Spectrum Of Molecular Alterations Research Articles

Targeting ATR in Cancer Medicine.

As a key component of the DNA Damage Response, the Ataxia telangiectasia and Rad3-related (ATR) protein is a promising druggable target that is currently widely evaluated in phase I-II-III clinical trials as monotherapy and in combinations with other rational antitumor agents, including immunotherapy, DNA repair inhibitors, chemo- and radiotherapy. Ongoing clinical studies for this drug class must address the optimization of the therapeutic window to limit overlapping toxicities and refine the target population that will most likely benefit from ATR inhibition. With advances in the development of personalized treatment strategies for patients with advanced solid tumors, many ongoing ATR inhibitor trials have been recruiting patients based on their germline and somatic molecular alterations, rather than relying solely on specific tumor subtypes. Although a spectrum of molecular alterations have already been identified as potential predictive biomarkers of response that may sensitize to ATR inhibition, these biomarkers must be analytically validated and feasible to measure robustly to allow for successful integration into the clinic. While several ATR inhibitors in development are poised to address a clinically unmet need, no ATR inhibitor has yet received FDA-approval. This chapter details the underlying rationale for targeting ATR and summarizes the current preclinical and clinical landscape of ATR inhibitors currently in evaluation, as their regulatory approval potentially lies close in sight.

Abstract 76: Comprehensive genomic profiling as an approach to guide therapeutic planning in pediatric patients with high-risk solid tumors

Abstract Despite the great achievements in treating pediatric cancer patients in the last several decades, approximately one fifth of patients remains uncurable using standard therapeutic modalities and require search for innovative therapeutic approaches. Advances in sequencing techniques and bioinformatic data processing enabled identification of wide spectrum of molecular alterations including single nucleotide variants, copy number aberrations, fusion genes or changes in expression and methylation patterns, which could serve as therapeutic targets. Translation of comprehensive molecular profiling into clinical practice is still limited, however, multiple precision oncology initiatives have already explored feasibility of this approach. From September 2016 to December 2020, a total of 160 patients with high-risk solid tumors that were treated or consulted at Department of Pediatric Oncology of University Hospital Brno were subjected to molecular analysis of tumor tissue using whole-exome sequencing, targeted RNA sequencing, whole-transcriptome profiling and array-CGH. In 18 patients, 2 or more biopsies were analyzed due to relapse or progression of the disease. In the cohort, CNS tumors were the most prevalent (41%), followed by sarcomas (33%) and neuroblastoma (9%). All patients were presented at multidisciplinary molecular tumor board, where treatment recommendations were discussed. In 37% of patients (n = 59), therapeutic targets were identified. Most commonly identified targets included BRAF (n = 9), FGFR1 (n = 7), NF1 (n = 6), NRAS (n = 5) and PIK3CA (n = 4), making RAS/MAPK signaling most frequently altered pathway in the subgroup. Single nucleotide variants or small indels accounted for 65% of actionable findings, followed by fusion genes (12%), copy number aberrations (9%), CD274 expression (7%, confirmed by IHC staining for PD-L1 protein), and high tumor mutational burden (7%). Clinically relevant fusions were found in 25% of patients and 20% of identified fusions were targetable. 8 patients were eligible for immunotherapy based on either PD-L1 expression, or high tumor mutational burden (>10 mut/Mb). Using molecular-based approach in treating high-risk patients represents a promising strategy and helps to understand the complexity of pediatric malignancies though examining tumor biology at multiple levels. Implementing the concept of precision oncology into clinical practice could not only be beneficial in the context of chances for improved survival of high-risk patients, but might also be convenient for other patients, whose successful treatment comes at cost of various secondary complications due to intensive chemotherapy/radiotherapy approaches. Supported by Ministry of Health of the Czech Republic, grant nr. NV19-03-00562, NV19-03-00501, NV19-03-00559 and NU20-03-00240. All rights reserved. Citation Format: Petra Pokorna, Hana Palova, Tina Catela Ivkovic, Sona Adamcova, Michal Kyr, Vojtech Bystry, Robin Jugas, Karolina Trachtova, Dagmar Al Tukmachi, Tomas Merta, Jaroslav Juracek, Jiri Sana, Sona Mejstrikova, Marta Jezova, Peter Mudry, Zdenek Pavelka, Jaroslav Sterba, Ondrej Slaby. Comprehensive genomic profiling as an approach to guide therapeutic planning in pediatric patients with high-risk solid tumors [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 76.

Early-onset metastatic and clinically advanced prostate cancer is a distinct clinical and molecular entity characterized by increased TMPRSS2\u2013ERG fusions

BackgroundMen with early-onset prostate cancer are at increased risk for cancer-related mortality, yet the prevalence and spectrum of molecular alterations in this patient population is unknown. Here, we analyze comprehensive genomic profiling data to characterize the molecular drivers of early-onset prostate cancer in patients with clinically advanced and metastatic disease.MethodsNext-generation sequencing was ordered as a part of routine clinical care for 10,189 patients with prostate cancer between 02/2013 and 03/2020 using commercially available comprehensive genomic profiling.ResultsDeidentified genomic data for 10,189 unique patients with prostate cancer were obtained (median age = 66 y, range = 34–90 y). 439 patients were ≤50 y (4.3%), 1928 patients were between ages of 51 and 59 y (18.9%), and 7822 patients were ≥60 y (76.8%). Of metastatic biopsy sites, lymph node, liver, and bone were the most common in all groups, accounting for 60.2% of all specimens. Overall, 97.4% of patients harbored pathologic genomic alterations. The most commonly altered genes were TP53, TMPRSS2–ERG, PTEN, AR, MYC, MLL2, RAD21, BRCA2, APC, SPOP, PIK3CA, RB1, MLL3, CDK12, ATM, and CTNNB1. Patients ≤50 y harbored significantly more TMPRSS2–ERG fusions than patients ≥60 y, while AR copy number alterations as well as SPOP and ASXL1 mutations were significantly less frequent.ConclusionsClinically advanced and metastatic early-onset prostate cancer is a distinct clinical subgroup with characteristic genomic alterations including increased frequency of TMPRSS2–ERG fusions and fewer AR, SPOP, and ASXL1 alterations.

Abstract 4341: Large mutational spectrum of cutaneous melanoma in a Brazilian population: The experience of A.C. Camargo Cancer Center

Abstract Introduction: Cutaneous melanoma (CM) is an aggressive type of malignancy, with elevated mortality rates. The Cancer Genome Atlas Network (TCGA) recently reported the molecular classification of CM and divided these lesions according to their somatic mutation profile in 4 categories: BRAF, NRAS or NF1 mutated, and also the triple-negative group. The aim of this study is to describe the spectrum of molecular alterations from a Brazilian population of CM patients. Methods: DNA was extracted from formalin-fixed, paraffin-embedded (FFPE) tissue from primary and metastatic melanoma samples from A.C. Camargo Cancer Center molecular pathology section. Next-generation sequencing (Ion Torrent®) targeting a 14-gene panel was performed, targeting the following genes: BRAF (códon 600), NRAS (códons 12, 13, 61, 117 and 146) e KIT (éxon 11, 13, 17), KRAS, CTNNB1, IDH1, EGFR, HRAS, PDGFR-a, PIK3CA, RET, JAK2, MET, and CDH1. Results: 131 cutaneous melanoma samples from different patients were sequenced. The majority of the samples (57%) showed mutation in at least one gene. BRAF was the most frequent detected mutation, found in 40% of the cases, and p.V600E, p.V600K and p.V600R represented 90%, 8% and 2% of BRAF mutations, respectively. NRAS mutation was detected in 10% of the cases, and among those 88% involved codon 61. KIT mutation was identified in 10% of the cases. Mutations in KRAS, CTNNB1, PDGFRa, PIK3CA, EGFR and HRAS were identified in 5%, 4%, 4%, 3%, 2% and 1% of the cases, respectively. No mutations in IDH1, JAK2, MET or RET was identified. Most of the mutated cases showed mutation in only one tested gene (71%), while 14%, 10% and 5% showed mutations in 2, 3 or 4 genes respectively. None of the cases showed simultaneous mutation involving combinations of BRAF, NRAS or KIT mutations. Discussion and Conclusion: The BRAF, NRAS and KIT mutation frequency in this population with CM diagnosis is similar to the one described in the world literature for this disease, as well as the distribution of the most frequent mutated regions and specific types of mutations. These results add the mutational spectrum of CM of a large Brazilian cohort to the world literature. Treatment of CM with targeted therapies aiming the MAP-Kinase pathway, and especially blocking BRAF, are a reality in the clinical oncology routine for treating CM patients, but there are still many obstacles in order to fully understand the resistance mechanism and the possibility of drug combinations. Additionally, new targeted agents are under development, such as the ones for NRAS mutated cases, and in this way the understanding of the large mutational spectrum of melanoma is of extreme importance in the clinical scenario. Citation Format: Mariana Petaccia de Macedo, Felipe Fidaldo, Clovis Lopes Pinto, João Pedreira Duprat, Maria Dirlei S.f Begnami, Dirce Maria Carraro, Isabela Werneck Cunha. Large mutational spectrum of cutaneous melanoma in a Brazilian population: The experience of A.C. Camargo Cancer Center [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4341.

Mutational landscape of goblet cell carcinoids and adenocarcinoma ex goblet cell carcinoids of the appendix is distinct from typical carcinoids and colorectal adenocarcinomas

AbstractThere is limited data on the spectrum of molecular alterations in goblet cell carcinoids and adenocarcinoma ex goblet cell carcinoids of the appendix. We used next generation sequencing to determine mutations of potential pathogenetic and therapeutic significance in this rare group of tumors. Adequate DNA was successfully extracted in 34/46 cases and the final group included 18 goblet cell carcinoids and 16 adenocarcinoma ex goblet cell carcinoids. Illumina TruSeq™ was used for sequencing exons of a custom 282 gene panel using an Illumina HiSeq 2000. All cases had a minimum coverage depth of at least 50 reads. After filtering through the Exome Sequencing Project, the number of mutations per case ranged from 0–9 (mean:3). The mutational burden in adenocarcinoma ex goblet cell carcinoids was significantly higher than goblet cell carcinoids (mean 5 vs. 3; p < 0.05) but the spectrum of alterations overlapped between the two groups. The most frequent mutations included ARID1A (4/34), ARID2 (4/34), CDH1 (4/34), RHPN2 (4/34), and MLL2 (3/34). Some mutations typically seen in conventional colorectal adenocarcinomas were also identified but with much lower frequency (APC :4/34; KRAS :2/34). MLL2 and KRAS mutations were only seen in adenocarcinoma ex goblet cell carcinoids and TP53 mutations were limited to poorly differentiated adenocarcinoma ex goblet cell carcinoids (2/34). Copy number changes could be evaluated in 15/34 cases and showed low copy number gains in CDKN1B (6/15) and NFKBIA (6/15), among others. The overlapping molecular alterations suggest that goblet cell carcinoids and adenocarcinoma ex goblet cell carcinoids are best considered two grades of differentiation of the same tumor rather than two distinct histological types. Mutations in TP53, CDH1 and MLL2 mutations were predominantly present in the adenocarcinoma ex goblet cell carcinoid group consistent with transformation to a higher grade lesion. The unique mutational profile also offers an explanation for the poor chemosensitivity in these tumors and highlights the need for developing new targeted therapies.

Abstract PD4-3: Use of community-based next-generation sequencing (NGS) in advanced breast cancer: Identification of actionable targets to guide clinical trial selection

Abstract Background: Molecularly targeted drugs specific for mutated genes are increasingly the focus of novel clinical trials. However, molecular profiling of tumors is largely unavailable in community cancer centers, where nearly 80% of cancer patients (pts) are treated. In October 2012, Sarah Cannon Research Institute (SCRI) launched a community-based molecular profiling initiative to characterize the spectrum of molecular alterations in tumors. The profiling panel focused on potentially actionable mutations for the purpose of identifying candidates for treatment with specific targeted agents (FDA approved or investigational). Herein, we report the initial data from breast cancers (BC) profiled between October 2012 and May 2013. Methods: Metastatic breast cancer (MBC) pts &amp;gt; 18 years of age with ECOG PS ≤ 2 who were candidates for treatment provided consent for tumor molecular profiling. Archival tumor specimens (tissue block or 10 unstained slides) obtained from either the primary or metastatic disease were collected and interrogated by NGS (1000X average coverage) in a CLIA/CAP laboratory to detect oncogenic hotspot mutations in 35 cancer-related genes. Results were reported to the treating physician within 12 calendar days of receipt of suitable tissue and were stored in a database to enable correlation with clinical outcomes. Detection of relevant molecular abnormalities was used to identify pts appropriate for clinical trials of targeted agents. Results: As of May 31 2013, a total of 594 tumor samples were profiled, 101 (17%) of which were BC samples. 8% (8/101) of the BC samples were inadequate for assay. Of the remaining 93 samples, 60 (65%) had no mutations detected. 28% of BC had single mutations and 7% had multiple mutations. PIK3CA mutations (24%) were the most frequently identified alteration. Other genetic alterations identified included RUNX1 (4%) and FGFR3 (2%) while mutations in PIK3R1, MET, KRAS, KIT, FGFR2, HER2, BRAF, SMO, MYC, DDR2 and AKT1 were infrequent, each identified in 1 pt. Patterns and frequency of mutations in the 35 genes assayed differed in the various subtypes of BC. 6% (6/93) of BC pts with appropriate tumor mutations identified by molecular profiling have been enrolled into phase I clinical trials with PI3K or mTORC1/2 inhibitors; updated treatment results will be presented. An additional 27 patients are potentially eligible for ongoing trials at SCRI. Conclusions: This community-based molecular profiling initiative has been well accepted by patients and physicians, and provides timely results. Potentially actionable mutations were identified in 35% of BCs tested; PIK3CA mutations accounted for 70% of all actionable mutations detected. Identification of BC patients with actionable mutations may add to treatment options and improve results, and will also accelerate development of new targeted agents. Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr PD4-3.

Spectrum of molecular alterations in colorectal, upper urinary tract, endocervical, and renal carcinomas arising in a patient with hereditary non-polyposis colorectal cancer

Hereditary nonpolyposis colon cancer (HNPCC) syndrome is the most frequent hereditary cancer syndrome predisposing to cancers of various locations, especially colon, endometrium, stomach, and upper urinary tract. Carcinomas of the kidney parenchyma are not considered as an HNPCC-related tumor. HNPCC tumors are characterized by microsatellite instability (MSI) due to a defect in mismatch repair (MMR) and carry somatic frameshift mutations in mononucleotide repeats within the coding regions of key genes. We report the first case of a papillary carcinoma of the kidney in an HNPCC patient who developed carcinomas of the upper urinary tract, endocervix, and colon. Whereas the HNPCC-related tumors demonstrated MSI phenotype, loss of MSH2 protein expression, and frameshift mutations in several of the 13 target genes analyzed, the kidney cancer displayed MSS phenotype, normal MMR protein expression, and no frameshift mutation in target genes. Our observations do not support the possibility that papillary carcinomas are part of HNPCC syndrome.

Simultaneous analysis of 1176 gene products in normal human aorta and abdominal aortic aneurysms using a membrane-based complementary DNA expression array

Background: A number of changes in gene expression have been described in abdominal aortic aneurysms (AAAs), but the spectrum of molecular alterations in this disease is unknown. The purpose of this study was to characterize the expression of approximately 1000 gene products in human AAA tissue and to compare the profile of genes expressed in AAAs with that observed in normal aorta. Materials and Methods: Total RNA was isolated from abdominal aortic wall tissues (4 AAAs and 4 normal aortas), and array-specific [32P]–labeled complementary DNA (cDNA) probes were created with reverse transcription. The cDNA probes were hybridized with nylon membranes containing an array of 1176 cDNA clones (AtlasArray Human 1.2 I; Clontech, Palo Alto, Calif), and autoradiographs were scanned to identify the patterns of gene expression characteristic of each tissue type. Densitometric analysis was used to standardize the expression of individual genes to a panel of housekeeping controls, and differential gene expression was defined by a signal ratio of at least 2:1. Results: One hundred forty-five (12.3%) of the 1176 genes were consistently expressed in aortic tissue. Thymosin β-4 was the most abundant of 101 transcripts detected in both AAAs and normal aorta, whereas 44 genes exhibited differential patterns of expression (39 predominant in AAAs and 5 in normal aorta). Densitometric analysis confirmed differences in expression for 20 of these gene products between AAAs and normal aorta, with the greatest increases seen for myeloid cell nuclear differentiation antigen (31-fold), cathepsin H (30-fold), platelet-derived growth factor–A (23-fold), apolipoprotein E (13-fold), gelatinase B/matrix metalloproteinase-9 (12-fold), and interleukin-8 (11-fold). The only gene products substantially decreased in AAAs were myosin light chain kinase (39-fold) and β-1 integrin (twofold). AAA tissues thereby exhibited a distinct pattern of gene expression reflecting chronic inflammation, extracellular matrix degradation, atherosclerosis, and smooth muscle cell depletion. Conclusions: cDNA expression arrays provide a powerful new approach to help identify the molecular mechanisms responsible for aneurysmal degeneration. Further studies will be needed to elucidate the functional and pathophysiologic significance of the individual genes that exhibit altered levels of expression in AAA tissue. (J Vasc Surg 2001;34:143-50.)

Field cancerisation of the oral cavity: comparison of the spectrum of molecular alterations in cases presenting with both dysplastic and malignant lesions

Field cancerisation of the oral cavity: comparison of the spectrum of molecular alterations in cases presenting with both dysplastic and malignant lesions

The spectrum of molecular alterations in the evolution of chronic myelocytic leukemia.

DNA from 135 patients with chronic myelogenous leukemia (CML) at various clinical stages and Philadelphia (Ph1) chromosome positive acute lymphoblastic leukemia was investigated for alterations in a variety of proto-oncogenes which have been implicated in the evolution of CML from its chronic phase to blast crisis. The most common genetic change found in the evolution of typical Ph1 chromosome positive CML to blast crisis was an alteration of the p53 gene involving either a rearrangement, a deletion, or a point mutation in the coding sequence of the gene. Alterations of the p53 gene were found in the myeloid and the rare megakaryocytic variant of blast crisis but were absent in the lymphoid leukemic transformants. Gross structural alterations were seen in 11 of 54 (20%) of myeloid or unknown phenotypes of blast crisis and in only 1 of 44 chronic phase cases. Eight examples of mutations in the open reading frame of the p53 gene at codons 49, 53, 60, 140, 202, 204, 238, and 239 were observed in blast crisis patients. Mutations in the N-RAS gene were rare in typical blast crisis (2 of 27 cases) but were found in megakaryocytic and Ph1 negative myeloid blast crisis. We concluded that heterogeneous alterations in the p53 gene and occasionally in the N-RAS genes accompany the evolution of chronic phase CML to blast crisis.