Individual cancers harbor a set of genetic aberrations that can be informative for identifying rational therapies currently available or in clinical trials. We implemented a pilot study to explore ...the practical challenges of applying high-throughput sequencing in clinical oncology. We enrolled patients with advanced or refractory cancer who were eligible for clinical trials. For each patient, we performed whole-genome sequencing of the tumor, targeted whole-exome sequencing of tumor and normal DNA, and transcriptome sequencing (RNA-Seq) of the tumor to identify potentially informative mutations in a clinically relevant time frame of 3 to 4 weeks. With this approach, we detected several classes of cancer mutations including structural rearrangements, copy number alterations, point mutations, and gene expression alterations. A multidisciplinary Sequencing Tumor Board (STB) deliberated on the clinical interpretation of the sequencing results obtained. We tested our sequencing strategy on human prostate cancer xenografts. Next, we enrolled two patients into the clinical protocol and were able to review the results at our STB within 24 days of biopsy. The first patient had metastatic colorectal cancer in which we identified somatic point mutations in NRAS, TP53, AURKA, FAS, and MYH11, plus amplification and overexpression of cyclin-dependent kinase 8 (CDK8). The second patient had malignant melanoma, in which we identified a somatic point mutation in HRAS and a structural rearrangement affecting CDKN2C. The STB identified the CDK8 amplification and Ras mutation as providing a rationale for clinical trials with CDK inhibitors or MEK (mitogen-activated or extracellular signal-regulated protein kinase kinase) and PI3K (phosphatidylinositol 3-kinase) inhibitors, respectively. Integrative high-throughput sequencing of patients with advanced cancer generates a comprehensive, individual mutational landscape to facilitate biomarker-driven clinical trials in oncology.
Due to poor correlation between slice thickness and orientation, verification of medical imaging results by histology is difficult. Often validation of imaging findings of lesions suspicious for ...prostate cancer is driven by a subjective, visual approach to correlate in vivo images with histopathology. We describe fallacious assumptions in the correlation of imaging findings with pathology and identify the lack of accurate registration as a major obstacle in the validation of PET and PET/CT imaging in primary prostate cancer. Specific registration techniques that facilitate the most difficult part of the registration process—the mapping of pathology onto high-resolution imaging, preferably aided by the ex vivo prostate specimen—are discussed.
Use of next-generation sequencing (NGS) to identify clinically actionable genomic targets has been incorporated into routine clinical practice in the management of advanced solid tumors; however, the ...clinical utility of this testing remains uncertain.
To determine which patients derived the greatest degree of clinical benefit from NGS profiling.
Patients in this cohort study underwent fresh tumor biopsy and blood sample collection for genomic profiling of paired tumor and normal DNA (whole-exome or targeted-exome capture with analysis of 1700 genes) and tumor transcriptome (RNA) sequencing. Somatic and germline genomic alterations were annotated and classified according to degree of clinical actionability. Results were returned to treating oncologists. Data were collected from May 1, 2011, to February 28, 2018, and analyzed from May 1, 2011, to April 30, 2020.
Patients' subsequent therapy and treatment response were extracted from the medical record to determine clinical benefit rate from NGS-directed therapy at 6 months and exceptional responses lasting 12 months or longer.
During the study period, NGS was attempted on tumors from 1138 patients and was successful in 1015 (89.2%) (MET1000 cohort) (538 men 53.0%; mean SD age, 57.7 13.3 years). Potentially clinically actionable genomic alterations were discovered in 817 patients (80.5%). Of these, 132 patients (16.2%) received sequencing-directed therapy, and 49 had clinical benefit (37.1%). Exceptional responses were observed in 26 patients (19.7% of treated patients). Pathogenic germline variants (PGVs) were identified in 160 patients (15.8% of cohort), including 49 PGVs (4.8% of cohort) with therapeutic relevance. For 55 patients with carcinoma of unknown primary origin, NGS identified the primary site in 28 (50.9%), and sequencing-directed therapy in 13 patients resulted in clinical benefit in 7 instances (53.8%), including 5 exceptional responses.
The high rate of therapeutically relevant PGVs identified across diverse cancer types supports a recommendation for directed germline testing in all patients with advanced cancer. The high frequency of therapeutically relevant somatic and germline findings in patients with carcinoma of unknown primary origin and other rare cancers supports the use of comprehensive NGS profiling as a component of standard of care for these disease entities.
The MyProstateScore test was validated for improved detection of clinically significant (grade group ≥2) prostate cancer relative to prostate specific antigen based risk calculators. We sought to ...validate an optimal MyProstateScore threshold for clinical use in ruling out grade group ≥2 cancer in men referred for biopsy.
Biopsy naïve men provided post-digital rectal examination urine prior to biopsy. MyProstateScore was calculated using the validated, locked multivariable model including only serum prostate specific antigen, urinary prostate cancer antigen 3 and urinary TMPRSS2:ERG. The MyProstateScore threshold approximating 95% sensitivity for grade group ≥2 cancer was identified in a training cohort, and performance was measured in 2 external validation cohorts. We assessed the 1) overall biopsy referral population and 2) population meeting guideline based testing criteria (ie, prostate specific antigen 3-10, or <3 with suspicious digital rectal examination).
Validation cohorts were prospectively enrolled from academic (977 patients, median prostate specific antigen 4.5, IQR 3.1-6.0) and community (548, median prostate specific antigen 4.9, IQR 3.7-6.8) settings. In the overall validation population (1,525 patients), 338 men (22%) had grade group ≥2 cancer on biopsy. The MyProstateScore threshold of 10 provided 97% sensitivity and 98% negative predictive value for grade group ≥2 cancer. MyProstateScore testing would have prevented 387 unnecessary biopsies (33%), while missing only 10 grade group ≥2 cancers (3.0%). In 1,242 patients meeting guideline based criteria, MyProstateScore ≤10 provided 96% sensitivity and 97% negative predictive value, and would have prevented 32% of unnecessary biopsies, missing 3.7% of grade group ≥2 cancers.
In a large, clinically pertinent biopsy referral population, MyProstateScore ≤10 provided exceptional sensitivity and negative predictive value for ruling out grade group ≥2 cancer. This straightforward secondary testing approach would reduce the use of more costly and invasive procedures after screening with prostate specific antigen.
Fusions of androgen-regulated genes and v-ets erythroblastosis virus E26 oncogene homolog (avian) (ERG) occur in approximately 50% of prostate cancers, encoding a truncated ERG product. In ...prostatectomy specimens, ERG rearrangements are greater than 99% specific for prostate cancer or high-grade prostatic intraepithelial neoplasia adjacent to ERG-rearranged prostate cancer by fluorescence in situ hybridization and immunohistochemistry.
To evaluate ERG staining by immunohistochemistry on needle biopsies, including diagnostically challenging cases.
Biopsies from a retrospective cohort (n = 111) enriched in cores requiring diagnostic immunohistochemistry and a prospective cohort from all cases during 3 months (n = 311) were stained with an anti-ERG antibody (clone EPR3864).
Among evaluable cores (n = 418), ERG staining was confined to cancerous epithelium (71 of 160 cores; 44%), high-grade prostatic intraepithelial neoplasia (12 of 68 cores; 18%), and atypical foci (3 of 28 cores; 11%), with staining in only 2 of 162 cores (1%) diagnosed as benign. The ERG was expressed in about 5 morphologically benign glands across 418 cores and was uniformly expressed by all cancerous glands in 70 of 71 cores (99%).
ERG staining is more prostate cancer-specific than α-methylacyl-coenzyme A racemase, and staining in an atypical focus supports a diagnosis of cancer if high-grade prostatic intraepithelial neoplasia can be excluded. Thus, ERG staining shows utility in diagnostically challenging biopsies and may be useful in molecularly subtyping prostate cancer and in stratifying isolated high-grade prostatic intraepithelial neoplasia by risk of subsequent cancer.
Nephrogenic adenoma, also referred to as nephrogenic metaplasia, is an uncommon benign lesion of the urothelial tract, characterized by a circumscribed proliferation of tubules, cysts, and papillae ...lined by cells with low cuboidal to columnar epithelium. The diagnostic features that are useful in the recognition of this benign entity are the characteristic mixture of various architectural patterns, associated stromal edema and inflammation, hyaline sheath around tubules, eosinophilic colloidlike secretion within tubules, and lack of mitotic activity. Nephrogenic adenoma can be a significant diagnostic pitfall as certain histologic features, such as the presence of enlarged nuclei with prominent nucleoli, degenerative nuclear atypia, tiny tubules with blue mucin simulating signet ring cells, and focal invasion into superficial muscle, when taken out of context, can mimic malignancy. Herein, I report a case of nephrogenic adenoma with some worrisome histologic features and review the diagnostic criteria as well as pertinent morphologic malignant mimics of nephrogenic adenoma.
Renal medullary carcinomas (RMCs) and collecting duct carcinomas (CDCs) are rare subsets of lethal high-stage, high-grade distal nephron-related adenocarcinomas with a predilection for the renal ...medullary region. Recent findings have established an emerging group of fumarate hydratase (FH)-deficient tumors related to hereditary leiomyomatosis and renal cell carcinoma (HLRCC-RCCs) syndrome within this morphologic spectrum. Recently developed, reliable ancillary testing has enabled consistent separation between these tumor types. Here, we present the clinicopathologic features and differences in the morphologic patterns between RMC, CDC, and FH-deficient RCC in consequence of these recent developments. This study included a total of 100 cases classified using contemporary criteria and ancillary tests. Thirty-three RMCs (SMARCB1/INI1-deficient, hemoglobinopathy), 38 CDCs (SMARCB1/INI1-retained), and 29 RCCs defined by the FH-deficient phenotype (FH/2SC or FH/2SC with FH mutation, regardless of HLRCC syndromic stigmata/history) were selected. The spectrum of morphologic patterns was critically evaluated, and the differences between the morphologic patterns present in the 3 groups were analyzed statistically. Twenty-five percent of cases initially diagnosed as CDC were reclassified as FH-deficient RCC on the basis of our contemporary diagnostic approach. Among the different overlapping morphologic patterns, sieve-like/cribriform and reticular/yolk sac tumor-like patterns favored RMCs, whereas intracystic papillary and tubulocystic patterns favored FH-deficient RCC. The tubulopapillary pattern favored both CDCs and FH-deficient RCCs, and the multinodular infiltrating papillary pattern favored CDCs. Infiltrating glandular and solid sheets/cords/nested patterns were not statistically different among the 3 groups. Viral inclusion-like macronucleoli, considered as a hallmark of HLRCC-RCCs, were observed significantly more frequently in FH-deficient RCCs. Despite the overlapping morphology found among these clinically aggressive infiltrating high-grade adenocarcinomas of the kidney, reproducible differences in morphology emerged between these categories after rigorous characterization. Finally, we recommend that definitive diagnosis of CDC should only be made if RMC and FH-deficient RCC are excluded.
Abstract
Objectives
Biomarker expression evaluation for estrogen receptor (ER), progesterone receptor (PgR), and human epidermal growth factor receptor 2 (HER2) is an essential prognostic and ...predictive parameter for breast cancer and critical for guiding hormonal and neoadjuvant therapy. This study compared quantitative image analysis (QIA) with pathologists’ scoring for ER, PgR, and HER2.
Methods
A retrospective analysis was undertaken of 1,367 invasive breast carcinomas, including all histopathology subtypes, for which ER, PgR, and HER2 were analyzed by manual scoring and QIA. The resulting scores were compared, and in a subset of HER2 cases (n = 373, 26%), scores were correlated with available fluorescence in situ hybridization (FISH) results.
Results
Concordance between QIA and manual scores for ER, PgR, and HER2 was 93%, 96%, and 90%, respectively. Discordant cases had low positive scores (1%-10%) for ER (n = 33), were due to nonrepresentative region selection (eg, ductal carcinoma in situ) or tumor heterogeneity for PgR (n = 43), and were of one-step difference (negative to equivocal, equivocal to positive, or vice versa) for HER2 (n = 90). Among HER2 cases where FISH results were available, only four (1.0%) showed discordant QIA and FISH results.
Conclusions
QIA is a computer-aided diagnostic support tool for pathologists. It significantly improves ER, PgR, and HER2 scoring standardization. QIA demonstrated excellent concordance with pathologists’ scores. To avoid pitfalls, pathologist oversight of representative region selection is recommended.
Abstract Objective Androgen-induced E26 transformation-specific (ETS) gene fusion–positive tumors have been associated with aggressive prostate cancer. The aim is to evaluate the ETS gene ...rearrangement status on initial biopsy of patients registered in the Reduction by Dutasteride of Clinical Progression Events in Expectant Management trial study and determine if gene fusion status was associated with disease progression. Materials and methods Initial biopsy material from 146 men registered in Reduction by Dutasteride of Clinical Progression Events in Expectant Management trial study treated with dutasteride (73/146, 50%) and as placebo (73/146, 50%) were reviewed, and ERG and SPINK1 immunohistochemistry was performed. ERG- and SPINK1-negative cancer samples were evaluated for ETV1 , ETV4, and ETV5 rearrangements by fluorescence in situ hybridization. Frequency of ETS gene aberrations in both groups was correlated with cancer progression including prostate-specific antigen progression, Gleason progression, and progression-free survival by logistic analysis, pairwise differences, and chunk likelihood ratio tests for the genotype groups. Results and conclusions Of the 146 patients, 99 (67.8%) (placebo, 51; dutasteride, 48) samples displayed the following Gleason patterns: 3+3 = 6 in 80 (54.8%) (placebo, 39; dutasteride, 41), 3+4 = 7 in 18 (12.3%) (placebo, 11; dutasteride, 7), and 4+4 = 8 in 1(0.68%) (placebo, 1). The remaining 47 samples showed atypical glands in 5 (3.4%) (placebo, 2; dutasteride, 3), HGPIN in 9 (6.1%) (placebo, 5; dutasteride, 4), and benign in 33 (22.6%) (placebo, 15; dutasteride, 18). Immunohistochemistry findings were positive for ERG and SPINK1 in 56 (56%) (placebo, 31; dutasteride, 25) and 9 (6.1%) (placebo, 5; dutasteride, 4) cases, respectively. ETV1 and ETV4 rearrangements were noted in 2 cases (1.4%) (placebo, 1; dutasteride, 1) and 1 (0.7%) (placebo, 1) case, respectively. No significant differences in the incidence of prostate cancer molecular aberrations between the groups were observed. There was no evidence that ETS fusion status was associated with disease progression.
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