaluable patients was 30% (95% confidence interval [CI] 16–47): three complete responses, eight partial responses, 21 stable disease (16 patients ≥24 weeks), and five progressive disease. The 24-week DCR was 73% (95% CI 56–86) for all patients, 68% (95% CI 45–86) for patients with HGG, and 89% (95% CI 52–100) for patients with LGG. Twenty-five of 31 patients (81%) with measurable disease at baseline had tumor shrinkage. Median time to response was 1.9 months. Median duration of response (DoR) was not reached; median follow-up was 25.6 months. The 12-month DoR rate was 64%. Median progression-free survival (PFS) was 16.5 months (95% CI 6.7–not estimable); median follow-up was 27.4 months. Median overall survival (OS) was not reached; median follow-up was 26.7 months. The 24-month OS rate was 65%. Treatment duration ranged from 0.1+ to 38.7+ months. Twenty-two patients (58%) progressed on treatment and three continued treatment post-progression for ≥4 weeks. Treatment-related adverse events (TRAEs) were reported in 21 patients (55%); the majority of these patients (18/21 [86%]) reported Grade 1 or 2 TRAEs. No Grade 3 or higher treatment-related neurological adverse events were reported. There were no treatment discontinuations due to TRAEs. Conclusions: Larotrectinib achieved a high DCR, rapid and durable responses, and a manageable safety profile in patients with TRK fusion primary CNS tumors. These results support testing for NTRK gene fusions in patients with CNS tumors. Clinical trial information: NCT02637687, NCT02576431.

Characteristics of fusion gene expression in acute lymphoblastic leukemia

Objective: To analyze the genetic landscape of 52 fusion genes in patients with de novo acute lymphoblastic leukemia (ALL) and to investigate the characteristics of other laboratory results. Methods: The fusion gene expression was retrospectively analyzed in the 1 994 patients with de novo ALL diagnosed from September 2016 to December 2020. In addition, their mutational, immunophenotypical and karyotypical profiles were investigated. Results: In the 1 994 patients with ALL, the median age was 12 years (from 15 days to 89 years). In the panel of targeted genes, 15 different types of fusion genes were detected in 884 patients (44.33%) and demonstrated a Power law distribution. The frequency of detectable fusion genes in B-cell ALL was significantly higher than that in T-cell ALL (48.48% vs 18.71%), and fusion genes were almost exclusively expressed in B-cell ALL or T-cell ALL. The number of fusion genes showed peaks at<1 year, 3-5 years and 35-44 years, respectively. More fusion genes were identified in children than in adults. MLL-FG was most frequently seen in infants and TEL-AML1 was most commonly seen in children, while BCR-ABL1 was dominant in adults. The majority of fusion gene mutations involved signaling pathway and the most frequent mutations were observed in NRAS and KRAS genes. The expression of early-stage B-cell antigens varied in B-cell ALL patients. The complex karyotypes were more common in BCR-ABL1 positive patients than others. Conclusion: The distribution of fusion genes in ALL patients differs by ages and cell lineages. It also corresponds to various gene mutations, immunophenotypes, and karyotypes.

Diagnostic testing approaches for the identification of patients with TRK fusion cancer prior to enrollment in clinical trials investigating larotrectinib

IntroductionNTRK gene fusions are targetable oncogenic drivers independent of tumor type. Prevalence varies from highly recurrent in certain rare tumors to <1% in common cancers. The selective TRK inhibitor larotrectinib was shown to be highly active in adult and pediatric patients with tumors harboring NTRK gene fusions. MethodsWe examined the techniques used by local sites to detect tumor NTRK gene fusions in patients enrolled in clinical trials of larotrectinib. We also report the characteristics of the detected fusions in different tumor types. ResultsThe analysis included 225 patients with 19 different tumor types. Testing methods used were next-generation sequencing (NGS) in 196 of 225 tumors (87%); this was RNA-based in 96 (43%); DNA-based in 53 (24%); DNA/RNA-based in 46 (20%) and unknown in 1 (<1%); FISH in 14 (6%) and PCR-based in 12 (5%). NanoString, Sanger sequencing and chromosome microarray were each utilized once (<1%). Fifty-four different fusion partners were identified, 39 (72%) of which were unique occurrences. ConclusionsThe most common local testing approach was RNA-based NGS. Many different NTRK gene fusions were identified with most occurring at low frequency. This supports the need for validated and appropriate testing methodologies that work agnostic of fusion partners.

Prognostic significance of DEK-NUP214 fusion gene in patients with acute myeloid leukemia after allogeneic hematopoietic stem cell transplantation

Objective: To investigate the dynamic change and clinical impact of DEK-NUP214 fusion gene in patients with acute myeloid leukemia (AML) receiving allogeneic hematopoietic stem cell transplantation (allo-HSCT). Methods: Real-time quantitative polymerase chain reaction (RQ-PCR) and multicolor flow cytometry (FCM) were used to detect DEK-NUP214 gene expression and leukemia-associated immunophenotype (LAIP) in 15 newly diagnosed patients with positive DEK-NUP214 and receiving allo-HSCT from September 2012 to September 2017 at Peking University People's Hospital. The clinical outcome was analyzed using Kaplan-Meier survival curves. The impact of DEK-NUP214 expression was analyzed by log-rank test. Results: The subjects were followed-up with a median period of 657 (62-2 212) days. The median DEK-NUP214 expression level at diagnosis was 488% (274%-1 692%). Thirteen patients achieved complete remission before allo-HSCT. Thirteen patients had a residual DEK-NUP214 expression of 0.38% (0.029%-738.9%) before allo-HSCT. After allo-HSCT, DEK-NUP214 expression in 9/13 patients remained positive, which dropped by around 500 folds (5.7-5 663.0 folds) within a month post-transplant. Five patients died and 2 patients relapsed. The 3-year cumulative incidence of relapse in patients with positive DEK-NUP214 before transplant was 17.5%±11.3% and the 3-year overall survival was 60.5%±13.8%. After allo-HSCT, DEK-NUP214-negative patients had a better outcome. Conclusion: Quantitative monitor of DEK-NUP214 fusion gene could be a sensitive indicator of MRD status after allo-HSCT.

Combined use of interferon alpha-1b, interleukin-2, and thalidomide to reverse the AML1-ETO fusion gene in acute myeloid leukemia

This study aims to explore the effect of the ITI (interferon alpha-1b, thalidomide, and interleukin-2) regimen on the AML1-ETO fusion gene in patients with t(8;21) acute myeloid leukemia (AML) who were in hematologic remission but positive for the AML1-ETO fusion gene. From September 2014 to November 2020; 20 patients with AML (15 from The Affiliated Cancer Hospital of Zhengzhou University, 4 from The First Affiliated Hospital; and College of Clinical Medicine of Henan University of Science and Technology, and 1 from Anyang District Hospital) with hematological remission but AML1-ETO fusion gene positivity were treated with different doses of the ITI regimen to monitor changes in AML1-ETO fusion gene levels. Twenty patients were treated with a routine dose of the ITI regimen, including 13 males and 7 females. The median patient age was 38 (14–70 years). The fusion gene was negative in 10 patients after 1 (0.5 ~ 8.6) month, significantly decreased in 4 patients after 2.8 (1 ~ 6) months, increased in 4 patients, and unchanged in 2 patients. The 4 patients with elevated levels of the fusion gene were treated with an increased dose of the ITI regimen, and all four patients became negative, for a total effective rate of 90%. The ITI regimen reduces AML1-ETO fusion gene levels in patients with AML who are in hematologic remission but are fusion gene–positive. Improvement was observed in patients’ response to a higher dose administration, and patients tolerated the treatment well.

Abstract CT020: Long-term outcomes of patients with TRK fusion cancer treated with larotrectinib

Abstract Introduction: Neurotrophic tyrosine receptor kinase (NTRK) gene fusions are oncogenic drivers in various tumor types. Larotrectinib is a first-in-class, highly selective, central nervous system (CNS)-active TRK inhibitor approved in over 40 countries, including the US, for the treatment of adult and pediatric patients with TRK fusion cancer. Larotrectinib was approved by the FDA in 2018 based on efficacy and safety outcomes in a primary analysis cohort of 55 patients with TRK fusion cancer from 3 clinical trials (Drilon A et al. NEJM. 2018). Here, we report long-term efficacy follow-up for larotrectinib and molecular data on co-occurring mutations in this primary analysis cohort. Methods: Patients with non-primary CNS TRK fusion cancer treated with larotrectinib were identified from 3 clinical trials (NCT02122913, NCT02576431, NCT02637687). NTRK gene status was determined by local molecular testing. Adult and pediatric patients received larotrectinib 100 mg and 100 mg/m2 twice daily, respectively. The primary endpoint was investigator-assessed objective response rate (ORR) (per RECIST v1.1). Next-generation sequencing was performed on pre-treatment tumor samples from a subset of patients with evaluable tumor material (n=31) using the FoundationOne® CDx assay. The data cut-off was July 15, 2019. Results: A total of 55 patients with 17 different tumor types were included in the primary analysis cohort. Median age was 45 years (range 0.3-76 years). Patients had gene fusions involving NTRK1 (45%), NTRK2 (2%), or NTRK3 (53%). For 31 patients the detailed genomic profile, including co-occurring mutations, will be presented. Forty-four (80%) patients had received prior systemic therapy, with a median of 2 prior therapies (range 0-10). ORR with larotrectinib was 80% (95% confidence interval [CI] 67-90%); 13 (24%) patients had a complete response (CR), 31 (56%) patients had a partial response (PR), 5 (9%) patients had stable disease, and 6 (11%) patients had progressive disease. With longer follow-up, best response for 4 patients improved from PR to CR. Median duration of response and progression-free survival were 35.2 months (95% CI 19.8-not estimable [NE]) and 25.8 months (95% CI 9.9-NE), respectively. Median overall survival (OS) was not reached (95% CI 44.4-NE) over a median follow-up of 32.5 months. The 36-month OS rate was 76% (95% CI 63-89%). In an expanded safety population (n=279), larotrectinib-related adverse events were mainly Grade 1-2. Conclusions: Larotrectinib demonstrated a robust response rate with long durability and extended survival benefits in adult and pediatric patients with TRK fusion cancer. These data highlight the importance of identifying NTRK gene fusions in patients with cancer. Citation Format: Alexander Drilon, Shivaani Kummar, Catherine M. Albert, Ramamoorthy Nagasubramanian, Jaclyn F. Hechtman, John A. Reeves, Georg Beckmann, Marion Rudolph, Justyna A. Wierzbińska, Laura Dima, Nicoletta Brega, Theodore W. Laetsch, David S. Hong. Long-term outcomes of patients with TRK fusion cancer treated with larotrectinib [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr CT020.

SO-29 Efficacy and safety of larotrectinib in patients with tropomyosin receptor kinase fusion-positive gastrointestinal cancer: An expanded dataset

Neurotrophic tyrosine receptor kinase (NTRK) gene fusions are oncogenic drivers in a range of adult and pediatric malignancies but are generally rare in patients with gastrointestinal (GI) cancer, with a prevalence of around 0.3% in colorectal cancer (CRC; Forsythe et al, Ther Adv Med Oncol 2021). Larotrectinib is a first-in-class, central nervous system (CNS)-active, highly selective tyrosine receptor kinase (TRK) inhibitor approved for the treatment of adult and pediatric patients with TRK fusion-positive cancer, demonstrating an objective response rate (ORR) of 78% across 175 adult and pediatric patients with various non-CNS cancers (McDermott et al, ESMO 2020). We report data on an expanded dataset of patients with TRK fusion-positive GI tumors. Patients with TRK fusion-positive GI cancer treated with larotrectinib in the phase II clinical trial NAVIGATE (NCT02576431) were included in this analysis. Response was investigator-assessed using RECIST v1.1. As of July 20, 2020, 18 patients with metastatic TRK fusion-positive GI cancer were enrolled. Median age was 67.0 years (range 32.0 to 84.0 years). Of the 10 patients with CRC, 7 were microsatellite instability-high (MSI-H), 2 were microsatellite stable (MSS) and phenotype was unknown in 1 patient. The other tumor types were cholangiocarcinoma (n=3), pancreatic (n=2), appendiceal (n=1), esophageal (n=1), and hepatocellular carcinoma (n=1). Overall, 13 patients (72%) had received ≥2 prior lines of therapy, 3 (17%) of whom had received immunotherapy. The best response to last prior therapy was 2 partial responses (PR), 6 stable disease (SD), 3 progressive disease (PD), and 7 unknown, unevaluable or not applicable. ORR in the 17 evaluable patients was 41% (95% CI 18–67): 1 complete response (CR), 6 PR (1 pending confirmation), 7 SD, 2 PD and 1 not determined. Median time to response in the 6 confirmed responders was 1.9 months (range 1.7 to 5.0 months). Median duration of response (DoR) was 5.5 months (95% CI 3.5–27.3). Median progression-free survival (PFS) was 5.4 months (95% CI 2.2–11.6) at a median follow-up of 20.3 months. Median overall survival (OS) was 14.1 months (95% CI 2.8–33.4) at a median follow-up of 7.8 months. In the 10 patients with CRC, ORR was 50% (95% CI 19–81): 1 CR, 4 PR (1 pending confirmation), and 5 SD. For these patients, median DoR was 15.5 months (95% CI 3.7–27.3), median PFS was 5.5 months (95%CI 2.2–29.4) and median OS was 29.4 months (95% CI 2.8–36.5). Duration of treatment for all GI patients ranged from 0.26+ to 29.3 months. At data cut-off, 10 patients had progressed, with 3 continuing treatment post-progression. Adverse events were mostly Grade 1–2. Treatment-related adverse events (TRAEs) occurred in 11 patients. Grade 3/4 TRAEs occurred in 2 patients (increased alanine aminotransferase, increased aspartate aminotransferase, and nausea). There were no treatment discontinuations due to TRAEs. In patients with TRK fusion-positive GI cancer, larotrectinib demonstrated rapid responses with high survival rates and a favorable safety profile. These results support testing for NTRK gene fusions in patients with GI cancer, particularly in patients with MSI-H CRC.