Everolimus for the treatment of advanced renal cell carcinoma

INTRODUCTION

The efficacy of sequential everolimus (RAD001, Afinitor®), an orally administered inhibitor of mammalian target of rapamycin (mTOR), is one of the therapeutic options in patients with advanced renal cell cancer (RCC). The purpose of this review is to discuss the mTOR pathway and to update current knowledge of the role of everolimus in metastatic RCC.

AREAS COVERED

The function of mTOR and its inhibition, the early development trials of everolimus, the Phase II trial that lead to the Phase III study and ultimately to FDA approval are all discussed in this review. Literature utilized for this review consists of PUBMED for both description of the mTOR pathway and its role, in addition to publications using everolimus in RCC.

EXPERT OPINION

Everolimus is currently the only agent with a proven progression-free survival improvement for patients who progressed on a vascular endothelial growth factor receptor-tyrosine kinase inhibitor. Future studies may further shed light on the most optimal use of everolimus.

Hyperthyroidism in men with germ cell tumors and high levels of beta-human chorionic gonadotropin

A retrospective review was done on all high volume choriocarcinomas and other germ cell tumors of men with serum beta-human chorionic gonadotropin (beta-HCG) levels greater than 50,000 mIU/ml to determine the incidence and characteristics of hyperthyroidism in this setting. Nineteen patients were identified with high beta-HCG levels, but because 2 did not have thyroid function tests performed, the cases of only 17 patients were evaluable. Of these, 14 (82%) had primary testicular carcinoma and 3 (18%) had extragonadal tumors. Beta-HCG levels on presentation ranged from 80,000 to 3,058,000 mIU/ml, with a median of 243,500 mIU/ml. Seven of the 17 evaluable cases (41%) had T4 serum levels higher than 12 micrograms/dl (normal level 4 to 12 micrograms/dl) with a median value of 15.4 micrograms/dl (range, 12.6 to 33.5 micrograms/dl); serum T4 levels correlated with beta-HCG levels (r = 0.84). All seven patients with elevated T4 levels had beta-HCG values greater than 200,000 mIU/ml, and three of these seven had clinical manifestations that could be attributed to an elevated serum T4; only one patient required specific antithyroid treatment; and after control of primary disease, all other patients had normalization of thyroid function. The most common manifestations of hyperthyroidism in our series were tachycardia, hypertension, and a systolic flow murmur; none of the patients had thyroid gland enlargement. We conclude that subclinical hyperthyroidism is a relatively common phenomenon in germ cell tumors of men with high levels of beta-HCG and that control of the primary disease results in serum T4 level normalization.

A phase I study of everolimus plus sorafenib in patients with metastatic renal cell carcinoma (mRCC)

e16056

Background: Everolimus, a mTOR inhibitor and Sorafenib, a Raf kinase inhibitor had shown their efficacy in RCC, as single agents. Combining these two active agents could have potential additive or synergistic effects. We conducted a phase I study to evaluate the maximum tolerated dose (MTD) of this combination in patients with progressive mRCC. Methods: Patients predominantly had clear cell RCC, and progressive measurable diseases on prior treatments including immunotherapy, TKI and/or Everolimus. Patients were evaluated weekly for toxicities and every 8 weeks for radiological response, including at least both PET/CT and CT scans at baseline and 1st staging. Patients received daily Everolimus and twice daily sorafenib both orally at escalating dose levels of 2.5mg/400mg (dose level 0), 5mg/400mg (+1), and 10mg/400mg (+2). Results: 18 patients with mRCC were enrolled and 15 patients were evaluable. 6 patients were treated on dose level 0, dose- limited toxicity (DLT) was found in 2/6 patients, one with thrombocytopenia/leukopenia, the other with pneumonitis; 6 patients were treated on dose level +1, DLT of pulmonary embolism was found in 1/6 patient; and 3 patients were treated on dose level +2, without DLT. The most common side effect was grade 1/2 hand-foot syndrome (4/15, 27%). The MTD was dose level +2. Overall response by RECIST was 27% (4/15 patients): pathological complete response (CR) was 6% (1/15); radiographic CR was 6% (1/5); surgical CR after resection was 6% (1/15). 47% (7/15) of the patients had stable disease. Decreased FDG uptake was found in 67% (10/15) of the patients. The median PFS was 5.53 months (range, 1.4–14.7), and OS was 7.9 months (range, 2.3–23). Conclusions: The MTD of combining daily Everolimus 10mg and twice daily sorafenib 400mg are safe and effective for progressive metastatic RCC. The phase II trial is planned to start in early 2009.

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Granulocyte macrophage: Colony stimulating factor (GM-CSF), ketoconazole, and mitoxantrone as second-line therapy in patients (Pts) with progressive hormone refractory prostate cancer (HRPC)

e16033

Background: A variety of docetaxel regimens have been tested in HRPC pts, yielding response rates between 38% - 69%. Docetaxel therapy has been widely used as first line therapy. Second line therapies, which are non - taxane based with comparable activities do not exist. This trial is built on the significant body of work which has demonstrated anti-tumor activity of GM-CSF, Ketoconazole and Mitoxantrone alone and in combination in pts with HRPC. The trial is designed to assess the combination of all three agents. Methods: No more than two prior chemotherapy regimens (one which contained docetaxel), progressive disease, and adequate marrow / organ function. Treatment consisted of: Ketoconazole daily 400mg po tid, GM-CSF subcutaneous 250mcg / m2 (14 days on/ 7 days off) and Mitoxantrone 12mg / m2 every 3 weeks (maximum cumulative dose of 140mg / m2), until either the completion of Mitoxantrone or maximum anti-tumor benefit. Pts continued Ketoconazole/ GM-CSF until disease progression. PSA was evaluated every 3 weeks and radiographic studies were performed every 9 weeks. Results: 31 pts were enrolled; 4 pts with PSA only, 9 bone only, 5 soft tissue only, and 13 bone and soft tissue. 2 pts withdrew from study due to toxicity. 8 pts had a PSA response of ≥ 50%, 5 pts had a PSA response of ≥ 80%, and 7 pts had a PSA response of ≥ 90%. 9 pts progressed. The majority of pts had stabilization of their bone and soft tissue involvement and 2 pts with nodal involvement demonstrated a radiographic CR. Significant adverse events included grade III/IV neutropenia, thrombocytopenia, and nausea. Median duration of treatment was 6.22 months (range 2 months - 20.5 months). Conclusions: GM-CSF, Ketoconazole and Mitoxantrone in combination demonstrate significant anti-tumor activity and reversible toxicity in pts who have failed prior docetaxel therapy. Information regarding PSA response, radiographic outcome and adverse event data will be presented. This data warrants further investigation such as a randomized phase II study.

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Vaccination of renal cell cancer (RCC) patients with modified vaccinia Ankara (MVA) delivering tumor antigen 5T4 administered alone or with interleukin 2 (IL-2) or interferon-alpha (IFN)

3026

Background: The attenuated vaccinia virus (MVA) has been engineered to deliver the tumor antigen 5T4 (TroVax). More than 90% of RCCs overexpress the 5T4 antigen. A series of clinical trials were conducted to evaluate the effectiveness of MVA 5T4 as a single agent or in combination with either IL-2 or IFN. Methods: Eligibility: Pathologic diagnosis of clear cell or papillary RCC, progressive measurable metastases, any prior therapy, adequate physiological parameters, Karnofsky performance status ≥ 80%, and no active CNS involvement. A regimen of MVA 5T4 alone or in combination with IL-2 or IFN was given. Results: A total of 53 pts received MVA 5T4 alone or in combination with IL-2 or IFN. 13 pts received MVA 5T4 alone, 25 pts received low dose subcutaneous IL-2, and 15 pts received IFN. Clinical responses were assessed by measuring changes in tumor burden via computed tomography or magnetic resonance imaging scan. 5T4-specific cellular and humoral responses were monitored throughout the study. 5T4 was well tolerated with no serious adverse events attributed to vaccination. Of 48 intention-to-treat pts, 43 mounted 5T4-specific antibody responses. 2 pts showed a complete response for > 36 months and 2 other pts had a partial response for > 24 months and 12 months respectively. 20 pts demonstrated disease stabilization for ≥ 3 months. Median progression-free survival and overall survival for all pts was 3.6 months (range 0.8–29.7) and 13.2 months (range 1–38) respectively. A significant relationship was detected between the magnitude of 5T4-specific antibody response and overall survival. Conclusions: 5T4, whether administered alone or in combination, was well tolerated. High frequency of 5T4-specific immune responses and associated enhanced patient survival is encouraging and warrants further investigation.

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Virtual karyotyping with SNP microarrays reduces uncertainty in the diagnosis of renal epithelial tumors

Background

Renal epithelial tumors are morphologically, biologically, and clinically heterogeneous. Different morphologic subtypes require specific management due to markedly different prognosis and response to therapy. Each common subtype has characteristic chromosomal gains and losses, including some with prognostic value. However, copy number information has not been readily accessible for clinical purposes and thus has not been routinely used in the diagnostic evaluation of these tumors. This information can be useful for classification of tumors with complex or challenging morphology. 'Virtual karyotypes' generated using SNP arrays can readily detect characteristic chromosomal lesions in paraffin embedded renal tumors and can be used to correctly categorize the common subtypes with performance characteristics that are amenable for routine clinical use.

Methods

To investigate the use of virtual karyotypes for diagnostically challenging renal epithelial tumors, we evaluated 25 archived renal neoplasms where sub-classification could not be definitively rendered based on morphology and other ancillary studies. We generated virtual karyotypes with the Affymetrix 10 K 2.0 mapping array platform and identified the presence of genomic lesions across all 22 autosomes.

Results

In 91% of challenging cases the virtual karyotype unambiguously detected the presence or absence of chromosomal aberrations characteristic of one of the common subtypes of renal epithelial tumors, while immunohistochemistry and fluorescent in situ hybridization had no or limited utility in the diagnosis of these tumors.

Conclusion

These results show that virtual karyotypes generated by SNP arrays can be used as a practical ancillary study for the classification of renal epithelial tumors with complex or ambiguous morphology.

Stereotactic body radiotherapy in the management of painful bone metastases

More than 100,000 new cases of bone metastases are diagnosed each year, and they present an important clinical problem. They cause significant morbidity and quality-of-life issues in cancer patients. Conventional external-beam radiotherapy is currently the most common method to treat these metastases, with several randomized controlled trials showing no difference in effectiveness between multiple- and single-dosing treatment regimens. A newer technology to treat bone metastases is stereotactic body radiotherapy (SBRT), a radiation delivery method that allows for a large ablative dose to be accurately given to the target over one to a few fractions. This review details the role of SBRT in painful bone metastases, primarily in the vertebral column, but in other bony sites as well, its unique advantages and disadvantages, and its role in the treatment of tumors traditionally deemed radioresistant. Toxicity to surrounding normal tissues and patterns of local failures are also addressed.

A phase II trial of RAD001 in patients (Pts) with metastatic renal cell carcinoma (MRCC)

5107

Background: RAD001 is an oral mammalian target of Rapamycin (mTOR) inhibitor. Three mechanisms of anti-tumor activity; shuts down tumor response to nutrients and growth factors; cell cycle arrest at late G1 and anti-angiogenesis via VEGF. Molecular alterations in the mTOR modular pathway increase sensitivity in PTEN deficient tumors such as RCC. Endpoints: time-to-progression (TTP), response rate (RR), overall survival (OS), toxicity, and to assess changes in metabolic imaging utilizing CT-PET. Methods: Eligibility included; predominant clear cell, progressive measurable MRCC, adequate organ/marrow function, zubrod performance status (ZPS) = 2, no more than 1 prior therapy, and no active CNS involvement. RAD001 is given orally at a dose of 10mg daily without an interruption (28-day cycle), with dose modifications for toxicity. Re-evaluation was assessed every 2 cycles (8 weeks). RECIST criteria is utilized. TTP and OS are determined from entry into the study. Results: 41 pts have been enrolled. 37 pts are evaluable for response/toxicity. 2 pts toxicity only. 2 pts screened failures. 31 were male/8 female, median age 60 (38–80) years. 31 pts received prior therapy. 23 pts had a ZPS of 0, 13 /1 and 3/2. Sites of disease included; lung, nodal, liver, bone, adrenal, and kidney. 9 pts had 1 metastatic site, 17 pts/2 and 13 pts/3 or more. 15 pts continue to receive RAD001. 12 pts had partial responses, 19 pts were stable for 3+ months. Median duration of therapy is 8+ (range 01–20+) months. Treatment related adverse events; mucositis, skin rash, pneumonitis, hypophosphatemia, hyperglycemia, hypertriglyceridemia, hypercholesterolemia, thrombocytopenia, anemia and elevated LFTs. PET scans have demonstrated decreased metabolic activity in responding or stable pts. Median overall survival is 11.5+ months (range 01–20+). Conclusion: RAD001 has promising anti-tumor activity in pts with MRCC demonstrated by partial response rate. Anti-tumor activity is further suggested by prolonged TTP =3 months. Anti-tumor activity, toxicity and metabolic imaging correlation will be presented. An additional 40 pts who failed prior sunitinib or sorafenib therapy are being enrolled.

No significant financial relationships to disclose.

Activity of MVA 5T4 alone or in combination with either interleukin-2 (IL-2) or interferon-α (IFN) in patients (Pts) with metastatic renal cell cancer (MRCC)

3069

Background: MVA 5T4 consists of the highly attenuated modified Vaccinia Ankara virus containing the gene encoding the human TAA 5T4. Ninety percent or more of RCCs overexpress the 5T4 antigen. A series of clinical trials were conducted to evaluate the effectiveness of MVA 5T4 as a single agent or in combination with Interleukin-2 or Interferon Alpha 2B. Methods: Eligibility: pathologic diagnosis of clear cell or papillary RCC, progressive measurable metastases, any prior therapy, adequate physiologic parameters, Karnofsky performance status (KPS) = 80%, and no active CNS involvement. A regimen of MVA 5T4 alone or in combination with IFN or IL-2 was given. Results: A total of 41 patients received MVA 5T4 alone or in combination. 33 patients received MVA 5T4 with low dose IL-2 or IFN. 23 pts had clear cell; 12 papillary; 5 mixed clear cell; and 1 mixed papillary. 19 pts continue to receive therapy. 2 pts (both clear cell RCC) developed complete responses, 3 pts/partial responses (2 clear cell, 1 papillary) 8 pts/stable for 3+months and 6 pts are too early to be staged at this time. Median duration of therapy is 3.0+ (1+-13+) months. Conclusion: Although comparable antibody response were observed in papillary and clear cell histotypes, clear cell patients appeared to be more likely to respond in terms of clinical benefit parameters, to be presented. Of note is that preliminary analysis of clear cell patients suggests a relationship between the anti-5T4 immune response and tumor response. With the immunological potency and encouraging clinical activity, the future research will focus on the phase 3 randomized, double-blind, placebo controlled parallel group study to investigate whether MVA 5T4, added to first line standard of care therapy, prolongs the survival of patients with locally advanced or metastatic clear cell as well as studies to further optimize MVA 5T4 potency.

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A phase II study of FolateImmune (EC90 with GP1–0100 adjuvant followed by EC17) with low dose cytokines interleukin-2 (IL-2) and interferon-α (IFN-α) in patients with refractory or metastatic cancer

13516

Background: FolateImmune is a folate-receptor (FR)-targeted immunotherapy that induces an immune response against tumor cells by marking them with a folate-hapten conjugate. The conjugate is specifically designed to target FR, which is over-expressed in a variety of cancers. FolateImmune therapy is comprised of a vaccine fluorescein conjugate (EC90), an adjuvant (GP-0100), and a folate-hapten conjugate (EC17). Patients (pts) receive a series of subcutaneous (SQ) injections of EC90 vaccine to stimulate the production of antibodies to the fluorescein-hapten, followed by SQ injections of EC17, which forms a molecular bridge between the tumor cell and the endogenous circulating anti-fluorescein IgG antibody. This is thought to initiate an Fc-mediated immune response leading to antibody-dependent cellular cytotoxicity and/or phagocytosis. IL-2 and IFN are utilized at low doses (7 MIU and 3 MIU, respectively) to further promote an immune response. The Phase Ib objective is to determine the safety of EC90 vaccine/EC17 folate-targeted therapy in combination with IL-2 and IFN. The previous phase I trial explored the safety of FolateImmune without cytokines. Methods: This phase 1b safety study treated eligible patients with FolateImmune therapy at dose levels of 1.2 mg EC90 and EC17 of 0.3 mg/kg. Results: As of Jan 2, 2007, all patients have tolerated therapy without significant toxicity. Grade 1–2 toxicity included: chills, fever, and nausea. One patient has had a minor response and continues on study. Laboratory studies revealed decline in circulating FR+ cells. Of 6 pts enrolled, 5 had a pathologic classification of renal cell cancer (RCC). Conclusion: Preliminary data suggest that FolateImmune therapy, with the addition of low dose cytokines, may be administered in a safe and well-tolerated manner. Phase II trials are planned for RCC.

No significant financial relationships to disclose.

Pathologic Complete Response in Renal Cell Carcinoma Brain Metastases Treated with Stereotactic Radiosurgery

Renal cell carcinoma (RCC) is often regarded as a radiation-resistant tumor. However, radiation therapy (RT) in the form of stereotactic radiosurgery (SRS) or whole-brain irradiation has been used to treat brain metastases from RCC. To date, there have been no clinical pathologic correlative findings before and after RT. Herein, we present a case of a patient with brain metastases from RCC treated with SRS. The diagnosis of clear-cell RCC was made in 2001 after right radical nephrectomy. He was also found to have lung metastases at diagnosis. He presented with neurologic symptoms in 2004, and magnetic resonance imaging showed 3 brain lesions with a significant amount of edema consistent with brain metastases. The largest lesion caused a midline shift and was surgically resected. Pathology revealed metastatic RCC. The other 2 smaller brain lesions were treated at 20 Gy respectively with shaped-beam SRS using the BrainLab Novalis system. No whole-brain irradiation was delivered. However, the patient had difficulty weaning off his steroids, and a magnetic resonance imaging performed 6 months after SRS was read as "progression of the lesions." He then underwent resection of both the irradiated brain lesions. Pathologic examination revealed necrotic tissues without any viable tumor identified. The patient has since been doing very well, now 18 months after SRS and 5 years from the initial diagnosis. This is the first reported case that demonstrates that precise high-dose radiation in the form of SRS can cause significant tumor cell death (pathologic complete response) in radiation-resistant brain metastases from RCC. This finding also provides a rationale to deliver stereotactic body RT for primary and metastatic RCC extracranially. A prospective clinical trial using stereotactic body RT for primary and metastatic RCC is under way.

Antitumor effects of two newly constructed oncolytic herpes simplex viruses against renal cell carcinoma

Conditionally replicating (oncolytic) herpes simplex viruses (HSVs) have shown clear potential as effective agents for the treatment of solid tumors such as renal cell carcinoma (RCC). To enhance the oncolytic capabilities of first-generation HSVs, we recently developed two new constructs. Synco-2D is derived from HSV-1 and contains two mechanisms to induce cell membrane fusion. FusOn-H2 is derived from HSV-2. It selectively targets the activated Ras signaling pathway in tumor cells and also has the ability to induce cell membrane fusion and apoptosis. We studied the in vitro and in vivo antitumor effects of both Synco-2D and FusOn-H2 against RCC. Both Synco-2D and FusOn-H2 lysed human RCC cells in vitro much more readily than did Baco-1. For in vivo studies, the oncolytic viruses were administered either intratumorally or intravenously to nude mice bearing xenografted human RCC, and the tumor growth rate and animal survival were monitored after treatment. In most instances, the results were compared with those for a first-generation non-fusogenic oncolytic HSV (Baco-1). A single intratumoral injection of either Synco-2D or FusOn-H2 produced a striking effect against xenografted human RCC, in contrast to Baco-1, which produced only moderate antitumor activity. Two intravenous injections of Synco-2D also inhibited the growth of human RCC xenografts, while Baco-1 injections via the same route lacked any measurable antitumor effect. These data demonstrate that the newly constructed oncolytic HSVs have potent activity against established RCC in animal models. Clinical trials to validate these results in cancer patients appear warranted.

Phase II study of lenalidomide in patients (pts) with metastatic renal cell cancer (MRCC)

4533

Background: Immunomodulatory drugs are compounds that originated via the deliberate structural modification of thalidomide. Lenalidomide (Revlimid) is a derivative with enhanced immunological and anti-angiogenic properties lacking toxicities associated with thalidomide. Objectives were to determine response rate, time to progression (TTP), one-year survival, and toxicity in patients with progressive MRCC. Methods: Eligibility included: progressive measurable MRCC, adequate organ/marrow function, zubrod performance status (ZPS) ≤ 2, ≤ 1 prior therapy, and no active CNS involvement. Lenalidomide is administered orally at a dose of 25mg daily for 21 days with 7 days rest (28-day cycle), with dose modifications for toxicity. Re-evaluation is done every 3 cycles (12 weeks). RECIST criteria is utilized to determine response rate. TTP is determined from entry into study. Results: 40 pts enrolled. 30 male/10 female, range 38–73 (median 63) years. 38 pts had clear cell carcinoma; 2 pts with papillary. 24 pts received prior immunotherapy and/or chemotherapy. 3 pts met criteria for good prognosis, 33 intermediate and 4 poor. Sites of disease included: lung, nodal, bone, adrenal, kidney, and liver. 17 pts had 1 metastatic site, 13 pts 2 metastatic sites, and 10 pts 3 or more metastatic sites. 36 pts completed at least 12 weeks of therapy. 4 pts had early progressive disease. 1 pt had a CR, 2 pts achieved a PR. 52% of pts had a prolonged TTP ≥ 6 months and 25% ≥ 12 months. Median overall survival of 14.8 months (4.1− 22.2+). Treatment related adverse events included: reversible grade 1/2 non-hematologic toxicity consisting of: nausea, diarrhea, constipation, myalgia and fatigue. 19 pts with grade 3/4 neutropenia and 9 pts with grade 3/4 thrombocytopenia. Median duration of therapy is 6 months (2 - 22). Conclusion: Lenalidomide was well tolerated. Anti-tumor activity has been demonstrated by the following: tumor regression and delayed TTP. The tumor effect was also demonstrated as a second line therapy following cytokine failure.

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Gene expression profiling identifies two distinct papillary renal cell carcinoma (RCC) subgroups of contrasting prognosis

4503

Background: Despite the moderate incidence of papillary renal cell carcinoma (PRCC), there is a disproportionately limited understanding of its underlying genetic programs. There is no effective therapy for metastatic PRCC, and patients are often excluded from kidney cancer trials. A morphological classification of PRCC into Type 1 and Type 2 tumors has been recently proposed, but its biological relevance remains uncertain. Methods: We studied the gene expression profiles of 34 cases of PRCC using Affymetrix HGU133 Plus 2.0 arrays (54,675 probe sets) using both unsupervised and supervised analysis. Comparative genomic microarray analysis (CGMA) was used to infer cytogenetic aberrations, and pathways were ranked with a curated database. Expression of selected genes was validated by immunohistochemistry in 34 samples, with 15 independent tumors. Results: We identified two highly distinct molecular PRCC subclasses with morphologic correlation. The first class, with excellent survival, corresponded to three histological subtypes: Type 1, low-grade Type 2 and mixed Type 1/low-grade Type 2 tumors. The second class, with poor survival, corresponded to high-grade Type 2 tumors (n = 11). Dysregulation of G1/S and G2/M checkpoint genes were found in Class 1 and Class 2 tumors respectively, alongside characteristic chromosomal aberrations. We identified a 7-transcript predictor that classified samples on cross-validation with 97% accuracy. Immunohistochemistry confirmed high expression of cytokeratin 7 in Class 1 tumors, and of topoisomerase IIα in Class 2 tumors. Conclusions: We report two molecular subclasses of PRCC, which are biologically and clinically distinct, which may be readily distinguished in a clinical setting. This may also have therapeutic implications.

No significant financial relationships to disclose.

Radiation therapy in the management of brain metastases from renal cell carcinoma

Brain metastases from renal cell carcinoma (RCC) cause significant morbidity and mortality. More effective treatment approaches are needed. Traditionally, whole-brain radiotherapy has been used for palliation. With advances in radiation oncology, stereotactic radiosurgery and hypofractionated stereotactic radiotherapy have been utilized for RCC brain metastases, producing excellent outcomes. This review details the role of radiotherapy in various subgroups of patients with RCC brain metastases as well as the associated toxicities and outcomes. Newer radiosensitizers (eg, motexafin gadolinium [Xcytrin]) and chemotherapeutic agents (eg, temozolomide [Temodar]) used in combination with radiotherapy will also be discussed.

A multi-step approach to time series analysis and gene expression clustering

MOTIVATION

The huge growth in gene expression data calls for the implementation of automatic tools for data processing and interpretation.

RESULTS

We present a new and comprehensive machine learning data mining framework consisting in a non-linear PCA neural network for feature extraction, and probabilistic principal surfaces combined with an agglomerative approach based on Negentropy aimed at clustering gene microarray data. The method, which provides a user-friendly visualization interface, can work on noisy data with missing points and represents an automatic procedure to get, with no a priori assumptions, the number of clusters present in the data. Cell-cycle dataset and a detailed analysis confirm the biological nature of the most significant clusters.

AVAILABILITY

The software described here is a subpackage part of the ASTRONEURAL package and is available upon request from the corresponding author.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

A Molecular Classification of Papillary Renal Cell Carcinoma

Despite the moderate incidence of papillary renal cell carcinoma (PRCC), there is a disproportionately limited understanding of its underlying genetic programs. There is no effective therapy for metastatic PRCC, and patients are often excluded from kidney cancer trials. A morphologic classification of PRCC into type 1 and 2 tumors has been recently proposed, but its biological relevance remains uncertain. We studied the gene expression profiles of 34 cases of PRCC using Affymetrix HGU133 Plus 2.0 arrays (54,675 probe sets) using both unsupervised and supervised analyses. Comparative genomic microarray analysis was used to infer cytogenetic aberrations, and pathways were ranked with a curated database. Expression of selected genes was validated by immunohistochemistry in 34 samples with 15 independent tumors. We identified two highly distinct molecular PRCC subclasses with morphologic correlation. The first class, with excellent survival, corresponded to three histologic subtypes: type 1, low-grade type 2, and mixed type 1/low-grade type 2 tumors. The second class, with poor survival, corresponded to high-grade type 2 tumors (n = 11). Dysregulation of G1-S and G2-M checkpoint genes were found in class 1 and 2 tumors, respectively, alongside characteristic chromosomal aberrations. We identified a seven-transcript predictor that classified samples on cross-validation with 97% accuracy. Immunohistochemistry confirmed high expression of cytokeratin 7 in class 1 tumors and of topoisomerase IIalpha in class 2 tumors. We report two molecular subclasses of PRCC, which are biologically and clinically distinct and may be readily distinguished in a clinical setting.