Chromosome 17p Deletion Research Articles

Abstract 282: MicroRNAs located at chromosome 8p21-22 region as novel factors underlying racial disparities in prostate cancer aggressiveness

Abstract The mechanistic basis of racial disparities in prostate cancer (PCa) aggressiveness between African American (AA) and Caucasian (CA) men are not yet fully understood. Further, molecular biomarkers to predict aggressive disease at its onset have been studied primarily in CAs, the relevance of these biomarkers to AAs are largely unknown. We propose a novel, paradigm-shifting hypothesis that expression of microRNA (miRNA) genes-miR-3622a and miR-383-located within frequently deleted chr8p21-22 region constitute important molecular factors contributing to racial disparities in PCa aggressiveness in AA vs CA men. Chromosome 8p deletions are a frequent alteration of PCa genome, with a common region of loss of heterozygosity at the chr8p21-22 locus. We previously showed that this region is associated with a set of tumor suppressive miRNAs (miR-3622a/b, -383, -4288) that are downregulated in PCa with important causal roles in tumor progression, recurrence and metastasis. Chr8p deletions increase significantly with tumor grade and are associated with poor prognosis. These deletions are well studied in CA men. However, there have been conflicting reports on frequency of chr8p deletions in AA men. In view of these conflicting studies and in light of our paradigm-shifting studies establishing the link between chr8p deletions and loss of miRNA genes in this region, we examined the expression of these miRNAs in AA vs CA clinical PCa tissues. We found that miR-3622a and miR-383 expression is significantly lower in AA men as compared to age, tumor stage and grade matched CAs. To examine if these miRNAs constitute causal factors contributing to PCa racial disparities, we overexpressed miR-3622a/miR-383/control miR in AA and CA PCa cell lines followed by functional assays. We found that these miRNAs exert more prominent effects on cellular proliferation and apoptosis in AA cell lines. To understand molecular mechanisms contributing to disparate functional effects of these miRNAs in AA vs CA cell lines, we examined potential miRNA target genes and found that miR-3622a regulates PCa stem cell marker, CD44 while miR-383 represses LEF1 and ZEB1 in a race-specific manner. Further, we determined the mechanistic basis of differential expression of miR-3622a in AAs vs CAs by examining copy number alterations (CNAs) and methylation at this locus using PCa clinical samples. Our analyses showed that while this locus is genomically altered at a lower frequency in AAs, significantly increased frequency of miRNA promoter hypermethylation was found in AAs as compared to CAs. In conclusion, our data suggests that miRNAs located in frequently deleted chr8p21-22 region constitute important causal factors contributing to racial disparities in PCa aggressiveness and clinical outcomes and are potential biomarkers to predict PCa aggressiveness and tumor recurrence in AA men. Citation Format: Divya Bhagirath, Nikhil Patel, Santu Ghosh, Roni Bollag, Sharanjot Saini. MicroRNAs located at chromosome 8p21-22 region as novel factors underlying racial disparities in prostate cancer aggressiveness [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 282.

Refinement of the critical genomic region for congenital hyperinsulinismin the Chromosome 9p deletion syndrome.

Background: Large contiguous gene deletions at the distal end of the short arm of chromosome 9 result in the complex multi-organ condition chromosome 9p deletion syndrome. A range of clinical features can result from these deletions with the most common being facial dysmorphisms and neurological impairment. Congenital hyperinsulinism is a rarely reported feature of the syndrome with the genetic mechanism for the dysregulated insulin secretion being unknown. Methods: We studied the clinical and genetic characteristics of 12 individuals with chromosome 9p deletions who had a history of neonatal hypoglycaemia. Using off-target reads generated from targeted next-generation sequencing of the genes known to cause hyperinsulinaemic hypoglycaemia (n=9), or microarray analysis (n=3), we mapped the minimal shared deleted region on chromosome 9 in this cohort. Targeted sequencing was performed in three patients to search for a recessive mutation unmasked by the deletion. Results: In 10/12 patients with hypoglycaemia, hyperinsulinism was confirmed biochemically. A range of extra-pancreatic features were also reported in these patients consistent with the diagnosis of the Chromosome 9p deletion syndrome. The minimal deleted region was mapped to 7.2 Mb, encompassing 38 protein-coding genes. In silico analysis of these genes highlighted SMARCA2 and RFX3 as potential candidates for the hypoglycaemia. Targeted sequencing performed on three of the patients did not identify a second disease-causing variant within the minimal deleted region. Conclusions: This study identifies 9p deletions as an important cause of hyperinsulinaemic hypoglycaemia and increases the number of cases reported with 9p deletions and hypoglycaemia to 15 making this a more common feature of the syndrome than previously appreciated. Whilst the precise genetic mechanism of the dysregulated insulin secretion could not be determined in these patients, mapping the deletion breakpoints highlighted potential candidate genes for hypoglycaemia within the deleted region.

Refinement of the critical genomic region for congenital hyperinsulinism in the Chromosome 9p deletion syndrome

Background: Large contiguous gene deletions at the distal end of the short arm of chromosome 9 result in the complex multi-organ condition chromosome 9p deletion syndrome. A range of clinical features can result from these deletions with the most common being facial dysmorphisms and neurological impairment. Congenital hyperinsulinism is a rarely reported feature of the syndrome with the genetic mechanism for the dysregulated insulin secretion being unknown. Methods: We studied the clinical and genetic characteristics of 12 individuals with chromosome 9p deletions who had a history of neonatal hypoglycaemia. Using off-target reads generated from targeted next-generation sequencing of the genes known to cause hyperinsulinaemic hypoglycaemia (n=9), or microarray analysis (n=3), we mapped the minimal shared deleted region on chromosome 9 in this cohort. Targeted sequencing was performed in three patients to search for a recessive mutation unmasked by the deletion. Results: In 10/12 patients with hypoglycaemia, hyperinsulinism was confirmed biochemically. A range of extra-pancreatic features were also reported in these patients consistent with the diagnosis of the Chromosome 9p deletion syndrome. The minimal deleted region was mapped to 7.2 Mb, encompassing 38 protein-coding genes. In silico analysis of these genes highlighted SMARCA2 and RFX3 as potential candidates for the hypoglycaemia. Targeted sequencing performed on three of the patients did not identify a second disease-causing variant within the minimal deleted region. Conclusions: This study identifies 9p deletions as an important cause of hyperinsulinaemic hypoglycaemia and increases the number of cases reported with 9p deletions and hypoglycaemia to 15 making this a more common feature of the syndrome than previously appreciated. Whilst the precise genetic mechanism of the dysregulated insulin secretion could not be determined in these patients, mapping the deletion breakpoints highlighted potential candidate genes for hypoglycaemia within the deleted region.

Abstract A44: Functional models of chromosome arm-level aneuploidies in cancer

Abstract Aneuploidy, whole-chromosome or chromosome arm copy number imbalance, is a near-universal characteristic of human cancers. We previously applied methods that define chromosome arm-level aneuploidy and a global cancer aneuploidy score to 10,522 tumors of 33 types in The Cancer Genome Atlas (TCGA). Aneuploidy level was correlated with TP53 mutation, somatic mutation rate, and expression of proliferation genes. Overall aneuploidy was anti-correlated with expression of immune signaling genes, due to decreased leukocyte infiltrates in high-aneuploidy samples. In contrast, some individual chromosome arm alterations correlated with higher expression of immune signaling genes, including deletion of chromosome 3p, 8p, and 17p. Cancer subtypes are often characterized by tumor specific patterns of arm-level copy number alterations; for example, squamous cell carcinomas (SCCs) from different tissues of origin (including lung, esophagus, and bladder) have a pattern of chromosome 3p loss and chromosome 3q gain. Although yeast and mammalian models of whole-chromosome aneuploidies have been extensively investigated, chromosome arm-level aneuploidies have rarely been modeled. However, recent advances in genome engineering and targeting of endonucleases allow generation of large chromosomal alterations. We used the CRISPR-Cas9 system to delete one copy of chromosome 3p in human immortalized lung epithelial cells, validated in 8 clones by whole-genome sequencing. Consistent with patient data, expression of 3p genes was decreased upon deletion, as well as increased expression of interferon response genes. Phenotypic characterization revealed that cells with chromosome 3p deletion initially proliferated more slowly than their siblings. These chromosome 3p-deleted cells had increased G1 arrest but did not undergo increased apoptosis or cell death. Interestingly, after several passages in culture, the proliferation defect was rescued in chromosome 3p-deleted cells; genome sequencing and karyotype analyses suggested that this was partially the result of chromosome 3 duplication. With our cellular model of chromosome arm-level aneuploidy, we uncovered a selection mechanism that allowed aneuploidy tolerance in vitro. We have also grown these cells in spheroid and organoid culture systems to assess the effects of chromosome 3 arm-level aneuploidies on cytokine production and squamous differentiation and are using these systems to identify how chromosome 3p deletion affects drug sensitivity. In conclusion, our genome engineering approach to model chromosome arm-level deletions provides a robust model that will address a gap in our understanding of aneuploidy in cancer. Citation Format: Alison M. Taylor, Sejal Jain, Juliann Shih, Andrew D. Cherniack, Rameen Beroukhim, Matthew Meyerson. Functional models of chromosome arm-level aneuploidies in cancer [abstract]. In: Proceedings of the AACR Special Conference on the Evolving Landscape of Cancer Modeling; 2020 Mar 2-5; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2020;80(11 Suppl):Abstract nr A44.

The impact of cytogenetic evolution and acquisition of del(17p) on the prognosis of patients with multiple myeloma.

Prognosis of patients with newly diagnosed multiple myeloma (MM), a third most common hematological cancer, is dependent on baseline cytogenetics. However, little is known about the prognostic significance of cytogenetic evolution (CE) at the time between the diagnosis and relapse of MM. Here, we retrospectively analyzed the prognostic impact of CE detected in a routine interphase fluorescence in situ hybridization (FISH) test in a cohort of patients with MM. Among 650 patients evaluated with the FISH MM panel at our center between 2014 and 2019, we identified 29 individuals with MM who had been tested twice, at the time of diagnosis and relapse. Cytogenetic evolution was defined as the acquisition or loss of at least 1 cytogenetic abnormality at relapse (FISH2) compared with the baseline test result (FISH1). Cytogenetic evolution was seen in 14 patients (48%), whereas 15 had stable cytogenetics. Acquired chromosome 17p deletion (del[17p]) was the most common type of CE, found in 7 patients (24%). In univariable analysis, stable cytogenetics predicted longer overall survival (median not reached vs 3.8 years; hazard ratio [HR], 0.15; P = 0.04; median follow‑up of 3.1 years) and longer overall survival after FISH2 (median not reached vs 0.8 years; HR, 0.13; P = 0.002; median follow‑up of 0.6 years). In multivariable analysis, acquired del(17p) predicted shorter progression‑free survival and the overall survival after FISH2 (HR, 9.3 and 18.8; P = 0.005 and P = 0.004, respectively). Presence of CE and, particularly, the acquisition of new del(17p) at relapse, negatively affect the outcome of MM. Therefore, re‑evaluation of FISH at MM relapse should be included in routine clinical practice.

An Updated Perspective on Current Prognostic and Predictive Biomarkers in Chronic Lymphocytic Leukemia in the Context of Chemoimmunotherapy and Novel Targeted Therapy.

Chronic lymphocytic leukemia (CLL) is a heterogeneous disease with a variable clinical course. Novel biomarkers discovered over the past 20 years have revolutionized the way clinicians approach prognostication and treatment especially in the chemotherapy-free era. Herein, we review the best established prognostic and predictive biomarkers in the setting of chemoimmunotherapy (CIT) and novel targeted therapy. We propose that TP53 disruption (defined as either TP53 mutation or chromosome 17p deletion), unmutated immunoglobulin heavy chain variable region gene status (UM IGHV), NOTCH1 mutation, and CD49d expression are the strongest prognosticators of disease progression and overall survival in the field of novel biomarkers including recurrent gene mutations. We also highlight the predictive role of TP53 disruption, UM IGHV, and NOTCH1 mutation in the setting of CIT and TP53 disruption and CD49d expression in the setting of novel targeted therapy employing B-cell receptor (BCR) and B-cell lymphoma-2 (BCL2) inhibition. Finally, we discuss future directions in the field of biomarker development to identify those with relapsed/refractory disease at risk for progression despite treatment with novel therapies.

Gene signatures associated with genomic aberrations predict prognosis in neuroblastoma.

BackgroundNeuroblastoma (NB) is a heterogeneous disease with respect to genomic abnormalities and clinical behaviors. Despite recent advances in our understanding of the association between the genetic aberrations and clinical features, it remains one of the major challenges to predict prognosis and stratify patients for determining personalized therapy in this disease. The aim of this study was to develop an effective prognosis prediction model for NB patients.MethodsWe integrated diverse computational analyses to define gene signatures that reflect MYCN activity and chromosomal aberrations including deletion of chromosome 1p (Chr1p_del) and chromosome 11q (Chr11q_del) as well as chromosome 11q whole loss (Chr11q_wls). We evaluated the prognostic and predictive values of these signatures in seven NB gene expression datasets (the number of samples ranges from 94 to 498, with a total of 2120) generated from both RNA sequencing and microarray platforms.ResultsMYCN signature was a more effective prognostic marker than MYCN amplification status and MYCN expression. Similarly, the Chr1p_del score was more prognostic than Chr1p status. The activity scores of MYCN, Chr1p_del and Chr11q_del were associated with poor prognosis, while the Chr11q_wls score was linked to good outcome. We integrated the activity scores of MYCN, Chr1p_del, Chr11q_del, and Chr11q_wls and clinical variables into an integrative prognostic model, which displayed significant performance over the clinical variables or each genomic aberration alone.ConclusionsOur integrative gene signature model shows a significantly improved forecast performance with prognostic and predictive information, and thereby can be served as a biomarker to stratify NB patients for prognosis evaluation and surveillance programs.

Abstract P3-10-19: Precise targeting of POLR2A for treating triple negative breast cancer with Chr17p loss

Abstract Triple-negative breast cancer (TNBC) is a molecularly diverse and clinically heterogeneous disease. The challenges for developing novel treatment approaches for TNBC are the paucity of actionable targets, lack of targeted therapies, and poor prognosis of patients. Breast cancer genomics revealed that heterozygous deletion of chromosome 17p (Chr17p) is the most prevalent (53%) event in TNBC. Within the 17p deletion region is the tumor suppressor TP53 (encoding p53), whose deletion or mutation has been long known as a primary tumorigenic driver. However, it remains unclear whether the deletion event, which often includes as many as 200 genes, impacts tumorigenesis beyond TP53 loss alone. While p53 aberrancy promotes proliferation, metabolism and metastatic potential of the TNBC cells, we found that heterozygous deletion of Chr17p is tightly correlated with poor cytotoxicity of tumor infiltrating lymphocytes (TILs) and poor clinical outcomes in patients with TNBC. This result suggests that selective advantage due to Chr17p loss reflects the combined impact of TP53 loss and the reduced dosage of co-deleted genes. Our recent study also identified POLR2A in the TP53-neighboring region as a collateral vulnerability target in the TNBC tumors with Chr17p loss, suggesting that inhibition of POLR2A may be a precision therapy approach for TNBC. As a proof-of-concept, we designed pH-activated nanoparticles (termed as nanobomb) for delivery of POLR2A siRNA, which enhances bioavailability and improves endo/lysosomal escape of the siRNA. In this study (Nature Nanotechnology, 2019)1, we demonstrated that suppressing POLR2A expression with the siRNA-laden nanoparticles led to marked growth reduction of TNBC tumors with 17p loss. Despite recent success of the first FDA-approved RNAi-based therapy for polyneuropathy, the issues of RNAi-based drugs, such as non-specific and incomplete knockdown, can make RNAi unpredictable, slow, and risky, in particular in drug discovery, where speed and reliability of results are crucial factors. To accelerate the translational development of our important finding, we will use α-amanitin, a natural small compound isolated from Amanita phalloides, to specifically inhibit POLR2A (Kd ∼10−9 M). However, free form of α-amanitin causes liver toxicity via the interaction with the hepatocyte-specific OATP1B3 transporter, limiting its clinical applications. To overcome the drug toxicity of α-amanitin, we have been developing α-amanitin-based antibody-drug conjugates (ADC). This approach inhibits the specific uptake of α-amanitin into hepatocytes and increases tumor-specific targeting using tumor-specific monoclonal antibodies. This type of ADC showed significant efficacy in inhibiting the growth of colorectal tumors with heterozygous deletion of TP53 and POLR2A (Nature, 2015)2. Here, we propose that heterozygous deletion of Chr17p not only contributes to TNBC tumorigenesis, but also confers therapeutic vulnerabilities, which can be utilized to develop novel targeted cancer therapy. Refernces 1. Xu,J. et al. Precise targeting of POLR2A as a therapeutic strategy for human triple negative breast cancer. Nat. Nanotechnol. 14, 388-397 (2019). 2. Liu,Y. et al. TP53 loss creates therapeutic vulnerability in colorectal cancer. Nature 520, 697-701 (2015). Citation Format: Xiongbin Lu, Yujing Li, Yifan Sun, Kevin Van der Jeught, Michael Kulke, Pahl Andreas, Xinna Zhang, Xiaoming He, Chi Zhang. Precise targeting of POLR2A for treating triple negative breast cancer with Chr17p loss [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P3-10-19.

Prognosis, Biology, and Targeting of TP53 Dysregulation in Multiple Myeloma.

Multiple myeloma (MM) is the second most common hematological cancer and is characterized by genetic features including translocations, chromosomal copy number aberrations, and mutations in key oncogene and tumor suppressor genes. Dysregulation of the tumor suppressor TP53 is important in the pathogenesis of many cancers, including MM. In newly-diagnosed MM patients, TP53 dysregulation occurs in three subsets: monoallelic deletion as part of deletion of chromosome 17p (del17p) (~8%), monoallelic mutations (~6%), and biallelic inactivation (~4%). Del17p is an established high-risk feature in MM and is included in current disease staging criteria. Biallelic inactivation and mutation have also been reported in MM patients but are not yet included in disease staging criteria for high-risk disease. Emerging clinical and genomics data suggest that the biology of high-risk disease is complex, and so far, traditional drug development efforts to target dysregulated TP53 have not been successful. Here we review the TP53 dysregulation literature in cancer and in MM, including the three segments of TP53 dysregulation observed in MM patients. We propose a reverse translational approach to identify novel targets and disease drivers from TP53 dysregulated patients to address the unmet medical need in this setting.

Cardiomyopathy due to PRDM16 mutation: First description of a fetal presentation, with possible modifier genes.

PRDM16 (positive regulatory domain 16) is localized in the critical region for cardiomyopathy in patients with deletions of chromosome 1p36, as defined by Gajecka et al., American Journal of Medical Genetics, 2010, 152A, 3074-3083, and encodes a zinc finger transcription factor. We present the first fetal case of left ventricular non-compaction (LVNC) with a PRDM16 variant. The third-trimester obstetric ultrasound revealed a hydropic fetus with hydramnios and expanded hypokinetic heart. After termination of pregnancy, foetopathology showed a eutrophic fetus with isolated cardiomegaly. Endocardial fibroelastosis was associated with non-compaction of the myocardium of the left ventricle. Exome sequencing (ES) identified a de novo unreported p.(Gln353*) heterozygous nonsense variant in PRDM16. ES also identified two rare variants of unknown significance, according to the American College of Medical Genetics and Genomics guidelines, in the titin gene (TTN): a de novo missense p.(Lys14773Asn) variant and a c.33043+5A>G variant inherited from the mother. Along with the PRDM16 de novo probably pathogenic variant, TTN VOUS variants could possibly contribute to the severity and early onset of the cardiac phenotype. Because of the genetic heterogeneity of cardiomyopathies, large panels or even ES could be considered as the main approaches for the molecular diagnosis, particularly in fetal presentations, where multiple hits seem to be common.

Renal Cell Carcinoma with Clear Cell Papillary Features: Perspectives of a Differential Diagnosis

Thirty-one cases of low-grade renal cell carcinoma (RCC) with clear cells and tubulopapillary/papillary architecture were analyzed retrospectively with immunohistochemical and genetic markers to gain more experience with the differential diagnosis of such cases. All samples coexpressed CK7 and CA9; the TFE3 or TFEB reactions were negative; the CD10 and the AMACR stainings were negative in 27 cases and 30 cases, respectively. The FISH assays for papillary RCC, available in 27 cases, and deletion of chromosome 3p, available in 29 cases, gave negative results. The results for 3p deletion, VHL gene mutation or VHL gene promoter region hypermethylation testing, along with the diffuse CD10-positivity in 2 cases confirmed 21 cases as clear cell papillary RCC (CCPRCC; CK7+, CA9+; no 3p loss, no VHL abnormality) and 10 cases as clear cell RCC (CCRCC; CK7+, CA9+; no 3p loss, VHL abnormality mutation/hypermethylation present). In CCPRCCs, the representative growth pattern was branching tubulo-acinar, commonly accompanied by cyst formation. The linear nuclear arrangement or cup-shaped staining of CA9 did not necessarily indicate CCPRCC, and the absence of these did not exclude the diagnosis of CCPPRC. One tumor infiltrated the renal sinus; the others exhibited pT1 stage; and metastatic outcome was not recorded. The CCRCC cases were in pT1 stage; 6 exhibited cup-shaped staining of CA9, and 1 displayed lymph node metastasis at the time of surgery. Distant metastatic disease was not observed. In summary, the VHL abnormalities distinguished the subset of CCRCC with diffuse CK7-positivity and no 3p loss from cases of CCPRCC.

Refinement of the critical genomic region for hypoglycaemia in the Chromosome 9p deletion syndrome

Background: Large contiguous gene deletions at the distal end of the short arm of chromosome 9 result in the complex multi-organ condition chromosome 9p deletion syndrome. A range of clinical features can result from these deletions with the most common being facial dysmorphisms and neurological impairment. Congenital hyperinsulinism is a rarely reported feature of the syndrome with the genetic mechanism for the dysregulated insulin secretion being unknown. Methods: We studied the clinical and genetic characteristics of 12 individuals with chromosome 9p deletions who had a history of neonatal hypoglycaemia. Using off-target reads generated from targeted next-generation sequencing of the genes known to cause hyperinsulinaemic hypoglycaemia (n=9), or microarray analysis (n=3), we mapped the minimal shared deleted region on chromosome 9 in this cohort. Targeted sequencing was performed in three patients to search for a recessive mutation unmasked by the deletion. Results: In 10/12 patients with hypoglycaemia, hyperinsulinism was confirmed biochemically. A range of extra-pancreatic features were also reported in these patients consistent with the diagnosis of the Chromosome 9p deletion syndrome. The minimal deleted region was mapped to 7.2 Mb, encompassing 38 protein-coding genes. In silico analysis of these genes highlighted SMARCA2 and RFX3 as potential candidates for the hypoglycaemia. Targeted sequencing performed on three of the patients did not identify a second disease-causing variant within the minimal deleted region. Conclusions: This study identifies 9p deletions as an important cause of hyperinsulinaemic hypoglycaemia and increases the number of cases reported with 9p deletions and hypoglycaemia to 15 making this a more common feature of the syndrome than previously appreciated. Whilst the precise genetic mechanism of the dysregulated insulin secretion could not be determined in these patients, mapping the deletion breakpoints highlighted potential candidate genes for hypoglycaemia within the deleted region.

Large deletions (>10.9 MB) in 17p and bi-allelic TP53 inactivation events in newly-diagnosed multiple myeloma are associated with higher clonal cell fraction and poor prognosis

Deletions in Chromosome 17p (del17p) are associated with poor outcome in Multiple Myeloma (MM). We compiled a cohort of 139 whole-exome and whole-genome sequenced del17p newly diagnosed patient tumors and correlated the size of the deletion, as calculated by controlFreec, against progression-free and overall survival. Large (> 10.9MB) deletions in chromosome 17p that included TP53 region were significantly associated with poorer overall survival (mOS = 28.8 months vs. mOS = 45.0 months, pval= 0.047).

Loss of TRIM33 in Multiple Myeloma correlates with increased genomic instability

Genomic instability is a hallmark of Multiple Myeloma (MM), with almost all patients displaying cytogenetic abnormalities including ploidy changes, deletions, amplifications and translocations. A common recurrent genetic event in MM with prognostic significance is the deletion of chromosome 1p. TRIM33, an E3 ligase, is located within this deleted region at 1p13. Recent studies demonstrate a role for TRIM33 in the PARP-dependent DNA Damage Response (DDR) and showed that loss of TRIM33 results in the accumulation of chromosomal abnormalities.

Targeting lysosome function causes selective cytotoxicity in VHL-inactivated renal cell carcinomas.

The inactivation of the tumor suppressor gene, von Hippel-Lindau (VHL), has been identified as the earliest event in renal cell carcinoma (RCC) development. The loss of heterogeneity by chromosome 3p deletion followed by inactivating mutations on the second VHL copy are events present in close to 90% of patients. Our study illustrates a lysosomal vulnerability in VHL-inactivated RCC in vitro. By investigating the mechanism of action of the previously identified STF-62247, a small bioactive compound known for its selective cytotoxic properties towards VHL-defective models, we present the promising approach of targeting truncal-driven VHL inactivation through lysosome disruption. Furthermore, by analyzing the open platform for exploring cancer genomic data (cbioportal), we uncover the high alteration frequency of essential lysosomal and autophagic genes in sequenced biopsies from clear cell RCC patient primary tumors. By investigating lysosome physiology, we also identify VHL-inactivated cells' inability to maintain their lysosomes at the perinuclear localization in response to STF-62247-induced stress and accumulate cytoplasmic inclusion bodies in response to an inefficient lysosomal degradative capacity. Finally, by testing other known lysosomal-disrupting agents (LDAs), we show that these are selectively cytotoxic to cells lacking VHL functions. Our study builds a strong platform that could specifically link genetic clonal ccRCC evolution to lysosomal and trafficking vulnerabilities.

The Implication of Cytogenetic Alterations in Pancreatic Ductal Adenocarcinoma and Intraductal Papillary Mucinous Neoplasm Identified by Fluorescence In Situ Hybridization and Their Potential Diagnostic Utility

Background/AimsWe investigated chromosomal aberrations in patients with pancreatic ductal adenocarcinoma (PDAC) and intraductal papillary mucinous neoplasm (IPMN) by fluorescence in situ hybridization (FISH) to identify cytogenetic changes and molecular markers that may be useful for preoperative diagnosis.MethodsTissue samples from 48 PDAC and 17 IPMN patients were investigated by FISH analysis using probes targeting chromosomes 7q, 17p, 18q, 20q, and 21q and the pericentromeric region of chromosome 18 (CEP18).ResultsThe PDAC samples harbored 17p deletion (95.8%), 18q deletion (83.3%), CEP18 deletion (81.2%), 20q gain (81.2%), 21q deletion (77.1%), and 7q gain (70.8%). The IPMN samples had 17p deletion (94.1%), CEP18 deletion (94.1%), 21q deletion (70.6%), 18q deletion (58.8%), 20q gain (58.8%), and 7q gain (58.8%). A significant difference in CEP18 gain was identified between the PDAC and IPMN groups (p=0.029). Detection of 17p or 18q deletion had the highest diagnostic accuracy (80.0%) for PDAC.ConclusionsChromosomal alterations were frequently identified in both PDAC and IPMN with similar patterns. CEP18 gain and 17p and 18q deletions might be involved in the later stages of PDAC tumorigenesis. Chromosome 17p and 18q deletions might be excellent diagnostic markers.

Venetoclax for the Treatment of Chronic Lymphocytic Leukemia.

This review summarizes the role of BCL-2 in the pathogenesis of CLL, and the clinical data evaluating safety and efficacy of venetoclax, in treatment of patients with CLL, in the context of other available targeted agents. Venetoclax, alone or in combination with other targeted agents results in high rate of durable responses and undetectable measurable residual disease. Venetoclax maintains activity across all clinical and biologic subgroups, including those with high risk disease, including CLL with chromosome 17p deletion. TLS risk can be mitigated with risk stratification and five-week administration ramp-up schedule. Venetoclax, a novel, orally bioavailable inhibitor of BCL-2 has demonstrated substantial clinical activity in the treatment of CLL. In combination with other targeted agents it can induce high disease response rates and potentially lead to MRD-negative durable remissions.

Chronic lymphocytic leukemia with TP53 gene alterations: a detailed clinicopathologic analysis.

TP53 alteration in chronic lymphocytic leukemia indicates a high-risk disease that is usually refractory to chemotherapy. It may be caused by deletion of 17p involving the loss of TP53 gene, which occurs in low percentage of patients at diagnosis but can be acquired as the disease progresses. Since patients may harbor TP53 mutation without chromosome 17p deletion, consensus recommendations call for both cytogenetic and PCR mutation analysis of TP53 in chronic lymphocytic leukemia. We conducted a single-institution retrospective study to investigate the clinicopathologic features of chronic lymphocytic leukemia with TP53 alterations as well as the utility of different diagnostic modalities to identify p53 alterations. Forty percent of chronic lymphocytic leukemia patients with TP53 alterations demonstrated atypical lymphocytes with cleaved/irregularly shaped nuclei and/or large atypical lymphoid cells with abundant cytoplasm in the peripheral blood. Progression was also observed in lymph node and bone marrow samples (21% with Richter transformation; 33% with findings suggestive of "accelerated phase" of chronic lymphocytic leukemia including prominent proliferation centers and/or increased numbers of prolymphocytes). However, the presence of the morphologic features suggestive of "accelerated phase" had no effect on overall survival within the chronic lymphocytic leukemia group with TP53 abnormalities (p > 0.05). As previously reported by others, a subset of patients with TP53 alterations were only identified by either PCR mutation analysis (12%) or cytogenetic studies (14%). p53 immunostain positivity was only identified in approximately half of the patients with TP53 alterations identified by either method, and it failed to identify any additional patients with p53 abnormalities. In summary, chronic lymphocytic leukemia patients with TP53 alterations frequently show atypical morphologic features. Use of multiple modalities to identify p53 abnormalities is recommended to ensure optimal sensitivity and specificity.

Clinical Utility of Fluorescence In Situ Hybridization (FISH) for Deletion of Chromosome 3p in the Work-up of Renal Masses.

Chromosome 3p deletion is a well-established genetic aberration in clear cell renal cell carcinoma (RCC). We aimed to evaluate the clinical utility of 3p fluorescence in situ hybridization (FISH) on formalin-fixed paraffin-embedded tissue in surgical pathology specimens. 3p:3q <0.8 was established as the cut-off for 3p loss. The 2015 Medicare allowable billing rates were used to estimate the cost. Over 2.5 years (2013 to 2015), 3p FISH was performed on 18 cases per year. Among tested cases, 70% (30/43) were nephrectomies and 30% (14/43) metastases. 3p loss was detected in 44% (19/43) of cases, with a higher rate of loss in radical compared with partial nephrectomies (71% vs. 15%; P=0.003). A definitive RCC subtype was assigned in 65% (28/43) of cases. More partial nephrectomies had a definitive subtype assigned, compared with radical nephrectomies (92% vs. 59%; P=0.04), possibly related to more high-grade, high-stage tumors in submitted radical nephrectomies. Tested nephrectomies were most commonly diagnosed as clear cell (41%) or clear cell papillary RCC (32%). Half of unclassifiable RCCs had 3p loss (53%, 8/15). Annual 3p FISH costs were $3446.64, with 79% of costs from ancillary studies attributable to immunostains. 3p FISH was performed infrequently in nephrectomy specimens and was not cost prohibitive. RCC cases that are unclassifiable by morphology and other ancillary tests, but which have 3p FISH deletion may merit a comment in the pathology report, raising the possibility of clear cell RCC, as the oncologic approach may be altered despite the lack of a definitive RCC subtype.

Efficacy of venetoclax in relapsed chronic lymphocytic leukemia is influenced by disease and response variables

AbstractTo define the efficacy of venetoclax with extended follow-up and identify clinical or biological treatment effect modifiers, updated data for previously treated patients with chronic lymphocytic leukemia (CLL) or small lymphocytic lymphoma (SLL) enrolled in 4 early-phase trials were pooled. Rates of response, complete remission (CR/CRi), and undetectable minimal residual disease (U-MRD) were analyzed for all patients (n = 436) and for those patients who were planned to receive 400 mg/day monotherapy (n = 347). Univariate and multiple regression analyses were performed to identify the pretreatment factors associated with response rates and duration of response (DoR). Objective responses were documented in 75% of all patients, including 22% CR/CRi. Overall, 27% and 16% of the patients achieved U-MRD in blood and marrow, respectively. Estimated median progression-free survival (PFS), DoR, and time to progression were 30.2, 38.4, and 36.9 months, respectively. Similar efficacy outcomes were observed within the 400 mg/day monotherapy subset. For those who achieved CR/CRi, the 3-year PFS estimate was 83%. DoR was superior for patients achieving CR/CRi or U-MRD in landmark analyses. In multiple regression analyses, bulky lymphadenopathy (≥5 cm) and refractoriness to B-cell receptor inhibitor (BCRi) therapy were significantly associated with lower CR rate and shorter DoR. Fewer prior therapies were associated with higher CR rate, but not DoR. Chromosome 17p deletion and/or TP53 mutation and NOTCH1 mutation were consistently associated with shorter DoR, but not probability of response. Thus, both pretreatment factors and depth of response correlated with DoR with venetoclax. Patients without bulky lymphadenopathy, BCRi-refractory CLL, or an adverse mutation profile had the most durable benefit.