Targetable Genes Research Articles

Abstract 2277: Evaluation of mutation profile of oncogenic signalling pathway in breast cancer among Indian population

Abstract Introduction: Genomic profile of breast cancer is diverse in nature and complex due to heterogeneity among racial groups. In India, it is the leading cause of cancer death and accounts for 13.5% of the total incidence of new cancer cases with a mortality rate of 10.6% irrespective of age and sex in 2020. The growing incidence marks the importance of profiling driver genes that are usually involved in proliferation, cell survival, oxidative stress response, progenitor phenotype, cell growth, apoptosis, and cell cycle regulation. In order to evaluate the mutation profile within breast tumor, we carried out Whole Exome Sequencing (WES) followed by gene analysis which is implicated in oncogenic pathways. Experimental procedures: 40 primary breast cancer patients were recruited from the clinical follow-up at AIIMS, New Delhi, India. With informed consent, tumor and blood were collected after surgery followed by genomic DNA extraction. Library preparation was done by adopting a protocol developed by Illumina. Exonic regions were captured by using Trueseq Exome kit which covers ≥ 80% of whole-exome and sequencing was performed by utilizing Illumina platform as per the manufacturer’s instruction. Bioinformatics analyses were carried out through an in-house developed pipeline. We identified altered genes by comparing them with the matched control and further filtered them on the basis of their functional impact. Results: In our study, a recurrent mutation in RTK-RAS, Notch, PI3K, WNT, Hippo, Myc, cell cycle, p53, TGF-β, NRF2 pathways were reported among 40 individuals. We found a total of 263 altered genes, out of these 186 genes were driver genes comprise 88 tumor suppressor genes and 98 oncogenes while the rest are passenger genes. In terms of SNP Class- >58%- missense, <4%-silent, <38%-nonsense mutations. These SNPs have their phenotypic impact such as high, moderate, modifier, and low which accounts <2.4%, 8-12%, >75%, and <10% respectively. Missense mutation has a greater fraction of C>T transitions followed by C>A transversion. Moreover, we also identified p53, PIK3CA, EIF4EBP1 and ALK as a top mutated genes. A hotspot mutation H1047R in PIK3CA and R56W, as well as R99S in EIF4EBP1, were account for subsequently 20%, 25%, and 15% samples along with hotspot region in MAML3. Conclusions: Here we demonstrate exclusive molecular profiling of the oncogenic pathways of breast cancer in the Indian population. Apart from nonsynonymous substitution, we also revealed recurrent mutation within a specific position or region of gene involved in the RTK-RAS, Notch, and PIK3CA network. Overall this study will improve insight for commonly mutated genes with a primary objective of screening, diagnosis, prognosis along risk stratification. In addition, this could be used to identify specific targetable candidate mutation gene panels with an overall objective of personalized drug therapy. Citation Format: Rahul Kumar, Anurag Srivastava, Usha Agrawal, S.V.S. Deo, Sandeep R. Mathur, Ajay Gogia, Pranay Tanwar. Evaluation of mutation profile of oncogenic signalling pathway in breast cancer among Indian population [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2277.

Abstract 2989: FAP facilitates ovary tumorigenesis through the NF-κB/survivin funcational axis

Abstract Ovarian cancer is the deadliest gynecologic cancer, mainly attributing to lack of early diagnosis of the diseases. Current mainstay treatment for ovarian cancer is surgical removal followed by chemotherapy. Although patients initially respond well, most of patients suffer from relapse and die from metastasis. Therefore, developing successful approaches combatting metastasis is most likely to prolong patients’ survival and improve their life quality. Toward this goal, we analyzed The Cancer Genome Atlas ovarian cancer patient dataset to reach for targetable genes preferentially elevated in advanced ovarian cancer. Among them, we found that knockdown of fibroblast activation protein alpha (FAP) led to dramatic apoptosis in mesenchymal-like ovarian cancer cells. To elucidate the underlying mechanism, we performed RNAseq and identified that TNF-alpha/NF-κB signaling pathway was impaired in FAP-knockdown cells. NF-κB signaling pathway is well characterized to promote cell survival by elevating the expression of pro-survival genes. In fact, the level of survivin was diminished upon FAP-knockdown. As forced expression of survivin almost completely abrogated apoptosis elicited by FAP-knockdown and survivin inhibitor also induced robust apoptosis in ovarian cancer cells, we reason that FAP participates in ovarian cancer development by promoting cell survival through activation of NF-κB/survivin axis. With the aid of EpCAM aptamer as delivering cargo, we demonstrated that FAP siRNA was able to suppress intraperitoneal ovarian cancer development. This study suggests that FAP is an ideal therapeutic target against mesenchymal-like ovarian cancer. Citation Format: Bin Li, Shuang Huang. FAP facilitates ovary tumorigenesis through the NF-κB/survivin funcational axis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2989.

Abstract 5779: Colorectal cancer and its molecular differences between sexes

Abstract Introduction: Although the risk of colorectal cancer is roughly equal between sexes (slightly higher in males), the molecular profile between the two varies significantly. Many genes identified have a distinctive effect on outcome between these two subgroups, including actionable genes, the most frequently altered genes, and the most significantly altered genes. The molecular basis is important for understanding etiology and treatment options. Uncovering these molecular differences could help optimize screening and treatment and improve outcomes for colorectal cancer for both sexes. Materials and Methods: This study used molecular data from three TCGA Colorectal Adenocarcinoma studies (Firehose Legacy, Nature 2012, and PanCancer Atlas) on cBioPortal. The two subgroups, males and females, were separated and analyzed for molecular differences. 1496 cases (790 male, 706 female) were analyzed on cBioPortal for molecular characteristics including alterations (mutations, deletions, amplifications), overall survival, and mRNA expression vs. copy number variation (CNV). Significant differences were noted, and OncoPrints and survival curves were generated. Results: The genes analyzed on cBioPortal showed similar alteration rates between males and females, although differences were depicted between sex and specific genes. Out of the 17 actionable genes, four had a significant effect on one sex, but not the other. ARID1A alterations increased the probability of male survival (p-value = 0.0219), ERRB2 (0.0467) and NRAS (1.118e-3) decreased survival odds for males, and NF1 (0.0107) decreased survival odds for females. CDK12 and ERBB2 co-amplification was identified for both sexes, but more prominent in males. Multiple altered genes also had a lower probability of survival in only females. Of the most altered genes, RBFOX1 (0.0312), CSDM1 (8.631e-3), TTN (4.374e-4), WWOX (2.226e-4), CCSER1 (5.048e-3), MACROD2 (0.0366), and a 20q co-amplification cluster of CHD6 (7.313e-3), PREX1 (5.422e-3), and ZNF335 (0.0439) were significant in females. Also, among the most significant genes between males and females, TENM1 alteration (found in 11% of females and 4% of males) lowered the probability of survival in females (1.384e-6). Lastly, 75% of females remained disease free after 70 months, compared to 45% of males (8.849e-3). Conclusion: Molecular differences in colorectal cancer between males and females are significant. TTN is important to note due to its comparison to tumor mutational burden (TMB); TTN, combined with MUC4 and MUC16, can predict TMB and may be used as a convenient biomarker for effective immunotherapy in females. ERBB2 is potentially targetable with anti HER2 therapeutics, thus may improve the worse outcome observed in males with ERBB2 alterations. Colorectal cancer has different targetable genes expressed differentially among males and females. This needs to be considered when developing screening and treatment strategies. Citation Format: Roy Khalife, Genevra Magliocco, So Hyeon Park, Anthony Magliocco. Colorectal cancer and its molecular differences between sexes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5779.

Heterogeneity of triple negative breast cancer: Understanding the daedalian labyrinth and how it could reveal new drug targets

Introduction : Triple negative breast cancer (TNBC) is considered the most aggressive breast cancer subtype with the least favorable outcomes. However, recent research efforts have generated an enhanced knowledge of the biology of the disease and have provided a new, more comprehensive understanding of the multifaceted ecosystem that underpins TNBC. Areas covered : In this review, the authors illustrate the principal biological characteristics of TNBC, the molecular driver alterations, targetable genes, and the biomarkers of immune engagement that have been identified across the subgroups of TNBC. Accordingly, the authors summarize the landscape of the innovative and investigative biomarker-driven therapeutic options in TNBC that emerge from the unique biological basis of the disease. Expert opinion The therapeutic setting of TNBC is rapidly evolving. An enriched understanding of the tumor spatial and temporal heterogeneity and the surrounding microenvironment of this complex disease can effectively support the development of novel and tailored opportunities of treatment.

HGG-23. The presence ofROS1 fusions are not limited only to infantile hemispheric glioma.

INTRODUCTION: Diffuse pediatric-type high-grade gliomas are diffuse gliomas with histological features of malignancy, typically occurring in children, and infants. For these tumors, precise classification, identification of prognostic and predictive factors requires molecular analysis. The ROS proto-oncogene 1 (ROS1) gene encodes a receptor tyrosine kinase that is involved in chromosomal rearrangements in numerous malignancies, and may be an attractive therapeutic target, since specific inhibitors have been approved for several neoplasms. Molecular evaluation including detection of ROS1 fusions in pediatric gliomas are not included in standard diagnostic tests so far, therefore data on its significance is still limited. We present two cases of pediatric ROS1 fusion-positive brain tumors. METHODS AND RESULTS: The patient no.1 was 1 year old boy with disseminated brain lesions. Histopathological examination displayed the presence of a neoplasm, which was composed of round and spindle-shaped cells with palisading necrosis, mitotic activity, and microvascular proliferation. The patient no.2 is 9 years old girl with tumor located in left frontal lobe. Microscopically, the neoplasm revealed the presence of oligodenroglial-like component with microvascular proliferation, and high mitotic activity. Targeted gene sequencing panel - Ampliseq Childhood Cancer Panel for Illumina was used to detect diagnostic and targetable gene fusions. In both of patients ROS1:GOPC gene fusions were detect. Identified fusions allowed to established diagnosis - infant-type hemispheric glioma with ROS1 fusion (patient no 1) and - diffuse pediatric-type high grade glioma with ROS1 fusion (patient no 2). CONCLUSIONS: Our results indicate, that the presence of ROS1 fusions are not limited to the infant-type hemispheric gliomas only and may play a role in other glioma entities. It may be worth to include this biomarker in the diagnostic panel of pediatric brain tumors to establish a more precise diagnosis and a potential therapeutic target. Funded by National Science Centre, Poland (2016/23/B/NZ2/03064).

Comprehensive genomic profiling of MET rare tumors in China.

e15058 Background: The mesenchymal epithelial transition factor receptor (MET) is a potential therapeutic target in a number of cancers, commonly activated by amplification, mutation and fusion. Methods: Rare tumor was defined as solid tumors with an incidence lower than 2.5/100,000 per year. We retrospectively analyzed the next-generation sequencing and clinicopathological data of 3453 Chinese rare tumors patients in the Geneplus database, including 1021 genes, MSI loci, tumor mutational burden (TMB), and programmed cell death ligand-1 (PD-L1) expression analysis information. Results: MET-positive was identified in 115 patients (3.3%), including 109 cases of amplification (3.2%), 8 cases of exon 14 skipping (0.2%) and 1 cases of fusion. The prevalence of MET-positive varied widely across tumors systems and subtypes. Urinary, neural, skin and respiratory systems were the top 4 systems with 8.3% (1/12), 7.9% (58/732), 4.2% (1/24) and 2.9% (6/207) MET-positive rate, respectively. Considering the tumor subtypes, glioblastoma, sarcomatoid carcinoma, neuroendocrine tumor and glioma were higher, reaching 15.7% (16/102), 13.2% (7/53), 9.8% (4/41), and 7.4% (36/487) respectively (Table). Totally, 73.0% of patients had at least one common targetable gene mutation, including ATM，BRAF，BRCA，CDKN2A，EGFR substitution, ERBB2, FGFR1,2,3, KIT, NF1, PIK3CA, PTEN and RET. The proportions of TMB-H (≥9 mut/Mb) and MSI-H were very low, with only 8.9% and 2.2%, while PD-L1 positive rate reached to 60.9%. Conclusions: The treatment options for rare tumors are still limited. The approval of MET receptor tyrosine kinase has brought hope to patients with Non-Small Cell Lung Cancer. The MET-positive rate in rare tumors is higher than 2.7% in lung adenocarcinoma, so MET receptor tyrosine kinase have great application potential in rare tumors. However, since most patients co-occurred with other targetable driver mutations or PD-L1 positive, how to choose the best treatment strategy should be solved. The deployment of the best treatment strategy is a problem that should be solved in the follow-up study.[Table: see text]

GemOX plus immune checkpoint inhibitor in combination with lenvatinib or NGS-guided targeted therapy in patients with biliary tract cancers.

e16133 Background: The combination of gemcitabine-based chemotherapy and immune checkpoint inhibitors has made great progress recently in advanced biliary tract cancer (BTC). Multi-target TKI lenvatinib or next-generation sequencing (NGS)-guided molecular targeted therapy are also promising. The aim of this study was to explore the anti-tumor effects of combined GemOX plus anti-PD-1 sintilimab and TKI either by lenvatinib or by NGS-guided targeted therapy if there is available target for local advanced or metastatic BTCs. Methods: This is a prospective single arm clinical study. Patients with local advanced or metastatic BTC were given intravenous infusion of standard GemOX (85mg/m2 oxaliplatin on day 1 and gemcitabine 1000mg/m2 on a 1-8-day schedule of a 3-week treatment cycle) plus 200mg q3w of sintilimab and lenvatinib or targeted therapy based on NGS (olaparib for BRCA1/2 mutation, dasatinib for IDH1/2 mutation, afatinib for EGFR mutation, lenvatinib for PDGFR and KIT mutation, lenvatinib for FGFR/KIT mutation). The primary end point was objective response rate (ORR), and the secondary end points were progression-free survival (PFS) and overall survival (OS). Tumor response was evaluated according to RECIST v1.1 criteria. Results: From November 2020 to December 2021, 22 patients with locally advanced or metastatic BTCs (6 GBC, 14 iCCA, 1 pCCA and 1 dCCA) were enrolled in the regimen, with an average age of 58.4 years. Partial response (PR) was achieved in 10 cases, stable disease (SD) in 9 cases and progression disease (PD) in 3 cases (13.6 %). The objective response rate (ORR) was 45.5%, and the disease control rate (DCR) was 86.4%. By December 31st, 2021, the median follow-up time was 13.1 months. The most common adverse events were anorexia (68.2%), nausea (68.2%), vomiting (36.36%), hair loss (45.5%) and bone marrow suppression (63.6%). During the treatment, the incidence of adverse reactions was 81.8%, and the incidence of grade 3/4 adverse events was 9.09%. For 14 patients with NGS, 5 patients were treated by targeting IDH2, EGFR, FGFR2, PDGFRA/KIT, BRCA2 and resulted in 1 SD and 4 PR with an ORR of 80% and DCR of 100%. The ORR and DCR were both 100% for 4 patients with programmed cell death ligand-1 (PD-L1) expression. While for the 3 patients with supper-progression markers such as RET, MDM2 and FGF14/STK24, there were 2 SD and 1 PD with an ORR of 0% and DCR of only 33%. Conclusions: In patients with advanced BTCs, the combination of GemOX plus sintilimab and lenvatinib or NGS-guided targeted therapy showed promising ORR and DCR, especially for the patients with positive PD-L1 expression and targetable gene alterations.

Increasing targeted therapy options for patients with relapsed cancer with broader somatic gene panel analysis from the primary tumor: The Profiler02 randomized phase II trial.

3130 Background: PROFILER-02 is a multicenter randomized prospective study comparing the proportion of metastatic cancer patients (pts) with Targeted Agent (TA) recommendation provided by large NGS panel (FOne panel, 324 genes) vs home 87-gene NGS panel (CTRL) (PMID 30865223). Methods: Adult pts with advanced/metastatic cancer during 1st or 2nd line of therapy without known targetable gene alteration were eligible and randomized (1:1) to FOne vs CTRL panel. Both panels were performed for each patient. The randomization arm defined the first panel reviewed by dedicated Molecular Tumor Board (MTB) at disease progression while the 2nd panel remained blinded. The primary objective was the pts rate with at least one TA recommendation by the MTB using either FOne or CTRL panel. The study was designed in order to detect difference in proportions of 10% between the two panels. A sample size of 289 pts with both panels were requested to show this difference with an expected proportion of discordant pairs of 20% using a McNemar's test with 98% power and 5% two-sided significance level. Secondary endpoints included number of pts receiving at least one TA, progression free survival (PFS) and overall survival (OS). Results: From June 2017 to June 2019, among the 339 included pts 171 and 168 pts were randomized in FOne or CTRL panels’ first use, respectively. Median age was 57 years [19.0 - 85.0]; 54.9% were female. The median time from randomization to first MTB was 7.62 months [range 0.80 - 48.1]. Among the 339 pts, 147 pts (43.4%) had no TA recommendation, 108 pts (31.9%) had at least one TA recommendation according to both panels, 67 pts (19.8%) had one or more TA recommendation according to FOne panel only and 17 pts (5%) according to CTRL panel only (McNemar p < 0.001). At the time of the analysis, 51/339 (15%) pts started recommended treatment: 27 pts (8%) with TA recommendation from both panels, 21 pts (6.2%) from FOne only and 3 pts (0.3%) from CTRL only. Main initiated TA were PARP inh. (FOne n = 12; CTRL n = 9), PI3K/AKT/mTOR inh. (FOne n = 10; CTRL n = 9) and immunotherapy (ICI) (FOne n = 7; CTRL n = 0). Median PFS following first MTB were 3.2 months (95% CI 2.5-3.8) and 2.6 months (95% CI 2.0-3.8), median OS were 8.7 months (95% CI 6.6-10.8) and 8.4 months (95% CI 6.4-9.7), in the FOne and CTRL arm, respectively. Conclusions: Larger NGS panel including Tumor Mutational Burden increased the number of recommended options (TA and ICI), as well as the number of treatment initiation. Clinical trial information: NCT03163732.

Evaluation of somatic and germline variants in patients with small bowel adenocarcinoma reveals clinically actionable targets.

4159 Background: Small bowel adenocarcinoma (SBA) is a rare gastrointestinal cancer with a poor prognosis and limited treatment options. Because the treatments for colorectal cancer showed limited efficacy in SBA, the NCCN guide strongly encourages SBA patients to participate in clinical trials. In this study, we aimed to explore clinically actionable variants in a large cohort of patients with SBA to assist oncologists to select the matched trials for patients. Methods: To explore therapeutic targets in 84 Chinese SBA patients, a deep sequencing panel (OncoPanscan, Genetron health) was used to characterize somatic alterations including point mutations, indels, copy number alterations, gene fusions as well as pathogenic germline variants. Results: Recurrent somatic mutations included TP53 (57%), KRAS (56%), APC (31%), SMAD4 (21%), MDM2 (13%), CTNNB1 (12%), KMT2C (12%), SOX9 (12%), ARID2 (12%), FAT3 (11%), FBXW7 (10%), SPTA1(10%) and PIK3CA (10%). Of the entire cohort, we observed five activating PIK3CA mutations (R108H; G364R; E542K; E545K, n = 2) which may be sensitive to FDA-approved PIK3CA inhibitor alpelisib. Additionally, patients with loss-of-function mutation in NF1 (n = 2), STK11 (n = 1) and PTEN (n = 1) can be targeted with MEK inhibitor selumetinib and mTOR inhibitor everolimus, respectively. Except for one V600E mutation, all mutations in BRAF are either type 2 (L597R, n = 1) or type 3 (N581S, n = 1; D594N, n = 4) which were sensitive to MEK inhibitor trametinib. We also found four type 2 MAP2K1 activating mutations (K57E, K57N, and F53L) which can be targeted by trametinib. Furthermore, oncogenic ERBB2/HER2 mutations were seen in 4 patients including S310F (n = 1), V842I (n = 2) and V777L (n = 1). We also found one patient harbored ERBB2/HER2 high magnification amplification. These five patients were candidates for HER2-targeted therapy clinical trials. Interestingly, one IDH1 mutation (R132C) carrier in our cohort might benefit from ivosidenib. In addition, we observed targetable gene amplification of MDM2 (n = 2) and FGF3/4/19 (n = 2). There were two patients with MLH1 loss-of-function germline mutations that may benefit from immunotherapy. Among 78 patients with available MSI status, three were designated as microsatellite instability. The median TMB of microsatellite stable patients was 2.82 mutations/Mb. Lastly, we observed five deleterious germline mutations, three for SBDS, one each for APC and ERCC5. Taken together, at least 33 (39%) patients in our cohort harbored actionable genetic alterations. Conclusions: Through comprehensive genomic characterization of Chinese SBA patients, we identified actionable variants of multiple signaling pathways in plenty. NGS profiling results can guide physicians to enroll a significant portion of SBA patients in genomically-matched clinical trials.

Clonal evolution after treatment pressure in multiple myeloma: heterogenous genomic aberrations and transcriptomic convergence

We investigated genomic and transcriptomic changes in paired tumor samples of 29 in-house multiple myeloma (MM) patients and 28 patients from the MMRF CoMMpass study before and after treatment. A change in clonal composition was found in 46/57 (82%) of patients, and single-nucleotide variants (SNVs) increased from median 67 to 86. The highest increase in prevalence of genetic aberrations was found in RAS genes (60% to 72%), amp1q21 (18% to 35%), and TP53 (9% to 18%). The SBS-MM1 mutation signature was detected both in patients receiving high and low dose melphalan. A total of 2589 genes were differentially expressed between early and late samples (FDR < 0.05). Gene set enrichment analysis (GSEA) showed increased expression of E2F, MYC, and glycolysis pathways and a decreased expression in TNF-NFkB and TGFbeta pathways in late compared to early stage. Single sample GSEA (ssGSEA) scores of differentially expressed pathways revealed that these changes were most evident in end-stage disease. Increased expression of several potentially targetable genes was found at late disease stages, including cancer-testis antigens, XPO1 and ABC transporters. Our study demonstrates a transcriptomic convergence of pathways supporting increased proliferation and metabolism during disease progression in MM.

Rational testing for gene fusion in colorectal cancer: MSI and RAS-BRAF wild-type metastatic colorectal cancer as target population for systematic screening

Gene fusions provide access to new therapeutic opportunities for patients treated for a colorectal cancer (CRC). However, they do not excess 1% of patients. A better identification of patients in whom gene fusions are highly prevalent is a major issue in a therapeutic and medico-economics perspective. This study assesses the rates of gene fusions in CRC patients with MSI/RAS-BRAFWT in our routine practice detected with a commercially available NGS-based fusion panel. Among the 130 MSI CRC tumors, 43 (33%) were KRAS-NRAS-BRAFWT. A gene fusion was detected in 7 (25.9%) of the 27 MSI/RAS-BRAFWT samples, which had RNA suitable for analysis after quality control. These fusions involved mainly NTRK1/3 (n = 5), as well as ALK (n = 1) and BRAF (n = 1). In the present study, we confirm that patients with MSI/RAS-BRAFWT CRCs represent a subpopulation in which targetable gene fusions are overrepresented. Our results support the use of a two-step algorithm for molecular screening, in which metastatic CRC patients would have routine MSI and RAS/BRAF testing, and then only those with MSI/RAS-BRAFWT would be screened with dedicated NGS RNA panel for gene fusions.

The Molecular Landscape of Pancreatobiliary Cancers for Novel Targeted Therapies From Real-World Genomic Profiling.

Chemotherapies have limited efficacy in pancreatic cancer (PC) and biliary tract cancer (BTC), underscoring the need for new regimens. Recently, tumor-agnostic approaches have been developed for some targeted therapies in advanced solid tumors; however, the frequency of alterations by clinical and genomic background is unclear in PC and BTC. To assess the frequencies of druggable gene alterations and investigate new potential therapeutic targetable genomic alterations, advanced PC and BTC patients were tested with comprehensive genomic profiling at Foundation Medicine during the course of clinical care. A total of 16 913 PC patients and 3031 BTC patients were available for analyses, and frequencies of genomic alterations were stratified by age (≥40 years or <40 years), microsatellite instability status, tumor mutational burden status (high ≥10 or low <10 Muts/Mb), and select genomic alterations. Alterations in BRCA2, BRAF, ERBB2, CDK12, PIK3CA, FGFR2, EGFR, and other potential targets were seen across cohorts, with enrichment observed within particular subsets such as in PC patients lacking a KRAS mutation. In BTC patients, the rate of ERBB2 amplification was statistically significantly higher in the tumor mutational burden-high population (23.3% vs 13.7%). Interestingly, CDK12 rearrangement was observed in BTC patients with ERBB2 amplification tumors. In patients younger than 40 years, FGFR2 rearrangement (4%) was observed in PC: GATA6 amplification (11.1%) and rearrangement of BRAF (2.8%)FGFR2 (5.6%) was observed in BTC patients. We identified an appreciable frequency of immunotherapy biomarkers and targetable gene alterations in both PC and BTC, with notable frequencies in PC samples lacking KRAS mutations and children or adolescent and young adult populations, that should encourage comprehensive genomic profiling testing.

Functional genetic screen identifies ITPR3/calcium/RELB axis as a driver of colorectal cancer metastatic liver colonization.

Metastatic colonization is the primary cause of death from colorectal cancer (CRC). We employed genome-scale invivo short hairpin RNA (shRNA) screening and validation to identify 26 promoters of CRC liver colonization. Among these genes, we identified a cluster that contains multiple targetable genes, including ITPR3, which promoted liver-metastatic colonization and elicited similar downstream gene expression programs. ITPR3 is a caffeine-sensitive inositol 1,4,5-triphosphate (IP3) receptor that releases calcium from the endoplasmic reticulum and enhanced metastatic colonization by inducing expression of RELB, a transcription factor that is associated with non-canonical NF-κB signaling. Genetic, cell biological, pharmacologic, and clinical association studies revealed that ITPR3 and RELB drive CRC colony formation by promoting cell survival upon substratum detachment or hypoxic exposure. RELB was sufficient to drive colonization downstream of ITPR3. Our findings implicate the ITPR3/calcium/RELB axis in CRC metastatic colony formation and uncover multiple clinico-pathologically associated targetable proteins as drivers of CRC metastatic colonization.

Oncogenic Fusions in Gliomas: An Institutional Experience

Gliomas are primary malignancies of the central nervous system (CNS). High-grade gliomas are associated with poor prognosis and modest survival rates despite intensive multimodal treatment strategies. Targeting gene fusions is an emerging therapeutic approach for gliomas that allows application of personalized medicine principles. The aim of this study was to identify detectable fusion oncogenes that could serve as predictors of currently available or newly developed targeted therapeutics in cross-sectional samples from glioma patients using next-generation sequencing (NGS). A total of 637 patients with glial and glioneuronal tumours of the CNS who underwent tumour resection between 2017 and 2020 were enrolled. Detection of fusion transcripts in FFPE tumour tissue was performed by a TruSight Tumour 170 assay and two FusionPlex kits, Solid Tumour and Comprehensive Thyroid and Lung. Oncogene fusions were identified in 33 patients. The most common fusion was the KIAA1549-BRAF fusion, detected in 13 patients, followed by FGFR fusions (FGFR1-TACC1, FGFR2-CTNNA3, FGFR3-TACC3, FGFR3-CKAP5, FGFR3-AMBRA1), identified in 10 patients. Other oncogene fusions were also infrequently diagnosed, including MET fusions (SRPK2-MET and PTPRZ1-MET) in 2 patients, C11orf95-RELA fusions in 2 patients, EGFR-SEPT14 fusion in 2 patients, and individual cases of SRGAP3-BRAF, RAF1-TRIM2, EWSR1-PALGL1 and TERT-ALK fusions. The introduction of NGS techniques provides additional information about tumour molecular alterations that can aid the multimodal management of glioma patients. Patients with gliomas positive for particular targetable gene fusions may benefit from experimental therapeutics, enhancing their quality of life and prolonging survival rates.

Germline mutation landscape of DNA damage repair genes in African Americans with prostate cancer highlights potentially targetable RAD genes

In prostate cancer, emerging data highlight the role of DNA damage repair genes (DDRGs) in aggressive forms of the disease. However, DDRG mutations in African American men are not yet fully defined. Here, we profile germline mutations in all known DDRGs (N = 276) using whole genome sequences from blood DNA of a matched cohort of patients with primary prostate cancer comprising of 300 African American and 300 European Ancestry prostate cancer patients, to determine whether the mutation status can enhance patient stratification for specific targeted therapies. Here, we show that only 13 of the 46 DDRGs identified with pathogenic/likely pathogenic mutations are present in both African American and European ancestry patients. Importantly, RAD family genes (RAD51, RAD54L, RAD54B), which are potentially targetable, as well as PMS2 and BRCA1, are among the most frequently mutated DDRGs in African American, but not in European Ancestry patients.

Transcriptional Profiling of Malignant Melanoma Reveals Novel and Potentially Targetable Gene Fusions.

Simple SummaryMalignant melanoma is a complex disease that is estimated to claim over 7000 lives in the United States in 2021. Although recent advances in genomic technology have helped with the identification of driver variants, molecular studies and clinical trials have often focused on prevalent alterations, such as the BRAF-V600E mutation. With the inclusion of whole transcriptome sequencing, molecular profiling of melanomas has identified gene fusions and revealed gene expression profiles that are consistent with the activation of signaling pathways by common driver mutations. Patients harboring such fusions may benefit from currently approved targeted therapies and should be considered in the design of future clinical trials to further personalize treatments for patients with malignant melanoma.Invasive melanoma is the deadliest type of skin cancer, with 101,110 expected cases to be diagnosed in 2021. Recurrent BRAF and NRAS mutations are well documented in melanoma. Biologic implications of gene fusions and the efficacy of therapeutically targeting them remains unknown. Retrospective review of patient samples that underwent next-generation sequencing of the exons of 592 cancer-relevant genes and whole transcriptome sequencing for the detection of gene fusion events and gene expression profiling. Expression of PDL1 and ERK1/2 was assessed by immunohistochemistry (IHC). There were 33 (2.6%) cases with oncogenic fusions (14 novel), involving BRAF, RAF1, PRKCA, TERT, AXL, and FGFR3. MAPK pathway-associated genes were over-expressed in BRAF and RAF1 fusion-positive tumors in absence of other driver alterations. Increased expression in tumors with PRKCA and TERT fusions was concurrent with MAPK pathway alterations. For a subset of samples with available tissue, increased phosphorylation of ERK1/2 was observed in BRAF, RAF1, and PRKCA fusion-positive tumors. Oncogenic gene fusions are associated with transcriptional activation of the MAPK pathway, suggesting they could be therapeutic targets with available inhibitors. Additional analyses to fully characterize the oncogenic effects of these fusions may support biomarker driven clinical trials.

Anaplastic thyroid cancer: genome-based search for new targeted therapy options.

ObjectiveAnaplastic thyroid cancer (ATC) is one of the most lethal human cancers with meager treatment options. We aimed to identify the targeted drugs already approved by the Food and Drug Administration (FDA) for solid cancer in general, which could be effective in ATC.DesignDatabase mining.MethodsFDA-approved drugs for targeted therapy were identified by screening the databases of MyCancerGenome and the National Cancer Institute. Drugs were linked to the target genes by querying Drugbank. Subsequently, MyCancerGenome, CIViC, TARGET and OncoKB were mined for genetic alterations which are predicted to lead to drug sensitivity or resistance. We searched the Cancer Genome Atlas database (TCGA) for patients with ATC and probed their sequencing data for genetic alterations which predict a drug response.Results In the study,155 FDA-approved drugs with 136 potentially targetable genes were identified. Seventeen (52%) of 33 patients found in TCGA had at least one genetic alteration in targetable genes. The point mutation BRAF V600E was seen in 45% of patients. PIK3CA occurred in 18% of cases. Amplifications of ALK and SRC were detected in 3% of cases, respectively. Fifteen percent of the patients displayed a co-mutation of BRAF and PIK3CA. Besides BRAF-inhibitors, the PIK3CA-inhibitor copanlisib showed a genetically predicted response. The 146 (94%) remaining drugs showed no or low (under 4% cases) genetically predicted drug response.ConclusionsWhile ATC carrying BRAF mutations can benefit from BRAF inhibitors and this effect might be enhanced by a combined strategy including PIK3CA inhibitors in some of the patients, alterations in BRAFWT ATC are not directly targeted by currently FDA-approved options.

Mediastinal germ cell tumours: where we are and where we are going-a narrative review.

In this review, we summarize the current state of the art of primary mediastinal germ cell tumours (PMGCTs) and we highlight challenges and future research directions for this disease. PMGCTs account for 1-3% of all germ cell malignancies and for 15% of adult anterior mediastinal cancers. In 60-70% of cases PMGCTs are represented by nonseminomatous germ cell tumours (GCTs), and in 30-40% of cases by seminomas. Even if PMGCTs share histological and biochemical characteristics with gonadal GCTs, they have peculiar clinical and biological features. Nonseminomatous PMGCTs have a poor prognosis, with a 5-year overall survival (OS) rate of 40-50% after platinum-based chemotherapy and surgery, and a long-term OS of only 10% after salvage treatment. Due to the rarity of this disease, no level 1 evidence is available from randomised trials for PMGCTs. The combination of bleomycin, etoposide, and cisplatin (BEP) or etoposide, ifosfamide and cisplatin (VIP) for 4 cycles are recommended as first line treatment options for nonseminomatous PMGCTs. Surgery of the residual disease after chemotherapy is fundamental in the treatment of nonseminomatous PMGCTs. PMGCTs have high TP53 pathway gene alterations, while targetable gene alterations are rarely identified, thus challenging the advance of precision medicine in this field. We performed a narrative review of international literature published in English on PMGCTs, focusing the attention on clinical trials, international guidelines and translational studies. Treatment of patients with PMGCTs is challenging and should be performed in experienced centers. International collaborations should become a priority to ensure optimal patient management. Clinical investigation of new therapeutic options remains an important unmet clinical need, and inclusion of patients in clinical trials should be encouraged. Liquid biopsy is a new promising strategy in PMGCTs.

Comprehensive genomic profiling (CGP) of fibrolamellar oncocytic hepatoma (FLO) and conventional hepatocellular carcinomas (HCC): An observational study.

474 Background: FLO is a rare variant of liver cancer that disproportionately affects young adults and is frequently progressive and fatal as it is often detected in a clinically advanced stage. It is seldom associated with cirrhosis of liver, viral hepatitis or other risk factors associated with conventional HCC. Treatment options are largely limited to surgical resection, and there is dearth of effective targeted therapies for FLO. Methods: Comprehensive genomic profiling (CGP) was performed using the Foundation Medicine Inc. (FMI) data base on 63 FLO and 1,793 HCC clinically advanced cases between 6/2013-12/2020 using a hybrid capture-based assay of up to 324 genes a to detect genomic alterations (GA), tumor mutational burden (TMB) and microsatellite instability (MSI). PD-L1 expression in tumor cells (Dako 22C3) was measured by IHC and scored using the tumor proportion score (TPS) method. Results: The FLO patients (pts) were significantly younger than HCC pts (median age 20 vs. 64, respectively) and the male preponderance was similar. The HCC group featured significantly more GA/tumor than FLO group (3.74 vs 1.31 p&lt;.0001). In the currently untargetable GA group, CTNNB1, TERT and TP53 GA were significantly more frequent in HCC than FLO. GA in potentially targetable genes were extremely uncommon in both FLO and HCC with HCC featuring slightly more MTOR pathway targets ( PTEN, TSC2, NF1). GA in DNA damage and repair (DDR) pathway including BRCA2 were infrequent in both groups. GA in targetable kinases including EGFR, ERBB2, ALK, RET and PIK3CA were extremely uncommon in both groups. GA associated with intrahepatic cholangiocarcinoma (IDH1, FGFR2) were extremely uncommon in these tumors. Although the mean TMB was significantly higher in HCC than FLO, overall TMB was low with very few cases having TMB &gt; 10 mutations/Mb. PD-L1 expression was relatively low in both groups. GA in genes associated with immune checkpoint inhibitors (ICPI) drug response like PBRM1, CD274, MDM2, STK11 were rarely identified in both groups. Additional details are illustrated in the table. Conclusions: Comparison of CGP of FLO with HCC illustrates the multifarious nature of these cancers. In HCC, there is a high prevalence of GA in TERT, CTNNB1 and TP53. CGP identified certain targetable GA in the MTOR and DDR pathways and TMB was higher in HCC. These findings warrant further evaluation of clinically advanced FLO and HCC pts by CGP to identify possible targetable genomic pathways. [Table: see text]

Next-generation sequencing of endoscopically obtained tissues from patients with all stages of pancreatic cancer.

Routinely available clinical samples of all stages of pancreatic cancer are used in the present study to elucidate its molecular mechanisms and identify novel therapeutic targets. We evaluated the use of next‐generation sequencing (NGS) of endoscopically obtained pancreatic cancer tissues. We enrolled 147 patients who underwent endoscopic ultrasound‐guided fine‐needle aspiration or endoscopic biopsy. The quantity and quality of the extracted DNA was assessed. Tissue samples were used for NGS of 78 cancer‐related genes, from which gene alterations and microsatellite instability (MSI) were extracted. NGS was successful in 141 out of 147 (96%) cases. Gene alterations were detected in 134 out of 141 (91%) samples, among which eight out of 10 samples with a DNA concentration below the detection limit had some type of gene alteration. Targetable genes were detected in 28 (19.9%) cases. MSI and germline mutations in homologous recombination repair associated genes were detected in 5% and 3% of cases, respectively. Cox regression analysis revealed that metastasis (P < .005; hazard ratio [HR], 3.30) was associated with poor prognosis in all pancreatic cancer patients. In addition, fewer than three mutations (P = .03; HR, 2.48) and serum carcinoembryonic antigen levels >5 ng/mL (P < .005; HR, 3.94) were associated with worse prognosis in cases without and with metastasis, respectively. Targeted sequencing of all stages of pancreatic cancer using available samples from real clinical practice could be used to determine the relationship between gene alterations and prognosis to help determine treatment choices.