Loss Of Tumor Suppressor Genes Research Articles

Sarcomatoid (srcRCC) versus clear cell (ccRCC) renal cell carcinoma: A comparative comprehensive genomic profiling (CGP) study.

349 Background: srcRCC is a well-described histologic entity often featuring rapid progression and aggressive clinical course when compared with classic ccRCC. We queried whether CGP would uncover opportunities for targeted and immunotherapy (IO) for srcRCC patients that could individualize their treatment and entry into clinical trials. Methods: Using a hybrid capture-based CGP assay to evaluate all classes of genomic alterations (GA), 160 cases of srcRCC and 1,664 cases of ccRCC were sequenced from FFPE tissue samples. Tumor mutational burden (TMB) was determined on up to 1.1 Mbp of sequenced DNA and microsatellite instability (MSI) was determined on up to 114 loci. PD-L1 expression was determined by IHC (Dako 22C3) with low tumor cell positive staining set at 1-49% and high staining >50% expression. Results: Gender and age distributions for both tumor types were similar. srcRCC featured significantly higher GA/tumor than ccRCC (P < .0001). CGP revealed major differences with ccRCC associated more frequently with tumor suppressor gene (TSG) losses in VHL, PBRM1, TSC2 and SETD2 (all P < .0001). In contrast, srcRCC is associated with cell proliferation with increased inactivation of cell cycle regulatory genes including TP53, CDKN2A/B, MDM2 and TERT (all P < .0001). RB1 GA in srcRCC may reflect neuroendocrine differentiation occasionally found in these tumors. NF2 GA were more frequent in srcRCC (P < .0001). Conclusions: CGP reveals striking differences between srcRCC and ccRCC which may in part explain the differing histologic appearances and typical clinical course of these 2 aggressive malignancies. ccRCC is driven more by TSG loss and srcRCC is driven more by cell cycle dysregulation. Targeted therapy opportunities were uncommon for both tumor types although each featured biomarkers potentially predictive of mTOR inhibitor responses ( TSC2 in ccRCC and NF2 in srcRCC). Although the higher PBRM1 GA frequency in ccRCC may explain the IO benefit well-known for this tumor type, the srcRCC group features significantly increased TMB, CD274 amplification and PD-L1 staining which may also create IO opportunities for srcRCC patients. [Table: see text]

Overall survival of patients with metastatic castrate-resistant prostate cancer (mCRPC) who have PTEN tumor suppressor gene loss of function.

58 Background: It is estimated that more than 40% of patients with mCRPC have functional loss of phosphatase and tensin homolog (PTEN) tumor suppressor gene, which is associated with unfavorable prognosis and reduced response to androgen receptor-targeting therapy. We describe patient characteristics and survival outcomes by PTEN LOF status among patients with mCRPC in real-world clinical practice. Methods: We conducted a retrospective cohort study using data from the nationwide Flatiron Health-Foundation Medicine mCRPC Clinico-Genomic database (FH-FMI CGDB), a de-identified database linking data derived from electronic health records with genomic data derived from FMI comprehensive genomic profiling (CGP) tests. The study included patients ≥18 years old, with a primary diagnosis of mCRPC between 1/1/2013 and 6/30/2019 who underwent FMI CGP testing and who had a valid PTEN LOF status. Patients were included if their PTEN report date and mCRPC diagnosis date occurred before death or censoring. PTEN LOF status was identified via FMI’s CGP testing. Kaplan-Meier (KM) methods assessed overall survival (OS) by PTEN LOF status from the date of mCRPC diagnosis (later of metastasis and castration resistance) until death or end of study follow-up. A stratified Cox regression model was used to estimate the hazard of death. The Cox model was adjusted for age, race and sequence of metastasis/CRPC diagnoses, and was stratified by the year of mCRPC diagnosis. Adjustments to account for left-truncation and survivorship bias were made in the KM analysis and the Cox regression model. Results: Among the 458 patients who met the eligibility criteria, 174 (38%) had PTEN LOF. The majority of the study sample (76%) was diagnosed with castration-resistance after metastasis. The PTEN LOF group had a higher percentage of white patients (80% vs. 68%; p= 0.01) compared to the PTEN non-LOF group. The mean age of the study sample was 68 years, and there was no difference in mean age at diagnosis by PTEN LOF status ( p= 0.17). Based on the KM estimates adjusted for left-truncation, the median OS was 14.3 months (95% confidence interval [CI]: 11.1-19.7) in the PTEN LOF group compared to 18.3 months (95%CI: 15.5-21.5) in the PTEN non-LOF group (log-rank p= 0.049). In the multivariable Cox model, the PTEN LOF group had numerically 30% higher risk of death compared to the PTEN non-LOF group (hazard ratio = 1.30; 95% CI: 0.99-1.71; p= 0.057). Conclusions: Among real-world patients with mCRPC in the CGDB, PTEN LOF could be associated with poorer survival outcomes, potentially highlighting the unmet need among these patients. Additional studies with larger cohorts are needed to better evaluate the survival outcomes of patients with PTEN LOF. Therapeutic agents acting on the PTEN/PI3K/AKT/mTOR pathway are being tested in clinical trials, and could potentially improve outcomes in this subgroup of patients with mCRPC.

T-ALL can evolve to oncogene independence.

The majority of cases of T-cell acute lymphoblastic leukemia (T-ALL) contain chromosomal abnormalities that drive overexpression of oncogenic transcription factors. However, whether these initiating oncogenes are required for leukemia maintenance is poorly understood. To address this, we developed a tetracycline-regulated mouse model of T-ALL driven by the oncogenic transcription factor Lmo2. This revealed that whilst thymus-resident pre-Leukemic Stem Cells (pre-LSCs) required continuous Lmo2 expression, the majority of leukemias relapsed despite Lmo2 withdrawal. Relapse was associated with a mature phenotype and frequent mutation or loss of tumor suppressor genes including Ikzf1 (Ikaros), with targeted deletion Ikzf1 being sufficient to transform Lmo2-dependent leukemias to Lmo2-independence. Moreover, we found that the related transcription factor TAL1 was dispensable in several human T-ALL cell lines that contain SIL-TAL1 chromosomal deletions driving its overexpression, indicating that evolution to oncogene independence can also occur in human T-ALL. Together these results indicate an evolution of oncogene addiction in murine and human T-ALL and show that loss of Ikaros is a mechanism that can promote self-renewal of T-ALL lymphoblasts in the absence of an initiating oncogenic transcription factor.

Mutations that collaborate with IL-7Ra signaling pathways to drive ALL.

The IL-7 pathway is required for normal T cell development and survival. In recent years the pathway has been shown to be a major driver of acute lymphoblastic leukemia (ALL), the most common cancer in children. Gain-of-function mutations in the alpha chain of the IL-7 receptor found in ALL patients clearly demonstrated that this pathway was a driver. However mutant IL-7R alone was insufficient to transform primary T cell progenitors, indicating that cooperating mutations were required. Here we review evidence for additional oncogenic mutations in the IL-7 pathway. We discuss several oncogenes, loss of tumor suppressor genes and epigenetic effects that can cooperate with mutant IL-7 receptor. These include NRas, HOXA, TLX3, Notch 1, Arf, PHF6, WT1, PRC, PTPN2 and CK2. As new therapeutics targeting the IL-7 pathway are developed, combination with agents directed to cooperating pathways offer hope for novel therapies for ALL.

Mitochondrial metabolism-mediated redox regulation in cancer progression

Cancer cells display abnormal metabolic activity as a result of activated oncogenes and loss of tumor suppressor genes. The Warburg Effect is a common metabolic feature of cancer that involves a preference for aerobic glycolysis over oxidative phosphorylation to generate ATP and building blocks for biosynthesis. However, emerging evidence indicates that mitochondrial metabolic pathways are also reprogrammed in cancer and play vital roles in bioenergetics, biosynthesis, and managing redox homeostasis. The mitochondria act a central hub for metabolic pathways that generate ATP and building blocks for lipid, nucleic acid and protein biosynthesis. However, mitochondrial respiration is also a leading source of reactive oxygen species that can damage cellular organelles and trigger cell death if levels become too high. In general, cancer cells are reported to have higher levels of reactive oxygen species than their non-cancerous cells of origin, and therefore must employ diverse metabolic strategies to prevent oxidative stress. However, mounting evidence indicates that the metabolic profiles between proliferative and disseminated cancer cells are not the same. In this review, we will examine mitochondrial metabolic pathways, such as glutaminolysis, that proliferative and disseminated cancer cells utilize to control their redox status.

Synthetic Lethal Interaction between the ESCRT Paralog Enzymes VPS4A and VPS4B in Cancers Harboring Loss of Chromosome 18q or 16q

SUMMARYFew therapies target the loss of tumor suppressor genes in cancer. We examine CRISPR-SpCas9 and RNA-interference loss-of-function screens to identify new therapeutic targets associated with genomic loss of tumor suppressor genes. The endosomal sorting complexes required for transport (ESCRT) ATPases VPS4A and VPS4B score as strong synthetic lethal dependencies. VPS4A is essential in cancers harboring loss of VPS4B adjacent to SMAD4 on chromosome 18q and VPS4B is required in tumors with co-deletion of VPS4A and CDH1 (E-cadherin) on chromosome 16q. We demonstrate that more than 30% of cancers selectively require VPS4A or VPS4B. VPS4A suppression in VPS4B-deficient cells selectively leads to ESCRT-III filament accumulation, cytokinesis defects, nuclear deformation, G2/M arrest, apoptosis, and potent tumor regression. CRISPR-SpCas9 screening and integrative genomic analysis reveal other ESCRT members, regulators of abscission, and interferon signaling as modifiers of VPS4A dependency. We describe a compendium of synthetic lethal vulnerabilities and nominate VPS4A and VPS4B as high-priority therapeutic targets for cancers with 18q or 16q loss.

Abstract PO-011: Synthetic lethal interaction between the ESCRT paralog enzymes VPS4A and VPS4B in SMAD4 or CDH1-deleted cancers

Abstract Somatic copy number alterations that result in loss of tumor suppressor gene function are important drivers of tumorigenesis. However, few existing therapeutic options to target oncogenic processes evoked by tumor suppressor gene inactivation exist. The discovery of synthetic lethal interactions with genetic drivers of cancer may yield new therapeutic strategies with cancer selective potential. We examined genome-scale CRISPR-SpCas9 and RNA interference screens to uncover new synthetic lethal vulnerabilities associated with the loss of common tumor suppressor genes (TSGs). The ATPases Vacuolar protein sorting 4 homolog A (VPS4A) and B (VPS4B) scored as strong synthetic lethal dependencies, with VPS4A selectively essential in cancers harboring loss of VPS4B adjacent to SMAD4 and VPS4B required in tumors with co-deletion of VPS4A and CDH1 (encoding E-cadherin). VPS4B resides 12.3 Mb away from the SMAD4 TSG on chromosome 18q and is lost in approximately 33% of all cancers, suggesting broad clinical applicability. Moreover, VPS4B is commonly lost in pancreatic cancer due to the frequent loss of SMAD4, highlighting VPS4A represents a promising target for this deadly cancer. VPS4A and VPS4B function as AAA ATPases forming a multimeric protein complex within the endosomal sorting complex required for transport (ESCRT) pathway to regulate membrane remodeling in a range of cellular processes. VPS4A suppression in cells with VPS4B/SMAD4 loss led to accumulation of ESCRT-III filaments, cytokinesis defects, nuclear deformation and micronucleation, which ultimately resulted in G2/M cell cycle arrest and apoptosis. Furthermore, upon VPS4A suppression, we observed potent in vivo tumor regression, which led to extended survival, in mouse subcutaneous xenograft models utilizing a pancreatic or rhabdomyosarcoma cancer cell line harboring VPS4B loss. CRISPR-SpCas9 screening and integrative genomic analysis revealed other ESCRT members, regulators of abscission and interferon signaling as modifiers of VPS4A dependency. Using the most comprehensive available CRISPR-SpCas9 and RNA-interference screening datasets to date, we provide a compendium of synthetic lethal vulnerabilities with TSG loss and credential VPS4A as a new and promising therapeutic target in cancers with VPS4B/SMAD4 deletion. Citation Format: Jasper E. Neggers, Brenton R. Paolella, Adhana Asfaw, Michael V. Rothberg, Thomas A. Skipper, Radha L. Kalekar, Michael J. Krill-Burger, Neekesh V. Dharia, Guillaume Kugener, Adam D. Durbin, Annan Yang, Nancy Dumont, Yvonne Y. Li, Brian M. Wolpin, Federica Piccioni, David E. Root, Jesse S. Boehm, Andrew D. Cherniack, Aviad Tsherniak, Andrew L. Hong, William C. Hahn, Kimberly Stegmaier, Todd R. Golub, Francisca Vazquez, Andrew J. Aguirre. Synthetic lethal interaction between the ESCRT paralog enzymes VPS4A and VPS4B in SMAD4 or CDH1-deleted cancers [abstract]. In: Proceedings of the AACR Virtual Special Conference on Pancreatic Cancer; 2020 Sep 29-30. Philadelphia (PA): AACR; Cancer Res 2020;80(22 Suppl):Abstract nr PO-011.

Curcumin against Prostate Cancer: Current Evidence.

Cancer is a condition characterized by remarkably enhanced rates of cell proliferation paired with evasion of cell death. These deregulated cellular processes take place following genetic mutations leading to the activation of oncogenes, the loss of tumor suppressor genes, and the disruption of key signaling pathways that control and promote homeostasis. Plant extracts and plant-derived compounds have historically been utilized as medicinal remedies in different cultures due to their anti-inflammatory, antioxidant, and antimicrobial properties. Many chemotherapeutic agents used in the treatment of cancer are derived from plants, and the scientific interest in discovering plant-derived chemicals with anticancer potential continues today. Curcumin, a turmeric-derived polyphenol, has been reported to possess antiproliferative and proapoptotic properties. In the present review, we summarize all the in vitro and in vivo studies examining the effects of curcumin in prostate cancer.

Modeling tumors of the peripheral nervous system associated with Neurofibromatosis type 1: Reprogramming plexiform neurofibroma cells.

Plexiform neurofibromas (pNFs) are benign tumors of the peripheral nervous system (PNS) that can progress towards a deadly soft tissue sarcoma termed malignant peripheral nerve sheath tumor (MPNST). pNFs appear during development in the context of the genetic disease Neurofibromatosis type 1 (NF1) due to the complete loss of the NF1 tumor suppressor gene in a cell of the neural crest (NC) - Schwann cell (SC) axis of differentiation. NF1(-/-) cells from pNFs can be reprogrammed into induced pluripotent stem cells (iPSCs) that exhibit an increased proliferation rate and maintain full iPSC properties. Efficient protocols for iPSC differentiation towards NC and SC exist and thus NC cells can be efficiently obtained from NF1(-/-) iPSCs and further differentiated towards SCs. In this review, we will focus on the iPSC modeling of pNFs, including the reprogramming of primary pNF-derived cells, the properties of pNF-derived iPSCs, the capacity to differentiate towards the NC-SC lineage, and how well iPSC-derived NF1(-/-) SC spheroids recapitulate pNF-derived primary SCs. The potential uses of NF1(-/-) iPSCs in pNF modeling and a future outlook are discussed.

4 Oral - Synthetic lethal interaction between the ESCRT paralog enzymes VPS4A and VPS4B in cancers with chromosome 18q or 16q deletion

Somatic copy number alterations constitute distinctive driver events of tumorigenesis. Hence, the identification of pharmacologically tractable targets related to somatic copy number alterations represents an opportunity for drug discovery to achieve cancer-selective therapeutics. Here, we examined genome-scale CRISPR-SpCas9 and RNA-interference loss-of-function screens to identify new cancer therapeutic targets associated with genomic loss of common tumor suppressor genes. The ESCRT ATPases VPS4A and VPS4B scored as strong synthetic lethal dependencies, with VPS4A selectively essential in cancers harboring loss of VPS4B adjacent to SMAD4 on chromosome 18q and VPS4B required in tumors with co-deletion of VPS4A and CDH1 (encoding E-cadherin) on chromosome 16q.

Oncogenic Gene-Expression Programs in Leiomyosarcoma and Characterization of Conventional, Inflammatory, and Uterogenic Subtypes.

Leiomyosarcoma (LMS) is a mesenchymal neoplasm with complex copy-number alterations and characteristic loss of tumor suppressor genes without known recurrent activating mutations. Clinical management of advanced LMS relies on chemotherapy and complementary palliative approaches, and research efforts to date have had limited success identifying clinically actionable biomarkers or targeted therapeutic vulnerabilities. To explore the biological underpinning of LMS, we evaluated gene-expression patterns of this disease in comparison with diverse sarcomas, nonmesenchymal neoplasms, and normal myogenic tissues. We identified a recurrent gene-expression program in LMS, with evidence of oncogenic evolution of an underlying smooth-muscle lineage-derived program characterized by activation of E2F1 and downstream effectors. Recurrently amplified or highly expressed genes in LMS were identified, including IGF1R and genes involved in retinoid signaling pathways. Though the majority of expressed transcripts were conserved across LMS samples, three separate subtypes were identified that were enriched for muscle-associated transcripts (conventional LMS), immune markers (inflammatory LMS), or a uterine-like gene-expression program (uterogenic LMS). Each of these subtypes expresses a unique subset of genes that may be useful in the management of LMS: IGF1R was enriched in conventional LMS, worse disease-specific survival was observed in inflammatory LMS, and prolactin was elaborated by uterogenic LMS. These results extend our understanding of LMS biology and identify several strategies and challenges for further translational investigation. IMPLICATIONS: LMS has a recurrent oncogenic transcriptional program and consists of molecular subtypes with biological and possible clinical implications.

Abstract LB-053: VPS4A is a synthetic lethal target in VPS4B-deficient cancers due to co-deletion with SMAD4

Abstract Somatic copy number alterations that result in loss of tumor suppressor gene function are important drivers of tumorigenesis. However, few existing therapeutic options to target oncogenic processes evoked by tumor suppressor gene inactivation exist. The discovery of synthetic lethal interactions with genetic drivers of cancer may yield new therapeutic strategies with cancer selective potential. We examined genome-scale CRISPR-SpCas9 and RNA interference screens to uncover new synthetic lethal vulnerabilities associated with the loss of common tumor suppressor genes (TSGs). Vacuolar protein sorting 4 homolog A (VPS4A) scored as a strong, selective dependency in cancer cells with genomic loss of the SMAD4 tumor suppressor due to co-deletion of VPS4A's paralog gene, VPS4B. VPS4B resides 12.3 Mb away from the SMAD4 TSG on chromosome 18q and is lost in approximately 33% of all cancers, suggesting broad clinical applicability. VPS4A and VPS4B function as AAA ATPases forming a multimeric protein complex within the endosomal sorting complex required for transport (ESCRT) pathway to regulate membrane remodeling in a range of cellular processes. VPS4A suppression in cells with VPS4B/SMAD4 loss led to accumulation of ESCRT-III filaments, cytokinesis defects, nuclear deformation and micronucleation, which ultimately resulted in G2/M cell cycle arrest and apoptosis. Furthermore, upon VPS4A suppression, we observerd potent in vivo tumor regression, which led to extended survival, in mouse subcutaneous xenograft models with human cancer cell lines harboring VPS4B loss. Finally, genome-scale CRISPR-SpCas9 loss-of-function screening revealed other ESCRT pathway members and regulators of cellular abscission as modifiers of VPS4A dependency. Using the most comprehensive available CRISPR-SpCas9 and RNA-interference screening datasets to date, we provide a compendium of synthetic lethal vulnerabilities with TSG loss and credential VPS4A as a new and promising therapeutic target in cancers with VPS4B/SMAD4 deletion. Citation Format: Jasper E. Neggers, Brenton R. Paolella, Adhana Asfaw, Michael V. Rothberg, Thomas A. Skipper, Radha L. Kalekar, John M. Krill-Burger, Andrew L. Hong, Guillaume Kugener, Jeremie Kalfon, Annan Yang, Chen Yuan, Nancy Dumont, Alfredo Gonzalez, Mai Abdusamad, Yvonne Y. Li, Liam F. Spurr, Westley W. Wu, Federica Piccioni, Brian M. Wolpin, David E. Root, Jesse S. Boehm, Andrew D. Cherniack, Aviad Tsherniak, Todd R. Golub, Francisca Vazquez, Andrew J. Aguirre. VPS4A is a synthetic lethal target in VPS4B-deficient cancers due to co-deletion with SMAD4 [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 LB-053.

Abstract 5861: BOP1 expression contributes to the proliferative/invasive phenotype in melanoma

Abstract We recently performed whole exome sequencing of 30 melanocytic nevi which surprisingly revealed numerous regions of copy number loss. It was found that common reticular nevi (mostly with a junctional component) have a high incidence of copy number aberrations (CNA). Importantly, concurrent with the loss of tumor suppressor genes (e.g. CDKN2A, TP53, and NF1) was the loss of potent oncogenes (e.g. NRAS, MITF, and MDM2). We postulated that the balanced nature of these CNAs confers protection from transformation, thus keeping the lesion in the benign state. Along with copy-number loss of these well-known genes, further interrogation of these data revealed a loss on chr8q24.3 which was frequently observed in 7/30 (23%) nevi. In the smallest region of overlap, the block of proliferation 1 (BOP1) gene was identified as a candidate for functional validation. BOP1 is part of the trimeric “PeBoW” complex, essential for ribosome biogenesis and cell cycle progression. In melanoma cell lines (MM96L, HT144, and MM253), we used siRNA mediated gene targeting to achieve differing BOP1 expression levels (high, low, absent), which resulted in altered cell states. For example, high BOP1 expression caused an increase in proliferation and colony formation, whereas low BOP1 expression conferred reduced proliferation, colony formation, and a senescent like phenotype. Interestingly, low BOP1 expression also resulted in increased migration and invasive capacity. BOP1 immunofluorescence assessment of benign nevi revealed limited expression whereas in early invasive melanomas, BOP1 expression was clearly evident in proliferative melanoma nests. These data support the role of BOP1 playing a role in melanoma progression by contributing to phenotype switching. Citation Format: Mitchell S. Stark, Sabrina Hammerlindl, Lisa Tom, Kasturee Jagirdar, Jean-Marie Tan, Helmut Schaider, Richard A. Sturm, Blake O'Brien, Michael Walsh, Angus Collins, H.Peter Soyer. BOP1 expression contributes to the proliferative/invasive phenotype in melanoma [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 5861.

Abstract 6007: Post-fasting refeeding enhances intestinal stem cell-mediated regeneration and tumorigenesis

Abstract Although short-term fasting interventions improve intestinal stem cell (ISC) function, little is known about how much of this benefit comes from fasting versus the post-fasting refeeding response. Given the central role that ISCs play in driving injury-induced repair and in initiating early intestinal tumors, it is possible that fasting by boosting ISC function not only improves regeneration but also unexpectedly elevates intestinal tumorigenesis. To understand how fasting/refeeding interventions influence the role of ISCs in regeneration and early tumor formation, we assessed the function of ISCs to repair the intestinal lining after injury and to contribute to intestinal tumors. Notably, we find that 24 hours post-fasting refeeding boosts intestinal stem and progenitor cells proliferation and increases ISC function in organoid and in fate mapping assays compared to AL and fasted cohorts. Mechanistically, elevated mammalian target of rapamycin (mTOR) activity mediates the effects of refeeding in ISCs as treatment with mTOR inhibitor blocks these effects. Surprisingly, loss of the APC tumor suppressor gene in ISCs increased intestinal tumor numbers in the refed state compared to the AL and fasted states in an mTOR dependent manner. We propose that refeeding through mTOR signaling stimulates ISC function and in a context-dependent manner this can either improve repair after injury or promote intestinal tumorigenesis. Citation Format: Shinya Imada. Post-fasting refeeding enhances intestinal stem cell-mediated regeneration and tumorigenesis [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 6007.

Nutritional Indexes as Predictors of Survival and Their Genomic Implications in Gastric Cancer Patients

Gastric cancer is an aggressive malignancy with poor prognosis. Although obesity is a risk factor, an association between overweight and better survival has been reported. We explored the genomic implications of such association. Data from 940 patients were analyzed using Cox regression models and ROC curves to assess body mass index (BMI) and prognostic nutritional index (PNI) as predictors of survival. The exome sequencing of a random subset was analyzed to determine copy number variation (CNV) and single nucleotide variation (SNV), using Kruskal-Wallis and chi-square tests to evaluate their clinical implications. Overall survival was lower in patients with BMI ≤ 24.9 and PNI ≤ 29 (p < 0.001). BMI and survival were directly correlated (HR: 0.972, 95% CI: 0.953, 0.992; p-value < 0.007). A higher PNI correlated with improved survival (HR: 0.586, 95% CI: 0.429, 0.801; p-value <0.001). We found a PNI cutoff point of 41.00 for overall survival. Genomic analysis showed an association between lower BMI, less CNV events (p-value = 0.040) and loss of tumor suppressor genes (p-value = 0.021). BMI and PNI are independent factors for overall survival in gastric cancer, probably linked to variations in genomic intratumoral alterations.

Sequential ctDNA whole-exome sequencing in advanced lung adenocarcinoma with initial durable tumor response on immune checkpoint inhibitor and late progression.

BackgroundDespite prolonged tumor response to immune checkpoint inhibitors (ICIs) for a subset of patients with advanced non-small cell lung cancer (NSCLC), a secondary resistance will occur for a majority of these patients. The understanding of late progression mechanisms with ICIs is important to improve future treatment strategies.MethodsWe performed whole-exome sequencing (WES) on circulating tumor DNA and compared molecular profiles between the beginning of ICI treatment and tumor progression in patients with advanced NSCLC treated with ICIs and who had initial and prolonged tumor response with secondary progression, after at least 6 months of treatment.ResultsWe identified eight patients who experienced initial and durable tumor response, and secondary tumor progression after 6 months of treatment, with available paired blood samples (diagnosis and progression). All had lung adenocarcinoma, three had programmed-death ligand-1 expression ≥50% in immunohistochemistry and all presented low blood tumor mutational burden (bTMB). Seven patients received nivolumab in second-line or more, and one received pembrolizumab as first-line treatment. WES at progression showed clonal selection with molecular alterations of Wnt pathway-related genes, increase of copy number aberrations in cancer-related genes and loss of tumor-suppressor genes (such as PTEN) or of genes associated with immune response (such as B2M). No difference in term of bTMB was observed at progression.ConclusionsThis is the first study describing putative molecular mechanisms associated with late progression under ICI in lung cancer. Studies on treatment strategies adapted to these mechanisms are needed.

Abstract A20: Persistent high-risk HPV infection in the development of uterine cervical cancer

Abstract The early detection and treatment of preneoplastic uterine cervical lesions is certainly a major challenge for developing countries. Preneoplastic lesions result from human papilloma virus (HPV) infection in cells located in the transformation zone of the cervical epithelial tissue, causing low-grade or high-grade lesions. HPV infections are transient and most of the time cleared within a couple of years following exposure. However, 10–20% of infections persist latently, leading to disease progression and, ultimately, various forms of invasive cancer. The transformation of preneoplastic lesions in invasive cancer cells is provoked at least partly by HPV, especially through gene and protein expression modulation. This modulation involves tissue oxygenation, oncogene activation, loss of tumor suppressor genes and aberrant molecular signaling pathways (such as Insulin-like growth factor-1 receptor (IGF-1R). In recent studies, it was reported that IGF1R is overexpressed by effect of E6 AA-a and E-G350 HPV-16 variants. The aim of the present study was to prospectively and retrospectively report the detection of HPV-16 variants and IGF1R expression in patients with cervical cancer and assess the relationship with development of uterine cervical cancer. Sixty consecutive patients with invasive cervical cancer were assessed for HPV-16. A total of 35 patients (58.3%) were infected with HPV-16, with a mean age of 51 years (range: 30–76 years). Thirty patients (85.7%) were diagnosed with European HPV-16 variant and five patients (14.3%) were diagnosed with non-European HPV-16 variants. European HPV-16 variants (E-HPV-16) were mainly E-G350 (n = 14; 41.1%) and E-T350 (n = 12; 35.2%) subclasses. Of these 35 patients, 15 received exclusive radiotherapy and four radiochemotherapy, and the remaining 16 did not complete the treatment (NCT). Of the patients who presented an incomplete response, overexpression of IGF1R was detected in all. Of patients NCT, we retrospectively studied one case in IIIB stage FIGO. Samples of preneoplastic lesions and invasive cervical cancer were analyzed to confirm histopathologic diagnosis and detect the presence of HPV variants and overexpression of IGF-1R. Of the results found in this case, in which the patient was diagnosed in 1986 with a high-grade squamous intraepithelial cervical lesion, HPV-16 E-G350 and HPV-33 coinfection as low expression of IGF1R were detected and for the invasive cancer diagnosed in 2002, the presence of HPV-16 AA-c and overexpression of IGF1R was detected. The detection of high-risk HPV in samples of preneoplastic lesions and invasive cancer in a 60-year-old patient at the time of diagnosis showed that HPV33 infection was eliminated. Results such as these suggest that persistent infection with HPV-16 variants, overexpression of IGF1R, such as viral load and age, could be necessary factors for disease progression, and thus contribute to the identification of patients with a high risk of viral persistence and development of cervical neoplasia. Note: This abstract was not presented at the conference. Citation Format: Pablo Moreno Acosta, Diana Mayorga, Nicolas Magné. Persistent high-risk HPV infection in the development of uterine cervical cancer [abstract]. In: Proceedings of the AACR Special Conference on the Microbiome, Viruses, and Cancer; 2020 Feb 21-24; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2020;80(8 Suppl):Abstract nr A20.

Abstract P4-10-24: Cyclin E overexpression is associated with high risk 70 gene signature, and may indicate intrinsic resistance to CDK4/6 inhibitors

Abstract Background: The use of CDK4/6 inhibitors (CDK4/6i) is a promising therapeutic strategy for recurrent ER+, HER2- breast cancers that have escaped previous treatment targeting the endocrine pathway. A number of adjuvant and neoadjuvant trials with CDK4/6i in early breast cancer are also underway. However, no clear predictive biomarkers for resistance are available other than loss of the RB1 tumor suppressor gene. Cyclin E genes (CCNE1, CCNE2) play a critical role in cell cycle control with approximately 25% of breast cancer overexpressing CCNE2, and there is a significant correlation between CCNE2 and CCNE1 expression1,2,3. Furthermore, a positive correlation between expression of CCNE1 and resistance to CDK4/6i (i.e. palbociclib)4,5,6 has been reported in vitro and in a gene expression analysis from the PALOMA-3 trial. The 70-gene MammaPrint® (MP) signature is a prognostic assay that stratifies early-stage breast cancer (ESBC) patients into Low and High-risk of distant relapse. One of the 70 genes is CCNE2, shown to be associated with resistance to both endocrine therapy and CDK4 inhibition7. Considering the potential role of the Cyclin E genes as biomarker of resistance for CDK4/6i, we assessed the expression of CCNE2 in a large series of ESBCs with respect to their MP risk profile. Methods: The mRNA expression of CCNE2 (and CCNE1) was measured in a series of 5022 breast cancer samples for which FFPE microarray full-transcriptome data were available for testing. Intensities were Lowess normalized and log2 transformed. The 80-gene BluePrint (BP) profile8 was used in combination with MP to stratify patient samples based on their molecular subtype: Luminal A- (MP Low Risk, BP Luminal), Luminal B- (MP High Risk, BP Luminal), HER2- and Basal-type. Wilcoxon rank sum test was used to examine expression differences. Results: CCNE2 is significantly higher expressed in MP High risk compared to MP Low risk tumors when all samples are included (p &amp;lt;0.0001). When looking at the clinically ER positive BP Luminal group, CCNE2 is significantly higher expressed in the Luminal B compared to the Luminal A tumors (p &amp;lt;0.0001). However, we observe a broad distribution of CCNE2 expression within the Luminal group, indicating a biological diversity in both Luminal A and B tumors, which CCNE2 may help to further define. Specifically, Luminal B tumors have a range of CCNE2 expression with the highest levels being in the highest MP risk interval (Ultra High). Of importance, CCNE1 showed similar expression patterns as CCNE2. Conclusions: Our preliminary results show that MP could help in stratifying BP Luminal-type B tumors in subgroups with differential CCNE2 expression. Since increased CCNE1 expression is correlated with CDK4/6i resistance, and CCNE2 is a functionally-related gene whose expression correlates to some extent with CCNE1, it is reasonable to speculate that high CCNE2 expression and MP High Risk Luminal B may also correlate with CDK4/6i resistance, a testable hypothesis. This warrants additional analyses that integrate treatment response data to support and further investigate these observations. Our exploratory analysis also highlights the added value of a multi-gene signature profile versus single-gene testing as tool for patient stratification and treatment recommendation. Refernces: 1. Asghar U et al Nat Rev Drug Discov. 2015 2. Caldon C et al Cell Div. 2010 3. Payton M et al Oncogene. 2002 4. Turner N et al. J Clin Oncol. 2019 5. Chandarlapaty S et al J Clin Oncol. 2019 6. Guarducci C et al NPJ Br Cancer. 2018 7. Caldon CE et al Mol Cancer Ther. 2012 8. Krijgsman O et al BRCT 2012 Citation Format: Lorenza Mittempergher, Joe McKelley, Rajith Bhaskaran, Sahra Uygun, René Bernards, Laura J van 't Veer, Annuska M Glas, William Audeh. Cyclin E overexpression is associated with high risk 70 gene signature, and may indicate intrinsic resistance to CDK4/6 inhibitors [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 P4-10-24.

The study on copy number alteration of clear cell renal cancer in Chinese population.

Objectives: Copy number alteration (CNA) is one of the important genetic variations. Although there are many studies on renal cancer CNA, few studies are based on the Chinese population. In our study, our objective is to acquire the whole-genome CNA landscape in Chinese population and explore the tumor risk-associated functional genes in the CNA regions, by detecting whole-genome in the clear cell renal cancer (ccRCC) tissues.Methods: We enrolled 35 formalin fixed paraffin embedded samples, which were processed by Oncoscan assay, and then acquired the data of whole-genome CNA. Then genes annotation and enrichment analyzing were processed. Furthermore, the gene burden and the affected bp (base pair) per Mbp (million bp) regions in whole-genome were analyzed by comparison of different T stage affected by CNA.Results: We acquired the whole-genome CNA landscape by Oncoscan detection, and found out the high-frequency CNA regions which were not reported in previous studies, for example, 11P11, 22q11.23, 20q11.3 (PDRG1), and Xp22.33 so on. During the analyzing of genes annotation and enrichment, we found out some ccRCC functional genes in the CNA regions which might play a role in the biological process, for example, the copy number loss of DNA repair genes (TTC5、PARP2, etc.) and tumor suppressor genes (TADA3, VHL, BAP1, ERC2-IT1, etc.), the copy number gain of oncogenes (ABL2, MET, HUWE1, etc.) and Notch signal pathway genes (MDK, etc.). Besides, gene fusion (GSTTP and GSTTP2) was noticed at 22q11.23 which copy number loss occurred, and the frequency is 46%. And between the different T stage patients affected by CNA, the T2+T3 group carried more high-frequency CNA regions (P-value was 0.012).Conclusions: In this study, the whole-genome ccRCC CNA landscape in Chinese population was acquired, a few functional genes and fusion genes were found out. However, a larger scale of samples is still needed to validate our results.

Biomarker-guided targeted and immunotherapies in malignant pleural mesothelioma.

Malignant pleural mesothelioma (MPM) is a lethal thoracic malignancy whose incidence is still increasing worldwide. MPM is characterized by frequent inactivation of tumor-suppressor genes (TSGs), e.g., the homozygous deletion of CDKN2A/2B and various genetic alterations that inactivate BAP1, NF2, LATS1/2, and TP53. The leading cause for the poor prognosis of patients with MPM is the lack of effective treatment options, with conventional chemotherapy being the standard of care in the clinic, which has remained unchanged for almost 20 years. Precision oncology, a burgeoning effort to provide precise cancer treatment tailored to unique molecular changes in individual patients, has made tremendous progress in the last decade in several cancers, but not in MPM. Recent studies indicate a high degree of tumor heterogeneity in MPM and the importance to optimize histological and molecular classifications for improved treatment. In this review, we provide an up-to-date overview of recent advances in MPM by focusing on new stratifications of tumor subgroups, specific vulnerabilities associated with functional loss of TSGs and other biomarkers, and potential clinical implications. The molecularly based subdivisions not only deepen our understanding of MPM pathobiology, but more importantly, they may raise unprecedented new hopes for personalized treatment of MPM patients with biomarker-guided targeted and immunotherapies.