ETS Gene Family Research Articles

Abstract 4349: Characterization of a centrosome loss-induced tumorigenic signature in prostate epithelial cells

Abstract Prostate cancer (PCa) stands as the second leading cause of cancer death in American men, with overtreatment being common given the difficulty in distinguishing between indolent and aggressive cases. Unlike many cancers, PCa lacks hallmark mutations in key oncogenes and tumor-suppressor genes. Instead, PCa exhibit extensive genomic rearrangements and chromosomal instability (CIN). CIN occurs during PCa progression, producing ETS gene family fusions, PTEN loss and androgen receptor amplification. Importantly, the mechanism underlying CIN in PCa remains unclear. Previously, we found that cell within early-grade human primary prostate adenocarcinomas (PRAD) frequently lack centrosomes, and this frequency correlates with tumor grade. We demonstrated that transient removal of centrosomes within non-tumorigenic human prostate epithelial cells (hPrEC) induces CIN and was, strikingly, sufficient to transform subpopulations of cells capable of producing xenograft tumors in mice. To unravel the molecular mechanisms underlying this path to tumorigenesis, we isolated DNA and RNA from parental hPrECs, clonal lines subjected to transient centrosome loss, and xenograft tumor cells and performed whole genome sequencing (WGS) and bulk RNA-seq. This allowed us to characterize the genomic profiles induced by centrosome loss and to identify an associated mutational signature. We used MUTECT2 to identify single nucleotide variants. Kataegis loci were observed on multiple chromosomes in all transient centrosome removal samples. Copy number variations were also detected in these samples using FACETS and SEQUENZA. Next, we extracted the copy number (CN) signature with SigProfiler and Sigminer, comparing it to COSMIC CN signatures and WGS data from PRAD patients. Our results revealed that the transient centrosome loss signature bears similarity to CN signatures associated with chromothripsis, loss of heterozygosity, and homologous recombination repair deficiency. Patients with PRAD displaying the centrosome loss CN signature had a poorer prognosis. Additionally, our CN analysis discovered that centrosome loss induced mosaic loss of chromosome Y in our samples. To detect structural variations, we employed DELLY, MANTA, SVABA, revealing a high occurrence of both non-clustered and clustered translocations in transient centrosome loss samples. These translocations were validated in our RNA-seq data using STAR-Fusion. Ongoing analyses include inferring CNV from PCa scRNA-seq data, and determining cell populations with the centrosome loss CN-signature and their associated transcriptome features. This work unveils a comprehensive genomic profile stemming from centrosome loss and demonstrates its role in driving oncogenesis in PCa. These findings have the potential to establish centrosome loss as a hallmark in PCa stratification, and lead to a significant advancement in prostate tumor treatment. Citation Format: Jiawen Yang, Diogo de Oliveira Pessoa, John M. Ryniawec, Emily Loertscher, Anne E. Cress, Megha Padi, Gregory C. Rogers. Characterization of a centrosome loss-induced tumorigenic signature in prostate epithelial cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4349.

Machine Learning–Supported Diagnosis of Small Blue Round Cell Sarcomas Using Targeted RNA Sequencing

Small blue round cell sarcomas (SBRCSs) are a heterogeneous group of tumors with overlapping morphologic features but markedly varying prognosis. They are characterized by distinct chromosomal alterations, particularly rearrangements leading to gene fusions, whose detection currently represents the most reliable diagnostic marker. Ewing sarcomas (ESs) are the most common SBRCSs, defined by gene fusions involving EWSR1 and transcription factors of the ETS gene family, while the most frequent non-EWSR1-rearranged SBRCSs harbor a CIC rearrangement. Unfortunately, the identification of CIC::DUX4 translocation events, the most common CIC rearrangement, is challenging with current methods. Here, a machine-learning approach to support SBRCS diagnosis relying on gene expression profiles measured via targeted sequencing is presented. The analyses on a curated cohort of 69 soft tissue tumors (STT) showed markedly distinct expression patterns for SBRCS subgroups. A random forest (RF) classifier trained on ES and CIC-rearranged cases predicted probabilities of being CIC-rearranged > 0.9 for CIC-rearranged-like sarcomas and < 0.6 for other SBRCS. Testing on a retrospective cohort of 1335 routine diagnostic cases identified 15 candidate CIC-rearranged tumors with a probability > 0.75, all of which supported by expert histopathological reassessment. Furthermore, the multi-gene RF classifier appeared advantageous over using high ETV4 expression alone, previously proposed as surrogate to identify CIC rearrangement. Taken together, the expression-based classifier can offer valuable support for SBRCS pathological diagnosis.

Genome-wide identification and characteristic analysis of ETS gene family in blood clam Tegillarca granosa

BackgroundETS transcription factors, known as the E26 transformation-specific factors, assume a critical role in the regulation of various vital biological processes in animals, including cell differentiation, the cell cycle, and cell apoptosis. However, their characterization in mollusks is currently lacking.ResultsThe current study focused on a comprehensive analysis of the ETS genes in blood clam Tegillarca granosa and other mollusk genomes. Our phylogenetic analysis revealed the absence of the SPI and ETV subfamilies in mollusks compared to humans. Additionally, several ETS genes in mollusks were found to lack the PNT domain, potentially resulting in a diminished ability of ETS proteins to bind target genes. Interestingly, the bivalve ETS1 genes exhibited significantly high expression levels during the multicellular proliferation stage and in gill tissues. Furthermore, qRT-PCR results showed that Tg-ETS-14 (ETS1) is upregulated in the high total hemocyte counts (THC) population of T. granosa, suggesting it plays a significant role in stimulating hemocyte proliferation.ConclusionOur study significantly contributes to the comprehension of the evolutionary aspects concerning the ETS gene family, while also providing valuable insights into its role in fostering hemocyte proliferation across mollusks.

Erythroblast transformation-specific transcription factor fusions in prostate cancer.

224 Background: Common drivers in advanced prostate cancer (PC) involve fusions of the 3’ DNA binding domain-containing region of an Erythroblast Transformation Specific (ETS) transcription factor gene with a 5’ region of another gene, often one that is androgen-regulated. Previous work indicates that PCs harboring TMPRSS2:ERG fusions are more dependent on androgen signaling, and men with such tumors may, therefore, be more responsive to the effects of androgen deprivation therapy than men lacking this fusion. In this study, we examined the frequency of fusions involving ETS-family genes, including TMPRSS2:ERG, and determined how often such fusions would be missed if detection relied solely on DNA sequencing. Methods: To identify fusions and compare DNA-only versus DNA plus RNA sequencing, we utilized the Oncomap ExTra genomic profiling assay. This assay performs whole-exome, whole-transcriptome DNA and RNA sequencing of tumor and matched normal samples to identify somatic alterations in tumors. Single-nucleotide variants, indels, copy number alterations, alternative transcripts, and gene fusions are all detected. We specifically searched for fusions involving ETS transcription factor genes ERG and ETV1- 7. Results: A total of 512 PC patient samples assayed between April 2018 and July 2022 were included in the analysis; 226 ETS fusions were present in 223 (43.6%) patients; 3 patients carried two fusions. There were 196 ERG fusions including 185 (36.1%) patients having the familiar TMPRSS2: ERG fusion and 8 (1.6%) patients with a SLC45A3: ERG fusion, which is known to be associated with particularly poor prognosis. ETV1, 4, and 5 fusions were found in 29 (5.7%) patients and involved 12 different 5’ partner genes, the most common of which were SLC45A3 (6 fusions) and CANT1 (4 fusions). The two partner genes were on the same chromosome in 192 fusions, with 190 requiring a single deletion to create the fusion and 2 requiring a single inversion. For the 34 fusions involving genes on different chromosomes, a single translocation would be sufficient to produce the fusion gene in 23 cases; in 11 cases more than one structural rearrangement would be required. A total of 66 (29.6%) fusions were not detected in the DNA sequencing data, including 40 (21.6%) TMPRSS2: ERG fusions. In addition, 16 fusions were detected only in the DNA data, as RNA could not be sequenced, including 13 TMPRSS2: ERG fusions. Conclusions: In addition to TMPRSS2: ERG, the Oncomap ExTra assay identified several low frequency ETS fusions, all of which could be used to assist patients and physicians to select appropriate treatments. The identification of ETS fusions appears to be limited when using only DNA sequencing. Oncomap ExTra RNA analysis identified 66 additional fusions, representing almost 30% of those present, not identified by whole-exome DNA sequencing, suggesting RNA plus DNA assays detect fusions more reliably than DNA-only assays.

Symphony in the crowd: Key genetic alterations in prostate cancer.

Androgen receptor (AR) signaling have been frequently targeted for treating prostate cancer (PCa). Even though primarily patients receive a good therapeutic outcome by targeting AR signaling axis, eventually it emerges resistance by altering the genetic makeup of prostate cells. However, to develop an effective therapeutic regime, it is essential to recognize key genetic alterations in PCa. The most common genetic alterations that give rise to distinct androgen different differentiation states are gene fusion of TMPRSS2 with ETS family genes, deletion, or mutation of tumor suppressor PTEN and TP53 gene, amplification or splicing of AR, altered DNA repair genes. In this review, we describe key genes and genetic changes that have been recognized to contribute to altered prostate environment.

Sarcoma of the right femur with heterogeneous morphology similar to myoepithelial carcinoma and amplification of the EWSR1 gene in a 14-year-old boy. Clinical observation and literature review

Ewing sarcoma (ES) is one of the most frequent primary bone tumors and has a well-studied diagnostically important genetic background. However, there are primary bone round-cell tumors with atypical morphology different from conventional ES, tumors with rearrangement of the EWSR1 gene with partner genes not from the ETS gene family, tumors with unusual changes in the EWSR1 gene (amplification or deletion), which can cause significant diagnostic difficulties. In this article, we will describe a case of a primary bone tumor with an atypical morphology similar to myoepithelial carcinoma, where an amplification of the EWSR1 gene was detected. According to morphological, immunological, genetic and clinical signs, this tumor was classified as a sarcoma from the EWSR1::non-ETS group of round-cell sarcomas, namely a sarcoma with EWSR1::NFATC2 rearrangement, first formalized in the WHO classification of soft tissue tumors in 2020.

Clinical and morphological characteristics of Ewing's sarcoma and the algorithm for diagnosing undifferentiated round cell sarcomas

The group of undifferentiated round cell sarcomas, according to the World Health Organization Classification, in addition to Ewing's sarcoma (ES), includes round cell sarcoma with rearrangement of the EWSR1 gene with partners not from the ETS gene family, sarcoma with BCOR gene alterations, CIC -rearranged sarcoma. Despite the fact that all tumors have clear histological and immunological criteria, their diagnosis can be difficult, given the fact that there are overlapping variants of the morphological picture and immunophenotype both within the group and with other round cell tumors. Present a comparative analysis of genetically verified ES, sarcoma with BCOR gene alterations and CIC-rearranged sarcoma. A comparative study of biopsy specimens of bones, soft tissues and internal organs was carried out in 118 patients with ES, 10 with BCOR gene alterations and 8 with CIC-rearranged sarcomas. All cases were genetically verified. The following research methods were used: histological, immunohistochemical, RT-PCR, RNA sequencing and FISH. Within our cohort, it was shown that ES predominantly affects bones, while soft tissue localization is more typical for the other two undifferentiated round cell sarcomas. Histologically, in the overwhelming majority of cases, ES is characterized by a monomorphic round-cell structure; on the contrary, heterogeneous structure is typical for sarcoma with alterations of the BCOR gene, CIC-rearranged sarcoma. High sensitivity and specificity of CD99/NKX2.2 co-expression for ES, BCOR/SATB2/TLE1 for sarcoma with BCOR gene alterations, high specificity and low sensitivity of WT1/ETV4 co-expression for CIC-rearranged sarcoma was shown. For the differential diagnosis of undifferentiated round-cell sarcomas, it is necessary to take into account the clinical, morphology when compared with the data of the IHC study, and verification by molecular genetic methods is necessary to improve the accuracy of diagnosis.

In situ expression of ERG protein in the context of tumor heterogeneity identifies prostate cancer patients with inferior prognosis.

Prognostic biomarkers for prostate cancer are needed to improve prediction of disease course and guide treatment decisions. However, biomarker development is complicated by the common multifocality and heterogeneity of the disease. We aimed to determine the prognostic value of candidate biomarkers transcriptional regulator ERG and related ETS family genes, while considering tumor heterogeneity. In a multisampled, prospective, and treatment‐naïve radical prostatectomy cohort from one tertiary center (2010–2012, median follow‐up 8.1 years), we analyzed ERG protein (480 patients; 2047 tissue cores), and RNA of several ETS genes in a subcohort (165 patients; 778 fresh‐frozen tissue samples). Intra‐ and interfocal heterogeneity was identified in 29% and 33% (ERG protein) and 39% and 27% (ETS RNA) of patients, respectively. ERG protein and ETS RNA was identified exclusively in a nonindex tumor in 31% and 32% of patients, respectively. ERG protein demonstrated independent prognostic value in predicting biochemical (P = 0.04) and clinical recurrence (P = 0.004) and appeared to have greatest prognostic value for patients with Grade Groups 4–5. In conclusion, when heterogeneity is considered, ERG protein is a robust prognostic biomarker for prostate cancer.

Osteosarcoma/Ewing Sarcoma

Osteosarcoma/Ewing Sarcoma

Genetic alterations in Ewing’s sarcoma: What do we know so far?

Ewing’s sarcoma (EwS) is the second most common cancer that affects bone in children and adolescents. EwS is an aggressive malignancy with a projected overall survival of 70% for the low risk localized and 30% for the metastatic tumors. EwS is genetically described by its unique translocation that fuses FET family genes with the ETS family genes encoding transcription factors. The most frequent molecular event in over 90% of EwS cases is the translocation between EWSR1–FLI1. Additional events, ingincluding TP53, mutations, and CDKN2A deletions, have been reported but in low incidences. Hitherto, new research on EwS molecular processes is needed to lead to early diagnosis, disease monitoring, treatment development, improve patients’ survival, and quality of life. In this review, we outline the presently available information on the genetics underlying EwS carcinogenesis, investigate the existing understanding of the genetics underpinning EwS, and discuss the future directions for research on EwS.

Implementation of a prostate cancer-specific targeted sequencing panel for credentialing of patient-derived cell lines and genomic characterization of patient samples.

Primary and metastatic prostate cancers have low mutation rates and recurrent alterations in a small set of genes, enabling targeted sequencing of prostate cancer-associated genes as an efficient approach to characterizing patient samples (compared to whole-exome and whole-genome sequencing). For example, targeted sequencing provides a flexible, rapid, and cost-effective method for genomic assessment of patient-derived cell lines to evaluate fidelity to initial patient tumor samples. We developed a prostate cancer-specific targeted next-generation sequencing (NGS) panel to detect alterations in 62 prostate cancer-associated genes as well as recurring gene fusions with ETS family members, representing the majority of common alterations in prostate cancer. We tested this panel on primary prostate cancer tissues and blood biopsies from patients with metastatic prostate cancer. We generated patient-derived cell lines from primary prostate cancers using conditional reprogramming methods and applied targeted sequencing to evaluate the fidelity of these cell lines to the original patient tumors. The prostate cancer-specific panel identified biologically and clinically relevant alterations, including point mutations in driver oncogenes and ETS family fusion genes, in tumor tissues from 29 radical prostatectomy samples. The targeted panel also identified genomic alterations in cell-free DNA and circulating tumor cells (CTCs) from patients with metastatic prostate cancer, and in standard prostate cancer cell lines. We used the targeted panel to sequence our set of patient-derived cell lines; however, no prostate cancer-specific mutations were identified in the tumor-derived cell lines, suggesting preferential outgrowth of normal prostate epithelial cells. We evaluated a prostate cancer-specific targeted NGS panel to detect common and clinically relevant alterations (including ETS family gene fusions) in prostate cancer. The panel detected driver mutations in a diverse set of clinical samples of prostate cancer, including fresh-frozen tumors, cell-free DNA, CTCs, and cell lines. Targeted sequencing of patient-derived cell lines highlights the challenge of deriving cell lines from primary prostate cancers and the importance of genomic characterization to credential candidate cell lines. Our study supports that a prostate cancer-specific targeted sequencing panel provides an efficient, clinically feasible approach to identify genetic alterations across a spectrum of prostate cancer samples and cell lines.

Abstract PO-102: Multifocal analysis of the ETS (-) subtypes, mutated SPOP and overexpression of SPINK-1, in prostate cancer from Colombian patients as a process of understanding the carcinogenesis model of the disease

Abstract The Cancer Genome Atlas (TCGA) Research Network defined the SPOP-mutant subset of prostate cancers (PCa) had frequent overexpression of SPINK1 mRNA, which suggests a relationship in these subtypes that had not been evaluated simultaneously in other studies on ETS(-) subtypes as a key feature in the molecular taxonomy of prostate cancer. However, this analysis was performed on the index tumors and it is suggested that a better knowledge of the different molecular profiles of different neoplastic foci, in the same prostate, could be affecting the relationship of the molecular subtypes and prognosis of the disease. With an approximate 50% prevalence of ETS family gene fusions, attempts to molecularly characterize PCa often begin with the division into ETS(-) and ETS (+). To represent the molecular heterogeneity of PCa, which could improve medical decision-making, we aim to study it through the expression of SPINK-1 and mutations in SPOP; as well as the TMPRSS2-ERG fusion status, in order to assess the clonality of the foci in each patient and also the possible association of this alteration with different degrees of differentiation and lymph node metastasis. FFPE samples of different foci with different lesion degrees: High-Grade Prostatic Intraepithelial Neoplasia (n=17), PCa foci with different Gleason scores (n= 53; GL3: (n=23); GL4: (n=23) and GL5: (n=7)), and positive lymph node (LN) (n=13) from radical prostatectomy from twenty patients were used to analyse the presence of TMPRSS2-ERG fusion and expression levels of ERG and SPINK-1 using RT-PCR. Sanger sequencing was used in exon 6 and 7 to analyze mutations in SPOP. The molecular concordance between the different prostatic foci of the same patient was determined, taking into account subclonal events. The LN were compared with prostatic foci to try to establish its clonal origin. The results indicate that multifocal PCa may have monoclonal or multiclonal origin. SPINK-1 overexpression was the predominant pattern in the LN, while the opposite was the most frequent in the HGPIN samples. None of the thirteen analyzed LN showed the same pattern of other PCa foci from each patient. Metastasis have less molecular heterogeneity than pre-neoplastic lesions. The ERG(+) subtype was found in 54.7% of the foci and 70% of the patients. No mutations were found in SPOP. The frequency of overexpressed SPINK-1 in the 20 patients was 60%. In this study, the frequency of SPINK-1 cases overexpressed in ERG(-) taking into account all the samples analyzed as independent, even if they were from the same patient, due to the high heterogeneity in PCa, coincides with that expected (11%), but it should be taken into account that the foci that tested positive did not show total exclusivity with ERG(+), and in fact, there were more associated with it (74%), which does not agree with what was found in other studies that had not taken into account samples of patients from our country, which highlights the importance of personalized medicine and of not extrapolating results from other populations in our population. Citation Format: Yenifer Y. Segura Moreno, María C. Sanabria Salas, Jorge A. Mesa López De Mesa, Rodolfo Varela Ramirez, Natalia L. Acosta Vega, Martha L. Serrano López. Multifocal analysis of the ETS (-) subtypes, mutated SPOP and overexpression of SPINK-1, in prostate cancer from Colombian patients as a process of understanding the carcinogenesis model of the disease [abstract]. In: Proceedings of the AACR Virtual Conference: 14th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2021 Oct 6-8. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr PO-102.

ETS Family Transcription Factor Fusions in Childhood AML: Distinct Expression Networks and Clinical Implications

The ETS family of genes encode transcription factors (TFs) containing the ETS DNA binding domain, which have roles in cellular growth and development, including embryonic hematopoiesis. Dysregulation of these genes is associated with malignant transformation and tumorigenesis. In childhood acute myeloid leukemia (AML), the MNX1-ETV6 t(7;12)(q36;p13) and FUS-ERG t(16;21)(p11;q22) fusions are associated with adverse outcome. However, the biological and clinical implications of other ETS oncofusions in pediatric AML remain unknown.We identified 62 ETS gene fusions in 1,473 primary diagnostic AML samples (4.2%) using whole transcriptome RNA-sequencing and karyotype data. Four ETS family genes were identified to be involved in fusions with various partner genes: ETV6, ERG, FEV, and FLI1. Fusions with ETV6 were the most abundant (58%, 36/62) while FEV and FLI1 were the least; 21 fusion partners were identified where many function as TFs and co-activators (Figure 1A). MNX1-ETV6 (N=16) is enriched in infants (87.5% < 3 years, p < 0.001, Figure 1B), consistent with previous reports. ETV6 fusions with various partners (ETV6-Other, N=20) were likewise enriched in infants (50% < 3 years) and were significantly younger than patients without ETS fusions (median age: 3.0 vs 9.6 years, p = 0.025). FUS-ERG (N=10), HNRNPH1-ERG (N=8), and ETS fusions with various partners (ETS-Other, N=8) were primarily identified in patients 5-18 years old.Outcomes for patients with ETS fusions was determined after censoring for stem cell transplantation. Patients with ETS fusions as a collective group had adverse outcome with an EFS of 17.7% vs 39.9% (p = 0.047, Figure 1C), similar to high-risk cases in the reference group (22%), suggesting that patients with any ETS fusion may be considered high risk. Evaluation of outcomes by individual fusion groups at 3 years from diagnosis demonstrated an EFS of 0% for HNRNPH1-ERG, 18.0% for FUS-ERG, 14.2% for ETV6-Other, 20.8% for ETS-Other, and 28.4% for those with MNX1-ETV6. Twenty-one patients (37.5%) with ETS family fusions received stem cell transplant (SCT) in first complete remission, including HNRNPH1-ERG (N=5), FUS-ERG (N=3), ETV6-Other (N=5), ETS-Other (N=2), and MNX1-ETV6 (N=6). For these SCT recipients, OS at 3 years after transplant was 60.2%.We investigated whether ETS family fusions might have similar transcriptome profiles. Unsupervised uniform manifold approximation and projection (UMAP) on RNA-seq gene expression data followed by Leiden clustering found that individual fusions clustered in the same 3D space. More importantly, ETS fusion groups clustered closely to one another, indicating a shared transcriptional profile (Figure 1D, circle). Next, ETS fusion groups were each independently compared to the reference cohort (N=1421) using differential expression (DE) analysis. Intersection of DE genes revealed 17 overexpressed genes common to ETS fusions and 9/17 (52%) were also dysregulated when contrasting ETS cohorts to healthy normal marrows' transcriptome (N=68, Figure 1E). The minimal set of dysregulated genes included an adhesion molecule EDIL3, a prostaglandin (PG) enzyme HPGD, and a tyrosine phosphatase PTP4A3, which is strongly associated with progression in lymphoblastic leukemia and multiple myeloma. EDIL3 was reported to be overexpressed in MNX1-ETV6 and we found this molecule is a common feature of ETS fusions and their cellular dysregulation. The minimal set of 9 genes were further investigated using protein interaction networks defined from Pathway Commons v11. FUS-ERG and HNRNPH1-ERG both had significantly (adj. p < 0.001) activated HPGD networks; PG-E synthase and > 10 PG metabolism genes were upregulated. PG metabolism has important roles in regulating hematopoietic stem and progenitor (HSPC) functions and PG-E2 was shown to increase HSPC survival. ETV6-MXN1, ETV6-Other, and FUS-ERG had activated PTP4A3 networks and its expression was associated with sensitivity to BET inhibitors (BETi) in myeloma. They also exhibited increased activity of an ERG network with the overexpression of upstream regulators CBFA2T3 and GATA, and downstream targets like VWF and ZBTB16.Overall, we show that ETS fusions are uniformly high risk and share dysregulated cell adhesion (EDIL3) and transcriptional networks for ERG, HPGD, and PTP4A3, which provide opportunities for further research into the metabolome and therapeutics (BETi) in these fusions. [Display omitted] DisclosuresShaw: T-Cell and/or Gene Therapy for Cancer: Patents & Royalties.

MP60-08 DEEP TRANSCRIPTOMIC PROFILING OF PROSTATE CANCER WITH QUANTITATIVE MEASURES: A SPECTRA APPROACH

You have accessJournal of UrologyProstate Cancer: Markers (MP60)1 Sep 2021MP60-08 DEEP TRANSCRIPTOMIC PROFILING OF PROSTATE CANCER WITH QUANTITATIVE MEASURES: A SPECTRA APPROACH Heidi Hanson, Jacob Ambrose, Brock O'Neil, Greg Lee, Claire Leiser, Rosalie Waller, Joemy Ramsay, Michael Madsen, Rupam Das, Christopher Dechet, Brian Avery, and Nicola Camp Heidi HansonHeidi Hanson More articles by this author , Jacob AmbroseJacob Ambrose More articles by this author , Brock O'NeilBrock O'Neil More articles by this author , Greg LeeGreg Lee More articles by this author , Claire LeiserClaire Leiser More articles by this author , Rosalie WallerRosalie Waller More articles by this author , Joemy RamsayJoemy Ramsay More articles by this author , Michael MadsenMichael Madsen More articles by this author , Rupam DasRupam Das More articles by this author , Christopher DechetChristopher Dechet More articles by this author , Brian AveryBrian Avery More articles by this author , and Nicola CampNicola Camp More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000002095.08AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Abstract INTRODUCTION AND OBJECTIVE: Methods that embrace the complexity of prostate cancer (CaP) gene expression are necessary for accurate phenotypic characterization. We previously presented a novel agnostic computational framework, SPECTRA, to describe RNA sequencing (RNAseq) data using multiple quantitative expression variables, or transcriptomic spectra (TrS). Here, we implement this technique to derive a set of TrS variables for CaP tumors from The Cancer Genome Atlas (TCGA). We compare the identified TrS with clinical and sample characteristics, progression-free interval, and previously established CaP subtypes. METHODS: Gene-level RNAseq data were downloaded from the Genomic Data Commons (GDC) Data Portal. Data were preprocessed using the SPECTRA protocol (nsamples=480, ngenes = 10,438) and matrix factorization was used to derive quantitative measures for each TrS. Linear, logistic, multinomial logistic, and Cox regression were used to assess the relationship between TrS and age, Gleason Risk Score, tumor stage, and progression free interval. Two approaches were used to select TrS associated with demographic, clinical, and molecular features of the tumors; “hard-thresholding” (Bonferonni corrected p-value) and lasso regularization. We compare model fit statistics to determine the difference in predictive power between our TrS and previously defined molecular subtypes defined by fusion of ETS family genes. RESULTS: We identified 21 TrS in our data that together explain 65.5% of the variance in global gene expression across CaP tumors in TCGA. Many of the TrS were associated with demographic and clinical characteristics of the patients and progression-free interval, with TrS3 having the strongest associations (Figure 1). The difference in predictive power of the TrS vs the previously identified molecular subtypes was substantial, with the difference in pseudo R-square in the range of 30% on average. This suggests that more information can be gained from quantitative vs. qualitative measures of gene expression. CONCLUSIONS: This approach had substantially better model fit than traditional qualitative tumor classifications and could lead to innovative ways to understanding gene expression patterns driving individual risk, treatment response and survival. Source of Funding: 5K07CA230150-03 © 2021 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 206Issue Supplement 3September 2021Page: e1044-e1044 Advertisement Copyright & Permissions© 2021 by American Urological Association Education and Research, Inc.MetricsAuthor Information Heidi Hanson More articles by this author Jacob Ambrose More articles by this author Brock O'Neil More articles by this author Greg Lee More articles by this author Claire Leiser More articles by this author Rosalie Waller More articles by this author Joemy Ramsay More articles by this author Michael Madsen More articles by this author Rupam Das More articles by this author Christopher Dechet More articles by this author Brian Avery More articles by this author Nicola Camp More articles by this author Expand All Advertisement Loading ...

Prostate cancer.

Prostate cancer is a complex disease that affects millions of men globally, predominantly in high human development index regions. Patients with localized disease at a low to intermediate risk of recurrence generally have a favourable outcome of 99% overall survival for 10 years if the disease is detected and treated at an early stage. Key genetic alterations include fusions of TMPRSS2 with ETS family genes, amplification of the MYC oncogene, deletion and/or mutation of PTEN and TP53 and, in advanced disease, amplification and/or mutation of the androgen receptor (AR). Prostate cancer is usually diagnosed by prostate biopsy prompted by a blood test to measure prostate-specific antigen levels and/or digital rectal examination. Treatment for localized disease includes active surveillance, radical prostatectomy or ablative radiotherapy as curative approaches. Men whose disease relapses after prostatectomy are treated with salvage radiotherapy and/or androgen deprivation therapy (ADT) for local relapse, or with ADT combined with chemotherapy or novel androgen signalling-targeted agents for systemic relapse. Advanced prostate cancer often progresses despite androgen ablation and is then considered castration-resistant and incurable. Current treatment options include AR-targeted agents, chemotherapy, radionuclides and the poly(ADP-ribose) inhibitor olaparib. Current research aims to improve prostate cancer detection, management and outcomes, including understanding the fundamental biology at all stages of the disease.

Detection of tmprss2-erg and tmprss2-egr1 gene fusion in prostate cancer from a Chinese population

BackgroundTMPRSS2: ETS gene fusion occurs recurrently in a high proportion of prostate cancer (PCa) patients in Western countries. However, for Chinese PCa patients, no solid conclusion could be drawn from the present studies, as the results varied considerably between the limited reports.ResultsIn this study, we evaluated the prevalence of such gene rearrangements in a small number of Chinese PCa patients and discovered that 6 out of 27 (22.2%) were found to harbor the TMPRSS2: ERG fusion, the ratio was much lower than that in Western countries. Furthermore, we first identified TMPRSS2: EGR1 gene fusion, suggesting other chromosome rearrangements besides ETS gene family harbor in prostate cancer. The hybrid transcript was predicted to encode a truncated EGR1 protein by ORF finder, which might play a key role in prostate cancer.ConclusionsWe reported that the total occurrence rate of TMPRSS2: ERG fusion gene in this small group of Chinese patients was lower than the reported frequencies in European descent patients but comparable to other reported frequencies in Asian populations. The occurrence of TMPRSS2: EGR1 gene fusion suggested other chromosome rearrangements in prostate cancer.

Sarcome avec transcrit de fusion EWSR1-PATZ1 Une nouvelle observation avec revue de la littérature

Sarcoma with EWSR1-PATZ1 gene fusion is an exceedingly rare and newly described Ewing-like sarcoma harboring EWSR1 rearrangements involving fusion partners other than ETS family genes. The clinical, histopathologic and immunophenotypic features of cases reported in literature are fairly diverse and not specific. We report a new case report posing real challenges for histological and molecular diagnosis.

Abstract 2012: Recurrent rearrangements of NAALADL2 in prostate, breast, cervical, head and neck and lung squamous cell carcinoma

Abstract Prostate cancer is a heterogeneous disease with unique molecular aberrations present in patient sub-groups. Distinct prostate cancer molecular changes have been shown to associate with specific clinical outcomes, suggesting the potential of molecular markers as diagnostic and prognostic biomarkers for prostate cancer. Recurrent ETS family gene fusions, BRAF and SPINK1 overexpression account for about 50-60% of the prostate cancer cases. Genetic aberrations in the remaining 40-50% of the cases is not known. Our attempt to identify new molecular markers in prostate cancer led to the identification of NAALADL2 gene shown to be associated with aggressive prostate cancer. In this study, we carried out a comprehensive analysis of genomic changes of NAALADL2 in prostate and other solid cancers by analyzing copy number changes and gene expression using TCGA next generation RNA sequencing data. We observed recurrent amplification, rearrangement, deletion, mutations and over-expression of NAALADL2 in prostate cancer cases. Notably, we observed mutually exclusive aberrations in NAALADL2 when compared to other cases with known prostate cancer aberrations including ETS gene fusions, indicating NAALADL2 as a distinct molecular sub-set of prostate cancer. Independent validation by fluorescent in situ hybridization (FISH) analysis using break apart probe for NAALADL2 on 874 prostate cancer revealed recurrent amplification and rearrangements in about 8% (71/874) [PN1] of the cases with higher prevalence in Caucasian American than African American cases. Based on these results, we explored prostate cancer TGCA gene fusion database and identified additional cases with gene fusions involving NAALADL2. We selected one of the gene fusions identified in the TCGA database involving NAALADL2-PIK3CA and conducted in vitro functional characterization studies and showed its oncogenic properties. Gene expression microarray analysis of RWPE1 cells transfected with NAALADL2-PIK3CA showed dysregulation of genes involved in cancer related pathways, further suggesting a role for NAALADL2-PIK3CA in prostate cancer development. Based on these studies, we explored the incidence of NAALADL2 gene fusion in other solid cancers including lung squamous cell cancer (LUSC), ovarian cancer, head and neck cancer, cervical cancer and breast cancer shown to have recurrent gene fusions identified in the TCGA gene fusion database. Notably, recurrent rearrangements and amplification are seen in a large subset (45%) of LUSC patients, but not in lung adenocarcinoma, suggesting that NAALADL2 could be developed as a novel biomarker in LUSC. Further validation studies using FISH in our independent cohort of LUSC and breast cancer patients including 79 patients from Ghana confirmed recurrent rearrangements and amplification in a subset of cases. In conclusion, similar to ERG, BRAF and FGFR genes, we show recurrent gene fusions of NAALADL2 across multiple solid cancer with potential applications as a pan cancer molecular marker for cancer diagnosis and a potential target for drug development. Citation Format: Pavithra D. Arachchige, Shannon Carskadon, James Hu, Justin Fernando, Darshan S. Chandrashekar, Nilesh S. Gupta, Sean R. Williamson, Dhananjay A. Chitale, Craig G. Rogers, James O. Peabody, Mani Menon, Tarek A. Bismar, Evelyn Jiagge, Sooryanarayana Varambally, Nallasivam Palanisamy. Recurrent rearrangements of NAALADL2 in prostate, breast, cervical, head and neck and lung squamous cell carcinoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2012.

Prevalence and genetic features of TMPRSS2-ERG fusion in Chinese patients with prostate cancer.

e17529 Background: Prostate cancer (PCa) is one of the most common malignancies, with rising incidence rate in China. The Cancer Genome Atlas (TCGA) revealed 53% of patients with PCa had ETS family gene fusions. The most frequent fusion type of ETS fusions is TMPRSS2-ERG, which may predicts resistance to taxane and androgen-deprivation therapies. The prevalence of TMPRSS2-ERG fusion in Chinese PCa patients evaluated by fluorescence in situ hybridization (FISH) or immunohistochemistry (IHC) varied from 7.5% to 78.0%. However, the sample sizes were small. In the present study, we investigated the prevalence and genetic features of TMPRSS2-ERG fusion by next generation sequencing (NGS) in a larger Chinese PCa cohort. Methods: Genomic profiling was performed through NGS from Chinese patients with PCa between January, 2017 and November, 2019. Formalin fixed paraffin-embedded (FFPE) tumor specimens or blood samples from participants were collected for NGS. IHC staining for PD-L1 expression was performed using PD-L1 IHC 22C3 pharmDx assay or Ventana PD-L1 SP263 assay. Data analyses were performed using SPSS and R 3.6.1. Results: A total of 526 Chinese PCa patients were included in this study. The median age was 70 (range, 29-90) years old. We observed 13.1% patients with a positive PD-L1 expression, 3.0% patients with MSI-H, and a median TMB of 4.0 muts/Mb (range: 0-72.9). TMPRSS2 fusions were detected in 47 (8.9%) PCa patients, and 6.8% of patients had TMPRSS2-ERG fusion, which is significantly lower than that of Caucasian patients. The PD-L1 expression pattern and TMB distribution of the TMPRSS2-ERG fusion-positive patients were similar with TMPRSS2-ERG fusion-negative patients, however no fusion-positive patients were identified as MSI-H. Among these 36 TMPRSS2-ERG fusion-positive patients, the most frequently somatic mutations were detected in TP53 (38.9%), AR (11.1%), ATM (11.1%), and PTEN (11.1%). 9 (22.2%) patients harbored somatic mutations in PI3K/ AKT/mTOR pathway that has been previously demonstrated to collaborate with ERG to promote prostate cancer progression. Conclusions: This study revealed the prevalence and genetic features of TMPRSS2-ERG fusion in Chinese PCa patients by NGS in the first time. Our results provide a better understanding of molecular features in Chinese TMPRSS2-ERG fusion-positive PCa patients.

Practical Molecular Testing in a Clinical Genitourinary Service

Molecular testing is increasingly playing a key role in the diagnosis, prognosis, and treatment of neoplasms of the genitourinary system. To provide a general overview of the clinically relevant molecular tests available for neoplasms of the genitourinary tract. Relevant medical literature indexed on PubMed. Understanding of the molecular oncology of genitourinary neoplasms is rapidly advancing, and the pathologist must be aware of the practical implications of molecular testing. While many genomic abnormalities are not yet clinically relevant, there is an increasing library of ancillary tests that may guide diagnosis, prognosis, and/or treatment of many neoplasms. Recurrent genomic abnormalities have been identified in many types of renal cell carcinoma, and some types of renal cell carcinoma are specifically defined by the molecular abnormality. Two major routes of developing urothelial carcinoma have been molecularly described. Recurrent translocations involving ETS family genes are found in approximately half of prostate cancer cases. Testicular germ cell tumors typically harbor i(12p). Penile neoplasms are often high-risk human papillomavirus-driven cancers. Nonetheless, even as genitourinary neoplasms are increasingly better understood at the molecular level, further research with eventual clinical validation is needed for optimal diagnosis, prognosis, and treatment of aggressive malignancies in the genitourinary tract.