Abstract 4497: Distinct structural classes of activating FOXA1 alterations in prostate cancer progression

Forkhead box A1 (FOXA1) is a pioneer transcription factor that is essential for the normal development of several endoderm-derived organs, including the prostate gland. FOXA1 is frequently mutated in the hormone-receptor driven prostate, breast, bladder, and salivary gland tumors. In prostate luminal epithelial cells, wild-type FOXA1 delimits tissue-specific enhancers that are transcriptionally activated by AR, and extensively reprograms AR-activity in the transformed prostate epithelia. However, how FOXA1 alterations affect cancer development is unclear, with FOXA1 previously ascribed both tumor suppressive and oncogenic roles. In this study, we assemble an aggregate cohort of 1546 prostate cancers (PCa) and, for the first time, show that FOXA1 alterations fall into three distinct structural classes that diverge in clinical incidence, genetic co-alteration profiles, and oncogenic gain-of-functions. Notably, we find the three classes of FOXA1 alterations to collectively recur at a frequency of 35% in metastatic PCa. Class1 activating mutations originate in early PCa without concurrent ETS or SPOP alterations, selectively recur within the Wing2-region of the DNA-binding Forkhead domain (FKHD), confer enhanced chromatin mobility and binding frequency, and strongly trans-activate a luminal androgen receptor (AR) program of prostate oncogenesis. By contrast, class2 activating mutations are acquired in metastatic PCa, truncate the C-terminal regulatory domain of FOXA1, confer chromatin-binding dominance by increasing DNA affinity, and aberrantly activate the WNT/β-Catenin pathway to enable PCa metastasis. Finally, class3 genomic rearrangements are comprised of tandem duplications and translocations within the highly-syntenic FOXA1 locus. These structural variations amplify or reposition a conserved enhancer element, which we named FOXA1 Mastermind (FOXMIND), to drive overexpression of FOXA1 or other oncogenes, respectively. In summary, our study reaffirms the central role of FOXA1 in mediating AR-driven oncogenesis, and provides mechanistic insights into how different classes of FOXA1 alterations uniquely promote PCa initiation and/or metastatic progression. Furthermore, these results have direct implications in understanding the biology of other hormone-receptor driven cancers where similar FOXA1 alterations are found, and rationalize therapeutic co-targeting of oncogenic FOXA1-activity to extort more potent and durable disease remissions.

Citation Format: Abhijit Parolia, Marcin Cieslik, Shih-Chun Chu, Lanbo Xiao, Takahiro Ouchi, Yuping Zhang, Xiaoju Wang, Pankaj Vats, Xuhong Cao, Fengyun Su, Rui Wang, Felix Feng, Yi-Mi Wu, Robert Lonigro, Dan R. Robinson, Arul M. Chinnaiyan. Distinct structural classes of activating FOXA1 alterations in prostate cancer progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4497.

Publisher Correction: The long tail of oncogenic drivers in prostate cancer

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Abstract PD9-12: Integrative molecular profiling of breast cancer brain metastasis and patient-derived xenograft organoids from resected breast cancer brain metastases to interrogate and prioritize therapeutic personalized strategies

Background: Breast cancer brain metastasis (BM) is an area of unmet need in metastatic breast cancer patients. Novel therapeutic interventions to help prevent and treat BM are warranted. We conducted integrative molecular profiling of BM and matched primary tumors (PT) using next-generation DNA and RNA sequencing to examine the molecular landscape. In addition, we established patient-derived xenograft/organoid (PDX/PDO) to examine drug sensitivity according to the molecular and clinical features of the BM.

Methods: Archived, formalin fixed paraffin-embedded BM was collected retrospectively. BM were also collected prospectively at the time of clinically indicated surgical resection through the central nervous system tissue banking and the Michigan Oncology Sequencing Center (MI-ONCOSEQ) protocols. Matched archived PT tissues were collected when available. Integrative next-generation sequencing was conducted using the MI-ONCOSEQ platform. The prospectively collected BM were further used to establish PDXs/ PDOs. Successfully established PDXs/PDOs were used for ex vivo drug testing via MiDrugScreen, a novel drug sensitivity testing platform, where testing was performed in a dose-response format with drug selection prioritized by clinical scenario and molecular alterations if known a priori.

Results: 12 matched BM-PT pairs were analyzed: 6 triple negative, 5 HER2 positive, and 1 ER positive HER2 negative. All except one (11/12) had TP53 mutations. When present, TP53 mutations in BM were also found in PT (except for 1 unknwon case in PT due to low coverage). ER+HER2- was the only one without TP53 mutation but had hyper-mutation (APOBEC signature). Driver mutations and unique copy number alterations (CDKN2A loss in 1/12, mutations in PIK3CA in 1/12 and ESR1 in 1/12, CCNE1 amplification in 1/12) were noted in BMs. In 75% of cases, mutational burden was higher in BM vs. PT. 2 PDX/PDO were available for drug testing. PDO-BC9 was noted to have RB1 (splice acceptor) and LOH. As predicted by this alteration, PDO-BC9 was insensitive to CDK4/6 inhibitors (palbociclib, abemaciclib) tested on MiDrugScreen panel. PDX-BC4 was established from PIK3CA and ESR1 mutated BM from an ER+HER2- patient who had previously progressed on endocrine therapy with a CDK4/6 inhibitor. As predicted, the PDX-BC4 was resistant to CDK4/6 inhibitor but interestingly sensitive to PIK3CA, ERK, and MEK inhibitors.

Conclusions: TP53 mutation was highly prevalent and may be a biomarker for increased risk of BM. Further study is warranted to see if specific TP53 mutations are associated with a risk of BM development and can be used in risk stratification for BM specific intervention. Unique molecular alterations in BM compared to matched PT may have a therapeutic implication as a target or resistance biomarker. Conducting drug testing in addition to molecular profiling has the strong potential of being informative in tailoring or prioritizing therapeutic agents in the era of precision medicine. Additional BM PDXs/PDOs from breast and other solid tumors are being examined using this novel therapeutic tailoring approach with the combination of MIONCOSEQ and MiDrugScreen.

Citation Format: Morikawa A, Robinson DR, Soellner M, Wu Y-M, Lonigro R, Gilani R, Cheng X, Lachacz E, Thomas D, McMurray K, Smerage J, Henry NL, Heth J, Chinnaiyan A, Hayes DF, Merajver S. Integrative molecular profiling of breast cancer brain metastasis and patient-derived xenograft organoids from resected breast cancer brain metastases to interrogate and prioritize therapeutic personalized strategies [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr PD9-12.

Abstract 5342: Somatic bi-allelic loss of TSC genes in eosinophilic solid and cystic renal cell carcinoma (ESC RCC)

Renal cell carcinoma (RCC) subtypes with overlapping histomorphologic features pose diagnostic challenges. For instance, a unique category of sporadic renal tumors with eosinophilic cytoplasm and solid and cystic growth pattern (ESC RCC) may mimic a RCC subtype usually encountered in patients with germline aberrations of tuberous sclerosis complex (TSC) genes (TSC RCC). Here, we used next-generation sequencing (NGS) technology to interrogate the clinicopathologic and molecular profiles of ESC RCC tumors. Mutational and copy number analysis of NGS data from ESC RCC tumors revealed a somatic bi-allelic loss of TSC family genes, specifically TSC1 or TSC2, in six out of seven profiled cases. However, the corresponding background kidney showed only wild type alleles, thus excluding any germline involvement and differentiating ESC RCC from TSC RCC. Furthermore, bi-allelic loss of the TSC genes occurred in a mutually exclusively manner in this cohort. Our study clarifies the molecular identity of ESC RCC, and can thus guide future therapeutic strategies and provide a basis for the revision of current RCC classification.

Citation Format: Nicole D. Lee, Pankaj Vats, Xuhong Cao, Fengyun Su, Robert Lonigro, Kumpati Premkumar, Kiril Trpkov, Jesse K. McKenney, Rohit Mehra, Saravana M. Dhanasekaran, Arul M. Chinnaiyan. Somatic bi-allelic loss of TSC genes in eosinophilic solid and cystic renal cell carcinoma (ESC RCC) [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 5342.

Somatic Bi-allelic Loss of TSC Genes in Eosinophilic Solid and Cystic Renal Cell Carcinoma

Renal cell carcinomas (RCC) with overlapping histomorphologic features poses diagnostic challenges. This is exemplified in RCCs with eosinophilic cytoplasm that include eosinophilic solid and cystic RCC (ESC RCC), RCCs in germline aberrations of tuberous sclerosis complex (TSC) genes mutated (TSC RCC) individuals, and other RCC subtypes. We used next-generation sequencing (NGS) technology to molecularly profile seven ESC RCC tumors. Mutational and copy number analysis of NGS data revealed mutually exclusively somatic bi-allelic loss of TSC1 or TSC2 genes-both negative regulators of the mammalian target of rapamycin (mTOR) pathway in 85% (6/7) of evaluated cases. Thus, lack of germline TSC aberration in matched non-neoplastic renal parenchyma distinguishes ESC RCC from TSC RCC. Immunohistochemistry data shows mTOR pathway activation in all tumors, thus supporting a pathognomonic role for TSC aberrations in ESC RCC. Our study clarifies the molecular identity of ESC RCC, provides basis for the revision of current RCC classification, and may guide future therapeutic strategies.

PATIENT SUMMARY

Molecular characterization of eosinophilic solid and cystic renal cell carcinomas (ESC RCC) revealed recurrent and mutually exclusive somatic homozygous loss of tuberous sclerosis complex family genes. This observation provides greater insight into the unique biology of this novel type of tumor and potentially expands the therapeutic options for ESC RCC patients.

Clinical validation of the Tempus xO assay

We have developed a clinically validated NGS assay that includes tumor, germline and RNA sequencing. We apply this assay to clinical specimens and cell lines, and we demonstrate a clinical sensitivity of 98.4% and positive predictive value of 100% for the clinically actionable variants measured by the assay. We also demonstrate highly accurate copy number measurements and gene rearrangement identification.

Clinically Integrated Sequencing Alters Therapy in Children and Young Adults With High-Risk Glial Brain Tumors

Purpose

Brain tumors have become the leading cause of cancer-related mortality in young patients. Novel effective therapies on the basis of the unique biology of each tumor are urgently needed. The goal of this study was to evaluate the feasibility, utility, and clinical impact of integrative clinical sequencing and genetic counseling in children and young adults with high-risk brain tumors.

Patients and Methods

Fifty-two children and young adults with brain tumors designated by the treating neuro-oncologist to be high risk (> 25% chance for treatment failure; mean age, 10.2 years; range, 0 to 39 years) were enrolled in a prospective, observational, consecutive case series, in which participants underwent integrative clinical exome (tumor and germline DNA) and transcriptome (tumor RNA) sequencing and genetic counseling. Results were discussed in a multi-institutional brain tumor precision medicine teleconference.

Results

Sequencing revealed a potentially actionable germline or tumor alteration in 25 (63%) of 40 tumors with adequate tissue, of which 21 (53%) resulted in an impact on treatment or change of diagnosis. Platelet-derived growth factor receptor or fibroblast growth factor receptor pathway alterations were seen in nine of 20 (45%) glial tumors. Eight (20%) sequenced tumors harbored an oncogenic fusion isolated on RNA sequencing. Seventeen of 20 patients (85%) with glial tumors were found to have a potentially actionable result, which resulted in change of therapy in 14 (70%) patients. Patients with recurrent brain tumors receiving targeted therapy had a median progression-free survival (from time on therapy) of 4 months.

Conclusion

Selection of personalized agents for children and young adults with highrisk brain tumors on the basis of integrative clinical sequencing is feasible and resulted in a change in therapy in more than two thirds of children and young adults with high-risk glial tumors.

The long tail of oncogenic drivers in prostate cancer

Comprehensive genomic characterization of prostate cancer has identified recurrent alterations in genes involved in androgen signaling, DNA repair, and PI3K signaling, among others. However, larger and uniform genomic analysis may identify additional recurrently mutated genes at lower frequencies. Here we aggregate and uniformly analyze exome sequencing data from 1,013 prostate cancers. We identify and validate a new class of E26 transformation-specific (ETS)-fusion-negative tumors defined by mutations in epigenetic regulators, as well as alterations in pathways not previously implicated in prostate cancer, such as the spliceosome pathway. We find that the incidence of significantly mutated genes (SMGs) follows a long-tail distribution, with many genes mutated in less than 3% of cases. We identify a total of 97 SMGs, including 70 not previously implicated in prostate cancer, such as the ubiquitin ligase CUL3 and the transcription factor SPEN. Finally, comparing primary and metastatic prostate cancer identifies a set of genomic markers that may inform risk stratification.

Comprehensive Mutation and Copy Number Profiling in Archived Circulating Breast Cancer Tumor Cells Documents Heterogeneous Resistance Mechanisms

Addressing drug resistance is a core challenge in cancer research, but the degree of heterogeneity in resistance mechanisms in cancer is unclear. In this study, we conducted next-generation sequencing (NGS) of circulating tumor cells (CTC) from patients with advanced cancer to assess mechanisms of resistance to targeted therapy and reveal opportunities for precision medicine. Comparison of the genomic landscapes of CTCs and tissue metastases is complicated by challenges in comprehensive CTC genomic profiling and paired tissue acquisition, particularly in patients who progress after targeted therapy. Thus, we assessed by NGS somatic mutations and copy number alterations (CNA) in archived CTCs isolated from patients with metastatic breast cancer who were enrolled in concurrent clinical trials that collected and analyzed CTCs and metastatic tissues. In 76 individual and pooled informative CTCs from 12 patients, we observed 85% concordance in at least one or more prioritized somatic mutations and CNA between paired CTCs and tissue metastases. Potentially actionable genomic alterations were identified in tissue but not CTCs, and vice versa. CTC profiling identified diverse intra- and interpatient molecular mechanisms of endocrine therapy resistance, including loss of heterozygosity in individual CTCs. For example, in one patient, we observed CTCs that were either wild type for ESR1 (n = 5/32), harbored the known activating ESR1 p.Y537S mutation (n = 26/32), or harbored a novel ESR1 p.A569S (n = 1/32). ESR1 p.A569S was modestly activating in vitro, consistent with its presence as a minority circulating subclone. Our results demonstrate the feasibility and potential clinical utility of comprehensive profiling of archived fixed CTCs. Tissue and CTC genomic assessment are complementary, and precise combination therapies will likely be required for effective targeting in advanced breast cancer patients.Significance: These findings demonstrate the complementary nature of genomic profiling from paired tissue metastasis and circulating tumor cells from patients with metastatic breast cancer. Cancer Res; 78(4); 1110-22. ©2017 AACR.

Abstract P2-09-26: Frequency and mechanisms of elevated somatic mutation burden in metastatic breast cancer and response to immune checkpoint blockade

Background: Immune checkpoint blockade (ICB) is effective in the treatment of various malignancies. Thus far, however, results in breast cancer have been mixed. Elevated tumor mutational load, and subsequent increased likelihood of forming immunogenic neoantigens, has been correlated with response to ICB. Mutational load observed in breast cancers varies widely. However, most studies have assessed mutational load using primary tumors. Few studies have explored the frequency of high mutational load, molecular mechanisms accounting for this phenomenon, and its potential impact on response to ICB in metastatic breast cancer (MBC).

Methods: From 2011-2016, 124 patients (pts) with MBC of varying subtypes underwent research biopsy of their metastatic disease for whole genome, exome and transcriptome sequencing of tumor and matched normal sample through the Michigan Oncology Sequencing Center (Mi-OncoSeq). Those pts with elevated somatic mutation load were defined as having greater than 10 mutations per megabase of targeted sequencing and mutational signatures accounting for high mutation load were noted. Pts treated subsequently with ICB were followed to assess response.

Results: Twelve MBC pts had high mutation load (10% of cohort). Eight pts had estrogen receptor (ER) positive MBC and 4 pts had metastatic triple negative breast cancer (TNBC). In 5 cases, a clear mutational signature accounting for high mutation load was evident. Two TNBC cases harbored an APOBEC mutational signature in addition to 1 TNBC and 2 ER positive tumors displaying a microsatellite instability signature (MSI-H). Among the tumors with MSI-H signature, 1 case was associated with a pathogenic germline alteration in MLH1. Two pts were subsequently treated with ICB on a clinical trial. One pt came off study after 3 months due to progressive brain metastases and another had partial response to therapy lasting 7 months.

Conclusions: Elevated somatic mutation burden in MBC is observed in approximately 10% of pts, and is detected in both ER positive and TNBC. Since high mutation burden has been associated with increased likelihood of response to ICB, identification of this genomic feature could have important therapeutic implications for MBC pts.

Citation Format: Cobain EF, Robinson DR, Wu Y-M, Lonigro R, Vats P, Rabban E, Kumar-Sinha C, Schott AF, Smerage JB, Morikawa A, Burness ML, Van Poznak CH, Griggs J, Wicha M, Hayes DF, Chinnaiyan AM. Frequency and mechanisms of elevated somatic mutation burden in metastatic breast cancer and response to immune checkpoint blockade [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-09-26.

Blood-brain barrier-adapted precision medicine therapy for pediatric brain tumors

Targeted chemotherapeutics provide a promising new treatment option in neuro-oncology. The ability of these compounds to penetrate the blood-brain barrier is crucial for their successful incorporation into patient care. "CNS Targeted Agent Prediction" (CNS-TAP) is a multi-institutional and multidisciplinary translational program established at the University of Michigan for evaluating the central nervous system (CNS) activity of targeted therapies in neuro-oncology. In this report, we present the methodology of CNS-TAP in a series of pediatric and adolescent patients with high-risk brain tumors, for which molecular profiling (academic and commercial) was sought and targeted agents were incorporated. Four of five of the patients had potential clinical benefit (partial response or stable disease greater than 6 months on therapy). We further describe the specific drug properties of each agent chosen and discuss characteristics relevant in their evaluation for therapeutic suitability. Finally, we summarize both tumor and drug characteristics that impact the ability to successfully incorporate targeted therapies into CNS malignancy management.

Gene Copy Number Estimation from Targeted Next-Generation Sequencing of Prostate Cancer Biopsies: Analytic Validation and Clinical Qualification

Purpose: Precise detection of copy number aberrations (CNA) from tumor biopsies is critically important to the treatment of metastatic prostate cancer. The use of targeted panel next-generation sequencing (NGS) is inexpensive, high throughput, and easily feasible, allowing single-nucleotide variant calls, but CNA estimation from this remains challenging.Experimental Design: We evaluated CNVkit for CNA identification from amplicon-based targeted NGS in a cohort of 110 fresh castration-resistant prostate cancer biopsies and used capture-based whole-exome sequencing (WES), array comparative genomic hybridization (aCGH), and FISH to explore the viability of this approach.Results: We showed that this method produced highly reproducible CNA results (r = 0.92), with the use of pooled germline DNA as a coverage reference supporting precise CNA estimation. CNA estimates from targeted NGS were comparable with WES (r = 0.86) and aCGH (r = 0.7); for key selected genes (BRCA2, MYC, PIK3CA, PTEN, and RB1), CNA estimation correlated well with WES (r = 0.91) and aCGH (r = 0.84) results. The frequency of CNAs in our population was comparable with that previously described (i.e., deep deletions: BRCA2 4.5%; RB1 8.2%; PTEN 15.5%; amplification: AR 45.5%; gain: MYC 31.8%). We also showed, utilizing FISH, that CNA estimation can be impacted by intratumor heterogeneity and demonstrated that tumor microdissection allows NGS to provide more precise CNA estimates.Conclusions: Targeted NGS and CNVkit-based analyses provide a robust, precise, high-throughput, and cost-effective method for CNA estimation for the delivery of more precise patient care. Clin Cancer Res; 23(20); 6070-7. ©2017 AACR.

Abstract LB-044: Copy number estimation from targeted amplicon-based next-generation sequencing of castration-resistant prostate cancer biopsies: analytic validation and clinical qualification for a iPARP clinical trial

Prostate cancer is a highly heterogeneous disease with distinct genomic underpinnings and generally presents a modest number of genome wide somatic single point mutations and indels at approximately one or two per megabase, but frequently has large-scale somatic copy number and structural alterations. We recently showed that 25-30% of prostate tumors bear defects in double-strand DNA repair genes that render them sensitive to treatment with PARP inhibition, and that these are commonly mediated through copy number events. Accurately estimate gene copy number variation (CNV) is crucial to understanding the genomic background of advanced prostate tumours. However, it has been challenging in targeted amplicon-based next generation sequencing (NGS).

Here, we describe the analytical validation and clinical qualification of a CNV assessment, based on targeted amplicon sequencing of a focused biomarker gene panel dedicated to identifying DNA repair defects, with an aim to identify patients that may benefit from PARP inhibitor treatment.

Our targeted NGS protocol is used to profile a cohort of 110 castration-resistant prostate cancer patients. The key findings include AR amplification (Log2 > 2) in 45.5% (50/110) of samples and commonly shared loss of BRCA2 and RB1 (88% of samples reporting any BRCA2 loss also had some loss of RB1, while 33.8% of samples with RB1 loss had loss of BRCA2). Moreover, we validated our results using other CNV estimation platforms to establish that: 1) the protocol produces highly reproducible results (r = 0.98); 2) in the covered regions, CNV estimated from targeted amplicon NGS is comparable with capture based whole exome sequencing (r = 0.86) as well as array CGH (r = 0.81); and 3) CNV estimation can be validated by orthogonal methods such as ddPCR and FISH. The approach has the benefit of estimating CNV from tumour-only sample by using pooled (n=34) germline sequencing data as a reference.

In this study, we have developed an accurate, affordable and rapid approach to estimate copy number aberrations using targeted gene panel sequencing. We demonstrated high reproducibility, validating our results with different orthogonal copy number estimation platforms. And this protocol has potential to be integrated with other protocols for patient assessment and precision medicine.

Citation Format: George Seed, Wei Yuan, Joaquin Mateo, Suzanne Carreira, Maryou Lambros, Gunther Boysen, Roberta Ferraldeschi, Susana Miranda, Ines Figueiredo, Ruth Riisnaes, Mateus Crespo, Daniel Nava Rodrigues, Eric Talevich, Dan Robinson, Priya Kunju, Yi-mi Wu, Robert Lonigro, Shahneen Sandhu, Arul Chinnayan, Johann De Bono. Copy number estimation from targeted amplicon-based next-generation sequencing of castration-resistant prostate cancer biopsies: analytic validation and clinical qualification for a iPARP clinical trial [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-044. doi:10.1158/1538-7445.AM2017-LB-044

Biallelic Alteration and Dysregulation of the Hippo Pathway in Mucinous Tubular and Spindle Cell Carcinoma of the Kidney

Mucinous tubular and spindle cell carcinoma (MTSCC) is a relatively rare subtype of renal cell carcinoma (RCC) with distinctive morphologic and cytogenetic features. Here, we carry out whole-exome and transcriptome sequencing of a multi-institutional cohort of MTSCC (n = 22). We demonstrate the presence of either biallelic loss of Hippo pathway tumor suppressor genes (TSG) and/or evidence of alteration of Hippo pathway genes in 85% of samples. PTPN14 (31%) and NF2 (22%) were the most commonly implicated Hippo pathway genes, whereas other genes such as SAV1 and HIPK2 were also involved in a mutually exclusive fashion. Mutations in the context of recurrent chromosomal losses amounted to biallelic alterations in these TSGs. As a readout of Hippo pathway inactivation, a majority of cases (90%) exhibited increased nuclear YAP1 protein expression. Taken together, nearly all cases of MTSCC exhibit some evidence of Hippo pathway dysregulation.

SIGNIFICANCE

MTSCC is a rare and relatively recently described subtype of RCC. Next-generation sequencing of a multi-institutional MTSCC cohort revealed recurrent chromosomal losses and somatic mutations in the Hippo signaling pathway genes leading to potential YAP1 activation. In virtually all cases of MTSCC, there was evidence of Hippo pathway dysregulation, suggesting a common mechanistic basis for this disease. Cancer Discov; 6(11); 1258-66. ©2016 AACR.This article is highlighted in the In This Issue feature, p. 1197.

Inherited DNA-Repair Gene Mutations in Men with Metastatic Prostate Cancer

BACKGROUND

Inherited mutations in DNA-repair genes such as BRCA2 are associated with increased risks of lethal prostate cancer. Although the prevalence of germline mutations in DNA-repair genes among men with localized prostate cancer who are unselected for family predisposition is insufficient to warrant routine testing, the frequency of such mutations in patients with metastatic prostate cancer has not been established.

METHODS

We recruited 692 men with documented metastatic prostate cancer who were unselected for family history of cancer or age at diagnosis. We isolated germline DNA and used multiplex sequencing assays to assess mutations in 20 DNA-repair genes associated with autosomal dominant cancer-predisposition syndromes.

RESULTS

A total of 84 germline DNA-repair gene mutations that were presumed to be deleterious were identified in 82 men (11.8%); mutations were found in 16 genes, including BRCA2 (37 men [5.3%]), ATM (11 [1.6%]), CHEK2 (10 [1.9% of 534 men with data]), BRCA1 (6 [0.9%]), RAD51D (3 [0.4%]), and PALB2 (3 [0.4%]). Mutation frequencies did not differ according to whether a family history of prostate cancer was present or according to age at diagnosis. Overall, the frequency of germline mutations in DNA-repair genes among men with metastatic prostate cancer significantly exceeded the prevalence of 4.6% among 499 men with localized prostate cancer (P<0.001), including men with high-risk disease, and the prevalence of 2.7% in the Exome Aggregation Consortium, which includes 53,105 persons without a known cancer diagnosis (P<0.001).

CONCLUSIONS

In our multicenter study, the incidence of germline mutations in genes mediating DNA-repair processes among men with metastatic prostate cancer was 11.8%, which was significantly higher than the incidence among men with localized prostate cancer. The frequencies of germline mutations in DNA-repair genes among men with metastatic disease did not differ significantly according to age at diagnosis or family history of prostate cancer. (Funded by Stand Up To Cancer and others.).

The use of exome capture RNA-seq for highly degraded RNA with application to clinical cancer sequencing

RNA-seq by poly(A) selection is currently the most common protocol for whole transcriptome sequencing as it provides a broad, detailed, and accurate view of the RNA landscape. Unfortunately, the utility of poly(A) libraries is greatly limited when the input RNA is degraded, which is the norm for research tissues and clinical samples, especially when specimens are formalin-fixed. To facilitate the use of RNA sequencing beyond cell lines and in the clinical setting, we developed an exome-capture transcriptome protocol with greatly improved performance on degraded RNA. Capture transcriptome libraries enable measuring absolute and differential gene expression, calling genetic variants, and detecting gene fusions. Through validation against gold-standard poly(A) and Ribo-Zero libraries from intact RNA, we show that capture RNA-seq provides accurate and unbiased estimates of RNA abundance, uniform transcript coverage, and broad dynamic range. Unlike poly(A) selection and Ribo-Zero depletion, capture libraries retain these qualities regardless of RNA quality and provide excellent data from clinical specimens including formalin-fixed paraffin-embedded (FFPE) blocks. Systematic improvements across key applications of RNA-seq are shown on a cohort of prostate cancer patients and a set of clinical FFPE samples. Further, we demonstrate the utility of capture RNA-seq libraries in a patient with a highly malignant solitary fibrous tumor (SFT) enrolled in our clinical sequencing program called MI-ONCOSEQ. Capture transcriptome profiling from FFPE revealed two oncogenic fusions: the pathognomonic NAB2-STAT6 inversion and a therapeutically actionable BRAF fusion, which may drive this specific cancer's aggressive phenotype.

Abstract 4681: Inhibition of poly (ADP-ribose) polymerase-1 (PARP-1) as a strategy for targeted therapy in Ewing's sarcoma

The Ewing's sarcoma family of tumors (ESFTs) are aggressive malignancies which frequently harbor EWS-FLI1 or EWS-ERG genomic fusions. Here, we demonstrate that these fusion products interact with, and depend on, poly (ADP-ribose) polymerase 1 (PARP1), a DNA damage response protein and transcriptional co-regulator. This interaction occurs in a DNA-independent manner. ESFT cell lines and xenografts are preferentially sensitive to PARP1 inhibition, and the addition of a PARP1 inhibitor to the second-line chemotherapeutic agent temozolamide resulted in complete response of all treated tumors in an EWS-FLI1 ESFT xenograft model. PARP inhibition blocked Ewing's cell line, but not control osteosarcoma or rhabdomyosarcoma cell line invasion, as well as the formation of lung metastasis in a xenograft model of ESFT. Mechanistically, the EWS-FLI1 and EWS-ERG fusions induce DNA damage, which is potentiated by PARP1 inhibition in ESFT cell lines. In a positive feedback loop, EWS-FLI1 fusions maintain the expression of PARP1 by direct regulation of the PARP1 promoter. This regulation is independently supported by a gene expression array data set of 20 ESFT patient tumors (Spearman r = 0.8165). Finally, because front-line therapy for this disease includes an intense regimen of five cytotoxic chemotherapy agents from which patients can quickly relapse with even more aggressive disease, we studied the effect of PARP inhibition in two Ewing's sarcoma cell line models derived after patient relapse. Importantly, these two cell lines maintained a preferential sensitivity to PARP1 inhibition despite their general chemoresistance. These findings suggest that targeting the EWS-FLI1: PARP1 interaction axis is a promising therapeutic strategy for the Ewing's sarcoma family of tumors.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4681. doi:1538-7445.AM2012-4681

PARP-1 inhibition as a targeted strategy to treat Ewing's sarcoma

Ewing's sarcoma family of tumors (ESFT) refers to aggressive malignancies which frequently harbor characteristic EWS-FLI1 or EWS-ERG genomic fusions. Here, we report that these fusion products interact with the DNA damage response protein and transcriptional coregulator PARP-1. ESFT cells, primary tumor xenografts, and tumor metastases were all highly sensitive to PARP1 inhibition. Addition of a PARP1 inhibitor to the second-line chemotherapeutic agent temozolamide resulted in complete responses of all treated tumors in an EWS-FLI1-driven mouse xenograft model of ESFT. Mechanistic investigations revealed that DNA damage induced by expression of EWS-FLI1 or EWS-ERG fusion genes was potentiated by PARP1 inhibition in ESFT cell lines. Notably, EWS-FLI1 fusion genes acted in a positive feedback loop to maintain the expression of PARP1, which was required for EWS-FLI-mediated transcription, thereby enforcing oncogene-dependent sensitivity to PARP-1 inhibition. Together, our findings offer a strong preclinical rationale to target the EWS-FLI1:PARP1 intersection as a therapeutic strategy to improve the treatment of ESFTs.

Abstract 2815: Urine TMPRSS2:ERG for prostate cancer risk stratification in men with elevated serum PSA

Background: Over 1,000,000 men undergo prostate biopsy each year in the U.S., most for “elevated” serum PSA. Given the lack of sensitivity and specificity, and unclear mortality benefit of PSA testing, methods to individualize management of elevated PSA are needed. We evaluated urine expression of TMPRSS2:ERG, a gene fusion occurring in 50% of prostate cancers, for risk-stratifying men presenting for biopsy.

Methods: TMPRSS2:ERG was measured by a clinical grade, transcription-mediated-amplification assay in prospectively collected whole-urine from 1,094 men undergoing biopsy at 10 academic and community clinics.

Findings: Urine TMPRSS2:ERG was associated with indicators of clinically significant cancer at biopsy and prostatectomy, including tumor size, high prostatectomy Gleason score and upgrading at prostatectomy. TMPRSS2:ERG in combination with urine PCA3, improved the multivariate PCPT risk calculator performance for predicting cancer on biopsy (AUC in test set, 0.79 vs. 0.64, p&lt;0.001). Using a three-class stratification, men in the highest and lowest TMPRSS2:ERG+PCA3 score groups had markedly different rates of cancer (69% vs. 21%, p&lt;0.001), clinically significant cancer by Epstein criteria (61% vs. 15%, p&lt;0.001) and high grade cancer (40% vs. 7%, p&lt;0.001) on biopsy.

Interpretation: Urine TMPRSS2:ERG, in combination with urine PCA3, enhances the utility of serum PSA for predicting prostate cancer and clinically relevant cancer on biopsy.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2815. doi:10.1158/1538-7445.AM2011-2815

Abstract 953: Mechanistic rationale for inhibition of Poly(ADP-Ribose) Polymerase in ETS gene fusion positive prostate cancer

Recurrent fusions of ETS genes are considered driving mutations in a diverse array of cancers including Ewing's sarcoma, acute myeloid leukemia, and epithelial tumors such as prostate cancer. However, transcription factors like the ETS genes have been notoriously difficult to target therapeutically. In fact, while approximately 50% of all prostate cancers harbor ETS gene fusions, the most common variant fuses an androgen regulated promoter and the 5’-UTR of TMPRSS2 to the second exon of ERG resulting in the pathogenic overexpression of a slightly truncated ERG transcription factor. Here, we use IP-mass spectrometry to characterize the ETS protein interactome in prostate cancer. We show that the TMPRSS2:ERG gene fusion product interacts with the enzymes poly(ADP-ribose)polymerase 1 (PARP1) and the catalytic subunit of DNA protein kinase (DNA-PKcs) in a DNA-independent manner in both prostate cancer cells and tissues. ETS gene fusion-mediated transcription of several target genes including the invasion associated gene EZH2 requires both PARP1 and DNA-PKcs expression and activity. Likewise, cell invasion driven by ETS gene overexpression is inhibited by small molecule inhibitors or siRNA against these enzymes in matrigel coated transwell invasion assays (in vitro) as well as chicken chorioallantoic membrane intravasation and metastasis assays (in vivo). Importantly, pharmacological inhibition of PARP1 selectively inhibited the growth of 4 ETS positive, but not 5 ETS negative, prostate cancer cell xenografts. This analysis includes several prostate cancer cell lines, an isogenic model of hormone refractory prostate cancer and primary human tumors that were serially grown in mice. Finally, we find that TMPRSS2:ERG gene fusion overexpression leads to increased DNA double strand breaks as assessed by gamma-H2A.X staining and COMET assays. This DNA damage is then potentiated by PARP1 inhibition in a manner similar to that of BRCA1/2-deficiency.Thus, we propose that the ETS:PARP1 interaction axis may represent a novel target for therapeutic intervention in cancers with ETS gene fusions and that future clinical trials will help determine if this subgroup of patients preferentially benefits from the addition of PARP inhibitor therapy. Moreover, our study suggests that inhibition of co-factors necessary for function may represent a new paradigm of treatment for malignancies driven by oncogenic transcription factors.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 953. doi:10.1158/1538-7445.AM2011-953

Abstract 2795: An onco-protein axis linking polycomb repressive complex 2 and polycomb repressive complex 1 through miRNAs in cancer

Enhancer of Zeste Homolog 2 (EZH2) is the catalytic histone methyltransferase subunit of the Polycomb Repressive Complex 2 (PRC2), that trimethylates histone H3 at lysine 27 (H3K27me3) resulting in the silencing of target genes. PRC2 plays a critical role in many basic cellular processes including cell proliferation, differentiation, early embryogenesis, and X chromosome inactivation. In cancer, EZH2 upregulation is implicated in metastasis and tumor aggressiveness of prostate and breast cancer and several other solid tumors. Recently our lab reported the genomic loss of miR-101 microRNA accompanying EZH2 overexpression in tumor cells. Here we identified several microRNAs that were downregulated by EZH2 and their levels were restored upon EZH2 depletion in cancer cell lines, and expression levels of these microRNAs were negatively correlated with EZH2 in human prostate tumors. Additionally, H3K27me3 modification was observed in the upstream regions of the miRNAs, suggesting a direct role for EZH2 in their regulation. Ectopic overexpression of the miRNAs suppressed cell proliferation, invasion, anchorage-independent growth, sphere formation and xenograft tumor growth of aggressive prostate and breast cancer cell lines. Finally, our investigations showed that the miRNAs also repress the expression of Polycomb Repressive Complex 1 (PRC1) members BMI1 and RING2, leading to a global decrease in the epigenetic marker, ubiquityl-H2A-K119 (uH2A) in cells, a key step in PRC1-mediated silencing. Our findings provide compelling argument for a regulatory axis joining PRC2 and PRC1 through miRNAs. This novel link between PRC2 and PRC1 indicates a coordinated mechanism by polycomb group proteins to promote an aggressive cancer phenotype.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2795. doi:10.1158/1538-7445.AM2011-2795

Expert panel on weight loss surgery: executive report update

Rapid shifts in the demographics and techniques of weight loss surgery (WLS) have led to new issues, new data, new concerns, and new challenges. In 2004, this journal published comprehensive evidence-based guidelines on WLS. In this issue, we've updated those guidelines to assure patient safety in this fast-changing field. WLS involves a uniquely vulnerable population in need of specialized resources and ongoing multidisciplinary care. Timely best-practice updates are required to identify new risks, develop strategies to address them, and optimize treatment. Findings in these reports are based on a comprehensive review of the most current literature on WLS; they directly link patient safety to methods for setting evidence-based guidelines developed from peer-reviewed scientific publications. Among other outcomes, these reports show that WLS reduces chronic disease risk factors, improves health, and confers a survival benefit on those who undergo it. The literature also shows that laparoscopy has displaced open surgery as the predominant approach; that government agencies and insurers only reimburse procedures performed at accredited WLS centers; that best practice care requires close collaboration between members of a multidisciplinary team; and that new and existing facilities require wide-ranging changes to accommodate growing numbers of severely obese patients. More than 100 specialists from across the state of Massachusetts and across the many disciplines involved in WLS came together to develop these new standards. We expect them to have far-reaching effects of the development of health care policy and the practice of WLS.

Best practices in policy and access (coding and reimbursement) for weight loss surgery

To update evidence-based best practice guidelines for coding and reimbursement and establish policy and access standards for weight loss surgery (WLS). Systematic search of English-language literature on WLS and health-care policy, access, insurance reimbursement, coding, private payers, public policy, and mandated benefits published between April 2004 and May 2007 in MEDLINE, EMBASE, and the Cochrane Library. Use of key words to narrow the search for a selective review of abstracts, retrieval of full articles, and grading of evidence according to systems used in established evidence-based models. We identified 51 publications in our literature search; the 20 most relevant were examined in detail. These included reviews, cost-benefit analyses, and trend and cost studies from administrative databases. Literature on policy issues surrounding WLS are very sparse and largely focused on economic analyses. Reports on policy initiatives in the public and private arenas are primarily limited to narrative reviews of nonsurgical efforts to fight obesity. A substantial body of work shows that WLS improves or reverses most obesity-related comorbidities. Mounting evidence also indicates that WLS confers a significant survival advantage for those who undergo it. WLS is a viable and cost-effective treatment for an increasingly common disease, and policy decisions are more frequently being linked to incentives for national health-care goals. However, access to WLS often varies by payer and region. Currently, there are no uniform criteria for determining patient appropriateness for surgery.

APE/Ref-1 is controlled by both redox and cAMP-dependent mechanisms in rat thyroid cells

APE/Ref-1 is a multifunctional protein possessing both redox and DNA repair functions. Through its redox activity, APE/Ref-1 controls the DNA-binding function of several transcriptional regulators (AP1, NF-kappaB, p53, Pax proteins). We have previously shown that APE/Ref-1 upregulates the transcriptional activity of the thyroid-specific transcription factor Pax8. In thyroid cells, APE/Ref-1 can be detected both in the nuclear and cytoplasmatic compartments. In this study regulatory mechanisms acting on APE/Ref-1 were revealed using the FRTL-5 cell line. TSH induces both cytoplasm-to-nucleus translocation and neosynthesis of APE/Ref-1 protein. Interestingly, only neosynthesis is dependent on cAMP signalling. In contrast, the cytoplasm-to-nucleus translocation is dependent on redox-mediated mechanisms. Based upon the data shown in this study and in others, a bimodal control of APE/Ref-1 by TSH can be delineated.

Nestin is a neuroepithelial target gene of thyroid transcription factor-1, a homeoprotein required for forebrain organogenesis

Thyroid transcription factor-1 (TTF-1, also known as NKX2.1 and T/EBP), a transcription factor belonging to the NKX-2 family of homeodomain-containing genes, plays an essential role in the organogenesis of the thyroid gland, lung, and ventral forebrain. Nestin is an intermediate filament protein strongly expressed in multipotential neuroepithelial stem cells and rapidly down-regulated during postnatal life. Here we show that stable fibroblastic clones expressing TTF-1 acquire a phenotype reminiscent of neuroepithelial cells in culture and up-regulate the endogenous nestin gene. TTF-1 transactivates in HeLa and NIH3T3 cells a reporter gene driven by a central nervous system-specific enhancer element from the second intron of the rat nestin gene, where it recognizes a DNA-binding site (NestBS) whose sequence resembles a nuclear hormone/cAMP-responsive element very different from canonical TTF-1 binding sites. Nuclear extracts from the head of mouse embryos form a retarded complex with NestBS of the same mobility of the extracts obtained from TTF1-expressing clones, which is either abolished or supershifted in the presence of two different antibodies recognizing the TTF-1 protein. Thus, the neuroepithelial marker nestin is a direct central nervous system-specific target gene of TTF-1, leading to the hypothesis that it might be the effector through which TTF-1 plays its role in the organogenesis of the forebrain.

Missense mutations of human homeoboxes: A review

The homeodomain (encoded by the homeobox) is the DNA-binding domain of a large variety of transcriptional regulators involved in controlling cell fate decisions and development. Mutations of homeobox-containing genes cause several diseases in humans. A variety of missense mutations giving rise to human diseases have been described. These mutations are an excellent model to better understand homeodomain molecular functions. To this end, homeobox missense mutations giving rise to human diseases are reviewed. Seventy-four independent homeobox mutations have been observed in 17 different genes. In the same genes, 30 missense mutations outside the homeobox have been observed, indicating that the homeodomain is more easily affected by single amino acids changes than the rest of the protein. Most missense mutations have dominant effects. Several data indicate that dominance is mostly due to haploinsufficiency. Among proteins having the homeodomain as the only DNA-binding domain, three "hot spot" regions can be delineated: 1) at codon encoding for Arg5; 2) at codon encoding for Arg31; and 3) at codons encoding for amino acids of recognition helix. In the latter, mutations at codons encoding for Arg residues at positions 52 and 53 are prevalent. In the recognition helix, Arg residues at positions 52 and 53 establish contacts with phosphates in the DNA backbone. Missense mutations of amino acids that contribute to sequence discrimination (such as those at positions 50 and 54) are present only in a minority of cases. Similar data have been obtained when missense mutations of proteins possessing an additional DNA-binding domain have been analyzed. The only exception is observed in the POU1F1 (PIT1) homeodomain, in which Arg58 is a "hot spot" for mutations, but is not involved in DNA recognition.

Thyroid-specific gene expression is differentially influenced by intracellular glutathione level in FRTL-5 cells

Alteration of the redox potential has been proposed as a mechanism influencing gene expression. Reduced glutathione (GSH) is one of the cellular scavengers involved in the regulation of the redox potential. To test the role that GSH may play in thyroid cells, we cultured a differentiated rat thyroid cell strain (FRTL-5) in the presence of L-buthionine-(S,R)-sulfoximine (BSO). BSO affects GSH synthesis by irreversibly inhibiting gamma-glutamylcysteine synthetase (EC 6.3.2.2), a specific enzyme involved in GSH synthesis. BSO-treated FRTL-5 cells show a great decrease in the GSH level, whereas malondialdehyde increases in the cell culture medium as a sign of lipid peroxidation. In these conditions the activity of two thyroid-specific promoters, thyroglobulin (Tg) and thyroperoxidase (TPO), is strongly reduced in transient transfection experiments. As both Tg and TPO promoters depend upon the thyroid-specific transcription factors, thyroid-specific transcription factor-1 (TTF-1) and Pax-8 for full transcriptional activity, we tested whether reduction of GSH concentration impairs the activity of these transcription factors. After BSO treatment of FRTL-5 cells, both transcription factors fail to trans-activate the respective chimerical targets, C5 and B-cell specific activating protein promoters, containing, respectively, multimerized TTF-1- or Pax-8-binding sites only as well as the Tg and TPO natural promoters. Northern analysis revealed that endogenous Tg messenger RNA (mRNA) expression is also reduced by BSO treatment, whereas endogenous TPO expression is not modified. Furthermore, the Pax-8 mRNA steady state concentration does not change in BSO-treated cells, whereas TTF-1 mRNA slightly decreases. Immunoblotting analysis of FRTL-5 nuclear extracts does not show significant modification of the Pax-8 concentration in BSO-treated cells, whereas a decrease of 25% in TTF-1 protein is revealed. Furthermore, BSO treatment decreases the DNA-binding activity to the respective consensus sequence of both transcription factors. Finally, different mechanisms seem to act on TTF-1 and Pax-8 functional impairment in BSO-treated cells. Indeed, with a lowered GSH concentration, the overexpressed Pax-8 still activates transcription efficiently, whereas, on the contrary, the overexpressed TTF-1 does not recover its transactivation capability when the respective chimerical target sequences are used (C5 and BSAP). When the natural Tg and TPO promoter sequences are used, overexpression of Pax-8 parallels the effect on both promoters observed using the chimeric target sequences, whereas overexpression of TTF-1 increases TPO promoter transcriptional activity only.

Correlations between individual clinical manifestations and CTG repeat amplification in myotonic dystrophy

Myotonic dystrophy (DM) is a multisystemic disease caused by the expansion of a CTG repeat, located in the 3'-untranslated region of the DMPK gene. The number of CTG repeats broadly correlates with the overall severity of the disease. However, correlations between CTG repeat number and presence/absence or severity of individual clinical manifestations in the same patients are yet scarce. In this study the number of CTG repeats detected in blood cells of 24 DM subjects was correlated with the severity of single clinical manifestations. The presence/absence of muscular atrophy, respiratory insufficiency, cardiac abnormalities, diabetes, cataract, sleep disorders, sterility or hypogonadism is not related to the number of CTG repeats. Muscular atrophy and respiratory insufficiency are present with the highest frequency, occurring in 96 and 92% of the cases, respectively. A significant correlation was found with age of onset (r = -0.57, p<0.01), muscular disability (r = 0.46, p<0.05), intellective quotient (r = -0.58, p<0.01) and short-term memory (r= -0.59, p<0.01). Therefore, the CTG repeat number has a predictive value only in the case of some clinical manifestations, this suggesting that pathogenetic mechanisms of DM may differ depending on the tissue.

In the TTF-1 homeodomain the contribution of several amino acids to DNA recognition depends on the bound sequence

The thyroid transcription factor-1 homeodomain (TTF-1HD) shows a peculiar DNA binding specificity, preferentially recognizing sequences containing the 5'-CAAG-3' core motif. Most other homeodomains instead recognize sites containing the 5'-TAAT-3' core motif. Here, we show that TTF-1HD efficiently recognizes another sequence, called D1, devoid of the 5'-CAAG-3' core motif. Different experimental approaches indicate that TTF-1HD contacts the D1 sequence in a manner which is different to that used to interact with sequences containing the 5'-CAAG-3' core motif. The binding activities that mutants of TTF-1HD display with the D1 sequence or with the sequence containing the 5'-CAAG-3' core motif indicate that the role of several DNA-contacting amino acids is different. In particular, during recognition of the D1 sequence, backbone-interacting amino acids not relevant in binding to sequences containing the 5'-CAAG-3' core motif play an important role. In the TTF-1HD, therefore, the contribution of several amino acids to DNA recognition depends on the bound sequence. These data indicate that although a common bonding network exists in all of the HD/DNA complexes, peculiarities important for DNA recognition may occur in single cases.

A network of specific minor-groove contacts is a common characteristic of paired-domain-DNA interactions

Pax proteins are a family of transcription factors conserved during evolution and able to bind specific DNA sequences through a domain called a "paired domain'. The DNA-binding specificity of the Pax-8 paired domain was investigated. Site-selection experiments indicate that Pax-8 binds to a consensus sequence similar to those bound by Pax-2 and Pax-5. When consensus sequences of various paired domains are observed in light of recent structural studies describing paired-domain-DNA interaction [Xu, Rould, Jun, Desplan and Pabo (1995) Cell 80, 639-650], it appears that base-pairs contacted in the minor groove are conserved, while most of the base-pairs contacted in the major groove are not. Therefore a network of specific minor groove contacts is a common characteristic of paired-domain-DNA interactions. The functional importance of such a network was successfully tested by analysing the effect of consensus-based mutations on the Pax-8 binding site of the thyroglobulin promoter.

TTF-1 gene expression in human lung tumours

Tissue-specific transcription factors control cell determination and differentiation. TTF-1 is a tissue-specific transcription factor expressed in the thyroid and lung. We investigated the expression of TTF-1 in normal human lung, and in various histopathological types of lung cancers by immunohistochemistry. In normal lung, TTF-1 expression was restricted to bronchial and alveolar epithelial cells. TTF-1 expression was found in 7 of the 29 cases of non-small cell lung carcinomas. In these tumours, the expression of TTF-1 did not correlate with the histological degree of differentiation. Results obtained using RNase protection assay confirmed that TTF-1 was expressed only in a subset of non-small cell carcinomas. TTF-1, as expected, was not expressed in neoplasms having a neuroendocrine cell origin, such as carcinoids. Interestingly, TTF-1 was always expressed in small cell lung carcinomas. These findings indicate that: (i) small cell lung carcinomas could originate from the endothermal cell lineage and (ii) dedifferentiation processes that operate in these neoplasms do not affect molecular mechanisms necessary for TTF-1 gene expression.

Expression of thyroid transcription factor 1 gene can be regulated at the transcriptional and posttranscriptional levels

The complete structure of the gene for thyroid transcription factor 1 (TTF-1), both in rats and humans, has been determined. The rat TTF-1 gene shows three transcriptional start sites and contains two introns, one of which is alternatively spliced. Nuclear run-on and transient transfection experiments indicate that TTF-1 gene expression can be controlled at different levels. Using thyroid and nonthyroid cell lines, it can be shown that transcriptional mechanisms are involved in controlling thyroid-specific expression of the TTF-1 gene. In contrast, in thyroid cells expressing an activated Ki-ras oncogene, the steady-state level of TTF-1 mRNA is greatly reduced, while transcription of the TTF-1 gene is only moderately affected, suggesting that the accumulation of TTF-1 mRNA can be regulated by a posttranscriptional, Ras-sensitive mechanism.

Definition of the DNA-binding specificity of TTF-1 homeodomain by chromatographic selection of binding sequences

The homeodomain of the thyroid transcription factor-1 (TTF-1HD) shows a peculiar DNA-binding specificity, preferentially recognizing sequences having the 5'-CAAG-3' core motif. In order to detail the DNA-binding specificity of this protein, a TTF-1HD-Sepharose column chromatography was used. A sequential selection and amplification of sequences was performed. TTF-1HD binding activity for selected and unselected sequences was measured. The presence of the 5'-CAAG-3' core motif was necessary, but not sufficient, to obtain the maximal binding activity for TTF-1HD. However, several of the selected sequences do not contain the 5'-CAAG-3' core motif and are bound by TTF-1HD only 2-fold less with respect to sequences bound with the highest affinity. Therefore, these data indicate that TTF-1HD specifically recognizes a spectrum of sequences wider than previously determined.

The thyroid transcription factor-1 gene is a candidate target for regulation by Hox proteins

Vertebrate Hox homeobox genes are transcription factors which regulate antero-posterior axial identity in embryogenesis, presumably through activation and/or repression of downstream target genes. Some of these targets were reported to code for molecules involved in cell-cell interactions, whereas no relationship has yet been demonstrated between Hox genes and other transcription factors involved in determining and/or maintaining tissue specificity. The thyroid transcription factor-1 (TTF-1) is a homeodomain-containing protein required for expression of thyroid-specific genes. A 862 bp 5' genomic fragment of the rat TTF-1 gene, conferring thyroid-specific expression to a reporter gene, was sufficient to mediate transactivation by the human HOXB3 gene in co-transfection assay in both NIH3T3 or HeLa cells. HOXB3 is expressed in early mammalian embryogenesis in the anterior neuroectoderm, branchial arches and their derivatives, including the area of the thyroid primordia and thyroid gland. Transcription of the TTF-1 promoter is induced only by HOXB3, while its paralogous gene HOXD3 or other Hox genes expressed more posteriorly (HOXA4, HOXD4, HOXC5, HOXC6, HOXC8 and Hoxd-8) have no effect. Transactivation by HOXB3 is mediated by two binding sites containing an ATTA core located at -100 and +30 from the transcription start site. DNase I footprinting experiments show that the two sites bind HOXB3 protein synthesized in both Escherichia coli and eukaryotic cells, as well as nuclear factor(s) present in protein extracts obtained from mouse embryonic tissues which express group 3 Hox genes and TTF-1. Some of the DNA-protein complexes formed by the embryonic extracts are indistinguishable from those generated by HOXB3.(ABSTRACT TRUNCATED AT 250 WORDS)

The tissue-specific expression of the thyroglobulin gene requires interaction between thyroid-specific and ubiquitous factors

Thyroid-specific expression of the rat thyroglobulin gene is mediated by transcriptional control. Sufficient DNA sequence information to confer thyroid-specific expression to a heterologous gene is contained between positions -168 and +39. DNA-binding studies have demonstrated that this region interacts with two thyroid-specific factors (TTF-1 and TTF-2), and a ubiquitous factor (UFA). Here we have characterized three elements within the promoter, A, K, and C, which are important for promoter activity in thyroid cells. We have shown by mutational analysis that the interaction of TTF-1 with the A and C regions. UFA with the A region, and TTF-2 with the K region are required for full promoter activity. The complex interactions in the A region can be replaced by the substitution of the UFA/TTF-1-binding site with a high-affinity TTF-1 binding site. There is a correlation between the presence of TTF-1 and TTF-2 DNA-binding activities and the expression of thyroglobulin, which implies that the mechanism restricting thyroglobulin expression to thyroid cells is mediated through the control of the expression, or the activity, of TTF-1 and TTF-2.

A thyroid-specific nuclear protein essential for tissue-specific expression of the thyroglobulin promoter

A rat thyroglobulin promoter fragment, capable of directing thyroid-specific transcription, binds at least three different factors, TTF-1, TTF-2 and UFA, which are all present in nuclear extracts of the differentiated rat thyroid cell line FRTL-5. TTF-1 and TTF-2 are FRTL-5 specific, as demonstrated by their absence in nuclear extracts prepared from cell lines that do not express any thyroid-differentiated function, while UFA is present in all cell lines tested. TTF-1 has been extensively purified. It binds to the rat thyroglobulin promoter at three different sites which share sequence homology. Mutations in two of the three sites decrease both binding of TTF-1 in vitro and promoter function in vivo. This suggests that the tissue-specific expression of the thyroglobulin genes is mediated, at least in part, by the presence of a transcription factor exclusively in thyroid cells.

Tightly bound non-histone proteins in nucleosomes from pig-liver chromatin

Core particles prepared by micrococcal nuclease digestion of pig liver chromatin have been adsorbed on hydroxyapatite and dissociated by gradual increase in ionic strength and finally by urea and guanidine. By this method non-histone proteins have been found to be associated with the core particles. Proteins tightly bound to the core particle DNA (i.e. dissociated only by urea and guanidine) have also been found: these are proteins with a limited heterogeneity, with respect to their molecular weights, since only six components are present with molecular weights ranging from 71000 to 20000. They show, furthermore, a peculiar amino acid composition. Other tightly bound proteins have been shown to be present only in the spacer regions. The existence of two different classes of tightly bound proteins probably reflects different modes of binding to the DNA, which are compatible or incompatible, respectively, with the simultaneous binding of the histone octamer.