Cancer-relevant Pathways Research Articles

Chemical Proteomics–Guided Discovery of Covalent Ligands for Cancer Proteins

Advances in genome sequencing and editing technologies have enriched our understanding of the biochemical pathways that drive tumorigenesis. Translating this knowledge into new medicines for cancer treatment, however, remains challenging, and many oncogenic proteins have proven recalcitrant to conventional approaches for chemical probe and drug discovery. Here, we discuss how innovations in chemical proteomics and covalent chemistry are being integrated to identify and advance first-in-class small molecules that target cancer-relevant proteins. Mechanistic studies have revealed that covalent compounds perturb protein functions in cancer cells in diverse ways that include the remodeling of protein–protein and protein–RNA complexes, as well as through alterations in posttranslational modification. We speculate on the attributes of chemical proteomics and covalent chemistry that have enabled targeting of previously inaccessible cancer-relevant pathways and consider technical challenges that remain to be addressed in order to fully realize the druggability of the cancer proteome.

Abstract 3366: FoRx-06-428 is a novel PARG inhibitor with potent anti-tumor efficacy in preclinical cancer models

Abstract The formation of poly(ADP-ribose) (PAR) chains from NAD+ precursors by PARP enzymes is a characteristic posttranslational modification during DNA damage repair. PAR chains function as docking platforms for DNA repair proteins that are required to resolve DNA lesions. Equally important is the subsequent removal of PAR chains from protein substrates to conclude the repair process and restore genomic integrity. Poly(ADP-ribose) glycohydrolase (PARG) is the key enzyme in this process and has recently garnered significant attention as a novel cancer target. FoRx-06-428 is a novel, orally bioavailable and highly potent, low molecular weight PARG inhibitor. It binds to the catalytic domain of human PARG with high affinity, as evidenced by surface plasmon resonance (SPR), and displays potent inhibition of enzymatic activity. FoRx-06-428 shows selective reduction of viability in a panel of cancer cell lines highlighting therapeutic potential in multiple cancer indications. Pharmacological inhibition of PARG leads to accumulation of PAR chains and is indicative of target engagement, accompanied by modulation of DNA damage response markers, such as phosphorylation of replication protein A (pRPA) and phosphorylation of H2AX (γH2AX). Compelling anti-tumor efficacy as single agent was observed in several xenograft models (breast and gastric cancer) with excellent tolerability. Dose-dependent accumulation of PAR chains was demonstrated in vivo and constitutes a tractable target engagement biomarker for clinical exploration. Sensitivity to PARG inhibition is partly driven by distinct genomic instabilities, such as defects in homologous recombination (HR) repair, however the activity of PARG inhibitors is also influenced by aberrations in other cancer-relevant pathways. This report represents the first disclosure of the pharmacological characterization of FoRx-06-428 and highlights the value of PARG inhibition as a novel targeted approach to treat DNA repair-deficient cancers. Citation Format: Olivier Querolle, Ulrich Lücking, Luca Iacovino, Alena Freudenmann, Giacomo Rossetti, Marina Gysin, Serena Bologna, Vasilis Dionellis, Marta Malattia, Alessandro Potenza, Nicolas Bocquet, Irena Konstantinova, Andreas Goutopoulos, Sotirios Sotiriou, Thanos Halazonetis, Tarig Bashir, Frank Zenke. FoRx-06-428 is a novel PARG inhibitor with potent anti-tumor efficacy in preclinical cancer models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3366.

Blood-Based microRNA Biomarker Signature of Early-Stage Pancreatic Ductal Adenocarcinoma With Lead-Time Trajectory in Prediagnostic Samples

Clinically validated biomarker of pancreatic ductal adenocarcinoma (PDAC), carbohydrate antigen 19-9 (CA19-9), has limited sensitivity and specificity for early-stage disease. Circulating miRNAs in plasma associated with cancer relevant pathways were developed as early detection biomarkers. 2083 miRNAs in 15 μl of plasma from multicenter age-matched cohorts (N= 203: healthy controls, n= 46; pancreatitis controls, n= 36; diagnosed cases: n= 121) and a prediagnostic Prostate, Lung, Colorectal, and Ovarian age- and gender-matched cohort (N=96; controls, n= 48; prediagnosed cases, n= 48) were interrogated. A three-miRNA biomarker signature was developed for early-stage PDAC. The three-miRNA signature (let-7i-5p, miR-130a-3p and miR-221-3p) detected PDAC from healthy controls independently (area under the curve [AUC] of stage I, II, I-IV= 0.970, 0.975, 0.974) and in combination with CA19-9 (AUC of stage I, II, I-IV= 1.000, 0.992, 0.995). It also discriminated chronic pancreatitis (AUC of stage I, II, I-IV= 0.932, 0.931, 0.929), improving performance of CA19-9 alone (AUC of stage I, II, I-IV= 0.763, 0.701, 0.735) in combination (AUC of stage I, II, I-IV= 0.971, 0.943, 0.951). Blinded validation in prediagnostic Prostate, Lung, Colorectal, and Ovarian cohort revealed lead-time trajectory increase in AUC from 0.702 to 0.729 to 0.757 at twelve-, six-, and three-months before PDAC diagnosis, respectively. The signature also helped stratification of patients with different circulating tumor DNA and imaging subtypes. Plasma miRNAs associated with oncogenic pathways may serve as PDAC early detection biomarkers.

The Role of Curcumin in Gastric Carcinoma by Modulating the Immune System and its SAR

The second most prevalent cancer in the world and the fifth most common malignant tumour is gastric carcinoma. It is thought that several factors, including genetics, epigenetics, and environmental impacts, contribute to the development of gastric cancer. One of the main pathogenic variables associated with stomach cancer risk has been identified as inflammation. There are currently few methods to treat the gastric carcinoma. Therefore, an alternative plan is urgently needed. Explaining the importance of curcumin derived from Curcuma longa Linn. in stomach cancer is the goal of this review. According to recent research, Curcumin (CUR) has a great effect against stomach mucosal injury brought on by non-steroidal anti-inflammatory medicines, gastric mucosal injury in rats, stress haemorrhage, and Helicobacter pylori infection. In this review article, we have discussed the chemistry of CUR, the role of CUR in immunomodulation, and gastric cancer. We have also highlighted the various signalling pathway of gastric cancer where CUR work. By controlling miRNAs on gastric cancer and other relevant signal pathways, CUR exhibits notable anti-inflammatory and anti-cancer properties. In future there are more research work will be done on CUR.

Epigenomic reprogramming of therapy-resistant circulating tumor cells in colon cancer.

Therapy resistance is a major challenge in colorectal cancer management. Epigenetic changes, such as DNA methylation, in tumor cells are involved in the development of acquired resistance during treatment. Here, we characterized the DNA methylation landscape of colon circulating tumor cells (CTCs) during cancer progression and therapy resistance development. To this aim, we used nine permanent CTC lines that were derived from peripheral blood samples of a patient with metastatic colon cancer collected before treatment initiation (CTC-MCC-41) and during treatment and cancer progression (CTC-MCC-41.4 and CTC-MCC-41.5 [A-G]). We analyzed the DNA methylome of these nine CTC lines using EPIC arrays and also assessed the association between DNA methylation and gene expression profiles. We confirmed DNA methylation and gene expression results by pyrosequencing and RT-qPCR, respectively. The global DNA methylation profiles were different in the pre-treatment CTC line and in CTC lines derived during therapy resistance development. These resistant CTC lines were characterized by a more hypomethylated profile compared with the pre-treatment CTC line. Most of the observed DNA methylation differences were localized at CpG-poor regions and some in CpG islands, shore regions and promoters. We identified a distinctive DNA methylation signature that clearly differentiated the pre-treatment CTC line from the others. Of note, the genes involved in this signature were associated with cancer-relevant pathways, including PI3K/AKT, MAPK, Wnt signaling and metabolism. We identified several epigenetically deregulated genes associated with therapy resistance in CTCs, such as AP2M1. Our results bring new knowledge on the epigenomic landscape of therapy-resistant CTCs, providing novel mechanisms of resistance as well as potential biomarkers and therapeutic targets for advanced CRC management.

PhosphoDisco: A Toolkit for Co-regulated Phosphorylation Module Discovery in Phosphoproteomic Data

Kinases are key players in cancer-relevant pathways and are the targets of many successful precision cancer therapies. Phosphoproteomics is a powerful approach to study kinase activity and has been used increasingly for the characterization of tumor samples leading to the identification of novel chemotherapeutic targets and biomarkers. Finding co-regulated phosphorylation sites which represent potential kinase-substrate sets or members of the same signaling pathway allows us to harness these data to identify clinically relevant and targetable alterations in signaling cascades. Unfortunately, studies have found that databases of co-regulated phosphorylation sites are only experimentally supported in a small number of substrate sets. To address the inherent challenge of defining co-regulated phosphorylation modules relevant to a given dataset, we developed PhosphoDisco, a toolkit for determining co-regulated phosphorylation modules. We applied this approach to tandem mass spectrometry based phosphoproteomic data for breast and non-small cell lung cancer and identified canonical as well as putative new phosphorylation site modules. Our analysis identified several interesting modules in each cohort. Among these was a new cell cycle checkpoint module enriched in basal breast cancer samples and a module of PRKC isozymes putatively co-regulated by CDK12 in lung cancer. We demonstrate that modules defined by PhosphoDisco can be used to further personalized cancer treatment strategies by establishing active signaling pathways in a given patient tumor or set of tumors, and in providing new ways to classify tumors based on signaling activity.

Genome-wide characterization of extrachromosomal circular DNA in gastric cancer and its potential role in carcinogenesis and cancer progression

Extrachromosomal circular DNAs (eccDNAs) carrying random genomic segments are broadly found across different cancer types, but their molecular functions and impact in gastric cancer (GC) are rarely known. In this study, we aimed to investigate the potential role of eccDNA in GC. Using the Circle-seq strategy, we observed the eccDNA abundance in gastric cancer tissues (GCT) was aberrantly higher than that of normal adjacent tissues (NAT). The high abundance of eccDNAs carrying oncogene-segments in GCT may represent the DNA damage products of amplified oncogenes. Analysis of GCT over-represented eccDNA carrying enhancer (eccEnhancer) based on data from FANTOM5 project combined with TCGA database suggested the GC over-represented eccEnhancers may contribute to development of GC. GC over-represented eccDNAs carrying pre-miRNA (eccMIR) were enriched to multiple cancer-relevant signal pathways by KEGG analysis. We then synthesized the top six GC over-represented eccMIRs and found four of them enabled high expression of miRNAs and down-regulation of miRNA-target genes in MGC803 cells. Furthermore, we observed the inheritance of GC over-represented eccMIRs benefited host cell proliferation and promoted the aggressive features of host cells. Altogether, this study revealed the GC over-represented eccDNAs carrying functional genomic segments were related to the carcinogenesis of GC and presented the capability to facilitate cancer progression, suggesting the cancerous eccDNAs may serve as a dynamic reservoir for genome plasticity and rapid adaptive evolution of cancer. Therefore, blocking the pathways for eccDNAs generation may provide a novel therapeutic strategy for the treatment of gastric cancer.

Abstract A001: Differential alternative RNA splicing and transcription events between Black and White prostate cancer patients involve genes promoting cancer aggressiveness and associate with patient survival

Abstract Black patients suffer disproportionately from prostate cancer (PCa) progression to lethal disease compared with Asian and White patients. Comparing the molecular landscape of PCa in Black and White men has the potential to identify targets for development of new precision medicine interventions. Alternative RNA splicing and transcription events (ARS/Ts) can alter gene function. Cancer may exploit ARS/Ts to enhance proliferation, metastasis, and drug resistance. Here, we isolated RNA from fresh frozen PCa specimens and tumor-associated normal (TAN) specimens from 35 self-reported Black and 37 self-reported White patients diagnosed with Gleason-high or -low PCa and undergoing radical prostatectomy or biopsy. Analysis of follow-up clinical data for patients participating in our study show an increased hazard ratio of PCa progression among Black patients compared to White patients (HR = 2.13 and p < 0.05). We performed comparative transcriptomic analysis between Gleason-high or -low tumor and TAN samples among Blacks, among Whites, or between Blacks and Whites with Gleason-high or –low PCa. Among differential ARS/Ts identified between tumors and TANs among Blacks, 532 are unique to Gleason-high and 673 are unique to Gleason-low. Among differential ARS/Ts between Blacks and Whites, 360 are unique to Gleason-high and 242 are unique to Gleason-low. Interestingly, we found that even in TANs, there are 802 differential ARS/Ts between Blacks and Whites, with 459 and 343 in Gleason-high and Gleason-low, respectively. Among the genes undergoing differential ARS/Ts between Blacks and Whites are FGFR1, AKT1, H6PD, MDM2, and RAD51D in Gleason-high and CDK7 and VEGFA in Gleason-low. Notably, the number of genes undergoing ARS/Ts between Blacks and Whites with Gleason-high or -low tumors was higher than the number of genes undergoing differential aggregate gene expression between Blacks and Whites. Using gene set enrichment analysis, we found that genes undergoing ARS/Ts function in cancer relevant pathways. For example, the genes undergoing ARS/Ts between Blacks and Whites with Gleason-high or -low tumors were enriched in spermatogenesis and P53 hallmark pathways, respectively. Importantly, survival analysis shows a number of differential ARS/Ts between Blacks and Whites with Gleason-high or -low tumors are individually associated with progression-free survival. In summary, we have investigated the biology of PCa and TAN tissue between Black and White patients at the exon level. A number of genes undergoing newly identified differential ARS/Ts between Blacks and Whites are in genes reported to promote cancer aggressiveness and a number are in genes whose function in cancer was unreported prior to our findings, and a number are associated with patient progression-free survival. Our findings have identified novel targets with potential for precision oncology for PCa. Estimation of genetic ancestry of study participants and in vitro and in vivo validation of prioritized targets for PCa biology are underway. Citation Format: Muthana Al Abo, Wen-Chi Foo, Lauren Howard, Monika Anand, Daniel J. George, Steven R. Patierno, Jennifer A Freedman. Differential alternative RNA splicing and transcription events between Black and White prostate cancer patients involve genes promoting cancer aggressiveness and associate with patient survival [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr A001.

Comprehensive plasma genotyping of patients with EGFR positive NSCLC as a monitoring tool for therapy response and disease progression.

e20598 Background: Targeted therapy against molecular drivers has revolutionized the NSCLC standard of care. EGFR activating mutations (mEGFR) are most prominent in Asian NSCLC patients and can benefit from tyrosine kinase inhibitor (TKi) therapy. NCCN guidelines recommend screening lung tumors for detecting mEGFR as a standard of care for TKi inhibitor therapy. However, a significant number of patients with mEGFR do not respond well to TKi due to naturally occurring or therapy-induced TKi blunting mutations. Small gene panels may fail to detect concomitant rare mutations, e.g genomic instability. We longitudinally monitored mEGFR dynamics and the presence of cooccurring clinically important mutations using a comprehensive gene panel in NSCLC patients. Methods: We retrospectively analyzed outcomes from the plasma genotyping of 150 samples from 25 mEGFR-positive NSCLC pts on TKi therapy. For NGS, ctDNA was isolated from longitudinally collected plasma samples (at diagnosis, and during Tx including PD). Libraries prepared using a custom-designed comprehensive gene panel OncoIndx to target 600 cancer-relevant exons, including MSI and HRR pathway genes, were target captured and sequenced in pair-end mode on Illumina platform Nextseq2000. Variant calling was performed using an in-house developed bioinformatics pipeline based on GATK environment. Results: ex 19 deletion variant was the most frequent (35 %) mEGFR followed by L858R (20 %) and T790M (10 %). Rest 10 % had other mutations, including TP53, KRAS, TGFBR1 and PTEN and 25 % of the longitudinal samples did not show any mutations. In 40 % of patients increase in mEGFR vaf correlated with the clinical progression. Surprisingly, these patients had either TP53, RB1 or TGFBR1 variants cooccurring with mEGFR. For the remaining patients, we did not observe a clear temporal correlation with mEGFR vaf. This was corroborated well by the absence of any TKi blunting mutations among these patients. T790M variants were detected only at the progression onset and were absent at earlier time points. MGA, TP53, and RB1 variants were detected along high mEGFR vaf in 10 % of patients around the time of clinical progression. At the genomic scale, TMB scores were low and did not vary longitudinally among the pts. HRD and LOH sores were high and correlated well in patients with mEGFR cooccurrence along variants such as KRAS, TP53, PTEN, and BAP1. Conclusions: Comprehensive plasma genotyping identified cooccurring key drivers that correlated with the clinical progression. Their presence may suggest the blunting effect of TKi and early progression. The patient with high genome instability scores may benefit from HRR inhibitor +TKi combination therapy in EGFR-positive pts. A small patient cohort limits the interpretation of this data and warrants further investigation through clinical trials.

Abstract 4811: Oxygen tension - dependent differences in cancer cell kinome

Abstract Current approaches to preclinical cancer research often fail to consider the impact of ambient oxygen (O2; ~21%) on cancer cells. This is also true for hypoxia studies that typically involves cancer cells previously grown in ambient O2 before subsequent transfer to hypoxia. However, the tumor microenvironment is characterized by significantly lower O2 levels. We have previously demonstrated the impact of ambient O2 on stem cell populations, signaling pathways and resistance to therapy. We developed an experimental approach that allows us to collect and process tumor tissues from transgenic mammary tumor mouse models and ovarian cancer patients under physioxia (3% O2), such that they are never exposed to ambient O2. In this study, our goal was to explore oxygen-dependent signaling pathway alterations and to determine how these pathways are influenced by targeted drugs in the context of physioxia or ambient air (AA). Our studies revealed increased basal phosphorylation levels of EGFR (Y1068) in the tumor cells in AA, relative to physioxia. However, downstream signaling effectors AKT and ERK showed higher phosphorylation levels under physioxia, compared to AA, suggesting that their activation is independent of EGFR signaling. These findings correlate with the decreased sensitivity of the tumor cells under physioxia to target drugs lapatinib and alpelisib. We then sought to examine basal and target drug induced kinome changes in tumor cells under physioxia and AA via Multiplexed Inhibitor Beads (MIBs) kinome assay. This assay revealed significant differences in the kinome of the tumor cells under physioxia compared to AA. Although direct comparison between vehicle and lapatinib treated cells in physioxia and ambient air showed very minimal changes, pairwise comparison between lapatinib treated physioxia cells and vehicle treated AA cells revealed an increase in the activity of PDGFRB in lapatinib treated physioxia cells. Similarly, a receptor tyrosine kinase (RTK) array and western blotting showed increased basal and lapatinib induced phosphorylation of PDGFRB (Y751) under physioxia. Next, we determined the potential role of PDGFRB in downstream signaling pathway activation of AKT and ERK and resistance to lapatinib. We found that sunitinib, a multitarget RTK inhibitor with high affinity for PDGFR effectively decreased PGDFRB activity under physioxia, with a concurrent decrease in the phosphorylation of AKT. Moreover, tumor cells under physioxia were more sensitive to sunitinib treatment, relative to ambient air. Furthermore, a combination of lapatinib and sunitinib rendered tumor cells under physioxia more sensitive to treatment than with lapatinib alone. These findings suggest that ambient and physioxic oxygen tensions differentially impact cancer relevant signaling pathways. Therefore, it may be necessary to carry out preclinical cancer studies in the context of physiologically relevant oxygen tensions to aid translatability. Citation Format: Adedeji K. Adebayo, Brijesh Kumar, Christopher Davis, Steven P. Angus, Harikrishna Nakshatri. Oxygen tension - dependent differences in cancer cell kinome. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4811.

462 RNA-Based Therapeutics Targeting the Oncogenic Splicing Factor TRA2β Rewire Glioblastoma Cell Transcriptomes and Inhibit Their Proliferation

INTRODUCTION: Glioblastomas are an aggressive brain tumor that, despite current treatment paradigms, carry a poor prognosis. Novel therapies aimed at specific glioblastoma alterations are needed. Alternative RNA splicing is a critical step in gene expression that allows a single gene to encode multiple RNA and subsequently protein isoforms. Alternative splicing becomes dysregulated in human tumors, including glioblastoma, through alterations in upstream regulatory splicing factor proteins such as TRA2β, an oncogene that enhances glioma cell proliferation. Despite these known alterations, targeting alternative splicing in glioblastomas has not been leveraged therapeutically. METHODS: U87MG glioblastoma cells were treated with splice-switching antisense oligonucleotides (ASOs) targeting the TRA2β transcript (ASO-1570) or non-targeting control (ASO-CTL). Cancer-relevant phenotypes, including proliferation and apoptosis, were measured using high-content imaging. Transcriptomic splicing signatures were defined using high-depth RNA-sequencing with computational tools that quantify percent splicing event inclusion (PSI) and validated using RT-PCR and western blotting. RESULTS: ASO-1570 treatment increased inclusion of a poison-exon in TRA2β leading to decreased coding transcripts and subsequent reductions in TRA2β protein expression compared to ASO-CTL. ASO-1570 significantly decreased cell proliferation and increased apoptosis. Mechanistically, ASO-1570 treated cells exhibited significant differences in alternatively spliced events, impacting genes involved in cancer-relevant pathways such as p53 and mTOR signaling. For example, ASO-1570 led to increased exon skipping in MDM2 leading to decreased MDM2 protein expression and increased p53 wild-type expression. ASO-1570 treatment also impacted growth of U87MG 3D-neurospheres, suggesting efficacy in advanced models that better capture in vivo conditions. CONCLUSIONS: Glioblastoma cells are sensitive to ASO-mediated TRA2β knockdown, which mechanistically induced transcriptome wide changes that impact cancer-related pathways. Further testing of this ASO in vivo may open novel avenues for its use as a targeted glioblastoma therapeutic.

Selection of Optimal Cell Lines for High-Content Phenotypic Screening

High-content microscopy offers a scalable approach to screen against multiple targets in a single pass. Prior work has focused on methods to select "optimal" cellular readouts in microscopy screens. However, methods to select optimal cell line models have garnered much less attention. Here, we provide a roadmap for how to select the cell line or lines that are best suited to identify bioactive compounds and their mechanism of action (MOA). We test our approach on compounds targeting cancer-relevant pathways, ranking cell lines in two tasks: detecting compound activity ("phenoactivity") and grouping compounds with similar MOA by similar phenotype ("phenosimilarity"). Evaluating six cell lines across 3214 well-annotated compounds, we show that optimal cell line selection depends on both the task of interest (e.g., detecting phenoactivity vs inferring phenosimilarity) and distribution of MOAs within the compound library. Given a task of interest and a set of compounds, we provide a systematic framework for choosing optimal cell line(s). Our framework can be used to reduce the number of cell lines required to identify hits within a compound library and help accelerate the pace of early drug discovery.

Abstract C049: Investigating cancer racial disparities through TCGA transcriptomic and proteomic database

Abstract In the United States, epidemiological studies have highlighted a disparity in cancer incidence and outcome rates between racial groups. This disparity is attributed to numerous factors, including gene polymorphisms, differences in lifestyle and environmental exposures, and socioeconomic factors. Although an abundance of tumor molecular data exists, the effect of race on gene expression signatures often remains unexplored. In this project, we investigated racial molecular differences in tumors of 10 carcinoma types. We used publicly available data from The Cancer Genome Atlas (TCGA) in conjunction with online analysis tools to identify patterns of differential gene expression in tumors obtained from 4,112 White, Black/African American, and Asian patients. We identified race-dependent expression of numerous genes whose mRNA transcript levels were significantly correlated with patient survival outcomes. A small subset of these genes was differentially expressed in multiple carcinomas, including genes involved in cell cycle progression such as CCNB1, CCNE1, CCNE2, and FOXM1. This suggests that cell cycle dysregulation is a major culprit in the health disparity. In contrast, genes such as transcriptional factor ETS1 and apoptotic gene BAK1 were differentially expressed and clinically significant only in specific cancer types. In numerous cancer types we also observed race-dependent regulation of cancer-relevant biological pathways, especially DNA repair mechanisms. This large-scale pan-cancer study refines our understanding of the molecular basis for the cancer racial health disparity and can help inform the use of novel biomarkers in clinical settings as well as the future development of precision therapies. Citation Format: Brian Lei, Anjana Saxena. Investigating cancer racial disparities through TCGA transcriptomic and proteomic database [abstract]. In: Proceedings of the 15th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2022 Sep 16-19; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr C049.

Anesthetic‑specific lncRNA and mRNA profile changes in blood during colorectal cancer resection: A prospective, matched‑case pilot study.

Prometastatic and antitumor effects of different anesthetics have been previously analyzed in several studies with conflicting results. Thus, the underlying perioperative molecular mechanisms mediated by anesthetics potentially affecting tumor phenotype and metastasis remain unclear. It was hypothesized that anesthetic‑specific long non‑coding RNA (lncRNA) expression changes are induced in the blood circulation and play a crucial role in tumor outcome. In the present study, high‑throughput sequencing and quantitative PCR were performed in order to identify lncRNA and mRNA expression changes affected by two therapeutic regimes, total intravenous anesthesia (TIVA) and volatile anesthetic gas (VAG) in patients undergoing colorectal cancer (CRC) resection. Total blood RNA was isolated prior to and following resection and characterized using RNA sequencing. mRNA‑lncRNA interactions and their roles in cancer‑related signaling of differentially expressed lncRNAs were identified using bioinformatics analyses. The comparison of these two time points revealed 35 differentially expressed lncRNAs in the TIVA‑group, and 25 in the VAG‑group, whereas eight were shared by both groups. Two lncRNAs in the TIVA‑group, and 23 in the VAG‑group of insilico identified target‑mRNAs were confirmed as differentially regulated in the NGS dataset of the present study. Pathway analysis was performed and cancer relevant canonical pathways for TIVA were identified. Target‑mRNA analysis of VAG revealed a markedly worsened immunological response against cancer. In this proof‑of‑concept study, anesthesic‑specific expression changes in lncRNA and mRNA profiles in blood were successfully identified. Moreover, the data of the present study provide the first evidence that anesthesia‑induced lncRNA pattern changes may contribute further in the observed differences in CRC outcome following tumor resection.

Deregulation of SPOP in Cancer.

Speckle-type POZ protein (SPOP) is a substrate-binding adaptor of the CULLIN3/RING-box1 E3 ubiquitin ligase complex. SPOP is frequently mutated in prostate and endometrial cancers, whereas it is overexpressed in renal cell carcinoma (RCC). SPOP can mediate both degradable and nondegradable polyubiquitination of a number of substrates with diverse biological functions such as androgen receptor (AR), SRC-3, TRIM24, BRD4, PD-L1, 53BP1, GLP/G9a, c-Myc, SENP7, among others. Cancer-associated SPOP mutants often impair SPOP binding and polyubiquitination of its substrates to influence various cancer-relevant pathways, which include androgen/AR signaling, DNA repair and methylation, cellular stress surveillance, cancer metabolism, and immunity. Although SPOP is recognized as a tumor suppressor in prostate and endometrial cancers, it acts like an oncoprotein in RCC. This review provides an overview of the recent progress in understanding of the upstream regulators of SPOP and its downstream targets, highlights the significant impact of SPOP mutations and overexpression on cancer pathogenesis, and discusses the potential of targeting SPOP for cancer treatment.

Nested Therapeutics rakes in $90 million series A

Nested Therapeutics has launched with $90 million in series A funding to develop small-molecule cancer medicines by identifying druggable pockets on proteins involved in cancer-relevant pathways. The company’s lead compound, NEST-1, is a molecular glue that targets the proteins involved in the MAPK cellular signaling pathway. One scientific cofounder is Kevan Shokat, a University of California, Berkeley, chemistry professor who first drugged the protein KRas.

ScAllele: A versatile tool for the detection and analysis of variants in scRNA-seq.

Single-cell RNA sequencing (scRNA-seq) data contain rich information at the gene, transcript, and nucleotide levels. Most analyses of scRNA-seq have focused on gene expression profiles, and it remains challenging to extract nucleotide variants and isoform-specific information. Here, we present scAllele, an integrative approach that detects single-nucleotide variants, insertions, deletions, and their allelic linkage with splicing patterns in scRNA-seq. We demonstrate that scAllele achieves better performance in identifying nucleotide variants than other commonly used tools. In addition, the read-specific variant calls by scAllele enables allele-specific splicing analysis, a unique feature not afforded by other methods. Applied to a lung cancer scRNA-seq dataset, scAllele identified variants with strong allelic linkage to alternative splicing, some of which are cancer specific and enriched in cancer-relevant pathways. scAllele represents a versatile tool to uncover multilayer information and previously unidentified biological insights from scRNA-seq data.

Using multi-omic network analysis to identify cancer-relevant signaling pathways and novel biomarkers

Using multi-omic network analysis to identify cancer-relevant signaling pathways and novel biomarkers

S-palmitoylation of PCSK9 induces sorafenib resistance in liver cancer by activating the PI3K/AKT pathway.

Sorafenib is currently the first-line treatment for advanced hepatocellular carcinoma (HCC). However, sorafenib resistance remains a significant challenge. Aberrant AKT signaling activation is a crucial mechanism driving sorafenib resistance in HCC. Proprotein convertase subtilisin/kexin type 9 (PCSK9) plays a vital role in antitumor immune responses. In this study, we demonstrate that aberrant PCSK9 upregulation promotes cell proliferation and sorafenib resistance in HCC by inducing AKT-S473 phosphorylation. After palmitoylation at cysteine 600, the binding affinity between PCSK9 and tensin homolog (PTEN) is dramatically increased, inducing lysosome-mediated PTEN degradation and subsequent AKT activation. We identify zinc finger DHHC-type palmitoyltransferase 16 (ZDHHC16) as a palmitoyltransferase that promotes PCSK9 palmitoylation at cysteine 600. We also develop a biologically active PCSK9-derived peptide that competitively inhibits PCSK9 palmitoylation, suppressing AKT phosphorylation and augmenting the antitumor effects of sorafenib in HCC.

Biomolecular Condensation: A New Phase in Cancer Research.

One of the fundamental functions of phase separation is to rapidly and dynamically respond to environmental perturbations. Importantly, these changes often lead to alterations in cancer-relevant pathways and processes. This review covers recent advances in the field, including emerging principles and mechanisms of phase separation in cancer.