Heinz-Josef Lenz

182Background: Sex-based disparities have been reported for mCRC both in incidence, males having higher incidence than females, and in outcome, younger females having better outcome than males of same age or older females. Tumor immune microenvironment is hypothesized to have role in this sexual dimorphic pattern. Herein, we explored the role of gene expression (exp) and genetic variation of IRGs on progression-free (PFS) and overall survival (OS) in mCRC pts. Methods: 21 IRGs with potential roles in CRC were identified from literature review. The association of tumor gene exp with PFS and OS was evaluated in pts with mCRC (433 pts, RNA seq) from CALGB/SWOG 80405. Subgroup analyses were based on treatment (bevacizumab [bev] (N = 226) / cetuximab [cet] (N = 207)) and sex (male (N = 271) / female (N = 162)). Further, the impact on outcome of 5 selected germline single nucleotide …

Background: Colorectal cancer (CRC) is the third most common cancer, and second cause of cancer death in the United States (US). Among US Hispanic/Latino/a/x (H/L) individuals, CRC represents the second and the third most common cancer and the most common cause of cancer death for men and women, respectively. Despite this, the tumor landscape, and key determinants of outcomes in CRC H/L patients are understudied. Methods: To address this need, we launched the ENLACE study, to engage H/L CRC patients in germline and somatic sequencing and identify the optimal approaches for patient participation. Through the Center for Patient Engagement in Cancer Characterization Studies (COPECC) patients were recruited from two healthcare facilities: a safety-net hospital (Los Angeles General Medical Center, LA Gen) and the USC Norris Comprehensive Cancer Center (Norris) a university medical …

174Background: Few genome-wide investigations have examined germline variants associated with mCRC outcomes following primary treatment. Here, we performed a GWAS meta-analysis to explore the impact of germline genetic variation on progression-free survival (PFS) and overall survival (OS) in four clinical trials of mCRC. Methods: The GWAS comprised 1,324 mCRC patients (pts) enrolled in four randomized Phase II/III trials for first line treatment: FIRE-3 (FOLFIRI-bevacizumab [bev]; FOLFIRI-cetuximab[cet]), MAVERICC (FOLFIRI-bev; FOLFOX6-bev), TRIBE (FOLFIRI-bev; FOLFOXIRI-bev), and TRIBE2 (mFOLFOX6-bev; FOLFOXIRI-bev). DNA isolated from blood was genotyped using the OncoArray and imputed against the Haplotype Reference Consortium panel. In each trial arm, associations between SNPs and PFS and OS were assessed using an additive coding in a Cox proportional hazard …

172Background: Lemur tail kinase 3 (LMTK3) plays a critical role in multiple cellular pathways such as Wnt signaling, KIT modulation, and the estrogen receptor pathway. We previously reported that LMTK3 gene polymorphisms are associated with clinical outcome in patients with CRC, and that LMTK3 and estrogen-mediated signaling play a crucial role in CRC tumorigenesis in vitro. Here, we aimed to characterize the molecular features associated with LMTK3 gene expression in CRC. Methods: 20,219 CRC were tested at Caris Life Sciences (Phoenix, AZ) with NextGen Sequencing on DNA (592 genes or WES) and RNA (WTS). Top quartile transcripts per million (TPM) for LMTK3 expression (Q4) were considered high while bottom quartile (Q1) low. Consensus molecular subtypes (CMS) were assessed using RNAseq. Cell infiltration (CI) in the tumor microenvironment (TME) was estimated by QuantiSEQ. X2 and …

Background: Plant-based diet is recommended by multiple cancer survivorship guidelines and was reported to be associated with better survival among patients with non-metastatic colorectal cancer. However, the association between plant-based diet and survival in metastatic colorectal cancer is unknown. Methods: Using an NCI-sponsored systemic therapy trial conducted from 2005 to 2015 (CALGB/SWOG 80405), we included 1,279 patients who completed validated food frequency questionnaires at the initiation of treatment for metastatic colorectal cancer. To emphasize different impact of healthful plant foods, less healthful plant foods, and animal foods, we used 18 food groups to calculate three plant-based indexes (ranges: 18-90 points): overall plant-based diet index (PDI), healthful plant-based diet index (hPDI), and unhealthful plant-based diet index (uPDI). The primary outcome was overall survival, and …

PurposeProgrammed death receptor ligand-1 (PD-L1) expression and tumor mutational burden (TMB) are approved screening biomarkers for immune checkpoint inhibition (ICI) in advanced triple negative breast cancer. We examined these biomarkers along with characterization of the tumor microenvironment (TME) between breast tumors (BrTs), axillary metastases (AxMs), liver metastases (LvMs), non-axillary lymph node metastases, and non-liver metastases to determine differences related to site of metastatic disease.Methods3076 unpaired biopsies from breast cancer patients were analyzed using whole transcriptome sequencing and NextGen DNA depicting TMB within tumor sites. The PD-L1 positivity was determined with VENTANA PD-L1 (SP142) assay. The immune cell fraction within the TME was calculated by QuantiSeq and MCP-counter.ResultsCompared to BrT, more LvM samples had a high TMB …

PURPOSECALGB (Alliance)/SWOG 80405 was a randomized phase III trial that in first-line patients with metastatic colorectal cancer (mCRC) treated with bevacizumab or cetuximab with chemotherapy. We aimed to discover novel mutated genes associated with prognosis and differential response to therapy with the biologics.METHODSPrimary tumor DNA from 548 patients was sequenced using FoundationOne. The effect of mutated genes and mutations on overall survival (OS) was tested adjusting for microsatellite instability status, BRAF V600E, all RAS mutations, arm, sex, and age.RESULTSThe median number (lower-upper quartile) of mutated genes was 5 (3-7), 5 (3-6) in microsatellite stable and 12.5 (4.5-32) in microsatellite instability-high tumors. Mutated KRAS and APC were more frequent in Black (53% and 85%) than White (27% and 65%, respectively) patients while BRAF V600E was less frequent in …

Prior observational studies suggest an association between intra-pancreatic fat deposition (IPFD) and pancreatic ductal adenocarcinoma (PDAC); however, the causal relationship is unclear. To elucidate causality, we conduct a prospective observational study using magnetic resonance imaging (MRI)-measured IPFD data and also perform a Mendelian randomization study using genetic instruments for IPFD. In the observational study, we use UK Biobank data (N = 29,463, median follow-up: 4.5 years) and find that high IPFD (>10%) is associated with PDAC risk (adjusted hazard ratio [HR]: 3.35, 95% confidence interval [95% CI]: 1.60–7.00). In the Mendelian randomization study, we leverage eight out of nine IPFD-associated genetic variants (p < 5 × 10−8) from a genome-wide association study in the UK Biobank (N = 25,617) and find that genetically determined IPFD is associated with PDAC (odds ratio [OR] per 1 …

Circadian clock genes are emerging targets in many types of cancer, but their mechanistic contributions to tumor progression are still largely unknown. This makes it challenging to stratify patient populations and develop corresponding treatments. In this work, we show that in breast cancer, the disrupted expression of circadian genes has the potential to serve as biomarkers. We also show that the master circadian transcription factors (TFs) BMAL1 and CLOCK are required for the proliferation of metastatic mesenchymal stem-like (mMSL) triple-negative breast cancer (TNBC) cells. Using currently available small molecule modulators, we found that a stabilizer of cryptochrome 2 (CRY2), the direct repressor of BMAL1 and CLOCK transcriptional activity, synergizes with inhibitors of proteasome, which is required for BMAL1 and CLOCK function, to repress a transcriptional program comprising circadian cycling genes in mMSL TNBC cells. Omics analyses on drug-treated cells implied that this repression of transcription is mediated by the transcription factor binding sites (TFBSs) features in the cis-regulatory elements (CRE) of clock-controlled genes. Through a massive parallel reporter assay, we defined a set of CRE features that are potentially repressed by the specific drug combination. The identification of cis-element enrichment may serve as a new way of defining and targeting tumor types through the modulation of cis-regulatory programs, and ultimately provide a new paradigm of therapy design for cancer types with unclear drivers like TNBC.

Neoadjuvant chemotherapy is a common treatment for patients with gastric cancer. Although its benefits have been demonstrated, neoadjuvant chemotherapy is underutilized in gastric cancer management, because of the lack of biomarkers for patient selection and a limited understanding of resistance mechanisms. Here, we performed whole-genome, whole-exome, and RNA sequencing on 84 clinical samples (including matched pre- and posttreatment tumors) from 35 patients whose responses to neoadjuvant chemotherapy were rigorously defined. We observed increased microsatellite instability and mutation burden in nonresponse tumors. Through comparisons of response versus nonresponse tumors and pre- versus posttreatment samples, we found that C10orf71 mutations were associated with treatment resistance, which was supported by drug response data and potentially through inhibition of cell cycle …

379Background: Histone-lysine N-methyltransferase 2 (KMT2) family proteins methylate lysine 4 on the histone H3 tail at important regulatory regions in the genome and thereby impart crucial functions through modulating chromatin structures and DNA accessibility, which is associated with tumorigenesis and immune tolerance, indicating its possible correlation with the efficacy of immunotherapy. Recurrent mutations of KMT2 have been identified in EC, but data addressing the molecular features of KMT2 mutated (MT) EC are lacking. We aimed to understand the molecular profile of KMT2 -MT EC. Methods: A total of 787 oesophageal carcinoma [adenocarcinoma (EAC), N=604; squamous cell carcinoma (ESCC), N=183] were analyzed using next-generation sequencing (NGS) and immunohistochemistry (Caris Life Sciences, Phoenix, AZ). Tumor mutational burden (TMB) was calculated based on somatic …

Background: Onvansertib (Onv) is an oral, small molecule, selective PLK1 kinase inhibitor that demonstrated clinical activity at tolerated drug exposures in combination with FOLFIRI/Bevacizumab (Bev) in the 2nd-line treatment of mutated KRAS (mKRAS) metastatic colorectal cancer (mCRC) (Lenz, JCO, 2022). Here we explored biomarkers of response to the combination therapy and their associated biology. Methods: In a Phase 1b/2 study, mKRAS mCRC patients with prior exposure to oxaliplatin (with or without Bev) were treated with Onv (Days 1-5 and 15-19) in combination with FOLFIRI/Bev (Days 1 and 15) of each 28-day cycle (NCT03829410). Efficacy endpoints included objective response rate (ORR, RECIST v1.1), progression-free survival (PFS) and duration of response (DoR). Preclinically, the combination of Onv and Bev was tested in 3 mKRAS CRC xenograft models. The role of PLK1 in hypoxia was …

Methods• Tumor profiling was performed for 13,942 samples by NextGen Sequencing on DNA (592-gene panel or WES) and RNA (WTS) at Caris Life Sciences (Phoenix, AZ).• 932 of these specimens were dMMR/MSI-H.• Cohorts were created based on top (Q4) and bottom (Q1) quartiles of CDK4/6 RNA expression (transcripts per million) and further divided based on TP53mt. TP53wt includes WT, VUS and benign/likely benign mutations• Chi-square, Fishers-exact, and Mann Whitney U tests were used to determine statistical significance and adjusted for multiple hypothesis testing by Benjamini-Hochberg (q< 0.05).• Cell infiltration in the TME was estimated by quanTIseq.

Background: Activating mutations in KRAS (including KRAS G12V) are well-described oncogenic drivers in solid tumors. Patients with KRAS driver mutations have a poor prognosis, and most KRAS-mutated cancers lack effective therapies. T cell receptor (TCR)-T cell therapies targeting mutant KRAS have demonstrated proof of concept in the clinic, but duration of response remains a challenge. AFNT-211 represents a novel strategy to address the immunosuppressive tumor microenvironment and improve response rate and duration in solid tumors. Rationale: AFNT-211 autologous CD4+ and CD8+ T cells are engineered to express a high avidity HLA-A*11:01restricted, KRAS G12V-specific, transgenic TCR; the wildtype CD8α/β coreceptor; and a FAS-41BB switch receptor. The intended mechanism of action is recognition and elimination of KRAS G12V-mutated tumor cells by AFNT-211. AFNT-211 is designed to …

BackgroundCDC37 is a key determinant of client kinase recruitment to the HSP90 chaperoning system. We hypothesized that kinase-specific dependency on CDC37 alters the efficacy of targeted therapies for metastatic colorectal cancer (mCRC).Material and methodsTwo independent mCRC cohorts were analyzed to compare the survival outcomes between CDC37-high and CDC37-low patients (stratified by the median cutoff values): the CALGB/SWOG 80405 trial (226 and 207 patients receiving first-line bevacizumab- and cetuximab-containing chemotherapies, respectively) and Japanese retrospective (50 refractory patients receiving regorafenib) cohorts. A dataset of specimens submitted to a commercial CLIA-certified laboratory was utilized to characterize molecular profiles of CDC37-high (top quartile, N = 5055) and CDC37-low (bottom quartile, N = 5055) CRCs.ResultsIn the bevacizumab-treated group …

BackgroundStandard first-line therapies for metastatic colorectal cancer (mCRC) include fluoropyrimidine-containing regimens with oxaliplatin and/or irinotecan and a biologic agent. Immunotherapy may enhance antitumor activity in combination with standard therapies in patients with mCRC. Here, we present phase 2 results of nivolumab plus standard-of-care therapy (SOC; 5-fluorouracil/leucovorin/oxaliplatin/bevacizumab) versus SOC in the first-line treatment of patients with mCRC (CheckMate 9X8).MethodsCheckMate 9X8 was a multicenter, open-label, randomized, phase 2/3 trial. Eligible patients were at least 18 years of age with unresectable mCRC and no prior chemotherapy for metastatic disease. Patients were randomized 2: 1 to receive nivolumab 240 mg plus SOC or SOC alone every 2 weeks. The primary endpoint was progression-free survival (PFS) by blinded independent central review (BICR) per …

Background: The identification of novel compounds that specifically target cancer cells while sparing normal tissues is crucial. The orphan tyrosine kinase-like receptor 1 (ROR1) is one such target expressed exclusively in various human malignancies, including pancreatic cancer, but not in normal adult tissues. Inhibiting ROR1 signaling shows promise in halting pancreatic cancer cell proliferation and invasion. In this study, lead compounds CSF1R-IN-1 and MCULE-8715589337 were found as potential inhibitors of the ROR1 and were further evaluated for its potential effect on pancreatic cancer cell viability. Method: We curated a compound library of 6 million from PubChem, 2 million lead-like compounds from ZINC15, and 2 million compounds from diverse vendors. Employing Glide’s HTVS followed by XP, we refined the selection based on docking scores lower than the reference molecule, Ponatinib …

LBA768Background: Patients (pts) with MSI-H/dMMR mCRC have poor outcomes with standard chemo ± targeted therapies. NIVO ± IPI are approved in previously treated pts with MSI-H/dMMR mCRC in many countries, based on the phase 2 CheckMate 142 study. CheckMate 8HW (NCT04008030) is a randomized phase 3 study comparing NIVO + IPI with NIVO or chemo in pts with MSI-H/dMMR mCRC. We report progression-free survival (PFS) by blinded independent central review (BICR) at a prespecified interim analysis for NIVO + IPI vs chemo in the 1L setting. Methods: Pts ≥ 18 years with recurrent or mCRC not amenable to surgery and MSI-H/dMMR status per local testing were enrolled across different lines of therapy. Previously untreated pts were randomized 2:2:1 to NIVO (240 mg) + IPI (1 mg/kg) Q3W (4 doses, then NIVO 480 mg Q4W), NIVO (240 mg) Q2W (6 doses, then NIVO 480 mg Q4W), or chemo …

TPS222Background: ME-344 is a synthetic small molecule that inhibits oxidative phosphorylation, resulting in energy starvation and cell death via caspase-dependent and -independent mechanisms. The activity of mitochondrial inhibitors is enhanced when mitochondrial respiration is upregulated, a situation achieved in solid tumors by inducing vascular normalization and hypoxia correction with antiangiogenics. In a CT26 colon carcinoma syngeneic murine model, ME-344 in combination with regorafenib showed significantly reduced tumor growth compared to regorafenib alone (Navarro et al. Cell Reports. 2016;15:2705). A randomized phase 0/1 window of opportunity study in HER2-negative breast cancer showed significant decrease in the proliferation marker Ki67 in patients administered ME-344 plus bevacizumab vs. bevacizumab alone (Quintela-Fandino et al, Clin Cancer Res. 2020;26:35). The current …

CONCLUSIONSThis is the largest molecular and clinical characterization of the myostatin activin cachexia pathway in PDAC. Our data shows that increased activation of the myostatin activin pathway is associated with immune mediators, lipid metabolism, and inflammatory gene activation. Activators and repressors are significant predictors of survival in PDAC, suggesting possible novel therapeutic targets.

Background: Lemur tail kinase 3 (LMTK3) is a serine/threonine protein kinase with roles in multiple cellular pathways, including Wnt signaling, KIT modulation, and the estrogen receptor pathway; identifying it as a potential target in various cancers. LMTK3 is highly expressed within the central nervous system (CNS) and has been demonstrated to influence neuronal signaling. This study aimed to investigate the potential connection between LMTK3 and neuronal signaling pathways in colorectal cancer (CRC). Methods: Using the Cre/loxP system, we generated a C57BL/6 mouse strain that lacks the expression of LMTK3. 1 × 106 MC38 cells were subcutaneously implanted into 8 weeks old male and female wildtype (WT) and knockout (KO) mice. Tumor growth was measured until endpoint was reached. Tumors were then processed for RNA sequencing. Differentially expressed genes (DEGs) for each comparison …

BackgroundThe majority of pancreatic ductal adenocarcinomas (PDACs) are driven by mutant (mt) KRAS. How mt KRAS and co-driver mutations affect the immune cell (IC) landscape of PDAC remains uncertain. Herein, we characterize the types of IC in the PDAC tumor microenvironment (TME) and the prevalence of immuno-oncologic (IO) biomarkers by genomic and transcriptomic analysis in the context of KRAS status.Materials and methods4142 PDAC and 3727 colorectal cancer (CRC) cases with KRAS mt were analyzed using next-generation DNA sequencing, immunohistochemistry, and whole-transcriptome RNA sequencing. Microsatellite instability and deficiency in mismatch repair (MSI-H/dMMR) and tumor mutational burden (TMB) were also assessed.ResultsWe found KRAS mt in 81% of PDAC, with the most common variant being G12D in PDAC, and fewer cases of KRAS mt were co-expressed with the …

TPS228Background: Colorectal cancer (CRC) is the third most frequently diagnosed cancer and the second leading cause of cancer-related mortality worldwide. PD-1/PD-L1 inhibition, in combination with other modalities, has demonstrated significant benefit in patients (pts) with microsatellite instability-high or mismatch repair–deficient CRC. However, these agents have limited, if any, clinical benefit in pts with microsatellite stable (MSS) or mismatch repair–proficient (pMMR) CRC. RP2 is an enhanced potency oncolytic herpes simplex virus type 1 which expresses the fusogenic gibbon ape leukemia virus glycoprotein with the R sequence deleted (GALV-GP-R–), granulocyte-macrophage colony-stimulating factor (GM-CSF), and an anti–CTLA-4 antibody-like molecule; RP3 additionally expresses 4-1BB and CD40 activating ligands but does not express GM-CSF. Both agents have demonstrated preliminary safety …

Background: Chemotherapy in combination with bevacizumab (Bev) has been a standard first-line treatment for RAS-mutated mCRC patients for the last 2 decades. The prognosis of these patients remains poor. Onvansertib is an orally available, highly potent, and selective inhibitor of Polo-like kinase 1 (PLK1), currently in clinical development. In a Phase 1b/2 study, onvansertib in combination with FOLFIRI + Bev demonstrated safety and promising efficacy in the second-line treatment of KRAS-mutated mCRC patients (NCT03829410). A subgroup analysis showed that patients not exposed to Bev (Bev-naïve) in the first-line setting had superior clinical benefit compared to Bev-exposed patients. Based on this data, we propose to investigate the combination of onvansertib with SoC (chemo + Bev) in the first-line treatment of RAS-mutated, Bev-naïve mCRC patients. Methods: This exploratory Phase 2, open-label …

Purpose Onvansertib is a highly specific inhibitor of polo-like kinase 1 (PLK1), with demonstrated safety in solid tumors. We evaluated, preclinically and clinically, the potential of onvansertib in combination with chemotherapy as a therapeutic option for KRAS-mutant colorectal cancer. Patients and Methods Preclinical activity of onvansertib was assessed (i) in vitro in KRAS wild-type and -mutant isogenic colorectal cancer cells and (ii) in vivo, in combination with irinotecan, in a KRAS-mutant xenograft model. Clinically, a phase Ib trial was conducted to investigate onvansertib at doses 12, 15, and 18 mg/m2 (days 1–5 and 14–19 of a 28-day cycle) in combination with FOLFIRI/bevacizumab (days 1 and 15) in patients with KRAS-mutant metastatic colorectal cancer who had prior oxaliplatin exposure. Safety, efficacy, and changes in circulating tumor DNA (ctDNA) were assessed …

BackgroundThe CC motif chemokine receptor 5 (CCR5)/CC motif chemokine ligand 5 (CCL5) axis plays a major role in colorectal cancer (CRC). We aimed to characterize the molecular features associated with CCR5/CCL5 expression in CRC and to determine whether CCR5/CCL5 levels could impact treatment outcomes.Methods7604 CRCs tested with NextGen Sequencing on DNA and RNA were analyzed. Molecular features were evaluated according to CCR5 and CCL5 tumor gene expression quartiles. The impact on treatment outcomes was assessed in two cohorts, including 6341 real-world patients and 429 patients from the Cancer and Leukemia Group B (CALGB)/SWOG 80405 trial.ResultsCCR5/CCL5 expression was higher in right-sided versus left-sided tumors, and positively associated with consensus molecular subtypes 1 and 4. Higher CCR5/CCL5 expression was associated with higher tumor …

46Background: LDH is a potential prognostic biomarker of outcomes for pts with mCRC. This retrospective, observational cohort study describes RW LDH testing patterns and assesses LDH as a prognostic factor for overall survival (OS) in pts receiving chemotherapy (CT) for mCRC in the USA. Methods: Pts with mCRC, ≥18 years (yrs) of age, who initiated first line (1L) CT (index date) between January 1, 2016, and November 30, 2022, were identified in the nationwide de-identified Flatiron Electronic Health Record-derived database. Practice patterns for LDH testing are described. Pts were categorized into normal vs abnormal LDH baseline (≤3 months prior to/at index date) value based on the lab reference range. Prognostic relationship between normal vs abnormal LDH baseline value and OS was assessed using Kaplan-Meier and multivariate Cox proportional-hazards model. Results: Of 15,329 eligible pts …

Oncogenic drivers such as KRAS extensively modulate the tumor inflammatory microenvironment (TIME) of colorectal cancer (CRC). The influence of KRAS on modulating immune cell composition remains unclear. The objective of this study was to identify signatures of infiltrative immune cells and distinctive patterns that differ between RAS wild-type (WT) and oncogenic mutant (MT) CRC that explain immune evasion in MT tumors. A total of 7,801 CRC specimens were analyzed using next-generation DNA sequencing, whole-exome sequencing, and/or whole transcriptome sequencing. Deficiency of mismatch repair (dMMR)/microsatellite instability (MSI) and tumor mutation burden (TMB) were also assessed. KRAS mutations were present in 48% of CRC, similarly distributed in patients younger than vs. 50 years and older. In microsatellite stable (MSS) KRAS MT tumors, composition of the TIME included higher …

Background: Myeloid cell leukemia 1 (MCL-1) is an anti-apoptotic member of the BCL-2 protein family which is involved in intrinsic (mitochondrial) pathway of apoptosis and is deregulated in several cancers. Current MCL-1 specific inhibitors have limitations in terms of efficiency, tolerability, and off-target effects and challenges associated with shallow binding groove of MCL-1. In this study, dihydroergotamine mesylate (DHE), an approved anti-migraine drug, was found as a potential ligand of the MCL-1 BH3-binding pocket and was further evaluated for its potential MCL-1 inhibition and effect on pancreatic cancer cells. Methods: PubChem Database was used for library preparation and virtual screening (OpenBabel and AutoDock Vina). The 55 crystal structures available for MCL-1 in Protein Data Bank (PDB) were clustered using principal component analysis with Bio3D R-package to select representative PDBs …

BackgroundWhile immune checkpoint inhibitors (ICI) were approved for head and neck squamous cell carcinomas (HNSCCs), the response rate remains relatively low. Mechanisms underlying ICI unresponsiveness versus sensitivity are not fully understood.MethodTo better delineate differential responses to ICI treatment, we employed mouse SCC models, termed KPPA tumors that were caused by deleting p53 and hyperactivating PIK3CA, two most frequently mutated genes in human HNSCCs. We transplanted two KPPA tumor lines (TAb2 versus TCh3) into C57BL/6 recipients and examined the immune tumor microenvironment using flow cytometry. Furthermore, we employed single-cell RNA sequencing to identify the difference in tumor infiltrating lymphocytes (TILs).ResultsWe found that different KPPA tumors exhibited heterogeneous immune profiles pre-existing treatment that dictated their sensitivity or …

Unlocking the full dimensionality of single-cell RNA sequencing data (scRNAseq) is the next frontier to a richer, fuller understanding of cell biology. We introduce q-diffusion, a framework for capturing the coexpression structure of an entire library of genes, improving on state-of-the-art analysis tools. The method is demonstrated via three case studies. In the first, q-diffusion helps gain statistical significance for differential effects on patient outcomes when analyzing the CALGB/SWOG 80405 randomized phase III clinical trial, suggesting precision guidance for the treatment of metastatic colorectal cancer. Secondly, q-diffusion is benchmarked against existing scRNAseq classification methods using an in vitro PBMC dataset, in which the proposed method discriminates IFN-γ stimulation more accurately. The same case study demonstrates improvements in unsupervised cell clustering with the recent Tabula Sapiens …

DNA methyltransferase inhibitors (DNMTi) have demonstrated benefit in reversing resistance to systemic therapies for several cancer types. In a phase II trial of guadecitabine and irinotecan compared to regorafenib or TAS‐102 in pts with advanced mCRC refractory to irinotecan. Patients with mCRC refractory to irinotecan were randomized 2:1 to guadecitabine and irinotecan (Arm A) vs standard of care regorafenib or TAS‐102 (Arm B) on a 28‐day cycle. Between January 15, 2016 and October 24, 2018, 104 pts were randomized at four international sites, with 96 pts undergoing treatment, 62 in Arm A and 34 in Arm B. Median overall survival was 7.15 months for Arm A and 7.66 months for Arm B (HR 0.93, 95% CI: 0.58–1.47, P = .75). The Kaplan–Meier rates of progression free survival at 4 months were 32% in Arm A and 26% in Arm B. Common ≥Grade 3 treatment related adverse events in Arm A were …

PurposeTo examine the prevalence of female sexual dysfunction (FSD), male erectile dysfunction (ED), and the prevalence and correlates of sexual health discussions between early-onset CRC survivors and their health care providers.MethodsAn online, cross-sectional survey was administered in partnership with a national CRC advocacy organization. Respondents (n = 234; diagnosed < 50 years, 6–36 months from diagnosis/relapse) were colon (36.8%) and rectal (63.3%) cancer survivors (62.5% male). The Female Sexual Function Index (FSFI-6) was used to measure FSD, and the International Index of Erectile Function (IIEF-5) was used to measure ED. Survivors reported whether a doctor communicated with them about sexual issues during/after treatment.ResultsAmong females (n = 87), 81.6% had FSD (mean FSFI-6 score = 14.3 [SD±6.1]). Among males (n = 145), 94.5% had ED (mean IIEF-5 …

While monoclonal antibody-based targeted therapies have substantially improved progression-free survival in cancer patients, the variability in individual responses poses a significant challenge in patient care. Therefore, identifying cancer subtypes and their associated biomarkers is required for assigning effective treatment. In this study, we integrated genotype and pre-treatment tissue RNA-seq data and identified biomarkers causally associated with the overall survival (OS) of colorectal cancer (CRC) patients treated with either cetuximab or bevacizumab. We performed enrichment analysis for specific consensus molecular subtypes (CMS) of colorectal cancer and evaluated differential expression of identified genes using paired tumor and normal tissue from an external cohort. In addition, we replicated the causal effect of these genes on OS using validation cohort and assessed their association with the Cancer Genome Atlas Program data as an external cohort. One of the replicated findings was WDR62, whose overexpression shortened OS of patients treated with cetuximab. Enrichment of its over expression in CMS1 and low expression in CMS4 suggests that patients with CMS4 subtype may drive greater benefit from cetuximab. In summary, this study highlights the importance of integrating different omics data for identifying promising biomarkers specific to a treatment or a cancer subtype.

The lemur family of protein kinases has gained much interest in recent years as they are involved in a variety of cellular processes including regulation of axonal transport and endosomal trafficking, modulation of synaptic functions, memory and learning, and they are centrally placed in several intracellular signalling pathways. Numerous studies have also implicated role of the lemur kinases in the development and progression of a wide range of cancers, cystic fibrosis, and neurodegenerative diseases. However, parallel discoveries and inaccurate prediction of their kinase activity have resulted in a confusing and misleading nomenclature of these proteins. Herein, a group of international scientists with expertise in lemur family of protein kinases set forth a novel nomenclature to rectify this problem and ultimately help the scientific community by providing consistent information about these molecules.

188Background: Cancer cachexia leads to reduced overall survival (OS) in mCRC. Novel therapeutics targeting the myostatin/activin pathway can reverse cachexia. Here we investigate the effect of myostatin/activin pathway gene expression and SNPs in mCRC patients (pts). Methods: Blood samples from 836 pts enrolled in 3 randomized first-line trials: TRIBE (FOLFIRI bevacizumab [bev]; FOLFOXIRI bev), FIRE-3 (FOLFIRI bev; FOLFIRI cetuximab [cet]) and MAVERICC (FOLFIRI bev; FOLFOX bev) were genotyped by Illumina OncoArray. The impact on outcome of 13 SNPs from 5 myostatin/activin genes (ACVR1B, ACVR2A, ACVR2B, MSTN, INHBA) was tested. Gene expression analysis included 433 mCRC pts treated with either bev (n = 226) or cet (n = 207) in combination with first-line chemotherapy from the CALGB/SWOG 80405 trial (NCT00265850). RNA isolated from FFPE tumor samples were sequenced …

Anti VEGF A antibody Bevacizumab combined with standard chemotherapy has improved outcomes for CRC patients. However, a subset of CRC patients acquires resistance to anti-VEGF treatment and underlying mechanism is poorly understood. Our recent study reported that circadian clock transcription factor BMAL1 drives transcription of VEGFA conferring resistance to bevacizumab treatment. Our rational is to stabilize negative regulator of circadian clock CRY protein to inhibit BMAL1 activity in a negative feedback loop. In this study, we evaluated whether CRY stabilizers SHP656 and SHP1705 in combination with bevacizumab can synergistically enhance anti-tumor effect in CRC mouse models. Methods: In vitro tube formation assay was performed with HUVECs cells to investigate the effect of CRY stabilizer on tube formation. For in vivo experiments, 106 HCT116 human CRC cells were injected …

552Background: Recognition of tumor neoantigens by autologous T cells activates immune surveillance and has been reported to promote sensitivity to immune checkpoint inhibitors (ICI) in mismatch repair deficient (MMRd)/microsatellite instability high (MSI-H) tumors. Neoantigen-targeted reactivity has also been reported in microsatellite stable (MSS) tumors. Neoantigens are emerging targets for novel immunotherapy strategies, including tumor vaccines, in BC and PC. We aimed to comprehensively assess the spectrum of immunogenic neoantigens in BC and PC. Methods: 3728 tumor specimens (1389 BC; 2339 PC) tested at Caris Life Sciences (Phoenix, AZ) with NextGen Sequencing on DNA (720-gene panel) and RNA (whole transcriptome) were analyzed. MSI status was determined by immunohistochemistry of MMR protein and/or NGS. Immune epitope prediction was performed on translated peptide …

198Background: Tissue factor (TF) is a transmembrane protein that plays a crucial role in thrombosis. TF expression is elevated in various types of cancer, including colorectal cancer (CRC) and is associated with more aggressive disease and poor prognosis. The aim of this study was to evaluate TF expression in patients (pts) with metastatic CRC (mCRC) enrolled in the CALGB (Alliance)/SWOG 80405 clinical trial. Understanding the relationship between TF expression and mCRC will provide insights into the role of coagulation in the progression and prognosis of this disease and may have therapeutic implications, particularly in the setting of recent approval of a TF antibody drug conjugate for metastatic cervical cancer and other agents in the pipeline. Methods: 433 pts with mCRC treated with bevacizumab (Bev, n = 226) or cetuximab (Cet, n =207) in combination with first-line chemotherapy in CALGB/SWOG …

Cachexia, marked by continuous skeletal muscle mass loss and severe metabolic disturbances, presents a substantial challenge for pancreatic ductal adenocarcinoma (PDAC) patients. Despite its prevalence and the adverse impact on quality of life and survival rates, effective clinical treatments for cachexia remain elusive. This study aims to bridge this gap by employing innovative in vitro models to investigate the underlying mechanisms of cachexia and identify potential therapeutic targets. To enhance the relevance of cell culture models, modifications were introduced to replicate in vivo conditions, where the muscle is exposed to the ongoing kinetics of constant tumor secretion of active factors. Patient-derived PDAC cells were cultured in a dense 3D stiffness extracellular matrix (ECM) to mimic the hypoxic desmoplastic tumor microenvironment. The conditioned medium from prolonged cultured patient-derived …

Genome-wide association studies (GWAS) have identified more than 200 common genetic variants independently associated with colorectal cancer (CRC) risk, but the causal variants and target genes are mostly unknown. We sought to fine-map all known CRC risk loci using GWAS data from 100,204 cases and 154,587 controls of East Asian and European ancestry. Our stepwise conditional analyses revealed 238 independent association signals of CRC risk, each with a set of credible causal variants (CCVs), of which 28 signals had a single CCV. Our cis-eQTL/mQTL and colocalization analyses using colorectal tissue-specific transcriptome and methylome data separately from 1299 and 321 individuals, along with functional genomic investigation, uncovered 136 putative CRC susceptibility genes, including 56 genes not previously reported. Analyses of single-cell RNA-seq data from colorectal tissues revealed 17 …

PURPOSEThe phase III Cancer and Leukemia Group B (CALGB)/SWOG 80405 trial found no difference in overall survival (OS) in patients with metastatic colorectal cancer receiving first-line chemotherapy in combination with either bevacizumab or cetuximab. We investigated the potential prognostic and predictive value of HER2 amplification and gene expression using next-generation sequencing (NGS) and NanoString data.PATIENTS AND METHODSPrimary tumor DNA from 559 patients was profiled for HER2 amplification by NGS (FoundationOne CDx). Tumor tissue from 925 patients was tested for NanoString gene expression using an 800-gene panel. OS and progression-free survival (PFS) were the time-to-event end points.RESULTSHigh HER2 expression (dichotomized at median) was associated with longer PFS (11.6 v 10 months, P = .012) and OS (32 v 25.3 months, P = .033), independent of treatment …

Purpose Suboptimal treatment outcomes with 5-fluorouracil (5-FU)/folate, the standard of care for metastatic colorectal cancer (mCRC), have generated interest in optimizing the folate. Arfolitixorin ([6R]-5,10-methylene-tetrahydrofolate) is an immediately active folate and may improve outcomes over the existing standard of care (leucovorin). Experimental Design AGENT was a randomized, phase III study (NCT03750786). Patients with mCRC were randomized to arfolitixorin (120 mg/m2 given as two intravenous bolus doses of 60 mg/m2) or leucovorin (400 mg/m2 given as a single intravenous infusion) plus 5-FU, oxaliplatin, and bevacizumab. Assessments were performed every 8 weeks. The primary endpoint was the superiority of arfolitixorin for overall response rate (ORR). Results Between February 2019 and April 2021, 490 patients were randomized …

e15612Background: The approach of collectively classifying TP53 mutations (mTP53) into gain-of-function (GOF) and non-GOF was proposed as a novel approach for prognostic stratification and incorporation in clinical trials design in colorectal cancer (CRC). We previously reported that the prognosis of CRC with mTP53 is independent of GOF. Here, we explored the underlying molecular signature of mTP53 in CRC based on GOF vs. non-GOF classification. Methods: CRC specimens (N = 13,976) were tested at Caris Life Sciences (Phoenix, AZ) with NextGen Sequencing (NGS) of DNA (592-gene panel or whole- exome sequencing). R175H, R248W, R248Q, R249S, R273H, R273L, and R282W were defined as GOF mTP53; all other mTP53 were defined as non-GOF. MSI-H/dMMR status was determined by immunohistochemistry of MMR protein and/or NGS. Statistical significance was determined using chi …

237Background: CDC37-HSP90 axis is an essential chaperoning system for stabilization of kinases. CDC37 determines selectivity of client kinases recognized by HSP90. We previously showed patients with CDC37-dependent (CDC37 high expression) colorectal cancer (CRC) derived more benefit from regorafenib and bevacizumab both of which target HSP90 client kinases or signaling pathway, but not from cetuximab which targets HSP90 non-client kinase. However, molecular characteristics and interaction with relevant signaling pathways in CDC37-dependent CRC are largely unknown. Methods: We retrospectively reviewed CRC patient samples submitted to a commercial CLIA-certified laboratory (Caris Life Sciences, Phoenix AZ). Next-generation sequencing of DNA and RNA (whole-transcriptome sequencing) and immunohistochemistry were performed. Molecular profiles between top quartile transcripts …

185Background: Down syndrome (DS), a genetic disorder caused by trisomy of chr 21, is associated with a considerably lower risk for solid tumors and other angiogenesis related diseases. DSCR1 belongs to a family of evolutionary conserved protein-coding genes located on chr 21 and is highly upregulated in DS patients. Its product, calcipressin-1, has been shown to reduce cancer risk by suppressing angiogenesis. We previously reported that a germline polymorphism in DSCR1 was associated with time to recurrence in resected CRC and anti-VEGF treatment outcomes in metastatic CRC. Here, we analyzed the molecular landscape of CRC according to DSCR1 expression levels. Methods: 20,237 samples from CRC tested at Caris Life Sciences (Phoenix, AZ) with WTS (Illumina NovaSeq) and NextGen DNA sequencing (NextSeq, 592 Genes and NovaSEQ, WES) were analyzed. Top quartile transcripts per …

A critical obstacle in the field of colorectal cancer (CRC) is the establishment of precise tumor subtypes to facilitate the development of targeted therapeutic regimens. While dysregulated mucin production is a histopathological feature of multiple CRC subtypes, it is not clear how well these pathologies are associated with the proportion of goblet cells in the tumor, or whether or not this proportion is variable across all CRC. This study demonstrates that consensus molecular subtype 3 (CMS3) CRC tumors and cell lines are enriched for the expression of goblet cell marker genes. Further, the proportion of goblet cells in the tumor is associated with the probability of CMS3 subtype assignment and these CMS3 subtype tumors are mutually exclusive from mucinous adenocarcinoma pathologies. This study provides proof of principle for the use of machine learning classification systems to subtype tumors based on cellular …

Background. Immune checkpoint inhibitors have substantial clinical success in MSI-H/dMMR metastatic CRC. However, only a subset of patients exhibits durable responses, emphasizing the importance of identifying mechanism of innate and acquired resistance. The relation between the circadian clock and the immune system is well established. We used a syngeneic mouse model of MSI-H CRC to investigate whether a targeted enhancement of clock repressor proteins cryptochrome 1/2 (CRY 1/2) may affect tumor growth and response to anti-PD1 (aPD1). Methods. 1 × 106 MC38 cells were subcutaneously implanted into the right flank of 8 weeks old C57BL/6 mice. Mice were randomized into 1 control and 3 treatment arms (10 mice/group): A. CRY stabilizer SHP656(10 mg/kg PO, 5 days/week); B. aPD1 (100 μg/mouse IP, twice/week administered for 2 weeks); C. combination SHP656 + aPD1. Tumors from 4 …

Polybromo-1 (PBRM1) loss of function mutations are present in a fraction of biliary tract cancers (BTCs). PBRM1, a subunit of the PBAF chromatin-remodeling complex, is involved in DNA damage repair. Herein, we aimed to decipher the molecular landscape of PBRM1 mutated (mut) BTCs and to define potential translational aspects. Totally, 1848 BTC samples were analyzed using next-generation DNA-sequencing and immunohistochemistry (Caris Life Sciences, Phoenix, AZ). siRNA-mediated knockdown of PBRM1 was performed in the BTC cell line EGI1 to assess the therapeutic vulnerabilities of ATR and PARP inhibitors in vitro. PBRM1 mutations were identified in 8.1% (n = 150) of BTCs and were more prevalent in intrahepatic BTCs (9.9%) compared to gallbladder cancers (6.0%) or extrahepatic BTCs (4.5%). Higher rates of co-mutations in chromatin-remodeling genes (e.g., ARID1A 31% vs. 16%) and …

Background Colorectal cancer (CRC) is the third most common cancer in California and second among Hispanic/Latinx (H/L) males. Data from the California Cancer Registry were utilized to investigate the differential impact on CRC outcomes from demographic and clinical characteristics among non‐Hispanic white (NHW), non‐Hispanic Black (NHB), U.S. born (USB), and non‐U.S. born (NUSB) H/L patients diagnosed during 1995–2020. Methods We identified 248,238 NHW, 28,433 NHB, and 62,747 H/L cases (32,402 NUSB and 30,345 USB). Disparities across groups were evaluated through case frequencies, odds ratios (OR) from logistic regression, and hazard ratios (HR) from Cox regression models. All statistical tests were two‐sided. Results NHB patients showed a higher proportion of colon tumors (75.8%) than NHW (71.5%), whereas both NUSB (65.9%) and USB (66.9%) H/L cases had less (p < 0 …

BackgroundThe treatment of locally advanced rectal cancer (LARC) has evolved following recent landmark trials of total neoadjuvant therapy (TNT)—the delivery of preoperative chemotherapy sequenced with radiation.AimTo assess the preferences of colorectal surgery (CRS), radiation oncology (RO) and medical oncology (MO) specialists attending the All-Ireland Colorectal Cancer Conference (AICCC) 2022 regarding the neoadjuvant management of LARC.MethodsA live electronic survey explored the preferred treatment approach and TNT regimen for early-, intermediate-, bad-, and advanced-risk categories of rectal cancer according to the European Society of Medical Oncology (ESMO) guidelines. The survey was preceded by an update from lead investigators of TNT trials (OPRA, PRODIGE-23 and RAPIDO), who then participated in a multidisciplinary panel discussion.ResultsTen CRS, 7 RO and 15 MO (32 …

Our recent work has shown that DCAF1 (also known as VprBP) is overexpressed in colon cancer and phosphorylates histone H2AT120 to drive epigenetic gene inactivation and oncogenic transformation. We have extended these observations by investigating whether DCAF1 also phosphorylates non-histone proteins as an additional mechanism linking its kinase activity to colon cancer development. We now demonstrate that DCAF1 phosphorylates EZH2 at T367 to augment its nuclear stabilization and enzymatic activity in colon cancer cells. Consistent with this mechanistic role, DCAF1-mediated EZH2 phosphorylation leads to elevated levels of H3K27me3 and altered expression of growth regulatory genes in cancer cells. Furthermore, our preclinical studies using organoid and xenograft models revealed that EZH2 requires phosphorylation for its oncogenic function, which may have therapeutic implications for …

2618Background: TMB is a predictive biomarker for immune checkpoint inhibitor treatment in dMMR/MSI-H cancers. We aimed to characterize specific molecular features of a large cohort of dMMR/MSI-H GI tumors with a range of TMB levels. Methods: A total of 2272 GI tumors tested as dMMR/MSI-H were analyzed using Next-generation sequencing (NGS) and immunohistochemistry (IHC) (Caris Life Sciences, Phoenix, AZ). MMR/MSI status was evaluated by a combination of IHC, Fragment Analysis and NGS. TMB-H were defined using differing TMB cutoffs (10, 20, 50 mutations/Mb). Molecular features were compared in four groups (TMB < 10 vs 10-20 vs 20-50 vs ≥50mutations/Mb) using Fisher-Exact or Chi-square and adjusted for multiple comparison by Benjamini-Hochberg. The impact of TMB on tumor immune environment was analyzed using a TCGA cohort. Significance was determined by adjusted (adj) P …

In the version of this article initially published, the author affiliations incorrectly listed “Candiolo Cancer Institute FPO-IRCCS, Candiolo (TO), Italy” as “Candiolo Cancer Institute, Candiolo, Italy.” The change has been made to the HTML and PDF versions of the article.

Background Colorectal cancer (CRC) is a heterogenous disease treated with FOLFOX, FOLFIRI, and FOLFOXIRI chemotherapy regimens. About 85% of CRC patients have microsatellite stable (MSS) tumors that resist immune checkpoint blockade (ICB). Some studies suggest that chemotherapy modulates the MSS CRC tumor microenvironment (TME) to enhance CD8+ T cell infiltration, but ICB remains ineffective. We evaluated the TME of MSS CRC patients to investigate chemotherapy impact on immune markers. Methods CRC patient samples (n= 16,827) underwent DNA (592-gene or whole exome)/RNA (whole transcriptome) sequencing at Caris Life Sciences. Immune cell fractions within TMEs were estimated from RNA deconvolution (quanTIseq; Finotello, 2019; n= 11,109). PDL1 expression was assessed by IHC (SP142;≥ 2+/5%). Patients who received FOLFOX (n= 425), FOLFIRI (n= 88), or FOLFOXIRI (n= 19)< 1 year prior to tumor collection or who didn’t receive these treatments> 4000 days before tumor collection (untreated, n= 6,608) were analyzed. Statistical significance was determined using chi-square, Fisher’s exact, and Mann-Whitney U tests, where appropriate. Results FOLFOX-treated CRC (n= 213) had a higher CD8+ T cell fraction vs untreated (n= 3,449, FC= 1.9, p< 0.01) CRC and there was no difference among FOLFIRI-treated (n= 37, FC= 1.1, p= 0.13) or FOLFOXIRI-treated (n= 9, FC= 2.2, p= 0.49) CRC. Survival outcomes were similar in FOLFOX-treated CD8+ T cellhigh (n= 82) vs low (n= 161, HR= 1.3, p= 0.12) and in FOLFOX-treated PDL1+(n= 13) vs PDL1-(n= 338) CRC (HR= 1.6, p= 0.14). The CD8+ T cell fraction …

287Background: Addition of immune checkpoint blockade to anti-HER2 therapy has improved outcomes in HER2-positive GEC. Anti-HER2 antibody-drug conjugates have shown activity in some HER2-L tumors in other tumor types. We aimed to compare the molecular profile and TIME of HER2-L and HER-H GEC. Methods: 8678 GEC (gastric, GE junction, and esophageal) adenocarcinoma and squamous cell carcinoma samples were analyzed by next-generation sequencing (NGS) of RNA (whole transcriptome, NovaSeq), DNA (592 genes, NextSeq, or whole exome sequencing, NovaSeq), and immunohistochemistry (IHC, Caris Life Sciences, Phoenix, AZ). Cohorts were stratified by IHC HER2 values of 0 (non-expressors), 1-2+ (HER2-L), or 3+ (HER2-H) and compared using X2 or Fisher-Exact. Statistical significance was determined as P-value adjusted for multiple comparisons (q < 0.05). Microenvironment cell …

4144 Background: Encouraging pre-clinical efficacy targeting Exportin-1 (XPO1) - a master regulator of tumor suppressor protein export - has been reported in pancreatic ductal adenocarcinoma (PDAC) and clinical trials are currently ongoing. However, limited data is available regarding expression and function of XPO1 in PDAC. Thus, we investigated XPO1 mRNA expression and its clinical and immune correlates in PDAC. Methods: 5,488 PDACs were tested at Caris Life Sciences (Phoenix, AZ) with NGS of DNA (WES) and RNA (WTS). TMB-H was defined as ≥10 mutations/MB. The cohort was stratified in quartiles according to XPO1 mRNA expression status, and XPO1-high (XPO1H) and XPO1-low (XPO1L) expression were defined as ≥top and XPO1. Results: Increased XPO1 mRNA expression was observed in metastatic lesions compared to primary tumors (p<0.001). Copy number amplification and …

250Background: Tissue factor (TF), a component of the coagulation cascade, transmembrane receptor, and cofactor for factor VII/VIIa is expressed by subendothelial cells and critical to hemostasis, thrombosis, cell proliferation, angiogenesis, and metastasis. TF is suggested to have a critical role in colorectal cancer (CRC). Here we assessed the clinico-molecular features associated with TF expression (exp) in CRC. Methods: Tumor molecular profiling was performed for 14,0786 samples by NextGen Sequencing on DNA (592 genes or WES) and RNA (WTS) and immunohistochemistry (IHC) at Caris Life Sciences (Phoenix, AZ). TF-high (TF-H) and TF-low (TF-L) RNA exp were defined as ≥ 75th- and < 25th-percetile of TF transcripts per million (TPM), respectively. X2/Fisher-exact and Mann Whitney U tests were used for comparison, and P-values were adjusted for multiple comparisons. Cell infiltration in the tumor …

Background Engaging diverse populations in cancer genomics research is of critical importance and is a fundamental goal of the NCI Participant Engagement and Cancer Genome Sequencing (PE-CGS) Network. Established as part of the Cancer Moonshot, PE-CGS is a consortium of stakeholders including clinicians, scientists, genetic counselors, and representatives of potential study participants and their communities. Participant engagement is an ongoing, bidirectional, and mutually beneficial interaction between study participants and researchers. PE-CGS sought to set priorities in participant engagement for conducting the network's research. Methods PE-CGS deliberatively engaged its stakeholders in the following four-phase process to set the network's research priorities in participant engagement: (i) a brainstorming exercise to elicit potential priorities; (ii) a 2-day virtual …

PURPOSEActivating mutations in KRAS, NRAS, and BRAF are known to cause resistance to anti–epidermal growth factor receptor (EGFR) therapy; however, only approximately 40% of patients with colorectal cancer (CRC) with RASWT tumors respond to anti-EGFR treatment. We sought to discover novel biomarkers to predict response to anti-EGFR antibody treatment in CRC and to understand mechanisms of resistance to anti-EGFR therapy.MATERIALS AND METHODSTranscriptomic profiles from three clinical and two preclinical cohorts treated with cetuximab were used to assign consensus molecular subtypes (CMS) to each sample and correlated with outcomes.RESULTSRestricting to RASWT patients, we observed that CMS2 tumors (canonical subtype) had significantly higher response rates relative to other CMS when treated with cetuximab combination with doublet chemotherapy (Okita et al cohort: 92 …

BackgroundHER2 is an actionable biomarker for mCRC, though the impact of concomitant genomic alterations is unknown. On the basis of the MOUNTAINEER study, TUC+ Tras was approved by the FDA for use in pts with chemo-refractory HER2+, RAS-WT mCRC. Here we present the impact of concomitant baseline genomic alterations on the clinical activity of TUC+ Tras.MethodsMOUNTAINEER enrolled pts w/locally assessed HER2+ mCRC by tissue immunohistochemistry (IHC), in situ hybridization (ISH), and/or next-generation sequencing (NGS). Baseline tissue and blood samples were retrospectively analyzed by IHC/FISH, PGDx tissue NGS and Guardant 360 blood NGS. cORRs (proportion of pts w/CR or PR per RECIST v1. 1 by BICR) and DoR were calculated for selected genomic alterations (SNVs and CNVs) occurring in≥ 5 pts treated with TUC+ Tras. This analysis was descriptive; no statistical …

Introduction: CRC is the second leading cause of cancer mortality in the United States. Clinical factors and molecular characteristics may impact therapeutics and prognosis. Scientific studies have uncovered significant aberrations, including critical genes and pathways. Despite these efforts, few studies have utilized similar sample sizes to TCGA, heterogeneous populations and integrative clinical data to compare their reported genomic changes, even though little is known about the tumor microenvironment and its significance for colorectal tumorigenesis. Methods: Clinical and DNA genomic data from 262 colorectal tumor/normal DNA samples were obtained for whole exome sequencing analysis from the Oncology Research Information Exchange Network and two colorectal tissue samples for Spatial Transcriptomics profiling from the USC colorectal cancer Moonshot project. Whole Exome Sequencing data …

Predictive and prognostic gene signatures derived from interconnectivity among genes can tailor clinical care to patients in cancer treatment. We identified gene interconnectivity as the transcriptomic-causal network by integrating germline genotyping and tumor RNA-seq data from 1,165 patients with metastatic colorectal cancer (CRC). The patients were enrolled in a clinical trial with randomized treatment, either cetuximab or bevacizumab in combination with chemotherapy. We linked the network to overall survival (OS) and detected novel biomarkers by controlling for confounding genes. Our data-driven approach discerned sets of genes, each set collectively stratify patients based on OS. Two signatures under the cetuximab treatment were related to wound healing and macrophages. The signature under the bevacizumab treatment was related to cytotoxicity and we replicated its effect on OS using an external cohort. We also showed that the genes influencing OS within the signatures are downregulated in CRC tumor vs. normal tissue using another external cohort. Furthermore, the corresponding proteins encoded by the genes within the signatures interact each other and are functionally related. In conclusion, this study identified a group of genes that collectively stratified patients based on OS and uncovered promising novel prognostic biomarkers for personalized treatment of CRC using transcriptomic causal networks.

1035Background: The androgen receptor (AR) is a hormone-regulated transcription factor that plays an important role in breast cancer (BC) pathogenesis. While estrogen receptor inhibitors are well-studied in BC, the role of AR on prognosis and therapy is less well-known. Here we aim to characterize the clinicopathologic and molecular features of AR expression in BC. Methods: 27,169 BC samples were tested by NGS (592, NextSeq; WES, NovaSeq), WTS (NovaSeq) (Caris Life Sciences, Phoenix, AZ). Microsatellite-instability (MSI) was tested by IHC and NGS. Tumor mutational burden (TMB) totaled somatic mutations per tumor (high≥10 mt/MB). Tumors with AR-high(H) and AR-low(L) expression were classified by top and bottom quartile, respectively. Real world overall survival (OS) and treatment-associated survival was obtained from insurance claims and calculated from tissue collection or treatment start to …

BackgroundAntiangiogenic drug (AAD)-triggered oxygen and nutrient depletion through suppression of angiogenesis switches glucose-dependent to lipid-dependent metabolism. Blocking fatty acid oxidation can enhance AAD-mediated anti-tumor effects in colorectal cancer (CRC). Therefore, we hypothesised that genetic variants in the lipid metabolism pathway may predict clinical outcomes [overall response rate (ORR), overall survival (OS) and progression-free survival (PFS)] in metastatic CRC (mCRC) patients receiving bevacizumab-based first-line treatment.MethodsGenomic DNA from blood samples of patients enrolled in FIRE-3 (a global, randomised, open-label, phase 3 trial, between 2007-6-23 and 2012-9-19, discovery cohort: FOLFIRI/bevacizumab arm, n = 107; control cohort: FOLFIRI/cetuximab arm, n = 129) and MAVERICC (a global, randomised, open-label, phase II study, between 2011–8 and …

BackgroundThe rarity of appendiceal adenocarcinoma (AC) presents challenges in understanding disease pathogenesis. We previously showed that AC has higher rates of mutations in KRAS and GNAS and lower rates of TP53, APC, and PIK3CA than CRC. The appendix also has many lymphoid clusters and regulates IgA production in the large bowel, suggesting that AC may be subject to more lymphocytic regulation than CRC. We sought to characterize the molecular profile and TME across AC histopathological types.

741Background: While pancreatic adenocarcinoma (PDAC) remains a leading cause of cancer-related deaths, the highly aggressive PDAC subtype of undifferentiated sarcomatoid carcinoma (USC) remains poorly characterized as it comprises only 2-3% of all PDAC histology. Previous case reports suggest that immune checkpoint inhibitors could be a promising treatment strategy for USC, but the prevalence of established predictive biomarkers of response are largely unknown in this unique subpopulation. We identified PDAC USC patient samples from a large dataset and performed comprehensive genomic profiling to determine the prevalence of biomarkers associated with response to immunotherapy. Methods: PDAC USC patient samples (N=43) underwent central pathology review to confirm this diagnosis and were compared to non-USC PDAC patient samples (N=5562). Next-generation sequencing of DNA …

3550Background: NIVO + IPI demonstrated robust, durable clinical benefit, and was well tolerated as a 1L therapy in pts with MSI-H/dMMR mCRC in the phase 2 CheckMate 142 study (NCT02060188), leading to the inclusion of NIVO + IPI in the NCCN guidelines as an initial therapy option for these pts. At 52-mo median follow-up, 1L NIVO + IPI continued to demonstrate durable clinical benefit, and no new safety signals were identified. Here we report longer follow-up results. Methods: Pts with MSI-H/dMMR mCRC and no prior treatment for metastatic disease received NIVO 3 mg/kg Q2W + IPI 1 mg/kg Q6W until disease progression or unacceptable toxicity. The primary endpoint was objective response rate (ORR) by investigator assessment (INV) per RECIST v1.1. Other key endpoints were disease control rate (DCR), duration of response (DOR), progression-free survival (PFS), all by INV; overall survival (OS); and …

184Background: 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 …

Background and Objectives Published data comparing peritoneal metastases from appendiceal cancers (pAC) and colorectal cancers (pCRC) remain sparse. We compared pAC and pCRC using comprehensive tumor profiling (CTP). Methods CTP was performed, including next‐generation sequencing and analysis of copy number variation (CNV), microsatellite instability (MSI) and tumor mutational burden (TMB). Results One hundred thirty‐six pAC and 348 pCRC samples underwent CTP. The cohorts' age and gender were similar. pCRC demonstrated increased pathogenic variants (PATHs) in APC (48% vs. 3%, p < 0.01), ARID1A (12% vs. 2%, p < 0.01), BRAF (12% vs. 2%, p < 0.01), FBXW7 (7% vs. 2%, p < 0.01), KRAS (52% vs. 41%, p < 0.05), PIK3CA (15% vs. 2%, p < 0.01), and TP53 (53% vs. 23%, p < 0.01), and decreased PATHs in GNAS (8% vs. 31%, p < 0.01). There was no …

BackgroundBotensilimab (BOT), a multifunctional Fc-enhanced anti-CTLA-4 antibody has previously shown durable objective responses in 9 immunotherapy-resistant/‘cold’tumors. BOT is designed to enhance T cell priming, activation, and memory formation; to deplete intratumoral T regulatory cells and activate antigen presenting cells; and to improve safety by reducing complement fixation. Here we present updated efficacy and safety data from an ongoing expanded phase Ib study investigating BOT±balstilimab (BAL; anti-PD-1) in patients with refractory metastatic microsatellite stable colorectal cancer (MSS or non-microsatellite instability-high CRC).MethodsPatients received BOT 1 or 2 mg/kg every 6 weeks (Q6W)+ BAL 3 mg/kg Q2W. RECIST 1.1 imaging assessments were performed at least once every 6 weeks. Primary and secondary endpoints included adverse events, objective response rate (ORR …

The Colon Cancer Family Registry (CCFR, www. coloncfr. org) is supported in part by funding from the National Cancer Institute (NCI), National Institutes of Health (NIH)(award U01 CA167551). Support for case ascertainment was provided in part from the Surveillance, Epidemiology, and End Results (SEER) Program and the following US state cancer registries: AZ, CO, MN, NC, NH; and by the Victoria Cancer Registry (Australia) and Ontario Cancer Registry (Canada). The CCFR Set-1 (Illumina 1M/1M-Duo) and Set-2 (Illumina Omni1-Quad) scans were supported by NIH awards U01 CA122839 and R01 CA143237 (to GC). The CCFR Set-3 (Affymetrix Axiom CORECT Set array) was supported by NIH award U19 CA148107 and R01 CA81488 (to SBG). The CCFR Set-4 (Illumina OncoArray 600K SNP array) was supported by NIH award U19 CA148107 (to SBG) and by the Center for Inherited Disease Research …

Transcription factors (TFs) are key regulators of homeostasis and cancer. Recent advances in pharmacological targeting of TFs makes them valuable targets in various diseases, but systems-level understanding of the function and regulation of TFs from different families in cancers remains lacking. Our lab and collaborators have been developing new small molecules to modulate the functions of key regulators of the circadian clock BMAL1 and CLOCK, which are bHLH family TFs that activate gene expression by binding to a DNA motif called E-box, with a consensus sequence of CANNTG. E-boxes are ubiquitous in the genome and broadly regulate essential physiological processes of the cell, but their molecular biology in cancer is largely unknown. In the current work we tested the ability of small molecules to regulate the expression of BMAL1 and CLOCK target genes. Across different cell lines of various cancer …

BackgroundOver 95% of patients with metastatic colorectal cancer (mCRC) are ineligible for immune checkpoint inhibitors as standard of care due to a lack of observed response in microsatellite stable/mismatch repair proficient (MSS/pMMR) tumors. Current standard of care includes chemotherapy and targeted therapy regimens. Botensilimab (BOT)–a multifunctional Fc-enhanced anti-CTLA-4 antibody designed to enhance T cell priming, activation, and memory formation; deplete intratumoral T reg cells; and minimize complement fixation–has demonstrated preclinical and promising early phase clinical data. In an ongoing Phase 1 study (NCT03860272), BOT±balstilimab (BAL; anti-PD-1) has shown responses across a wide variety of cold/IO refractory solid tumors, particularly in CRC patients without active liver metastases, with a managable safety profile. The aim of this randomized Phase 2 study is to evaluate …

3625Background: In colorectal cancer (CRC) and endometrial cancer (EC) patients (pts), preliminary data suggest a differential response to immune checkpoint inhibitors (ICIs) according to different MMR alterations. The drivers of this difference remain unknown and no reliable predictive biomarker has been found. We explored the genomic alterations, tumor mutation burden (TMB), immune-related gene expressions and signatures, tumor microenvironment (TME), neoantigen load and median overall survival (mOS) inCRC and EC pts treated with ICIs with different MMR alterations. Methods: 13,701 CRC and 3,315 EC specimens were tested at Caris Life Sciences (Phoenix, AZ) with Next Gen Sequencing (NGS) of DNA (592-gene or whole exome) and RNA (whole transcriptome). MMR/MSI status was determined by IHC of MMR protein and/or NGS. Immune cell abundance was quantified using quanTIseq. Gene …

Exploring the relationship between various neurotransmitters and breast cancer cell growth has revealed their likely centrality to improving breast cancer treatment. Neurotransmitters play a key role in breast cancer biology through their effects on the cell cycle, epithelial mesenchymal transition, angiogenesis, inflammation, the tumor microenvironment and other pathways. Neurotransmitters and their receptors are vital to the initiation, progression and drug resistance of cancer and progress in our biological understanding may point the way to lower-cost and lower-risk antitumor therapeutic strategies. This review discusses multiple neurotransmitters in the context of breast cancer. It also discusses risk factors, repurposing of pharmaceuticals impacting neurotransmitter pathways, and the opportunity for better integrated models that encompass exercise, the intestinal microbiome, and other non-pharmacologic …

3566Background: According to the various types of clinical trials for metastatic colorectal cancer (mCRC), ETS and DpR are suggested as the surrogates of OS. Whereas associations between ETS/DpR and OS/PPS in the era of chemotherapy (chemo) +anti-EGFR antibody (ab)/bevacizumab (bev) in 1st line therapy have not been elucidated. Methods: From 40,889 Individual patient data (IPD) from 59 studies in ARCAD mCRC database, 2,138 treatment-naïve pts with RAS wild-type (wt) mCRC were selected from 7 randomized studies (PRIME, CAIRO2, CRYSTAL, OPUS, CALGB80495, WJOG4407G, ATOM) of chemo with/without anti-EGFR ab or bev. The ETS was defined as 20%≥ tumor shrinkage at 8 ± 2wks (ETS+: ≥20%, ETS-: <20%). Multivariate Cox regression models for OS/PPS were performed to investigate associations between ETS+ and ETS- by primary tumor location (overall/left-sided/right-sided …

4151Background: Individuals with Down syndrome (DS) have a lower risk for solid tumors and angiogenesis related diseases. DSCR1 is highly upregulated in DS patients and its product, calcipressin-1, was shown to suppress angiogenesis and reduce cancer risk. High DSCR1 expression has been reported to decrease PDAC growth and metastasis in animal models. Here, we analyzed the molecular features and clinical outcomes associated with DSCR1 gene expression in PDAC. Methods: 8352 tumor samples tested at Caris Life Sciences (Phoenix, AZ) with WTS (Illumina NovaSeq) and NextGen DNA sequencing (NextSeq, 592 Genes and NovaSEQ, WES) were analyzed. Top quartile transcripts per million for DSCR1 expression were considered high (Q4) while bottom quartile low (Q1). Cell infiltration in the tumor microenvironment (TME) was estimated using QuantiSEQ. Interferon-gamma (IFG) and T-cell …

240Background: CD47 belongs to the immunoglobulin superfamily and is overexpressed in many tumor types. CD47 plays an important role in suppressing phagocytosis through binding to transmembrane protein SIRP-alpha on macrophages. Targeting CD47 is a novel strategy for cancer immunotherapy and is being evaluated in ongoing clinical trials. However, molecular characteristics of CD47-overexpressed colorectal cancer (CRC) are largely unknown. Methods: We retrospectively reviewed CRC patient samples (n = 14786) submitted to a commercial CLIA-certified laboratory (Caris Life Sciences, Phoenix AZ). Next-generation sequencing of DNA and RNA (whole-transcriptome sequencing) and immunohistochemistry were performed. Correlation of CD47 expression with danger-associated molecular pattern (DAMP)-related genes (HMGB1, CALR, ANXA1, HSP90AA1, HSPA1A, and CXCL10) expressions …

3528Background: Tucatinib (TUC) is a highly selective HER2-directed TKI approved by the FDA in combination w/trastuzumab (Tras) for treatment (tx) of pts w/ RAS wild-type HER2+ unresectable or metastatic colorectal cancer (mCRC) that has progressed following tx w/ fluoropyrimidine-, oxaliplatin-, and irinotecan-based chemotherapy. There are currently no established best practices for HER2 testing/interpretation in mCRC. Here we present results of central HER2 testing across multiple platforms and response to tx for MOUNTAINEER pts treated w/ TUC + Tras based on central HER2 status. Methods: MOUNTAINEER (NCT03043313) enrolled pts w/ local HER2+ mCRC using ≥1 method: IHC, ISH, and/or NGS testing; retrospective central assessment of HER2 status was performed on multiple platforms. Pts in cohorts A+B were treated w/ TUC + Tras; pts in cohort C were treated w/ TUC monotherapy …

Three-dimensional (3D) in vitro models are essential in cancer research, but they often neglect physical forces. In our study, we combined patient-derived tumor organoids with a microfluidic organ-on-chip system to investigate colorectal cancer (CRC) invasion in the tumor microenvironment (TME). This allowed us to create patient-specific tumor models and assess the impact of physical forces on cancer biology. Our findings showed that the organoid-on-chip models more closely resembled patient tumors at the transcriptional level, surpassing organoids alone. Using ‘omics’ methods and live-cell imaging, we observed heightened responsiveness of KRAS mutant tumors to TME mechanical forces. These tumors also utilized the γ-aminobutyric acid (GABA) neurotransmitter as an energy source, increasing their invasiveness. This bioengineered model holds promise for advancing our understanding of cancer …

Background. CRC is the third leading cause of cancer related deaths worldwide with age and diet are among the strongest risk factors. CRC characteristics appear to be distinct between younger and older patients. We evaluated the effects of age on CRC tumor biology using syngeneic mice models with a focus on a) specific differences in tumor growth patterns and the role of the tumor microenvironment (TME) in young versus old mice harboring CRC allografts; b) differential dietary effects in young versus old hosts. Methods. 1 × 106 MC38 cells were subcutaneously implanted into the right flank of young (6 weeks) or old (24 months) C57BL/6 male mice. Mice were randomized into 3 diet groups: A. Standard Chow (SC); B. Calorie Restriction (CR: 30% reduction in total calories); C. High Fat (HF). Parameters studied were daily food intake, body weight, tumor growth and survival. Once endpoint reached, tumors …

Epigenetic dysregulation is a prominent feature in cancer, as exemplified by frequent mutations in chromatin regulators, including the MLL/KMT2 family of histone methyltransferases. Although MLL1/KMT2A activity on H3K4 methylation is well documented, their non-canonical activities remain mostly unexplored. Here we show that MLL1/KMT2A methylates Borealin K143 in the intrinsically disordered region essential for liquid–liquid phase separation of the chromosome passenger complex (CPC). The co-crystal structure highlights the distinct binding mode of the MLL1 SET domain with Borealin K143. Inhibiting MLL1 activity or mutating Borealin K143 to arginine perturbs CPC phase separation, reduces Aurora kinase B activity, and impairs the resolution of erroneous kinetochore–microtubule attachments and sister-chromatid cohesion. They significantly increase chromosome instability and aneuploidy in a subset …

Objective: The objective of this Phase 2, open-label, multicenter study is to investigate the antitumor activity of navicixizumab monotherapy or in combination with chemotherapy in patients with advanced solid tumors. Cohort C will enroll triple-negative breast cancer (TNBC) patients. Background: Navicixizumab is a bispecific humanized monoclonal immunoglobulin G2 kappa antibody directed against human delta-like ligand 4, a critical ligand of the NOTCH pathway, and human vascular endothelial growth factor (VEGF). Aberrant NOTCH signaling is associated with chemotherapy resistance, tumor plasticity, enhanced metastatic potential, promotion of a cancer stem cell phenotype, and immune evasion. In TNBC, aberrant NOTCH expression is associated with poor prognosis, making targeting of this pathway an attractive therapeutic strategy. Additionally, NOTCH may mediate resistance to angiogenesis inhibition …

BackgroundLiver metastases arise frequently from primary colorectal, pancreatic, and breast cancers. Research has highlighted the patient’s frailty status as an important predictor of outcomes, but the literature evaluating the role of frailty in patients with secondary metastatic disease of the liver remains limited. Using predictive analytics, we evaluated the role of frailty in patients who underwent hepatectomy for liver metastases.MethodsWe used the Nationwide Readmissions Database from 2016-2017 to identify patients who underwent resection of a secondary malignant neoplasm of the liver. Patient frailty was evaluated using the Johns Hopkins Adjusted Clinical Groups (JHACG) frailty-defining diagnosis indicator. Propensity score matching was performed and Mann-Whitney U testing was used to analyze complication rates. Receiver operating characteristic (ROC) curves were created following creation of logistic …

LBA8Background: BOT promotes optimized T cell priming, activation and memory formation by strengthening antigen presenting cell/T cell co-engagement. As an Fc-enhanced next-generation anti–CTLA-4 antibody, BOT also promotes intratumoral regulatory T cell depletion and reduces complement fixation. We present results from patients with MSS CRC treated with BOT + BAL in an expanded phase 1a/1b study; NCT03860272. Methods: Patients (pts) with metastatic MSS CRC received BOT 1 or 2 mg/kg every 6 weeks (Q6W) + BAL 3 mg/kg every 2 weeks. Crossover from monotherapy to combination therapy was permitted (rescue) as well as fixed-dosing (150 mg BOT Q6W + 450 mg BAL every 3 weeks). Results: Fifty-nine combination pts were evaluable for efficacy/safety (treated as of 19 May 2022 with ≥1 Q6W imaging assessment), including one rescue and one fixed-dose pt. Median pt age was 57 (range …

3118Background: TROP2 expression is associated with decreased overall survival in colorectal and pancreatic cancers. The antibody drug conjugate sacituzumab delivers a SN38 toxic payload to TROP2-expressing cells and is approved for the treatment of breast cancer and urothelial carcinoma. We aimed to explore the genomic and immunological landscape of TACSTD2 (TROP2-encoding gene) in different solid tumors. Methods: Tumors from breast cancer (BC, N=11,246), colorectal carcinoma (CRC, N= 15,425), liver cancer (LC, N=433), pancreatic cancer (PC, N=5,488) and urothelial carcinoma (UC, N=5,488) were assessed at Caris Life Sciences (Phoenix, AZ) with NextGen Sequencing of DNA (592-gene or whole exome) and RNA (whole transcriptome). PD-L1 (SP142; Positive (+): ≥2+, ≥5%) expression was assessed by IHC. When investigating the genomic landscape, mutation prevalence was …

3578Background: The immune system is alerted for virally infected cells in the body by the antigen presentation pathway, which is in turn mediated by the major histocompatibility complex (MHC) class I and II molecules. Cancer cells overcome immune evasion as a major hallmark by downregulation of antigen presentation pathway molecules. Therefore, the present study aimed to explore the effect of genetic variants in MHC class I and II pathways on first-line treatment outcome in mCRC pts. Methods: Genomic DNA from blood samples of 775 pts enrolled in three independent, randomized, first-line trials: TRIBE (FOLFIRI-bevacizumab [bev], N = 215), FIRE-3 (FOLFIRI-bev, N = 107; FOLFIRI-cetuximab [cet], N = 129) and MAVERICC (FOLFIRI-bev, N = 163; FOLFOX-bev, N = 161) was genotyped through OncoArray, a custom array manufactured by Illumina including approximately 530K SNP markers. The impact on …

202Background: Large studies have identified immune checkpoint inhibitors (ICI) as an effective therapy for deficient mismatch repair/microsatellite instability high (dMMR/MSI-H) colorectal cancer (CRC). However, a subset of dMMR/MSI-H CRC patients exist that do not benefit from ICI and show rapid cancer progression within the first 6 months of therapy. Genetic alterations of the host immune system, including loss of β2M and single copy loss of HLA molecules, can contribute to innate resistance to ICI. In this study, we sought to analyze the role of expression of HLA genes and β2M as determinants of innate resistance to ICI by analyzing an extensive clinico-genomic database. Methods: Next-generation sequencing (NGS) of DNA (592-gene or whole exome) and RNA (whole transcriptome) was performed on CRC patient samples (n = 24,394) submitted to a CLIA-certified laboratory (Caris Life Sciences, Phoenix …

4108Background: The circadian clock mechanism controls the physiological homeostasis of the liver and plays a key role in hepatocarcinogenesis. Recent evidence unveiled core clock proteins as novel therapeutic targets in cancer. Our group showed that clock regulators BMAL1 and CLOCK can promote proliferation of liver cancer cells by modulating the cell cycle checkpoint kinase Wee1. Here we further evaluated the molecular landscape of clock pathway alterations in HCC leveraging multi-platform profiling of patient tumor samples. Methods: 780 HCC tested at Caris Life Sciences (Phoenix, AZ) with WTS (Illumina NovaSeq) and NextGen DNA sequencing (NextSeq, 592 Genes and NovaSEQ, WES) were analyzed. Clock gene Score (CS) was determined using expression of core clock genes Z scores (positives of CLOCK, ARNTL, RORA/B/C and negatives of repressors CRY1/2, PER1/2/3, REVERBA/B …

Background: Mitochondrial MAO A and MAO B isoenzymes catalyze oxidative deamination of neuroactive and vasoactive monoamines in CNS and peripheral tissues. MAO A inhibitors have been used as antidepressants; MAO B inhibitors have been used for Parkinson’s disease. Recently, we and others have shown MAO inhibitors can be repurposed for cancer therapy. This study focused on the MAO inhibitors as a novel therapeutic strategy for CRC utilizing patient derived xenograft (PDX) platform which recapitulates the patient’s molecular characteristics. Methods and Results: CRC PDX models were selected from our repository based on MAO A and B expression and activity. To establish two PDX models with high or low MAO A/B activity we implanted patient’s tumor samples (F0 generation) with high MAO A/B activity (MAO high) or low MAO A/B activity (MAO low) in 8 weeks NSG mice (F1 generation). F1 …

Background/ObjectiveImmune checkpoint inhibitors (CPIs) activate antitumoral immune responses and are used to treat multiple types of primary and metastatic malignancies. Thyroid dysfunction is a known immune-related adverse event of CPI therapy. There are few data on the effect of CPI and CPI-induced thyroiditis on primary papillary thyroid carcinoma (PTC). We present a patient who developed CPI-induced thyroiditis during treatment for a nonthyroid malignancy and subsequent regression of a coexisting untreated primary PTC.Case ReportA 49-year-old man with metastatic colon adenocarcinoma was found to have a large right thyroid nodule with biopsy confirmation of PTC. He did not have compressive symptoms or evidence of metastatic PTC. Resection was not performed because of colon cancer therapy. Treatment with CPI (ezabenlimab, an anti–programmed cell death protein 1 antibody) was …

The authors regret that Fig. 2B was accidently excluded from the final manuscript. This has now been corrected. The authors would like to apologise for any inconvenience caused [Formula presented].

The expression of the protein Mesothelin (MSLN) is highly variable in several malignancies including colorectal cancer (CRC) and high levels are associated with aggressive clinicopathological features and worse patient survival. CRC is both a common and deadly cancer; being the third most common in incidence and second most common cause of cancer related death. While systemic therapy remains the primary therapeutic option for most patients with stage IV (metastatic; m) CRC, their disease eventually becomes treatment refractory, and 85% succumb within 5 years. Microsatellite-stable (MSS) CRC tumors, which affect more than 90% of patients with mCRC, are generally refractory to immunotherapeutic interventions. In our current work, we characterize MSLN levels in CRC, specifically correlating expression with clinical outcomes in relevant CRC subtypes and explore how MSLN expression impacts the status of immune activation and suppression in the peritumoral microenvironment. High MSLN expression is highly prevalent in CMS1 and CMS4 CRC subtypes as well as in mCRC tissue and correlates with higher gene mutation rates across the patient cohorts. Further, MSLN-high patients exhibit increased M1/M2 macrophage infiltration, PD-L1 staining, immune-inhibitory gene expression, enrichment in inflammatory, TGF-β, IL6/JAK/STAT3, IL2/STAT5 signaling pathways and mutation in KRAS and FBXW7. Together, these results suggest MSLN protein is a potential target for antigen-specific therapy and supports investigation into its tumorigenic effects to identify possible therapeutic interventions for patients with high MSLN expressing …

Background: Disruption of circadian processes has been linked to cancer initiation, progression, metastasis, resistance, and mortality. Clock proteins are an emerging target for therapy in breast cancer. Circadian rhythms are controlled by a network of transcription/translation feedback loops primarily driven by BMAL and CLOCK and the transcriptional repressors period (PER1-3) and cryptochrome (CRY1-2). We investigated the molecular and clinical associations of clock genes in breast cancer. Methods: A total of 9563 breast tumors underwent molecular profiling (Caris Life Sciences). Analyses included next-generation sequencing of DNA (592 genes-NextSeq, WES-NovaSeq) and RNA (NovaSeq). Clock gene Score (CS) was determined using expression of clock pathway gene Z scores (positives of BMAL, CLOCK and negatives of PER1/2 and CRY1/2) and then stratified into quartiles. xCell was used to quantify …

BackgroundHER2 is an actionable target in metastatic colorectal cancer. We assessed the activity of tucatinib plus trastuzumab in patients with chemotherapy-refractory, HER2-positive, RAS wild-type unresectable or metastatic colorectal cancer.MethodsMOUNTAINEER is a global, open-label, phase 2 study that enrolled patients aged 18 years and older with chemotherapy-refractory, HER2-positive, RAS wild-type unresectable or metastatic colorectal cancer at 34 sites (clinics and hospitals) in five countries (Belgium, France, Italy, Spain, and the USA). Initially, the study was designed as a single-cohort study, which was expanded following an interim analysis to include more patients. Initially, patients were given tucatinib (300 mg orally twice daily) plus intravenous trastuzumab (8 mg/kg as an initial loading dose, then 6 mg/kg every 21 days; cohort A) for the duration of treatment (until progression), and after …

Methods• 28,576 CRC samples were analyzed by Caris Life Sciences (Phoenix, AZ) with WTS (Illumina NovaSeq) and NextGen DNA sequencing (NextSeq, 592 Genes and NovaSEQ, WES).