Platinum Sensitivity in IDH1/2 Mutated Intrahepatic Cholangiocarcinoma: Not All "BRCAness" Is Created Equal

Preclinical data suggest that IDH1/2 mutations result in defective homologous recombination repair (HRR). We hypothesized that patients with IDH1/2mt intrahepatic cholangiocarcinoma (IHCC) would benefit more from 1 L platinum chemotherapy than patients with wildtype (WT) tumors. We performed a multicenter retrospective study of 81 patients with unresectable IHCC treated with 1 L platinum with a primary endpoint of clinical benefit rate (CBR). Patients with IDH1/2mt tumors had a similar CBR and objective response rate compared to those with IDH WT disease (59 versus 54%; p = 0.803), suggesting that a relationship between platinum sensitivity and HRR gene defects may be specific to tumor context.

Characteristics Associated With Disparities Among Older Adults in Coronavirus Disease 2019 Outcomes in an Academic Health Care System

BACKGROUND

An improved understanding of the coronavirus disease 2019 (COVID-19) pandemic is needed to identify predictors of outcomes among older adults with COVID-19.

OBJECTIVE

The objective of this study was to examine patient and health system factors predictive of in-hospital mortality, intensive care unit (ICU) admission, and readmission among patients with COVID-19.

DESIGN, SETTING, AND PARTICIPANTS

A cohort study of patients aged 18 years and older with COVID-19 discharged from 5 New York hospitals within the Mount Sinai Health System (March 1, 2020-June 30, 2020).

MEASURES

Patient-level characteristics (age, sex, race/ethnicity, comorbidities/serious illness, transfer from skilled nursing facility, severe acute respiratory syndrome coronavirus 2 viral load, Sequential Organ Failure Assessment score, treatments); hospital characteristics.

OUTCOMES

All-cause in-hospital mortality; ICU admission; 30-day readmission.

RESULTS

Among 7556 subjects, mean age 61.1 (62.0) years; 1556 (20.6%) died, 949 (12.6%) had an ICU admission, and 227 (9.1%) had a 30-day readmission. Increased age [aged 55-64: odds ratio (OR), 3.28; 95% confidence interval (CI), 2.41-4.46; aged 65-74: OR, 4.67; 95% CI, 3.43-6.35; aged 75-84: OR, 10.73; 95% CI, 7.77-14.81; aged 85 y and older: OR, 20.57; 95% CI, 14.46-29.25] and comorbidities (OR, 1.11; 95% CI, 1.16, 2.13) were independent risk factors for in-hospital mortality. Yet older adults (aged 55-64 y: OR, 0.56; 95% CI, 0.40-0.77; aged 65-74: OR, 0.46; 95% CI, 0.33-0.65; aged 75-84: OR, 0.27; 95% CI, 0.18-0.40; aged above 85 y: OR, 0.21; 95% CI, 0.13-0.34) and those with Medicaid (OR, 0.74; 95% CI, 0.56-0.99) were less likely to be admitted to the ICU. Race/ethnicity, crowding, population density, and health system census were not associated with study outcomes.

CONCLUSIONS

Increased age was the single greatest independent risk factor for mortality. Comorbidities and serious illness were independently associated with mortality. Understanding these risk factors can guide medical decision-making for older adults with COVID-19. Older adults and those admitted from a skilled nursing facility were half as likely to be admitted to the ICU. This finding requires further investigation to understand how age and treatment preferences factored into resource allocation.

Primary hemangioblastoma of the kidney with molecular analyses by next generation sequencing: a case report and review of the literature

Background

Hemangioblastoma is an indolent mesenchymal tumor most frequently occurring in the central nervous system (CNS), but can also arise extraneuraxially, as part of Von Hippel-Lindau (VHL) disease or in sporadic tumors. Extraneuraxial hemangioblastomas occur outside the central nervous system. It includes tumors arising from the nervous paraneuraxial structures and visceral organs. Sporadic hemangioblastoma of the kidney, a rare subset of extraneuraxial hemangioblastomas, is an under-recognized renal neoplasm. There have been only 25 cases described to date in the English language literature. We report herein one additional sporadic tumor in a patient without VHL disease.

Case presentation

A 61 year old male presenting with gross hematuria was found to have a 3.5 cm renal mass at the lateral mid to lower pole of the left kidney on computed tomography urogram. The patient underwent a partial nephrectomy for the mass. Pathological examination showed a well-circumscribed non-encapsulated tumor composed of sheets of large polygonal cells traversed by a rich vascular network. The tumor cells showed clear to eosinophilic cytoplasm and overall bland nuclei. The diagnosis of hemangioblastoma was confirmed by positive immunostaining for alpha-inhibin, S100, neuron-specific enolase, and PAX8. No significant gene mutations, including VHL gene and copy number changes were detected in the tumor using next generation sequencing supporting the diagnosis of sporadic renal hemangioblastoma.

Conclusion

Sporadic renal hemangioblastoma is a rare subset of extraneuraxial hemangioblastomas. We report one such tumor in a patient without clinical or molecular evidence of VHL disease. The literature was reviewed to better understand the clinical, radiological, pathological, and molecular features of this neoplasm. The majority of renal hemangioblastomas showed positive immunostaining for PAX8, which supports the idea that the immunoprofiles of extraneuraxial hemangioblastomas can vary depending on sites of origin. Diagnosis of renal hemangioblastoma is challenging because of its rarity and overlapping microscopic and immunophenotypic features with other renal tumors, including clear cell renal cell carcinoma. In some cases, molecular or genetic studies may be necessary to obtain an accurate diagnosis. Since renal hemangioblastoma is clinically benign, recognition of this pathological entity is important to avoid unnecessary over-treatment.

Solitary Peutz-Jeghers Type Polyp of Jejunum with Gastric Fundic and Antral Gland Lining Mucosa: A Case Report and Review of Literature

Solitary Peutz-Jeghers type polyps are characterized by a hamartomatous polyp of the gastrointestinal (GI) tract in a patient without mucocutaneous pigmentation, family history of Peutz-Jeghers syndrome, or STK11/LKB1 mutations. Histologically identical to the polyps in Peutz-Jeghers syndrome, these sporadic polyps can arise anywhere along the GI tract, with typical arborizing smooth muscles extending from the muscularis mucosa. While the lining mucosa is generally the same as the organ in which it arises, gastric pyloric and osseous metaplasia have been reported in intestinal polyps in Peutz-Jeghers syndrome. Herein, the authors report the first case of a small intestinal solitary Peutz-Jeghers type polyp with gastric antral and fundic gland lining mucosa. A 43-year-old male was admitted for small bowel obstruction. Diagnostic laparoscopy revealed jejuno-jejunal intussusception with an associated polyp measuring 7.2 cm. Histological examination showed a hamartomatous polyp with arborizing smooth muscle bundles extending from the muscularis mucosae. The polyp was lined by non-dysplastic gastric antral and fundic gland mucosa, and was sharply demarcated from the adjacent non-polypoid intestinal mucosa. Colonoscopy, esophagogastroduodenoscopy and small bowel enteroscopy revealed no additional polyps or masses. Thorough investigation of the patient's family history was negative for Peutz-Jeghers syndrome or mucocutaneous pigmentation. Molecular analysis of the lesion was negative for STK11/LKB1 mutations. A diagnosis of solitary Peutz-Jeghers type polyp of the small bowel with gastric antral and fundic gland mucosal lining was rendered.

Anti-invasive efficacy and survival benefit of the YAP-TEAD inhibitor Verteporfin in preclinical glioblastoma models

BACKGROUND

Glioblastoma (GBM) remains a largely incurable disease as current therapy fails to target the invasive nature of GBM growth in disease progression and recurrence. Here we use the FDA-approved drug and small molecule Hippo inhibitor Verteporfin to target YAP-TEAD activity, known to mediate convergent aspects of tumor invasion/metastasis, and assess the drug's efficacy and survival benefit in GBM models.

METHODS

Up to eight low-passage patient-derived GBM cell lines with distinct genomic drivers, including three primary/recurrent pairs, were treated with Verteporfin or vehicle to assess in-vitro effects on proliferation, migration, YAP-TEAD activity, and transcriptomics. Patient-derived orthotopic xenograft models (PDX) were used to assess Verteporfin's brain penetrance and effects on tumor burden and survival.

RESULTS

Verteporfin treatment disturbed YAP/TAZ-TEAD activity; disrupted transcriptome signatures related to invasion, epithelial-to-mesenchymal, and proneural-to-mesenchymal transition, phenocopying TEAD1-knockout effects; and impaired tumor migration/invasion dynamics across primary and recurrent GBM lines. In an aggressive orthotopic PDX GBM model, short-term Verteporfin treatment consistently diminished core and infiltrative tumor burden, which was associated with decreased tumor expression of Ki67, nuclear YAP, TEAD1, and TEAD-associated targets EGFR, CDH2 and ITGB1. Finally, long-term Verteporfin treatment appeared non-toxic and conferred survival benefit compared to vehicle in two PDX models: as monotherapy in primary (de-novo) GBM and in combination with Temozolomide chemoradiation in recurrent GBM, where VP treatment associated with increased MGMT methylation.

CONCLUSIONS

We demonstrate combined anti-invasive and anti-proliferative efficacy for Verteporfin with survival benefit in preclinical GBM models, indicating potential therapeutic value of this already FDA-approved drug if repurposed for glioblastoma patients.

Urothelial carcinoma of the graft kidney with molecular analyses: a rare case report

Background

Malignancy after transplantation is a leading cause of death among kidney transplant recipients. However, donor-derived malignancies are rare. We report a case of a high grade papillary urothelial carcinoma arising in a transplanted kidney.

Case presentation

A 62-year-old female who received a kidney transplantation more than 30 years ago presented with urinary tract infection, acute renal failure, and hydronephrosis of the transplant kidney. Anterograde nephrostogram showed a large filling defect in the lower pole of the transplant kidney and in the proximal 3–4 cm of the ureter. A biopsy from the renal pelvic mass showed a high grade urothelial carcinoma. She underwent an anterior exenteration, resection of both transplant and native kidneys and bilateral pelvic lymph node dissection. Pathologic examination showed a high grade papillary urothelial carcinoma which appeared to arise in the pelvis of the graft kidney, involve the graft ureter and native urinary bladder. The tumor had metastasized to one left obturator lymph node but spared the two native kidneys and ureters. Short tandem repeat (STR) analysis confirmed the tumor to be of donor origin. Next-generation sequencing identified amplification of TERT and loss of CDKN2A/CDKN2B in the primary tumor.

Conclusion

While it is known that transplant recipients have an increased risk of urothelial carcinoma compared to the general population, the lack of the well-documented risk factors, such as older age at transplantation, BK polyomavirus infection, and prolonged post-transplantation history and dissemination of the tumor in this case shed light on the de novo tumorigenesis of the graft kidney within the host microenvironment. Amplification of Telomerase reverse transcriptase (TERT) and loss of cyclin dependent kinase inhibitor 2A/2B (CDKN2A/CDKN2B) detected in the tumor by next gene sequencing suggests that they may play an important role in this case.

Intestinal Host Response to SARS-CoV-2 Infection and COVID-19 Outcomes in Patients With Gastrointestinal Symptoms

BACKGROUND & AIMS

Given that gastrointestinal (GI) symptoms are a prominent extrapulmonary manifestation of COVID-19, we investigated intestinal infection with SARS-CoV-2, its effect on pathogenesis, and clinical significance.

METHODS

Human intestinal biopsy tissues were obtained from patients with COVID-19 (n = 19) and uninfected control individuals (n = 10) for microscopic examination, cytometry by time of flight analyses, and RNA sequencing. Additionally, disease severity and mortality were examined in patients with and without GI symptoms in 2 large, independent cohorts of hospitalized patients in the United States (N = 634) and Europe (N = 287) using multivariate logistic regressions.

RESULTS

COVID-19 case patients and control individuals in the biopsy cohort were comparable for age, sex, rates of hospitalization, and relevant comorbid conditions. SARS-CoV-2 was detected in small intestinal epithelial cells by immunofluorescence staining or electron microscopy in 15 of 17 patients studied. High-dimensional analyses of GI tissues showed low levels of inflammation, including down-regulation of key inflammatory genes including IFNG, CXCL8, CXCL2, and IL1B and reduced frequencies of proinflammatory dendritic cells compared with control individuals. Consistent with these findings, we found a significant reduction in disease severity and mortality in patients presenting with GI symptoms that was independent of sex, age, and comorbid illnesses and despite similar nasopharyngeal SARS-CoV-2 viral loads. Furthermore, there was reduced levels of key inflammatory proteins in circulation in patients with GI symptoms.

CONCLUSIONS

These data highlight the absence of a proinflammatory response in the GI tract despite detection of SARS-CoV-2. In parallel, reduced mortality in patients with COVID-19 presenting with GI symptoms was observed. A potential role of the GI tract in attenuating SARS-CoV-2-associated inflammation needs to be further examined.

Multiparametric MRI texture analysis in prediction of glioma biomarker status: added value of MR diffusion

Background

Early identification of glioma molecular phenotypes can lead to understanding of patient prognosis and treatment guidance. We aimed to develop a multiparametric MRI texture analysis model using a combination of conventional and diffusion MRI to predict a wide range of biomarkers in patients with glioma.

Methods

In this retrospective study, patients were included if they (1) had diagnosis of gliomas with known IDH1, EGFR, MGMT, ATRX, TP53, and PTEN status from surgical pathology and (2) had preoperative MRI including FLAIR, T1c+ and diffusion for radiomic texture analysis. Statistical analysis included logistic regression and receiver-operating characteristic (ROC) curve analysis to determine the optimal model for predicting glioma biomarkers. A comparative analysis between ROCs (conventional only vs conventional + diffusion) was performed.

Results

From a total of 111 patients included, 91 (82%) were categorized to training and 20 (18%) to test datasets. Constructed cross-validated model using a combination of texture features from conventional and diffusion MRI resulted in overall AUC/accuracy of 1/79% for IDH1, 0.99/80% for ATRX, 0.79/67% for MGMT, and 0.77/66% for EGFR. The addition of diffusion data to conventional MRI features significantly (P < .05) increased predictive performance for IDH1, MGMT, and ATRX. The overall accuracy of the final model in predicting biomarkers in the test group was 80% (IDH1), 70% (ATRX), 70% (MGMT), and 75% (EGFR).

Conclusion

Addition of MR diffusion to conventional MRI features provides added diagnostic value in preoperative determination of IDH1, MGMT, and ATRX in patients with glioma.

KRAS G12C-Mutant Non-Small Cell Lung Cancer: Biology, Developmental Therapeutics, and Molecular Testing

Mutation in the gene that encodes Kirsten rat sarcoma viral oncogene homolog (KRAS) is the most common oncogenic driver in advanced non-small cell lung cancer, occurring in approximately 30% of lung adenocarcinomas. Over 80% of oncogenic KRAS mutations occur at codon 12, where the glycine residue is substituted by different amino acids, leading to genomic heterogeneity of KRas-mutant tumors. The KRAS glycine-to-cysteine mutation (G12C) composes approximately 44% of KRAS mutations in non-small cell lung cancer, with mutant KRas^G12C present in approximately 13% of all patients with lung adenocarcinoma. Mutant KRas has been an oncogenic target for decades, but no viable therapeutic agents were developed until recently. However, advances in KRas molecular modeling have led to the development and clinical testing of agents that directly inhibit mutant KRas^G12C. These agents include sotorasib (AMG-510), adagrasib (MRTX-849), and JNJ-74699157. In addition to testing for known actionable oncogenic driver alterations in EGFR, ALK, ROS1, BRAF, MET exon 14 skipping, RET, and NTRK and for the expression of programmed cell-death protein ligand 1, pathologists, medical oncologists, and community practitioners will need to incorporate routine testing for emerging biomarkers such as MET amplification, ERBB2 (alias HER2), and KRAS mutations, particularly KRAS G12C, considering the promising development of direct inhibitors of KRas^G12C protein.

Gastrointestinal involvement attenuates COVID-19 severity and mortality

Given that gastrointestinal (GI) symptoms are a prominent extrapulmonary manifestation of coronavirus disease 2019 (COVID-19), we investigated intestinal infection with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and its effect on disease pathogenesis. SARS-CoV-2 was detected in small intestinal enterocytes by immunofluorescence staining or electron microscopy, in 13 of 15 patients studied. High dimensional analyses of GI tissues revealed low levels of inflammation in general, including active downregulation of key inflammatory genes such as IFNG, CXCL8, CXCL2 and IL1B and reduced frequencies of proinflammatory dendritic cell subsets. To evaluate the clinical significance of these findings, examination of two large, independent cohorts of hospitalized patients in the United States and Europe revealed a significant reduction in disease severity and mortality that was independent of gender, age, and examined co-morbid illnesses. The observed mortality reduction in COVID-19 patients with GI symptoms was associated with reduced levels of key inflammatory proteins including IL-6, CXCL8, IL-17A and CCL28 in circulation but was not associated with significant differences in nasopharyngeal viral loads. These data draw attention to organ-level heterogeneity in disease pathogenesis and highlight the role of the GI tract in attenuating SARS-CoV-2-associated inflammation with related mortality benefit.

One Sentence Summary

Intestinal infection with SARS-CoV-2 is associated with a mild inflammatory response and improved clinical outcomes.

Histology-specific FGFR2 alterations and FGFR2-TACC2 fusion in mixed adenoid cystic and neuroendocrine small cell carcinoma of the uterine cervix

Neuroendocrine small cell carcinoma of the uterine cervix portends a dismal prognosis with limited treatment options. Rarely, tumors of mixed-lineage appear in gynecologic malignancies. Here, we report a 77-year-old woman who presented with complete uterine prolapse and 4-month history of vaginal bleeding. Histopathologic evaluation revealed a mixed adenoid cystic carcinoma and neuroendocrine small cell carcinoma of the uterine cervix. The tumor was PD-L1 and HPV 35 positive. The patient was treated with up-front surgery and adjuvant radiation. Independent, histology-specific alterations in FGFR2 and a FGFR2-TACC2 fusion were identified. Progression of disease occurred within 6 months for which she received chemotherapy and immunotherapy. However, the patient expired within a year. We comprehensively review how screening for and targeting of FGFR alterations in recurrent and metastatic cervical cancer might serve as a touchstone for future treatment regimens.

Liquid phase human papillomavirus genotype analysis of aspirated metastatic head and neck squamous cell carcinoma: Fine needle aspiration supernatant is a rich source of tumor DNA that can increase the diagnostic yield

BACKGROUND

Most patients with human papillomavirus (HPV)-related head and neck squamous cell carcinoma (HNSC) present with lymph node metastasis. In these patients, fine needle aspiration (FNA) is not only a diagnostic tool, but a means for determining HPV status. HPV status, in turn, is used to determine tumor origin, prognosis, and even guide therapy. Thus, the limited sampling afforded by FNA must be optimized to meet heavy clinical demands.

PURPOSE

The purpose of this study was to determine whether the residual supernatant portion of the FNA could serve as a resource for reliable determination of HPV status DESIGN/METHOD: 25 FNAs from 24 patients with metastatic HNSC underwent HPV genotyping of post-centrifuged supernatant fluid from FNA needle rinses. HPV genotyping was performed using two real time PCR-based assays, the two-step LightCycler and the one-step automated cobas HPV tests. HPV status of the supernatant was compared with the paired FNA cell blocks and/or surgical tissue samples.

RESULTS

The supernatant was adequate for HPV testing in 24 (96%) of 25 cases. Of these, 14 (56%) were HPV positive and 11 (44%) negative by the LightCycler assay. HPV16 was the most commonly detected genotype (n = 12). When results of supernatant and paired cell block testing were compared, HPV status was concordant in all cases. The LightCycler method was more sensitive than the cobas assay due to its ability to detect an expanded profile of HPV variant genotypes.

CONCLUSION

The current standard of practice for patients with HNSC who undergo FNA is to construct a cell block and then discard the supernatant. This supernatant is a rich source of tumor DNA that can be used to detect HPV status. It should not be wasted.

Comparison of SARS-CoV-2 detection from nasopharyngeal swab samples by the Roche cobas 6800 SARS-CoV-2 test and a laboratory-developed real-time RT-PCR test

The urgent need to implement and rapidly expand testing for severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) infection has led to the development of multiple assays. How these tests perform relative to one another is poorly understood. We evaluated the concordance between the Roche Diagnostics cobas 6800 SARS‐CoV‐2 test and a laboratory‐developed test (LDT) real‐time reverse transcription‐polymerase chain reaction based on a modified Centers for Disease Control and Prevention protocol, for the detection of SARS‐CoV‐2 in samples submitted to the Clinical Laboratories of the Mount Sinai Health System. A total of 1006 nasopharyngeal swabs in universal transport medium from persons under investigation were tested for SARS‐CoV‐2 as part of routine clinical care using the cobas SARS‐CoV‐2 test with subsequent evaluation by the LDT. Cycle threshold values were analyzed and interpreted as either positive (“detected” or “presumptive positive”), negative (not detected), inconclusive, or invalid. Statistical analysis was performed using GraphPad Prism 8. The cobas SARS‐CoV‐2 test reported 706 positive and 300 negative results. The LDT reported 640 positive, 323 negative, 34 inconclusive, and 9 invalid results. When excluding inconclusive and invalid results, the overall percent agreement between the two platforms was 95.8%. Cohen's κ coefficient was 0.904 (95% confidence interval, 0.875‐0.933), suggesting almost perfect agreement between both platforms. An overall discordance rate of 4.2% between the two systems may reflect differences in primer sequences, assay limit of detection, or other factors, highlighting the importance of comparing the performance of different testing platforms.

In this study, we compared the detection of SARS‐CoV‐2 in clinical samples from patients being evaluated for CoVID‐19 infection by two different RT‐PCR assays, the cobas® 6800 SARS‐CoV‐2 test from Roche Molecular Systems and a laboratory‐developed test (LDT) using the Centers for Disease Control and Prevention 2019‐nCoV primers and probes. Overall there was excellent agreement between the two tests methods, although our results suggest that the cobas® SARSCoV‐2 test may have a lower limit of detection than the LDT.

Assessing Genomic Copy Number Alterations as Best Practice for Renal Cell Neoplasia: An Evidence-Based Review from the Cancer Genomics Consortium Workgroup

Renal cell neoplasia are heterogeneous with diverse histology, genetic alterations, and clinical behavior that are diagnosed mostly on morphologic features. The Renal Cell Neoplasia Workgroup of the Cancer Genomics Consortium systematically evaluated peer-reviewed literature on genomic studies of renal cell carcinoma (RCC), including clear cell RCC, papillary RCC, chromophobe RCC, and the translocation RCC involving TFE3, TFEB and MITF rearrangements, as well as benign oncocytoma, which together comprise about 95% of all renal cell neoplasia. The Workgroup curated recurrent copy number alterations (CNAs), copy-neutral loss-of-heterozygosity (cnLOH), rearrangements, and mutations, found in each subtype and assigned clinical relevance according to established criteria. In clear cell RCC, loss of 3p has a disease-initiating role and most likely also in progression with mutations detected in VHL and other genes mapped to this arm, and loss of 9p and/or 14q has well-substantiated prognostic utility. Gain of chromosomes 7 and 17 are hallmark CNAs of papillary RCC, but patterns of other CNAs as detected by chromosomal microarray analysis (CMA) afford sub-classification into Type 1 and 2 with prognostic value, and for further sub-stratification of Type 2. Inherent chromosome loss in chromophobe RCC as detected by CMA is useful for distinguishing the eosinophilic variant from benign oncocytoma which in contrast exhibits few CNAs or rearranged CCND1, but share mitochondrial DNA mutations. In morphologically atypical RCCs, rearrangement of TFE3 and TFEB should be considered in the differential diagnosis, portending an aggressive RCC subtype. Overall, this evidence-based review provides a validated role for assessment of CNAs in renal cell neoplasia in the clinical setting to assist in renal cell neoplasm diagnosis and sub-classification within subtypes that is integral to the management of patients, from small incidentally found renal masses to larger surgically resected specimens, and simultaneously identify the presence of key alterations portending outcome in malignant RCC subtypes.

Clinicopathological and Molecular Characterisation of Crohn's Disease-associated Small Bowel Adenocarcinomas

BACKGROUND AND AIMS

Small bowel adenocarcinoma [SBA] is a recognised complication of Crohn's disease [CD], but its low absolute prevalence limits opportunities for clinicopathological characterisation.

METHODS

We compared the clinical, pathological, and molecular features of 48 SBA from patients with CD [CDSBA] and 29 SBAs from patients without CD [NSBA] who underwent treatment at our tertiary care centre between 2000 and 2018.

RESULTS

Patients with CDSBA were younger than those with NSBA [mean age, 56 vs 64; p = 0.02]. Males predominated in both groups. Most CDSBA [69%] occurred in the ileum, whereas most NSBA occurred in the duodenum [38%] and jejunum [31%; p < 0.001]. Stage I tumours were more prevalent in the CDSBA [33% vs 3%; p = 0.002], although the rates of Stage IV disease and disease-specific mortality were similar in both groups. CDSBA were less likely to present a discrete mass [35% vs 93%; p < 0.001] and were more often stricturing or fistulising [75% vs 10%, respectively, p < 0.001] than NSBA. Microscopically, CDSBA were relatively heterogeneous, exhibiting at least three distinct growth patterns in 39% compared with 1% of NSBA [p = 0.01]. Low-grade tubuloglandular adenocarcinoma was the predominant pattern in 19% of CDSBA compared with 0% of NSBA [p = 0.003]. CDSBA were more frequently DNA mismatch repair proficient [90% vs 62%; p = 0.04] and exhibited profiles of frequently mutated genes similar to those of NSBA, except for IDH1 [18%] and SMAD4 [12%] mutations that occurred uniquely in CDSBA.

CONCLUSIONS

These observations, based on the largest single-centre series described hitherto, establish that CDSBA is a distinct clinical, pathological, and molecular entity.

Bone marrow morphologic features, MyPRS, and gene mutation correlations in plasma cell myeloma

Genetics has played an important role in risk stratification for plasma cell myeloma patients, providing therapeutic guidance. In this study, we investigated the correlation of bone marrow morphologic features and genetic aberrations, including gene expression profiles, translocations, and gene mutations. For the first time we show that high plasma cell volume, diffuse sheet growth pattern, immature cell morphology, high mitotic index, and increased reticulin fibrosis, significantly correlates with high risk disease determined by MyPRS gene expression profiles. Furthermore, we show the association between MyPRS risk stratification and chromosomal alterations and specific gene mutations. We also demonstrate the combinational effect of TP53 mutation and 17p loss on the histological changes in bone marrow.

Mutation profile of high-grade appendiceal mucinous neoplasm

AIMS

High-grade appendiceal mucinous neoplasm (HAMN) was recently proposed as a disease entity histologically analogous to low-grade appendiceal mucinous neoplasm (LAMN), but characterised by high-grade cytological atypia. The pathogenesis and clinical features of HAMN have not been fully elucidated.

METHODS AND RESULTS

Nine cases of HAMN, eight LAMN, 10 appendiceal mucinous adenocarcinomas (MACA) and five appendiceal serrated polyps resected between 2008 and 2017 contributed by three medical centres underwent targeted next-generation sequencing of 50 cancer-related genes. The patients in each category had similar profiles with respect to gender, age, tumour stage and follow-up intervals. Both LAMN and HAMN harboured mutations of KRAS [nine of nine and eight of eight (100%), respectively] and GNAS [five of eight (63%) and five of nine (56%), respectively] in significantly higher proportions than MACA [KRAS, seven of 10 (70%, P = 0.04); GNAS: one of 10 (10%, P = 0.02)] and serrated polyps [KRAS, one of five (20%, P = 0.0007); GNAS: none of five (0%, P = 0.04)]. Four cases of HAMN, but none of LAMN, harboured mutations of TP53 [four of nine (44%)] and/or ATM [two of nine (22%)]. Three cases of HAMN (33%) showed extra-appendiceal spread with retention of the same mutational profiles in the intra- and extra-appendiceal components. The 10 cases of MACA harboured a similar prevalence of TP53 mutations (n = 5, 50%) as HAMN but, unlike LAMN and HAMN, some harboured mutations in PIK3CA, APC, FBXW7, PTEN and SMAD4.

CONCLUSIONS

HAMN and LAMN share high rates of KRAS and GNAS co-mutations supporting a common histogenesis and distinguishing them from MACA. Acquisition of TP53 or ATM mutations by HAMN may drive its progression to a more advanced phenotype.

A phase I study of panobinostat and ruxolitinib in patients with primary myelofibrosis (PMF) and post--polycythemia vera/essential thrombocythemia myelofibrosis (post--PV/ET MF)

Ruxolitinib, a selective JAK1/JAK2 inhibitor, is the current first line therapy for myelofibrosis (MF), which reduces symptomatology and splenomegaly, but does not clearly modify disease course. Panobinostat, a histone deacetylase inhibitor, was shown to be safe and tolerable in phase I and II trials and demonstrated clinical activity in approximately a third of treated patients. Combination therapy of ruxolitinib and panobinostat showed synergistic activity in a preclinical MF model, which prompted clinical evaluation of this combination in both ruxolitinib naïve and treated MF patients. Herein, we report the results of an investigator-initiated, dose escalation, phase I trial of ruxolitinib and panobinostat in 15 patients with primary MF and post-polycythemia vera/essential thrombocythemia MF. This combination treatment proved to be safe and tolerable without dose limiting thrombocytopenia and a maximum tolerated dose of both agents in combination was not determined. The majority of patients maintained stable disease with this combination treatment and 40 % attained a clinical improvement (spleen n = 5, anemia n = 1) by modified IWG-MRT at the end of 6 cycles. This is one of the first attempts of rationally designed, JAK inhibitor-based, combination therapy studies and exemplifies the feasibility of such an approach in patients with advanced MF.

Clinicopathological characterization of SMAD4-mutated intestinal adenocarcinomas: A case-control study

The SMAD4 tumor suppressor gene product inhibits transforming growth factor-β-mediated signaling and is mutated in ~10% of colorectal carcinomas. The prognostic significance of SMAD4 mutations has been controversial. We studied the pathological and clinical characteristics of SMAD4-mutated intestinal adenocarcinomas using a retrospective case-control study design. Cases and controls were identified among 443 primary adenocarcinomas that had undergone next generation DNA sequencing (NGS) with the Ion AmpliSeq Cancer Hotspot Panel v2, which evaluates 50 cancer-related genes. Twenty-eight SMAD4-mutated (SMAD4m) patients were matched 1:2 with 56 consecutive SMAD4 wild-type (SMAD4wt) control patients from the same analysis stream. Compared with the SMAD4wt controls, the SMAD4m tumors were of higher stage (P = 0.026) and were more likely to feature mucinous differentiation (P = 0.0000), to occur in the setting of Crohn’s disease (P = 0.0041), and to harbor concurrent RAS mutations (P = 0.0178). Tumor mucin content was significantly correlated with mutations involving the MH2 domain of the SMAD4 protein (P = 0.0338). Correspondence between mutation sites and morphology was demonstrated directly in a mixed adenocarcinoma and neuroendocrine tumor where SMAD4 mutations involving different protein domains were found in histologically disparate tumor regions despite both containing identical KRAS and TP53 mutations.

Predictive genomic markers of response to VEGF targeted therapy in metastatic renal cell carcinoma

Background

First-line treatment for metastatic renal cell carcinoma (mRCC) is rapidly changing. It currently includes VEGF targeted therapies (TT), multi-target tyrosine kinase inhibitors (TKIs), mTOR inhibitors, and immunotherapy. To optimize outcomes for individual patients, genomic markers of response to therapy are needed. Here, we aim to identify tumor-based genomic markers of response to VEGF TT to optimize treatment selection.

Methods

From an institutional database, primary tumor tissue was obtained from 79 patients with clear cell mRCC, and targeted sequencing was performed. Clinical outcomes were obtained retrospectively. Progression-free survival (PFS) on first-line VEGF TT was correlated to genomic alterations (GAs) using Kaplan-Meier methodology and Cox proportional hazard models. A composite model of significant GAs predicting PFS in the first-line setting was developed.

Results

Absence of VHL mutation was associated with inferior PFS on first-line VEGF TT. A trend for inferior PFS was observed with GAs in TP53 and FLT1 C/C variant. A composite model of these 3 GAs was associated with inferior PFS in a dose-dependent manner.

Conclusion

In mRCC, a composite model of TP53 mutation, wild type VHL, and FLT1 C/C variant strongly predicted PFS on first-line VEGF TT in a dose-dependent manner. These findings require external validation.

Role of minimal residual disease in the management of acute myeloid leukemia-a case-based discussion

AML is stratified into risk-categories based on cytogenetic and molecular features that prognosticate survival and facilitate treatment algorithms, though there is still significant heterogeneity within risk groupings with regard to risk of relapse and prognosis. The ambiguity regarding prognosis is due in large part to the relatively outdated criteria used to determine response to therapy. Whereas risk assessment has evolved to adopt cytogenetic and molecular profiling, response criteria are still largely determined by bone marrow morphologic assessment and peripheral cell count recovery. Minimal residual disease refers to the detection of a persistent population of leukemic cells below the threshold for morphologic CR determination. MRD assessment represents standard of care for ALL and PML, but concerns over prognostic capability and standardization have limited its use in AML. However, recent advancements in MRD assessment and research supporting the use of MRD assessment in AML require the reconsideration and review of this clinical tool in this disease entity. This review article will first compare and contrast the major modalities used to assess MRD in AML, such as RQ-PCR and flow cytometry, as well as touching upon newer technologies such as next-generation sequencing and digital droplet PCR. The majority of the article will discuss the evidence supporting the use of MRD assessment to prognosticate disease at various time points during treatment, and review the limited number of studies that have incorporated MRD assessment into novel treatment algorithms for AML. The article concludes by discussing the current major limitations to the implementation of MRD assessment in this disease. The manuscript is bookended by a clinical vignette that highlights the need for further research and refinement of this clinical tool.

Amplification of specific chromosomal regions assessed by fluorescent in situ hybridization on Pap smears to be added as screening tool for identifying women at risk of progressing to cervical cancer

Cervical carcinoma is a frequent malignancy in developing countries despite being a preventable disease. For the first time, four screening tests were used simultaneously for identifying women with a risk of developing cervical cancer, to help clinicians and policy makers to implement the best strategy for reducing the burden of this disease. Women visiting a hospital in India were enrolled after institutional ethics clearance and informed consent. Visual inspection using acetic acid and Pap smear tests were performed on 2683 women, and 104 had abnormal cytology: atypical squamous cells of undetermined significance (n = 29), low-grade squamous intraepithelial lesion (n = 41), high-grade squamous intraepithelial lesion (n = 17), and squamous cell carcinoma (n = 17). These and 96 samples, with normal cytology, were subjected to high-risk human papilloma virus testing and fluorescent in situ hybridization evaluation. Women with abnormal cytology were followed for 5 years and evaluated with colposcopy-guided biopsy. Three accepted methods of screening and one novel fluorescent in situ hybridization assay were carried out in 200 cases. Cutoffs for fluorescent in situ hybridization were established. The screening methods had 88%-96% negative predictive value, while positive predictive value was low (20%) for visual inspection using acetic acid, 47% for fluorescent in situ hybridization, 56% for high-risk human papilloma virus, and 73% for combined high-risk human papilloma virus and fluorescent in situ hybridization. Combined high-risk human papilloma virus and fluorescent in situ hybridization had 94% sensitivity, specificity, and negative predictive value, suggesting that simultaneous screening with these two tests is appropriate for identifying women progressing to cervical cancer and not visual inspection using acetic acid, which has low positive predictive value and Pap cytology which requires to be repeated. Policy makers and clinicians can assess feasibility of incorporating this screening strategy to prevent cervical cancer.

NSD1 Inactivation and SETD2 Mutation Drive a Convergence toward Loss of Function of H3K36 Writers in Clear Cell Renal Cell Carcinomas

Extensive dysregulation of chromatin-modifying genes in clear cell renal cell carcinoma (ccRCC) has been uncovered through next-generation sequencing. However, a scientific understanding of the cross-talk between epigenetic and genomic aberrations remains limited. Here we identify three ccRCC epigenetic clusters, including a clear cell CpG island methylator phenotype (C-CIMP) subgroup associated with promoter methylation of VEGF genes (FLT4, FLT1, and KDR). C-CIMP was furthermore characterized by silencing of genes related to vasculature development. Through an integrative analysis, we discovered frequent silencing of the histone H3 K36 methyltransferase NSD1 as the sole chromatin-modifying gene silenced by DNA methylation in ccRCC. Notably, tumors harboring NSD1 methylation were of higher grade and stage in different ccRCC datasets. NSD1 promoter methylation correlated with SETD2 somatic mutations across and within spatially distinct regions of primary ccRCC tumors. ccRCC harboring epigenetic silencing of NSD1 displayed a specific genome-wide methylome signature consistent with the NSD1 mutation methylome signature observed in Sotos syndrome. Thus, we concluded that epigenetic silencing of genes involved in angiogenesis is a hallmark of the methylator phenotype in ccRCC, implying a convergence toward loss of function of epigenetic writers of the H3K36 histone mark as a root feature of aggressive ccRCC. Cancer Res; 77(18); 4835-45. ©2017 AACR.

Metastasis-associated mutations in clear cell renal cell carcinoma

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Background: Over 30% of patients with clear cell renal cell carcinoma (ccRCC) exhibit metastasis at the time of diagnosis and exhibit poor outcome. About 20-50% of patients with localized disease eventually develop metastasis after nephrectomy. The goal of the current study was to identify target gene mutations associated with ccRCC metastasis. Methods: In this IRB approved study, genomic DNA from 128 ccRCC resected specimens (128 unique patients) were profiled using a custom targeted next-generation sequencing (NGS) panel comprising 70 frequently mutated genes and prognostic SNPs in renal cancer. The specimen cohort consisted of 78 primary (29 stage I-III, 30 stage IV, 19 unknown) and 50 metastatic (10 lung, 9 bone, 25 other sites, 6 unknown) lesions. Following hybrid capture, sequencing was performed (MiSeq, Illumina) and variants identified using CLCbio (Qiagen). Chi-square test was used to test for significance. Results: The median specimen had 4 non-synonymous mutations (123/128 samples had at least one mutation). 66 genes showed a non-synonymous mutation in at least one specimen. There was no significant difference between total mutation count between primary and metastatic specimens (Mann-Whitney test). TSC1 mutation was significantly enriched in metastatic (8/50) compared with primary lesions (3/78). No TSC1 mutation was found in the 29 localized (stage I-III) primary lesions. Interestingly, TSC1 maps to 9q34 and our prior copy number studies indicated that loss of 9q is also enriched in metastatic lesions. Of the 11 specimens bearing TSC1 mutation in this cohort, 5 also had loss of 9q. In 44 specimens with known sites of resection, SETD2 and TSC1 mutations were not found in metastases to the lung but found in 30-40% of lesions at other sites, KDM5C and TSC1 mutations were not found in metastases to the bone while 25-30% of lesions at other sites exhibited these mutations. Due to the limited sample size, significance could not be determined for these associations. Conclusions: Preliminary results of this study implicated TSC1 in the metastasis of ccRCC. Since TSC1 mutation is known to confer sensitivity to mTOR inhibitors, our initial finding of absence of TSC1 mutation in lung and bone sites of metastasis may have therapeutic implications.

Clinical utility of a custom next-generation sequencing panel in the diagnosis of needle biopsies from renal masses

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Background: Image-guided core-needle biopsies are increasingly being utilized to assist in the management of patients with renal masses, where only limited material is available for analysis. In this study, the performance of a custom next-generation sequencing (NGS) panel was evaluated for diagnostic and prognostic utility in this setting. Methods: DNA was available for NGS from 41 of 48 core-needle biopsies from renal masses previously submitted to array-CGH (aCGH) in this IRB-approved study. The targeted NGS panel comprised genes mutated in renal cancer, prognostic SNPs, and a 3Mbp SNP backbone. After library preparation from as little as 25ng DNA, sequencing was performed (MiSeq, Illumina), variants identified using CLCbio, and genomic gain/loss estimated by CNVKit (Talevich E, et al, manuscript in preparation). A classification algorithm based on 15 copy number alterations (CNAs) was applied to aCGH and NGS CNA profiles (PMID: 25498568). Histology of the biopsy or resected specimen (if available) served as the gold standard. Results: By histology, the 41 profiled biopsies comprised: 13 clear cell RCC (ccRCC), 9 papillary RCC (pRCC), 2 chromophobe RCC (chrRCC), 12 benign neoplasms, 2 unclassified, 2 high grade/poorly differentiated RCC, and 1 non-diagnostic. Among ccRCC, aCGH correctly subtyped 8/13. No CNAs were detected in the remaining 5, but for which NGS detected CNAs in 3/5 and TET2 mutations in 1. Mutations in PBRM1 and BAP1 with reported prognostic significance in ccRCC were found in 3 and 1 specimens respectively. Apart from 1 without any detectable mutations or CNAs, aCGH and NGS correctly subtyped 8/9 pRCCs based on CNAs. Also, activating MET mutations were seen in 2 pRCC specimens. aCGH and NGS accurately diagnosed the 2 chrRCC and detected pRCC-related CNAs in 2/13 benign neoplasms. In the two unclassified specimens, both methods identified ccRCC-related CNAs. Notably, NGS identified CNAs and mutations in the biopsy non-diagnostic by histology. Conclusions: Overall, targeted NGS can robustly detect genomic alterations requiring only limited DNA, that together with histology, contributes important diagnostic and prognostic information in the management of renal mass patients.

Development and Validation of a Gene-Based Model for Outcome Prediction in Germ Cell Tumors Using a Combined Genomic and Expression Profiling Approach

Germ Cell Tumors (GCT) have a high cure rate, but we currently lack the ability to accurately identify the small subset of patients who will die from their disease. We used a combined genomic and expression profiling approach to identify genomic regions and underlying genes that are predictive of outcome in GCT patients. We performed array-based comparative genomic hybridization (CGH) on 53 non-seminomatous GCTs (NSGCTs) treated with cisplatin based chemotherapy and defined altered genomic regions using Circular Binary Segmentation. We identified 14 regions associated with two year disease-free survival (2yDFS) and 16 regions associated with five year disease-specific survival (5yDSS). From corresponding expression data, we identified 101 probe sets that showed significant changes in expression. We built several models based on these differentially expressed genes, then tested them in an independent validation set of 54 NSGCTs. These predictive models correctly classified outcome in 64–79.6% of patients in the validation set, depending on the endpoint utilized. Survival analysis demonstrated a significant separation of patients with good versus poor predicted outcome when using a combined gene set model. Multivariate analysis using clinical risk classification with the combined gene model indicated that they were independent prognostic markers. This novel set of predictive genes from altered genomic regions is almost entirely independent of our previously identified set of predictive genes for patients with NSGCTs. These genes may aid in the identification of the small subset of patients who are at high risk of poor outcome.

Cross-platform assessment of genomic imbalance confirms the clinical relevance of genomic complexity and reveals loci with potential pathogenic roles in diffuse large B-cell lymphoma

Genomic copy number alterations (CNAs) in diffuse large B-cell lymphoma (DLBCL) have roles in disease pathogenesis, but overall clinical relevance remains unclear. Herein, an unbiased algorithm was uniformly applied across three genome profiling datasets comprising 392 newly-diagnosed DLBCL specimens that defined 32 overlapping CNAs, involving 36 minimal common regions (MCRs). Scoring criteria were established for 50 aberrations within the MCRs while considering peak gains/losses. Application of these criteria to independent datasets revealed novel candidate genes with coordinated expression, such as CNOT2, potentially with pathogenic roles. No one single aberration significantly associated with patient outcome across datasets, but genomic complexity, defined by imbalance in more than one MCR, significantly portended adverse outcome in two of three independent datasets. Thus, the standardized scoring of CNAs currently developed can be uniformly applied across platforms, affording robust validation of genomic imbalance and complexity in DLBCL and overall clinical utility as biomarkers of patient outcome.

Interrogation of a context-specific transcription factor network identifies novel regulators of pluripotency

The predominant view of pluripotency regulation proposes a stable ground state with coordinated expression of key transcription factors (TFs) that prohibit differentiation. Another perspective suggests a more complexly regulated state involving competition between multiple lineage-specifying TFs that define pluripotency. These contrasting views were developed from extensive analyses of TFs in pluripotent cells in vitro. An experimentally validated, genome-wide repertoire of the regulatory interactions that control pluripotency within the in vivo cellular contexts is yet to be developed. To address this limitation, we assembled a TF interactome of adult human male germ cell tumors (GCTs) using the Algorithm for the Accurate Reconstruction of Cellular Pathways (ARACNe) to analyze gene expression profiles of 141 tumors comprising pluripotent and differentiated subsets. The network (GCT(Net)) comprised 1,305 TFs, and its ingenuity pathway analysis identified pluripotency and embryonal development as the top functional pathways. We experimentally validated GCT(Net) by functional (silencing) and biochemical (ChIP-seq) analysis of the core pluripotency regulatory TFs POU5F1, NANOG, and SOX2 in relation to their targets predicted by ARACNe. To define the extent of the in vivo pluripotency network in this system, we ranked all TFs in the GCT(Net) according to sharing of ARACNe-predicted targets with those of POU5F1 and NANOG using an odds-ratio analysis method. To validate this network, we silenced the top 10 TFs in the network in H9 embryonic stem cells. Silencing of each led to downregulation of pluripotency and induction of lineage; 7 of the 10 TFs were identified as pluripotency regulators for the first time.

Association of genome-wide copy number alterations with metastasis of clear cell renal cell carcinoma

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Background: About one-third of patients with clear cell renal cell carcinoma (ccRCC) exhibit metastasis at the time of diagnosis and show poor prognosis. The genetic and epigenetic alterations associated with metastasis in ccRCC have variably been studied, and their role in the metastatic process is unclear. The goals of the current study were to identify genomic copy number alterations (CNAs) associated with ccRCC metastasis and examine their clinical utility. Methods: In this IRB-approved study, genome-wide copy number profiling was performed on DNA from 144 ccRCC (81 primary and 63 metastatic lesions). Differential CNAs between primary and metastatic lesions and between different metastatic sites were identified using Fisher’s exact test. Associations between CNAs and overall survival (OS) were tested using the log rank statistic and Kaplan-Meier method. Genomic profiling data of 437 and 240 primary ccRCC (TCGA and PMID: 23797736, respecitively) were used for verification. Results: Between primary and metastatic lesions, 25 CNAs were significantly different (p<0.05). Of the 11 more frequent in metastatic lesions, nine retained significance when comparing stage IV and stage I TCGA ccRCC. For 368 TCGA locally-invasive tumors (stages I, II, and III), three CNAs (loss of 9p24.3-p13.3, 9p12-q11, and 9q21.12-q21.33) were associated with inferior survival (p=0.002). In the second dataset of 214 locally-invasive lesions, loss of 18q11.2-q23 correlated with shorter OS (p=0.025). Across metastatic lesions, nine CNAs were found to be significantly enriched in lung lesions and three in bone. In a subset of 127 ccRCC with known metastatic status at 5 years after diagnosis, two of these CNAs (gain of 7q36.1-36.3 in lung and loss of 22q13.2 in bone) were significantly enriched in the corresponding primary specimens. Conclusions: This study identified CNAs associated with ccRCC metastasis and common sites of metastasis that have the potential to serve as biomarkers to assist in better risk stratification of patients with this disease. Integrated analyses of genes mapping to the loci of genomic imbalance would further our understanding of the biology of metastasis in renal cancer.

A genomic algorithm for the molecular classification of common renal cortical neoplasms: development and validation

PURPOSE

Accurate discrimination of benign oncocytoma and malignant renal cell carcinoma is useful for planning appropriate treatment strategies for patients with renal masses. Classification of renal neoplasms solely based on histopathology can be challenging, especially the distinction between chromophobe renal cell carcinoma and oncocytoma. In this study we develop and validate an algorithm based on genomic alterations for the classification of common renal neoplasms.

MATERIALS AND METHODS

Using TCGA renal cell carcinoma copy number profiles and the published literature, a classification algorithm was developed and scoring criteria were established for the presence of each genomic marker. As validation, 191 surgically resected formalin fixed paraffin embedded renal neoplasms were blindly submitted to targeted array comparative genomic hybridization and classified according to the algorithm. CCND1 rearrangement was assessed by fluorescence in situ hybridization.

RESULTS

The optimal classification algorithm comprised 15 genomic markers, and involved loss of VHL, 3p21 and 8p, and chromosomes 1, 2, 6, 10 and 17, and gain of 5qter, 16p, 17q and 20q, and chromosomes 3, 7 and 12. On histological rereview (leading to the exclusion of 3 specimens) and using histology as the gold standard, 58 of 62 (93%) clear cell, 51 of 56 (91%) papillary and 33 of 34 (97%) chromophobe renal cell carcinomas were classified correctly. Of the 36 oncocytoma specimens 33 were classified as oncocytoma (17 by array comparative genomic hybridization and 10 by array comparative genomic hybridization plus fluorescence in situ hybridization) or benign (6). Overall 93% diagnostic sensitivity and 97% specificity were achieved.

CONCLUSIONS

In a clinical diagnostic setting the implementation of genome based molecular classification could serve as an ancillary assay to assist in the histological classification of common renal neoplasms.

Abstract 52: Identification of genomic alterations associated with metastasis in clear cell renal cell carcinoma

Clear cell renal cell carcinoma (ccRCC) is the most abundant and lethal form of RCC and about one third of patients exhibit metastasis with poor prognosis. At the molecular level, metastasis is accompanied by multiple genetic and epigenetic alterations including genomic copy number changes. Identification of novel genomic markers and underlying mechanisms associated with metastasis could result in better therapeutic management of ccRCC patients. In this study, aCGH was performed using Agilent 244K arrays on DNA from 83 primary and 64 metastatic unmatched ccRCC fresh-frozen specimens and profiles were compared using Fisher's Exact test (FDR, p-value ≤ 0.05), with a minimum threshold difference of 15%. Significant copy number changes were found at 15 loci between primary and metastatic lesions, after excluding loci enriched in normal CNVs. Loss of 2p16.1-p15, 2q33.1-q33.3, 3q11.1-q13.2, 3q22.3, 10q21.3-q22.1 and 11p15.4 were more frequent in primary lesions, while nine aberrations (gain of 5q23.3-q31.1, 7q21.3-q22.1, 16p11.2, 20q11.1-q13.12, 21p11.2-q11.1 and loss of 4p15.2-p14, 4q, 9p24.3-p13.3 and 18q21.2-q21.31) were more frequent in metastatic lesions. While some of these aberrations have previously been implicated in metastasis, nine were novel. In order to further examine the association of these aberrations with metastasis, the frequencies of the 15 aberrations were determined in primary ccRCCs publicly available from TCGA, stratified into low (stages I and II, n=287) and high stage groups (III and IV, n=202). Eight of the nine aberrations that were more frequent in metastatic lesions, were also observed at a higher frequency in high stage TCGA primary ccRCC (four were significantly higher between Stages I and IV). Little or no trend was observed for the six aberrations more frequent in primary lesions.

In order to identify alterations associated with specific metastatic sites, aCGH profiles were compared across metastatic lesions at sites represented by at least 6 specimens: 15 lung, 7 bone, 6 lymph node, 6 pancreas and 6 brain metastatic ccRCC specimens. Gain of 7q11 and 8p12-p11, and loss of 6q14-q22 and 10q were specifically observed in lung metastases. Gain of chr12 and loss of chr22 were frequent in bone, loss of 1q32-q41 and gain of 22q11 in lymph node, and loss of 2p22.3, 8p12, 8q12-q13 and 8q24 in pancreatic lesions. No specific aberrations were found in brain lesions.

In conclusion, this study has confirmed known and identified novel genomic loci associated with metastasis in ccRCC. Determination of candidate genes of the aberrations will further our understanding of metastatic progression of ccRCC and together with examination of metastatic site-specific alterations, may assist in selecting patients with metastatic disease for appropriate targeted therapy and lead to improved overall survival.

Citation Format: Venkata J. Thodima, Banumathy Gowrishankar, Ana Molina, Murielle Georges, RSK Chaganti, Robert J. Motzer, Jane Houldsworth. Identification of genomic alterations associated with metastasis in clear cell renal cell carcinoma. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 52. doi:10.1158/1538-7445.AM2014-52

Subtyping of renal cortical neoplasms in fine needle aspiration biopsies using a decision tree based on genomic alterations detected by fluorescence in situ hybridization

OBJECTIVES

To improve the overall accuracy of diagnosis in needle biopsies of renal masses, especially small renal masses (SRMs), using fluorescence in situ hybridization (FISH), and to develop a renal cortical neoplasm classification decision tree based on genomic alterations detected by FISH.

PATIENTS AND METHODS

Ex vivo fine needle aspiration biopsies of 122 resected renal cortical neoplasms were subjected to FISH using a series of seven-probe sets to assess gain or loss of 10 chromosomes and rearrangement of the 11q13 locus. Using specimen (nephrectomy)-histology as the 'gold standard', a genomic aberration-based decision tree was generated to classify specimens. The diagnostic potential of the decision tree was assessed by comparing the FISH-based classification and biopsy histology with specimen histology.

RESULTS

Of the 114 biopsies diagnostic by either method, a higher diagnostic yield was achieved by FISH (92 and 96%) than histology alone (82 and 84%) in the 65 biopsies from SRMs (<4 cm) and 49 from larger masses, respectively. An optimized decision tree was constructed based on aberrations detected in eight chromosomes, by which the maximum concordance of classification achieved by FISH was 79%, irrespective of mass size. In SRMs, the overall sensitivity of diagnosis by FISH compared with histopathology was higher for benign oncocytoma, was similar for the chromophobe renal cell carcinoma subtype, and was lower for clear-cell and papillary subtypes. The diagnostic accuracy of classification of needle biopsy specimens (from SRMs) increased from 80% obtained by histology alone to 94% when combining histology and FISH.

CONCLUSION

The present study suggests that a novel FISH assay developed by us has a role to play in assisting in the yield and accuracy of diagnosis of renal cortical neoplasms in needle biopsies in particular, and can help guide the clinical management of patients with SRMs that were non-diagnostic by histology.

Genomic imbalance defines three prognostic groups for risk stratification of patients with chronic lymphocytic leukemia

Array comparative genomic hybridization (aCGH) has yet to be fully leveraged in a prognostic setting in chronic lymphocytic leukemia (CLL). Genomic imbalance was assessed in 288 CLL specimens using a targeted array. Based on 20 aberrations in a hierarchical manner, all 228 treatment-naive specimens were classified into a group with poor outcome (20.6%) exhibiting at least one aberration that was univariately associated with adverse outcome (gain: 2p, 3q, 8q, 17q, loss: 7q, 8p, 11q, 17p, 18p), good outcome (32.5%) showing 13q14 loss without any of the other 10 aberrations (gain: 1p, 7p, 12, 18p, 18q, 19, loss: 4p, 5p, 6q, 7p) or intermediate outcome (remainder). The three groups were significantly separated with respect to time to first treatment and overall survival (p < 0.001), and validation of the stratification scheme was performed in two independent datasets. Gain of 3q and 8q, and 17p loss were determined to be independent unfavorable prognostic biomarkers. TP53, NOTCH1 and SF3B1 mutations correlated with the presence of one poor outcome aCGH marker, at a considerably higher frequency than when only considering poor risk aberrations routinely detected by fluorescence in situ hybridization (FISH). These data support genomic imbalance evaluation in CLL by aCGH to assist in risk stratification.

Abstract C09: Reduced proficiency in homologous recombination underlies the high sensitivity of embryonal carcinoma testicular germ cell tumors to cisplatin and poly (ADP-ribose) polymerase inhibition

Testicular Germ Cell Tumors (TGCT) and patient-derived cell lines are extremely sensitive to cisplatin and other interstrand cross-link (ICL) inducing agents. Nevertheless, a subset of TGCTs are either innately resistant or acquire resistance to cisplatin during treatment. Understanding the mechanisms underlying TGCT sensitivity/resistance to cisplatin as well as the identification of novel strategies to target cisplatin-resistant TGCTs have major clinical implications. Herein, we have examined the proficiency of five embryonal carcinoma (EC) cell lines to repair cisplatin-induced ICLs. Using γH2AX staining as a marker of double strand break formation, we found that EC cell lines were either incapable of or had a reduced ability to repair ICL-induced damage. The defect correlated with reduced Homologous Recombination (HR) repair, as demonstrated by the reduction of RAD51 foci formation and by direct evaluation of HR efficiency using a GFP-reporter substrate. HR-defective tumors cells are known to be sensitive to the treatment with poly(ADP-ribose) polymerase (PARP) inhibitor. In line with this observation, we found that EC cell lines were also sensitive to PARP inhibitor monotherapy. The magnitude of sensitivity correlated with HR-repair reduced proficiency and with the expression levels and activity of PARP1 protein. In addition, we found that PARP inhibition strongly enhanced the response of the most resistant EC cells to cisplatin, by reducing their ability to overcome the damage. These results point to a reduced proficiency of HR repair as a source of sensitivity of ECs to ICL-inducing agents and PARP inhibitor monotherapy, and suggest that pharmacological inhibition of PARP can be exploited to target the stem cell component of the TGCTs (namely ECs) and to enhance the sensitivity of cisplatin-resistant TGCTs to standard treatments.

Citation Format: Francesca Cavallo, Grazia Graziani, Cristina Antinozzi, Darren R. Feldman, Jane Houldsworth, George J. Bosl, Raju S. K. Chaganti, Mary Ellen Moynahan, Maria Jasin and Marco Barchi. Reduced proficiency in homologous recombination underlies the high sensitivity of embryonal carcinoma testicular germ cell tumors to cisplatin and poly (ADP-ribose) polymerase inhibition. [abstract]. In: Proceedings of the Third AACR International Conference on Frontiers in Basic Cancer Research; Sep 18-22, 2013; National Harbor, MD. Philadelphia (PA): AACR; Cancer Res 2013;73(19 Suppl):Abstract nr C09.

Chromosomal gains measured in cytology samples from women with abnormal cervical cancer screening results

OBJECTIVE

Chromosomal gains at 3q26, 5p15 and 20q13 have been described in cervical precancer and cancer. We evaluated a novel fluorescence in situ hybridization (FISH) assay that detects gains at these three loci simultaneously as a possible biomarker for detecting cervical precancer.

METHODS

Chromosomal copy numbers at 3q26, 5p15, 20q13 and the centromere of chromosome7 (cen7) in liquid-based cytology specimens from 168 women enrolled in the Biopsy Study were determined by FISH. The number of cells with ≥ 3 or ≥ 4 signals for a genomic locus was enumerated and diagnostic test performance measures were calculated using receiver operating characteristic (ROC) analyses. Sensitivity and specificity values were determined for the detection of CIN2+ and/or HSIL.

RESULTS

The median number of cells with ≥ 3 signals increased with the severity of cervical lesion for each genomic locus (p-trend<0.02 for each locus). ROC analysis for the number of cells with ≥ 3 signals resulted in area under the curve values of 0.70 (95% CI: 0.54-0.86), 0.67 (0.52-0.83), 0.67 (0.51-0.83) and 0.78 (0.64-0.92) for 3q26, 5p15, 20q13 and cen7, respectively, for the detection of CIN2+ and/or HSIL. Positivity for gains at multiple loci resulted in only slightly better test performance measures than those for the individual probes for four distinct combinations of probes.

CONCLUSIONS

Chromosomal gains at 3q26, 5p15, 20q13 and cen7 are associated with severity of cervical lesions. Further studies are required to quantify risk stratification of FISH assays for cervical cancer screening.

Fluorescence in situ hybridization (FISH) and array-comparative genomic hybridization (a-CGH) from percutaneous needle biopsy compared to renal mass histology

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Background: Image-guided percutaneous needle biopsies are increasingly utilized for the diagnosis of renal tumors. Histologic diagnosis of renal mass subtypes, including malignant clear cell (ccRCC), papillary (pRCC), chromophobe (chrRCC) renal cell carcinoma, and benign oncocytomas (OC) can be challenging due to the low cellularity and damaged architecture of needle biopsy specimens. However, each subtype exhibits unique genetic aberrations that can assist in histologic classification and potentially assist in guiding management decisions. We report our initial experience correlating renal mass histology to subtype-associated genomic alterations detected by FISH and a-CGH of percutaneous needle biopsy specimens. Methods: In an ongoing IRB-approved blinded study, 17 samples obtained from 15 patients with known renal masses were submitted to FISH (FReCaD) and targeted a-CGH (UroGenRA-Kidney). Specimens were classified using a subtype classification decision tree algorithm based on the presence/absence of genomic abnormalities. The results were compared to biopsy histology or surgical specimen when available. Results: Histology revealed ccRCC in 6 patients, pRCC in 4, OC in 2, Angiomyolipoma in 1, and unclassified type RCC in 2. In 6 of 9 cases FISH achieved a diagnosis, which correlated with histology in 4. FISH incorrectly classified as ccRCC two cases with pRCC on histology. A-CGH was diagnostic in 14 of 15 cases and correlated with histology in 13. In one case, a-CGH showed a genomic profile not consistent with ccRCC, pRCC, chrRCC, or OC according to the algorithm. Conclusions: The addition of genetic tumor tissue studies to complement histology from biopsy tissues may supplement or improve the accuracy of classification and biological characterization of renal tumor biopsies and influence treatment planning. In our initial experience, a-CGH showed better correlation with histology in subtype classification of malignant and benign renal masses than FISH. Prospective testing will be required to validate these results.

Abstract 4240: Transcription factor networks that regulate pluripotency and lineage differentiation in adult human male germ cell tumors

Recent interest and effort have been focused on identification of transcription factors (TFs) and TF networks that regulate pluripotency and lineage differentiation in human and murine cells. Yet, a complete repertoire of regulatory interactions supporting these processes remains elusive. Embryonic stem (ES) cells, induced pluripotent (iPS) cells, and embryonal carcinoma (EC) cells derived from germ cell tumors (GCTs) comprise the three classic pluripotent cell types. EC cells exhibit, in vivo and in vitro, many properties in common with ES cells, making them an excellent system to study pluripotency and lineage differentiation. We previously characterized the gene expression profile (GEP) of a panel of 135 GCT biopsies comprising all described in vivo differentiation lineages and 6 normal testes as controls, using the Affymetrix U133A+B arrays (Korkola et al. Cancer Res., 66: 820-7, 2006 and J. Clin. Oncol., 27: 5240-7, 2009). These GEP data were analyzed using the ARACNe reverse engineering algorithm (Basso et al., Nat. Genet., 37: 382-90, 2005) to reconstruct a global transcriptional interaction network regulating pluripotency and lineage differentiation in these tumors. The ensuing interactome, comprising 1312 TFs, displayed three strongly intra-connected modules: Module A, including 187 genes associated with regulation of development and differentiation, Module B, including 89 genes associated with regulation of immune response and B-cell development, and Module C, including 80 genes associated with regulation of transcription. Furthermore, the interactome recapitulated 830 regulatory targets of the core pluripotency TFs, POU5F1, NANOG, and SOX2 (369 of POU5F1, 375 of NANOG, and 306 of SOX2). Validation of these targets by ChIP-PCR and ChIP-seq in NT2/D1 (EC) and H9 (ES) cells revealed that all of the top 10 target genes of POU5F1 (NANOG, FAM46B, L1TD1, DND1, ZYG11, FRAT2, DPPA4, ARGEF1, KLRG2 and CBR3) and SOX2 (SEPHS1, PLCB2, ZNF518, ECE2, SLC26A3, GPM6B, PHLDA2, PATZ1, ADRB3 and MAP1A) could specifically bind the corresponding TF in their promoter regions, within both cell types. For NANOG, 9 of the top 10 targets (POU5F1, FAM46B, DPPA4, L1TD1, UTF1, FRAT2, RAB15, TEAD4 and ZYG11A) showed specific promoter binding of the TF in both cell types, while one target (DND1) showed specific binding only in H9 cells. ChIP-seq analysis was consistent with the results of ChIP-PCR. We sought functional validation of the targets by performing lentivirus-mediated shRNA silencing of POU5F1 in NT2/D1 cells. Results showed that the ARACNe-inferred targets were both positively and negatively regulated, consistently with regulation of pluripotency and/or differentiation. Taken together, these results define a novel and highly accurate regulatory model for the systems biology study of TFs involved in regulation of pluripotency and lineage differentiation in mammalian cells.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4240.