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Introduction and Background: Salmonella-IL2 (Saltikva) is an attenuated strain of orally administered Salmonella that carries the human gene for IL-2 that colonizes the tumor microenvironment and locally releases IL-2 without any untoward effects. Following significant anti-tumor responses during preclinical study in multiple tumor models; a Phase I trial in humans found a single dose to be not toxic and elevated the Natural Killer T cell populations in patients with advanced gastrointestinal (GI) cancers. Additionally, a Phase I multiple dose trial in companion dogs with metastatic osteosarcoma demonstrated a 22% complete response rate. A Phase II trial was performed studying the addition of Salmonella-IL2 to standard of care chemotherapy for stage 4 metastatic pancreatic cancer. Patients and Methods: A Health Canada and local IRB approved, non-randomized, two-arm study in patients with Stage 4 metastatic adenocarcinoma of the pancreas is currently underway. The goal is to recruit 30 patients per arm; Arm 1: Salmonella-IL2 with FOLFIRINOX and Arm 2: Salmonella-IL2 with Gemcitabine/Abraxane. The primary outcome is overall survival with secondary outcomes of response determined by CT imaging using RECIST 1.1 criteria and biomarker data. Outcomes were compared to patients with stage 4 metastatic pancreatic cancer administered FOLFIRINOX (n=37) or Gemcitabine/Abraxane (n=24) from 4 years prior to starting this trial (2016-2020) at the study site and to historical controls from the published literature. Salmonella-IL2 is orally administered concomitantly with the administration of the prescribed chemotherapy according to arm of enrollment. 109 cfu of attenuated Salmonella-IL2 was administered orally after ingestion of a gastric acid neutralizing agent and followed with 200ml of an isotonic crystalloid fluid. Results: A total of 28 patients have been enrolled into this clinical trial. 20 patients were administered Salmonella-IL2 orally every 2 weeks with FOLFIRINOX; mean age 59.4 (32-73) years; 12(60%) women, and 8 (40%) men. 8 patients were administered Salmonella-IL2 with Gemcitabine/Abraxane every 2/3 weeks; mean age is 68.8 (56-82); 6 (66.7%) women and 3 (33.3%) men. Median survival in the FOLFIRINOX arm was 24 months compared to 11.1 months in published historical controls and 13.1 months site specific controls (n=37) (P Conclusion: Addition of Salmonella-IL2 to FOLFIRINOX for stage 4 metastatic pancreatic cancer results in the near doubling of median survival when compared to historical and site-specific controls receiving FOLFIRNOX only. These findings strongly indicate that a larger pivotal phase 3 multicenter trial is warranted. Citation Format: Petr Kavan, Daniel A. Saltzman, Jule Muegge, Jordan Moradian, Gerald Batist. Addition of Salmonella-IL2 to FOLFIRINOX for metastatic stage 4 pancreatic cancer nearly doubles median survival [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr CT035.

Background: BOLD-100 is a first-in-class ruthenium-based anticancer agent in Phase 1b/2a clinical development for the treatment of advanced gastrointestinal (GI) cancers in combination with FOLFOX. BOLD-100 demonstrated synergy in established preclinical models in combination with various anticancer therapies, particularly in resistant cell lines. In the first interim analysis of the phase 1b dose-escalation component of the clinical trial, BOLD-100 plus FOLFOX was well-tolerated in patients (pts) with advanced GI solid cancers. Methods: This is a prospective, Phase 1b dose-escalation (Part A) and Phase 2a dose-expansion (Part B) study of BOLD-100 in combination with FOLFOX for colorectal (CRC), pancreatic (PDAC), gastric (GC) and biliary tract (BTC) cancers. Pts receive BOLD-100 with FOLFOX on day 1 of each 14-day cycle. In Part A, pts were enrolled in a 3+3 design to determine the combination recommended Phase 2 dose (RP2D), with BOLD-100 dose-escalation (420, 500 and 625 mg/m2). Part B comprises 4 cohorts treated at the RP2D of 625 mg/m2 until progressive disease or unacceptable toxicity. The primary objective of Part B is to evaluate the efficacy of BOLD-100 in three clinical endpoints (PFS, OS, and ORR). Bayesian modelling is used to continually reassess these endpoints; the posterior probability of superiority to a historical landmark for each endpoint. Results: As of 31 Dec 2022, 17 pts with advanced metastatic colorectal cancer median age 62 years were treated. Pts received a median of 4 prior systemic therapies, 14 had received prior FOLFOX and 16 (94%) were enrolled with stage IV disease. Median number of cycles completed was 7 (range 1-12). Median PFS was 4.7 [2.9,8.6] months, median OS 9.8 [5.2,22] months, and ORR 13% [3,36] compared to the historical benchmark of 2.0 months, 7.1 months, and 1.6% respectively for similar patients treated with approved standard of care. Two pts achieved a partial response and 11 pts had stable disease for an overall disease control rate of 87% (13/15 [64%,97%]). This compares favorably to the historical control 44%. 16 pts reported 1 or more treatment-emergent adverse events (AEs), most commonly neutrophil count decreased (n=9, 52.9%), fatigue (n=6, 35.3%), pyrexia (n=4, 23.5%), platelet count decreased (n=4, 23.5%) and decreased appetite (n=4, 23.5%). Most of the AEs were grade (G) 1-2. 12 G3 AEs were observed (mostly neutrophil count decreased [8]). Conclusion: BOLD-100 plus FOLFOX is an active and well-tolerated treatment regimen in the heavily pre-treated metastatic CRC trial population. There were no new safety signals. PK and PD data are forthcoming. The preliminary mPFS, mOS, ORR and DCR data in this interim analysis demonstrate significant improvement over the currently available approved therapies. Citation Format: Jennifer Spratlin, Grainne O'Kane, Do-Youn Oh, Sun Young Rha, Elaine McWhirter, Elena Elimova, Petr Kavan, Moon Ki Choi, Dae Won Kim, Rachel Goodwin, J Randolph Hecht, Seung Tae Kim, Dong-Hoe Koo, Khalif Halani, E Russell McAllister, Michelle Jones, Malcolm Snow, Yasmin Lemmerick, Gonzalo Spera, Jim Pankovich. BOLD-100-001 (TRIO039): a phase 1b/2a dose-escalation study of BOLD-100 in combination with FOLFOX chemotherapy in patients with pre-treated advanced colorectal cancer: interim efficacy, safety and tolerability analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr CT149.

Single-agent regorafenib is approved in Canada and in the US for patients with metastatic colorectal cancer (mCRC) who have failed previous lines of therapy1. Identification of prognostic biomarkers is crucial to ensure the best therapeutic strategies for mCRC patients. The goal of this clinical study (NCT01949194) was to explore putative molecular signatures of response and resistance to regorafenib in metastatic tumors and serial blood samples. We used a multi-omics approach to profile metastatic tumor tissues and serial blood samples from 47 mCRC patients who received single-agent regorafenib as second-line therapy after failing first-line therapy with an oxaliplatin or irinotecan-containing regimen with or without bevacizumab. Whole exome sequencing was performed to assess both the mutational and copy number (CN) landscapes of metastatic tissues from 29 patients and the transcriptome was interrogated using RNA sequencing. A 14-gene panel was used to profile serial plasma samples. Molecular aberrations were then correlated with lesion-specific treatment response using RECIST 1.1 and progression free survival (PFS) to investigate potential associations.The copy number aberration (CNA) landscape of metastatic tumors was assessed using Nexus Copy Number Software and 20 significant focal aberrations were identified using Genomic Identification of Significant Target in Cancer (GISTIC) test (q-bound Citation Format: Karen Gambaro, Maud Marques, Suzan McNamara, Mathilde Couetoux du Tertre, Cyrla Hoffert, Archana Srivastava, Sophie Mathieu, Anna schab, Thierry Alcindor, Adrian Langleben, Lucas Sideris, Mahmoud Adbelsalam, Mustapha Tehfe, Gerald Batist, Petr Kavan. A Phase II exploratory study to identify biomarkers prognostic of clinical response to regorafenib in patients with metastatic colorectal cancer who have failed first-line therapy [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4325.

Introduction: Colorectal cancer (CRC) is the third leading cause of cancer related deaths primarily due to its resistance to current treatments. Studies aiming at understanding mechanisms of resistance have largely investigated the genomic landscape of primary tumors at diagnosis. However, selective pressures during therapy can lead to the expansion of resistant clones and tumor heterogeneity. This highlights the need to characterize the molecular changes of metastasis over time of treatment and response to decipher tumor evolution and therapeutic resistance mechanisms. Methods: Metastatic liver tissue samples were collected at baseline (pre-biopsies) and at the time of resistance (post-biopsies) in responder and non-responder CRC patients undergoing the same first-line treatment. Paired pre/post biopsies were collected from 14 patients including 4 patients with multiple post-biopsies to assess temporal and spatio-temporal tumor heterogeneity following treatment exposure. Biopsies were profiled using exome and transcriptome sequencing as well as high-density Single-Nucleotide Polymorphism (SNP) array analysis to capture chromosomal anomalies, loss of heterozygosity and copy number (CN) variations. Results: Profiling of 45 samples with both high-density SNP array and exome sequencing revealed 97.4% similarity between both technologies in the identification of genes targeted by copy number changes. Using chemo-naïve biopsies, we identified 120 CN gains and 47 CN loss that were significantly associated with patient progression free survival. Integrative analysis with transcriptome data revealed that only 10% of the genomic CN gains and 17% of the CN loss correlated with their gene expression levels. Based on CN variants comparison between paired pre/post treatment samples, we found high temporal intra-patient heterogeneity over time of treatment. Interestingly, we observed a relationship between heterogeneity and tumor response; showing that acquired resistant tumors have the highest temporal variations. Conclusion: This study, using a multi-omic approach to profile serial liver metastatic samples in CRC patients, highlights the genomic changes in tumor composition after treatment exposure and constitutes an innovative approach to identify clinical biomarkers and molecular signatures of resistance. Citation Format: Mathilde Couetoux du Tertre, Maud Marques, Karen Gambaro, Michael Witcher, Benoit Samson, Bernard Lespérance, Yoo-Joung Ko, Richard Dalfen, Eve St-Hilaire, Lucas Sidéris, Félix Couture, Sabine Tejpar, Ronald Burkes, Mohammed Harb, Errol Camlioglu, Adrian Gologan, Vincent Pelsser, André Constantin, Suzan McNamara, Petr Kavan, Claudia Kleinman, Gerald Batist. Genomic profiling in serial metastatic colorectal tumors identifies copy number alterations and spatio temporal intra-patient heterogeneity profiles associated with clinical response. Q-CROC-01: NCT00984048 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-231.

Colorectal cancer (CRC) is the 2nd leading cause of cancer related-death in Canada. Clinical responses of metastatic (m)CRC to first-line treatment range from 35 to 60%, but even responders inevitably develop therapeutic resistance. Studies aiming at understanding mechanisms of resistance have largely investigated primary tumors. However, selective pressures during therapy can lead to the expansion of resistant clones and tumor heterogeneity. This highlights the need to characterize the molecular changes of metastasis and plasma over time of treatment and response to decipher tumor evolution and therapeutic resistance mechanisms. In this multicenter study, 52 tissue samples from liver metastasis were collected at baseline (pre-biopsies) and at the time of resistance (post-biopsies) in responder and non-responder mCRC patients (n=44) undergoing the same standard first-line treatments. Multiple post-biopsies also have been harvested in 4 patients, to allow the assessment of tumor heterogeneity and as well as the evolution of the genomic complexity after treatment exposure. Analyses were carried out across multiple omic platforms to identify resistant signatures and characterize molecular changes during treatment. Biopsies were profiled using exome and transcriptome sequencing as well as high-density SNP array analysis to capture chromosomal anomalies, loss of heterozygosity (LOH) and copy number variations (CNV). Additionally, serial blood samples were collected for proteomic, ctDNA and cytokine analysis. Our preliminary analysis of transcriptomes performed on serial biopsies from a set of 11 patients identified genes consistently overexpressed at resistance. Cytogenetics analysis showed similar genomic profiles of matched pre- and post-biopsies and allowed the establishment of LOH and CNV catalogues of liver metastasis, while exome sequencing revealed cumulative somatic mutations over time of treatment, which suggests subclonal and acquired “driver” mutations of resistance. Plasma-derived ctDNA analysis was performed to investigate the mutational status during treatment and whether they correlate with their relative levels in biopsies. Immune gene expression analysis of a test set of 27 metastases revealed strong clustering of 7 metastases due to overexpression of transcripts related to active immune response, allowing to define novel subgroups of patients based on immune response status. Our study, using a multi-omic strategy and integration of independent molecular platforms to profile liver metastasis samples of responder and non-responder mCRC patients, constitutes an innovative approach to identify clinical biomarkers and molecular signature of resistance, which may enhance individualization of cancer medicine and customized therapy. Citation Format: Karen Gambaro, Maud Marques, Ryan Morin, Claudia Kleinman, Michael Witcher, Simon Turcotte, Benoit Samson, Bernard Lespérance, Yoo-Joung Ko, Richard Dalfen, Eve St-Hilaire, Lucas Sideris, Felix Couture, Sabine Tejpar, Ronald Burkes, Mohammed Harb, Francine Aubin, Thierry Alcindor, Errol Camlioglu, Adriana Aguilar, Mathilde Couetoux du Tertre1, Suzan McNamara, Adrian Gologan, Petr Kavan, Gerald Batist. Integrating multiomics discovery approaches to identify biomarkers of therapeutic resistance in metastatic colorectal cancer through analyses of multiple sequential tumor and liquid biopsies; Qcroc01: NCT00984048 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2795. doi:10.1158/1538-7445.AM2017-2795

Therapeutic resistance remains a major obstacle in metastatic colorectal cancer (mCRC) and biomarkers to guide treatment are essential to improving survival and quality of life in mCRC patients. A biopsy-driven prospective study was designed to identify biomarkers and mechanisms of resistance to a standard first-line therapy in patients with mCRC which could be useful in guiding treatment selection (QCROC-01; NCT00984048). We also hoped to recognize molecular changes over time, or resulting from the selection pressure of treatment, which could have implications for subsequent therapy. This study is ongoing and approved at thirteen sites with one-hundred patients enrolled so far. Patients with mCRC receiving FOLFOX (5-fluorouracil, leucovorin and oxaliplatin) with bevacizumab consented to three needle core tumour biopsies at pre-treatment and at the time of resistance. The rate of both patient and physician acceptance of biopsies has steadily risen with time and experience. Serial bloods were also collected for proteomic analysis and circulating tumor DNA. Twenty-five biopsy samples were profiled using exome sequencing (tumor and germ line), RNAseq, low pass genome sequencing and miRNA analysis. Differential gene expression analysis revealed signatures associated with clinical response and resistance when comparing tumours obtained pre- and post-treatment. We detect changes in variant allele fraction including both depletion and enrichment of individual somatic mutations over the course of treatment, the latter of which may indicate subclonal and acquired “driver” mutations that confer therapeutic resistance. A small number of genes show recurrent evidence for changes in clonal enrichment at the time of relapse across multiple patients. These could also represent therapeutic targets for subsequent therapy for these patients, and as such, represent new treatment opportunities. Our findings provide insights into tumor evolution during first-line chemotherapy of mCRC that may hold clues to optimize current first-line therapeutic decision making and identifies potential target pathways for second-line stratification of patients. This study is part of the Canadian Colorectal Cancer Consortium which is a multi-site collaboration funded by the Terry Fox Research Institute and le fonds de recherche du québec - santé. Citation Format: Suzan McNamara, Ryan Morin, Mathilde Couëtoux du Tertre, Rosemary McCloskey, Rebecca Johnston, Daniel Fornika, Benoit Samson, Bernard Lespérance, Thierry Alcindor, Yoo-Joung Ko, Richard Dalfen, Eve St-Hilaire, Lucas Sideris, Felix Couture, Hans Prenen, Sabine Tejpar, Ronald Burkes, André Constantin, Errol Camlioglu, Adriana Aguilar, Adrian Gologan, Benoit Têtu, Celia M. Greenwood, Cyrla Hoffert, Samia Qureshi, Zuanel Diaz, Maud Marques, Micheal Witcher, Thérèse Gagnon-Kugler, Petr Kavan, Gerald Batist. Molecular profiling of sequential biopsies in patients with metastatic colorectal cancer identifies genomic alterations that evolve during first-line therapy and could have therapeutic implications: A prospective study to identify molecular mechanisms of clinical resistance (QCROC-01: NCT00984048). [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3888. doi:10.1158/1538-7445.AM2015-3888

Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL Introduction: The success of personalized medicine in oncology relies on translational research efforts to identify biomarkers that will influence clinical management. The discovery and validation of biomarkers is a concerted effort requiring an organizational framework that is often underestimated. The Quebec Clinical Research Organization in Cancer (Q-CROC) consortium is a multi-disciplinary and multi-institutional group of scientists and clinicians devoted to integrating and enhancing translational and clinical research capacity in Quebec. We describe here the organizational framework driving a multicenter, prospective study to identify biomarkers of clinical resistance to first-line therapy in metastatic colorectal cancer ([NCT00984048][1], Q-CROC-01). Results: The Q-CROC consortium has put in place an organizational infrastructure to support the activities and operations of its translational projects. We identified and addressed several critical issues during the course of the Q-CROC-01 translational project that were also common to our subsequent biomarker-driven trial in lymphoma (Q-CROC-02, [NCT01238692][2]) and breast cancer (Q-CROC-03, [NCT01276899][3]). Examples of these issues include: (i) feasibility and burden of tissue collection at participating sites, (ii) limiting pre-analytical variability in blood and tissue specimens for functional downstream applications, (iii) verification of tumor content on biopsy specimens, (iv) tracking sample flow, (v) integration of clinical data with discovery platforms, and (vi) engaging participation throughout all steps of the project. In part to address the above issues, we established five operational Cores: clinical, biobank, biospecimen processing, bioanalytical and bioinformatic. A further challenge was the integration between these Cores, who for the most part operated in silos. We observed that a critical element to unify all components of the consortium was a scientific project management team, consisting of dedicated individuals regularly interacting with each Core to ensure that objectives were aligned and deliverables were met. This academic framework for translational research may be comparable to that of multicenter clinical trials undertaken by industry, but some challenges, including financial and time constraints, data sharing and IP agreements, and engagement of its members, may be more palpable in the academic setting. Conclusion: Infrastructure science is underestimated and under-reported in translational cancer research and is crucial to the success of any large-scale biomarker discovery effort. Our experience with three multi-institutional biomarker-driven trials is that progress hinges upon the availability of an infrastructure that is not only the sum of its parts but that provides a concrete link between each component. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5534. doi:1538-7445.AM2012-5534 [1]: /lookup/external-ref?link_type=CLINTRIALGOV&access_num=NCT00984048&atom=%2Fcanres%2F72%2F8_Supplement%2F5534.atom [2]: /lookup/external-ref?link_type=CLINTRIALGOV&access_num=NCT01238692&atom=%2Fcanres%2F72%2F8_Supplement%2F5534.atom [3]: /lookup/external-ref?link_type=CLINTRIALGOV&access_num=NCT01276899&atom=%2Fcanres%2F72%2F8_Supplement%2F5534.atom