Insights From Targeted Genetic Analysis of 364 Adrenocortical Carcinomas

Abstract Adrenocortical carcinoma (ACC) is a rare endocrine malignancy affecting individuals across a broad age spectrum. Disease rarity, scarcity of pre-clinical models, lack of effective targeted therapy and limited clinical trials have contributed to poor prognosis for patients with ACC. Identifying targetable genetic drivers and pathways to guide precision medicine approaches is therefore critical to improve outcomes. The purpose of this study was to analyze the genomic profile of a large cohort of ACC to identify potential therapeutic targets. FoundationOne (Foundation Medicine Inc.; FMI, Cambridge, MA) is a next-generation sequencing-based platform for somatic genetic testing in solid tumors. The FoundationOne genomic data and limited demographic data through 2018 for 364 unique ACC specimens were analyzed. The cohort of 364 tumors were from 222 females and 141 males (1 gender unknown). The mean age (SD) was 48.6 (13.6) for females and 50.6 (12.20) for males with overall median age of 52 years. A total of 3117 genomic alterations were identified impacting 457 genes. The median number of genomic alterations per tumor was 7 (range 1–56), with single nucleotide variants and indels being the most common alterations (median=4), followed by copy number alterations (median=1) and rearrangements (median=0). The most frequently altered genes were TP53 (38%), CTNNB1 (28%), ZNRF3 (17%), CDKN2A (13%), ATRX (11%), TERT promoter (10%). Several novel recurrent alterations were identified including IL7R (6%), LRP1B (8%), FRS2 (4%), PTCH1 (4%) and KRAS (3%). Pathway enrichment analysis confirmed that tumor suppressor genes (51%) and Wnt signaling pathways (51%) are the most commonly dysregulated in ACC tumors. Epigenetic alterations, including histone modification (38%), SWI/SNF (21%) and DNA methylation (8%), affected upwards of one third of ACC tumors. Mutation signature analysis identified tumors with signatures 6, 15 and 26 associated with defective DNA mismatch repair (MMR), which was not reported previously. In addition, fifty ACCs (13.7%) exhibited 60 genomic alterations in MMR genes, MLH1, MSH2, MSH6 and PMS2, which included 49 SNVs/indels, 10 CNAs and one truncating rearrangement. In addition to MMR gene alterations, potentially actionable (www.oncokb.org) genomic alterations were found in 46 genes in 213 (58.5%) ACCs. In summary, this study represents the largest to date genomic analysis of ACC that showed that over 50% of ACC tumors had potentially actionable genomic alterations. Approximately 13% of tumors had an alteration in MMR pathway, suggesting that immunotherapy is a relevant therapeutic modality in a significant subset of patients with ACC.

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Genomic landscape of circulating tumor (ct)-DNA alterations in patients with penile cancer.

Journal of Clinical Oncology ◽

10.1200/jco.2019.37.15_suppl.e16027 ◽

2019 ◽

Vol 37 (15_suppl) ◽

pp. e16027-e16027

Author(s):

Archana Agarwal ◽

Amin Nassar ◽

Rebecca Nagy ◽

Catherine Curran ◽

Sarah Abou Alaiwi ◽

...

Keyword(s):

Penile Cancer ◽

Demographic Data ◽

Tumor Biology ◽

The United States ◽

Median Number ◽

Hpv Infection ◽

Single Nucleotide Variants ◽

Genomic Alterations ◽

Her Family ◽

Platinum Based Chemotherapy

e16027 Background: Penile cancer is a rare disease associated with HPV infection and is known to harbor recurrent somatic genomic alterations in the ERBB (HER)-family, CDKN2A, TP53, NOTCH1 and PIK3CA. ctDNA assay allows the noninvasive genomic profiling of malignancies and may assist with understanding molecular evolution of resistance. To our knowledge, the genomic alterations observed in ctDNA for penile cancer have not been described before. We report ctDNA profiling of patients with advanced penile cancer. Methods: Sixteen pts with metastatic penile cancer from multiple institutions in the United States that underwent ctDNA analysis using the Guardant360 platform were eligible. Three patients had at least one serial ctDNA sample. De-identified demographic data were collected. Guardant 360 is CLIA-certified ctDNA panel that assesses single nucleotide variants and copy number alterations in 68 to 73 genes for potentially actionable genomic alterations. Variants seen at least 3 times in the Catalogue of Somatic Mutations in Cancer (COSMIC) database or reported in OncoKB were considered pathogenic. Results: The median age was 64 years (range 40-77). 4 pts (25%) were documented to be post platinum-based chemotherapy. The median number of ctDNA alterations detected per sample was 2 (range 0-6). Overall, genomic alterations were detected in 15/16 patients (94%) across 21 genes (table 1). Alterations were most frequently detected in TP53 (9/16, 56%), CDKN2A (5/16, 31%), TERT promoter (5/16, 31%), PIK3CA (3/16, 19%) and ERBB2 (3/16, 19%). In 3 patients with serial samples, 9 novel pathogenic alterations were detected in the second sample including ATM, CDKN2A, ARID1A, CCND1, CDK6, EGFR, PDGFRA, PIK3CA, and SMAD4. Conclusions: ctDNA alterations in patients with advanced penile cancer were frequently detected with similar prevalences to previously described tumor tissue analyses. New alterations observed on serial ctDNA assays may provide insights regarding tumor biology and inform drug development. [Table: see text]

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Targeted genomic analysis of 364 adrenocortical carcinomas

Endocrine Related Cancer ◽

10.1530/erc-21-0040 ◽

2021 ◽

Vol 28 (10) ◽

pp. 671-681

Author(s):

Nikita Pozdeyev ◽

Lauren Fishbein ◽

Laurie M Gay ◽

Ethan S Sokol ◽

Ryan Hartmaier ◽

...

Keyword(s):

Tumor Suppressor Genes ◽

Wnt Signaling Pathway ◽

Genomic Analysis ◽

Genomic Alteration ◽

Genomic Alterations ◽

Dna Mismatch ◽

Significant Incidence ◽

Adrenocortical Carcinomas ◽

Telomere Lengthening ◽

Gene Alterations

Despite recent advances in elucidating molecular pathways underlying adrenocortical carcinoma (ACC), this orphan malignancy is associated with poor survival. Identification of targetable genomic alterations is critical to improve outcomes. The objective of this study was to characterize the genomic profile of a large cohort of patient ACC samples to identify actionable genomic alterations. Three hundred sixty-four individual patient ACC tumors were analyzed. The median age of the cohort was 52 years and 60.9% (n = 222) were female. ACC samples had common alterations in epigenetic pathways with 38% of tumors carrying alterations in genes involved in histone modification, 21% in telomere lengthening, and 21% in SWI/SNF complex. Tumor suppressor genes and WNT signaling pathway were each mutated in 51% of tumors. Fifty (13.7%) ACC tumors had a genomic alteration in genes involved in the DNA mismatch repair (MMR) pathway with many tumors also displaying an unusually high number of mutations and a corresponding MMR mutation signature. In addition, genomic alterations in several genes not previously associated with ACC were observed, including IL7R, LRP1B, FRS2 mutated in 6, 8 and 4% of tumors, respectively. In total, 58.5% of ACC (n = 213) had at least one potentially actionable genomic alteration in 46 different genes. As more than half of ACC have one or more potentially actionable genomic alterations, this highlights the value of targeted sequencing for this orphan cancer with a poor prognosis. In addition, significant incidence of MMR gene alterations suggests that immunotherapy is a promising therapeutic for a considerable subset of ACC patients.

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Circulating tumor (ct)-DNA alterations in patients with testicular germ tumors.

Journal of Clinical Oncology ◽

10.1200/jco.2019.37.15_suppl.e16063 ◽

2019 ◽

Vol 37 (15_suppl) ◽

pp. e16063-e16063 ◽

Cited By ~ 1

Author(s):

Amin Nassar ◽

Archana Agarwal ◽

Rebecca Nagy ◽

Catherine Curran ◽

Sarah Abou Alaiwi ◽

...

Keyword(s):

Somatic Mutations ◽

Demographic Data ◽

Germ Cell Tumors ◽

The United States ◽

Median Number ◽

Genomic Alterations ◽

Testicular Germ Cell ◽

Dna Alterations ◽

Ctdna Analysis ◽

Serial Samples

e16063 Background: Testicular germ cell tumors (GCT) infrequently harbor somatic mutations. ctDNA assay allows the noninvasive genomic profiling of malignancies and may assist with understanding molecular evolution of resistance. To our knowledge, ctDNA genomic alterations observed in in testicular GCTs have not been heretofore described. We report ctDNA profiling of patients (pts) with testicular GCTs. Methods: 31 Pts with testicular GCTs from multiple institutions in the United States that underwent ctDNA analysis using the Guardant360 platform were eligible. Two patients had one serial ctDNA sample. De-identified demographic data were collected in addition to data for ctDNA alterations. Guardant360 is a CLIA-certified ctDNA panel that assesses single nucleotide variant and copy number alterations in 68 to 73 genes for potentially actionable genomic alterations. Variants reported at least 3 times in the Catalogue of Somatic Mutations in Cancer (COSMIC) database or found in OncoKB were considered pathogenic. Results: Of 31 patients with testicular GCTs, 162 ctDNA alterations were detected in 26 patients (84%) across 41 genes (Table). A median number of 3 alterations (range 1-19) was detected per sample. Among the 162 alterations, 88 were believed to be pathogenic and detectable in 20 patients (65%). 12/31 pts (39%) were documented to be post systemic therapy. The median age was 38 years (range 20-61). The most common pathogenic somatic alterations were KRAS (n = 12/88, 14%), CCND2 (n = 8/88, 9%), MET (n = 8/88, 9%), CDK6 (n = 7/88, 8%), TP53 (n = 6/88, 7%), and RAF1 (n = 5/88, 6%). In 2 patients with serial samples, 5 novel pathogenic alterations were detected in the second sample including FGFR2, APC, CDK6, RAF1, and MAPK1. Conclusions: ctDNA alterations were frequently detected in resistant testicular GCTs and appear similar to alterations previously described in tumor tissue analyses of testicular GCTs. Given that ctDNA offers a non-invasive means of profiling tumor DNA, further development of this promising modality is warranted to determine it's relevance in clinical practice. [Table: see text]

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Targeting STAT3 Abrogates Tim-3 Upregulation of Adaptive Resistance to PD-1 Blockade on Regulatory T Cells of Melanoma

Frontiers in Immunology ◽

10.3389/fimmu.2021.654749 ◽

2021 ◽

Vol 12 ◽

Author(s):

Lili Huang ◽

Yu Xu ◽

Juemin Fang ◽

Weixing Liu ◽

Jianhua Chen ◽

...

Keyword(s):

Mononuclear Cells ◽

Genomic Analysis ◽

Enrichment Analysis ◽

Treg Cells ◽

The Cancer Genome Atlas ◽

Molecular Characteristics ◽

Pathway Enrichment Analysis ◽

Peripheral Blood Mononuclear ◽

Adaptive Resistance ◽

Melanoma Patients

BackgroundLess than 20% of melanoma patients respond to programmed cell death-1 (PD-1) blockade immunotherapies. Thus, it is crucial to understand the dynamic changes in the tumor microenvironment (TME) after PD-1 blockade, for developing immunotherapy efficacy.MethodsA genomic analysis was conducted by The Cancer Genome Atlas (TCGA) datasets and web platform TIMER2.0 datasets. Pathway enrichment analysis was performed using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. Peripheral blood mononuclear cells (PBMCs), regulatory T (Treg) cells, and B16-F10 melanoma mice were used as models. The cellular and molecular characteristics and mechanisms of Treg cells in melanoma were assessed by performing gene expression studies, immunohistochemistry, RNA sequencing, and flow cytometry.ResultsHere, we evaluate the countenance of T cell immunoglobulin and mucin-domain containing-3 (Tim-3), and various immunosuppressive factors within tumor-infiltrated Treg cells after treatment with anti-PD-1 or the indicator transduction and activator of transcription 3 (STAT3) inhibitors. Increased expression of Tim-3 is markedly observed within the tissues of the PD-1 blockade resistance of melanoma patients. Targeting STAT3 significantly boosts the response of resistant-PD-1 therapy within the melanoma mouse model. Mechanistically, the manifestation of STAT3 decreases the expression of Tim-3 and various cytokines in the purified Treg cells from individual PBMCs and the murine melanoma model, limiting the immunosuppression of Treg cells.ConclusionsOur findings indicate that Tim-3 expression on Treg cells within the TME is STAT3-dependent, providing support to STAT3 as a target and enhancing the immunotherapy for patients suffering from melanoma.

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Functional drug–target–disease network analysis of gene–phenotype connectivity for curcumin in cancer

10.21203/rs.3.rs-72811/v1 ◽

2020 ◽

Author(s):

Yuanyuan Zhao ◽

Jiahao Tao ◽

Zhuangzhong Chen ◽

Suihui Li ◽

Zeyu Liu ◽

...

Keyword(s):

Cancer Survival ◽

Genomic Analysis ◽

Enrichment Analysis ◽

Pathway Enrichment Analysis ◽

Mrna Levels ◽

Protein Targets ◽

Protein Protein Interaction ◽

Target Disease ◽

Hep3b Cells ◽

Underlying Mechanisms

Abstract Background The anti-tumor properties of curcumin have been elucidated in many cancer types. However, a systematic functional and biological analysis related to its target proteins has yet to be documented fully. The aim of this study was to explore the underlying mechanisms of curcumin and broaden the perspective of targeted therapies. Methods Direct protein targets (DPTs) of curcumin were searched in the DrugBank database. Using the STRING database, the interaction between curcumin and DPTs and indirect protein targets (IPTs) was documented. The protein–protein interaction (PPI) network of curcumin-mediated proteins was visualized using Cytoscape. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was performed for all curcumin-mediated proteins. Furthermore, the cancer targets were searched in the Comparative Toxicogenomics Database (CTD). The overlapping targets were studied using Kaplan–Meier analysis to evaluate cancer survival. Further genomic analysis of overlapping genes was conducted using the cBioPortal database. Lastly, CKK-8, qPCR, and WB analysis were used to validate the predicted results on HCC cells. Results A total of 5 DPTs and 199 IPTs were found. These protein targets were found in 121 molecular pathways analyzed via KEGG enrichment. Based on the anti-tumor properties of curcumin, two pathways were selected, including pathways in cancer (36 genes) and hepatocellular carcinoma (HCC) pathway (22 genes). Overlapping with 505 HCC-related gene sets identified in CTD, five genes (TP53、 RB1、 TGFB1、 GSTP1、 and GSTM1) were finally identified. High mRNA levels of TP53, RB1, and GSTM1 indicated a prolonged OS in HCC, while elevated mRNA levels of TGFB1 were correlated with poor prognosis. The viability of HepG2 cells and Hep3B cells can both be significantly reduced by curcumin at concentrations of 20 or 30 µM after 48 or 72 h of culture. At a concentration of 20 µM curcumin, the expression of TGFB1 and GSTP1 in Hep3B cells was reduced significantly in qPCR analysis, and reduced TGFB1 protein expression was also found in Hep3B cells. Conclusions The current results provided evidence that curcumin has the potential to become an alternative chemotherapy or chemoprevention for HCC.

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Genomic landscape of circulating tumor (ct)-DNA alterations in patients with penile cancer.

Journal of Clinical Oncology ◽

10.1200/jco.2020.38.6_suppl.6 ◽

2020 ◽

Vol 38 (6_suppl) ◽

pp. 6-6 ◽

Cited By ~ 1

Author(s):

Amin Nassar ◽

Archana Agarwal ◽

Rebecca Nagy ◽

Catherine Curran ◽

Sarah Abou Alaiwi ◽

...

Keyword(s):

Penile Cancer ◽

Demographic Data ◽

The United States ◽

Hpv Infection ◽

Tumor Evolution ◽

Single Nucleotide Variants ◽

Genomic Alterations ◽

Her Family ◽

Entire Cohort ◽

Platinum Based Chemotherapy

6 Background: Penile cancer is a rare disease associated with HPV infection and harbors recurrent somatic genomic alterations in the ERBB (HER)-family, CDKN2A, TP53, NOTCH1 and PIK3CA. ctDNA assay allows the noninvasive genomic profiling of malignancies and may assist with understanding molecular evolution. To our knowledge, the genomic alterations observed in ctDNA for penile cancer have not been described before. We report ctDNA profiling of patients with advanced penile cancer. Methods: Sixteen pts with metastatic penile cancer from multiple institutions in the United States that underwent ctDNA analysis using the Guardant360 platform were eligible. Three patients had at least one serial ctDNA sample. De-identified demographic data were collected. Guardant 360 is CLIA-certified ctDNA panel that assesses single nucleotide variants and copy number alterations in 68 to 73 genes for potentially actionable genomic alterations. Variants seen at least 3 times in the Catalogue of Somatic Mutations in Cancer (COSMIC) database or reported in OncoKB were considered pathogenic. Results: The median age was 64 years (range 40-77). 4 pts (25%) were documented to be post platinum-based chemotherapy. Among the entire cohort, 51 ctDNA alterations were detected (median=2, range 0-6) in 15/16 patients (94%) across 21 genes (table). Of the 51 alterations, 24 (47%) were actionable and had approved targeted therapies in other cancers. Alterations were most frequently detected in TP53 (9/16, 56%), CDKN2A (5/16, 31%), and TERT promoter (5/16, 31%) (table). In 3 patients with serial samples, 9 novel pathogenic alterations were detected in the second sample including ATM, CDKN2A, ARID1A, CCND1, CDK6, EGFR, PDGFRA, PIK3CA, and SMAD4. Conclusions: ctDNA alterations in patients with advanced penile cancer were frequently detected and appeared similar to previously described tumor tissue analyses. New alterations found on serial ctDNA assays shed light on patterns of tumor evolution and may inform drug development for this challenging orphan malignancy.[Table: see text]

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Genome Sequence and Comparative Analysis of Colletotrichum gloeosporioides Isolated from Liriodendron Leaves

Phytopathology ◽

10.1094/phyto-12-19-0452-r ◽

2020 ◽

Vol 110 (7) ◽

pp. 1260-1269

Author(s):

Fang-Fang Fu ◽

Zhaodong Hao ◽

Pengkai Wang ◽

Ye Lu ◽

Liang-Jiao Xue ◽

...

Keyword(s):

Structure Prediction ◽

Polyketide Synthase ◽

Colletotrichum Gloeosporioides ◽

Genomic Analysis ◽

Enrichment Analysis ◽

Comparative Genomic ◽

Pathway Enrichment Analysis ◽

Protein Coding ◽

Protein Coding Genes ◽

Species Specific

Colletotrichum gloeosporioides is a hemibiotrophic pathogen causing significant losses to economically important crops and forest trees, including Liriodendron. To explore the interaction between C. gloeosporioides and Liriodendron and to identify the candidate genes determining the pathogenesis, we sequenced and assembled the whole genome of C. gloeosporioides Lc1 (CgLc1) using PacBio and Illumina next generation sequencing and performed a comparative genomic analysis between CgLc1 and Cg01, the latter being a described endophytic species of the C. gloeosporioides complex. Gene structure prediction identified 15,744 protein-coding genes and 837 noncoding RNAs. Species-specific genes were characterized using an ortholog analysis followed by a pathway enrichment analysis, which showed that genes specific to CgLc1 were enriched for the arginine biosynthetic process. Furthermore, genome synteny analysis revealed that most of the protein-coding genes fell into collinear blocks. However, two clusters of polyketide synthase genes were identified to be specific for CgLc1, suggesting that they might have an important role in virulence control. Transcriptional regulators coexpressed with polyketide synthase genes were detected through a Weighted Correlation Network Analysis. Taken together, this work provides new insight into the virulence- and pathogenesis-associated genes present in C. gloeosporioides and its possible lifestyle.

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RARE-07. THE LANDSCAPE OF GENOMIC ALTERATIONS IN ADAMANTINOMATOUS CRANIOPHARYNGIOMAS

Neuro-Oncology ◽

10.1093/neuonc/noaa222.718 ◽

2020 ◽

Vol 22 (Supplement_3) ◽

pp. iii443-iii443

Author(s):

Prasidda Khadka ◽

Eric Prince ◽

Sophie Lu ◽

Sandro Santagata ◽

Keith Ligon ◽

...

Keyword(s):

Wnt Signaling Pathway ◽

Genomic Analysis ◽

Enrichment Analysis ◽

Gene Set Enrichment Analysis ◽

Structural Variations ◽

Genomic Alterations ◽

Normal Tissues ◽

Activating Mutations ◽

Ctnnb1 Gene ◽

Recurrent Mutations

Abstract INTRODUCTION Adamantinomatous craniopharyngiomas (ACPs) are characterized by activating mutations in the CTNNB1 gene. Here we perform a comprehensive genomic analysis of 23 ACPs to define the landscape of genomic alterations in this disease. METHODS We performed whole-genome sequencing of 24 ACPs and their matched normal tissues. We used Mutect 2.0 to detect mutations and indels in these samples and MutSig2CV to identify significant mutations. Copy numbers were called using the GATK4 pipeline and GISTIC 2.0 was applied to identify significant alterations. Finally, SvABA was applied to identify genome-wide structural variants and rearrangements. RESULTS 18/24 (75%) of the sequenced ACPs harbored activating mutations in exon 3 of CTNNB1 gene with an average variant allele fraction (VAF) of 0.4±0.1. These mutations have previously been shown to activate the WNT signaling pathway in these tumors. No other significantly recurrent mutations were detected in our samples. The ACPs were quiet with regard to copy number alterations and no recurrent amplifications or deletions were detected. 528 structural variations and rearrangements were detected in total in all 24 samples with an average of 22 variants per sample. Gene-Set Enrichment Analysis (GSEA) of the RNAseq data revealed upregulation of WNT/B-catenin (FDR q-value <0.25) in the CTNNB1 mutant samples compared to CTNNB1 WT samples. CONCLUSION Our study identified previously described activating CTNNB1 mutations in the majority of ACPs. In addition, we identified several rearrangements and structural variations in these tumors that could play an important role in the pathogenesis of the disease.

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