Identification Of Targetable Mutations Research Articles

Mutational profiling of 103 unresectable pancreatic ductal adenocarcinomas using EUS-guided fine-needle biopsy.

Pancreatic ductal adenocarcinoma (PDAC) is among the most lethal cancers, with a 5-year survival rate of around 9%. Only 20% are candidates for surgery. Most unresectable patients undergo EUS-guided fine-needle biopsy (EUS-FNB) for diagnosis. Identification of targetable mutations using next-generation sequencing (NGS) is increasingly requested. Data on feasibility of EUS-FNB for NGS and knowledge regarding mutational profile of unresectable PDAC are scarce. We evaluated the "technical yield" of EUS-FNB for NGS in unresectable PDAC: relative fraction of diagnostic EUS-FNBs meeting technical criteria. We also investigated the "molecular yield": relative fraction of EUS-FNBs included in NGS containing sufficient DNA for detection of at least one mutation. Furthermore, we determined the relative frequency of cancer-associated mutations in unresectable PDAC. Formalin-fixed and paraffin-embedded EUS-FNBs diagnostic of unresectable PDAC and fulfilling these criteria were included (n = 105): minimum 3-mm2 tissue, minimum of 2-mm2 tumor area, and minimum 20% relative tumor area. NGS was performed using Ion GeneStudio S5 Prime System and Oncomine™ Comprehensive Assay v.3 including 161 cancer-related genes. Technical yield was 48% (105/219) and molecular yield was 98% (103/105). Most frequently mutated genes were KRAS (89.3%) and TP53 (69.9%), followed by CDKN2A (24.3%), ARID1A (9.7%), SMAD4 (7.8%), TSC2 (7.8%), and CCND3 (6.8%). EUS-FNB for NGS of unresectable PDAC is feasible. Our technical criteria for NGS, using leftovers in formalin-fixed and paraffin-embedded blocks after routine pathology diagnosis, were met by around half of EUS-FNBs. Almost all EUS-FNBs fulfilling the technical criteria yielded a successful NGS analysis.

Molecular Characterization and Therapeutic Opportunities in KRAS Wildtype Pancreatic Ductal Adenocarcinoma.

To investigate the molecular characteristics of and potential for precision medicine in KRAS wildtype pancreatic ductal adenocarcinoma (PDAC). We investigated 27 patients with KRASWT PDAC at our institution. Clinical data were obtained via chart review. Tumor specimens for each subject were interrogated for somatic single nucleotide variants, insertion and deletions, and copy number variants by DNA sequencing. Gene fusions were detected from RNA-seq. A patient-derived organoid (PDO) was developed from a patient with a MET translocation and expanded ex vivo to predict therapeutic sensitivity prior to enrollment in a phase 2 clinical trial. Transcriptomic analysis showed our cohort may be stratified by the relative gene expression of the KRAS signaling cascade. The PDO derived from our patient harboring a TFG-MET rearrangement was found to have in vitro sensitivity to the multi-tyrosine kinase inhibitor crizotinib. The patient was enrolled in the phase 2 SPARTA clinical trial and received monotherapy with vebrelitinib, a c-MET inhibitor, and achieved a partial and durable response. KRASWT PDAC is molecularly distinct from KRASMUT and enriched with potentially actionable genetic variants. In our study, transcriptomic profiling revealed that the KRAS signaling cascade may play a key role in KRASWT PDAC. Our report of a KRASWT PDAC patient with TFG-MET rearrangement who responded to a cMET inhibitor further supports the pursuit of precision oncology in this sub-population. Identification of targetable mutations, perhaps through approaches like RNA-seq, can help enable precision-driven approaches to select optimal treatment based on tumor characteristics.

Liquid biopsy guides successful molecular targeted therapy of an inoperable pediatric brainstem neoplasm

Midline CNS tumors are occasionally inaccessible for surgical biopsies. In these instances, cell-free DNA (cfDNA) may serve as a viable alternative for molecular analysis and identification of targetable mutations. Here, we report a young child with an inoperable brainstem tumor in whom a stereotactic biopsy was deemed unsafe. The tumor progressed on steroids and after radiotherapy the patient developed hydrocephalus and received a ventriculoperitoneal shunt. Droplet digital PCR analysis of cfDNA from an intraoperative cerebrospinal fluid liquid biopsy revealed a BRAF V600 mutation enabling targeted treatment with MEK and BRAF inhibitors. The patient, now on trametinib and dabrafenib for 1 year, has had substantial tumor volume regression and reduction of contrast enhancement on MRIs and is making remarkable clinical progress. This case highlights that in a subset of CNS tumors, access to liquid biopsy analysis may be crucial to identify actionable therapeutic targets that would otherwise go undiscovered.

Utility of artificial intelligence-based genomic classification of occult malignancies in clinical practice.

3065 Background: Occult primary malignancies (OPM) are a significant clinical problem, representing 3 to 5% of advanced cancers. Patients with OPM have a worse prognosis and fewer treatment options than when the primary site of origin of cancer can be confidently identified. Novel artificial intelligence-based genomic classification of occult malignancies has been validated for clinical use by previous studies, but reports of clinical utility have not yet been published. We report our experience of consecutive cases where a commercial AI-based genomic classifier was used in routine practice at a high-volume community cancer center. Methods: Malignancies with uncertain pathological classification or site of origin were subjected to molecular profiling and AI-based genomic classification (GPSai) capable of recognizing a set of 115 distinct primary tumor sites and histology classes. Molecular profiling consisted of whole exome and whole transcriptome sequencing of FFPE tumor samples along with other predictive biomarkers assays performed by a commercial laboratory (Caris Life Sciences). The identification of targetable mutations was reported, but variants of unknown significance were excluded when reporting genomic alterations. Results: From 1,316 patients between October 2021-November 2022, we analyzed 70 (5.3%) patients with OPM, including 44 (62.9%) females and 26 (37.1%) males, with 34 (48.6%) being 65 or older. GPSai classification was ordered for 73 samples from 70 patients, which resulted in the classification of 33 (45.2%) tumors, inconclusive results in 36 (49.3%), and insufficient tissue quantity in 4 (5.5%). Of the 33 cases with a GPSai classification, the putative pathology diagnosis was concordant in 26 (78.8%) and discordant in 7 (21.2%) cases. We investigated discordance between the GPSai and pathological diagnoses in discordant cases . The pathological classification was favored over GPSai in all 7 discordant cases. Of the 36 cases that could not be confidently assigned a classification, 14 (38.9%) possessed potentially actionable alterations . 23 of the 36 had no presumptive site of origin. Of these, 10 of 23 (43.5%) were PD-L1 positive, 4 of 23 (17.4%) had a high TMB, and 1 of 23 (4.4%) had MMR deficiency. Additionally, based on molecular profile and examination of RNA expression levels, 2 cases were able to be classified with subsequent IHC confirmation. Based on the results from genomic testing, 55.7% of patients (39 of 70) had FDA-approved treatment options. Conclusions: Over a third of patients with OPM were able to be assigned a cancer diagnosis concordant with diagnoses by pathologists. Of those which could not be classified, targetable biomarkers were commonly found. AI-based genomic classification of occult primaries is useful in clinical practice to help discern the site of origin and identify treatment options.

An approach to genetic testing in patients with metastatic castration-resistant prostate cancer in Singapore.

There has been a rapid evolution in the treatment strategies for metastatic castration-resistant prostate cancer (mCRPC) following the identification of targetable mutations, making genetic testing essential for patient selection. Although several international guidelines recommend genetic testing for patients with mCRPC, there is a lack of locally endorsed clinical practice guidelines in Singapore. A multidisciplinary specialist panel with representation from medical and radiation oncology, urology, pathology, interventional radiology, and medical genetics discussed the challenges associated with patient selection, genetic counselling and sample processing in mCRPC. A clinical model for incorporating genetic testing into routine clinical practice in Singapore was formulated. Tumour testing with an assay that is able to detect both somatic and germline mutations should be utilised. The panel also recommended the "mainstreaming" approach for genetic counselling in which pre-test counselling is conducted by the managing clinician and post-test discussion with a genetic counsellor, to alleviate the bottlenecks at genetic counselling stage in Singapore. The need for training of clinicians to provide pre-test genetic counselling and educating the laboratory personnel for appropriate sample processing that facilitates downstream genetic testing was recognised. Molecular tumour boards and multidisciplinary discussions are recommended to guide therapeutic decisions in mCRPC. The panel also highlighted the issue of reimbursement for genetic testing to reduce patient-borne costs and increase the reach of genetic testing among this patient population. This article aims to provide strategic and implementable recommendations to overcome the challenges in genetic testing for patients with mCRPC in Singapore.

89P Genomic profiling of wild-type gastrointestinal stromal tumor (GIST) reveals targetable mutations in multiple signaling pathways

GIST is the most common mesenchymal tumor of the gastrointestinal tract. Clinical trials or targeted therapies are recommended for c-kit and PDGFRA wild-type GIST patients who are unable to obtain multi-target protein tyrosine kinase inhibitors therapy. Thus, the identification of targetable mutations will gain new insights into the etiology of c-kit and PDGFRA wild-type GIST.

Abstract 2183: Genomic profiling of small bowl adenocarcinoma reveals targetable mutations in multiple signaling pathways

Abstract Background: Small bowel adenocarcinoma (SBA) is a rare malignancy of the gastrointestinal (GI) tract without approved targeted therapy. Because the treatment approaches for colorectal cancer showed limited efficacy in SBA, the NCCN guide strongly encourages SBA patients to participate in clinical trials. The identification of targetable mutations through genomic profiling will gain new insights into the etiology of SBA and enable physicians to select the matched trials for patients. Methods: To characterize actionable targets in 50 Chinese SBA patients, a 830-gene next-generation sequencing panel was applied to assess the mutational status of their tumor tissues, including SNV, insertions/deletions, CNV and re-arrangements. Also, paired genomic DNA sample was extracted and analyzed by a 139-gene NGS panel to identify pathogenic germline variants. Results: The most frequently mutated genes in this SBA cohort were TP53 (68%), KRAS (56%), APC (38%), SMAD4 (20%), CTNNB1 (16%), ARID2 (14%), FAT3 (12%), FBXW7 (12%), KMT2C (12%) and PIK3CA (12%). Potentially targetable alterations include BRAF (10%), MDM2 (10%), ERBB2/HER2 (8%), PIK3CA (4%) and MAP2K1 (4%). Except one V600E mutation, all mutations in BRAF are either type 2 (L597R) or type 3 (N581S and D594N) which were sensitive to MEK inhibitor trametinib. We also found two MAP2K1 activating mutations (K57E and K57N) which can be targeted by trametinib. ERBB2/HER2 was highly amplified in one patient (copy number 25) and ERBB2/HER2 driver mutations were seen in 3 (6%) patients including V842I (n =2) and V777L (n =1). These four patients were good candidates for HER2-targeted therapy clinical trials. We also observed two activating PIK3CA mutations (R108H and G364R) which may be sensitive to PIK3CA inhibitor alpelisib. In addition, we observed targetable gene amplification of MDM2 (n =1) and FGF3/4/19 (n =2). Interestingly, one patient carried an activating ZKSCAN1-MET fusion gene which can be targeted by FDA-approved MET inhibitor carbozantinib. Among 46 patients with available MSI status, two were designated as microsatellite instability. The median TMB of microsatellite stable patients was 3.7 mutations/Mb. Lastly, we observed five deleterious germline mutations, two for SBDS, one each for APC, ERCC5 and MLH1. Overall, at least 18 (36%) patients harbored potentially actionable genetic mutations. Conclusions: The mutational landscape of our SBA cohort provided compelling evidence that multiple signaling pathways play a role in the pathogenesis of SBA and many driver mutations in these pathways are targetable. Our findings indicated that SBA patients should participate in matched clinical trials for better management of this disease. Citation Format: Rong Liu, Xiaomo Li, Zhiming Zhao, Tonghui Ma, Fei Wang, Si Liu. Genomic profiling of small bowl adenocarcinoma reveals targetable mutations in multiple signaling pathways [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 2183.

The Role of Surgery in Meningiomas.

This review presents the most recent evidences and recommendations in the pre-, intra-, and post-surgical management of patients harboring meningiomas. Due to the increasing relevance of multimodal approaches, in order to preserve patients' neurological function and quality of life (QoL), the role of observation and radiation treatments (as either primary or adjuvant therapy) has also been discussed. Multiple advances in neurosurgery, including the use of the microscope and endoscope, improved preoperative neuroimaging, intraoperative image-guided approaches, and intraoperative neurophysiological monitoring, have extended the neurosurgeon's ability to remove lesions that were previously considered only partially resectable or unresectable, while minimizing morbidity. On the other hand, the preservation of patients' neurological integrity and QoL are increasingly important issues, more than complete tumor resection, for both patients and neurosurgeons. In this setting, stereotactic radiosurgery (SRS) and radiotherapy (RT) may be considered safe and effective alternatives for asymptomatic small- to moderate-sized tumors that demonstrate growth on serial imaging, or in combination with planned subtotal resection (STR) for tumors in critical locations. Data supporting the use of pharmacotherapy in meningiomas are, to date, weak, but the strength of the evidence might improve in the next future with the identification of targetable mutations. Complete microsurgical resection remains the standard of care if it can be achieved with minimal or no morbidity. However, many studies have reported SRS/RT as safe and effective treatments, either as primary approach or as complementary to surgery, especially when dealing with critically located meningiomas (e.g., cranial base) or in patients with comorbidity or wishing to avoid invasive treatments. The management of meningiomas is a field of complementary disciplines: neurosurgeon needs to work closely with radiation oncologists while tailoring the optimal treatment for these patients in order to achieve the best results.

Histologic, immunohistochemical, and molecular features of pituicytomas and atypical pituicytomas

Pituicytoma is a rare, poorly characterized tumor of the sellar region that is thought to be derived from neurohypophyseal pituicytes. Resection of pituicytomas is often associated with significant morbidity including diabetes insipidus and panhypopituitarism. Most of the literature on this tumor exists as small case series or case reports. Here we describe a cohort of fourteen pituicytoma resections from eleven patients. The average follow-up on these cases is 3.7 years with some patients having over 10 years of follow-up data available in the electronic medical record. Pituicytomas were frequently misdiagnosed on pre-operative imaging, and surgical resection was associated with persistent endocrine abnormalities. Histologically, the tumors showed a range of morphologies from epithelioid to spindled. All tumors were positive for TTF-1 with variable immunostaining for other markers including GFAP, EMA, S100, SSTR2A, and synaptophysin. Within this cohort are two patients with atypical pituicytomas which showed increased cellularity, pleomorphism, mitoses and elevated Ki-67 proliferation indexes when compared to non-atypical pituicytomas. Next generation sequencing performed on three tumors revealed alterations in genes involved in the MAPK pathway. Additionally, immunohistochemical staining for phosphorylated-ERK was positive in the majority of tumors. Increased awareness of the neoplastic entity and identification of targetable mutations have the potential to decrease the morbidity associated with resection of pituicytomas.

Clinical applications of genetic sequencing in lymphoma: A retrospective review.

e23169 Background: Personalized therapy through the identification of targetable mutations within individual tumors has increasingly become a focus in the management of patients (pts) with relapsed/refractory malignancy. To better understand how this is clinically applied, we reviewed 29 cases of B- and T-cell lymphomas that had genetic sequencing of their tumor. Methods: The electronic medical records of 29 pts who underwent Michigan Oncology Sequencing (MI-ONCOSEQ) testing at the University of Michigan from 2013-2016 were reviewed for disease and treatment history. Reports from whole-genome tumor sequencing were obtained for each patient to identify putative molecular targets. Results: Sixteen male and 13 female pts had a median age of 59 years (range 30-80 years) and median disease stage of IV at diagnosis. Five had CTCL, 5 PTCL, 11 follicular, 1 CLL/ mantle cell (MC), 1 MC, 1 marginal zone, 1 Waldenstrom’s (WM) and 4 DLBCL. Pts received a median of 2 therapies prior to MI-ONCOSEQ biopsy. Targetable mutations were identified in 15 pts and a total of 5 pts underwent MI-ONCOSEQ-based treatments. Bosutinib was given for FYB-FGR fusion, imatinib for FLI1-PDGFRB fusion, and everolimus for activating mTOR mutation with an avg. treatment duration of 3.6 weeks due to progressive disease. Bosutinib and imatinib were 3rd line therapies and everolimus was 5th. Another 2 pts were treated with ibrutinib for transformed WM with MYD88 mutation and bortezomib after classification of DLBCL as ABC-type based on MI-ONCOSEQ results, with CR in both. Other targetable mutations identified include BRAF, CDK, BCL2, EZH2 and NOTCH. Of the remaining 12 pts with targetable mutations, 8 pursued clinical trials, 2 responded to standard therapy, 1 died shortly after genetic analysis and 1 declined further therapy. About 50% of these pts remain alive. Conclusions: Our results demonstrate that targeted therapy is favored after standard therapy or clinical trial options are exhausted. Barriers to its use include the availability of clinical trials, off-label drug access and our incomplete knowledge of driver mutations. With further understanding of disease pathogenesis, we expect personalized therapy will be possible for all patients.

To B-(RAF) or Not to Be

The identification of targetable mutations has revolutionized the therapy of metastatic melanoma. In particular, BRAF and MEK inhibitors have a well-documented impact on overall survival in metastatic disease. However, therapeutic success is highly dependent on the correct identification of these mutations. We discuss the impact of molecular heterogeneity in this context.