Abstract 1126: Disease monitoring with comprehensive genomics provides evidence of mechanism of action and immune evasion in patients receiving an individualized neoantigen cancer vaccine

Therapeutic vaccines hold promise to broaden the potency of immune checkpoint blockade (ICB) therapy in tumors lacking immune reactivity. A heterologous chimpanzee adenovirus (ChAd68) and self-amplifying mRNA (samRNA)-based individualized neoantigen vaccine regimen in combination with nivolumab 480 mg IV and ipilimumab 30mg SC (NCT03639714) has previously demonstrated safety, durable immunogenicity, and clinical benefit in patients with previously treated metastatic disease. Genomic correlates of response were studied over time in 29 patients (13 MSS-CRC, 13 GEA, 3 NSCLC) to understand novel mechanisms of action. Exome and transcriptome sequencing from archival biopsies was used for neoantigen selection. Monthly circulating tumor DNA (ctDNA) samples were collected for monitoring using a comprehensive tumor-naïve and tumor-informed hybrid-capture based ctDNA assay. Paired pre- and post-vaccine tumor transcriptomes were analyzed for 10 patients with 6 having accompanying DNA T cell receptor Β CDR3 repertoire sequencing (TCRseq) in biopsies and longitudinal PBMCs. Prior to vaccination patient tumors were not enriched for immune infiltration or tumor mutation burden (TMB), median 4.3 mut/Mb (range: 2-17 mut/Mb). Minimal neoantigen and mutation drift was observed with a median of 92.5% of neoantigens (range: 45-100%) and a median of 84% (range: 24-99%) of individual mutations detected in biopsies and ctDNA. Notably, paired pre- and post-vaccine biopsy gene expression analyses show upregulation in gene signatures associated with immune infiltration aligning with evidence of T cell expansion measured by significantly expanding CDR3 clonotypes (p &lt0.01). Longitudinal TCRseq in PBMCs demonstrate vaccine induced TCR repertoire dynamics and expanding and contracting clones observed in tumor biopsies could be monitored throughout treatment. In 4 patients the most drastic TCR repertoire changes were observed at time points measured after a 2nd dose of ChAd68. Lastly, we observe evidence of acquired immune evasion through ctDNA monitoring in two patients each following a year of study treatment. One GEA patient acquired HLA-LOH after remaining stable on treatment and one MSS-CRC with a molecular response (MR) for &gt7 months acquired novel biallelic loss-of-function mutations in TAP1 following 1 year of study treatment. We demonstrate that our neoantigen-directed immunotherapy regimen drives durable immune pressure on the tumor in patients with advanced disease where CPI alone has provided minimal benefit. Further, the evidence of acquired resistance supports the induction of immune pressure on tumors following individualized neoantigen vaccination. Comprehensive ctDNA longitudinal monitoring enables real-time assessment of clinical response and acquired resistance.

Citation Format: Desiree Schenk, Rita Zhou, Olivia Petrillo, Alexis Mantilla, Italo Faria do Valle, Steven Maron, Brian S. Henick, Chih-Yi Liao, Daniel V.T. Catenacci, Sameek Roychowdhury, Benjamin Solomon, Alexander I. Spira, Ankur Dhanik, Andrew R. Fergusson, Karin Jooss, Matthew Davis. Disease monitoring with comprehensive genomics provides evidence of mechanism of action and immune evasion in patients receiving an individualized neoantigen cancer vaccine [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1126.

Abstract 1238: Comprehensive ctDNA monitoring provides early signal of clinical benefit with a novel personalized neoantigen directed immunotherapy for late-stage cancer patients

Neoantigen directed immunotherapy holds promise to increase the likelihood of patients with solid tumor devoid of immune infiltration benefiting from immune checkpoint immunotherapy (CPI). A heterologous prime-boost vaccination approach consisting of Chimpanzee Adenovirus (ChAd) prime and multiple self-amplifying mRNA (SAM) boosts, delivering 20 neoantigens, has been evaluated in a Phase 1/2 clinical trial in late-stage solid tumor patients in combination with nivolumab and ipilimumab (NCT03639714). Neoantigen dynamics, tumor burden and genomic correlates of response were studied over time in 20 patients (8 GEA, 2 NSCLC, 10 MSS-CRC). Exome sequences from archival (sample used for neoantigen selection), baseline (start of immunization) and on-treatment biopsies were analyzed for 20, 16 and 10 patients respectively. Paired pre- and post-vaccine tumor transcriptomes were analyzed for 6 patients. Personalized capture baits were designed for all non-synonymous mutations detected in archival biopsies (mean 146; range: 67-402) for ctDNA monitoring. Longitudinal ctDNA samples were collected monthly on treatment (mean 7; range: 1-18). ctDNA duplex UMI libraries were captured and sequenced to a target mean raw depth >80,000x and reduced to 3x per strand consensus duplex reads. The majority of vaccine neoantigens were detected in ctDNA (87%; range 45%-100%) and mean neoantigen variant allele frequency (VAF) strongly correlated with all monitored mutations VAF (R2 = 0.90, p < 0.0001) through treatment. The percentage of vaccine neoantigens detected was higher than that for all monitored mutations in the same samples with a median of 80% (21%-98%) in ctDNA and 70% (44%-100%) in biopsies. Five of 9 MSS-CRC patients with measurable baseline ctDNA achieved molecular responses (MR, >50% reduction in ctDNA from baseline) that correlated with OS and PFS, and in some patients, was accompanied by radiologic tumor shrinkage. One MSS-CRC patient with MR for >7 months acquired novel biallelic loss-of-function mutations in TAP1 following 1 year of study treatment. Differential gene expression analysis from paired pre- and post-vaccine biopsies (including 2 MSS-CRC pairs with MR) demonstrated significant upregulation in gene signatures associated with immune-inflamed tumor microenvironments including interferon alpha and gamma responses. We demonstrate that tumor-informed neoantigen selection and vaccine manufacturing while patients receive chemotherapy is feasible, since the majority of neoantigens are retained in the tumor post-chemotherapy. Further, neoantigen-directed immunotherapy appears to drive clinical benefit in patients with advanced MSS-CRC tumors, where CPI alone has provided minimal benefit. Comprehensive ctDNA longitudinal monitoring enables real time assessment of clinical response and acquired resistance.

Citation Format: Desiree Schenck, Rita Zhou, Alexis Mantilla, Oliver Spiro, Taylor Patch, Adrienne Johnson, Daniel Navarro Gomez, Brian S. Henick, Chih-Yi Liao, Sameek Roychowdhury, Steve Maron, Benjamin Solomon, Alexander I. Spira, Daniel V. Catenacci, Andrew R. Fergusson, Raphael F. Rousseau, Karin Jooss, Matthew J. Davis. Comprehensive ctDNA monitoring provides early signal of clinical benefit with a novel personalized neoantigen directed immunotherapy for late-stage cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1238.

Photocatalytic behavior for the phenol degradation of ZnAl layered double hydroxide functionalized with SDS

Functionalized ZnAl layered double hydroxide based photocatalyst was obtained by the addition of sodium dodecyl sulfate (SDS) during the synthesis by the coprecipitation method, and further calcination at 400 °C. Bare and modified materials were characterized by X-ray diffraction, nitrogen adsorption-desorption, IR, UV-Vis, EPR and XPS spectroscopies, SEM and HRTEM. The synthesized material was evaluated in the photodegradation of phenol in a 40 ppm aqueous solution (4.25 × 10^-4 mol of phenol/L), under UV light irradiation. An increasing in the degradation of phenol from 62 to 95%, and from 62 to 82% in the mineralization of phenol was obtained using SDS functionalized ZnAl LDH, in comparison with the unmodified material. This increase could be attributed to the presence of sulfate radicals, confirmed by the EPR study.

Application of thermal lens microscopy (TLM) for measurement of Cr(VI) traces in wastewater

In this work, we demonstrate for the first time that Thermal Lens Microscopy technique (TLM) can be applied to monitor the dynamics of a photocatalytic process in-situ. The photocatalytic reduction of hexavalent chromium -Cr(VI)- in aqueous solution using CdS and irradiated with visible light is monitored by TLM. Since the values of Cr(VI) concentration obtained after the photocatalytic process were close to those imposed by the international regulations for drinking water, the use of TLM allowed its measurement with a better reliability than with UV spectroscopy, usually used in this kind of analysis.

Physicochemical and microbiological monitoring of anaerobic digestion at laboratory and low cost tubular digester

The aim of this work was to use an inexpensive technique, such as the most probable number, MPN to quantitatively and qualitatively examine microbial groups in anaerobic digestion, AD of cattle manure, CM. Different diluents and mixing ratios were evaluated in 100 mL reactors using biomethane potential, BMP, as output variable. MPN tests were performed to samples from a 23 L tank and 6.5 m³ low-cost tubular digester, LCTD. To monitor LCTD stability, volatile solids, VS, specific methanogenic activity, SMA, pH, volatile fatty acids, VFA, and chemical oxygen demand, COD were measured. Microbial characterization highlighted the optimal population essential to initiate the anaerobic digestion process. Bacteria domain were predominant over Archaea, with average abundance values of 78% and 22%, respectively. SMA of 0.0486 g COD g^-1 SV d^-1 was obtained at laboratory-scale and LCTD reached 83% of this value. Conditions selected are cost-effective to establish a biodigester in rural areas.

Photocatalytic degradation of 2,4-dichlorophenol with MgAlTi mixed oxides catalysts obtained from layered double hydroxides

MgAl and MgAlTi mixed oxides were obtained from the thermal treatment of LDH materials synthesized by the sol-gel method; these materials were characterized by N2 physisorption, XRD, UV-vis, XPS, EDS-SEM and TEM techniques. According to the results, Ti was incorporated in the LDH layer when content in the material was low. The MgAl and MgAlTi mixed oxides were evaluated in the photo-degradation of 2,4-dichlorophenol (2,4-DCP) in the presence of UV light. A superior efficiency in the photo-degradation of 2,4-DCP, in comparison with the Degussa P-25 TiO2 reference catalyst was observed, reaching a total decomposition of the 2,4-DCP molecule in less than 60 min. According to the results, Ti was incorporated in the LDH layer when the content in the material was low. The MgAl and MgAlTi mixed oxides were evaluated in the photo-degradation of 2,4-dichlorophenol (2,4-DCP) in the presence of UV light. A superior efficiency in the photo-degradation of 2,4-DCP with the MgAl and MgAlTi mixed oxides, in comparison with the Degussa P-25 TiO2 reference catalyst was observed, reaching a total decomposition of the 2,4-DCP molecule in less than 60 min.

High prevalence of RET tyrosine kinase activation in Mexican patients with papillary thyroid carcinomas

RET/PTC oncogene expression is restricted to papillary thyroid carcinomas (PTC). At least three forms of this oncogene have been described. These are generated by the rearrangement of the 5'-terminal region of different expressed genes with the tyrosine-kinase (TK) domain of the ret proto-oncogene. Several studies showing the correlation between the expression of this oncogene, clinical outcome, and histological subtypes have been published. Thirty-five paraffin-embedded PTC samples from patients without a history of radiation exposure were studied. Immunohistochemistry (IHC) and in situ hybridization (ISH) were used to determine a possible correlation between RET activation, clinical outcome, and tumor subtype. Almost half of the studied cases presented with tumoral extension or metastases. Ret gene transcripts and protein were found in all PTC variants as well as in their corresponding metastases. In contrast, none of the follicular adenomas, goiters, or normal follicular cells from the thyroid gland showed evidence of ret activation. We observed a high frequency of ret expression in PTCs, suggesting that ret activation is a common event in nonradiation-related PTC from Mexican patients.

[Acute fatty liver in pregnancy. A diagnosis to be considered]

The clinical records and follow up of two patients with jaundice in the third trimester of pregnancy and final diagnosis of acute fatty liver of pregnancy (AFLP) are reported. The purpose of this paper is to orient clinicians on the appropriate diagnostic approach in every woman with jaundice in the third trimester of pregnancy.