bluuebunny/crossref_metadata_2025 huggingface dataset:
Data from Preclinical Characterization and Phase I Trial Results of INBRX-109, A Third-Generation, Recombinant, Humanized, Death Receptor 5 Agonist Antibody, in Chondrosarcoma
Authors: Subbiah Vivek , Chawla Sant P. , Conley Anthony P. , Wilky Breelyn A. , Tolcher Anthony , Lakhani Nehal J. , Berz David , Andrianov Vasily , Crago William , Holcomb Monica , Hussain Abrahim , Veldstra Carson , Kalabus James , O’Neill Brianne , Senne Lane , Rowell Emily , Heidt Analeah B. , Willis Katelyn M. , Eckelman Brendan P.
Published: August 2023

AbstractPurpose:
Patients with unresectable/metastatic chondrosarcoma have poor prognoses; conventional chondrosarcoma is associated with a median progression-free survival (PFS) of <4 months after first-line chemotherapy. No standard targeted therapies are available. We present the preclinical characterization of INBRX-109, a third-generation death receptor 5 (DR5) agonist, and clinical findings from a phase I trial of INBRX-109 in unresectable/metastatic chondrosarcoma (NCT03715933).
Patients and Methods:
INBRX-109 was first characterized preclinically as a DR5 agonist, with binding specificity and hepatotoxicity evaluated in vitro and antitumor activity evaluated both in vitro and in vivo. INBRX-109 (3 mg/kg every 3 weeks) was then evaluated in a phase I study of solid tumors, which included a cohort with any subtype of chondrosarcoma and a cohort with IDH1/IDH2-mutant conventional chondrosarcoma. The primary endpoint was safety. Efficacy was an exploratory endpoint, with measures including objective response, disease control rate, and PFS.
Results:
In preclinical studies, INBRX-109 led to antitumor activity in vitro and in patient-derived xenograft models, with minimal hepatotoxicity. In the phase I study, INBRX-109 was well tolerated and demonstrated antitumor activity in unresectable/metastatic chondrosarcoma. INBRX-109 led to a disease control rate of 87.1% [27/31; durable clinical benefit, 40.7% (11/27)], including two partial responses, and median PFS of 7.6 months. Most treatment-related adverse events, including liver-related events, were low grade (grade ≥3 events in chondrosarcoma cohorts, 5.7%).
Conclusions:
INBRX-109 demonstrated encouraging antitumor activity with a favorable safety profile in patients with unresectable/metastatic chondrosarcoma. A randomized, placebo-controlled, phase II trial (ChonDRAgon, NCT04950075) will further evaluate INBRX-109 in conventional chondrosarcoma.
Data from Early Changes in Circulating Cell-Free KRAS G12C Predict Response to Adagrasib in KRAS Mutant Non–Small Cell Lung Cancer Patients
Authors: Paweletz Cloud P. , Heavey Grace A. , Kuang Yanan , Durlacher Emily , Kheoh Thian , Chao Richard C. , Spira Alexander I. , Leventakos Konstantinos , Johnson Melissa L. , Ou Sai-Hong Ignatius , Riely Gregory J. , Anderes Kenna , Yang Wenjing , Christensen James G. , Jänne Pasi A.
Published: August 2023

AbstractPurpose:
Non-invasive monitoring of circulating tumor DNA (ctDNA) has the potential to be a readily available measure for early prediction of clinical response. Here, we report on early ctDNA changes of KRAS G12C in a Phase 2 trial of adagrasib in patients with advanced, KRAS G12C-mutant lung cancer.
Experimental Design:
We performed serial droplet digital PCR (ddPCR) and plasma NGS on 60 KRAS G12C-mutant patients with lung cancer that participated in cohort A of the KRYSTAL-1 clinical trial. We analyzed the change in ctDNA at 2 specific intervals: Between cycles 1 and 2 and at cycle 4. Changes in ctDNA were compared with clinical and radiographic response.
Results:
We found that, in general, a maximal response in KRAS G12C ctDNA levels could be observed during the initial approximately 3-week treatment period, well before the first scan at approximately 6 weeks. 35 patients (89.7%) exhibited a decrease in KRAS G12C cfDNA >90% and 33 patients (84.6%) achieved complete clearance by cycle 2. Patients with complete ctDNA clearance at cycle 2 showed an improved objective response rate (ORR) compared with patients with incomplete ctDNA clearance (60.6% vs. 33.3%). Furthermore, complete ctDNA clearance at cycle 4 was associated with an improved overall survival (14.7 vs. 5.4 months) and progression-free survival (HR, 0.3).
Conclusions:
These results support using early plasma response of KRAS G12C assessed at approximately 3 weeks to anticipate the likelihood of a favorable objective clinical response.
Data from Bavituximab Decreases Immunosuppressive Myeloid-Derived Suppressor Cells in Newly Diagnosed Glioblastoma Patients
Authors: Ly K. Ina , Richardson Leland G. , Liu Mofei , Muzikansky Alona , Cardona Jonathan , Lou Kevin , Beers Andrew L. , Chang Ken , Brown James M. , Ma Xiaoyue , Reardon David A. , Arrillaga-Romany Isabel C. , Forst Deborah A. , Jordan Justin T. , Lee Eudocia Q. , Dietrich Jorg , Nayak Lakshmi , Wen Patrick Y. , Chukwueke Ugonma , Giobbie-Hurder Anita , Choi Bryan D. , Batchelor Tracy T. , Kalpathy-Cramer Jayashree , Curry William T. , Gerstner Elizabeth R.
Published: August 2023

AbstractPurpose:
We evaluated the efficacy of bavituximab—a mAb with anti-angiogenic and immunomodulatory properties—in newly diagnosed patients with glioblastoma (GBM) who also received radiotherapy and temozolomide. Perfusion MRI and myeloid-related gene transcription and inflammatory infiltrates in pre-and post-treatment tumor specimens were studied to evaluate on-target effects (NCT03139916).
Patients and Methods:
Thirty-three adults with IDH--wild-type GBM received 6 weeks of concurrent chemoradiotherapy, followed by 6 cycles of temozolomide (C1-C6). Bavituximab was given weekly, starting week 1 of chemoradiotherapy, for at least 18 weeks. The primary endpoint was proportion of patients alive at 12 months (OS-12). The null hypothesis would be rejected if OS-12 was ≥72%. Relative cerebral blood flow (rCBF) and vascular permeability (Ktrans) were calculated from perfusion MRIs. Peripheral blood mononuclear cells and tumor tissue were analyzed pre-treatment and at disease progression using RNA transcriptomics and multispectral immunofluorescence for myeloid-derived suppressor cells (MDSC) and macrophages.
Results:
The study met its primary endpoint with an OS-12 of 73% (95% confidence interval, 59%–90%). Decreased pre-C1 rCBF (HR, 4.63; P = 0.029) and increased pre-C1 Ktrans were associated with improved overall survival (HR, 0.09; P = 0.005). Pre-treatment overexpression of myeloid-related genes in tumor tissue was associated with longer survival. Post-treatment tumor specimens contained fewer immunosuppressive MDSCs (P = 0.01).
Conclusions:
Bavituximab has activity in newly diagnosed GBM and resulted in on-target depletion of intratumoral immunosuppressive MDSCs. Elevated pre-treatment expression of myeloid-related transcripts in GBM may predict response to bavituximab.
Data from Clinical Activity of Combined Telomerase Vaccination and Pembrolizumab in Advanced Melanoma: Results from a Phase I Trial
Authors: Ellingsen Espen B. , O'Day Steven , Mezheyeuski Artur , Gromadka Agnieszka , Clancy Trevor , Kristedja Timothy S. , Milhem Mohammed , Zakharia Yousef
Published: August 2023

AbstractPurpose:
Cancer vaccines represent a novel treatment modality with a complementary mode of action addressing a crucial bottleneck for checkpoint inhibitor (CPI) efficacy. CPIs are expected to release brakes in T-cell responses elicited by vaccination, leading to more robust immune responses. Increased antitumor T-cell responses may confer increased antitumor activity in patients with less immunogenic tumors, a subgroup expected to achieve reduced benefit from CPIs alone. In this trial, a telomerase-based vaccine was combined with pembrolizumab to assess the safety and clinical activity in patients with melanoma.
Patients and Methods:
Thirty treatment-naïve patients with advanced melanoma were enrolled. Patients received intradermal injections of UV1 with adjuvant GM-CSF at two dose levels, and pembrolizumab according to the label. Blood samples were assessed for vaccine-induced T-cell responses, and tumor tissues were collected for translational analyses. The primary endpoint was safety, with secondary objectives including progression-free survival (PFS), overall survival (OS), and objective response rate (ORR).
Results:
The combination was considered safe and well-tolerated. Grade 3 adverse events were observed in 20% of patients, with no grade 4 or 5 adverse events reported. Vaccination-related adverse events were mostly mild injection site reactions. The median PFS was 18.9 months, and the 1- and 2-year OS rates were 86.7% and 73.3%, respectively. The ORR was 56.7%, with 33.3% achieving complete responses. Vaccine-induced immune responses were observed in evaluable patients, and inflammatory changes were detected in posttreatment biopsies.
Conclusions:
Encouraging safety and preliminary efficacy were observed. Randomized phase II trials are currently ongoing.
Data from Discovery and Targeting of a Noncanonical Mechanism of Sarcoma Resistance to ADI-PEG20 Mediated by the Microenvironment
Authors: Rogers Leonard C. , Kremer Jeff C. , Brashears Caitlyn B. , Lin Zongtao , Hu Zhixian , Bastos Alliny C.S. , Baker Adriana , Fettig Nicole , Zhou Dong , Shoghi Kooresh I. , Dehner Carina A. , Chrisinger John S.A. , Bomalaski John S. , Garcia Benjamin A. , Oyama Toshinao , White Eileen P. , Van Tine Brian A.
Published: August 2023

AbstractPurpose:
Many cancers lack argininosuccinate synthetase 1 (ASS1), the rate-limiting enzyme of arginine biosynthesis. This deficiency causes arginine auxotrophy, targetable by extracellular arginine-degrading enzymes such as ADI-PEG20. Long-term tumor resistance has thus far been attributed solely to ASS1 reexpression. This study examines the role of ASS1 silencing on tumor growth and initiation and identifies a noncanonical mechanism of resistance, aiming to improve clinical responses to ADI-PEG20.
Experimental Design:
Tumor initiation and growth rates were measured for a spontaneous Ass1 knockout (KO) murine sarcoma model. Tumor cell lines were generated, and resistance to arginine deprivation therapy was studied in vitro and in vivo.
Results:
Conditional Ass1 KO affected neither tumor initiation nor growth rates in a sarcoma model, contradicting the prevalent idea that ASS1 silencing confers a proliferative advantage. Ass1 KO cells grew robustly through arginine starvation in vivo, while ADI-PEG20 remained completely lethal in vitro, evidence that pointed toward a novel mechanism of resistance mediated by the microenvironment. Coculture with Ass1-competent fibroblasts rescued growth through macropinocytosis of vesicles and/or cell fragments, followed by recycling of protein-bound arginine through autophagy/lysosomal degradation. Inhibition of either macropinocytosis or autophagy/lysosomal degradation abrogated this growth support effect in vitro and in vivo.
Conclusions:
Noncanonical, ASS1-independent tumor resistance to ADI-PEG20 is driven by the microenvironment. This mechanism can be targeted by either the macropinocytosis inhibitor imipramine or the autophagy inhibitor chloroquine. These safe, widely available drugs should be added to current clinical trials to overcome microenvironmental arginine support of tumors and improve patient outcomes.
Data from Dual Targeting of Apoptotic and Signaling Pathways in T-Lineage Acute Lymphoblastic Leukemia
Authors: Saygin Caner , Giordano Giorgia , Shimamoto Kathryn , Eisfelder Bart , Thomas-Toth Anika , Venkataraman Girish , Ananthanarayanan Vijayalakshmi , Vincent Tiffaney L. , DuVall Adam , Patel Anand A. , Chen Yi , Tan Fenlai , Anthony Stephen P. , Chen Yu , Shen Yue , Odenike Olatoyosi , Teachey David T. , Kee Barbara L. , LaBelle James , Stock Wendy
Published: August 2023

AbstractPurpose:
Relapsed T-acute lymphoblastic leukemia (T-ALL) has limited treatment options. We investigated mechanisms of resistance to BH3 mimetics in T-ALL to develop rational combination strategies. We also looked at the preclinical efficacy of NWP-0476, a novel BCL-2/BCL-xL inhibitor, as single agent and combination therapy in T-ALL.
Experimental Design:
We used BH3 profiling as a predictive tool for BH3 mimetic response in T-ALL. Using isogenic control, venetoclax-resistant (ven-R) and NWP-0476-resistant (NWP-R) cells, phosphokinase array was performed to identify differentially regulated signaling pathways.
Results:
Typical T-ALL cells had increased dependence on BCL-xL, whereas early T-precursor (ETP)-ALL cells had higher BCL-2 dependence for survival. BCL-2/BCL-xL dual inhibitors were effective against both subtypes of T-lineage ALL. A 71-protein human phosphokinase array showed increased LCK activity in ven-R cells, and increased ACK1 activity in ven-R and NWP-R cells. We hypothesized that pre-TCR and ACK1 signaling pathways are drivers of resistance to BCL-2 and BCL-xL inhibition, respectively. First, we silenced LCK gene in T-ALL cell lines, which resulted in increased sensitivity to BCL-2 inhibition. Mechanistically, LCK activated NF-κB pathway and the expression of BCL-xL. Silencing ACK1 gene resulted in increased sensitivity to both BCL-2 and BCL-xL inhibitors. ACK1 signaling upregulated AKT pathway, which inhibited the pro-apoptotic function of BAD. In a T-ALL patient-derived xenograft model, combination of NWP-0476 and dasatinib demonstrated synergy without major organ toxicity.
Conclusions:
LCK and ACK1 signaling pathways are critical regulators of BH3 mimetic resistance in T-ALL. Combination of BH3 mimetics with tyrosine kinase inhibitors might be effective against relapsed T-ALL.
Data from B-cell Receptor Pathway Mutations Are Infrequent in Patients with Chronic Lymphocytic Leukemia on Continuous Ibrutinib Therapy
Authors: Woyach Jennifer A. , Ghia Paolo , Byrd John C. , Ahn Inhye E. , Moreno Carol , O'Brien Susan M. , Jones Daniel , Cheung Leo W.K. , Chong Elizabeth , Kwei Kevin , Dean James P. , James Danelle F. , Wiestner Adrian
Published: August 2023

AbstractPurpose:
Acquired mutations in Bruton's tyrosine kinase (BTK) or phospholipase C-γ2 (PLCG2) genes are associated with clinical progressive disease (PD) in patients with chronic lymphocytic leukemia (CLL) treated with BTK inhibitors. Data on mutation rates in patients without PD on ibrutinib treatment are limited.
Experimental Design:
We evaluated frequency and time to detection of BTK and PLCG2 mutations in peripheral blood samples from 388 patients with previously untreated (n = 238) or relapsed/refractory (n = 150) CLL across five clinical trials.
Results:
With median follow-up of 35 months (range, 0–72) without PD at last sampling, mutations in BTK (3%), PLCG2 (2%), or both genes (1%) were rare in previously untreated patients. With median follow-up of 35 months (range, 1–70) without PD at last sample, mutations in BTK (30%), PLCG2 (7%), or both genes (5%) were more common in patients with relapsed/refractory CLL. Median time to first detection of BTK C481S mutation was not reached in previously untreated patients and was >5 years in patients with relapsed/refractory CLL. Among patients evaluable at PD, previously untreated patients (n = 12) had lower rates than those with relapsed/refractory disease (n = 45) of BTK (25% vs. 49%) and PLCG2 mutations (8% vs. 13%). Time from first detection of BTK C481S mutation to PD was 11.3 months in 1 previously untreated patient and median 8.5 months (range, 0–35.7) among 23 patients with relapsed/refractory CLL.
Conclusions:
This systematic investigation describes development of mutations over time in patients without PD and informs the potential clinical opportunity to optimize ongoing benefits for such patients.
Molecular Results and Potential Biomarkers Identified from the Phase 3 MILO/ENGOT-ov11 Study of Binimetinib versus Physician Choice of Chemotherapy in Recurrent Low-Grade Serous Ovarian Cancer
Authors: Grisham Rachel N. , Vergote Ignace , Banerjee Susana , Drill Esther , Kalbacher Elsa , Mirza Mansoor Raza , Romero Ignacio , Vuylsteke Peter , Coleman Robert L. , Hilpert Felix , Oza Amit M. , Westermann Anneke , Oehler Martin K. , Pignata Sandro , Aghajanian Carol , Colombo Nicoletta , Cibula David , Moore Kathleen N. , del Campo Josep M. , Berger Regina , Marth Christian , Sehouli Jalid , O'Malley David M. , Churruca Cristina , Kristensen Gunnar , Clamp Andrew , Farley John , Iyer Gopa , Ray-Coquard Isabelle , Monk Bradley J.
Published: August 2023

Purpose:

We present the results of a post hoc tumor tissue analysis from the phase 3 MILO/ENGOT-ov11 study (NCT01849874).

Patients and Methods:

Mutation/copy-number analysis was performed on tissue obtained pre-randomization. The Kaplan–Meier method was used to estimate progression-free survival (PFS). Unbiased univariate analysis, Cox regression, and binary logistic regression were used to test associations between mutation status and outcomes, including PFS and binary response by local RECIST 1.1.

Results:

MILO/ENGOT-ov11 enrolled 341 patients, ranging in age from 22 to 79, from June, 2013 to April, 2016. Patients were randomized 2:1 to binimetinib or physician's choice of chemotherapy (PCC). The most commonly altered gene was KRAS (33%). In 135 patients treated with binimetinib with response rate (RR) data, other detected MAPK pathway alterations included: NRAS (n = 11, 8.1%), BRAF V600E (n = 8, 5.9%), RAF1 (n = 2, 1.5%), and NF1 (n = 7, 5.2%). In those with and without MAPK pathway alterations, the RRs with binimetinib were 41% and 13%, respectively. PFS was significantly longer in patients with, compared with those without, MAPK pathway alterations treated with binimetinib [HR, 0.5; 95% confidence interval (CI) 0.31–0.79]. There was a nonsignificant trend toward PFS improvement in PCC-treated patients with MAPK pathway alterations compared with those without (HR, 0.82; 95% CI, 0.43–1.59).

Conclusions:

Although this hypothesis-generating analysis is limited by multiple testing, higher RRs and longer PFS were seen in patients with low-grade serous ovarian cancer (LGSOC) treated with binimetinib, and to a lesser extent in those treated with PCC, who harbored MAPK pathway alterations. Somatic tumor testing should be routinely considered in patients with LGSOC and used as a future stratification factor.
SPOP Mutations Target STING1 Signaling in Prostate Cancer and Create Therapeutic Vulnerabilities to PARP Inhibitor–Induced Growth Suppression
Authors: Geng Chuandong , Zhang Man-Chao , Manyam Ganiraju C. , Vykoukal Jody V. , Fahrmann Johannes F. , Peng Shan , Wu Cheng , Park Sanghee , Kondraganti Shakuntala , Wang Daoqi , Robinson Brian D. , Loda Massimo , Barbieri Christopher E. , Yap Timothy A. , Corn Paul G. , Hanash Samir , Broom Bradley M. , Pilié Patrick G. , Thompson Timothy C.
Published: August 2023

Purpose:

Speckle-type POZ protein (SPOP) is important in DNA damage response (DDR) and maintenance of genomic stability. Somatic heterozygous missense mutations in the SPOP substrate-binding cleft are found in up to 15% of prostate cancers. While mutations in SPOP predict for benefit from androgen receptor signaling inhibition (ARSi) therapy, outcomes for patients with SPOP-mutant (SPOPmut) prostate cancer are heterogeneous and targeted treatments for SPOPmut castrate-resistant prostate cancer (CRPC) are lacking.

Experimental Design:

Using in silico genomic and transcriptomic tumor data, proteomics analysis, and genetically modified cell line models, we demonstrate mechanistic links between SPOP mutations, STING signaling alterations, and PARP inhibitor vulnerabilities.

Results:

We demonstrate that SPOP mutations are associated with upregulation of a 29-gene noncanonical (NC) STING (NC-STING) signature in a subset of SPOPmut, treatment-refractory CRPC patients. We show in preclinical CRPC models that SPOP targets and destabilizes STING1 protein, and prostate cancer–associated SPOP mutations result in upregulated NC-STING–NF-κB signaling and macrophage- and tumor microenvironment (TME)–facilitated reprogramming, leading to tumor cell growth. Importantly, we provide in vitro and in vivo mechanism-based evidence that PARP inhibitor (PARPi) treatment results in a shift from immunosuppressive NC-STING–NF-κB signaling to antitumor, canonical cGAS–STING–IFNβ signaling in SPOPmut CRPC and results in enhanced tumor growth inhibition.

Conclusions:

We provide evidence that SPOP is critical in regulating immunosuppressive versus antitumor activity downstream of DNA damage–induced STING1 activation in prostate cancer. PARPi treatment of SPOPmut CRPC alters this NC-STING signaling toward canonical, antitumor cGAS–STING–IFNβ signaling, highlighting a novel biomarker-informed treatment strategy for prostate cancer.
Abstract A003: Kinome-wide siRNA screening identifies DCLK2 as a TBK1 activator and therapeutic target for ccRCC
Authors: Hu Lianxin , Zhang Qing
Published: August 2023

TBK1 has been identified as a potential therapeutic target in multiple cancers. However, it is challenging to target TBK1 in clinical practice due to lack of selectivity for TBK1 inhibitors and its role involved in innate immune signaling. To overcome this difficulty, one approach would be to identify a critical upstream regulator of TBK1 that can be targeted therapeutically, especially in clear cell Renal Cell Carcinoma (ccRCC) displaying hyper-activated TBK1 activity due to VHL loss. In this study, we perform a kinome-wide siRNA screening and identify Doublecortin like kinase 2 (DCLK2) as a novel TBK1 regulator in ccRCC. DCLK2 binds with TBK1 and directly phosphorylates TBK1 on Ser172. Depletion of DCLK2 inhibits anchorage independent colony growth of kidney cancer cells as well as kidney tumorigenesis in orthotopic xenograft models. DCLK2 gene product contains multiple isoforms. Among them, a short isoform called DCLK2203 expresses predominantly in ccRCC. Overexpression of DCLK2203 promotes ccRCC cell growth and tumorigenesis in vivo, which elicits its oncogenic signaling via activating TBK1 phosphorylation. Taken together, our work suggest that DCLK2 is a novel TBK1 activator and potential therapeutic target for ccRCC.

Citation Format: Lianxin Hu, Qing Zhang. Kinome-wide siRNA screening identifies DCLK2 as a TBK1 activator and therapeutic target for ccRCC [abstract]. In: Proceedings of the AACR Special Conference: Advances in Kidney Cancer Research; 2023 Jun 24-27; Austin, Texas. Philadelphia (PA): AACR; Cancer Res 2023;83(16 Suppl):Abstract nr A003.
Abstract B020: A mechanistic study of the TFE3-splicing machinery gene fusions reveals a new druggable target for translocation renal cell carcinoma
Authors: Fontane Ilaria Delle , Damayanti Nuri , Rupert Christopher , Heppner David E. , Pili Roberto
Published: August 2023

TFE3 is a member of basic helix-loop-helix leucine zipper MiT transcription factor family and its chimeric proteins are associated with translocation renal cell carcinoma (tRCC). Despite the variety of genes fusions, most of TFE3 fusions partner genes are linked to spliceosome machinery. Dissecting the function of TFE3 fused to spliceosome machinery factors (TFE3-SF) could direct the development of effective therapies for this lethal disease, which is refractory to standard treatments for kidney cancer. Here, by using a combination of in silico structure prediction, molecular cloning, next generation transcriptomics, FRET technology, mutagenesis, proteomics, and high-throughput high-content screening (HTHCS) we interrogated a series of oncogenic mechanisms of TFE3-SF-containing fusions, including spontaneous nuclear translocation, nuclear paraspeckle occupancy, enhanced in vitro proliferation and in vivo growth, transcriptome remodeling, alternative splicing reprogramming, and novel dimer partner recruitment. Molecular inhibition of TFE3-SF dimerization reverses its oncogenic activity and represents a potential new target for therapeutic intervention. Using HTHCS combined with FRET technology we screened FDA approved drugs library (LOPAC) and small molecule library (Microsource) and identified hits compounds which inhibit TFE3-SF dimerization. Hits compounds were validated in 2D and 3D models utilizing patient derived xenolines expressing TFE3-SF. Ouabain and terfenadine demonstrated decreased cell proliferation reduced spheroid growth and in vivo tumor growth. Overall, our results unmask synthetic vulnerabilities of TFE3-SF dimerization for novel therapeutic strategies in patients with this aggressive type of kidney cancer.

Citation Format: Ilaria Delle Fontane, Nuri Damayanti, Christopher Rupert, David E. Heppner, Roberto Pili. A mechanistic study of the TFE3-splicing machinery gene fusions reveals a new druggable target for translocation renal cell carcinoma [abstract]. In: Proceedings of the AACR Special Conference: Advances in Kidney Cancer Research; 2023 Jun 24-27; Austin, Texas. Philadelphia (PA): AACR; Cancer Res 2023;83(16 Suppl):Abstract nr B020.
Abstract IA012: Modelling childhood cancer using organoid technology
Authors: Drost Jarno
Published: August 2023

Cancer is still one of the leading causes of disease-related deaths in children. Survivors suffer from side effects of the, in most cases, intensive treatment regimens. Hence, there is an urgent need to develop improved, less toxic therapies. Our vision is that if we understand the processes that underpin the development of childhood cancer, we will facilitate improved cure rates and a better quality of life. However, therapeutic innovation is hampered by the lack of cell models representative of native tumor tissue. The organoid technology has revolutionized cancer research, as it allows for the ‘unlimited’ expansion of healthy and diseased tissue from individual patients in a dish, while retaining essential characteristics of native tissue. Organoids are therefore seen as avatars of the tissues they were derived from (Drost & Clevers, Nat Rev Cancer 2018). We recently succeeded in establishing culture protocols to grow organoids from a wide spectrum of pediatric malignancies such as Wilms tumors, renal cell carcinomas, as well as different rhabdoid tumor and soft tissue sarcoma subtypes. Subjecting our models to a comprehensive molecular profiling, we were able to demonstrate that pediatric cancer organoids retain many features of the tissues they were derived from (Calandrini et al., Nat Commun 2020; Calandrini et al., Cell Rep 2021; Meister et al., EMBO Mol Med 2022; Paassen et al., Oncogene 2023). Thus, we massively expanded the number of relevant pre-clinical in vitro model systems for cancers for which models were rare or even non-existing, including different pediatric kidney cancer subtypes. We use these models in combination with genetic engineering and (single-cell) omics technologies to study the very fundamental processes underlying tumorigenesis with the aim to find new therapies.

Citation Format: Jarno Drost. Modelling childhood cancer using organoid technology [abstract]. In: Proceedings of the AACR Special Conference: Advances in Kidney Cancer Research; 2023 Jun 24-27; Austin, Texas. Philadelphia (PA): AACR; Cancer Res 2023;83(16 Suppl):Abstract nr IA012.
Abstract IA016: Remodeling of tumor metabolism by L-2-hydroxyglutarate: Implications for renal cancer growth and progression
Authors: Sudarshan Sunil
Published: August 2023

Tumor cells remodel their metabolism to meet their unique demands in order to support tumor growth and progression. However, this reprogramming may create metabolic vulnerabilities. The small molecule L-2-hdroxyglutarate (L-2HG) is commonly elevated in clear cell renal cell carcinoma (ccRCC). Similar to other small molecules elevated in cancer, L-2HG has the potential to regulate gene expression by altering DNA, histone, and/or RNA methylation. Using unbiased profiling methodologies, we find that L-2HG remodels tumoral metabolism in renal cancer cells through the combined effects on histone methylation and RNA N6-methyladenosine (m6A). The combined effects of L-2HG result in a serine liability that renders tumors cells reliant on exogenous serine to support in vitro/vivo tumor growth and redox balance. In agreement with these data, raised L-2HG kidney tumors have reduced expression of serine biosynthetic enzymes. In summary, our data reveal that high L-2HG kidney tumors could be targeted by strategies that limit the availability of this now "essential" amino acid.

Citation Format: Sunil Sudarshan. Remodeling of tumor metabolism by L-2-hydroxyglutarate: Implications for renal cancer growth and progression [abstract]. In: Proceedings of the AACR Special Conference: Advances in Kidney Cancer Research; 2023 Jun 24-27; Austin, Texas. Philadelphia (PA): AACR; Cancer Res 2023;83(16 Suppl):Abstract nr IA016.
Abstract IA028: Renal medullary carcinoma: Discovery and validation of tailored treatment strategies
Authors: Msaouel Pavlos
Published: August 2023

Renal medullary carcinoma (RMC) is a rare but highly aggressive malignancy that predominantly afflicts young individuals of African descent harboring the sickle cell trait and is defined by loss of the SMARCB1 tumor suppressor. Notably, the anti-VEGF and mTOR targeted therapies and standard immune checkpoint inhibitor strategies developed for clear cell renal cell carcinoma (ccRCC) are completely ineffective against RMC. Conversely, platinum-based cytotoxic chemotherapy regimens are the preferred first-line therapy yielding a response rate of 29% and median survival of 13 months from diagnosis. There is clearly a need for tailored treatment strategies for this deadly disease. To meet this challenge, we have developed a dedicated research and clinical team and bench-to-bedside pipeline that supported the comprehensive profiling of patient samples and the development of multiple RMC cell lines, three patient-derived xenografts, and the first genetically engineered mouse model of RMC. These tools informed the development of the first three clinical trials dedicated to RMC (NCT03587662, NCT03274258, and NCT05347212 at clinicaltrials.gov), as well as the establishment of effective second-line, and more recently third-line, therapeutic strategies that produce objective responses and occasionally cures for this deadly disease. Using these approaches, the majority of patients diagnosed with RMC today will survive beyond a year from diagnosis. The progress made has been supported by a passionate patient advocacy group and the awareness raised has resulted in our current clinical volume of caring for 3-5 patients with RMC per week. Emerging insights into the pathophysiology of RMC have allowed us to uncover an "exercise paradox" whereby the hypoxia induced by high-intensity exercise in the setting of sickle cell trait may be the strongest modifiable risk factor for RMC. The unique biological processes behind the exercise paradox also underlie the distinct biological adaptation of RMC to true hypoxia via the loss of SMARCB1, as opposed to the pseudohypoxia observed in ccRCC driven by VHL loss. Whereas pseudohypoxic tumors are sensitive to VEGF targeting, SMARCB1 loss confers resistance to the hypoxia induced by in vivo inhibition of angiogenesis. These insights have allowed us to identify immediately actionable therapeutic targets paving the way for the next generation of clinical trials for RMC. The benchmark goal is to improve the median survival of patients with RMC to 24 months by 2025 and to 5 years by 2030.

Citation Format: Pavlos Msaouel. Renal medullary carcinoma: Discovery and validation of tailored treatment strategies [abstract]. In: Proceedings of the AACR Special Conference: Advances in Kidney Cancer Research; 2023 Jun 24-27; Austin, Texas. Philadelphia (PA): AACR; Cancer Res 2023;83(16 Suppl):Abstract nr IA028.
Abstract PR007: Von Hippel Lindau (VHL) tumor suppressor regulates m6A-dependent gene expression involved in renal tumorigenesis
Authors: Zhang Cheng , Zhang Zhao , Hepperla Austin , Yu Miaomiao , Zhou Jin , Hu Lianxin , Fang Jun , Liang Qian , Xu Kexin , Jia Liwei , Zhang Qing
Published: August 2023

Background: Renal cancer is the most common adult genitourinary cancer, of which ~85% is accounted for by the clear cell subtype (ccRCC). In the majority of ccRCC, as a result of VHL loss, HIF2a stabilization is sufficient and necessary for promoting ccRCC tumor growth. However, HIF-2 inhibitors have limited efficacy in cancer therapy, highlighting the importance of identifying additional therapeutic vulnerabilities. N6-Methyladenosine (m6A) is the most abundant internal post-translation modification, and its contribution to cancer evolution has just been appreciated. In renal cancer, previous research showed that m6A may play an important role but the molecular mechanism underlying m6A-regulated ccRCC tumorigenesis and aggression is still obscure. Approach and results: We demonstrate that VHL binds with m6A enzymatic complex proteins and regulates METTL3-METTL14 complex formation. VHL depletion suppresses mRNA m6A modification. By performing m6A RIP-Seq for renal cells with or without VHL coupled with RNA-Seq, we identified a selection of genes that their expression may be regulated by m6A. Specifically, PIK3R3 was identified to be one critical gene whose mRNA stability is regulated by VHL in a m6A-dependent but HIF-independent manner. Functionally, PIK3R3 depletion promoted renal cell growth and tumor growth while vice versa. Mechanistically, the VHL-m6A regulated PIK3R3 suppresses tumor growth by restraining PI3K/AKT activity. Conclusion: Taken together, we propose a new mechanism by which VHL regulates m6A through modulating METTL3-METTL14 protein complex formation, therefore promoting PIK3R3 mRNA stability and protein level that is critical for regulating ccRCC tumorigenesis.

Citation Format: Cheng Zhang, Zhao Zhang, Austin Hepperla, Miaomiao Yu, Jin Zhou, Lianxin Hu, Jun Fang, Qian Liang, Kexin Xu, Liwei Jia, Qing Zhang. Von Hippel Lindau (VHL) tumor suppressor regulates m6A-dependent gene expression involved in renal tumorigenesis [abstract]. In: Proceedings of the AACR Special Conference: Advances in Kidney Cancer Research; 2023 Jun 24-27; Austin, Texas. Philadelphia (PA): AACR; Cancer Res 2023;83(16 Suppl):Abstract nr PR007.
Abstract PR009: Linking VHL and SETD2 in a common oncogenic pathway that converges on the mitotic spindle
Authors: Dere Ruhee , Chowdhury Pratim , Jung Sung Yun , Aboulhassane Rim , Motrapu Manga , Wang Xiaoli , Han Richard , Walker Cheryl , Frew Ian , Rathmell W. Kimryn
Published: August 2023

Loss of chromosome 3p is a landmark event in clear cell renal cell carcinoma (ccRCC) that results in mono-allelic loss of VHL (von Hippel Lindau) and SETD2 (Set-domain containing 2) (and other tumor suppressors co-located on 3p). Second hits in VHL inactivate this key tumor suppressor initiating tumor progression. SETD2, a histone methyltransferase, was previously shown to have a dual function in methylating both histones and microtubules, thereby contributing to both the histone and tubulin codes. Methylation by SETD2 on microtubules occurs at the mitotic spindle and is essential for normal mitosis and cytokinesis, with loss of SETD2 acting as a strong driver of apoptosis. This raises a conundrum of how cancer cells survive early mono-allelic loss of SETD2, escaping cell death. We have identified the mitotic kinase, Aurora kinase A (AURKA), as a regulator of SETD2. Our data uncover SETD2 as a unique substrate for phosphorylation by AURKA, with mass spectrometry identifying serine 2080 (S2080) as the site of phosphorylation on SETD2. Phospho-SETD2 (S2080) localized at the spindle poles during mitosis, and this specific localization was modulated by AURKA enzymatic activity. Initial observations reveal a role for AURKA driven SETD2 phosphorylation at S2080 in nucleocytoplasmic shuttling of this methyltransferase. Our data suggest that phosphorylation of SETD2 by AURKA contributes to both its methyltransferase (i.e. enzymatic) activity and its geo-spatial location with the cell. Importantly, AURKA expression levels are high in VHL-null cells resulting from an inability of VHL to target AURKA for degradation and our data now highlight a direct link between VHL and SETD2, two tumor suppressors believed to independently drive RCC pathogenesis. In summary, our data reveal a tumor-specific vulnerability linked to mitotic fragility that can be precisely targeted to ultimately drive mitotic catastrophe.

Citation Format: Ruhee Dere, Pratim Chowdhury, Sung Yun Jung, Rim Aboulhassane, Manga Motrapu, Xiaoli Wang, Richard Han, Cheryl Walker, Ian Frew, W. Kimryn Rathmell. Linking VHL and SETD2 in a common oncogenic pathway that converges on the mitotic spindle [abstract]. In: Proceedings of the AACR Special Conference: Advances in Kidney Cancer Research; 2023 Jun 24-27; Austin, Texas. Philadelphia (PA): AACR; Cancer Res 2023;83(16 Suppl):Abstract nr PR009.
Abstract PR013: An integrative genomics approach converges on a critical OXPHOS program driven by MiT/TFE fusions in translocation renal cell carcinoma
Authors: Li Jiao , Gallant Danny S. , Sadagopan Ananthan , Li Bingchen , Xu Qingru , Viswanathan Srinivas R.
Published: August 2023

Translocation renal cell carcinoma (tRCC) is a rare and aggressive subtype of non-clear cell renal cell carcinoma (RCC) that represents 1-5% of kidney cancer in adults. Biologically, tRCC is driven by rearrangements that involve a member of the MiT/TFE transcription factor gene family, most commonly TFE3. There are currently no molecularly-targeted therapies specific to tRCC, owing in part to an incomplete mechanistic understanding of precisely how MiT/TFE gene fusions exert their oncogenic function. In prior work, we leveraged “histologic overlap” between tRCC and other RCC subtypes to identify tRCC cases from across multiple genomic, clinical trial, and retrospective RCC datasets, with the goal of defining the molecular landscape of this disease. Here, by analyzing pathways selectively activated in tRCC relative to other RCC subtypes in this aggregate dataset, we observed that tRCCs display strong enrichment for genes involved in oxidative phosphorylation (OXPHOS), reactive oxidative species (ROS) sensing, and the response to oxidative stress mediated by the transcription factor NRF2 (nuclear factor erythroid-derived2-like 2 [NFE2L2]). We performed chromatin immunoprecipitation and sequencing (ChIP-Seq) on a panel of tRCC and clear-cell RCC (ccRCC) cell lines, using antibodies against TFE3 as well as the active enhancer mark H3K27ac. We found that tRCC cell lines display a distinctive epigenomic profile characterized by activation of a host of genes involved in driving OXPHOS as well as NRF2 signaling. We further found that TFE3 fusions and NRF2 physically interact and genomically co-localize at multiple genes critical for mediating the response to antioxidant stress, suggesting that this metabolic phenotype is transcriptionally driven by TFE3 fusions. Genome-scale CRISPR screening in tRCC cell lines subsequently revealed tRCC-selective vulnerabilities in components of the OXPHOS machinery and in the NRF2 pathway, a distinction from most other kidney cancers in which aerobic glycolysis predominates. Overall, our genomic and functional studies implicate an essential transcriptional program driven by TFE3 fusions that converges on activation of the OXPHOS and NRF2 pathways. These molecular features provide mechanistic rationale for exploring the therapeutic targeting of OXPHOS and/or redox homeostasis pathways in tRCC.

Citation Format: Jiao Li, Danny S. Gallant, Ananthan Sadagopan, Bingchen Li, Qingru Xu, Srinivas R. Viswanathan. An integrative genomics approach converges on a critical OXPHOS program driven by MiT/TFE fusions in translocation renal cell carcinoma [abstract]. In: Proceedings of the AACR Special Conference: Advances in Kidney Cancer Research; 2023 Jun 24-27; Austin, Texas. Philadelphia (PA): AACR; Cancer Res 2023;83(16 Suppl):Abstract nr PR013.
Table S3 from Clinical benefit of autologous stem cell transplantation for multiple myeloma patients achieving undetectable minimal residual disease after induction treatment
Authors: Liu Jiahui , Yan Wenqiang , Fan Huishou , Xu Jingyu , Li Lingna , Du Chenxing , Mao Xuehan , Yan Yuting , Xu Yan , Sui Weiwei , Deng Shuhui , Yi Shuhua , Anderson Kenneth C. , Qiu Lugui , Zou Dehui , An Gang
Published: August 2023

Univariate analyses of PFS and OS in 407 transplant-eligible myeloma patients
Table S1 from Clinical benefit of autologous stem cell transplantation for multiple myeloma patients achieving undetectable minimal residual disease after induction treatment
Authors: Liu Jiahui , Yan Wenqiang , Fan Huishou , Xu Jingyu , Li Lingna , Du Chenxing , Mao Xuehan , Yan Yuting , Xu Yan , Sui Weiwei , Deng Shuhui , Yi Shuhua , Anderson Kenneth C. , Qiu Lugui , Zou Dehui , An Gang
Published: August 2023

Patient Characteristics, Treatments, and MRD detective methods: ASCT vs. Non-ASCT
Figure S2 from Clinical benefit of autologous stem cell transplantation for multiple myeloma patients achieving undetectable minimal residual disease after induction treatment
Authors: Liu Jiahui , Yan Wenqiang , Fan Huishou , Xu Jingyu , Li Lingna , Du Chenxing , Mao Xuehan , Yan Yuting , Xu Yan , Sui Weiwei , Deng Shuhui , Yi Shuhua , Anderson Kenneth C. , Qiu Lugui , Zou Dehui , An Gang
Published: August 2023

The prognostic impact of ASCT among all patients
Supplementary Table S1-S5 from Kinase Inhibitor Pulldown Assay Identifies a Chemotherapy Response Signature in Triple-negative Breast Cancer Based on Purine-binding Proteins
Authors: Wang Junkai , Saltzman Alexander B. , Jaehnig Eric J. , Lei Jonathan T. , Malovannaya Anna , Holt Matthew V. , Young Meggie N. , Rimawi Mothaffar F. , Ademuyiwa Foluso O. , Anurag Meenakshi , Kim Beom-Jun , Ellis Matthew J.
Published: August 2023

Supplementary Table S1-S5
Supplementary Figure 4 from Kinase Inhibitor Pulldown Assay Identifies a Chemotherapy Response Signature in Triple-negative Breast Cancer Based on Purine-binding Proteins
Authors: Wang Junkai , Saltzman Alexander B. , Jaehnig Eric J. , Lei Jonathan T. , Malovannaya Anna , Holt Matthew V. , Young Meggie N. , Rimawi Mothaffar F. , Ademuyiwa Foluso O. , Anurag Meenakshi , Kim Beom-Jun , Ellis Matthew J.
Published: August 2023

Supplementary Figure 4
Supplementary Figure 2 from Kinase Inhibitor Pulldown Assay Identifies a Chemotherapy Response Signature in Triple-negative Breast Cancer Based on Purine-binding Proteins
Authors: Wang Junkai , Saltzman Alexander B. , Jaehnig Eric J. , Lei Jonathan T. , Malovannaya Anna , Holt Matthew V. , Young Meggie N. , Rimawi Mothaffar F. , Ademuyiwa Foluso O. , Anurag Meenakshi , Kim Beom-Jun , Ellis Matthew J.
Published: August 2023

Supplementary Figure 2
FIGURE 5 from Kinase Inhibitor Pulldown Assay Identifies a Chemotherapy Response Signature in Triple-negative Breast Cancer Based on Purine-binding Proteins
Authors: Wang Junkai , Saltzman Alexander B. , Jaehnig Eric J. , Lei Jonathan T. , Malovannaya Anna , Holt Matthew V. , Young Meggie N. , Rimawi Mothaffar F. , Ademuyiwa Foluso O. , Anurag Meenakshi , Kim Beom-Jun , Ellis Matthew J.
Published: August 2023

The prognosis effects of the KIPA-based PBP signature in METABRIC dataset. A, Forest plot shows HRs and P values for disease-specific survival associated with the PBP signature and seven signature genes. HR and 95% confidence intervals were based on categorizing TNBC samples using a median mRNA expression cutoff for each gene or the PBP signature score in the METABRIC dataset. Survival analysis was also performed for clinical factors (lymph nodes number, tumor size, and tumor grade). Blue boxes indicate univariate analysis, and red boxes indicate multivariate analysis. B, Kaplan–Meier curve shows disease-specific survival of TNBC samples from the METABRIC dataset. Samples were categorized into mRNA-based PBP signature score high and low group based on the median cutoff.
Data from Clinical benefit of autologous stem cell transplantation for multiple myeloma patients achieving undetectable minimal residual disease after induction treatment
Authors: Liu Jiahui , Yan Wenqiang , Fan Huishou , Xu Jingyu , Li Lingna , Du Chenxing , Mao Xuehan , Yan Yuting , Xu Yan , Sui Weiwei , Deng Shuhui , Yi Shuhua , Anderson Kenneth C. , Qiu Lugui , Zou Dehui , An Gang
Published: August 2023

Abstract
Attaining undetectable minimal residual disease (MRD) is the current therapeutic goal for multiple myeloma (MM). But there is a current lack of data regarding the clinical benefit of autologous stem cell transplantation (ASCT) for myeloma patients achieving early MRD-negative status after induction treatment, in addition to the interaction of longitudinal MRD status with ASCT. The present study included 407 transplant-eligible MM patients with available MRD status from the National Longitudinal Cohort of Hematological Diseases in China (NCT04645199), of whom 147 (34.4%) achieved early undetectable MRD and 182 (44.7%) received ASCT. Early MRD-negative status was associated with a lower risk of disease progression (HR=0.447; 95%CI, 0.333-0.600; P<0.001) and death (HR=0.473; 95%CI, 0.320-0.700; P<0.001). Of note, patients who achieved undetectable MRD early still benefitted from ASCT, with a remarkable improvement in the median MRD-negative duration (33.5 to 58.0 months, P<0.001), progression-free survival (PFS; 46.0 to 88.3 months, P<0.001), and overall survival (OS; 76.4 months to not reached, P=0.003). These clinical benefits were more pronounced in patients with aggressive features (high-risk cytogenetic abnormalities or high tumor burden) compared to standard-risk patients. Similar results were observed in patients with detectable MRD after induction treatment. Additionally, we identified four MRD-status transformation patterns following ASCT, which were strongly correlated with diverse survival outcomes (P<0.001). Our study revealed the enhanced clinical significance of ASCT in transplant-eligible myeloma patients, regardless of early MRD status, particularly for high-risk patients. Subsequent prospective trials are essential to validate these observations.