RB1 Mutations Research Articles

Abstract PO1-14-08: Real-world clinical genomics study of HR+/HER2- metastatic breast cancers treated by CDK4/6i plus endocrine therapies revealed a drug resistant tumor segment characterized by ER independence

Abstract Background CDK4/6 inhibitors (CDK4/6i) plus endocrine therapies (ET) are the standard-of-care for hormone receptor–positive/human epidermal receptor 2–negative metastatic breast cancer (HR+/HER2− mBC). However, drug resistance remains a major unmet need. Investigations of drug resistance mechanisms has been hampered by a dearth of tumor molecular profiling data from the post-treatment setting. To address this challenge, we have conducted a real-world clinical genomics study to better understand the molecular mechanism of CDK4/6i resistance as well as to stratify patients based on integrated multi-omics profiles. Methods We retrospectively analyzed a multi-omics dataset of 400 HR+/HER2- mBC patients who had received CDK4/6i plus ET and developed progressive disease (PD) from the de-identified Tempus database. Pre-treatment and post-progression biopsies were taken  1 year prior to starting the CDK4/6i treatment or following PD respectively. Tempus xT next-generation sequencing (DNA-seq of 648 genes) and RNA sequencing assays were performed on 427 tumor FFPE samples, including 200 pre-treatment, 227 post-progression and 26 longitudinal pairs. Results The median age of the patients was 57 (54.9-57.4) and median progression free survival (PFS) is 379 (341-433) days. Two genes were found to harbor a significant increase in genomic alteration frequencies (GAF) after adjusting for FDR at post-progression vs. pre-treatment – ESR1 (41.9% vs. 15%, p=5.4e-10), RB1 (13.2% vs. 3%, p=8.5e-05). ESR1 and RB1 also harbored high frequencies of acquired genomic alterations among 26 paired samples at 34.6% and 11.5% respectively. TP53 mutation at baseline was significantly associated with shorter PFS at baseline (p=4.23e-05, HR=2.081) and TP53 GAF significantly increased after PD (37% vs. 28.5%, p=0.039). BRCA1/2 pathogenic mutations (p=1.63e-04, HR=3.066), APOBEC mutation signature S13 (p=0.0125, HR=1.55) and CCNE1 gene expression (p=0.024, HR=1.46) were significantly associated with shorter PFS. APOBEC signature (p=0.0035) and CCNE1 expression (p=1.33e-06) also significantly increased post-progression. Among the top molecular features associated with longer PFS were markers of estrogen signaling such as PGR gene expression (p=6.76e-04, HR=0.565) and the Hallmark estrogen response signature (p=0.021, HR=0.679). Applying a multi-omics pattern recognition algorithm, we identified a molecularly distinct cluster (IC1) characterized by down-regulation of estrogen signaling. IC1 is significantly associated with shorter PFS (p=3.72e-05, HR=0.22) and increased from 4% pre-treatment to 23% post-progression (p=7.3e-08). Further, IC1 is strongly enriched in markers previously implicated in CDK4/6i resistance including CCNE1 expression, RB1 mutation and MYC/E2F activation. We then developed machine learning models to predict gene-level dependency trained on cancer cell line expression and CRISPR-KO screen data. These models predicted decreased dependency on ESR1 and CDK4 and increased dependency on CDK2 in IC1, strengthening the association between ER independence and CDK4/6i resistance. Conclusions Our real-world clinical genomics study identified a comprehensive list of biomarkers associated with resistance to CDK4/6i plus ET and estimated patient prevalence for these markers in the post-treatment setting. Integrated and machine-learning analyses identified a subset of aggressive tumors with estrogen independence characteristics that are implicated in CDK4/6i resistance and suggested new therapeutic strategies. Citation Format: Zhengyan Kan, Ji Wen, Jennifer Webster, Vinicius Bonato, Whijae Roh, Xinmeng Jasmine Mu, Paul Rejto, Jadwiga Bienkowska. Real-world clinical genomics study of HR+/HER2- metastatic breast cancers treated by CDK4/6i plus endocrine therapies revealed a drug resistant tumor segment characterized by ER independence [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO1-14-08.

Abstract PS17-04: Clinical and Genomic Features of ER-Positive/HER2-negative Metastatic Breast Cancer in AURORA Molecular Screening Initiative (BIG 14-01): Mechanisms of Endocrine Therapy Resistance and Implications for Adjuvant Approaches

Abstract Background: Up to 30% of patients (pts) with ER-positive early breast cancers develop metastatic relapse. The molecular differences between endocrine therapy (ET)-sensitive and ET-resistant relapses, as well as the impact of specific adjuvant ET-based therapies, remain unclear. Methods: The AURORA program (NCT02102165) analyzed multi-omics data of paired primary (prim) and metastatic (meta) tumor tissue, along with plasma samples, from 1,156 patients with metastatic breast cancer (MBC). Targeted genome sequencing (TGS), RNA sequencing, and circulating tumor DNA analysis were performed. ET-resistance at MBC diagnosis was defined following the 5th ESO-ESMO ABC Guidelines. Results: We studied 628 pts with metastatic ER+/HER2- disease. Patient´s median age was 56 years, 133 (21%) were premenopausal, 314 (50%) had ET-resistance at recurrence (9% primary, 41% secondary), 132 (21%) had ET-sensitive recurrence, and the rest were ET-naive recurrences or de novo MBC. Adjuvant treatment was aromatase inhibitor (AI) +/- ovarian function suppression (OFS) in 288 (46%) pts, while 159 (25%) had tamoxifen only (+/- OFS). Gene expression correlation significantly differed (p < 0.005) based on ET-resistance in 92 paired samples. ET-sensitive (n=11) and de-novo tumors (n=41) showed higher correlation than primary (n=7) and secondary ET-resistance (n=32), regardless of adjuvant ET type. Prim and meta showed concordance in 91% of IHC subtypes and 62% of intrinsic subtypes. Intrinsic subtype showed 9% of prim luminal tumors switching to meta non-luminal, with 66% of Luminal A switching to Luminal B. Neither IHC nor intrinsic subtype switching was associated with the type of adjuvant ET or ET resistance. Pts with meta non-luminal intrinsic subtype (18%) had worse PFS on CDK4/6i (HR 4.0, 95% CI 1.9-8.7) and OS (HR 3.6, 95% CI 2.0-5.7) than luminal subtypes. TGS was performed in 534 meta (365 before 1L, 305 pairs). In meta before 1L, the dN/dS algorithm revealed selection in 17 genes, including TP53, PIK3CA, and ESR1. Mutations (mut) in ESR1, ERBB2, ERBB3, and RB1 among others, were specifically identified in meta. The incidence of ESR1mut was 3% in prim, 12.6% before 1L, 23.4% after 1L, and 4.7% in meta from ET-naive tumors (Table). Before 1L, ESR1mut was higher after adjuvant AI vs tamoxifen (21% vs. 4%, p< 0.001). ESR1mut incidence varied with ET-resistance (16% primary, 19% secondary, 9% sensitive, 4% ET-naïve/de novo, p< 0.01). Paired samples showed that ESR1mut were mainly acquired events and associated with higher ER mRNA signaling (hallmark estrogen response) compared to ESR1wt (p < 0.05). The agreement between ESR1mut detected in ctDNA and tissue was high before 1L (90%), and slightly lower after 1L (84%). In a multivariate model with relevant clinical factors, ESR1mut were associated with worse OS (HR 1.76, 95% CI 1.2-2.5, p=0.003), independently of TP53 and PIK3CA mutational status. Conclusion: AURORA study sheds light on metastatic tumor alterations acquired under anti-cancer therapy, in ER+/HER2- MBC. We observed a high prevalence of acquired ESR1mut prior to the initiation of first-line therapy, particularly in tumors exposed to adjuvant AI or with primary or secondary ET_resistance. The association of ESR1muts with poorer OS underscores the importance of implementing effective adjuvant ET strategies to prevent the emergence of these mutations. Frequency of driver gene mutations in primary and metastastic tumors before 1st-line treatment according to adjuvant ET and type of ET resistance Table. Citation Format: Angel Guerrero-Zotano, Matteo Benelli, Alexandre Irrthum, David Cameron, Lorenzo Ferrando, Dario Romagnoli, Marta Paoli, Arnau Llinas, Maya Dadiani, Danai Fimereli, Mafalda Oliveira, Carmela Caballero, Thayane Crestani, Elisa Agostinetto, Diogo Martins-Branco, Florentine Hilbers, Einav Gal-Yam, Marija Balic, Fatima Cardoso, Jorge Reis-Filho, Christos Sotiriou, Giuseppe Curigliano, Barbro Linderholm, Evandro de Azambuja, Susan Knox, Cristina Rotaru, Eva Ciruelos, Nancy E Davidson, Giuseppe Viale, Donatienne Taylor, Jean-Luc Canon, Lourdes Calvo, Joan Albanell, Marco Colleoni, Caroline Duhem, Nadia Harbeck, Catherine Herremans, Sibylle Loibl, Sandrine Marreaud, Elsemieke Scheepers, Alice Raimbault, Theodora Goulioti, Andrea Vingiani, Chiara Biagioni, Sebastian Vosberg, Gabriele Zoppoli, Jose Seoane, David Venet, Philippe Aftimos, Martine Piccart. Clinical and Genomic Features of ER-Positive/HER2-negative Metastatic Breast Cancer in AURORA Molecular Screening Initiative (BIG 14-01): Mechanisms of Endocrine Therapy Resistance and Implications for Adjuvant Approaches [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PS17-04.

Abstract PO4-24-01: Comprehensive Molecular and Immunological Characterization of Invasive Ductal Triple-Negative Breast Cancer

Abstract Background: Triple-negative breast cancer (TNBC) is a heterogeneous disease and characterized by poor outcomes with a lack of targeted therapies. A comprehensive analysis of the molecular and immune landscape of invasive ductal TNBC can help improve our understanding of TNBC biology and identify novel targets and/or pathways for better management of this disease. Here, we characterized the molecular and immune signature of invasive ductal (ID) TNBC. Methods: 13,036 BC samples (ID TNBC, n=392; ID non-TNBC, n=927) were analyzed by NGS (592, NextSeq; WES, NovaSeq), WTS (NovaSeq) (Caris Life Sciences, Phoenix, AZ). A total of 10 pro-apoptotic (BAX, BAK1, BID, BAD, BIK, BCL2L11, BMF, HRK, PMAIP1, BBC3) and 6 anti-apoptotic (BCL2, BCL2L1, BCL2L2, MCL1, BCL2A1, BCL2L10) BCL2 family genes were analyzed. Immune cell fractions were calculated by deconvolution of WTS: Quantiseq. Real world overall survival (OS) and treatment-associated survival was extracted from insurance claims and calculated from tissue collection or treatment start to last contact using Kaplan-Meier estimates. Statistical significance was determined using chi-square and Mann-Whitney U test with p-values adjusted for multiple comparisons (q < 0.05). Results: ID TNBC had a higher frequency of TP53, RB1, NF1, PIK3R1, NOTCH1, CREBBP, BRCA1, FANCI, and HRAS mutations (Table 1), NOTCH2 (4.3% vs 0.47%), EGFR (3.4% vs 0%), NFIB (4% vs 0.6%), MYB (3.5% vs 0.5%), CCNE1 (4.4% vs 1.1%) and AKT2 (2.4% vs 0.3%) copy number alterations, and NOTCH2 (1.6% VS 0.2%) fusion (all p < 0.05) compared to invasive ductal non-TNBC. Analysis of inferred immune cell infiltrates showed that ID TNBC had increased infiltration of Tregs (2% vs 1.7%), DC (3.2% vs 2.4%), CD8 T cells (0.5% vs 0.1%), and M1 macrophages (M) (3.4% vs 2.9%), but decreased infiltration of B cells (4.5% vs 6%) and M2M (2.9% vs 4.5%) (all p < 0.05). ID TNBC had increased T cell inflamed score (23 vs -9, p < 0.05), IFNy score (-0.24 vs -0.34, p < 0.05), MHC class I genes (HLA-A, HLA-B, TAP1, TAP2, FC: 1.1-1.5, all p < 0.05), immune checkpoint genes (CD274, PDCD1, CTLA4, PD-L2, FOXP3, IDO, FC: 1.1-2, all p < 0.05) and PD-L1 protein expression (SP142: 49.8% vs. 28.4%; 22c3: 41.7% vs. 16.8%, all p < 0.05). ID TNBC had differential expression of BCL2 family genes (upregulation: BAK1, BID, MCL1, BCL2A1, BCL2L10, FC: 1.1-2.0; downregulation: BAD, BIK, BBC3, BCL2, BCL2L1, BCL2L2, FC: 1.2-2.8, all p < 0.05) compared to invasive ductal non-TNBC. ID TNBC was associated with worse OS compared to ID non-TNBC (mOS: 24.5 vs 54.6 months; HR: 0.5, 95% CI 0.47-0.57; p < 0.00001) but trend towards better survival with pembrolizumab (mOS: 29.4 vs 8.8 month; HR: 0.67, 95% CI 0.28-1.5; p=0.3) treatment. No significant OS difference was noted for by high vs. low pro and anti-apoptotic BCL2 genes except for anti-apoptotic BCL2A1 (higher expression associated with better OS (mOS: 5.7 months, HR: 0.78, 95% CI 0.6-0.99; p=0.047). Conclusion: These data indicate that ID TNBC is associated with distinct mutational profile compared to non-TNBC, has increased T cell inflamed score, IFNy score, MHC class I and immune checkpoint gene expression, and differential immune cell infiltration. Interestingly, TNBC was associated with increased M1 and decreased M2M. There is evidence to suggest that transcriptomically defined M1 high tumors are clinically aggressive and have worse OS in TNBC. BCL2 family genes are not prognostic for TNBC outcomes except BCL2A1, which needs further prospective validation. Table 1: Mutation frequency in invasive ductal TNBC and invasive ductal non-TNBC Citation Format: Pooja Advani, Sachin Deshmukh, Sharon Wu, Jacob Andring, Joanne Xiu, Alex Farrell, Jose Leone, Priya Jayachandran, Stephanie Graff, Matthew Oberley, George Sledge Jr, Asher Chanan-Khan. Comprehensive Molecular and Immunological Characterization of Invasive Ductal Triple-Negative Breast Cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO4-24-01.

Role of RB1 in neurodegenerative diseases: inhibition of post-mitotic neuronal apoptosis via Kmt5b.

During the development of the vertebrate nervous system, 50% of the nerve cells undergo apoptosis shortly after formation. This process is important for sculpting tissue during morphogenesis and removing transiently functional cells that are no longer needed, ensuring the appropriate number of neurons in each region. Dysregulation of neuronal apoptosis can lead to neurodegenerative diseases. However, the molecular events involved in activating and regulating the neuronal apoptosis program are not fully understood. In this study, we identified several RB1 mutations in patients with neurodegenerative diseases. Then, we used a zebrafish model to investigate the role of Rb1 in neuronal apoptosis. We showed that Rb1-deficient mutants exhibit a significant hindbrain neuronal apoptosis, resulting in increased microglia infiltration. We further revealed that the apoptotic neurons in Rb1-deficient zebrafish were post-mitotic neurons, and Rb1 inhibits the apoptosis of these neurons by regulating bcl2/caspase through binding to Kmt5b. Moreover, using this zebrafish mutant, we verified the pathogenicity of the R621S and L819V mutations of human RB1 in neuronal apoptosis. Collectively, our data indicate that the Rb1-Kmt5b-caspase/bcl2 axis is crucial for protecting post-mitotic neurons from apoptosis and provides an explanation for the pathogenesis of clinically relevant mutations.

Genomic Correlates of Prostate-Specific Membrane Antigen Expression and Response to 177Lu-PSMA-617: A Retrospective Multicenter Cohort Study.

While 177Lu-PSMA-617 (LuPSMA) is an effective therapy for many patients with metastatic castration-resistant prostate cancer (mCRPC), biomarkers associated with outcomes are not well defined. We hypothesized that prostate cancer mutational profile may associate with clinical activity of LuPSMA. We devised a study to evaluate associations between mCRPC mutational profile with LuPSMA clinical outcomes. This was a multicenter retrospective analysis of patients with mCRPC with next-generation sequencing (NGS) who received LuPSMA. PSA50 response (ie, ≥50% decline in prostate-specific antigen [PSA]) rate, PSA progression free survival (PSA PFS), and overall survival (OS) were compared between genetically defined subgroups. One hundred twenty-six patients with NGS results who received at least one cycle of LuPSMA were identified. The median age was 73 (IQR, 68-78) years, 124 (98.4%) received ≥1 prior androgen receptor-signaling inhibitor, and 121 (96%) received ≥1 taxane-based chemotherapy regimen. Fifty-eight (46%) patients with a DNA damage repair gene mutation (DNA damage response group) and 59 (46.8%) with a mutation in TP53, RB1, or PTEN tumor suppressor genes (TSG group) were identified. After adjusting for relevant confounders, the presence of ≥1 TSG mutation was associated with shorter PSA PFS (hazard ratio [HR], 1.93 [95% CI, 1.05 to 3.54]; P = .034) and OS (HR, 2.65 [95% CI, 1.15 to 6.11]; P = .023). There was improved OS favoring the DNA damage response group (HR, 0.37 [95% CI, 0.14 to 0.97]; P = .044) on multivariable analysis. Univariate analysis of patients with ATM mutations had significantly higher rates of PSA50 response, PSA PFS, and OS. Outcomes on LuPSMA varied on the basis of mutational profile. Prospective studies to define the clinical activity of LuPSMA in predefined genomic subgroups are justified.

Diagnostic Imaging for Retinoblastoma Cancer Staging: Guide for Providing Essential Insights for Ophthalmologists and Oncologists.

Retinoblastoma is the most common cause of all intraocular pediatric malignancies. It is caused by the loss of RB1 tumor suppressor gene function, although some tumors occur due to MYCN oncogene amplification with normal RB1 genes. Nearly half of all retinoblastomas occur due to a hereditary germline RB1 pathogenic variant, most of which manifest with bilateral tumors. This germline RB1 mutation also predisposes to intracranial midline embryonal tumors. Accurate staging of retinoblastoma is crucial in providing optimal vision-, eye-, and life-saving treatment. The AJCC Cancer Staging Manual has undergone significant changes, resulting in a universally accepted system with a multidisciplinary approach for managing retinoblastoma. The authors discuss the role of MRI and other diagnostic imaging techniques in the pretreatment assessment and staging of retinoblastoma. A thorough overview of the prevailing imaging standards and evidence-based perspectives on the benefits and drawbacks of these techniques is provided. Published under a CC BY 4.0 license. Test Your Knowledge questions for this article are available in the supplemental material.

Abstract 6390: Exploratory biomarker analysis of phase 3 ASTRUM-005 study: Serplulimab versus placebo plus chemotherapy for extensive-stage small cell lung cancer

Abstract Background First-line serplulimab plus chemotherapy (chemo) significantly improved OS compared with chemo alone for patients with extensive-stage small cell lung cancer (ES-SCLC) in the phase 3 ASTRUM-005 study. In this exploratory biomarker analysis, we retrospectively evaluated the association of proteome signature, genetic mutations, and hematological indices with efficacy. Methods: Serum proteomics data were generated via Olink® Explore 3072 platform for 168 patients (training: 80; validation: 88). Genetic mutations were assessed by Med1CDxTM panel for 305 patients. Baseline neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR), and lactate dehydrogenase (LDH) levels were analyzed in all 585 patients. Clinical data cutoff date was June 13, 2022. Results: From Olink data, we generated a 15-protein signature. Results in the validation cohort are shown in the table below. Patients with upper signature score derived higher PFS (7.89 vs 4.17 mo, HR 0.37) and OS (17.18 vs 9.74 mo, HR 0.27) benefit from adding serplulimab, than those with lower signature score (PFS: 4.40 vs 4.34 mo, HR 0.68; OS: 9.05 vs 9.22 mo, HR 0.76). Patients with mutations in RB1 or NOTCH pathway had better tumor responses to the treatment of serplulimab-chemo (ORR: 80% and 86%, respectively) when compared to patients without mutations in RB1 or NOTCH pathway (ORR: 58% and 68%). Patients with NLR ≤4.6, PLR ≤338.3, and LDH ≤ upper limit of normal tended to have longer PFS and OS in both treatment groups; NLR and LDH were further proven to be independent prognostic biomarkers in multivariate regression (P = 0.002 and P <0.001, respectively). Conclusions: We found a 15-protein signature showing predictive power for serplulimab-chemo treatment; RB1 or NOTCH pathway mutations were enriched in serplulimab-chemo responders; baseline NLR and LDH were independent prognostic biomarkers for ES-SCLC. The above findings warrant further investigations. Serplulimab-chemo (n=48) Placebo-chemo (n=40) HR (95% CI) P Upper signature score, n 31 34 Median PFS (95% CI), months 7.89 (1.27, 10.74) 4.17 (2.96, 4.34) 0.37 (0.21, 0.66) <0.001 Median OS (95% CI), months 17.18 (11.01, NE) 9.74 (6.90, 12.65) 0.27 (0.15, 0.50) <0.001 Lower signature score, n 17 6 Median PFS (95% CI), months 4.40 (3.61, 5.75) 4.34 (2.66, NE) 0.68 (0.23, 2.02) 0.488 Median OS (95% CI), months 9.05 (6.67, 11.73) 9.22 (4.53, NE) 0.76 (0.29, 1.98) 0.570 Citation Format: Ying Cheng, Liang Han, Lin Wu, Jun Chen, Hongmei Sun, Guilan Wen, Yinghua Ji, Anastasia Zimina, Jianhua Shi, Zhijie Pan, Jinsheng Shi, Xicheng Wang, Fang Yang, Xinyi Yang, Mengkai Chen, Shiqi Zhong, Qingyu Wang, Jing Li, Jiancheng Cheng, Chen Ling, Yongqiang Shan, Jun Zhu, The ASTRUM-005 Study Group. Exploratory biomarker analysis of phase 3 ASTRUM-005 study: Serplulimab versus placebo plus chemotherapy for extensive-stage small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6390.

Abstract 5061: Improved survival and unique mutational signatures in small cell lung cancer arising in patients with limited tobacco use

Abstract Small-cell lung cancer (SCLC) remains the deadliest histologic lung cancer subtype with a median survival of only 12.3 months among trial-eligible patients with extensive-stage (ES-SCLC) disease, as demonstrated in the IMPower133 trial. Heavy tobacco use, >40 pack-years, is strongly associated with developing SCLC, which near universally harbors RB1 and TP53 co-mutations. However, there is a paucity of information regarding SCLC tumors that occur in patients with minimal tobacco use. This represents an unmet need given an increasing appreciation for low pack-year and never-smoker SCLC with some studies, like the CAPSTONE-1 trial, demonstrating an incidence of never-smoking SCLC >20%. To address this, we clinically characterized the treatments and outcomes of a 164 SCLC patient cohort with ≤10 pack year smoking histories treated at the University of Texas MD Anderson Cancer Center; 22 of which underwent whole-exome sequencing (WES). The overall survival of limited-stage (LS-SCLC) and extensive-stage (ES-SCLC) disease in the low pack-year cohort were 33.6 and 16.6 months, respectively (P=0.003); superior to historic medians of roughly 17.0 and 12.3 months, respectively. Among those with ES-SCLC, those who reported 1-10 pack-years had significantly improved median overall survival as compared to never-smokers; 19.5 vs 15.8 months, respectively (P=0.02). This trend was observed in LS-SCLC as well with 1-10 pack-year and never-smokers demonstrating median overall survivals of 88.6 vs 26.2 months, respectively (P=0.2). Demographic differences including age were similar across these cohorts. WES of tumors from 22 patients demonstrated significantly fewer mutations in RB1 and TP53 than was observed in previously reported cohorts of SCLC from smokers. Among the low-pack year cohort, 7/22 (32% vs 98.2%:P<0.001) harbored an RB1 alteration, 7/22 (32% vs 90.9%: P<0.001) harbored a TP53 mutation, and 4/22 (18% vs 90.9%: P<0.001) had co-occurring RB1/TP53 mutations. No patients harbored mutations in EGFR, HER2, or RET. Mutations in potentially targetable pathways were observed throughout the cohort including the DNA-damage repair pathways, RTK/RAS, and PI3K. Taken together, these data demonstrate that patients with low pack-year SCLC have improved overall survival compared to historic averages for SCLC patients with a history of heavy tobacco use. Paradoxically, however, light-smokers with SCLC live longer than never-smokers, and these patients may harbor a higher frequency of targetable alterations than typical SCLC patients, highlighting the importance of molecular profiling in SCLC patients with minimal tobacco use. Citation Format: Kyle Concannon, Moushumi Sahu, Whitney Lewis, Hai Tran, Lixia Diao, Yuanxin Xi, Benjamin Morris, Simon Heeke, Ximing Tang, John Stewart, Ivan Valiev, Gabriela Raso, Jing Wang, Koji Sasaki, Carl Gay, John Heymach, Lauren Byers. Improved survival and unique mutational signatures in small cell lung cancer arising in patients with limited tobacco use [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5061.

Abstract 3295: Pharmacological characterization of CYRS1542: A potent and orally available GSPT1 molecular glue degrader for the treatment of neuroendocrine solid cancer with a favorable safety profile

Abstract Neuroendocrine cancers (NECs) are relatively rare compared to other malignancies, but their clinical behavior can be exceptionally aggressive. Two particularly challenging subtypes of NECs, Small Cell Lung Cancer (SCLC) and Neuroendocrine Prostate Cancer (NEPC), are worthy of attention due to their rapid progression, limited treatment options, and high mortality rates. At the molecular level, SCLC and NEPCs necessitate the presence of TP53 and RB1 mutations (Beltran et al., 2016; George et al., 2015). The frequency of TP53 mutations in SCLC is particularly noteworthy, with studies consistently reporting a high incidence (89~92%) (Chen et al., 2022; Sivakumar et al., 2023). A recent study has unveiled intriguing parallels between NECs and hematological malignancies, shedding light on their shared genetic features and analogous patterns of therapeutic susceptibility (Balanis et al., 2019). GSPT1, a translation termination factor, plays a key role in releasing the complete polypeptide from the ribosome. As cancer cells are dependent on translation processes to express elevated levels of oncoproteins, GSPT1 degradation would have lethal consequences. Specific CRBN modulators possess the capability to induce GSPT1 degradation via the ubiquitin-proteasome pathway. GSPT1 degradation leads to a halt in translation termination, activating the Integrated Stress Response (ISR) and subsequently triggering TP53-independent apoptosis. Despite GSPT1 degradation in cancer cells is appealing due to its potential to disrupt the production of critical proteins necessary for cancer cell survival and growth, the challenge lies in doing so without causing excessive harm to normal cells, as GSPT1 is also indispensable for their vital cellular functions. Remarkably, the ongoing development of GSPT1-targeted agents in clinical trials has raised intriguing questions about the mechanisms by which a therapeutic index can be established. Recently, we have identified CYRS1542 as an orally bioavailable GSPT1 molecular glue degrader (MGD) (Joo et al., 2023). Here, we present a pharmacological characterization of CYRS1542 as a potent and orally bioavailable GSPT1 MGD with the ability to effectively treat aggressive neuroendocrine cancers. In various NEC in vivo models, including an orthotopic model, CYRS1542 demonstrated dose-dependent and excellent anti-tumor efficacy comparable to the clinical stage GSPT1 MGD. Furthermore, it demonstrates improved safety profiles in a broad spectrum of normal cells, resulting in a higher therapeutic index compared to the clinical GSPT1 MGD. Citation Format: Min Sung Joo, JaeYung Lee, Joonhyung Lee, Eun-Jung Kim, Seogbeom Song, Jeonghyeon Lee, Joonwoo Nam, Heuijoon Park, Jaewoo Park, Keon Wook Kang, Wooseok Han. Pharmacological characterization of CYRS1542: A potent and orally available GSPT1 molecular glue degrader for the treatment of neuroendocrine solid cancer with a favorable safety profile [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3295.

Abstract 5830: A first-of-its-kind model that reconstitutes targeted drug-induced cellular transdifferentiation

Abstract Introduction: Lung tumors treated with targeted therapies ultimately relapse due to intra-genic resistance mutations, bypass pathway activation, or cellular lineage changes. Newer precision therapies have higher selectivity and potency against both resistant and activating gene mutations, resulting in a significant increase in incidence of cellular transdifferentiation. The most common form of transdifferentiation is the change from lung adenocarcinomas (LUADs) to small cell lung cancer (t-SCLC) upon drug treatment which remains very poorly understood. Methods: We have combined patient derived xenografts (PDX) and ex vivo lines with multi-omic characterization, high-content image-based morphometry and fluorescence tracking, and single-cell barcode tracing to better understand the process of lung tumor transdifferentiation. Results: We have developed a first-of-its-kind t-SCLC model that reconstitutes ex vivo LUAD to SCLC transdifferentiation. Genomic and transcriptomic analyses of our NSCLC PDX collection identified tumors with mutation in TP53 and RB1, two genes that are altered in virtually all de novo SCLCs. PDX sample CBX336 was identified as having mutations in both TP53 and RB1, in addition to expressing the KRASG12C oncogene. Upon treatment with Sotorasib, CBX336 tumors initially demonstrated slow tumor growth, followed by a dramatic increase in the growth after prolonged drug exposure. Our experimental and computational data suggest a highly coordinated procession toward transdifferentiation with the parallel upregulation of the neuroendocrine transcription factor NEUROD1 across numerous epithelial cellular clones. Conclusions: Our new experimental system allows characterization at the single-cell level. Ongoing work includes the integration of new resources to study lineage reprogramming, and advancing new therapeutic strategies. Citation Format: Priyanka Gopal, Mohamed Abazeed. A first-of-its-kind model that reconstitutes targeted drug-induced cellular transdifferentiation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5830.

Abstract 972: Non-invasive detection of homologous recombination deficiency in metastatic prostate cancer patients

Abstract Background: The recent endorsement of poly ADP ribose polymerase inhibitors (PARPi) has been a breakthrough in managing prostate cancer (PCa) with homologous recombination deficiency (HRD). However, due to its propensity to metastasize to the bone, HRD assessment in tissue biopsy poses a challenge in advanced PCa. Circulating tumor DNA (ctDNA) as a tumor surrogate may be a promising substitute for pinpointing patients who may benefit from PARPi treatment. Methods: To test whether causes and consequences of HRD can be detected non-invasively in plasma, we pre-selected 139 plasma samples from PCa patients based on aneuploidy screening (mFAST-SeqS). We then applied targeted sequencing using a QIAseq panel including homologous recombination repair (HRR)-related genes as well as genes involved in cell cycle regulation (TP53, RB1, PTEN). Putative, pathogenic germline variants were sequencing in constitutional DNA using Sanger sequencing. Moreover, we performed low pass whole genome sequencing to determine the levels of genomic instability using the shallow HRD (sHRD) algorithm. Results: In our cohort, at least one pathogenic mutation was detected in 68/139 (48.9%) of the patients, of which the majority consisted of alterations in PTEN, TP53 or RB1 (44/139, 31.7%). Pathogenic BRCA1/2 mutations were detected in 13/139 patients (9.4%), the majority of which originated from the germline. In 8/139 patients (5.6%) a pathogenic variant in other HRR genes could be observed and in 3/139 patients (2.2%) CKD12 mutations were detected. As expected, samples with pathogenic HRR mutations and elevated tumor fraction, presented high sHRD scores (<20) in plasma DNA. In contrast, the majority of high ctDNA samples with mutations in PTEN, TP53 or RB1 had sHRD score below the cut-off of 20. However, the detection of genomic instability was clearly depending on tumor fractions. Conclusion: Our study indicates that a non-invasive assessment of root causes and subsequent effects of the HRD phenotype in prostate cancer is feasible, and that mutations in HRR correlate with a high genomic instability. However, to detect and quantify genomic instability in plasma, elevated ctDNA levels are required. Based on in-house data from mFAST-SeqS aneuploidy screening of over 900 plasma samples from advanced prostate cancer, approximately 30% of cfDNA samples would have sufficiently high ctDNA fractions for a combined assessment of causes and consequences of HRD, which might be most informative to direct PARPi treatment in PCa. Citation Format: Georgios Vlachos, Tina Moser, Anna Eberhard, Lisa Glaswitch, Jasmin Blatterer, Emil Bauernhofer, Nina Monsberger, Karl Kashofer, Jochen Geigl, Thomas Bauernhofer, Ellen Heitzer. Non-invasive detection of homologous recombination deficiency in metastatic prostate cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 972.

Abstract 1251: Tobacco smoke alters the adaptive landscape of lung adenocarcinoma and influences the strength of epistatic interactions

Abstract Tobacco smoke produces both mutagenic and physiological effects, altering the mutation rate of cells and the selection acting on them in the damaged lung environment, and facilitating its role in driving cancer progression. In addition to these gene-by-environment interactions, gene-by-gene epistatic interactions also shape the adaptive landscape, influencing the evolutionary trajectories of cancer. Understanding the influence of tobacco smoke on the epistatic trajectories of lung cancer progression would help guide the development of targeted therapies that are more effective for smoker or never-smoker populations. To address this need, we constructed a continuous-time Markov chain model for the evolutionary trajectories of lung adenocarcinoma (LUAD), the most common subtype of lung cancer and the most frequent subtype among never-smokers. Using thousands of tumor sample sequences aggregated across studies, we profiled the trajectories of LUAD in smokers and never-smokers and estimated the rates at which mutations are gained from each possible set of pre-existing mutations, or genetic states. We then accounted for differences in baseline mutation rates to quantify the selective benefit of mutations. We find that epistasis is prevalent in LUAD, with several strong synergistic interactions—such as between RB1 and EGFR mutations- and antagonistic interactions-such as between EGFR and KEAP1 or KRAS mutations. Additionally, we identify non-additive epistatic effects: STK11 mutations are synergistic with KEAP1 and KRAS mutations but do not experience additional selection when both are mutated. In contrast, GNAS mutations are not synergistic with KEAP1 or RBM10 mutations alone but are synergistic with their co-mutation. Smoking has a large influence on the adaptive landscape, with several common mutations being preferentially selected in never-smoker cancers, including EGFR, SMAD4, GNAS, and PIK3CA mutations. KEAP1, STK11, and KRAS mutations are preferentially selected in smoker cancers. Smoking’s physiological influence also affects the strength of certain epistatic interactions, such as between STK11 and KEAP1 mutations. Overall, we find that smoking not only increases the mutation rate of lung cells but also substantially alters the adaptive landscape of lung adenocarcinoma, leading to clinically relevant differences in selection on mutations between smoker and never-smoker cancers. We additionally detect frequent pairwise and higher-order epistatic effects in LUAD that may inform the personalized application of targeted therapies. Citation Format: Krishna Dasari, Jorge Alfaro-Murillo, Jeffrey Townsend. Tobacco smoke alters the adaptive landscape of lung adenocarcinoma and influences the strength of epistatic interactions [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1251.

Abstract 236: Modeling multi-step retinoblastoma genesis with cone reporter retinal organoids

Abstract Purpose: This study aims to develop a human retinoblastoma organoid (RBRO) model that recapitulates the cell-of-origin and multi-step retinoblastoma genesis. Background: Retinoblastomas originate from maturing cone photoreceptor precursors with biallelic RB1 inactivation. Rb1 mutant animal models fail to recapitulate retinoblastomagenesis with a cone precursor cell-of-origin, likely due to human-specific cone development features. In explanted fetal retina, pRB-depleted post-mitotic cone precursors proliferate, followed by a 3-5 month premalignant indolence phase before retinoblastoma-like masses emerge at tissue ages similar to retinoblastomas in vivo. However, tissue availability limits research with this disease model. RB1−/- retinal organoids (ROs) provide a potential alternative, as they demonstrate cone proliferation, but they deteriorate before forming indolent premalignant lesions or malignant retinoblastoma foci. Here, we developed methods with which to examine the effects of cone precursor pRB loss in otherwise healthy retinal tissue. Methods: We generated cone-reporter GNAT2-EGFP iPSC lines through CRISPR knock-in of EGFP-P2A at the N-terminus of GNAT2 in WTC11-mTagRFPT-LMNB1. A second round of CRISPR editing produced homozygous RB1 knockout. Chimeric RB1 WT ROs and RB1-null RBROs were generated from cone reporter iPSCs mixed with unedited parental iPSCs. ROs and RBROs were embedded in hydrogel and live-imaged episodically to track EGFP+ cone proliferation dynamics. scRNA-seq was carried out on FACS isolated EGFP+ RB1-null cones at various ages. Results: In RB1 WT ROs, EGFP+ cone precursors appeared at d34 and adopted cone morphology at ~d120, with rapid inner segment growth between ~d120 and ~d150. Immunohistochemistry confirmed cone-specific EGFP expression. In RB1-null RBROs, bi-weekly live confocal imaging revealed initial EGFP+ RB1−/− cone proliferation followed by a pre-malignant indolence phase starting at ~d150. The majority of the initially proliferating cones were Ki67-negative with some adopting mature cone photoreceptor morphology. Nascent retinoblastoma-like foci co-expressing EGFP, cone markers, and Ki67 formed in five of six RBROs after d281, a tissue age that equates to the first post-natal month when early retinoblastomas typically emerge. scRNA-seq of EGFP+ RB1−/− cones from the initial proliferation, indolence, and retinoblastoma-like stages revealed distinct molecular signatures. Conclusions: We generated a human retinoblastoma organoid model that recapitulates the cell-of-origin and timing of multi-step retinoblastomagenesis, with each tumorigenesis stage harboring distinct molecular signatures. This model may enable the identification of epigenetic and transcriptomic changes underlying malignant progression and screening for compounds that efficiently block this process. Citation Format: Jinlun Bai, David S. Koos, Kayla Stepanian, Kevin Stachelek, Bhavana Bhat, Scott Fraser, Rex Moats, David Cobrinik. Modeling multi-step retinoblastoma genesis with cone reporter retinal organoids [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 236.

Developing Novel Genomic Risk Stratification Models in Soft Tissue and Uterine Leiomyosarcoma.

Leiomyosarcomas (LMS) are clinically and molecularly heterogeneous tumors. Despite recent large-scale genomic studies, current LMS risk stratification is not informed by molecular alterations. We propose a clinically applicable genomic risk stratification model. We performed comprehensive genomic profiling in a cohort of 195 soft tissue LMS (STLMS), 151 primary at presentation, and a control group of 238 uterine LMS (ULMS), 177 primary at presentation, with at least 1-year follow-up. In STLMS, French Federation of Cancer Centers (FNCLCC) grade but not tumor size predicted progression-free survival (PFS) or disease-specific survival (DSS). In contrast, in ULMS, tumor size, mitotic rate, and necrosis were associated with inferior PFS and DSS. In STLMS, a 3-tier genomic risk stratification performed well for DSS: high risk: co-occurrence of RB1 mutation and chr12q deletion (del12q)/ATRX mutation; intermediate risk: presence of RB1 mutation, ATRX mutation, or del12q; low risk: lack of any of these three alterations. The ability of RB1 and ATRX alterations to stratify STLMS was validated in an external AACR GENIE cohort. In ULMS, a 3-tier genomic risk stratification was significant for both PFS and DSS: high risk: concurrent TP53 mutation and chr20q amplification/ATRX mutations; intermediate risk: presence of TP53 mutation, ATRX mutation, or amp20q; low risk: lack of any of these three alterations. Longitudinal sequencing showed that most molecular alterations were early clonal events that persisted during disease progression. Compared with traditional clinicopathologic models, genomic risk stratification demonstrates superior prediction of clinical outcome in STLMS and is comparable in ULMS.

High-Grade, Nonsarcomatoid Chromophobe Renal Cell Carcinoma: A Series of 22 Cases With Novel Molecular Features on a Subset

Chromophobe renal cell carcinoma (ChRCC) is the third most common subtype of renal cell carcinoma, and typically exhibits indolent behavior, though a rare subset can exhibit high-grade morphological features and are associated with a poor prognosis. Although there is limited data on the molecular characteristics of metastatic and sarcomatoid ChRCC, the molecular features of high-grade non-sarcomatoid ChRCC remain unexplored. Herein, we characterize 22 cases of ChRCC with high-grade, non-sarcomatoid components. High-grade ChRCC frequently demonstrated advanced stage at diagnosis (64% ≥pT3a or N1), with regions of extrarenal extension, nodal metastases, and vascular invasion consisting solely of high-grade ChRCC morphologically. We performed spatially guided panel-based DNA sequencing on 11 cases, comparing high- and low-grade regions (n = 22 samples). We identified recurring somatic alterations emblematic of ChRCC, including deletions of chromosomes 1, 2, 6, 10, 13, 17, and 21 in 91% (10/11) of cases and recurring mutations in TP53 (81.8%, n = 9/11) and PTEN (36.4%, n = 4/11). Notably, though PTEN and TP53 alterations were found in both high- and low- grade regions, private mutations were identified in 3 cases, indicating convergent evolution. Finally, we identified recurring RB1 mutations in 27% (n = 3) of high-grade regions leading to selective protein loss by immunohistochemistry not observed in adjacent low-grade regions. This finding was confirmed in the TCGA cohort where 2/66 cases contained RB1 mutations and demonstrated unequivocal high-grade, non-sarcomatoid morphology. We also detected multiple chromosomal gains confined to the high-grade regions, consistent with imbalanced chromosome duplication. These findings broaden our understanding of the molecular pathogenesis of ChRCC and suggest that subclonal RB1 mutations can drive the evolution to high-grade, non-sarcomatoid ChRCC.

The pancancer overexpressed NFYCAntisense 1 controls cell cycle mitotic progression through in cis and in trans modes of action

Antisense RNAs (asRNAs) represent an underappreciated yet crucial layer of gene expression regulation. Generally thought to modulate their sense genes in cis through sequence complementarity or their act of transcription, asRNAs can also regulate different molecular targets in trans, in the nucleus or in the cytoplasm. Here, we performed an in-depth molecular characterization of NFYCAntisense1 (NFYC-AS1), the asRNA transcribed head-to-head to NFYC subunit of the proliferation-associated NF-Y transcription factor. Our results show that NFYC-AS1 is a prevalently nuclear asRNA peaking early in the cell cycle. Comparative genomics suggests a narrow phylogenetic distribution, with a probable origin in the common ancestor of mammalian lineages. NFYC-AS1 is overexpressed pancancer, preferentially in association with RB1 mutations. Knockdown of NFYC-AS1 by antisense oligonucleotides impairs cell growth in lung squamous cell carcinoma and small cell lung cancer cells, a phenotype recapitulated by CRISPR/Cas9-deletion of its transcription start site. Surprisingly, expression of the sense gene is affected only when endogenous transcription of NFYC-AS1 is manipulated. This suggests that regulation of cell proliferation is at least in part independent of the in cis transcription-mediated effect on NFYC and is possibly exerted by RNA-dependent in trans effects converging on the regulation of G2/M cell cycle phase genes. Accordingly, NFYC-AS1-depleted cells are stuck in mitosis, indicating defects in mitotic progression. Overall, NFYC-AS1 emerged as a cell cycle-regulating asRNA with dual action, holding therapeutic potential in different cancer types, including the very aggressive RB1-mutated tumors.

Heterogeneous ERBB gene pathways, their targeted treatment and possible molecular mechanisms of resistance in metastatic gallbladder cancer

BackgroundERBB amplifications and mutations are known in metastatic gallbladder cancer (GBC). We conducted a prospective study on targeted therapy based on comprehensive genomic profiling (CGP). We report molecular pathways of ERBB gene and outcomes and explored the molecular mechanism of resistance. MethodsCGP was done for all consecutive GBC patients aged >18 years. Foundation medicines CDx and TarGT Absolute were used for analysis. Patients were enrolled from Jan 2017 till Dec 2022. Patient recruitment was done after ethics committee approval. Trastuzumab and/ or lapatinib were used as targeted therapy. ResultsTwenty-six patients out of 60 had ERBB1-4 gene alteration (amplification and/or mutation) that resulted in activation of PI3K/AKT/MTOR and RAS/RAF/MEK pathways. ERBB amplification (16%) was the most common genetic aberration. Mutations in TP53, RB1, CDKs, and cyclins lead to dysregulation of cell cycle and evasion of apoptosis. A total of 50% of ERBB2-positive patients carry CDK12 amplifications. The intrinsic resistance to anti-ERBB2 therapy was primarily due to downstream activation in ERBB pathway (PIK3CA) and its crosstalk with cell cycle pathway (TP53 and CDK12), JAK/STAT, VEGF, CTNNB1, and ARID1A that are known to drive MAPK/ERK signaling. Mesenchymal epithelial transition amplification or activating mutations is mechanism of resistance to anti-ERBB2 therapy. Kinase/Juxta membrane domain mutations in ERBB family proteins are also one of the potential mechanisms of resistance. ConclusionGBC is enriched with ERBB gene aberrations. Targeted therapy of ERBB pathway has shown encouraging responses. CDK12 gene amplification is a possible mechanism of resistance identified.

Impact of RB1 gene screening from blood collected on a single day from 411 family members of 113 Retinoblastoma survivors in India.

To analyse the profile and implication of genetic testing in a cohort of retinoblastoma (RB) patients and their families conducted on a single day during World Retinoblastoma Awareness Week 2017. Retrospective analysis of blood samples were collected from 411 subjects, including 113 probands at a camp organised for RB awareness and were analysed for RB1 mutations by Sanger sequencing and Multiplex Ligation-dependent Probe Amplification (MLPA). If germline mutations were detected, the parents and siblings of the proband were tested for the same mutation. Germline RB1 mutations were identified in 61/113(54%) probands with a mutation detection rate of 96% (47/49) and 22% (14/64) for bilateral and unilateral RB, respectively. Ten novel pathogenic mutations were identified. Splice mutation was most common (31%) followed by nonsense mutation (26%). The mean age at RB diagnosis was significantly lower in patients having germline RB1 mutation (mean 10.7 months ±2.5) compared to those without (mean 27.2 months ±6.5) (p = <0.0001). Parental transmission of the mutant allele was detected in 15/61(25%) cases of which 11(18%) parents were unaffected indicating incomplete penetrance. The origin of the variant allele was both paternal (n = 7) and maternal (n = 4) wherein 5 were bilateral and 6 unilateral. The detection of a germline mutation impacts the proband and family members due to its implications on change in prognosis, frequency of subsequent evaluations, screening for ocular and non-ocular cancers, and surveillance of family and future progeny.

Generation of an induced pluripotent stem cell line (LVPEIi002-A) with heterozygous RB1 mutation using peri-orbital fat derived mesenchymal cells of a patient with inherited retinoblastoma

Retinoblastoma is a pediatric intraocular cancer caused by biallelic inactivation of RB1 gene in retinal progenitor cells. Here, we report the generation of a patient-specific induced pluripotent stem cell (iPSC) line (LVPEIi002-A) from a patient diagnosed with retinoblastoma and showing familial inheritance of a nonsense mutation (c.1735C > T) within exon 18 of one of the two alleles. This RB1+/- iPSC line, LVPEIi002-A was generated by reprogramming the peri-orbital fat tissue derived mesenchymal cells and was stably expanded and characterized. It maintains the stemness, pluripotency, normal karyotype, and forms embryoid bodies comprising of all three lineage committed progenitor cells.

Predicting disease recurrence in limited disease small cell lung cancer using cell-free DNA-based mutation and fragmentome analyses.

Limited disease (LD) small cell lung cancer (SCLC) treated with definitive concurrent chemoradiotherapy (CCRT) potentially experience disease recurrence. We investigated the feasibility of circulating-tumor DNA (ctDNA)-based genomic and fragmentome analyses to assess the risk of recurrence. Targeted sequencing was conducted using pre-treatment and on-treatment blood samples from definitive CCRT-treated patients with LD-SCLC (n=50). Based on 12-month recurrence-free survival (RFS), patients were categorized into persistent-response (PeR, n=29) and non-PeR (n=21) groups. Fragmentome analysis was conducted using ctDNA fragments of different lengths: P1 (100-155 bp) and P2 (160-180 bp). Patients with TP53 (n=15) and RB1 (n=11) mutation in on-treatment samples demonstrated significantly shorter RFS than patients with wild-type (WT) (P=0.05, P=0.0014, respectively). Fragmentome analysis of all available on-treatment samples (n=26) revealed that the non-PeR group (n=10) had a significantly higher P1 range (P=0.003) and lower P2 range (P=0.002). The areas under the curves for P1, P2, and the fragmentation ratio (P1/P2) in distinguishing the PeR and non-PeR were 0.850, 0.725, and 0.900, respectively. Using optimal cut-off, longer RFSs were found with the low-fragmentation-ratio group than with the high-fragmentation-ratio group (not reached vs. 7.6 months, P=0.002). Patients with both WT RB1 and a low-fragmentation-ratio (n=10) showed better outcomes than patients with both mutated RB1 and a high-fragmentation-ratio (n=10; hazard ratio, 7.55; 95% confidence interval: 2.14-26.6; P=0.002). RB1 mutations and high fragmentation ratios correlated with early disease recurrence. Analyzing ctDNA could help in predicting early treatment failure and making clinical decisions for high-risk patients.