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(A) GOT2 western blot of HeLa cells stably silenced for GOT2 expression by shRNA transfection compared to non-silenced scrambled (Scr) control cells. β-actin was used as a loading control. (B) Number of GOT2 KD HeLa cells after transfection with empty vector (EV), GOT2- WT cDNA, and GOT2- c.357A>T. Cells were seeded into 12-well plates and incubated for various times, as indicated. The counts are reported as means (n=3). A t-test was applied to test for differences. n.s.: not significant.

Purpose and Methods: High-level DNA amplifications are recurrently found in breast cancer, and some of them are associated with poor patient prognosis. To determine their frequency and co-occurrence in familial breast cancer, we have analyzed 80 tumors previously characterized for BRCA1 and BRCA2 germ-line mutations (26 BRCA1, 18 BRCA2, and 36 non-BRCA1/2) using high-resolution comparative genomic hybridization.Results: Twenty-one regions were identified as recurrently amplified, such as 8q21-23 (26.25%), 17q22-25 (13.75%), 13q21-31 (12.50%), and 8q24 (11.25%), many of which were altered in each familial breast cancer group. These amplifications defined an amplifier phenotype that is correlated with a higher genomic instability. Based on these amplifications, two different genomic pathways have been established in association with 8q21-23 and/or 17q22-25 and with 13q21-31 amplification. These pathways are associated with specific genomic regions of amplification, carry specific immunohistochemical characteristics coincident with high and low aggressiveness, and have a trend to be associated with BRCA1 and BRCA2/X, respectively.Conclusion: In summary, our data suggest the existence of two different patterns of evolution, probably common to familial and sporadic breast tumors.

Genes included in the targeted next-generation sequencing panel

Supplementary Table 1 from The Accumulation of Specific Amplifications Characterizes Two Different Genomic Pathways of Evolution of Familial Breast Tumors

Purpose: Pheochromocytomas (PCC) and paragangliomas (PGL) are genetically heterogeneous neural crest–derived neoplasms. Recently we identified germline mutations in a new tumor suppressor susceptibility gene, MAX (MYC-associated factor X), which predisposes carriers to PCC. How MAX mutations contribute to PCC/PGL and associated phenotypes remain unclear. This study aimed to examine the prevalence and associated phenotypic features of germline and somatic MAX mutations in PCC/PGL.Design: We sequenced MAX in 1,694 patients with PCC or PGL (without mutations in other major susceptibility genes) from 17 independent referral centers. We screened for large deletions/duplications in 1,535 patients using a multiplex PCR-based method. Somatic mutations were searched for in tumors from an additional 245 patients. The frequency and type of MAX mutation was assessed overall and by clinical characteristics.Results: Sixteen MAX pathogenic mutations were identified in 23 index patients. All had adrenal tumors, including 13 bilateral or multiple PCCs within the same gland (P < 0.001), 15.8% developed additional tumors at thoracoabdominal sites, and 37% had familial antecedents. Age at diagnosis was lower (P = 0.001) in MAX mutation carriers compared with nonmutated cases. Two patients (10.5%) developed metastatic disease. A mutation affecting MAX was found in five tumors, four of them confirmed as somatic (1.65%). MAX tumors were characterized by substantial increases in normetanephrine, associated with normal or minor increases in metanephrine.Conclusions: Germline mutations in MAX are responsible for 1.12% of PCC/PGL in patients without evidence of other known mutations and should be considered in the genetic work-up of these patients. Clin Cancer Res; 18(10); 2828–37. ©2012 AACR.

Legends of the Supplementary Figures

Supplementary Table S1 from Estrogen Receptor Status Could Modulate the Genomic Pattern in Familial and Sporadic Breast Cancer

Supplementary Figures S1-S2 from Estrogen Receptor Status Could Modulate the Genomic Pattern in Familial and Sporadic Breast Cancer

Purpose: Mutations in Krebs cycle genes are frequently found in patients with pheochromocytomas/paragangliomas. Disruption of SDH, FH or MDH2 enzymatic activities lead to accumulation of specific metabolites, which give rise to epigenetic changes in the genome that cause a characteristic hypermethylated phenotype. Tumors showing this phenotype, but no alterations in the known predisposing genes, could harbor mutations in other Krebs cycle genes.Experimental Design: We used downregulation and methylation of RBP1, as a marker of a hypermethylation phenotype, to select eleven pheochromocytomas and paragangliomas for targeted exome sequencing of a panel of Krebs cycle-related genes. Methylation profiling, metabolite assessment and additional analyses were also performed in selected cases.Results: One of the 11 tumors was found to carry a known cancer-predisposing somatic mutation in IDH1. A variant in GOT2, c.357A>T, found in a patient with multiple tumors, was associated with higher tumor mRNA and protein expression levels, increased GOT2 enzymatic activity in lymphoblastic cells, and altered metabolite ratios both in tumors and in GOT2 knockdown HeLa cells transfected with the variant. Array methylation-based analysis uncovered a somatic epigenetic mutation in SDHC in a patient with multiple pheochromocytomas and a gastrointestinal stromal tumor. Finally, a truncating germline IDH3B mutation was found in a patient with a single paraganglioma showing an altered α-ketoglutarate/isocitrate ratio.Conclusions: This study further attests to the relevance of the Krebs cycle in the development of PCC and PGL, and points to a potential role of other metabolic enzymes involved in metabolite exchange between mitochondria and cytosol. Clin Cancer Res; 23(20); 6315–24. ©2017 AACR.

Supplementary Figure 1 from The Accumulation of Specific Amplifications Characterizes Two Different Genomic Pathways of Evolution of Familial Breast Tumors

Supplementary Table 2 from The Accumulation of Specific Amplifications Characterizes Two Different Genomic Pathways of Evolution of Familial Breast Tumors

Aldehyde dehydrogenase 1A1 (ALDH1A1) is a cancer stem cell (CSC) marker related to clinical outcomes in breast cancer (BC). The aim of this study was to analyze the relationship between ALDH1A1, programmed death ligand 1 (PD-L1) and tumor-infiltrating lymphocytes (TILs) in triple negative (TN) and human epidermal growth factor receptor 2-positive (HER2+) BC tumors, and its association with clinicopathological characteristics and outcomes. A retrospective, historical cohort study of patients diagnosed with early or locally advanced BC treated with neoadjuvant chemotherapy was conducted. ALDH1A1, PD-L1 expression and TILs were assessed using immunohistochemistry. A total of 75 patients were analyzed (42.7% TN, 57.3% HER2+ tumors). ALDH1A1+ was related to HTILs (p = 0.005) and PD-L1+ tumors (p = 0.004). ALDH1A1+ tumors presented higher CD3+ (p = 0.008), CD4+ (p = 0.005), CD8+ (p = 0.003) and CD20+ (p = 0.006) TILs. ALDH1A1+ (p = 0.018), PD-L1+ (p = 0.004) and HTILs (p < 0.001) were related to smaller tumors. ALDH1A1+ was related to pathologic complete response (pCR) (p = 0.048). At the end of the follow-up (54.4 [38.3–87.6] months), 47 patients (62.7%) remained disease-free, and 20 (26.7%) had died. HTILs were related to improved disease-free survival (p = 0.027). ALDH1A1+ was related to PD-L1+ and HITLs, that might be related to higher pCR rates with neoadjuvant therapy.

Background: Cytoplasmatic expression of Aldehyde dehydrogenase 1 A1 (ALDH1A1) has been identified as a cancer stem cell marker and related to an unfavorable prognosis. However, nuclear expression of ALDH1A1 has not been described in breast cancer (BC) patients yet. Methods: A retrospective, historical cohort study of patients diagnosed with early or locally advanced triple negative (TN) and human epidermal growth factor receptor 2 positive (HER2+) BC treated with neoadjuvant chemotherapy was conducted. Patients who had an available tumor sample from the diagnosis and who underwent surgery after the neoadjuvant treatment were included. Metastatic patients and non-evaluative biopsy sample cases were excluded. Immunostaining against ALDH1A1 was performed. The aim of this study was to assess the expression of nuclear ALDH1A1 in BC and its relation with clinicopathological features and outcomes.Results: 75 patients were analyzed (100% women, mean age 53.6±11.7 years, 42.7% TN, 57.3% HER2+ tumors). 28% had obesity, 32 (42.7%) had a tumor size ≤5 cm and 52 (69.3%) positive lymph nodes. 40 (53.3%) patients had cytoplasmatic ALDH1A1 expression. From them, 18 (24%) also expressed nuclear ALDH1A1 staining and 22 (29.3%) only had cytoplasmatic expression. 57 (76%) patients had negative nuclear ALDH1A1. At the end of the follow-up (54.4 [38.3-87.6] months), 47 patients (62.7%) remained disease free and 20 (26.7%) died. Patients with nuclear ALDH1A1 had higher prevalence of obesity when comparing to exclusively positive cytoplasmatic ALDH1A1 (p = 0.003) and versus those with negative ALDH1A1 expression (p = 0.017); and also, smaller size compared to those without nuclear ALDH1A1 staining (p = 0.044). Furthermore, in patients with positive nuclear ALDH1A1 a tendency to superior disease-free survival (DFS) and overall survival (OS) was observed when compared to positive cytoplasmatic and negative ALDH1A1 tumors, albeit not statistically significant. Conclusions: In this cohort, nuclear positive expression of ALDH1A1 was higher in patients with obesity and smaller tumors. Patients with positive nuclear ALDH1A1 carcinomas appear to have better DFS and OS, although this was not statistically significant. Further research studies are needed to understand the functions of this enzyme and its possible role as a predictive and prognostic marker in BC.

Pheochromocytomas and paragangliomas (PPGLs) provide some of the clearest genetic evidence for the critical role of metabolism in the tumorigenesis process. Approximately 40% of PPGLs are caused by driver germline mutations in 16 known susceptibility genes, and approximately half of these genes encode members of the tricarboxylic acid (TCA) cycle. Taking as a starting point the involvement of the TCA cycle in PPGL development, we aimed to identify unreported mutations that occurred in genes involved in this key metabolic pathway and that could explain the phenotypes of additional individuals who lack mutations in known susceptibility genes. To accomplish this, we applied a targeted sequencing of 37 TCA-cycle-related genes to DNA from 104 PPGL-affected individuals with no mutations in the major known predisposing genes. We also performed omics-based analyses, TCA-related metabolite determination, and (13)C(5)-glutamate labeling assays. We identified five germline variants affecting DLST in eight unrelated individuals (∼7%); all except one were diagnosed with multiple PPGLs. A recurrent variant, c.1121G>A (p.Gly374Glu), found in four of the eight individuals triggered accumulation of 2-hydroxyglutarate, both in tumors and in a heterologous cell-based assay designed to functionally evaluate DLST variants. p.Gly374Glu-DLST tumors exhibited loss of heterozygosity, and their methylation and expression profiles are similar to those of EPAS1-mutated PPGLs; this similarity suggests a link between DLST disruption and pseudohypoxia. Moreover, we found positive DLST immunostaining exclusively in tumors carrying TCA-cycle or EPAS1 mutations. In summary, this study reveals DLST as a PPGL-susceptibility gene and further strengthens the relevance of the TCA cycle in PPGL development.

The high percentage of patients carrying germline mutations makes pheochromocytomas/paragangliomas the most heritable of all tumors. However, there are still cases unexplained by mutations in the known genes. We aimed to identify the genetic cause of disease in patients strongly suspected of having hereditary tumors. Whole-exome sequencing was applied to the germlines of a parent–proband trio. Genome-wide methylome analysis, RNA-seq, CRISPR/Cas9 gene editing, and targeted sequencing were also performed. We identified a novel de novo germline mutation in DNMT3A, affecting a highly conserved residue located close to the aromatic cage that binds to trimethylated histone H3. DNMT3A-mutated tumors exhibited significant hypermethylation of homeobox-containing genes, suggesting an activating role of the mutation. CRISPR/Cas9-mediated knock-in in HeLa cells led to global changes in methylation, providing evidence of the DNMT3A-altered function. Targeted sequencing revealed subclonal somatic mutations in six additional paragangliomas. Finally, a second germline DNMT3A mutation, also causing global tumor DNA hypermethylation, was found in a patient with a family history of pheochromocytoma. Our findings suggest that DNMT3A may be a susceptibility gene for paragangliomas and, if confirmed in future studies, would represent the first example of gain-of-function mutations affecting a DNA methyltransferase gene involved in cancer predisposition.

When a patient with a previous history of neoplasm presents with a thyroid lesion, the possibility of it being metastatic should always be considered. In this series, we present the clinicopathological and immunohistochemical features of the thyroid metastases diagnosed in our department over the past 30 years. Here we present eight thyroidal metastases from clear cell renal cell carcinoma (ccRCCC), including a tumor to tumor metastasis, the patients being 2 men and 6 women with a median age of 62 years. The majority had a past history of goiter and a single and palpable metastasis. In one patient the thyroid metastases were the first sign of the ccRCCC. In the available cases, the metastasis showed positivity to PAX8 and CAIX and negativity to TTF1 and thyroglobulin. The median time from the detection of the primary renal tumor to thyroid metastasis and from thyroidectomy to last follow up were 84.17 and 54.50 months, respectively. After a median follow up of 158.50 months none of the patients had died from ccRCCC. Renal cell carcinoma (RCC) is the most frequent malignant neoplasm of the kidney and its incidence has increased over recent decades. In a clinical series, up to 1-3% of the oncologic thyroidectomies were due to thyroid metastases and the most frequent metastasizing tumor was RCC, followed by lung and breast cancer.

Enhancer of zeste homolog 2 (EZH2) is the catalitic subunit of polycomb repressive complex 2 and mediates gene silencing. EZH2 is overexpressed in many cancers and correlates with poor prognosis. The role of the gene EZH2 in colorectal cancer survival is uncertainly, the aim of this study is clear this relationship. Relevant literaure was searched from electronic databases. A meta-analysis was performed with elegible studies which quantitatively evaluated the relationship between EZH2 overexpression and survival of patients with colorectal cancer. Survival data were aggregated and quantitatively analyzed. We performed a meta-analysis of 8 studies (n = 1059 patients) that evaluated the correlation between EZH2 overexpression and survival in patients with colorectal cancer. Combined hazard ratios suggested that EZH2 overexpression was associated with better prognosis of overall survival (OS) HR(hazard ratio) = 0.61 95% CI (0.38–0.84) We performed bias analysis according Egger and Begg,s test and we did not find publication bias. EZH2 overexpression indicates a better prognosis for colorectal cancer.

Purpose: Mutations in Krebs cycle genes are frequently found in patients with pheochromocytomas/paragangliomas. Disruption of SDH, FH or MDH2 enzymatic activities lead to accumulation of specific metabolites, which give rise to epigenetic changes in the genome that cause a characteristic hypermethylated phenotype. Tumors showing this phenotype, but no alterations in the known predisposing genes, could harbor mutations in other Krebs cycle genes. Experimental Design: We used downregulation and methylation of RBP1, as a marker of a hypermethylation phenotype, to select eleven pheochromocytomas and paragangliomas for targeted exome sequencing of a panel of Krebs cycle-related genes. Methylation profiling, metabolite assessment and additional analyses were also performed in selected cases. Results: One of the 11 tumors was found to carry a known cancer-predisposing somatic mutation in IDH1. A variant in GOT2, c.357A>T, found in a patient with multiple tumors, was associated with higher tumor mRNA and protein expression levels, increased GOT2 enzymatic activity in lymphoblastic cells, and altered metabolite ratios both in tumors and in GOT2 knockdown HeLa cells transfected with the variant. Array methylation-based analysis uncovered a somatic epigenetic mutation in SDHC in a patient with multiple pheochromocytomas and a gastrointestinal stromal tumor. Finally, a truncating germline IDH3B mutation was found in a patient with a single paraganglioma showing an altered α-ketoglutarate/isocitrate ratio. Conclusions: This study further attests to the relevance of the Krebs cycle in the development of PCC and PGL, and points to a potential role of other metabolic enzymes involved in metabolite exchange between mitochondria and cytosol. Clin Cancer Res; 23(20); 6315–24. ©2017 AACR.

Prostate cancer (PC) is the most prevalent among men and yet its risk factors are little known. This article aims to determine the hospital incidence, trend and municipal distribution of PC in Health Area of León (HAL).We included new cases of prostate cancer (ICD-9: 185, ICD-10: C61) enrolled in the Hospital Tumor Registry of the Complejo Asistencial Universitario de León, between 1996 to 2010 with residence in HAL. We calculated crude triennial hospital incidences and adjusted at global and European population. As denominator we used the INE population data disaggregated by five-year age groups of residents in municipalities of the HAL. To analyze the spatial distribution, we estimated municipal relative risks (RR) smoothed by fitting the Besag, York and Mollié model and the posterior probability (PP) of RR1 using Bayesian methods.3,366 cases were included. Standardized rates at European population amounted of 30.3 (1996-98) to 119.0 (2008-2010) new cases per 100,000 men. The number of organ-confined cases were increased from 281 (1999-2001) to 999 (2008-2010). PSA determinations amounted from 30,985 (1999-2001) to 117 396 (2008-2010).A great increase was observed in the frequency of PC at the expense of organ-confined cases which correlate very well with PSA determinations performed in HAL. There were no differences of interest in the municipal distribution incidences.

Fundamentos. El cáncer de próstata (CaP) es el de mayor incidencia entre los varones y sin embargo se conoce muy poco sobre sus factores de riesgo. El presente artículo tiene por objetivo conocer la incidencia hospitalaria, tendencia y distribución municipal del CaP en el área de salud de León (ASL). Métodos. Fueron incluidos los casos nuevos de cáncer de próstata (CIE-9: 185, CIE-10: C61) del registro hospitalario de tumores del Complejo Asistencial Universitario de León, entre 1996 y 2010 en sujetos con residencia en el ASL. Se calcularon las incidencias hospitalarias brutas trienales y ajustadas a población mundial y europea. Como denominador se utilizaron los datos del Instituto Nacional de Estadística de población desagregada por grupos quinquenales de edad de residentes en municipios del ASL. Para el análisis de la distribución espacial se estimaron los riesgos relativos (RR) municipales suavizados mediante el ajuste del modelo de Besag, York y Mollié y sus probabilidades posteriores de que los RR fuesen > 1 (PP), utilizando métodos bayesianos. Resultados: Se incluyeron 3.366 casos. Las tasas estandarizadas con población europea ascendieron de 30,3 (1996-98) a 119,0 (2008-2010) casos nuevos por 100.000 hombres. El número de casos órgano-confinados pasó de 281 (1999-2001) a 999 (2008-2010). Las determinaciones de PSA ascendieron de 30.985 (1999-2001) a 117.396 (2008-2010). Conclusiones: Se observó un gran incremento de la frecuencia de CaP a expensas de los casos órgano-confinados, que correlacionan muy bien con las determinaciones de PSA llevadas a cabo en el ASL. No hubo diferencias de interés en la distribución municipal de las incidencias. Sí