bluuebunny/crossref_metadata_2025 huggingface dataset:
Investigation of synthetic lethality gene pairs in the DNA damage response pathway in response to immunotherapy in pan-cancer.
Authors: Huang Hongyan , Liu Miao , Zhang Ding
Published: June 2023

2567

Background: The concept of synthetic lethality (SL) refers to the phenomenon where the simultaneous loss of function of two genes leads to cell death, while the loss of function of either gene alone has no effect. PARP inhibitors target poly ADP ribose polymerase (PARP) enzymes, which are involved in DNA repair, are the successful cases of utilizing synthetic lethality-based therapy to treat cancers with DNA damage response (DDR) deficiency. The prognosis for cancer patients already has a combination of synthetic lethal mutations especially in DDR pathway can vary and it is not yet fully understood how these mutations may impact the response to immunotherapy. Methods: SL gene combinations in the DDR pathway were screened out from SynLethDB database (http://histone.sce.ntu.edu.sg/SynLethDB/). The immunotherapy cohort (Samstein 2019, n=1661) and non-immunotherapy cohort (Zehir 2017, n=10336) with solid tumor were used to Kaplan-Meier analyze the correlation between SL gene combinations and prognosis. TMB scores were compared between DDR co-mutation group and non DDR co-mutation group. For investigating the associations between immune infiltrates and genetic features, TIMER 2.0 database ( http://timer.cistrome.org/ ) was conducted to estimation of immune infiltration levels on DDR mutation genes in pan-cancer. Results: 430 pairs of DDR mutation combinations were used to subgroup stratification, the DDR co-mutation group was associated with worse prognosis in non-immunotherapy cohort (HR=1.305, p<0.0001) but better in immunotherapy cohort (HR=0.741,p<0.0061). Interestingly, the TMB score in the DDR co-mutation group was significantly higher than non DDR co-mutation group (mean 50.03 vs 8.868, p<0.0001) in immunotherapy cohort. The high-frequency mutation combinations (>10%) were ATM-POLE(14.40%), ATM-ATR (13.60%), ATR-BRCA2 (13.60%), ATM-BRCA2 (12.00%) and BRCA2-RECQL4 (10.40%), respectively. Comparing common immune component with statistically significant under different DDR mutant genes, the ATM-POLE co-mutation tumor tended to have more CD4+ T cell infiltration while the ATM-ATR co-mutation tumor appeared to have more myeloid dendritic cell infiltration. Conclusions: The combinations of DDR SL mutation tumor might result to worse prognosis whereas these patients might benefit from immunotherapy. Our results will help to shed light on the complex interplay for the combinations of SL mutation in DDR pathway between cancer cells and the immune system and provide new insights into the development of effective cancer treatments.
SpliceIO: A robust platform for the discovery and validation of splicing-derived neoantigens.
Authors: Arun Gayatri , Anderson Kendall , Manzanares Miguel Angel , Gera Sakshi , Zumrut Hasan , Smith Shaleigh , Floyd Taylor , Shah Sanjana , Habib Nayab , Trahan Devon , Akerman Martin
Published: June 2023

2581

Background: Splicing dysregulation is a major hallmark of cancer, affecting tumor progression, metastasis, and therapy resistance. Aberrant alternative splicing plays a critical role in generating tumor-specific neoantigens targetable through an arsenal of immunotherapeutic modalities. Such neoantigens cannot be discovered using conventional DNA-based tools; they require specialized software for alternative splicing analysis using RNA-seq data. Methods: Envisagenics has developed SpliceIO, a proprietary software platform for splicing-derived neoantigen discovery. SpliceIO uses RNA-seq data to uncover extracellular neoantigens encoded by transmembrane proteins or presented to immune cells through the MHC complex. This predictive ensemble maximizes the value of RNA-seq data to predict fundamental aspects of neoantigen activity, such as their protein localization, MHC binding affinity, epitope accessibility and cancer pathway relevance. Here, we summarize the discovery and validation of novel splicing-derived neoantigens identified using SpliceIO in acute myeloid leukemia and colorectal cancer. Results: We analyzed >10,000 RNA-seq samples from the four tumor types and controls derived from 32 normal tissues. To maximize the prevalence of neoantigen target candidates in patient subpopulations, RNA-seq samples were pre-stratified using SpliceSlice, a proprietary software for spliceosomal profiling. As a result, patients sharing common spliceosome alterations were grouped into 11 coherent subsets that are distinct from normal tissue. Using this approach, we have discovered several promising candidates that we prioritized for experimental validations. SpliceIO target candidates were validated experimentally in cancer cell lines and primary tumor tissues to confirm RNA expression, translation, and membrane localization. Additionally, we performed proteomics to evaluate the presence of neopeptides generated from the unique splicing events. Using this approach, we have discovered and validated several tumor specific splicing derived neoantigens that are also recurrent in >15 % of the population. Conclusions: Together, our results strongly support the role of aberrant splicing as a major source of tumor-specific neoantigens. Our combined computational and experimental approach promotes novel target discovery, enabling the development of novel immunotherapeutics for cancer treatment.
Clinical outcomes in phase 1 clinical trials (Ph1-CT) when treating patients (pts) with novel immunotherapy (IT) agents at early lines for advanced disease.
Authors: Soto Juan José , Llop-Serna Sandra , Stradella Agostina , Villanueva Rafael , Calvo Mariona , Jove Maria , Ruffinelli Jose Carlos , Cuadra Amor Carmen , Salazar Ramon , Gil Gil Miguel J. , Gil-Martin Marta , Oliva Marc , Martin Liberal Juan
Published: June 2023

2586

Background: Cancer pts can be offered IT drugs within Ph1-CT before having exhausted standard of care (SoC) therapies. However, whether this strategy may improve pts’ outcomes remains unclear. We assess the benefits of receiving novel IT compounds within Ph1-CT at early lines for advanced disease. Methods: We retrospectively reviewed a correlative series of pts with advanced solid tumors treated with IT within Ph1-CT at the Phase 1 Unit of Catalan Institute of Oncology (ICO), Barcelona, Spain, from January 2018 to July 2022. Primary aim was to assess clinical outcomes measured by median progression-free survival (mPFS) and median overall survival (mOS) according to number of prior lines (PL) for recurrent/metastatic disease, prior IT, availability of alternative SoC in our country, IT biomarker-selected population and grade 3-4 toxicity (G3-4 Tox) by multivariate analysis (MVA). Overall response rate (ORR) was evaluated by RECIST 1.1. Clinical benefit rate (CBR) was defined as complete/partial response + stable disease for ≥6 months (m). PFS/OS were calculated by Kaplan-Meier method. Log-rank test was used for comparisons. MVA was performed by Cox regression. Results: A total of 228 pts were assessed: IT monotherapy = 49 (21.5%), IT combinations = 179 (78.5%) (IT+IT = 111 [48.7%], IT+targeted therapy = 24 [10.5%], IT+others = 44 [19.3%]). Forty-nine (21.5%) pts were included according to IT biomarkers (PDL1, TIM3 expression, MSI-H, others). Median age was 62 y (24-83), 62.7% were men. All pts had ECOG ≤1. The 4 most frequent cancer types were HNSCC (19.7%), NSCLC (15.4%), glioblastoma (10.5%) and urothelial (10.1%). Number of PL: 0 = 33 (14.5%) pts, 1 = 92 (40.3%) pts, ≥2 = 103 (45.2%) pts. Sixty-three (27.6%) pts had received prior IT and 159 (69.7%) had alternative available SoC. Overall G3-4 Tox rate was 21.5% (20.6% in pts IT-treated). ORR and CBR were higher in pts IT-naïve than in pts IT-treated (21.2% vs 12.7% [p .18] and 35.7% vs 25.4% [p .26], respectively). With a median follow-up of 19m, overall mPFS and mOS were 3.5m (2.7-3.9) and 9.8m (8.5-11.5), respectively. In the MVA, lesser number of PL, SoC availability and biomarker selection positively impacted on mOS. After Ph1-CT treatment, 111 (48.7%) pts received further treatment: 19.3% within clinical trial, 29.4% with SoC. Conclusions: In our cohort of pts treated within IT Ph1-CT, those with less PL of treatment, with available alternative SoC and/or selected by biomarker achieved higher PFS and OS. These results suggest that treating pts with novel IT agents at early lines might positively impact on survival. [Table: see text]
Differences in real-world pembrolizumab dosing patterns (every 3 weeks versus every 6 weeks) across a large cancer center network.
Authors: Natesan Divya , Chablani Priyanka Vinod , Wang Hong , Jelinek Mark , Rosenzweig Margaret Q. , Wong Risa Liang
Published: June 2023

2592

Background: Pembrolizumab (pembro) is an intravenous immune checkpoint inhibitor used for anti-cancer treatment, with equivalent monotherapy dosing options of 200 mg every 3 weeks (Q3W) or 400 mg every 6 weeks (Q6W). Pembro Q6W dosing was approved for use in April 2020 after the Q3W dose had already been established. As pembro dosing patterns in real-world practice are not well-described, we evaluated this in a large cancer center network consisting of a central site (CS) and 36 community network sites (NS). Methods: We retrospectively reviewed the charts of all patients who received pembro monotherapy for cancer treatment between 4/2020 – 4/2022 at UPMC Hillman Cancer Center sites across the state of Pennsylvania, as well as sites in New York and Ohio. We performed statistical comparisons using the Fisher’s exact test and Wilcoxon rank-sum test. Results: We identified 1,640 patients who received pembro monotherapy, including 377 patients at the CS and 1,263 patients in the NS, with characteristics displayed. Pembro Q6W dosing was significantly more common at the CS than in the NS (42% vs. 15%, p<0.0001). When analyzed by tumor type, pembro Q6W dosing was significantly more common at the CS than in the NS for head & neck (53% vs. 11%, p<0.0001), thoracic (49% vs. 15%, p<0.0001), skin (60% vs. 19%, p<0.0001), and genitourinary (30% vs. 16%, p=0.015) cancers, but not for other tumor types. Within the NS, 30% (11/36) of sites only utilized pembro Q3W dosing and never administered Q6W dosing to patients. Of note, some patients who received pembro Q6W dosing received pembro Q3W dosing initially, either as part of a pembro-containing multidrug regimen or as monotherapy. Excluding patients initially treated with a multidrug regimen to reduce confounding factors, we found that of the patients who received pembro Q6W dosing, 47% (65/137) at the CS and 28% (48/169) in the NS were initially treated with pembro Q3W monotherapy before transitioning to Q6W monotherapy (p=0.0008). Conclusions: In our large cancer center network, pembro Q6W dosing was significantly more common at the CS than in the NS. Switching from pembro Q3W to Q6W dosing was also significantly more common at the CS. Further work is needed to clarify the patient, provider, and institutional factors influencing differences in pembro dosing patterns in real-world practice, as well as the impact of dosing patterns on care delivery outcomes such as cost and accessibility. [Table: see text]
Phase II basket trial evaluating the efficacy of pembrolizumab (PE) combined with vorinostat (VO) in patients (pts) with recurrent and/or metastatic squamous cell carcinoma (SCC).
Authors: Le Tourneau Christophe , Bigot Frédéric , Vansteene Damien , Kamal Maud , Ghiringhelli François , Mazzarella Luca , Borel Christian , Chaltiel Raphael , You Benoit , Gomez-Roca Carlos A. , Cousin Sophie , Coquan Elodie , Lambert Aurélien , Saada-Bouzid Esma , Durando Xavier , Legrand François , Lusque Amellie , Andre Fabrice , Filleron Thomas
Published: June 2023

2597

Background: Epigenetic modulation plays a major role in escaping tumor immunosurveillance and confers resistance to immune checkpoint inhibitors. Preclinical evidence suggests that modulating the epigenome might improve the efficacy of immunotherapy. Patients and Methods: PEVOsq is an open-label, non-randomized, multi-center, basket phase II trial, evaluating the efficacy of pembrolizumab in combination with vorinostat in patients with recurrent and/or metastatic squamous cell carcinoma of the cervix, head and neck, anus, vulva/vagina, penis, and lung. Patients had to be PD1/PD-L1 antagonist-naïve. There was no selection based on PD-L1 expression nor on HPV status, and no restriction in terms of prior lines of treatments. Pembrolizumab dose was 200 mg Q3W IV, and vorinostat 400 mg QD PO. Sample size was determined for each cohort using an A’Hern design. Primary endpoint was objective response rate (ORR) according to RECISTv1.1. Secondary endpoints included safety, progression-free survival (PFS), overall survival (OS), and duration of response (DOR). Results: Among 112 included patients, 111 were evaluable for safety and 107 for efficacy. The lung cohort was closed prematurely because of lack of enrollment. Median age was 61 years old [range: 18-85] and the median number of prior lines of therapies was 1 [range: 0-4]. ORR, PFS, G3/4 treatment related adverse events (TRAE), and OS are reported. 28 patients (26%) had an objective response and median DOR was 9.7 months [95%CI: 3.1-15.2]. Results per PD-L1 status will be presented at the meeting. Pembrolizumab and vorinostat were stopped for toxicity in 9% and 39% of patients, respectively. 60% of patients had a dose-reduced of vorinostat for toxicity. Pembrolizumab safety was as expected. Main vorinostat toxicities included hematological toxicity, gastrointestinal disorders, and asthenia and creatinine increase. Conclusions: Pembrolizumab combined with vorinostat showed encouraging antitumor activity in squamous cell carcinoma with unselected PD1/PD-L1 status, especially in cervical and anal cancer, although vorinostat dose had to be reduced because of toxicity in a substantial proportion of patients. Clinical trial information: NCT04357873 . [Table: see text]
PD-1 inhibitors combined with radiotherapy and GM-CSF, sequentially followed by IL-2 (PRaG 2.0) regimen in advanced refractory solid tumors: A prospective, multicenter, single-arm clinical trial.
Authors: Xing Pengfei , Yang Jiabao , Xu Meiling , Wang Jian , Han Dali , Kong Yuehong , Zhang Junjun , Zhang Liyuan
Published: June 2023

2603

Background: Low frequency of durable responses in patients treated with immune checkpoint inhibitors demands taking complementary strategies in order to boost immune responses against cancer. Our previous PRaG trial also demonstrated that PD-1 inhibitors in combination with radiotherapy and granulocyte macrophage-colony stimulating factor (GM-CSF) could improve clinical response in patients with advanced refractory solid tumors (ChiCTR1900026175). In an effort to further enhance efficacy, we conducted the PRaG 2.0 trial (ClinicalTrials.gov: NCT04892498) and optimized the PRaG regimen by incorporating interleukin-2 (IL-2). Methods: The PRaG 2.0 regimen was administered to patients with advanced refractory solid tumors who lacked or were unable to tolerate standard-of-care treatments. A treatment cycle consisted of radiotherapy (5 or 8Gy×2-3f) delivered for one metastatic lesion, PD-1 inhibitor dosing within one week after completion of radiotherapy, GM-CSF 200μg subcutaneous (SC) injection once daily for 7 days, and then sequentially followed by IL-2 2million IU SC once daily for 7 days. PRaG 2.0 regimen was repeated every 21 days for at least 2 cycles until no appropriate lesions for irradiation or reached the tolerance dose of normal tissues. Patients who could not continue radiotherapy and had not yet developed progression disease (PD) allowed PD-1 inhibitors to be continued as maintenance therapy until PD or unacceptable toxicity but no more than one year. The primary endpoint was Progression-Free Survival (PFS). Results: As of 31st October 2022, 51 patients were enrolled in the study, and 42 completed at least one tumor assessment. The median Progression-Free Survival (PFS) was 5.8 months, and the median overall survival (OS) was 13.5 months. The objective response rate (ORR) was 21.4%, and the disease control rate (DCR) was 61.9% according to RECIST version 1.1. Lower plasma levels of Interleukin (IL)-6 and IL-17 at baseline were found to be associated with improved PFS. Treatment-related adverse events (TRAE) experienced in 34 of 42 (78.6%) patients, with 4 patients (9.5%) experiencing Grade ≥ 3 TRAEs. TRAEs leading to discontinuation of all study treatments occurred in three patients (7.1%). Conclusions: The PRaG 2.0 trial demonstrates that PD-1 inhibitors in combination with radiotherapy, GM-CSF, and IL-2 could be a potential treatment regimen for patients with advanced refractory solid tumors, with an acceptable benefit/risk profile. Clinical trial information: NCT04892498 .
Durvalumab + tremelimumab in biologically selected advanced/metastatic solid tumors.
Authors: De La Fouchardiere Christelle , Gomez-Roca Carlos A. , De Montfort Aymeric , Italiano Antoine , Gilabert Marine , Tredan Olivier , Korakis Iphig nie , Ray-Coquard Isabelle Laure , Rochefort Pauline , Dufresne Armelle , Cousin Sophie , Le Tourneau Christophe , You Benoit , Bertucci Francois , Cassier Philippe Alexandre , Attignon Valéry , Mayet Romaine , Garin Gwenaelle , Pérol David , Blay Jean-Yves
Published: June 2023

2604

Background: Tremelimumab (T) in combination with Durvalumab (D) is approved by the FDA for the treatment of unresectable hepatocellular carcinoma and metastatic non–small cell lung cancer. We prospectively examined its clinical activity in a cohort of biologically-selected advanced/metastatic solid tumors from the MOST Plus clinical trial (NCT NCT02029001). Methods: Adult patients (pts) previously treated by at least one prior line but immunotherapy-naive were eligible if their tumor harbored TMB-H (>10mut/Mb) and/or MSI/dMMR (by PCR and IHC tests), and/or PD1/PD-L1/CTLA4 amplification and/or POLD1 or POLE mutation. T was administered for up to 4 cycles (75mg, IV, Q4W) and D (1500mg, IV, Q4W) until disease progression, unacceptable toxicity or patient/investigator decision. Tumor response was assessed as per RECIST 1.1 and adverse events reported according to NCI-CTCAE v4.03. Results: 70 patients were enrolled (24 male, median age: 65 years [33-88], MSI n=56, TMB-H n=10, PDL1 and PDL2 ampl. n=1, POLE mut. n=1, MSH6 mut. n=1, MSH2 mut. n=1). The median number of prior lines of systemic therapy was 1 (range: 0-4). Main tumor types were colorectal (44%), endometrial (19%), and stomach (7%) carcinomas. As of October 2022, overall response (ORR) rate was 52.8% (21.4% CR, 31.4% PR). With a median follow-up of 37 months, median PFS and OS were 8.4 months [95% CI: 4.4- 22.1] and 37.2 months [95% CI: 10.4-NE], respectively. Median duration response of response was not reached. Overall, 24.3% of patients experienced at least one serious treatment-related (TR) adverse event. Two TR-deaths were reported (haemophagocytic lymphohistiocytosis and nephritis). ORR, median PFS and OS are reported. Conclusions: T+D is a highly efficient combination in biologically selected tumors leading to a high complete response rate. Enrolment is still ongoing, to further evaluate the utility of a maintenance treatment, i.e the optimal treatment duration. Clinical trial information: NCT02029001 . [Table: see text]
Prospective cardiovascular surveillance of immune checkpoint inhibitor-based combination therapy in patients with early-stage, triple-negative breast cancer.
Authors: Venkatesh Vishnu , Yen Christine , Zhang Ray , Rao Anjali , Chandra Alvin , Zaha Vlad , Vallabhaneni Srilakshmi , Zhang Kathleen W
Published: June 2023

2607

Background: Both pembrolizumab and anthracyclines (AC) can cause adverse cardiovascular events; combination therapy is approved for high-risk, early-stage, triple-negative breast cancer (TNBC) and may further increase real-world cardiovascular risk. Cardiac surveillance with serial troponin measurements has been advocated in this population, though evidence supporting this approach is lacking. Methods: High-sensitivity troponin I (hs-TnI) was prospectively measured at baseline and with each treatment cycle in cancer patients receiving immune checkpoint inhibitors (ICI) at a single center as part of an institutional surveillance protocol for ICI-related adverse events from 2020-2022. Acute cardiac injury was defined as ≥1 abnormal hs-TnI value (>17ng/dL in women and >35ng/dL in men) with normal baseline hs-TnI, or at least 20% increase in hs-TnI from abnormal baseline. The incidence of acute cardiac injury and all-cause mortality were compared between patients receiving ICI in combination with AC versus ICI without AC. Results: Among 215 patients treated with ICI with baseline and ≥1 follow-up hs-TnI value, 28 patients (13%) received ICI with AC, all of whom were women with early-stage TNBC receiving pembrolizumab and AC-containing chemotherapy. 187 patients (87%) received ICI without AC for other oncological indications. Patients receiving ICI with AC were younger and more likely to be female than patients receiving ICI without AC (p<0.001) with lower rates of smoking, hypertension, and diabetes (p<0.04). Acute cardiac injury was observed in 33 patients, 21% of those receiving ICI with AC (N=6) and 14% of those receiving ICI without AC (N=27; p=0.34). Among these 33 patients, 2 patients were treated for ICI-associated myocarditis (1 receiving ICI with AC, 1 receiving ICI without AC); 67% of those receiving ICI with AC (N=4) were continued on ICI while only 30% of those receiving ICI without AC (N=8) were continued on ICI (p=0.16). The rate of all-cause mortality was significantly lower in patients receiving ICI with AC (0%) as compared to patients receiving ICI without AC (40%, p<0.001). Conclusions: Among women with early stage TNBC receiving pembrolizumab with AC, the rate of acute cardiac injury by surveillance troponin measurements was numerically but not statistically higher than for patients receiving ICI without AC for other oncological indications, though the rate of all-cause mortality was significantly lower. These findings suggest that surveillance troponin monitoring may have less clinical utility among women with early-stage TNBC receiving ICI-based combination therapy as compared to other patient populations receiving ICI. Further study is needed to understand the mechanistic and prognostic significance of acute cardiac injury in patients with TNBC receiving ICI-based combination chemotherapy.
Artificial intelligence (AI) –powered spatial analysis of macrophages in tumor microenvironment and its association with interferon-gamma (IFNG) signature and immune phenotype (IP) in pan-cancer dataset.
Authors: Oum Chiyoon , Park Gahee , Song Heon , Lee Jinhee , Pereira Sergio , Song Sanghoon , Kim Sukjun , Jung Wonkyung , Ock Chan-Young
Published: June 2023

2621

Background: Macrophages are known to play a crucial role in cancer progression, but few studies have reported macrophage spatial distribution and its association with genomic signatures and tumor-infiltrating lymphocytes (TIL). Here, we applied an AI-powered Whole Slide Image (WSI) analyzer in The Cancer Genome Atlas (TCGA) pan-cancer dataset to show correlation between specific localization of macrophage and anti-tumor activity, which is reflected by IFNG signature and IP based on spatial TIL density. Methods: For spatial macrophage analysis in TCGA pan-cancer dataset, we used Lunit SCOPE IO, an AI-powered H&E WSI analyzer, which identifies and quantifies various classes of cells such as tumor cell, macrophage, and TIL within cancer or stroma area. IPs were defined as follows: inflamed IP (IIP) as high intratumoral TIL (iTIL) and stromal TIL (sTIL); immune-excluded IP (IEP) as low iTIL and high sTIL; immune-desert IP (IDP) as low TIL overall. The immune cell profiling and quantification of the IFNG signature score were analyzed by using CIBERSORT and RSEM. Results: In TCGA dataset (N = 7,402), median macrophage density in total TME area (tMP) was 19.9 /mm2 (interquartile range [IQR] 9.0-44.9), and it was highly enriched in lung adenocarcinoma (median 65.1, IQR 34.3-110.0), lung squamous cell carcinoma (61, 32.4-101.3), and head and neck squamous cell carcinoma (39.4, 19.6-77.3). Based on IP classification, tMP was highly enriched in IIP (37.8, 18.7-73.8) compared to IEP (25.5, 13.8-48.6) and IDP (8.9, 4.4-17.1). Interestingly, spatial analysis showed that intratumoral macrophage density (iMP) in IIP was highly enriched compared to the others (mean fold change 2.57) and the difference of stromal macrophage density (sMP) among IPs was relatively smaller (mean fold change x1.85). Classified into four groups based on median values of iMP and sMP, high-iMP/high-sMP group had the highest proportion of IIP (47.3% vs 18.7%, p < 0.001), whereas low-iMP/high-sMP group had the highest one of IEP (54.9% vs 32.3%, p < 0.001) compared to the others, respectively. Moreover, the high-iMP/high-sMP group had the highest level of IFNG signature score among 4 groups (x2.13 times higher, p < 0.001). Notably, both iMP and sMP were significantly correlated with CD68 expression (rho 0.292 and 0.287) but CSF1R expression was more strongly correlated with iMP (rho 0.259) compared to sMP (rho 0.078). Conclusions: IIP, IFNG signature, and CSF1R expression are more strongly correlated with intratumoral macrophage density versus stromal macrophage density, suggesting a relationship between macrophage location and function in the TME warranting further investigation.
Role of HLA class-I antigen peptide loading complex components in immune evasion and treatment sensitivity in human lung cancer.
Authors: Costantini Adrien , Ranjan Kishu , Ferrone Soldano , Schalper Kurt A.
Published: June 2023

2623

Background: Determinants of sensitivity and resistance to immune checkpoint inhibitors (ICIs) are poorly understood. An intact HLA class-I antigen presentation machinery (APM) is necessary for tumor-antigen recognition by effector T-cells and disruptions to the APM can cause ICI resistance. The peptide loading complex (PLC) is a multi-chaperone complex located in the endoplasmic reticulum in which tapasin (Tap), calreticulin (CalR) and ERp57 play major roles. The PLC allows for optimal peptide selection and loading onto HLA class-I heavy chain and is critical for adequate cell surface presentation of peptide-HLA complexes. We studied the frequency and clinical significance of cancer-cell selective PLC protein defects in human NSCLC. Methods: Multiplex quantitative immunofluorescence (mQIF) was performed to simultaneously and spatially measure cytokeratin (CK), Tap, CalR, ERp57 and CD8 protein levels in 1,031 primary NSCLCs from 5 independent cohorts represented in tissue microarrays. The protein levels were measured in CK-positive cancer-cells and in CK-negative stromal cells. The presence of lower marker levels in malignant cells relative to stromal cells within the same sample was considered as cancer-cell selective downregulation. Cohorts #1-3 included baseline samples from patients treated without ICIs and Cohort #4 included samples from patients treated with ICIs. Cohort #5 contained lung adenocarcinomas clinically tested for EGFR and KRAS mutations. The association between the levels of Tap, CalR and ERp57, their association with clinicopathologic variables, CD8+ T-cell levels and outcomes were studied. Results: mQIF analysis identified cancer-cell selective downregulation of Tap, CalR and/or ERp57 in 73%, 81%, 68% and 75% of cases from Cohorts #1-4, respectively. The most common PLC alterations were cancer-cell downregulation of Tap alone in Cohorts #1 (32%), #3 (34%) and #4 (36%); and Tap-CalR in Cohort #2 (29%). Tap and ERp57 levels were significantly higher in stage IV than in earlier stage tumors. The PLC marker levels and the frequency of cancer-cell selective downregulation were comparable across EGFR and KRAS mutated samples. NSCLCs with cancer-cell Tap downregulation had lower CD8+ T-cell infiltration and shorter OS across all cohorts that reached statistical significance in Cohort #4 (median OS 12.08 vs 21.00, HR=1.72, 95% CI 1.02-2.89, p=0.034). The cancer-cell selective downregulation of CalR was associated with shorter OS in cohorts #1 and #3. Conclusions: HLA class-I PLC components show variable levels in treatment naïve NSCLCs. Downregulation of Tap in cancer-cells, alone or in combination with other PLC members occurs in up to 60% of cases and is associated with reduced CD8+ TILs and shorter OS preferentially in patients treated with ICIs. Cancer-cell Tap downregulation could mediate primary ICI resistance and has biomarker potential.
Using machine learning to characterize lung cancer microenvironment and the development of a model to predict the presence of similar microenvironment in other cancers.
Authors: Charifa Ahmad , Zhang Hong , Ip Andrew , Estella Jeffrey , Ma Wanlong , Mohtashamian Arash , Gutierrez Martin , Pecora Andrew L , Goy Andre , Albitar Maher
Published: June 2023

2634

Background: Poor response to immune checkpoint inhibitors (ICI) in colorectal cancer (CRC) is believed to be due to lack of immune suppressive tumor microenvironment (TME). In contrast, lung cancer TME is believed to be significantly more immunologically active and responsible for the relative success of ICI in lung cancer. We evaluated the TME in lung cancer and CRC using 43 immune biomarkers quantified using RNA sequencing and developed a model to classify TME into immunologically active (similar to lung cancer) vs inactive (similar to colorectal). These 43 immune biomarkers included B- and T-cell markers, cytokines and chemokines. Methods: RNA was extracted from FFPE samples from 707 patients with lung cancer, 227 patients with CRC, 131 patients with breast cancer, 111 patients with ovarian cancer, and 72 patients with pancreatic cancer. The expression levels of the 42 immunological markers were quantified using next generation sequencing (NGS) as a part of larger targeted RNA sequencing panel of 1408 genes. Using a machine learning algorithm, we first selected the relative genes that distinguish between two classes using two criteria: performance of each gene with K-fold cross-validation (K=12) and second based on stability measure using statistical significance tests. The selected genes were then used to predict one class from the other using random forest classifier. Samples were divided into a training set (67%) and testing set (33%). Results: A Bayesian-based algorithm selected the expression of 20 genes that were significantly relevant in differentiating between immunologically active and inactive TME. Using these 20 genes in Random Forest model, we can distinguish between lung and CRC with AUC of 0.997 (95% CI: 0.992-1.00) in the training set and AUC of 0.923 (95% CI: 0.880-0.966) in the testing set. Testing 131 breast cancer samples showed 23 (18%) with TME that can be classified as immunologically active. Of 111 ovarian samples 13 (12%) showed immunologically active TME and of 72 pancreatic samples, 17 (24%) showed microenvironment classified as active. The 20 genes that were adequate to distinguish between TME active vs inactive are: CD74, FCGBP, IL1R1, CD44, CD274, FCGR2B, IL21R, IL1RAP, IL7R, CD79A, CCL2, CYFIP2, CD19, IL2RA, CD8A, CD79B, ID1, CD22, FZD10, and IL1B, listed in order of their importance. Conclusions: This data shows that lung cancer TME is significantly different from that of CRC. Only 20 immune biomarkers adequate to distinguish between the two TME. The relevant biomarkers included CD274 (PD-L1) as well as one marker for T-cells (CD8A) but three markers for B-cells (CD19, CD22 and CD79B). This suggests that B-cells play a significant role in immunologically active TME and should be explored further as biomarkers for predicting response to ICI therapy.
Timing of immunotherapy-induced pneumonitis in patients with primary lung malignancy.
Authors: Winter Megan , Gilani Madiha Atif , Anipindi Manasa , Venigalla Tejaswi , Doreswamy Shriya
Published: June 2023

2647

Background: Pneumonitis is a widely recognized side effect of immunotherapy with increased incidence in non-small cell lung cancers as compared to other solid organ malignancies. A review of the literature demonstrates an incidence of 5% in patients receiving PD-1/PD-L1 inhibitors. While biopsy provides definitive diagnosis of immunotherapy-induced pneumonitis, clinical symptoms and radiologic features are most utilized with treatment guided by the grade of toxicity. The ability to predict the timing, which patients, and to what extent pneumonitis will present has been a significant challenge. Our study aims to look at the timing of onset of immunotherapy-induced pneumonitis in patients treated with checkpoint inhibitors for primary lung cancer to elicit patterns which may assist in diagnosis and appropriate treatment. Methods: This is a single-institution, retrospective study reviewing patients with primary lung cancer who received checkpoint inhibitors between January 2018 and January 2023. The focus was on the date of initiation of therapy and the date of onset of pneumonitis. Immunotherapy-induced pneumonitis was defined as development of abnormal imaging findings with or without respiratory symptoms following initiation of immunotherapy and graded by the Common Terminology Criteria for Adverse Events (CTCAE). Additional patient demographics were collected to assess secondary patterns. Results: A total of 117 patients met the specified search criteria. Of these, 10 patients (8.5%) met the criteria for immunotherapy-induced pneumonitis. The average time between receiving the first dose of immunotherapy and the development of immunotherapy-induced pneumonitis was 66.5 days (range of 1 to 163 days). The average number of cycles received before diagnosis was 3.7, with most cases occurring after less than 5 cycles provided (7 out of 10). The grade of pneumonitis ranged from 1 to 5. All patients had non-small cell lung cancer, with the most prevalent histology being squamous cell carcinoma, ranging from stage III to stage IV. Durvalumab was the most prevalent immunotherapy (6 of the 10). Conclusions: The timing of immunotherapy-induced pneumonitis, while variable, occurred after receiving less than 5 cycles in majority of our cases, with most occurring after just 1 cycle. Interestingly, durvalumab was the most common immunotherapy in these cases. While our study is limited by the number of patients, the incidence of pneumonitis in our study was close to that of the national average and may, also, be reflective of the timing of immunotherapy-induced pneumonitis. Additional studies with larger numbers of patients are needed.
Risk of immune-related adverse events (irAE) with immune checkpoint inhibitors (ICI) in patients (pts) with family history (FH) of autoimmune disease (AID).
Authors: Grover Piyush , Li Isabel , Menzies Alexander M. , Long Georgina V.
Published: June 2023

2648

Background: Pts with personal history (PH) of AID are at increased risk of irAE following ICI. Risk of irAE in pts with FH of AID is unknown. Methods: In this retrospective cohort study, consecutive pts were recruited from 2 Australian melanoma cancer centers. Pts who received anti-PD-1 (PD1) based ICI with FH of AID were eligible. Pts with PH of AID were excluded. Toxicity data (CTCAE v5.0) was obtained and stratified by FH of AID (first/second/third degree relative). Descriptive statistics and Fisher’s Exact test were used for analysis. Results: 396 melanoma cases were screened, of which 44 (11.1%) were eligible for inclusion. Baseline characteristics are summarized. 57 irAE occurred in 44 pts. The most common irAE were dermatological (n=11; 19.3%), colitis (n=8; 14.0%), endocrinopathies (n=8; 14.0%), hepatitis (n=7; 12.3%) and arthritis (n=7; 12.3%). Among 57 irAE, frequency of Grade 1,2,3 and 4 irAE was 16 (28.1%), 26 (45.6%), 12 (21.0%) and 3 (5.3%) respectively. Corticosteroids were used for 31 (54.4%) irAE. Hospital admission for management of irAE occurred in 11 pts (25.0%). ICI was discontinued in 20 pts (45.5%) due to irAE. In pts with irAE, FH of that irAE/AID was present in 6 pts (13.6%) (n= 2 x arthritis, n= 2 x psoriasis, n= 1 x Crohn’s disease, n= 1 x Grave’s disease), and 4 of these patients had a first-degree relative with an AID. 3/6 pts had ICI ceased due to an irAE (peak toxicity Grade was 3) and 4/6 pts had RECIST response. There was no association in development of irAE between patients with FH of AID in a first-degree relative and those with FH of AID in second or third degree relative (p=0.17). Rate of irAE in pts with FH of AID was not statistically higher to that reported in registration trials of similar regimens (p=0.40). Conclusions: FH of AID is common in melanoma pts and was not associated with higher rate or morbidity of irAE. FH AID should be routinely collected, and larger scale studies need to be performed. [Table: see text]
Mirzotamab clezutoclax as monotherapy and in combination with taxane therapy in relapsed/refractory solid tumors: Dose expansion results.
Authors: Carneiro Benedito A. , Perets Ruth , Dowlati Afshin , LoRusso Patricia , Yonemori Kan , He Lei , Munasinghe Wijith , Noorani Behnam , Johnson Eric Feral , Zugazagoitia Jon
Published: June 2023

3027

Background: Mirzotamab clezutoclax (ABBV-155; Mirzo-C) is a first-in-class antibody-drug conjugate with three components: an anti–B7-H3 monoclonal antibody, a solubilizing linker, and a BCL-XL inhibitor payload. By specific targeting of BCL-XL, synergy with other anticancer agents was observed in preclinical models. When combined with a taxane, clinical antitumor activity was reported in relapsed and/or refractory (R/R) solid tumors during the dose escalation phase of an ongoing Phase 1, open-label study (NCT03595059). Methods: In the dose expansion phase of the Phase 1 study, patients were treated as follows: (i) R/R small cell lung cancer (SCLC) with Mirzo-C monotherapy, (ii) non-small cell lung cancer (NSCLC) with Mirzo-C + docetaxel, and (iii) hormone positive, Her2 negative, post–CDK4/6 inhibitor breast cancer (BrCa) with Mirzo-C + paclitaxel. Mirzo-C was administered at the recommended Phase 2 dose determined at dose escalation. Primary objectives were safety and overall response rate (ORR). Results: As of November 18, 2022, 78 patients were enrolled (SCLC n=14; NSCLC n=36; BrCa n=28). The median (range) follow-up was 2.0 (0.6–9.1) months for the SCLC cohort, 4.9 (0.6–8.5) for NSCLC, and 10.4 (0.8–13.3) for BrCa. The median number of prior lines of systemic therapy was 2 in the SCLC cohort, 2 in NSCLC, and 6 in BrCa. Prior taxane therapy was received by 7% of patients in the SCLC cohort, 36% in NSCLC, and 64% in BrCa. The most common adverse events (AEs) in SCLC were fatigue, increased aspartate aminotransferase, diarrhea, and headache (21%, n=3 for each AE); fatigue was the most common AE in NSCLC (58%, n=21; Grade 3/4: 3%, n=1) and in BrCa (61%, n=17). Thrombocytopenia, a result of the systemic effects of BCL-XL inhibitors, was not observed in the Mirzo-C monotherapy cohort. Neutropenia/decreased neutrophil count was not observed in the SCLC monotherapy cohort but was common with BrCa paclitaxel combo (64%, n=18; Grade 3/4: 29%, n=8) and NSCLC docetaxel combo (53%, n=19; Grade 3/4: 44%, n=16); 5 patients in the NSCLC cohort (14%) and 1 in BrCa (4%) had febrile neutropenia. Confirmed ORR was 0% in the SCLC cohort, 11% in NSCLC, and 18% in BrCa. Conclusions: Mirzo-C demonstrated a tolerable safety profile as monotherapy and with taxanes. No thrombocytopenia or neutropenia was observed with monotherapy. No single-agent activity of Mirzo-C was observed in SCLC. Combination treatments were active with high best overall response (BOR) and disease control rates in heavily pretreated NSCLC and BrCa patients, where Grade 3/4 neutropenia was observed. It is unknown if Mirzo-C exacerbated the neutropenia risk associated with taxanes. Clinical trial information: NCT03595059 . [Table: see text]
Construction of DNA methylation-based biomarkers for diagnosis of hepatocellular carcinoma.
Authors: Xu Ximing , Chen Jiayu , Shen Yang
Published: June 2023

3048

Background: Hepatocellular carcinoma is the most common malignant tumor in China. Most of the patients are found in the advanced stage, which causes its low survival rate. According to the latest epidemiological data, hepatocellular carcinoma is the second leading cause of cancer mortality. DNA methylation is closely related to tumor development. In this study, differentially expressed methylated genes related to tumorigenesis and development were screened from the database and the diagnostic model was constructed for early screening. Methods: Limma package was used to analyze the differences between TCGA _ LIHC liver cancer and GSE113409 normal blood methylation sites and differentially expressed methylation sites (logFC>1，p<0.05) were identified. The TCGA _ LIHC methylation database was used as the training set. Lasso method, and random forest method were used for screening the differentially expressed methylation sites for the construction of the diagnostic model. After that, the characteristic coefficient of methylation sites and ROC curve of the diagnostic model were obtained from the training set. According to the cd-score, HCC patients could be diagnosed in the early stage, thus improved their survival. Results: Limma package was used to analyze the differences between TCGA _ LIHC liver cancer and GSE113409 normal blood methylation sites and 7109 differentially expressed methylation sites (logFC>1，p<0.05) were identified. Then the top 1000 differentially expressed methylation sites were selected. The TCGA _ LIHC methylation database was used as the training set. 30 methylation sites were screened by lasso method, and 20 methylation sites were screened by random forest. Taking the intersection, a total of 6 methylation sites were obtained for diagnostic model: cg00346208, cg00084798, cg00458878, cg00006397, cg00325910, cg00399027. The characteristic coefficient of methylation sites were displayed in the table below and the AUC of the diagnostic model was 0.9991579. High cd-score tended to have hepatocellular carcinoma, and vice versa. Conclusions: We have identified several DNA methylation markers for the diagnosis of hepatocellular carcinoma from GEO and TCGA databases. This model can predict hepatocellular carcinoma and the AUC is higher than that of AFP, which means it may become a more sensitive indicator for the diagnosis of liver cancer. [Table: see text]
Tumor mutational burden as a predictive biomarker for molecularly matched therapy in two independent pan-cancer cohorts.
Authors: Rieke Damian Tobias , de Bortoli Till , Benary Manuela , Horak Peter , Lamping Mario , Stintzing Sebastian , Tinhofer Inge , Leyvraz Serge , Schäfer Reinhold , Klauschen Frederick , Keller Ulrich , Stenzinger Albrecht , Froehling Stefan , Kurzrock Razelle , Jelas Ivan , Keilholz Ulrich
Published: June 2023

3066

Background: Personalized cancer therapy based on molecular tumor aberrations has shown efficacy in a subset of tumors. Novel biomarkers are warranted to help extend this benefit to a larger patient population. Tumor mutational burden (TMB) is an established predictive biomarker for immune checkpoint inhibition. Its role for molecularly matched therapy is unknown. Methods: Comprehensive molecular profiling including whole-exome and RNA-sequencing was performed in 104 patients with advanced cancer within the DKTK MASTER program. 55 patients received a systemic therapy excluding immunotherapy. TMB and survival were analyzed in patients receiving molecularly matched therapy (n=34) or non-molecularly matched therapy (n=21) as well as in an independent published cohort of patients receiving molecularly matched (n=68) or non-molecularly matched (n=40) therapy (excluding immunotherapy). TMB and co-occurring driver mutations were analyzed in the DKTK MASTER cohort. Results: The median TMB of 1.68 mutations per megabase (mut/Mb) in the 34 patients receiving molecularly matched therapy was used to stratify patients into TMB-high and -low groups. Median overall survival (OS) and progression-free survival (PFS) were significantly shorter in the TMB-high than in the TMB-low group (OS: 4 months [95% CI, 3.3 to 7.6] versus 19 months [95%CI, 10.0 to not reached] p < 0.001, Hazard Ratio (HR) 4.4 [95%CI, 1.9 to 10.2], p<0.001; PFS 1.8 months [95%CI, 1.1 to 3.6] versus 8.5 months [95% CI, 2.8 to 17.0] p = 0.004, HR 2.9 [95%CI, 1.4 to 6.2], p=0.005). No significant differences were observed in patients receiving non-molecularly informed systemic therapy (OS HR 0.7 [95%CI, 0.2 to 2.6], p=0.635 and PFS HR 1.2 [95%CI, 0.4 to 3.5] p=0.701). In the validation cohort, shorter progression-free survival was also identified in the TMB-high group (median TMB cut-off of 4 mut/Mb; HR 2.2 [95%CI, 1.3 to 3.7] p=0.005) treated with molecularly matched therapy but not with non-molecularly informed therapy (HR 1.1 [95%CI, 0.5 to 2.2] p=0.848). TMB was associated with co-occurring driver mutations (n=104, r = 0.78 [95%CI, 0.68 to 0.85], p<0.001). Conclusions: High TMB was previously established as a positive predictive biomarker associated with efficacy of immune checkpoint inhibitor treatments. Our study reveals high TMB as a negative predictive biomarker associated with low efficacy of molecularly informed systemic therapy, potentially due to co-occurring driver mutations. Thus, TMB is a candidate predictive pan-cancer biomarker for combined precision oncology and immunotherapy programs.