Evidence for causal effects of neuropsychiatric conditions on risk of venous thromboembolism: A univariable and multivariable Mendelian randomization study

BACKGROUND

Substantial observational evidence suggests an association between neuropsychiatric conditions and venous thromboembolism (VTE). However, the causal relationship between these two conditions requires further investigation. Therefore, we used a two-sample Mendelian randomization (MR) approach to assess the bidirectional causal effects between four neuropsychiatric conditions and VTE, deep vein thrombosis, and pulmonary embolism (PE).

METHODS

Genetic variants associated with four neuropsychiatric conditions (ie, schizophrenia, major depressive disorder [MDD], bipolar disorder, and epilepsy) and VTE, deep vein thrombosis, and PE were selected. Bidirectional univariable and multivariable MR methods were applied to evaluate the causal relationships among these conditions. The primary causal estimates were obtained using the inverse variance weighted method with multiplicative random effects, supplemented by MR Egger regression, weighted median, simple mode, and weighted mode. Sensitivity analysis was conducted using the MR pleiotropy residual sum, funnel plots, and outlier (MR pleiotropy and residual sum and outlier) method.

RESULTS

Univariable MR results showed that genetic susceptibility to MDD increases the risk of VTE and PE (VTE: odds ratio [OR], 1.25; 95% confidence interval [CI], 1.08-1.46; P = .004; PE: OR, 1.36; 95% CI, 1.09-1.69; P = .006) and that PE has an adverse causal effect on MDD (OR, 1.02; 95% CI, 1.00-1.04; P = .026). Adjustment for confounders such as obesity, sleep duration, smoking, physical activity, and alcohol consumption revealed that increased genetic susceptibility to MDD is also associated with VTE and PE.

CONCLUSIONS

Our results suggest that genetic susceptibility to MDD might have an adverse causal effect on the risk of VTE and PE and that PE has a reverse causal effect on MDD. Prevention and early diagnosis of depression are crucial in the management of VTE and PE.

MMP-9-dependent proteolysis of the histone H3 N-terminal tail: a critical epigenetic step in driving oncogenic transcription and colon tumorigenesis

Matrix metalloproteinase 9 (MMP-9) is a member of the MMP family and has been recently identified as a nuclear protease capable of clipping histone H3 N-terminal tails (H3NT). This MMP-9-dependent H3NT proteolysis is critical for establishing an active state of gene transcription during osteoclast differentiation and melanoma development. However, whether H3NT cleavage by MMP-9 plays a similar role in other cellular events has not been explored. Here, we dissect the functional contribution of MMP-9-dependent H3NT clipping to colonic tumorigenesis by using a combination of genome-wide transcriptome data, ChIP/ChIPac-qPCR, CRISPR/dCas9 gene-targeting system, and in vivo xenograft models. We show that MMP-9 is overexpressed in colon cancer cells and catalyzes H3NT proteolysis to drive transcriptional activation of growth stimulatory genes. Our studies using knockdown and inhibition approaches clearly indicate that MMP-9 mediates transcriptional activation and promotes colonic tumorigenesis in a manner dependent on its protease activity toward H3NT. Remarkably, artificial H3NT proteolysis at target gene promoters with dCAS9-MMP-9 is sufficient for establishing their transcriptional competence in colon cancer cells, underscoring the importance of MMP-9-dependent H3NT proteolysis per se in the transactivation process. Our data establish new functions and mechanisms for MMP-9 in driving the oncogenic transcription program in colon cancer through H3NT proteolysis, and demonstrate how this epigenetic pathway can be exploited as a potential therapeutic target for cancer treatment.

Nivolumab Plus 5-Azacitidine in Pediatric Relapsed/Refractory Acute Myeloid Leukemia (AML): Phase I/II Trial Results from the Therapeutic Advances in Childhood Leukemia and Lymphoma (TACL) Consortium

Improvements in survival have been made over the past two decades for childhood acute myeloid leukemia (AML), but the approximately 40% of patients who relapse continue to have poor outcomes. A combination of checkpoint-inhibitor nivolumab and azacitidine has demonstrated improvements in median survival in adults with AML. This phase I/II study with nivolumab and azacitidine in children with relapsed/refractory AML (NCT03825367) was conducted through the Therapeutic Advances in Childhood Leukemia & Lymphoma consortium. Thirteen patients, median age 13.7 years, were enrolled. Patients had refractory disease with multiple reinduction attempts. Twelve evaluable patients were treated at the recommended phase II dose (established at dose level 1, 3 mg/kg/dose). Four patients (33%) maintained stable disease. This combination was well tolerated, with no dose-limiting toxicities observed. Grade 3-4 adverse events (AEs) were primarily hematological. Febrile neutropenia was the most common AE ≥ grade 3. A trend to improved quality of life was noted. Increases in CD8+ T cells and reductions in CD4+/CD8+ T cells and demethylation were observed. The combination was well tolerated and had an acceptable safety profile in pediatric patients with relapsed/refractory AML. Future studies might explore this combination for the maintenance of remission in children with AML at high risk of relapse.

SETD2 Deficiency Confers Sensitivity to Dual Inhibition of DNA Methylation and PARP in Kidney Cancer

SETD2 deficiency alters the epigenetic landscape by causing depletion of H3K36me3 and plays an important role in diverse forms of cancer, most notably in aggressive and metastatic clear-cell renal cell carcinomas (ccRCC). Development of an effective treatment scheme targeting SETD2-compromised cancer is urgently needed. Considering that SETD2 is involved in DNA methylation and DNA repair, a combination treatment approach using DNA hypomethylating agents (HMA) and PARP inhibitors (PARPi) could have strong antitumor activity in SETD2-deficient kidney cancer. We tested the effects of the DNA HMA 5-aza-2'-dexoxydytidine (DAC), the PARPi talazoparib (BMN-673), and both in combination in human ccRCC models with or without SETD2 deficiency. The combination treatment of DAC and BMN-673 synergistically increased cytotoxicity in vitro in SETD2-deficient ccRCC cell lines but not in SETD2-proficient cell lines. DAC and BMN-673 led to apoptotic induction, increased DNA damage, insufficient DNA damage repair, and increased genomic instability. Furthermore, the combination treatment elevated immune responses, upregulated STING, and enhanced viral mimicry by activating transposable elements. Finally, the combination effectively suppressed the growth of SETD2-deficient ccRCC in in vivo mouse models. Together, these findings indicate that combining HMA and PARPi is a promising potential therapeutic strategy for treating SETD2-compromised ccRCC.

SIGNIFICANCE

SETD2 deficiency creates a vulnerable epigenetic status that is targetable using a DNA hypomethylating agent and PARP inhibitor combination to suppress renal cell carcinoma, identifying a precision medicine-based approach for SETD2-compromised cancers.

Comprehensive Evaluation of The Infinium Human MethylationEPIC v2 BeadChip

Infinium Methylation BeadChips are widely used to profile DNA cytosine modifications in large cohort studies for reasons of cost-effectiveness, accurate quantification, and user-friendly data analysis in characterizing these canonical epigenetic marks. In this work, we conducted a comprehensive evaluation of the updated Infinium MethylationEPIC v2 BeadChip (EPICv2). Our evaluation revealed that EPICv2 offers significant improvements over its predecessors, including expanded enhancer coverage, applicability to diverse ancestry groups, support for low-input DNA down to one nanogram, coverage of existing epigenetic clocks, cell type deconvolution panels, and human trait associations, while maintaining accuracy and reproducibility. Using EPICv2, we were able to identify epigenome and sequence signatures in cell line models of DNMT and SETD2 loss and/or hypomorphism. Furthermore, we provided probe-wise evaluation and annotation to facilitate the use of new features on this array for studying the interplay between somatic mutations and epigenetic landscape in cancer genomics. In conclusion, EPICv2 provides researchers with a valuable tool for studying epigenetic modifications and their role in development and disease.

VprBP/DCAF1 Triggers Melanomagenic Gene Silencing through Histone H2A Phosphorylation

Vpr binding protein (VprBP), also known as DDB1- and CUL4-associated factor1 (DCAF1), is a recently identified atypical kinase and plays an important role in downregulating the transcription of tumor suppressor genes as well as increasing the risk for colon and prostate cancers. Melanoma is the most aggressive form of skin cancer arising from pigment-producing melanocytes and is often associated with the dysregulation of epigenetic factors targeting histones. Here, we demonstrate that VprBP is highly expressed and phosphorylates threonine 120 (T120) on histone H2A to drive the transcriptional inactivation of growth-regulatory genes in melanoma cells. As is the case for its epigenetic function in other types of cancers, VprBP acts to induce a gene silencing program dependent on H2AT120 phosphorylation (H2AT120p). The significance of VprBP-mediated H2AT120p is further underscored by the fact that VprBP knockdown- or VprBP inhibitor-induced lockage of H2AT120p mitigates melanoma tumor growth in xenograft models. Collectively, our results establish VprBP-mediated H2AT120p as a key epigenetic signal for melanomagenesis and suggest the therapeutic potential of targeting VprBP kinase activity for effective melanoma treatment.

VprBP/DCAF1 triggers melanomagenic gene silencing through histone H2A phosphorylation

Background Melanoma is the most aggressive form of skin cancer arising from pigment-producing melanocytes and is often associated with dysregulation of epigenetic factors targeting histones. VprBP, also known as DCAF1, is a recently identified kinase and plays an important role in downregulating the transcription of tumor suppressor genes as well as increasing the risk for colon and prostate cancers. However, it remains unknown whether VprBP is also involved in triggering the pathogenesis of other types of cancer. Results We demonstrate that VprBP is highly expressed and phosphorylates threonine 120 (T120) on histone H2A to drive transcriptional inactivation of growth regulatory genes in melanoma cells. As is the case for its epigenetic function in colon and prostate cancers, VprBP acts to induce gene silencing program dependently of H2AT120 phosphorylation (H2AT120p). The significance of VprBP-mediated H2AT120p is further underscored by the fact that VprBP knockdown- or VprBP inhibitor-induced lockage of H2AT120p mitigates melanoma tumor growth in xenograft models. Moreover, artificial tethering of VprBP wild type, but not VprBP kinase-dead mutant, to its responsive genes is sufficient for achieving an inactive transcriptional state in VprBP-depleted cells, indicating that VprBP drives gene silencing program in an H2AT120p-dependent manner. Conclusions Our results establish VprBP-mediated H2AT120p as a key epigenetic signal for melanomagenesis and suggest the therapeutic potential of targeting VprBP kinase activity for effective melanoma treatment.

VprBP/DCAF1 triggers melanomagenic gene silencing through histone H2A phosphorylation

Background

Melanoma is the most aggressive form of skin cancer arising from pigment-producing melanocytes and is often associated with dysregulation of epigenetic factors targeting histones. VprBP, also known as DCAF1, is a recently identified kinase and plays an important role in downregulating the transcription of tumor suppressor genes as well as increasing the risk for colon and prostate cancers. However, it remains unknown whether VprBP is also involved in triggering the pathogenesis of other types of cancer.

Results

We demonstrate that VprBP is highly expressed and phosphorylates threonine 120 (T120) on histone H2A to drive transcriptional inactivation of growth regulatory genes in melanoma cells. As is the case for its epigenetic function in colon and prostate cancers, VprBP acts to induce gene silencing program dependently of H2AT120 phosphorylation (H2AT120p). The significance of VprBP-mediated H2AT120p is further underscored by the fact that VprBP knockdown- or VprBP inhibitor-induced lockage of H2AT120p mitigates melanoma tumor growth in xenograft models. Moreover, artificial tethering of VprBP wild type, but not VprBP kinase-dead mutant, to its responsive genes is sufficient for achieving an inactive transcriptional state in VprBP-depleted cells, indicating that VprBP drives gene silencing program in an H2AT120p-dependent manner.

Conclusions

Our results establish VprBP-mediated H2AT120p as a key epigenetic signal for melanomagenesis and suggest the therapeutic potential of targeting VprBP kinase activity for effective melanoma treatment.

DNA strand asymmetry generated by CpG hemimethylation has opposing effects on CTCF binding

CpG methylation generally occurs on both DNA strands and is essential for mammalian development and differentiation. Until recently, hemimethylation, in which only one strand is methylated, was considered to be simply a transitory state generated during DNA synthesis. The discovery that a subset of CCCTC-binding factor (CTCF) binding sites is heritably hemimethylated suggests that hemimethylation might have an unknown biological function. Here we show that the binding of CTCF is profoundly altered by which DNA strand is methylated and by the specific CTCF binding motif. CpG methylation on the motif strand can inhibit CTCF binding by up to 7-fold, whereas methylation on the opposite strand can stimulate binding by up to 4-fold. Thus, hemimethylation can alter binding by up to 28-fold in a strand-specific manner. The mechanism for sensing methylation on the opposite strand requires two critical residues, V454 and S364, within CTCF zinc fingers 7 and 4. Similar to methylation, CpG hydroxymethylation on the motif strand can inhibit CTCF binding by up to 4-fold. However, hydroxymethylation on the opposite strand removes the stimulatory effect. Strand-specific methylation states may therefore provide a mechanism to explain the transient and dynamic nature of CTCF-mediated chromatin interactions.

A Multi-Omics Overview of Colorectal Cancer to Address Mechanisms of Disease, Metastasis, Patient Disparities and Outcomes

Human colorectal cancer (CRC) is one of the most common malignancies in men and women across the globe, albeit CRC incidence and mortality shows a substantial racial and ethnic disparity, with the highest burden in African American patients. Even with effective screening tools such as colonoscopy and diagnostic detection assays, CRC remains a substantial health burden. In addition, primary tumors located in the proximal (right) or distal (left) sides of the colorectum have been shown to be unique tumor types that require unique treatment schema. Distal metastases in the liver and other organ systems are the major causes of mortality in CRC patients. Characterizing genomic, epigenomic, transcriptomic and proteomic (multi-omics) alterations has led to a better understanding of primary tumor biology, resulting in targeted therapeutic advancements. In this regard, molecular-based CRC subgroups have been developed that show correlations with patient outcomes. Molecular characterization of CRC metastases has highlighted similarities and differences between metastases and primary tumors; however, our understanding as to how to improve patient outcomes based on metastasis biology is lagging and remains a major obstacle to improving CRC patient outcomes. In this review, we will summarize the multi-omics features of primary CRC tumors and their metastases across racial and ethnic groups, the differences in proximal and distal tumor biology, molecular-based CRC subgroups, treatment strategies and challenges for improving patient outcomes.

Diagnostic Aqueous Humor Proteome Predicts Metastatic Potential in Uveal Melanoma

Gene expression profiling (GEP) is clinically validated to stratify the risk of metastasis by assigning uveal melanoma (UM) patients to two highly prognostic molecular classes: class 1 (low metastatic risk) and class 2 (high metastatic risk). However, GEP requires intraocular tumor biopsy, which is limited by small tumor size and tumor heterogeneity; furthermore, there are small risks of retinal hemorrhage, bleeding, or tumor dissemination. Thus, ocular liquid biopsy has emerged as a less-invasive alternative. In this study, we seek to determine the aqueous humor (AH) proteome related to the advanced GEP class 2 using diagnostic AH liquid biopsy specimens. Twenty AH samples were collected from patients with UM, grouped by GEP classes. Protein expression levels of 1472 targets were analyzed, compared between GEP classes, and correlated with clinical features. Significant differentially expressed proteins (DEPs) were subjected to analysis for cellular pathway and upstream regulator identification. The results showed that 45 DEPs detected in the AH could differentiate GEP class 1 and 2 at diagnosis. IL1R and SPRY2 are potential upstream regulators for the 8/45 DEPs that contribute to metastasis-related pathways. AH liquid biopsy offers a new opportunity to determine metastatic potential for patients in the absence of tumor biopsy.

SETD2 gene expression and the molecular landscape of colorectal cancer (CRC)

184

Background: SETD2, a key methyltransferase modulating histone 3 gene transcription, has been shown to act as a tumor suppressor gene by reducing oxidative stress, colonic inflammation and tumorigenesis in animal models. SETD2 gene expression has been reported to be significantly downregulated in CRC and linked with poorer patient survival. Additionally, SETD2 plays an important role in DNA repair and loss of function mutations have been associated with increased tumor mutational burden (TMB), mismatch repair (MMR) deficiency, and benefit from immunotherapy. Hence, we aimed to characterize the molecular features associated with SETD2 gene expression in CRC. Methods: 15,425 CRC tumors tested at Caris Life Sciences (Phoenix, AZ) with NextGen Sequencing on DNA (592 genes or whole exome sequencing), RNA (whole transcriptome sequencing), and IHC were analyzed. SETD2-high and -low expression were defined as ≥ top and < bottom quartile of SETD2 transcripts per million (TPM), respectively. Cell infiltration in the tumor microenvironment (TME) was estimated by QuantiSEQ. Mann-Whitney U and X2/Fisher-Exact tests were applied where appropriate, with P-values adjusted for multiple comparisons ( q < .05). Gene expression profiles were analyzed for transcriptional signatures predictive of response to immunotherapy (T cell-inflamed) and MAPK pathway activation (MPAS). Real-world overall survival information was obtained from insurance claims data and Kaplan-Meier estimates were calculated for molecularly defined patients. Results: SETD2 expression was significantly increased in left-sided/rectal compared to right-sided tumors (median TPM [mTPM] 55.8 vs 51.1, q < .001). SETD2 mutations were associated with reduced SETD2 expression in pMMR/MSS CRC (mTPM 37.9 vs 54.3 in WT, q < .001), although not statistically significant in dMMR/MSI-H CRC (mTPM 43.6 vs 51.7 in WT, P = .17). Compared to SETD2-high tumors, SETD2-low was associated with increased rates of TMB-high (10.4% vs 8.2%, P = .009), dMMR/MSI-H (7.3% vs 5.6%, P = .02), and PD-L1 IHC levels (4.4% vs 2.5%, q < .002). Only minor differences in gene mutation and copy number rates were observed between SETD2-high and -low tumors , whereas SETD2-high TME was associated with increased immune cell infiltration, including neutrophils, B cells, NK cells, M2 macrophages, and dendritic cells ( q < .05). SETD2-high was also associated with increased T cell-inflamed and MPAS signatures (152% and 159% median increase, respectively, q < .001), regardless of tumor MMR status. Among dMMR/MSI-H CRC, SETD2-high tumors receiving immune checkpoint inhibitors had longer time-on-treatment (HR: 0.39, 95% CI: 0.2-0.76, P = .005) and a trend towards longer OS (HR: 0.29, 95% CI: 0.07-1.2, P = .069). Conclusions: Our data show distinct immune biomarkers and TME cell infiltration associated with SETD2 gene expression in CRC. These findings support a key role for SETD2 in modulating anti-tumor immunity and TME.

RNA mis-splicing drives viral mimicry response after DNMTi therapy in SETD2-mutant kidney cancer

Tumors with mutations in chromatin regulators present attractive targets for DNA hypomethylating agent 5-aza-2'-deoxycytidine (DAC) therapy, which further disrupts cancer cells' epigenomic fidelity and reactivates transposable element (TE) expression to drive viral mimicry responses. SETD2 encodes a histone methyltransferase (H3K36me3) and is prevalently mutated in advanced kidney cancers. Here, we show that SETD2-mutant kidney cancer cells are especially sensitive in vitro and in vivo to DAC treatment. We find that the viral mimicry response are direct consequences of mis-splicing events, such as exon inclusions or extensions, triggered by DAC treatment in an SETD2-loss context. Comprehensive epigenomic analysis reveals H3K9me3 deposition, rather than DNA methylation dynamics, across intronic TEs might contribute to elevated mis-splicing rates. Through epigenomic and transcriptomic analyses, we show that SETD2-deficient kidney cancers are prone to mis-splicing, which can be therapeutically exacerbated with DAC treatment to increase viral mimicry activation and provide synergy with combinatorial immunotherapy approaches.

Molecular mechanisms of resistance to tyrosine kinase inhibitor in clear cell renal cell carcinoma

Clear cell renal cell carcinoma (ccRCC) is the most common subtype of renal cell carcinoma (RCC). Loss of von Hippel-Lindau tumor suppressor gene is frequently observed in ccRCC and increases the expression of hypoxia-inducible factors and their targets, including epidermal growth factor, vascular endothelial growth factor, and platelet-derived growth factor. Tyrosine kinase inhibitors (TKIs) offer a survival benefit in metastatic renal cell carcinoma (mRCC). Recently, immune checkpoint inhibitors have been introduced in mRCC. Combination therapy with TKIs and immune checkpoint inhibitors significantly improved patient outcomes. Therefore, TKIs still play an essential role in mRCC treatment. However, the clinical utility of TKIs is compromised when primary and acquired resistance are encountered. The mechanism of resistance to TKI is not fully elucidated. Here, we comprehensively reviewed the molecular mechanisms of resistance to TKIs and a potential strategy to overcome this resistance. We outlined the involvement of angiogenesis, non-angiogenesis, epithelial-mesenchymal transition, activating bypass pathways, lysosomal sequestration, non-coding RNAs, epigenetic modifications and tumor microenvironment factors in the resistance to TKIs. Deep insight into the molecular mechanisms of resistance to TKIs will help to better understand the biology of RCC and can ultimately help in the development of more effective therapies.

DNMT and EZH2 inhibitors synergize to activate therapeutic targets in hepatocellular carcinoma

The development of more effective targeted therapies for hepatocellular carcinoma (HCC) patients due to its aggressiveness is urgently needed. DNA methyltransferase inhibitors (DNMTis) represented the first clinical breakthrough to target aberrant cancer epigenomes. However, their clinical efficacies are still limited, in part due to an "epigenetic switch" in which a large group of genes that are demethylated by DNMTi treatment remain silenced by polycomb repressive complex 2 (PRC2) occupancy. EZH2 is the member of PRC2 that catalyzes the placement of H3K27me3 marks. EZH2 overexpression is correlated with poor HCC patient survival. We tested the combination of a DNMTi (5-aza-2'-deoxycytidine, DAC) and the EZH2 inhibitor (EZH2i) GSK126 in human HCC cell lines on drug sensitivity, DNA methylation, nucleosome accessibility, and gene expression profiles. Compared with single agent treatments, all HCC cell lines studied showed increased sensitivity after receiving both drugs concomitant with prolonged anti-proliferative changes and sustained reactivation of nascently-silenced genes. The increased number of up-regulated genes after combination treatment correlated with prolonged anti-proliferation effects and increased nucleosome accessibility. Combination treatments also activate demethylated promoters that are repressed by PRC2 occupancy. Furthermore, 13-31% of genes down-regulated by DNA methylation in primary HCC tumors were reactivated through this combination treatment scheme in vitro. Finally, the combination treatment also exacerbates anti-tumor immune responses, while most of these genes were downregulated in over 50% of primary HCC tumors. We have linked the anti-tumor effects of DAC and GSK126 combination treatments to detailed epigenetic alterations in HCC cells, identified potential therapeutic targets and provided a rationale for treatment efficacy for HCC patients.

Characterizing DNA methylation signatures of retinoblastoma using aqueous humor liquid biopsy

Retinoblastoma (RB) is a cancer that forms in the developing retina of babies and toddlers. The goal of therapy is to cure the tumor, save the eye and maximize vision. However, it is difficult to predict which eyes are likely to respond to therapy. Predictive molecular biomarkers are needed to guide prognosis and optimize treatment decisions. Direct tumor biopsy is not an option for this cancer; however, the aqueous humor (AH) is an alternate source of tumor-derived cell-free DNA (cfDNA). Here we show that DNA methylation profiling of the AH is a valid method to identify the methylation status of RB tumors. We identify 294 genes directly regulated by methylation that are implicated in p53 tumor suppressor (RB1, p53, p21, and p16) and oncogenic (E2F) pathways. Finally, we use AH to characterize molecular subtypes that can potentially be used to predict the likelihood of treatment success for retinoblastoma patients.

[A case of ocular siderosis caused by iron ore]

A patient complained of vision loss of his left eye which was crushed by iron ore for 11 months. The cornea of the injured eye was thin and swollen, and a large amount of rust-like material was observed to be deposited. An intraocular foreign body was found by orbital CT. During vitrectomy, a piece of metal sheet was found near the ora serrate, and the intraocular structure was severely damaged, and characterized by vitreous brown turbidity, a white optic disc, occlusion of blood vessels in the fundus, and peripheral retinal atrophy with degeneration. The patient was diagnosed as ocular siderosis in the left eye.

The Multi-Omic Landscape of Primary Breast Tumors and Their Metastases: Expanding the Efficacy of Actionable Therapeutic Targets

Breast cancer (BC) mortality is almost exclusively due to metastasis, which is the least understood aspect of cancer biology and represents a significant clinical challenge. Although we have witnessed tremendous advancements in the treatment for metastatic breast cancer (mBC), treatment resistance inevitably occurs in most patients. Recently, efforts in characterizing mBC revealed distinctive genomic, epigenomic and transcriptomic (multi-omic) landscapes to that of the primary tumor. Understanding of the molecular underpinnings of mBC is key to understanding resistance to therapy and the development of novel treatment options. This review summarizes the differential molecular landscapes of BC and mBC, provides insights into the genomic heterogeneity of mBC and highlights the therapeutically relevant, multi-omic features that may serve as novel therapeutic targets for mBC patients.

Abstract 3736: SETD2 aberrancy enhanced the synergetic anti-tumor effects of DNA hypomethylating agents and PARP inhibitors in aggressive clear cell renal cell carcinoma

Purpose: SETD2 aberrancy, as the main reason of depleted levels of H3K36me3, plays an important role in diverse forms of cancer and is most notably in clear cell renal cell carcinoma (ccRCC). Altered chromatin modelers related to impaired H3K36me3 occupancy are linked to renal cancer aggressiveness and metastasis, where the latter dramatically drops the relative 5-year survival rate of ccRCC from 91% to 11%. Developing novel treatment targeting H3K36me3-compromised cancer cell is urgently needed for diagnostic and treatment purposes.

Methods: Phenotypic and animal experiments were conducted to test the sensitivity of kidney cancer cells with impaired H3K36me3 to hypomethylating agent (HMA), PARP inhibitor (PARPi), and HMA + PARPi combination treatments. Comet assay, flow cytometry, western blot and bioinformatic analysis were performed to explore the mechanism beneath.

Results: Combination treatment of 5-Aza-CdR (DAC) and Talazoparib (PARPi) generate more cytotoxicity in SETD2-altered ccRCC cell lines than in SETD2-intact cell lines, including inhibited cell growth, incomplete colony formation, more apoptosis, increased DNA damage and impaired DNA damage repair. The up-regulation of STING and transposable element (TE), as well as the loss of chromatin stability, were more remarkable in SETD2-altered ccRCC cell lines when treated with DAC + PARPi.

Conclusion: Combination treatment of DAC and Talazoparib showed greater synergistic anti-tumor effect in SETD2 aberrant than in SETD2 wild-type ccRCC cells, making it a potential treatment strategy for H3K36me3-compromised cancers. Further pre-clinical studies should be conducted to make a precise medicine-based approach.

Citation Format: Xinyi Zhou, Guanghou Fu, Hong-Tao Li, Hemant Gujar, Daniel J. Weisenberger, David I. Quinn, Bo Han, Gangning Liang. SETD2 aberrancy enhanced the synergetic anti-tumor effects of DNA hypomethylating agents and PARP inhibitors in aggressive clear cell renal cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3736.

Abstract 3618: Loss of SETD2 sensitizes kidney cancer cells to DNA methylation inhibitors by inducing viral mimicry and RNA mis-splicing

Large-scale sequencing efforts of human cancers have identified recurrent mutations and deletions in a variety of chromatin-regulating proteins that modulate DNA methylation, histone modifications, and nucleosome positioning. The dysregulation of histone H3 lysine 36 (H3K36) methyltransferase, SETD2, through transcriptional or genetic aberrations is associated with worse clinical outcomes and metastasis in kidney cancer. Limited targeted therapeutic interventions are available for aggressive SETD2-mutant ccRCC tumors. Here, we reveal that kidney cancer cells displaying diminished H3K36 trimethylation levels, a consequence of SETD2 deficiency, show increased sensitivity of anti-tumor effects to DNA hypomethylating agent (HMA). We discovered that HMA treatment induced stronger viral mimicry activation and immune upregulation, which is potentiated by higher transposable element (TE) expression in SETD2-mutant cancer cells. Mechanistically, we provide evidence that substantial number of the HMA-induced TE expression is a consequence of mis-splicing, which is associated deficient in slicing in SETD2-loss content along with rapid gain of H3K9me3 across exons. These all suggested HMA could turn immune-cold tumor to immune-hot tumor and sensitize tumors to immune therapy. Then we performed in vivo assay in immune competent mice. Indeed, SETD2 deficient tumors were extremely sensitive to combination treatment of HMA and immune checkpoint inhibitor. Our finding provides one of the first preclinical and in vivo evidence that demonstrates the SETD2 dysregulation can be an epigenetic therapeutic target in ccRCC, especially in combination with immune checkpoint inhibitors, for future clinical trials.

Citation Format: Hong-Tao Li, Hyo Sik Jang, Krizia Rohena-Rivera, Hemant Gujar, Minmin Liu, Justin Kulchycki, Xinyi Zhou, Shuqing Zhao, Peter Jones, Neil Bhowmick, Gangning Liang. Loss of SETD2 sensitizes kidney cancer cells to DNA methylation inhibitors by inducing viral mimicry and RNA mis-splicing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3618.

Bactericidal efficacy of low concentration of vaporized hydrogen peroxide with validation in a BSL-3 laboratory

BACKGROUND

Highly infective pathogens are cultured and studied in biosafety laboratories. It is critical to thoroughly disinfect these laboratories to prevent laboratory infection. A whole-room, non-contact, reduced corrosion disinfection strategy using hydrogen peroxide was proposed and evaluated.

AIM

To evaluate the bactericidal efficacy of 8% and 10% vaporized hydrogen peroxide( VHP) in a laboratory setting with spores and bacteria as bioindicators.

METHODS

Spores of B. atrophaeus and B. stearothermophilus, along with bacteria E. coli, S. aureus, and S. epidermidis were placed in pre-selected locations in a sealed laboratory and an OXY-PHARM NOCOSPRAY2 vaporized hydrogen peroxide generator was applied. Spore killing efficacy was qualitatively evaluated, and bactericidal efficacy was quantitatively analyzed, and the mean log10 reduction was determined. Finally, the optimized disinfection strategy was verified in a BSL-3 laboratory.

FINDINGS

Significant reductions in microbial load were obtained for each of the selected spores and bacteria when exposed to VHP in concentrations of 8% and 10% for 2～3 h. S. aureus was found to be more resistant than E. coli and S. epidermidis. Tests with 8% hydrogen peroxide and exposure for more than 3 h completely killed B. atrophaeus on surfaces and equipment in the BSL-3 laboratory.

CONCLUSION

The vaporized hydrogen peroxide generator is superior in terms of good diffusivity and low corrosiveness and is time-effective in removing the disinfectant residue. This study provides reference for the precise disinfection of air and object surfaces in biosafety laboratories under varying conditions.

Genes regulated by DNA methylation are involved in distinct phenotypes during melanoma progression and are prognostic factors for patients

In addition to mutations, epigenetic alterations are important contributors to malignant transformation and tumor progression. The aim of this work was to identify epigenetic events in which promoter or gene body DNA methylation induces gene expression changes that drive melanocyte malignant transformation and metastasis. We previously developed a linear mouse model of melanoma progression consisting of spontaneously immortalized melanocytes, premalignant melanocytes, a nonmetastatic tumorigenic, and a metastatic cell line. Here, through the integrative analysis of methylome and transcriptome data, we identified the relationship between promoter and/or gene body DNA methylation alterations and gene expression in early, intermediate, and late stages of melanoma progression. We identified adenylate cyclase type 3 (Adcy3) and inositol polyphosphate 4-phosphatase type II (Inpp4b), which affect tumor growth and metastatic potential, respectively. Importantly, the gene expression and DNA methylation profiles found in this murine model of melanoma progression were correlated with available clinical data from large population-based primary melanoma cohorts, revealing potential prognostic markers.

KRT13 promotes stemness and drives metastasis in breast cancer through a plakoglobin/c-Myc signaling pathway

Background

Keratins (KRTs) are intermediate filament proteins that interact with multiple regulatory proteins to initiate signaling cascades. Keratin 13 (KRT13) plays an important role in breast cancer progression and metastasis. The objective of this study is to elucidate the mechanism by which KRT13 promotes breast cancer growth and metastasis.

Methods

The function and mechanisms of KRT13 in breast cancer progression and metastasis were assessed by overexpression and knockdown followed by examination of altered behaviors in breast cancer cells and in xenograft tumor formation in mouse mammary fat pad. Human breast cancer specimens were examined by immunohistochemistry and multiplexed quantum dot labeling analysis to correlate KRT13 expression to breast cancer progression and metastasis.

Results

KRT13-overexpressing MCF7 cells displayed increased proliferation, invasion, migration and in vivo tumor growth and metastasis to bone and lung. Conversely, KRT13 knockdown inhibited the aggressive behaviors of HCC1954 cells. At the molecular level, KRT13 directly interacted with plakoglobin (PG, γ-catenin) to form complexes with desmoplakin (DSP). This complex interfered with PG expression and nuclear translocation and abrogated PG-mediated suppression of c-Myc expression, while the KRT13/PG/c-Myc signaling pathway increased epithelial to mesenchymal transition and stem cell-like phenotype. KRT13 expression in 58 human breast cancer tissues was up-regulated especially at the invasive front and in metastatic specimens (12/18) (p < 0.05). KRT13 up-regulation in primary breast cancer was associated with decreased overall patient survival.

Conclusions

This study reveals that KRT13 promotes breast cancer cell growth and metastasis via a plakoglobin/c-Myc pathway. Our findings reveal a potential novel pathway for therapeutic targeting of breast cancer progression and metastasis.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13058-022-01502-6.

Effects of chronic intranasal dantrolene on nasal mucosa morphology in mice

OBJECTIVE

We have previously shown that the intranasal administration of dantrolene ameliorated cognitive dysfunction in the 5XFAD mouse model of Alzheimer's disease. This study examines the morphology of the nasal mucosa after 10 months of intranasal dantrolene in 5XFAD mice.

MATERIALS AND METHODS

5XFAD mice were either treated with intranasal dantrolene (5 mg/kg, 3 times/wk) from 2 months to 12 months of age or given no treatment at all. The mice were euthanatized at 12 months of age and the snouts were processed for histological examination. The morphology of the nasal mucosa was assessed and compared between the two groups.

RESULTS

There were no significant differences in the thickness of the olfactory epithelium or the proportion of the thickness of the glandular layer to the wall of mucosa and submucosa in the nasal passages.

CONCLUSIONS

Long-term intranasal administration of dantrolene did not significantly change the nasal mucosa morphology in 5XFAD mice.

Malnutrition Increases the Risk of Left Ventricular Remodeling

OBJECTIVES

Malnutrition is associated with increased incidence of heart failure (HF). Left ventricular (LV) remodeling is one of the most important processes in the occurrence and evolution of HF. However, the association between nutritional status and LV remodeling is not well known. The study aimed to investigate the association between malnutrition and LV remodeling.

DESIGN

The study was a retrospective observation study.

SETTING AND PARTICIPANTS

We included patients from the registry of Cardiorenal Improvement study from January 2007 to December 2018 at Guangdong Provincial People's Hospital.

MEASUREMENTS

The primary endpoint was LV remodeling, defined as an absolute decrease in LV ejection fraction ≥10% after discharge compared with baseline. Nutritional status was assessed by the Controlling Nutritional Status (CONUT) score. Eligible patients were divided into absent-mild malnutrition group (CONUT score ≤4) and moderate-severe malnutrition group (CONUT score >4). Univariable and multivariable logistic regression was performed to verify the association between malnutrition and left ventricular remodeling.

RESULTS

A total of 7,217 patients (mean age 61.3±10.5 years, 71.7% male) were included in the final analysis, among which 712 (9.9%) had LV remodeling. The incidence of LV remodeling in moderate-severe malnutrition group was significantly higher than that in absent-mild malnutrition group (12.9% vs. 9.5%, p=0.002). In multivariable logistic regression, moderate-severe malnutrition group was significantly associated with 1.69-fold increased risk of LV remodeling after adjusting confounders (OR: 1.69, CI: 1.32-2.16). Similar results were observed in subgroup stratified by age, gender, and coronary artery disease.

CONCLUSION

Nearly one eighth of patients were classified as moderate-severe malnutrition, 12% of whom had LV remodeling. Moderate-severe malnutrition was associated with 69% increased risk of LV remodeling. Further studies are needed to prospectively evaluate the nutrition-oriented managements on outcomes in LV remodeling.

Inhibition of myeloid differentiation factor 2 by MAC28 suppresses reactive oxygen species, inflammation and improves mitochondrial function, leading to improved cardiac function in prediabetic rats

Background

Chronic inflammation involves in the left ventricular (LV) dysfunction in high-fat diet (HFD)-induced prediabetes, along with cardiac mitochondrial dysfunction. This involved an activation of myeloid differentiation factor 2 (MD2)/toll-like receptor 4 (TLR4) by lipopolysaccharide, leading to inflammatory cytokines production in the heart. MAC28 is a novel MD2 inhibitor, which had been shown to provide effects against LPS-induced cytokine secretion from macrophages. However, the potential benefits of MAC28 on the LV function and its underlying mechanisms in HFD-induced prediabetic rats are unknown.

Purpose

We tested the hypothesis that MAC28 improves LV function in prediabetic rats by reducing cardiac oxidative stress, inflammation, and cardiac mitochondrial dysfunction.

Methods

Male Wistar rats were fed either a normal diet (ND, n=8) or HFD (n=24) for 16 weeks. At week 12, HFD-fed rats developed prediabetes and LV dysfunction. At this time, these HFD-fed rats were divided into 3 treatment groups (n=8/group): 1) vehicle (HFDV; 1% Na-carboxymethyl cellulose; p.o.); 2) MAC28 (40 mg/kg; p.o.); 3) metformin (300 mg/kg; p.o.; a positive control), the ND-fed rats received a vehicle (NDV). Rats were received their treatment for 4 weeks. Then, LV function and heart rate variability (HRV) were examined, and the heart was removed to determinecardiac malondialdehyde (MDA), cardiac inflammation (TNF-α) and mitochondrial function.

Results

HFD-induced prediabetes, together with depressed HRV and %LV ejection fraction (LVEF) (Fig. 1A). Moreover, cardiac oxidative stress and inflammation overproduction, and cardiac mitochondrial dysfunction was also observed, shown by elevated cardiac MDA, cardiac TNF-α protein levels, and mitochondrial ROS levels, mitochondrial depolarization and swelling (Fig. 1B). Notably, treatment with MAC28 effectively improved HRV and %LVEF and HRV (Fig. 1A), compared to HFDV group. Moreover, MAC28 significantly reduced cardiac MDA levels, cardiac TNF-α protein levels and cardiac mitochondrial dysfunction in HFD-induced prediabetic rats (Fig. 1B). These beneficial effects were also observed in metformin-treated rats (Fig. 1A, B).

Conclusion

MAC28 exerts cardioprotection in prediabetic rats by reducing cardiac oxidative stress, inflammation, and mitochondrial dysfunction, leading to restoring LV function.

Funding Acknowledgement

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): This work was supported by the Thailand Science Research and Innovation

Taurine Reduces Liver Damage in Non-Alcoholic Fatty Liver Disease Model in Rats by Down-Regulating IL-9 and Tumor Growth Factor TGF-β

The study employed a rat model to examine the effects of taurine (Tau) on prevention and therapy of non-alcoholic fatty liver disease (NAFLD). In model rats maintained on a high-fat diet (HFD), the serum levels of ALT, AST, triglycerides, cholesterol, and LDL were higher than the corresponding levels in normal control and NP groups (p<0.05). In Tau-prevention and Tau-treatment groups, the serum levels of AST and triglycerides were lower than in HFD rats (p<0.05). In HFD rats, diffuse fatty degeneration and infiltration with inflammatory cells was observed in the liver; in the ileal mucosa, the villi were fractured or absent, the epithelium was exfoliated and infiltrated with inflammatory cells. The levels of TGF-β, IL-9, and their mRNA in the liver and ileal mucosa of HFD rats were significantly higher than in normal control and NP groups (p<0.05). In Tau-prevention and Tau-treatment groups, these levels were significantly lower than in HFD rats (p<0.05). Thus, TGF-β and IL-9 can be implicated in NAFLD genesis, while Tau can preventively or therapeutically diminish the damage to the liver and ileal mucosa in rats with this disease by down-regulating the expression of TGF-β and IL-9.

Immunogenic cell death pathway polymorphisms for predicting oxaliplatin efficacy in metastatic colorectal cancer

Background

Immunogenic cell death (ICD) is a tumor cell death involving both innate and adaptive immune responses. Given published findings that oxaliplatin, but not irinotecan, drives ICD, we investigated whether single nucleotide polymorphisms (SNPs) in the ICD pathway are associated with the efficacy of oxaliplatin-based chemotherapy in metastatic colorectal cancer (mCRC).

Methods

Two randomized clinical trials data were analyzed: discovery cohort, FOLFOX/bevacizumab arm (MAVERICC); validation cohort, FOLFOXIRI/bevacizumab arm (TRIBE); and two control cohorts, FOLFIRI/bevacizumab arms (both trials). Genomic DNA extracted from blood samples was genotyped. Ten SNPs in the ICD pathway were tested for associations with clinical outcomes.

Results

In total, 648 patients were included. In the discovery cohort, three SNPs were significantly associated with clinical outcomes in univariate analysis: CALR rs1010222 with progression-free survival (G/G vs any A, HR=0.61, 95% CI 0.43–0.88), ANXA1 rs1050305 with overall survival (OS) (A/A vs any G, HR=1.87, 95% CI 1.04–3.35), and LRP1 rs1799986 with OS (C/C vs any T, HR=1.69, 95% CI 1.07–2.70). Multivariate analysis confirmed the trend, but statistical significance was not reached. In the validation cohort, ANXA1 rs1050305, and LRP1 rs1799986 were validated to have the significant associations with clinical outcome. No significant associations of these SNPs were observed in the two control cohorts. Treatment-by-SNP interaction test confirmed the predictive values.

Conclusions

The predictive utility of ICD-related SNPs for the efficacy of oxaliplatin-based chemotherapy was demonstrated, warranting further validation studies to be translated into personalized treatment strategies using conventional cytotoxic agents in mCRC.

Albumin levels predict prognosis in advanced renal cell carcinoma treated with tyrosine kinase inhibitors: a systematic review and meta-analysis

PURPOSE

With the development of therapy and prognostic criteria for metastatic Renal Cell Carcinoma (mRCC), the prognostic value of serum albumin level has remained in dispute. The aim of this meta-analysis was to evaluate the role of pre-treatment albumin in predicting the prognosis of mRCC patients in the era of tyrosine kinase inhibitor (TKI) treatments.

METHODS

The qualitative and quantitative synthesis was conducted of studies retrieved from PubMed, Embase, and Cochrane library from inception of these databases to July 19, 2020. The hazard ratio (HR) and its 95% confidence interval (CI) of overall survival (OS) and progression-free survival (PFS) were extracted from studies comparing different levels of pre-treatment serum albumin (as a dichotomous or continuous variable) in mRCC patients treated with TKI agents.

RESULTS

Within 5,638 primitive records, 16 were eligible and 14 had adequate data for quantitative analysis (N = 2,863 participants). Random-effects meta-analysis showed that lower albumin was related to poorer OS (dichotomous: HR = 2.01, 95% CI: 1.64-2.46, P < 0.001, I² = 28.8%; continuous: HR =0.93, 95% CI: 0.86-1.00, P = 0.040, I² = 67.5%) and PFS (dichotomous: HR = 1.45, 95% CI: 1.04-2.01, P = 0.029, I² = 57.4%; continuous: HR = 0.89, 95% CI: 0.80-0.98, P = 0.023, I² = 93.3%).

CONCLUSION

Lower pre-treatment serum albumin level is an independent adverse predictor of prognosis of mRCC patients receiving TKI therapy.

REGISTRATION

PROSPERO ID: CRD42020196802 Sep. 2^nd, 2020.

Characterizing DNA methylation signatures and their potential functional roles in Merkel cell carcinoma

BACKGROUND

Merkel cell carcinoma (MCC) is a rare but aggressive skin cancer with limited treatment possibilities. Merkel cell tumors display with neuroendocrine features and Merkel cell polyomavirus (MCPyV) infection in the majority (80%) of patients. Although loss of histone H3 lysine 27 trimethylation (H3K27me3) has been shown during MCC tumorigenesis, epigenetic dysregulation has largely been overlooked.

METHODS

We conducted global DNA methylation profiling of clinically annotated MCC primary tumors, metastatic skin tumors, metastatic lymph node tumors, paired normal tissues, and two human MCC cell lines using the Illumina Infinium EPIC DNA methylation BeadArray platform.

RESULTS

Significant differential DNA methylation patterns across the genome are revealed between the four tissue types, as well as based on MCPyV status. Furthermore, 964 genes directly regulated by promoter or gene body DNA methylation were identified with high enrichment in neuro-related pathways. Finally, our findings suggest that loss of H3K27me3 occupancy in MCC is attributed to KDM6B and EZHIP overexpression as a consequence of promoter DNA hypomethylation.

CONCLUSIONS

We have demonstrated specific DNA methylation patterns for primary MCC tumors, metastatic MCCs, and adjacent-normal tissues. We have also identified DNA methylation markers that not only show potential diagnostic or prognostic utility in MCC management, but also correlate with MCC tumorigenesis, MCPyV expression, neuroendocrine features, and H3K27me3 status. The identification of DNA methylation alterations in MCC supports the need for further studies to understand the clinical implications of epigenetic dysregulation and potential therapeutic targets in MCC.

O-137 Salpingectomy versus neosalpingostomy in women with hydrosalpinx: a prospective cohort study with long-term follow-up

Study question

What is the comparative effectiveness between salpingectomy and neosalpingostomy in the treatment of bilateral severe hydrosalpinx?

Summary answer

In women with bilateral severe hydrosalpinx, salpingectomy combined with In Vitro Fertilization (IVF) treatment resulted in a higher cumulative live birth rate than neosalpingostomy.

What is known already

Hydrosalpinx accounts for 25% to 35% of female subfertility and has a negative effect on pregnancy rates in women who undergo IVF. So far salpingectomy before in vitro fertilization treatment has been suggested for the treatment of hydrosalpinx in order to improve the chance of a live birth. Previous studies have reported a pooled live birth rate of 25% through natural conception after neosalpingostomy and an ongoing pregnancy rate of 55.8% after salpingectomy with IVF. Direct comparison of the cumulative live birth rate after salpingectomy versus neosalpingostomy, both followed by IVF is lacking.

Study design, size, duration

We performed a single center, prospective comparative cohort study in the International Peace Maternity and Child Health Hospital affiliated to Shanghai Jiao Tong University School of Medicine, China. We studied women diagnosed with tubal subfertility with bilateral hydrosalpinx between January 2005 and December 2012. Based on a shared decision approach, they had bilateral salpingectomy or neosalpingostomy followed by IVF. They were annually followed up until July 2020 for the occurrence of live birth.

Participants/materials, setting, methods

Out of 113 women, 55 had bilateral salpingectomy and 58 had bilateral neosalpingostomy. Primary outcome was cumulative live birth rate, defined as the cumulative birth rate of the first living neonate through either natural conception or in vitro fertilization. Both intention-to-treat (ITT) and per-protocol (PP) analysis were processed. Cox proportional hazards regression model with potential variables was performed to identify predictors of successful live birth.

Main results and the role of chance

Baseline characteristics were comparable between two groups. There were 42 live births in the salpingectomy and 36 in the neosalpingostomy group. When the result of IVF was incorporated (55/55 in salpingectomy group and 25/58 in neosalpingostomy group underwent IVF), salpingectomy resulted in a higher cumulative live birth rate (85.3% vs 76.0%; hazard ratio of the whole survival curve, 2.18; 95% CI, 1.37 - 3.45; P = 0.001), a lower risk of ectopic pregnancy (1.8% vs 20.7%; risk ratio, 0.07; 95% CI, 0.01 - 0.57; P = 0.013), and a shorter time to live birth (19 [14,27] versus 36 [17,76] months, P = 0.001).The number of live birth rates after natural conception was 0% (0/55) in the salpingectomy group and 28% (16/58) in neosalpingostomy group.The results of PP analyses were comparable with the ITT analyses apart from the biochemical pregnancy rate and the overall live birth rate, they were higher (the former: 76% (42/55) versus 58% (29/50), P = 0.045; the latter: 76% (42/55) versus 56% (28/50), P = 0.027) in salpingectomy group.

Limitations, reasons for caution

This is an observational study. The small sample size along with the data was obtained from a cohort study in a single center.

Wider implications of the findings

In women with confirmed bilateral severe hydrosalpinx, salpingectomy followed by IVF results in a higher cumulative live birth rate and decreases the risk of EP as compared to neosalpingostomy. However, neosalpingostomy is the only option to achieve a live birth by natural conception that should be discussed with patients preoperatively.

Trial registration number

not applicable

Bone marrow mesenchymal stem cells-induced exosomal microRNA-486-3p protects against diabetic retinopathy through TLR4/NF-κB axis repression

AIM

Diabetic retinopathy (DR) is a chronic disease causing health and economic burdens on individuals and society. Thus, this study is conducted to figure out the mechanisms of bone marrow mesenchymal stem cells (BMSCs)-induced exosomal microRNA-486-3p (miR-486-3p) in DR.

METHODS

The putative miR-486-3p binding sites to 3'untranslated region of Toll-like receptor 4 (TLR4) was verified by luciferase reporter assay. High glucose (HG)-treated Muller cells were transfected with miR-486-3p or TLR4-related oligonucleotides and plasmids to explore theirs functions in DR. Additionally, HG-treated Muller cells were co-cultured with BMSC-derived exosomes, exosomes collected from BMSCs that had been transfected with miR-486-3p or TLR4-related oligonucleotides and plasmids to explore their functions in DR. MiR-486-3p, TLR4 and nuclear factor-kappaB (NF-κB) expression, angiogenesis-related factors, oxidative stress factors, viability and apoptosis in HG-treated Muller cells were detected by RT-qPCR, western blot analysis, ELISA, MTT assay and flow cytometry, respectively.

RESULTS

MiR-486-3p was poorly expressed while TLR4 and NF-κB were highly expressed in HG-treated Muller cells. TLR4 was a target of miR-486-3p. Upregulating miR-486-3p or down-regulating TLR4 inhibited oxidative stress, inflammation and apoptosis, and promoted proliferation of HG-treated Muller cells. Meanwhile, BMSC-derived exosomes inhibited oxidative stress, inflammation and apoptosis, and promoted proliferation of HG-treated Muller cells. Restoring miR-486-3p further enhanced, while up-regulating TLR4 reversed, the improvement of exosomes treatment.

CONCLUSION

Our study highlights that up-regulation of miR-486-3p induced by BMSC-derived exosomes played a protective role in DR mice via TLR4/NF-κB axis repression.

Dantrolene repurposed to treat sepsis or septic shock and COVID-19 patients

OBJECTIVE

Disruption of intracellular Ca2+ homeostasis via excessive and pathological Ca2+ release from the endoplasmic reticulum (ER) and/or sarcoplasmic reticulum (SR) through ryanodine receptor (RyRs) Ca2+ channels play a critical role in the pathology of systemic inflammatory response syndrome (SIRS) and associated multiple organ dysfunction syndrome (MODS) in sepsis or septic shock. Dantrolene, a potent inhibitor of RyRs, is expected to ameliorate SIRS and MODS and decrease mortality in sepsis or septic shock patients. This review summarized the potential mechanisms of therapeutic effects of dantrolene in sepsis or septic shock at molecular, cell, and organ levels and provided suggestions and strategies for future clinical studies.

Clinical evaluation of Bladder CARE, a new epigenetic test for bladder cancer detection in urine samples

Background

Bladder cancer (BC) is the 5th most common cancer in the USA. Non-muscle invasive bladder cancer represents about 70% of all cases and has generally a favorable outcome. However, recurrence rates as high as 60 to 70% and progression rates of 10 to 20% necessitate intensive surveillance with cystoscopy. The invasiveness and high cost of cystoscopy poses significant burden on BC patients as well as on the healthcare system. In this study we test the feasibility of a simple, sensitive, and non-invasive detection of BC using Bladder CARE test in urine samples.

Results

Urine from 136 healthy and 77 BC subjects was collected using the at-home Bladder CARE Urine Collection Kit and analyzed with Bladder CARE test. The test measures the methylation level of three BC-specific biomarkers and two internal controls using methylation-sensitive restriction enzymes coupled with qPCR. Bladder CARE showed an overall sensitivity of 93.5%, a specificity of 92.6%, and a PPV and NPV of 87.8% and 96.2%, respectively. Bladder CARE has an LOD as low as 0.046%, which equates to detecting 1 cancer cell for every 2,200 cells analyzed. We also provided evidence that bisulfite-free methods to assess DNA methylation, like Bladder CARE, are advantageous compared to conventional methods that rely on bisulfite conversion of the DNA.

Conclusion

Highly sensitive detection of BC in urine samples is possible using Bladder CARE. The low LOD of the test and the measurement of epigenetic biomarkers make Bladder CARE a good candidate for the early detection of BC and possibly for the routine screening and surveillance of BC patients. Bladder CARE and the at-home urine sample collection system have the potential to (1) reduce unnecessary invasive testing for BC (2) reduce the burden of surveillance on patients and on the healthcare system, (3) improve the detection of early stage BC, and (4) allow physicians to streamline the monitoring of patients.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13148-021-01029-1.

A Novel DNA Methylation Signature as an Independent Prognostic Factor in Muscle-Invasive Bladder Cancer

Background

Muscle-invasive bladder cancer (MIBC) accounts for approximately 20% of all urothelial bladder carcinomas (UBC) at time of diagnosis, and up to 30% of patients with non-muscle invasive UBC will progress to MIBC over time. An increasing body of evidence has revealed a strong correlation between aberrant DNA methylation and tumorigenesis in MIBC.

Results

Using The Cancer Genome Atlas (TCGA) molecular data for 413 patients, we described a DNA methylation-based signature as a prognostic factor for overall survival (OS) in MIBC patients. By using a least absolute shrinkage and selection operator (LASSO) model, differentially methylated regions were first identified using multiple criteria followed by survival and LASSO analyses to identify DNA methylation probes related to OS and build a classifier to stratify patients with MIBC. The prognostic value of the classifier, referred to as risk score (RS), was validated in a held-out testing set from the TCGA MIBC cohort. Finally, receiver operating characteristic (ROC) analysis was used to compare the prognostic accuracy of the models built with RS alone, RS plus clinicopathologic features, and clinicopathologic features alone. We found that our seven-probe classifier-based RS stratifies patients into high- and low-risk groups for overall survival (OS) in the testing set (n = 137) (AUC at 3 years, 0.65; AUC at 5 years, 0.65). In addition, RS significantly improved the prognostic model when it was combined with clinical information including age, smoking status, Tumor (T) stage, and Lymph node metastasis (N) stage.

Conclusions

The DNA methylation-based RS can be a useful tool to predict the accuracy of preoperative and/or post-cystectomy models of OS in MIBC patients.

Could dantrolene be explored as a repurposed drug to treat COVID-19 patients by restoring intracellular calcium homeostasis?

Dantrolene, an FDA approved drug to treat malignant hyperthermia and muscle spasm, has been demonstrated to inhibit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mediated toxicity of host cells. Ryanodine receptor overactivation and associated disruption of intracellular Ca2+ homeostasis play important roles in SARS-CoV-2 infection and replication of host cells. Dantrolene, as an inhibitor of RyRs, is expected to ameliorate these detrimental effects of SARS-CoV-2 in host cells. Additionally, dantrolene has also been shown to inhibit multiple cell or organ damage induced by hypoxia/ischemia, mitochondria damage, oxidative stresses, inflammation, impairment of autophagy and apoptosis, etc., which are often the causes of severity and mortality of COVID-19 patients. We have repurposed that dantrolene has a high potential at treating COVID-19 patients and reducing its morbidity and mortality.

Identification of risk factors for falls in postmenopausal women: a systematic review and meta-analysis

The purpose of this study was to identify risk factors for falls in postmenopausal women and provide evidence for the primary prevention of falls in postmenopausal women. The protocol for this meta-analysis is registered with PROSPERO (CRD42020170927). We searched PubMed, the Cochrane Library and EMBASE for observational studies on the risk factors for falls in postmenopausal women. Review Manager 5.3 was used to calculate the relative risk (RR) or weighted mean difference (WMD) of potential risk factors related to falls. STATA 14.0 was used for the quantitative evaluation of publication bias. Eleven studies with 42,429 patients from 7 countries were included. The main risk factors for falls in postmenopausal women were patient sociodemographic risk factors (age: WMD = 0.37, 95% CI 0.07 to 0.68; body weight: WMD = 0.88, 95% CI 0.56 to 1.12; BMI: WMD = 0.34, 95% CI 0.21 to 0.46; exercise: RR = 0.97, 95% CI 0.94 to 0.99; and FES-I: WMD = 6.60, 95% CI 0.72 to 12.47) and medical risk factors (dietary calcium intake: WMD = - 16.91, 95% CI - 25.80 to - 8.01; previous fracture history: RR = 1.21, 95% CI 1.13 to 1.29; previous falls: RR = 2.02, 95% CI 1.91 to 2.14; number of diseases, ˃ 2: RR = 1.17, 95% CI 1.11 to 1.23; and number of reported chronic health disorders: WMD = 0.30, 95% CI 0.10 to 0.49). Knowledge of the many risk factors associated with falls in postmenopausal women can aid in fall prevention. However, we cannot rule out some additional potential risk factors (age at the onset of menopause, years since last menstruation, hormone therapy and BMD) that need further clinical research.

Structure of nucleosome-bound DNA methyltransferases DNMT3A and DNMT3B

CpG methylation by de novo DNA methyltransferases (DNMTs) 3A and 3B is essential for mammalian development and differentiation and is frequently dysregulated in cancer1. These two DNMTs preferentially bind to nucleosomes, yet cannot methylate the DNA wrapped around the nucleosome core2, and they favour the methylation of linker DNA at positioned nucleosomes3,4. Here we present the cryo-electron microscopy structure of a ternary complex of catalytically competent DNMT3A2, the catalytically inactive accessory subunit DNMT3B3 and a nucleosome core particle flanked by linker DNA. The catalytic-like domain of the accessory DNMT3B3 binds to the acidic patch of the nucleosome core, which orients the binding of DNMT3A2 to the linker DNA. The steric constraints of this arrangement suggest that nucleosomal DNA must be moved relative to the nucleosome core for de novo methylation to occur.

Abstract 2295: Bladder care epigenetic test allows the sensitive early detection of bladder cancer from urine samples

Introduction:

Bladder cancer (BC) is the 5th most common cancer in the USA, with 81,190 new cases and 17,240 deaths in 2018. The high recurrence rate of BC requires a lifelong patient follow-up with cystoscopy. However, the invasiveness of cystoscopy and the high costs associated to this procedure, poses a significant burden on patients as well as on the healthcare system. Several tests for the non-invasive detection of BC have been developed in the past years however, because of relatively low sensitivities and/or specificities (especially for low-grade tumors), these tests have not been adopted for the routine clinical use. Therefore, a non-invasive, simple and sensitive test for detection and routine monitoring of BC is needed.

Methods:

Bladder CARE is a new non-invasive and quantitative test that measures the methylation levels of three BC specific biomarkers and two internal controls in urine samples. Contrary to other epigenetic tests, Bladder CARE analyzes DNA methylation without converting the DNA with sodium bisulfite, thus minimizing the degradation of the target DNA. In this clinical study, we evaluated the performance of this test using voided urine samples collected from 136 healthy individuals and 77 BC patients with no prior history of bladder cancer. Urine specimens were collected and stabilized using Bladder CARE at-home urine sample collection kit and BC detection was performed by a CLIA-certified and CAP-accredited laboratory (Pangea Laboratory LLC) using Bladder CARE. The results were then compared to the clinical information (cystoscopy). Additionally, the test linearity and limit of detection (LOD) were determined by analyzing artificial samples with Bladder CARE test.

Results:

Bladder CARE was able to discriminate BC from healthy control samples with a sensitivity of 93.5%, a specificity of 92.6%, and a positive and negative predictive value of 87.8% and 96.2%, respectively. Remarkably, low-grade tumors were detected with a sensitivity of 90.0%. We also found that Bladder CARE test has a LOD of 0.046% (the equivalent of detecting 1 cancer cell in a sample containing 2,200 normal cells).

Conclusions:

While cystoscopy remains the gold standard to confirm the presence of BC, the superior sensitivity of Bladder CARE test, together with its low LOD, make this test an effective early indicator of low-grade tumors and for routine recurrence monitoring of BC patients. In addition, Bladder CARE urine collection kit allows to collect and stabilize the urine specimen comfortably at-home and mail it to the testing laboratory at room temperature, streamlining the patients' detection and monitoring process.

Citation Format: Paolo Piatti, Michiko Suwoto, Taikun Jamada, Yap Ching Chew, Gangning Liang, Saum Ghodossipour, Siamak Daneshmand, Xi-Yu Jia. Bladder care epigenetic test allows the sensitive early detection of bladder cancer from urine samples [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 2295.

Abstract 462: The mutated chromatin modifier gene, H3F3AK27M, is a druggable target of DNA hypomethylating agents in pediatric high-grade glioma

Purpose: With the current standard of care for Pediatric high-grade glioma (pHGG) patients the 5-year survival rate remain low at 5-35%. Thus, there is an urgent need to develop improved therapies for pHGG patients. A specific point mutation of histone H3 (H3F3A) has been identified at amino acid 27 (lysine to methionine (K27M)), resulting in inhibition of EZH2 (histone H3K27 tri-methylase), and reduced global levels of H3K27 tri-methylation (H3K27me3). The H3K27M alteration can be found in the majority (~80%) of pHGGs and represents an attractive target for diagnostic and treatment. Since the H3K27me3 mark correlate with gene silencing, mutations resulting in global decrease in H3K27me3 may result in aberrant gene regulation. Majority of demethylated promoters remain silenced after treatment with hypomethylating agent (HMA) due to the presence of repressive H3K27me3. HMAs treatment is also rendered ineffective in case of repression of endogenous retroviruses (ERVs) due to the presence of H3K27me3. Hence, pHGGs harboring the H3K27M mutation with low levels of H3K27me3 represent an attractive therapeutic target for treatment with HMAs. HMAs are approved by FDA for treatment of several forms of human cancers.

Methods: We had introduced mutant H3K27M in human pediatric glioma cell (SF188). Pediatric glioma cell lines (wild type and endogenous or endogenous expressed with H3K27M) were treated with DNA hypomethylating agents (HMAs). Cell doubling time was calculated. DNA methylation and gene expression were monitored at different time points. Additional RNA-seq data were obtained from pediatric glioma patient and patient derived cell lines.

Results: We demonstrate that pHGG cells carrying H3K27M mutation are more aggressive and showed down-regulation of innate immune response genes (immune deficient or immune cold) and up-regulation of cancer stem like genes as compared to the wild-type pHGG cells. These findings are further confirmed with published data from patient-derived pHGG cells. The prolonged antitumor effects in pHGG cells with H3K27M mutation observed after HMA treatment may be due to the failure of DNA remethylation and upregulated innate immune response pathway genes due to ERV reactivation.

Conclusion: Our findings suggest that HMA treatment may be effective against pHGGs with the H3K27M mutation and critical for converting immune deficient cells into immune reactive cells (immune hot). The success of this project will lead to clinical trials for pHGG patients to evaluate HMAs with immune-based therapies in pHGG patients, for whom there are currently no effective treatments.

Citation Format: Hemant Gujar, Lian Zhang, Hong-Tao Li, Hitoshi Otani, Daniel J. Weisenberger, Anat Erdreich-Epstein, Gangning Liang. The mutated chromatin modifier gene, H3F3AK27M, is a druggable target of DNA hypomethylating agents in pediatric high-grade glioma [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 462.

Abstract 1078: The nucleosomal acidic patch helps anchor of de novo DNA methyltransferase DNMT3A2/3B3 complex

CpG methylation by de novo DNA methyltransferases (DNMT) 3A and 3B is essential for mammalian development and differentiation, and is frequently dysregulated in cancer. DNMT3s preferentially bind nucleosomes yet can not methylate the DNA wrapped around the nucleosome core, and favor the methylation of linker DNA at positioned nucleosomes. Here we present the cryo-EM structure of a ternary complex of catalytically active DNMT3A2, the catalytically inactive accessory subunit DNMT3B3, and a nucleosome core particle flanked with linker DNA. We find that the catalytic-like domain (CLD) of the accessory DNMT3B3 binds the acidic patch of the nucleosome core, which orients the binding of the catalyticaly active DNMT3A2 to linker DNA. The sterical constraints of this arrangement suggest that nucleosomal DNA must be moved relative to the nucleosome core for de novo methylation to occur.

Citation Format: Ting-Hai Xu, Minmin Liu, Edward Zhou, Gangning Liang, Eric H. Xu, Karsten Melcher, Peter A. Jones. The nucleosomal acidic patch helps anchor of de novo DNA methyltransferase DNMT3A2/3B3 complex [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 1078.

Abstract 140: Deregulated genes by abnormal promoter methylation in early and late stages in a linear model of melanoma progression

Metastatic melanomas are extremely aggressive tumors, accounting for 70% of skin cancer deaths, which incidence is increasing globally. Despite the advances in their treatment, metastatic melanomas are still associated with a poor prognosis, with a median survival of 6 to 12 months. The study of the molecular alterations affecting key pathways during melanoma progression may contribute to a better understanding of the biology underlying the aggressiveness of the disease and lead to the identification of biomarkers for prognosis and novel targets for therapy. In addition to mutations, epigenetic alterations are important contributors to malignant transformation and tumor progression. Aberrant DNA methylation is an epigenetic hallmark of cancer, known to play important roles in melanoma development. Although different genes were described as presenting methylation alterations in their promoters in melanomas, the dynamics of these alterations along melanocyte malignant transformation and melanoma progression is still unclear. Our laboratory developed a linear model of melanoma progression in which different pre-malignant and melanoma cell lines were established after subjecting murine melanocytes to a sustained stressful condition (adhesion impediment). In this study, we used the spontaneously immortalized melanocyte lineage (melan-a); pre-malignant melanocytes (4C), obtained after subjecting melan-a cells to 4 cycles of adhesion impediment; a non-metastatic tumorigenic cell line (4C11-), obtained after a limiting dilution of spheroids formed by 4C adhesion impediment; and a metastatic cell line (4C11+), resulting from the spontaneously loss of p53 by 4C11- cells. The aim of this work was to identify genes that have their expression altered by promoter and gene body methylation that are related to the malignant transformation of melanocytes and metastasis. Through the integrative analysis of methylome (ERRBS) with transcriptome (RNAseq) data, it was possible to identify the dynamic changes in DNA methylation in promoters and gene bodies, and their relation with gene expression in both early and late stages of melanoma progression. Among those genes are Foxd1, Lrrk2, Adcy1 and Adcy3, which had their expression validated by qPCR, and their epigenetic regulation validated by the treatment of the cells with epigenetic drugs (5-aza-2'-deoxycytidine and Trichostatin A). The gene expression and promoter methylation profiles found in the murine model of melanoma progression were correlated with clinical data from melanoma patients available in cancers cohorts, revealing potential novel prognostic markers. Supported by FAPESP, CNPQ and CAPES

Citation Format: Débora Papaiz, Flávia E. Rius, Diogo Pessoa, Eduardo M. Reis, Christopher E. Mason, Gangning Liang, Miriam G. Jasiulionis. Deregulated genes by abnormal promoter methylation in early and late stages in a linear model of melanoma progression [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 140.

Abstract B14: Epigenetic remodeling of cancer metabolisms in cisplatin-resistant bladder cancer

Introduction and Objective: Alterations in DNA methylation are important epigenetic markers in bladder cancer (BC). These epigenome modifications drive the mechanisms of aggressive chemoresistant BC. Clinicopathologic biomarkers that indicate chemotherapeutic resistance are critical for better assessing treatment strategies for individual patients. Thus, in this study, we aimed to determine whether DNA methylation of certain metabolic enzymes is significantly altered in cisplatin-resistant BC cells.

Methods: To characterize CpG methylation and nucleosome accessibility in cisplatin-resistant BC cells, the Illumina Infinium HM450 DNA methylation assay was performed. Perturbed gene expression was found to be associated with cisplatin resistance, and the biologic roles of spermidine/spermine N1-acetyltransferase (SAT1) and argininosuccinate synthase 1 (ASS1) were further studied using qRT-PCR analysis and various cell biology assays, including Western blot.

Results: ASS1 and SAT1, genes for amino acid and polyamine metabolism catalysts, respectively, were found to be vastly hypermethylated, resulting in greatly downregulated expression. ASS1 expression is of particular interest because prior studies have demonstrated its potential association with BC stage and recurrence. In regard to chemoresistance, we found that aberrant expression or induced stimulation of SAT1 restored cisplatin sensitivity in the cell culture system. We also found that the addition of exogenous arginine deiminase through administration of ADI-PEG 20 (pegylated arginine deiminase) increased ASS1 expression and enhanced cisplatin's apoptotic effects.

Conclusions: Our study demonstrates a novel mechanistic link between the epigenetic perturbation of SAT1 and ASS1 and cancer metabolism in cisplatin-resistant bladder cancer cells. These findings suggest potential utility of SAT1 and ASS1 as predictive biomarkers in resensitizing bladder cancer to chemotherapy and personalizing therapy.

Citation Format: Austin Yeon, Sungyong You, Minhyung Kim, Amit Gupta, Myung Hee Park, Daniel Weisenberger, Gangning Liang, Jayoung Kim. Epigenetic remodeling of cancer metabolisms in cisplatin-resistant bladder cancer [abstract]. In: Proceedings of the AACR Special Conference on Bladder Cancer: Transforming the Field; 2019 May 18-21; Denver, CO. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(15_Suppl):Abstract nr B14.

Activation of a Subset of Evolutionarily Young Transposable Elements and Innate Immunity Are Linked to Clinical Responses to 5-Azacytidine

The DNA methyltransferase inhibitors (DNMTi) 5-azacytidine and 5-aza-2-deoxycytidine have been approved for the treatment of different types of hematologic malignancies. However, only about 50% of patients respond to treatment. Therefore, a more comprehensive understanding of the molecular changes in patients treated with DNMTi is needed. Here, we examined gene expression profiles in a total of 150 RNA samples from two adult cohorts and one pediatric cohort with hematologic cancers taken before, during, and after treatment with 5-azacytidine (40 patients; 15 nonresponders, 25 responders). Using each patient as their own control, malignant cells showed preferential activation of a subset of evolutionarily young transposable elements (TE), including endogenous retroviral long terminal repeats (LTR), short and long interspersed nuclear elements (SINE and LINE), and the type I IFN pathway in responders, all independent of disease classification. Transfection of eight upregulated LTRs into recipient human cells in culture showed robust and heterogenous activation of six genes in the type I IFN pathway. These results, obtained in diverse hematologic disease entities, show that common targets (TE) activated by the same drug (5-azacytidine) elicit an immune response, which may be important for patient's responses to DNMTi. SIGNIFICANCE: Activation of specific classes of evolutionarily young transposable elements can lead to activation of the innate immune system.

Epigenetic plasticity potentiates a rapid cyclical shift to and from an aggressive cancer phenotype

Highly tumorigenic, drug-resistant cancer stem-like cells drive cancer progression. These aggressive cells can arise repeatedly from bulk tumor cells independently of mutational events, suggesting an epigenetic mechanism. To test this possibility, we studied bladder cancer cells as they cyclically shifted to and from a cancer stem-like phenotype, and we discovered that these two states exhibit distinct DNA methylation and chromatin accessibility. Most differential chromatin accessibility was independent of methylation and affected the expression of driver genes such as E2F3, a cell cycle regulator associated with aggressive bladder cancer. Cancer stem-like cells exhibited increased E2F3 promoter accessibility and increased E2F3 expression that drove cell migration, invasiveness and drug resistance. Epigenetic interference using a DNA methylation inhibitor blocked the transition to a cancer stem-like state and reduced E2F3 expression. Our findings indicate that epigenetic plasticity plays a key role in the transition to and from an aggressive, drug-resistant phenotype.

Genetic variants in immunogenic cell death (ICD) relating genes to predict outcome in metastatic colorectal cancer (mCRC): Data from FIRE-3, TRIBE and MAVERICC trials

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Background: ICD is an immune response against dead-cell antigens from cancer cells treated with cytotoxic and/or targeted therapies. Oxaliplatin (OHP) and cetuximab (Cet) are distinct drugs to elicit ICD, while most other anticancer agents kill cancer cells in a nonimmunogenic manner. We hypothesized that genetic variants in ICD-related genes could predictive efficacy of OHP and/or Cet in mCRC. Methods: We analyzed data of mCRC patients enrolled in three 1st-line randomized trials [FIRE-3: FOLFIRI+Cet vs FOLFIRI+bevacizumab (Bev), TRIBE: FOLFOXIRI+Bev vs FOLFIRI+Bev and MAVERICC: FOLFOX+Bev vs FOLFIRI+Bev]. Genomic DNA from blood samples was genotyped through the OncoArray, a custom array manufactured by Illumina. Candidate 14 SNPs in five ICD-related genes ( CALR, HMGB1, ANXA1, LRP1 and P2RX7) were tested for association with progression-free survival (PFS) and overall survival (OS), using Cox proportional hazards model. We tested treatment-by-SNP interactions in the following cohorts: combined TRIBE and MAVERICC (OHP-containing treatment vs non-OHP-containing treatment), and FIRE-3 (FOLFIRI+Cet vs FOLFIRI+Bev). An interaction p-value (i p) < 0.05 was considered significant. Results: Totally, 890 patients’ SNPs were available (FIRE-3: n = 236, TRIBE: n = 324, and MAVERICC: n = 330). In the combined TRIBE and MAVERICC cohorts [the reference of hazard ratio (HR) is non-OHP-containing treatment], a significant interaction was observed in ANXA1 rs1050305 (A/A: HR 0.96, Any G: HR 2.62, i p < 0.01), LRP1 rs1466535 (G/G: HR 1.39, Any A: HR 0.91, i p = 0.02), P2RX7 rs2230911 (C/C: HR 0.98, Any G: HR 1.76, i p = 0.03) and P2RX7 rs208294 (C/C: HR 1.82, Any T: HR 0.93, i p < 0.01) on OS. For PFS, that was observed in CALR rs110222 (G/G: HR 1.30, Any A: HR 0.87, i p = 0.02), HMGB1 rs1045411 (C/C: HR 0.85, Any T: HR 1.30, i p = 0.04) and HMGB1 rs1360485 (T/T: HR 0.81, Any C: HR 1.40, i p < 0.01). However, in the FIRE-3 cohort, no significant interactions were observed in any SNPs. Conclusions: Our results showed for the first time that SNPs in ICD-related genes may predict efficacy of OHP-containing treatment in mCRC. But the predictive values for Cet efficacy was not evident.

AMPK variant, a candidate of novel predictor for chemotherapy in metastatic colorectal cancer: A meta-analysis using TRIBE, MAVERICC and FIRE3

AMP-activated protein kinase (AMPK) is a key sensor of energy homeostasis and regulates cell metabolism, proliferation and chemotherapy/radiotherapy sensitivities. This study aimed to explore the relationship between the AMPK pathway-related single nucleotide polymorphisms (SNPs) and clinical outcomes in patients with metastatic colorectal cancer (mCRC). We analyzed a total of 884 patients with mCRC enrolled in three randomized clinical trials (TRIBE, MAVERICC and FIRE-3: where patients were treated with FOLFIRI, mFOLFOX6 or FOLFOXIRI combined with bevacizumab or cetuximab as the first-line chemotherapy). The association between AMPK pathway-related SNPs and clinical outcomes was analyzed across the six treatment cohorts, using a meta-analysis approach. Our meta-analysis showed that AMPK pathway had significant associations with progression-free survival (PFS; p < 0.001) and overall survival (OS; p < 0.001), but not with tumor response (TR; p = 0.220): PRKAA1 rs13361707 was significantly associated with favorable PFS (log HR = -0.219, SE = 0.073, p = 0.003), as well as PRKAA1 rs10074991 (log HR = -0.215, SE = 0.073, p = 0.003), and there were suggestive associations of PRKAG1 rs1138908 with unfavorable OS (log HR = 0.170, SE = 0.083, p = 0.041), and of UBE2O rs3803739 with unfavorable PFS (log HR = 0.137, SE = 0.068, p = 0.042) and OS (log HR = 0.210, SE = 0.077, p = 0.006), although these results were not significant after false discovery rate adjustment. AMPK pathway-related SNPs may be predictors for chemotherapy in mCRC. Upon validation, our findings would provide novel insight for selecting treatment strategies.