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Adult-type granulosa cell tumors (aGCT) are rare ovarian sex cord tumors with few effective treatments for recurrent disease. The objective of this study was to characterize the tumor microenvironment (TME) of primary and recurrent aGCTs and to identify correlates of disease recurrence. Total RNA sequencing (RNA-seq) was performed on 24 pathologically confirmed, cryopreserved aGCT samples, including 8 primary and 16 recurrent tumors. After read alignment and quality-control filtering, DESeq2 was used to identify differentially expressed genes (DEG) between primary and recurrent tumors. Functional enrichment pathway analysis and gene set enrichment analysis was performed using “clusterProfiler” and “GSVA” R packages. TME composition was investigated through the analysis and integration of multiple published RNA-seq deconvolution algorithms. TME analysis results were externally validated using data from independent previously published RNA-seq datasets. A total of 31 DEGs were identified between primary and recurrent aGCTs. These included genes with known function in hormone signaling such as LHCGR and INSL3 (more abundant in primary tumors) and CYP19A1 (more abundant in recurrent tumors). Gene set enrichment analysis revealed that primarily immune-related and hormone-regulated gene sets expression was increased in recurrent tumors. Integrative TME analysis demonstrated statistically significant depletion of cancer-associated fibroblasts in recurrent tumors. This finding was confirmed in multiple independent datasets. Implications: Recurrent aGCTs exhibit alterations in hormone pathway gene expression as well as decreased infiltration of cancer-associated fibroblasts, suggesting dual roles for hormonal signaling and TME remodeling underpinning disease relapse.

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Adult-type granulosa cell tumors (aGCT) are rare ovarian sex cord tumors with few effective treatments for recurrent disease. The objective of this study was to characterize the tumor microenvironment (TME) of primary and recurrent aGCTs and to identify correlates of disease recurrence. Total RNA sequencing (RNA-seq) was performed on 24 pathologically confirmed, cryopreserved aGCT samples, including 8 primary and 16 recurrent tumors. After read alignment and quality-control filtering, DESeq2 was used to identify differentially expressed genes (DEG) between primary and recurrent tumors. Functional enrichment pathway analysis and gene set enrichment analysis was performed using “clusterProfiler” and “GSVA” R packages. TME composition was investigated through the analysis and integration of multiple published RNA-seq deconvolution algorithms. TME analysis results were externally validated using data from independent previously published RNA-seq datasets. A total of 31 DEGs were identified between primary and recurrent aGCTs. These included genes with known function in hormone signaling such as LHCGR and INSL3 (more abundant in primary tumors) and CYP19A1 (more abundant in recurrent tumors). Gene set enrichment analysis revealed that primarily immune-related and hormone-regulated gene sets expression was increased in recurrent tumors. Integrative TME analysis demonstrated statistically significant depletion of cancer-associated fibroblasts in recurrent tumors. This finding was confirmed in multiple independent datasets.Implications:Recurrent aGCTs exhibit alterations in hormone pathway gene expression as well as decreased infiltration of cancer-associated fibroblasts, suggesting dual roles for hormonal signaling and TME remodeling underpinning disease relapse.

S1. Heatmap of unsupervised hierarchical clustering of the top 1000 most variable genes.S2. Violin plots showing the expression levels of genes previously identified as differentially expressed genes between primary and recurrent tumors in Haltia et al., 2020.S3. Gene set enrichment analysis performed with GO terms and KEGG pathways showing that primarily immune-related and hormone-regulated gene sets expression are altered between primary and recurrent aGCTs.S4. Gene set enrichment analysis results showing that top enriched gene sets are significantly enriched in recurrent tumors in comparison with primary tumors.S5. Boxplot showing the fraction of each noncancerous cell type identified by CIBERSORTx (A) and xCell (B) in primary and recurrent tumor samples.S6. Heatmap showing the correlation between immune cells fractions.

Objective The objective of this study was to determine the prevalence of predictive biomarkers associated with FDA-approved therapies in molecularly defined adult-type ovarian granulosa cell tumors (aGCTs). Methods We performed a retrospective cross-sectional cohort study of tumor profiles using the inclusion criteria of molecularly defined (FOXL2 c.C402G positive) aGCTs previously sequenced at Foundation Medicine, Inc. The dataset included coding variants for up to 406 genes, microsatellite instability, tumor mutational burden, and genomic loss of heterozygosity (gLOH). PD-L1 expression was determined using the tumor proportion score, as measured using the DAKO 22C3 immunohistochemistry assay. Results 423 tumor profiles met inclusion criteria. The median age at the time of sample submission was 57 years (interquartile range 48–65). The mean tumor mutational burden was 1.8 mutations per megabase (range 0–8.8). No tumors exhibited microsatellite instability, and none were gLOH-High (≥16%). Sixty-seven tumors had PD-L1 expression measurement, and 94% were negative. Potentially actionable variants including MTAP deletion (12/173, 5.8%) and activating PIK3CA mutations (23/423, 5.4%) were identified. TP53-mutated aGCT had a higher tumor mutational burden (mean 2.4 mut/Mb, 95% CI 1.7–3.0 mut/Mb vs mean 1.7 mut/Mb, 95% CI 1.5–1.9 mut/Mb; P = .02) and higher gLOH score (mean 4.4%, 95% CI 2.7–6.1% vs mean 1.4%, 95% CI 1.2–1.6%; P = .002) than TP53 non-mutated tumors. Conclusions No women with molecularly defined aGCT in this large cohort would be eligible for FDA-approved pembrolizumab based on either microsatellite instability or high tumor mutational burden. TP53 mutation identified a subset of this tumor type with distinct molecular features. The development of precision treatment options remains a critical unmet need for this rare disease.

Recurrent high-grade neuroendocrine carcinoma of the cervix has a very poor prognosis and limited active treatment options.To evaluate the efficacy of the three-drug regimen topotecan, paclitaxel, and bevacizumab (TPB) in women with recurrent high-grade neuroendocrine carcinoma of the cervix.This retrospective cohort study used data from the Neuroendocrine Cervical Tumor Registry (NeCTuR), which includes data abstracted directly from medical records of women diagnosed with high-grade neuroendocrine carcinoma of the cervix from English- and Spanish-speaking countries. The study compared women with recurrent high-grade neuroendocrine carcinoma of the cervix who received TPB as first- or second-line therapy for recurrence and women with recurrent high-grade neuroendocrine carcinoma of the cervix who received chemotherapy but not TPB. Patients continued chemotherapy until disease progression or development of unacceptable toxic effects. Progression-free survival from the start of treatment for recurrence to the next recurrence or death, overall survival from first recurrence, and response rates were evaluated.The study included 62 patients who received TPB as first- or second-line treatment for recurrence and 56 patients who received chemotherapy but not TPB for recurrence. Median progression-free survival was 8.7 months in the TPB group compared to 3.7 months in the non-TPB group, with a hazard ratio for progression of 0.27 (95% CI 0.17-0.48; P0.0001). In the TPB group, 15% had stable disease, 39% had a partial response, and 18% had a complete response. Significantly more patients in the TPB group than in the non-TPB group remained on treatment at 6 months (67% vs. 31%, P = 0.0004) and 1 year (24% vs. 9%, P = 0.02). Median overall survival was 16.8 months in the TPB group compared to 14.0 months in the non-TPB group, with a hazard ratio for death of 0.87 (95% CI 0.55-1.37).TPB is an active regimen in women with recurrent high-grade neuroendocrine carcinoma of the cervix and improves progression-free survival while decreasing the hazard ratio for progression.

Background: Adult-type granulosa cell tumors (AGCT) are rare ovarian sex cord tumors that exhibit near-universal FOXL2 c.C402G (p.Cys134Trp) hotspot mutations. AGCT recurrence is difficult to predict and is almost always incurable after relapse. Little is known about the relationship between intra-tumor immune and stromal composition and AGCT relapse. Objective: To compare global gene expression profiles between primary and recurrent AGCTs, characterize the tumor microenvironment (TME), and identify correlates of disease recurrence. Methods: Total RNA sequencing was performed on 24 pathologically confirmed, cryopreserved AGCT samples, including 8 primary and 16 recurrent tumors. Standard methods were applied for read alignment, quality control, and quantification of gene-specific read counts. DESeq2 was used to identify statistically significant (adjusted P-value < 0.05) differentially expressed genes between primary and recurrent tumors with fold change > 2. Gene set enrichment analysis was performed using clusterProfiler. Integrative TME composition de-convolution was performed using multiple published algorithms including CIBERSORTx, quanTIseq, xCell, MCP-counter, and EPIC. TME analysis results were externally validated using data from smaller, previously published RNA sequencing datasets. Results: Thirty-one genes were identified as differentially expressed between primary and recurrent AGCTs, including NELL2, GDF6, TUBB2B, AQP3. These included genes with known function in hormone signaling such as LHCGR (adjusted P-value = 0.002) and INSL3 (adjusted P-value = 0.017) which were highly expressed in primary tumors and CYP19A1 (adjusted P-value = 0.009) which was highly expressed in recurrent tumors. Gene set enrichment analysis revealed increased expression of hormone-regulated and immune-related gene sets in recurrent tumors. Integrative, multi-platform TME analysis showed recurrent AGCT to exhibit reduced fractions of cancer-associated fibroblasts and enrichment of myeloid lineages such as neutrophils and macrophages. Conclusions: Recurrent AGCTs exhibit alterations in hormone pathway gene expression as well as decreased infiltration of cancer-associated fibroblasts, suggesting dual roles for hormonal signaling and TME remodeling underpinning disease relapse. Citation Format: Eleonora Khlebus, Veena K. Vuttaradhi, Thomas Welte, Namrata Khurana, Joseph Celestino, Hannah C. Beird, Curtis Gumbs, Latasha Little, Alejandra Flores Legarreta, Tri Nguyen, Barrett Lawson, Russell R. Broaddus, David M. Gershenson, P. Andrew Futreal, R. Tyler Hillman. Tumor microenvironment composition correlates with relapse in ovarian granulosa cell tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2503.

Adult granulosa cell tumor (AGCT) is a subtype of sex-cord stromal tumors and accounts for ~5% of all ovarian neoplasms. Nearly 100% of AGCT cases are caused by an oncogenic point mutation in the Forkhead Box L2 (FOXL2) transcription factor. Weis-Banke et al. found this gain-of-function mutation (FOXL2C134W) allows FOXL2 to hijack the nuclear SMAD2/3/4 complex, the downstream effector of transforming growth factor- ß (TGF-ß), and redirect to novel transcription sites, inducing transcription of epithelial to mesenchymal transition (EMT) and other oncogenes. We hypothesized that FOXL2 mutant AGCT would be sensitive to TGF-ß inhibition. To test this hypothesis, we treated two GCT cell lines with TP-6379, an orally available, investigational small molecule kinase inhibitor of TGFBR1 that has been shown to block the phosphorylation and nuclear translocation of SMAD2 and SMAD3 in cells. TP-6379 was tested in the KGN cell line, derived from an AGCT patient and heterozygous for the FOXL2C134W mutation, and the COV434 cell line, derived from a juvenile GCT patient, which is FOXL2 wild type (WT). KGN cells (IC50 = 135 nM) were observed to be more than 70-fold more sensitive to TP-6379 treatment than COV434 (IC50 = >10,000 nM), after a 6- and 7- day treatment, respectively. KGN cells that were edited to remove the WT FOXL2 or both the WT and FOXL2C134W alleles were observed to be 1.6-fold more sensitive to TP-6379 and 22-fold less sensitive than the parental KGN cells. In vivo testing using KGN cells is ongoing. Viably cryopreserved dissociated tumor cells (DTCs) from two AGCT patients and one JGCT patient, which contain a mixture of tumor, immune, endothelial, and other stromal cells, were also tested in proliferation assays with TP-6379. All three ex vivo samples were positive for the FOXL2C134W mutation as detected by a qPCR genotyping assay and were sensitive to TP-6379 (IC50 = 555-1600 nM) after 6-day treatment. Xenograft models using these patient samples are currently under development. TGF-ß signaling is also a master regulator of the tumor microenvironment (TME) and immune evasion by modulating deposition of extracellular matrix and suppression of immune cells. We performed an immunophenotyping assay in tissue microarrays of thin-needle biopsy cores of multiple cancer types by looking at the distribution of CD8 T cells within tumor and stroma. AGCT showed the strongest excluded and desert phenotype among the tested cancer types, where CD8 T cells were confined to the stroma or absent entirely. TP-6379 treatment was observed to increase expression and reverse TGF-ß induced suppression of HLA class I in KGN cells. These data suggest that TGF-ß may play a significant role in the TME of AGCT. In conclusion, preclinical data shows inhibition of TGFß signaling with TP-6379 in FOXL2C134W mutant AGCT is active at blocking cell growth and may prove to be a potential therapy in this rare disease. Citation Format: Curtis A. Allred, Richard E. Heinz, Yuta Matsumura, Tetyana V. Forostyan, David Kircher, Salah Sommakia, Thomas Welte, Veena Vuttaradhi, Jason M. Foulks, Steven L. Warner, R Tyler Hillman. TGFBR1 as a novel therapeutic target in adult granulosa cell tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1617.

OBJECTIVE. To identify clinical and demographic characteristics associated with the absence of opioid usage on the day before discharge among patients undergoing open gynecologic surgery within an enhanced recovery after surgery (ERAS) program. METHODS. This was a single institution retrospective cohort study including all patients who underwent elective open gynecologic surgery as part of an ERAS program between November 1, 2014 and September 30, 2018 and who were discharged between post-operative day 2 and 7. Patients were excluded if they reported preexisting chronic opioid use or underwent total pelvic exenteration. Descriptive statistics were used and multivariable logistic regression was used to identify factors associated with the absence of opioid usage on the day before discharge, after adjustment for relevant covariates. RESULTS. A total of 971 were included with a median length of stay of 3 days, and of these 526 (54.2%) used opioids on day before discharge and 445 (45.8%) did not. Absence of opioid use on the day before discharge was associated with age (P < .001), race (P = .04), Charlson Co-morbidity Index (P < .001), marital status (P = .004), and smoking status (P = .002) by univariate analysis. In a multivariable model, older age (adjusted OR 1.04; 95% CI 1.02–1.06; P < .001), current smoker status (adjusted OR 0.42; 95% CI 0.20–0.81; P = .01), and white or Caucasian race (adjusted OR 0.59; 95% CI 0.38–0.91; P = .02) were significantly associated with the absence of opioid use on the day prior to discharge. CONCLUSIONS. Nearly half of patients undergoing open gynecologic surgery within an established ERAS program did not consume any opioids on day before discharge. Safe, evidence-based reductions in post-operative opioid prescribing may be feasible for a subset of gynecologic surgery patients.

ObjectiveTo determine post-discharge patient-reported symptoms before and after implementation of restrictive opioid prescribing among women undergoing minimally invasive gynecologic surgery.MethodsWe compared clinical outcomes and symptom burden among a cohort of 389 women undergoing minimally invasive gynecologic surgery at a single institution before and after implementation of a restrictive opioid prescribing quality improvement initiative in July 2018. Post-discharge symptom burdens were collected up to 42 days after discharge using the MD Anderson Symptom Inventory and analyzed using linear mixed effects models.ResultsThe majority of women included in this study were white non-smokers and the median age was 55 (range 23–83). Most women underwent hysterectomy (64%), had surgery for malignancy (71%), and were discharged from the hospital on the day of surgery (65%). Women in the restrictive opioid prescribing group had a median reduction in morphine equivalent dose prescribed at discharge of 83%, corresponding to a median reduction in 25 tablets of 5 mg oxycodone per person. There was no difference between opioid prescribing groups in either the rate of refill requests (P=1) or hospital re-admission (P=1) up to 30 days after discharge. After adjustment for co-variates, there was no statistically significant difference in post-discharge symptom burden including patient-reported pain (P=0.08), sleep (P=0.30), walking interference (P=0.64), activity interference (P=0.12), or affective interference (P=0.67). There was a trend toward less reported constiptation in the restrictive opioid prescribing group that did not reach statistical significance (P=0.05).ConclusionWe found that restrictive post-operative opioid prescribing was not associated with differences in longitudinal symptom burden among women undergoing minimally invasive gynecologic surgery. These results provide the most comprehensive picture to date of post-operative symptom recovery under different opioid prescribing approaches, lending additional support for existing recommendations to reduce opioid prescribing following gynecologic surgery.

In order to improve treatment selection for high grade neuroendocrine carcinomas of the cervix (NECC), we performed a comparative genomic analysis between this rare tumor type and other cervical cancer types, as well as extra-cervical neuroendocrine small cell carcinomas of the lung and bladder. We performed whole exome sequencing on fresh-frozen tissue from 15 NECCs and matched normal tissue. We then identified mutations and copy number variants using standard analysis pipelines. Published mutation tables from cervical cancers and extra-cervical small cell carcinomas were used for comparative analysis. Descriptive statistical methods were used and a two-sided threshold of P < .05 was used for significance. In the NECC cohort, we detected a median of 1.7 somatic mutations per megabase (range 1.0–20.9). PIK3CA p.E545K mutations were the most frequency observed oncogenic mutation (4/15 tumors, 27%). Activating MAPK pathway mutations in KRAS (p.G12D) and GNAS (p.R201C) co-occurred in two tumors (13%). In total we identified PI3-kinase or MAPK pathway activating mutations in 67% of NECC. When compared to NECC, lung and bladder small cell carcinomas exhibited a statistically significant higher rate of coding mutations (P < .001 for lung; P = .001 for bladder). Mutation of TP53 was uncommon in NECC (13%) and was more frequent in both lung (103 of 110 tumors [94%], P < .001) and bladder (18 of 19 tumors [95%], P < .001) small cell carcinoma. These comparative genomics data suggest that NECC may be genetically more similar to common cervical cancer subtypes than to extra-cervical small cell neuroendocrine carcinomas of the lung and bladder. These results may have implications for the selection of cytotoxic and targeted therapy regimens for this rare disease.

Adult-type granulosa cell tumors of the ovary (aGCTs) are rare gynecologic malignancies that exhibit a high frequency of somatic FOXL2 c.C402G (p.Cys134Trp) mutation. Treatment of relapsed aGCT remains a significant clinical challenge. Here we show, using whole-exome and cancer gene panel sequencing of 79 aGCTs from two independent cohorts, that truncating mutation of the histone lysine methyltransferase gene KMT2D (also known as MLL2) is a recurrent somatic event in aGCT. Mono-allelic KMT2D-truncating mutations are more frequent in recurrent (10/44, 23%) compared with primary (1/35, 3%) aGCTs (p = 0.02, two-sided Fisher’s exact test). IHC detects additional non-KMT2D-mutated aGCTs with loss of nuclear KMT2D expression, suggesting that non-genetic KMT2D inactivation may occur in this tumor type. These findings identify KMT2D inactivation as a novel driver event in aGCTs and suggest that mutation of this gene may increase the risk of disease recurrence., Adult-type granulosa cell tumors of the ovary (aGCTs) are rare and recurrence is difficult to treat. Here, the authors observe in aGCT a novel recurrent somatic truncating mutation of KMT2D, more frequent in recurrent aGCT, and also non-genetic loss of KMT2D expression.

Objective To examine the association between living in a county with gynecologic oncologist provision, the performance of fertility sparing surgery, and survival among young women with early epithelial ovarian cancer. Methods The present retrospective cohort study was based on the SEER 18 dataset of the US National Cancer Institute. Women younger than 45 years with early stage epithelial ovarian cancer diagnosed between 2000 and 2012 were included. Logistic regression and Cox proportional hazards methods were used to analyze all-cause survival. Adjustment was made for relevant clinical and demographic variables. Results In total, 1499 women were included. Women living in a county with gynecologic oncologist provision were less likely to undergo hysterectomy (adjusted odds ratio, 0.69; 95% confidence interval, 0.52–0.93) at the time of primary surgery. Women who underwent hysterectomy had a similar risk of mortality as women with uterine preservation (adjusted hazard ratio [HR], 0.73; 95% CI, 0.41–1.30). Living in a county with gynecologic oncologist provision was associated with reduced risk of mortality (adjusted HR, 0.53; 95% CI, 0.31–0.92). Conclusion Living in a county with gynecologic oncologist provision was independently associated with the use of fertility sparing surgery among young women with early epithelial ovarian cancer.

Objective. This study was designed to evaluate the ability of commercial molecular tumor profiling to discover actionable mutations and to identify barriers that might prevent patient access to personalized therapies. Methods. We conducted an IRB-approved retrospective review of 26 patients with gynecologic malignancies who underwent commercial tumor profiling at our institution during the first 18 months of test availability. Tumor profiles reported targeted therapies and clinical trials matched to patient-specific mutations. Data analysis consisted of descriptive statistics. Results. Most patients who underwent tumor profiling had serous epithelial ovarian, primary peritoneal, or fallopian tube carcinoma (46%). Patients underwent profiling after undergoing a median of two systemic therapies (range 0 to 13). A median of one targeted therapy was suggested per patient profile. Tumor profiling identified no clinically actionable mutations for seven patients (27%). Six patients sought insurance approval for a targeted therapy and two were declined (33%). One patient (4%) received a targeted therapy and this was discontinued due to tumor progression. Conclusions. There are formidable barriers to targeted therapy for patients with gynecologic malignancies. These barriers include a dearth of FDA-approved targeted agents for gynecologic malignancies, lack of third party insurance coverage and limited geographic availability of clinical trials.

SummarySonic hedgehog (Shh) signaling is critical in development and oncogenesis, but the mechanisms regulating this pathway remain unclear. Although protein phosphorylation clearly affects Shh signaling, little is known about phosphatases governing the pathway. Here, we conducted a small hairpin RNA (shRNA) screen of the phosphatome and identified Eya1 as a positive regulator of Shh signaling. We find that the catalytically active phosphatase Eya1 cooperates with the DNA-binding protein Six1 to promote gene induction in response to Shh and that Eya1/Six1 together regulate Gli transcriptional activators. We show that Eya1, which is mutated in a human deafness disorder, branchio-oto-renal syndrome, is critical for Shh-dependent hindbrain growth and development. Moreover, Eya1 drives the growth of medulloblastoma, a Shh-dependent hindbrain tumor. Together, these results identify Eya1 and Six1 as key components of the Shh transcriptional network in normal development and in oncogenesis.

We have recently shown that a third of reliably-inferred alternative mRNA isoforms are candidates for nonsense-mediated mRNA decay (NMD), an mRNA surveillance system (Lewis et al., 2003; Proc. Natl Acad. Sci. USA, 100, 189–192). Rather than being translated to yield protein, these transcripts are expected to be degraded and may be subject to regulated unproductive splicing and translation (RUST). Our initial experimental studies are consistent with these predictions and suggest an unappreciated role for NMD in several human diseases. Contact: brenner@compbio.berkeley.edu *To whom correspondence should be addressed.

Few nonviral techniques exist for efficient and stable eukaryotic gene transfer and fewer still are broadly useful in both cell culture and whole-organism applications. ɸC31 integrase, a site-specific bacteriophage recombinase, is able to catalyze chromosomal transgene insertion under a diverse range of experimental and therapeutic conditions. The enzyme recognizes and catalyzes unidirectional recombination between attachment motifs found in phage and bacterial genomes (attP and attB sites, respectively). Use of ɸC31 integrase for gene transfer requires that an attB sequence be cloned into a transgene-bearing plasmid. When this modified plasmid is introduced into cells alongside integrase-expressing plasmid, ɸC31 integrase is able to catalyze insertion of the transgene plasmid into one of a limited pool of sites in the target genome that show sequence similarity to wild-type attP. Efficient delivery of ɸC31 integrase and attB donor plasmid to the tissue or cells of interest remains the most challenging aspect of the system. Unlike viral methods of genome manipulation, use of ɸC31 integrase almost always requires an additional method of stimulating cellular DNA uptake. However, the relative simplicity of the plasmid-based system means that nearly any proven method of introducing exogenous DNA into cells can be used with ɸC31 integrase. This protocol describes the use of ɸC31 integrase in mammalian cell culture for the creation of clonal lines showing robust and stable expression of an experimental transgene.

The Hedgehog (Hh) pathway is essential for vertebrate embryogenesis, and excessive Hh target gene activation can cause cancer in humans. Here we show that Neuropilin 1 (Nrp1) and Nrp2, transmembrane proteins with roles in axon guidance and vascular endothelial growth factor (VEGF) signaling, are important positive regulators of Hh signal transduction. Nrps are expressed at times and locations of active Hh signal transduction during mouse development. Using cell lines lacking key Hh pathway components, we show that Nrps mediate Hh transduction between activated Smoothened (Smo) protein and the negative regulator Suppressor of Fused (SuFu). Nrp1 transcription is induced by Hh signaling, and Nrp1 overexpression increases maximal Hh target gene activation, indicating the existence of a positive feedback circuit. The regulation of Hh signal transduction by Nrps is conserved between mammals and bony fish, as we show that morpholinos targeting the Nrp zebrafish ortholog nrp1a produce a specific and highly penetrant Hh pathway loss-of-function phenotype. These findings enhance our knowledge of Hh pathway regulation and provide evidence for a conserved nexus between Nrps and this important developmental signaling system.

Background: Nonsense-mediated mRNA decay (NMD) is a eukaryotic mRNA surveillance mechanism that detects and degrades mRNAs with premature termination codons (PTC + mRNAs). In mammals, a termination codon is recognized as premature if it lies more than about 50 nucleotides upstream of the final intron position. More than a third of reliably inferred alternative splicing events in humans have been shown to result in PTC + mRNA isoforms. As the mechanistic details of NMD have only recently been elucidated, we hypothesized that many PTC + isoforms may have been cloned, characterized and deposited in the public databases, even though they would be targeted for degradation in vivo. Results: We analyzed the human alternative protein isoforms described in the SWISS-PROT database and found that 144 (5.8% of 2,483) isoform sequences amenable to analysis, from 107 (7.9% of 1,363) SWISS-PROT entries, derive from PTC+ mRNA. Conclusions: For several of the PTC+ isoforms we identified, existing experimental evidence can be reinterpreted and is consistent with the action of NMD to degrade the transcripts. Several genes with mRNA isoforms that we identified as PTC + - calpain-10, the CDC-like kinases (CLKs) and LARD - show how previous experimental results may be understood in light of NMD.