Abstract 3410: Identifying potential mechanisms of resistance to erdafitinib (erda) via longitudinal analysis of circulating tumor (ct)-DNA of patients (pts) with advanced/metastatic urothelial cancer (mUC)

Background: The fibroblast growth factor receptor (FGFR) inhibitor erda is the only FDA-approved targeted treatment (tx) for mUC with FGFR2/3 alterations (alt). Median progression-free survival on erda is 5.5 months and mechanisms of resistance remain poorly characterized. Analysis of ctDNA offers an opportunity to longitudinally and non-invasively assess for mechanisms of resistance.

Methods: Plasma was collected from mUC pts on erda at baseline, on-tx, and at disease progression (PD). Clinical characteristics were recorded. Pre-tx tumors were sequenced with MSK-IMPACT and plasma samples with MSK-ACCESS, a cell-free DNA assay sequencing 129 genes with unique molecular indexes to generate >15,000x coverage for detection of mutations to an allele frequency of 0.1%.

Results: Between 8/2019-9/2021, 18 pts received erda. Median progression-free survival was 4.2 months, range 1.4-10.8. Tx was discontinued in 14 pts for PD, 3 for toxicity, and 1 death unrelated to erda/PD. During tx, several pts acquired new alts in ctDNA compared to pre-tx tumor/ctDNA, most commonly in TP53 (n = 5) and FGFR3 (n = 4) (Table 1). Of 9 newly acquired FGFR2/3 alts observed in ctDNA on-tx, 3 were hotspots. Several acquired FGFR3 alts have been shown to impact binding of erda to FGFR3 in vitro (Table 1). Of 5 pts with primary refractoriness to erda, 3 had baseline activating alts of signaling downstream or parallel to FGFR, including alts of PIK3CA (n = 1), TSC1 (n = 1), and HER2 (n = 2). Of 3 pts with TP53 alts in baseline ctDNA, 2 had PD as best response to erda.

Conclusions: Pts with mUC treated with erda demonstrated on-tx acquisition of ctDNA alts of FGFR2/3 and TP53 and activating alts downstream or parallel to FGFR signaling. Most pts with TP53 alts in baseline ctDNA were refractory to erda. Acquired FGFR2/3 alts on erda may drive resistance through interference with drug-target binding.

Case # Pre-tx FGFR2/3 alts Alts acquired on erda related to TP53 and FGFR signaling 1 FGFR3 Y373C TP53 K132M; TP53 R158L 2 FGFR3 S371C; FGFR3 R399C; FGFR3 R248C; FGFR3 S249C; FGFR3-TACC3 fusion FGFR3 R669G&; FGFR3 V553M&; FGFR3 N540S&; FGFR3 H673Y; FGFR3 K649_K650delinsIE; TP53 S241C; BRAF-CLIP2 fusion 3 FGFR3 S249C TP53 E287Q 4 FGFR3 S249C FGFR3 V553M&; FGFR3 K650M; FGFR2 R255W; AKT1 E17K 5 FGFR3 S249C FGFR3 R248C 6 FGFR3 S249C TP53 I195T 7 FGFR3 Y373C TP53 R248W; TP53 S241Y 8 FGFR3 S249C; FGFR3 L645V FGFR3 S424C & Alts likely to impact erda binding to FGFR3.

Citation Format: Brendan J. Guercio, Michal Sarfaty, Min Yuen Teo, Samuel A. Funt, Chung-Han Lee, David H. Aggen, Neha Ratna, Ashley M. Regazzi, Ziyu Chen, Michael Lattanzi, Hikmat A. Al-Ahmadie, A. Rose Brannon, Michael F. Berger, David B. Solit, Jonathan E. Rosenberg, Dean F. Bajorin, Gopa Iyer. Identifying potential mechanisms of resistance to erdafitinib (erda) via longitudinal analysis of circulating tumor (ct)-DNA of patients (pts) with advanced/metastatic urothelial cancer (mUC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3410.

The Role of the TP53 Pathway in Predicting Response to Neoadjuvant Therapy in Esophageal Adenocarcinoma

PURPOSE

In patients with locally advanced esophageal adenocarcinoma, response to neoadjuvant therapy strongly predicts survival, but robust molecular predictors of response have been lacking. We therefore sought to discover meaningful predictors of response in these patients.

EXPERIMENTAL DESIGN

We retrospectively identified all patients with adenocarcinoma of the lower esophagus or gastroesophageal junction who (i) were treated with multimodality therapy with curative intent at our institution from 2014 through 2020 and (ii) underwent prospective sequencing by Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets. Clinicopathologic and genomic data were analyzed to identify potential genomic features, somatic alterations, and oncogenic pathways associated with treatment response.

RESULTS

In total, 237 patients were included. MDM2 amplification was independently associated with poor response to neoadjuvant therapy [OR, 0.10 (95% confidence interval, 0.01-0.55); P = 0.032], when accounting for significant clinicopathologic variables, including clinical stage, tumor grade, and chemotherapy regimen. Moreover, TP53 pathway alterations, grouped according to inferred severity of TP53 dysfunction, were significantly associated with response to neoadjuvant therapy (P = 0.004, q = 0.07). Patients with MDM2 amplifications or truncating biallelic TP53 mutations had similar outcomes in terms of poor responses to neoadjuvant therapy and, consequently, shorter progression-free survival, compared with patients with TP53 pathway wild-type tumors. Thus, worsening TP53 dysfunction was directly correlated with worse outcomes.

CONCLUSIONS

MDM2 amplification and TP53 status are associated with response to therapy in patients with esophageal adenocarcinoma. Given the dearth of actionable targets in esophageal adenocarcinoma, MDM2 inhibition, in combination with cytotoxic chemotherapy, may represent an important therapeutic strategy to overcome treatment resistance and improve outcomes in these patients.

Allelic dosage of RB1 drives CDK4/6 inhibitor treatment resistance in metastatic breast cancer

1010

Background: We recently reported inferior outcomes to CDK4/6 inhibitors and endocrine therapy (CDK4/6i-ET) associated with germline BRCA2 (g BRCA2) in a cohort of estrogen receptor (ER) positive breast cancers. Co-occurrence of gBRCA2 with loss of heterozygosity (LOH) of neighboring RB1 was found to portend particularly poor outcomes. Here, we sought to define the effects of pre-treatment RB1 allelic copy number status on outcomes of CDK4/6i-ET and the likelihood of developing RB1 loss-of-function (LOF) mutations on CDK4/6i through the analysis of an expanded cohort of metastatic ER+ breast cancer patients. Methods: Patients who underwent sequencing on MSK-IMPACT from April 2014 to May 2021 were included. For every sample preceding CDK4/6i-ET, we performed FACETS to infer RB1 allele specific copy number, ploidy, tumor purity and fraction genome altered (FGA). Patients were categorized based on RB1 allelic status: HetLoss (total of one allelic copy), copy neutral LOH (CNLOH), other allelic imbalance including all other aneuploidy states, and diploid. Progression free survival (PFS) was assessed using univariate and multivariate Cox proportional hazard models adjusted for ET partner and FGA. Firth penalized logistic regression was used to study association of pre-treatment RB1 status with acquired RB1 LOF variants in paired post-CDK4/6i samples. Results: Of 2,630 potentially eligible patients, 279 patients had genomic sequencing performed prior to 1st line CDK4/6i-ET. Of these, 75 (26.8%) exhibited RB1 HetLoss, 39 (14.0%) had CNLOH of RB1, 111 (39.7%) exhibited diploid RB1 state, while 54 (19.4%) had other patterns of RB1 allelic imbalance. All non-diploid RB1 states were associated with significantly shortened PFS relative to diploid (univariate HetLoss HR: 2.05, 95% CI: 1.42, 2.97; CNLOH HR: 2.08, 95% CI: 1.32, 3.25; other imbalance HR: 1.70, 95% CI: 1.11, 2.58). Only HetLoss remained significant when adjusted for FGA (HR 1.61, 95% CI: 1.09, 2.38, p = 0.017). RB1 LOF was rare in pre-CDK4/6i tumors (< 1%); excluding these cases did not change our results. Of the 176 patients with paired pre- and post-CDK4/6i samples, only RB1 HetLoss in pre-CDK4/6i sample was significantly associated with development of RB1 LOF mutations in post-CDK4/6i sample (18.4%) as compared to diploid (4.2%, OR 4.25, 95% CI 1.02, 17.7, p = 0.047). These results indicate that tumors with one functional copy of RB1 are more likely to acquire RB1 LOF on CDK4/6i to achieve biallelic RB1 loss as a mechanism of CDK4/6i resistance. Conclusions: We demonstrate that LOH and allelic imbalance of RB1 are associated with shorter PFS on CDK4/6-ET. We postulate this may occur partly as a result of more frequent acquired RB1 LOF mutations under selective pressure of CDK4/6i. These data supports the implementation of more refined allele-specific copy number methods and identifies a high-risk population for escalated monitoring and treatment approaches.

Targeting HER2 mutation–positive advanced biliary tract cancers with neratinib: Final results from the phase 2 SUMMIT basket trial

4079

Background: HER2 mutations are infrequent genomic events in biliary tract cancers (BTCs) and are associated with poor overall survival (OS) in patients with metastatic disease. HER2 overexpression is associated with an increased risk of disease recurrence in patients with resected BTC. There is limited data on targeting HER2 in BTC harboring activating somatic HER2 mutations. Neratinib, an irreversible, pan-HER, oral tyrosine kinase inhibitor, interferes with constitutive receptor kinase activation and has demonstrated activity in several HER2-mutant solid tumors. Methods: SUMMIT is an open-label, single-arm, multi-cohort, phase 2, ‘basket’ trial of neratinib in patients with solid tumors harboring oncogenic HER2 somatic mutations. The primary objective of the BTC cohort was to estimate objective response rate (ORR). Secondary objectives were clinical benefit rate (CBR), progression-free survival (PFS), OS, response duration, safety, and tolerability. Retrospective central confirmation of locally reported HER2 mutation (next-generation sequencing on archival or fresh tumor tissue using MSK-IMPACT or in cfDNA extracted from plasma by MSK-ACCESS) and association with outcome was an exploratory endpoint. This trial is registered with ClinicalTrials.gov (NCT01953926). Results: 25 treatment-refractory patients with metastatic BTC were enrolled (11 cholangiocarcinoma, 10 gallbladder, 4 ampullary cancers). ORR was 16% (95% CI 4.5–36.1%) and CBR was 28% (95% CI 12.1–49.4%). Median PFS and OS were 2.8 (95% CI 1.1–3.7) and 5.4 (95% CI 3.7–11.7) months, respectively. Median PFS for the gallbladder, cholangiocarcinoma and ampulla cohorts was 3.7 (95% CI 0.8–6.4), 1.4 (95% CI 0.5–9.1), and 1.1 (95% CI 1.1–3.8) months, respectively. Corresponding median OS values in these cohorts were 9.8 (95% CI 2.4–NE), 5.4 (95% CI 0.8–16.2), and 5.0 (95% CI 3.7–10.2) months, respectively. Central mutation confirmation was feasible for 23 of 25 patients; 22 were concordant with enrolment assays. The most common HER2 mutations were S310F (n = 11; 48%) and V777L (n = 4; 17%). Exploratory analyses suggested worse outcomes for HER2-mutant tumors with co-occurring oncogenic TP53 and CDKN2A alterations. Loss of amplified HER2 S310F and acquisition of multiple previously undetected oncogenic co-mutations were identified at progression in one of four responders. Diarrhea (56% any grade) was the most common toxicity. Conclusions: Neratinib is tolerable with modest antitumor activity in patients with BTC harboring HER2 mutations. Although the primary endpoint was met, future studies should evaluate rational combinations to augment and/or prolong responses. Clinical trial information: NCT01953926.

Clinical and Genomic Characterization of Bladder Carcinomas With Glandular Phenotype

PURPOSE

To compare oncologic outcomes and genomic alteration profiles in patients with bladder and urachal adenocarcinoma, urothelial carcinoma (UC) with glandular differentiation, and UC, not otherwise specified (NOS) undergoing surgical resection, with emphasis on response to systemic therapy.

METHODS

We identified patients with bladder cancer with glandular variants who underwent surgical resection at Memorial Sloan Kettering from 1995 to 2018 (surgical cohort) and/or patients who had tumor sequencing using a targeted next-generation sequencing platform (genomics cohort). Pathologic complete and partial response rates to neoadjuvant chemotherapy (NAC) and recurrence-free and cancer-specific survival were measured. Alteration frequencies between histologic subtypes were compared.

RESULTS

Thirty-seven patients with bladder adenocarcinoma, 46 with urachal adenocarcinoma, 84 with UC with glandular differentiation, and 1,049 with UC, NOS comprised the surgical cohort. Despite more advanced disease in patients with bladder and urachal adenocarcinoma, no significant differences in recurrence or cancer-specific survival by histology were observed after adjusting for stage. In patients with UC with glandular differentiation, NAC resulted in partial (≤ pT1N0) and complete (pT0N0) responses in 28% and 17%, respectively. Bladder and urachal adenocarcinoma genomic profiles resembled colorectal adenocarcinoma with frequent TP53, KRAS, and PIK3CA alterations while the genomic profile of UC with glandular differentiation more closely resembled UC, NOS. Limitations include retrospective nature of analysis and small numbers of nonurothelial histology specimens.

CONCLUSION

The genomic profile of bladder adenocarcinomas resembled colorectal adenocarcinomas, whereas UC with glandular differentiation more closely resembled UC, NOS. Differences in outcomes among patients with glandular bladder cancer variants undergoing surgical resection were largely driven by differences in stage. Cisplatin-based NAC demonstrated activity in UC with glandular differentiation, suggesting NAC should be considered for this histologic variant.

Next-generation sequencing (NGS) of circulating cell-free DNA (cfDNA) in patients (pts) with advanced hepatocellular carcinoma (HCC)

4110

Background: HCC is often diagnosed based on high-quality cross-sectional imaging, and when a biopsy is pursued, acquisition of tissue may be of limited quantity and quality or complicated by underlying medical comorbidities. NGS of tumor derived circulating cfDNA represents an investigational tool for non-invasive molecular profiling, that has the potential to aid in diagnosis, prognosis, and in monitoring disease status. Although prior reports have evaluated such technologies, few studies have included tumor tissues to confirm histology and to explore plasma-tissue gene concordance. Methods: The primary objective of this retrospective cohort study was to define genomic alterations in circulating cfDNA and to explore plasma-tissue genotype concordance in HCC pts. HCC pts underwent collection of cfDNA for NGS using the MSK-ACCESS 129-gene assay between August 2019 and February 2021. Matched tissue-based NGS with the FDA authorized MSK-IMPACT gene assay was completed when tumor tissue was available. Clinical actionability of sequence variants was annotated by OncoKB, an FDA recognized knowledge base. Clinicopathologic characteristics were extracted, and all data were reported with descriptive statistics. Results: 51 unique patients with 53 plasma samples had an HCC histological diagnosis. Pts were male (39, 76%), median age 69 (42-87), viral hepatitis-related (24, 47%), and advanced stage (Stage III:9, 18%; Stage IV:38, 74.5%). Extrahepatic disease and macrovascular involvement were observed in 28 (55%) and 19 (38%) pts, respectively. 22 (43%) pts had AFP ≥400 ng/mL. 49 (92.5%) of 53 plasma samples had detectable genomic alterations. Median cfDNA yield after extraction was 39.43 ng (range: 7.93-287.68). The most frequently mutated genes occurring in > 10% of patients were TERT (57%), TP53 (47%), CTNNB1 (37%), ARID1A (18%) and TSC2 (14%). The most common oncogenic pathways that contained alterations were WNT-β-Catenin (45%) and PIK3-AKT-TOR (25%). 37 (73%) pts underwent tissue sequencing with MSK-IMPACT with a median time of 9.0 months to the time cfDNA testing. MSK-ACCESS identified mutations observed in tumor in most cases: TERT (20/22; 91%), TP53 (16/17; 94%), CTNNB1 (11/12; 92%), ARID1A (6/6; 100%) and TSC2 (6/7; 86%). In 18 (49%) of 37 paired samples, additional mutations in cfDNA not seen in tumor were detected and included KRAS, EGFR, and TP53 alterations. Potentially actionable mutations were identified through cfDNA in 37% of cases including TSC1/2 (18%), BRCA1/ 2 (8%) and PIK3CA (8%). Conclusions: Circulating cfDNA genotyping with MSK-ACCESS identifies previously reported HCC tumor genomic profiles and revealed tumor-associated mutations in 92.5% of plasma samples. Ongoing efforts will explore predictive and prognostic implications of NGS at different HCC stages as well as kinetics of treatment response.

Overcoming barriers to tumor genomic profiling through direct patient social media outreach

6532

Background: Tumor genomic profiling is increasingly used to identify actionable genomic alterations as a guide to therapy selection. To overcome barriers to genomic testing for patients with rare cancers, we initiated a program to offer free clinical tumor genomic testing worldwide to patients with select rare cancer subtypes. Methods: Patients were recruited through social media outreach, engagement with disease advocacy groups, or via physician referral, with a focus on recruiting patients with histiocytosis, germ cell tumors and rare pediatric cancers. Tumor and patient-matched germline DNA were analyzed using the MSK-IMPACT targeted sequencing next generation sequencing panel with return of results to patients and their local physicians. Whole exome recapture of MSK-IMPACT DNA sequencing libraries was performed for patients with female germ cell tumors to define the genomic landscape of this rare cancer subtype. Results: 359 cancer patients expressed interest in the Make-an-IMPACT program, of whom 333 were enrolled. Tumor tissue was received for 288 (86.4%), with 250 (86.8%) having tumor DNA of sufficient quantity and quality for MSK-IMPACT testing. 14 histiocytosis patients have received genomically guided therapy to date, of whom 13 (93%) have had clinical benefit based on local MD response assessment with a mean treatment duration of 16.7 months (range 3-32+). Whole exome sequencing of ovarian GCTs identified a subset with fully haploid genotypes, a phenotype rarely observed in other cancer types. Actionable genomic alterations were rare in ovarian GCT (28%), however, 2 ovarian GCTs and squamous transformation had high tumor mutational burden, one of whom had a complete response to pembrolizumab. Conclusions: Social media outreach can facilitate the assembly of cohorts of rare cancers of sufficient size to define their genomic landscape. By profiling tumors in a clinical laboratory, results could be reported to patients and their local physicians where they could be used to guide treatment selection. This can also open the door to diversifying and being able to study the genomic landscape in a diverse cohort.

Immunogenomic characterization of biliary tract cancers: Biomarker enrichment for benefit to immune checkpoint blockade

4083

Background: Several immunomodulatory molecules (PD-L1, B7H4, and CD276) have been associated with biliary tract cancer (BTC) subgroups, suggesting potential value to immune checkpoint blockade (ICB) in this lethal disease. Phase II monotherapy (pembrolizumab or nivolumab), and combination (atezolizumab and cobimetinib) ICB trials reported low response rates in unselected advanced BTC with a wide range of responses. A recent randomized phase III trial (TOPAZ-1) reported an overall survival (OS) benefit among patients (pts) with advanced BTC treated with chemotherapy and anti-PD-L1 ICB. However, no correlation between PD-L1 expression and OS was noted and biomarker enrichment strategy in BTC for immunotherapy remains a key to optimize OS. Methods: From our comprehensive clinico-genomic database for BTC at Memorial Sloan Kettering (MSK), a retrospective genomic landscape and neoantigen analysis was performed using MSK-IMPACT. Potential immunogenic subgroups were evaluated: homologous recombination deficiency (HRD) defined by pathogenic alterations in BRCA1/2, PALB2, and BAP1, microsatellite stability high (MSI-H) defined by MSIsensor score ≥10, and tumor mutation burden (TMB)>10. Clinical outcomes with anti-PD-1 ICB were evaluated. Results: Among N=1,190 pts with BTC, N=1,346 samples were sequenced between 03/2014 and 01/2022. Key actionable alterations included (%): IDH1, 2 (13, 3), FGFR2 fusions (9), ERBB2 amplification (5), BRAF V600E (2), RNF43 (2), POLE (2), NTRK1 fusion (<1). There were N=230 (17%) patients with putatively more immunogenic BTC (iBTC) identified by HRD [ BRCA1/2 (1, 2.4), PALB2 (1), BAP1 (9)], TMB>10, and MSI-H. Frequency, location (intrahepatic, ICC; extrahepatic, ECC; gallbladder, GBC), TMB, and genomic instability score (GIS) are summarized (Table). Among iBTC subgroup, N=32 pts received ICB. Their median follow up was 29.1 months. Median lines of prior therapy was 3. Median PFS was 5.6 M (95%CI: 1.2-10.1) and OS was 33.4 M (23.1-43.6). Conclusion: A subgroup of BTC pts (iBTC) benefit from ICB. Apart from MSI-H and TMB>10, other genomically-defined subgroups such as HRD may benefit from ICB. Prospective studies are needed to evaluate a better biomarker enrichment strategy beyond PD-L1 and TMB, that can represent other immunogenic aspects of tumor neoantigen and microenvironment. [Table: see text]

AKT mutant allele-specific activation dictates pharmacologic sensitivities

AKT- a key molecular regulator of PI-3K signaling pathway, is somatically mutated in diverse solid cancer types, and aberrant AKT activation promotes altered cancer cell growth, survival, and metabolism1-8. The most common of AKT mutations (AKT1 E17K) sensitizes affected solid tumors to AKT inhibitor therapy7,8. However, the pathway dependence and inhibitor sensitivity of the long tail of potentially activating mutations in AKT is poorly understood, limiting our ability to act clinically in prospectively characterized cancer patients. Here we show, through population-scale driver mutation discovery combined with functional, biological, and therapeutic studies that some but not all missense mutations activate downstream AKT effector pathways in a growth factor-independent manner and sensitize tumor cells to diverse AKT inhibitors. A distinct class of small in-frame duplications paralogous across AKT isoforms induce structural changes different than those of activating missense mutations, leading to a greater degree of membrane affinity, AKT activation, and cell proliferation as well as pathway dependence and hyper-sensitivity to ATP-competitive, but not allosteric AKT inhibitors. Assessing these mutations clinically, we conducted a phase II clinical trial testing the AKT inhibitor capivasertib (AZD5363) in patients with solid tumors harboring AKT alterations (NCT03310541). Twelve patients were enrolled, out of which six harbored AKT1-3 non-E17K mutations. The median progression free survival (PFS) of capivasertib therapy was 84 days (95% CI 50-not reached) with an objective response rate of 25% (n = 3 of 12) and clinical benefit rate of 42% (n = 5 of 12). Collectively, our data indicate that the degree and mechanism of activation of oncogenic AKT mutants vary, thereby dictating allele-specific pharmacological sensitivities to AKT inhibition.

Anatomic position determines oncogenic specificity in melanoma

Oncogenic alterations to DNA are not transforming in all cellular contexts1,2. This may be due to pre-existing transcriptional programmes in the cell of origin. Here we define anatomic position as a major determinant of why cells respond to specific oncogenes. Cutaneous melanoma arises throughout the body, whereas the acral subtype arises on the palms of the hands, soles of the feet or under the nails3. We sequenced the DNA of cutaneous and acral melanomas from a large cohort of human patients and found a specific enrichment for BRAF mutations in cutaneous melanoma and enrichment for CRKL amplifications in acral melanoma. We modelled these changes in transgenic zebrafish models and found that CRKL-driven tumours formed predominantly in the fins of the fish. The fins are the evolutionary precursors to tetrapod limbs, indicating that melanocytes in these acral locations may be uniquely susceptible to CRKL. RNA profiling of these fin and limb melanocytes, when compared with body melanocytes, revealed a positional identity gene programme typified by posterior HOX13 genes. This positional gene programme synergized with CRKL to amplify insulin-like growth factor (IGF) signalling and drive tumours at acral sites. Abrogation of this CRKL-driven programme eliminated the anatomic specificity of acral melanoma. These data suggest that the anatomic position of the cell of origin endows it with a unique transcriptional state that makes it susceptible to only certain oncogenic insults.

Upper tract urothelial carcinoma transcriptome profiling and immune microenvironment characterization

564

Background: Upper tract urothelial carcinoma (UTUC) is an aggressive disease that is risk-stratified by clinicopathological factors due to an incomplete understanding of its molecular features. Thus, we performed transcriptomic profiling of UTUC tumors from radical nephroureterectomy specimens and compared their molecular characterization to survival outcomes. Methods: 100 UTUC tumors from 100 patients were subject to RNA sequencing and a hybridization capture-based assay for deep sequencing of cancer-associated genes, followed by unsupervised nonnegative matrix factorization clustering based on the top 10% of variant genes. Gene Set Enrichment and immune deconvolution analyses assessed for differences in the tumor microenvironments (TME) between clusters. Results: Consensus clustering analysis identified 5 biologically distinct clusters (Cluster 1 (C1) = 17, C2 = 18, C3 = 30, C4 = 11, and C5 = 24 patients), which were associated with significant differences in disease-free (DFS) (p < 0.01) and overall survival (OS) (p = 0.03). C1 and C2 were associated with pT3/4 stages and worse DFS and OS, while C5 was associated with pTa/1 stages and better DFS and OS. In terms of somatic mutation frequency differences, C3 and C4 had overall higher tumor mutation burden and mutations in epigenetic modulators, which corresponds with the transcriptomic finding of higher microsatellite instability expression signatures in these two clusters as well. Of note, all Lynch patients (N = 4) were in C3. C3 was enriched for the presence of FGFR3 driver mutations in 93% of tumors, and TP53 mutations were frequent in C2 and C4 in 47 and 55% of tumors, respectively. Differentially expressed genes and Gene Set Enrichment analyses revealed that C1 and C2 were enriched with several Hallmark inflammation signatures, such as TNF-α signaling via NF-kB, allograft rejection, inflammatory response, IL6 JAK/STAT3 signaling, and IL2 STAT5 signaling. C1 demonstrated a particularly inflammatory phenotype enriched with INF-γ and INF-α response gene sets. Lastly, in the TME deconvolution analysis, C1 and C2 had higher expression of PDL-1, immune checkpoint, immune suppression, cancer-associated fibroblasts, and myeloid inflammation surrogate signatures. C2 and C3 were enriched with CD8 T-cells, while C1 was enriched for INF-γ and hypoxia signatures. C2 had the least hypoxic TME, which may be related to stronger stromal, EMT, and angiogenesis signature signals seen. These results were then validated using an outside institution’s published cohort. Conclusions: Several differences in transcriptomic features indicate heterogeneity among UTUC tumors. Two clusters with high rates of recurrence and worse prognosis are associated with higher immune and myeloid cell infiltration. In addition to clinicopathologic factors, tumor microenvironment immune features may have potential use for disease prognostication.

Human epidermal growth factor receptor 2 (HER2) and fibroblast growth factor receptor 3 (FGFR3) mutations to reveal biological pathways in urothelial carcinoma

567

Background: Human epidermal growth factor receptor 2 (HER2) (gene name: ERBB2) is a member of the epidermal growth factor receptor (EGFR) family and when mutated, associated with higher grade and stage of localized bladder cancer. Two HER2-targeted antibody-drug conjugates (ADC), trastuzumab emtansine and trastuzumab deruxtecan, are currently approved by the Food and Drug Administration (FDA) for use in gastric/breast cancers with promising application in urothelial carcinoma. Fibroblast growth factor receptor 3 ( FGFR3) is the target of another FDA-approved tyrosine kinase inhibitor erdafitinib and generally associated with more favorable prognosis as well as upper tract carcinoma. The purpose of this study is to characterize ERBB2 and FGFR3 mutations in a prospectively collected cohort of urothelial cancers. Methods: Patients with localized upper or lower tract urothelial carcinoma diagnosed between 2014 and 2020 who underwent a targeted exome sequencing panel of up to 468 cancer genes were identified. If multiple tumors were sequenced, only the diagnostic specimen was included. Analysis of gene alterations, frequency, and associated co-mutations was performed. Descriptive statistics were used to compare baseline patient characteristics. Results: 381 unique ERBB2 or FGFR3 mutated urothelial carcinoma specimens were included in this study. Of note, ERBB2 and FGFR3 mutations were essentially mutually exclusive and included 122 (66%) ERBB2 mutated tumors and 259 (34%) FGFR3 mutated tumors. Patients with tumors harboring FGFR3 mutations were younger (median 70 years IQR 60-76 vs. 74 years IQR 66-78, p<0.05), while patients with ERBB2 mutated tumors were more likely to be male (85% vs 73%, p<0.05). At the time of diagnosis, ERBB2 tumors were more likely to present with advanced (pT2 or higher) disease compared to FGFR3 mutated tumors (48% vs 24%). ERBB2 mutated tumors were more likely associated with RB1, P53, and ARID1A mutations, while FGFR3 mutated tumors were more likely associated with CDKN2A/B and STAG2 mutations (Table). Conclusions: These data highlight divergent biological pathways for patients with targetable mutations in ERBB2 and FGFR3 and are consistent with prior findings in non-muscle invasive bladder cancer. ERBB2 mutated tumors are associated with male gender, more aggressive pathological features and co-mutations with RB1, P53, and ARID1A.[Table: see text]

Defining hereditary upper tract urothelial carcinoma: Implications for genetic testing and clinical management

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Background: Despite being a rare cancer, upper tract urothelial carcinoma (UTUC) is the third most common core cancer associated with Lynch syndrome (LS) after colorectal and endometrial cancers. Yet, there is no established guideline to identify patients with UTUC who are at risk of carrying germline mutations in LS-associated genes. The objective of this study is to define selection criteria for patients with UTUC for LS screening. Methods: We retrospectively identified patients with UTUC who underwent germline sequencing of ≥77 cancer susceptibility genes using next generation sequencing (NGS) as part of a prospective matched tumor-normal genomic profiling initiative from 04/2015 to 04/2021. Mismatch repair protein status was evaluated by immunohistochemical (IHC) staining for MMR genes MSH2, MSH6, MLH1, and PMS2. Microsatellite instability (MSI) status was determined using NGS. Diagnostic performance of clinical and tumor-based screening criteria was assessed by the presence of germline pathogenic/likely pathogenic variants (PGVs) in MMR genes. Results: A total of 232 patients with UTUC underwent germline testing; median age of diagnosis was 67 years (interquartile range 59 – 73). Of these patients, 70% were male, 43% had UTUC diagnosed before the age of 65, 85% had high grade UTUC,12% had bilateral UTUC, 11% had metastasis at diagnosis, 10% and 31% had personal and family history of LS-associated cancers, respectively. PGVs in moderate or high-penetrance genes were identified in 31 (13%) patients including 6 (3%) in BRCA1/ 2 and 21 (9%) in MMR genes (13 MSH2, 4 MSH6, 4 MLH1). A total of 10/21 (48%) patients with MMR PGVs developed UTUC as their first cancer diagnosis. Of patients with MMR PVGs, 15/16 (94%) had MMR-deficient tumors and 12/18 (67%) had MSI-high tumors. Personal and family history of LS core cancers (p < 0.001), age of diagnosis < 65 (p = 0.008), MSI-high (p < 0.001), and MMR-deficiency (p < 0.001) were associated with MMR carrier status. Female gender (p = 0.7), HG UTUC (p = 0.5), and bilateral UTUC (p = 0.7) were not associated with MMR PGVs. Current NCCN genetic referral criteria for Lynch syndrome has high specificity in identifying patients with LS (100%) but missed 11/21 (52%) patients with UTUC and MMR PGVs. Conclusions: Current genetic referral guidelines for Lynch syndrome may miss a significant portion of patients with LS-associated UTUC. UTUC tumor should be investigated for MMR protein and MSI status with IHC or next generation sequencing methods to augment LS-screening of patients with UTUC and inform systemic treatment selection.

Incidence and clinical outcomes of HER2-altered bladder cancer (BC) patients (pts)

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Background: Bladder cancer has one of the highest rates of human epidermal growth factor receptor 2 (HER2) alteration. Novel HER2-directed agents are being investigated in metastatic BC. We sought to define the incidence and clinical characteristics of HER2-altered BC across disease states. Methods: We retrospectively analyzed our single-institution, clinically annotated cohort of urothelial BC pts with available genomic profiling data (MSK-IMPACT). We quantified the prevalence of HER2 alterations, defined as driver mutation (based on OncoKB), and/or amplification, across BC disease states. We examined the association between HER2 alteration and disease progression and survival. The Kaplan-Meier method was used for time-to-event analyses. Results: A total of 1073 BC pts underwent MSK IMPACT profiling of tumor tissue derived from the following disease states: 36% (n = 380) non-muscle invasive (NMI)BC, 41% (n = 443) muscle invasive (MI)BC, and 23% (n = 250) (met)BC. At initial diagnosis, the median age was 67 years, 77% (n = 822) were male, 86% (n = 928) were white, and 66% (n = 710) were smokers. Overall, 16% (n = 177) of pts had any oncogenic HER2 alteration (Table), including 11% with a HER2 driver mutation and 7% with HER2 amplification The most frequent mutations were S310F (40%, n = 53) and S310Y (14%, n = 19). The rate of HER2 amplification was different among the three groups (p = 0.002), 9% in MIBC and metBC compared to 3% in NMIBC. Among 514 pts with NMIBC, the median time to progression (TTP) to MIBC or metBC was 111.6 months (95% Cl: 85.7-NR). Among NMIBC pts, TTP was significantly shorter for HER2-amplified (n = 17) vs. non-amplified (n = 497) (HR = 1.99, 95%CI: 1.05-3.76, p = 0.034, median 26 vs. 114 months). Among pts with metBC receiving frontline platinum-based chemotherapy (n = 143), the median overall survival (OS) was 25.3 months (95%CI: 18.5-33.9). OS was numerically higher in pts with any oncogenic HER2 alteration (n = 26) compared to wild-type (n = 117) (HR = 0.59, 95% Cl: 0.33-1.07, p = 0.082), though this difference was not statistically significant. The median OS for platinum-refractory metBC pts receiving 2nd line immunotherapy (n = 63) was 10.3 months (95%CI: 7.2-31.6), and the association between OS and HER2 alteration was not significant (HR = 0.57, 95%CI: 0.24-1.37, p = 0.2). Conclusions: HER2 amplification is more frequent in MIBC and metBC than in NMIBC. In NMIBC, HER2 amplification is associated with shorter TTP to MIBC or metBC. HER2 alteration in metBC is associated with a non-significant trend towards improved OS in frontline platinum-treated pts, though this analysis is limited by small sample size.[Table: see text]

Abstract OT2-23-01: A Phase 1b/2a, open-label platform study to evaluate mirdametinib in combination with fulvestrant in ER+ metastatic breast cancers harboring MAPK-activating mutations

Background: Approximately 70% of all metastatic breast cancers (MBCs) express estrogen receptor (ER). Hormonal therapies targeting ER are highly active against these cancers and have been remarkably successful in improving outcomes. Unfortunately, resistance to hormonal therapy is nearly universal and over 90% of patients develop resistance to various drugs targeting ER. We have identified mutations in three non-overlapping gene sets that are associated with the hormone-resistant phenotype: (1) ESR1, (2) MAPK pathway, and (3) transcription factors. The finding of mutations that might activate MAPK signaling was particularly striking given the known oncogenic function of this pathway in other cancers and the potential to target this pathway with selective inhibitors. Indeed, in preclinical models, the combination of an allosteric MEK inhibitor with an ER antagonist induced tumor regression in NF1-null, ER+ xenografts that were resistant to antiestrogen monotherapy. These data suggest that MAPK pathway alterations promote resistance to ER-targeted therapies in MBC and lead us to hypothesize that MAPK-targeted therapies will prove highly effective in such patients. However, NF1 (prevalence 6%) is only one of several RAS modulators that are associated with hormone resistance, and KRAS and HRAS mutations were also present in this dataset. Further, receptor tyrosine kinase (RTK) alterations (EGFR amplification and ERBB2 somatic mutations) and mutations in the RAF/MEK kinase cascade (BRAF and MEK1) are present and may comparably confer resistance to hormonal therapy and sensitivity to MAPK pathway inhibition. We hypothesize that MAPK pathway-activated MBCs can be effectively treated using MAPK targeted therapies in combination with hormonal therapy. Patient Accrual:The workflow to enroll patients to clinical trials at MSKCC is automated such that genomic alterations that are deposited on the cBioPortal are matched with appropriate clinical trials using database queries. A recent query of cBioPortal data from ER+ MBC patients treated at MSKCC showed 216 patients harboring actionable alterations in the MAPK pathway. Clinical Trial Design: This investigator-initiated trial being performed in collaboration with SpringWorks Therapeutics is IRB-approved and anticipated to open at MSKCC in August 2021. This is a Phase IB/IIA clinical trial of the allosteric MEK1/2 inhibitor mirdametinib (oral, daily) with the ER antagonist fulvestrant (500mg IM monthly). Inclusion criteria for the study will include ER+ tumor (ASCO-CAP guidelines), MAPK-activating genomic alteration documented by a CLIA-certified NGS assay at any time before the start of treatment, measurable disease, and at least one line of prior endocrine therapy. The feasibility of the combination will be established in a brief safety run-in of full-dose fulvestrant together with mirdametinib with dose de-escalation planned if two Dose Limiting Toxicities (DLT) are observed in the first six patients. This drug combination will then be expanded in three cohorts of patients defined by tumor genotype: (1) RAS activating: NF1 loss, KRAS or HRAS activating mutation, (2) RTK: EGFR amplification or ERBB2 hotspot mutation, (3) RAF/MEK: activating mutation in BRAF, CRAF, or MEK1/2. The primary endpoint for the study will be safety and tolerability of mirdametinib in combination with fulvestrant, and secondary endpoints include Overall Response Rate (ORR), Progression Free Survival (PFS), Clinical Benefit Rate (CBR), and Duration of Response (DOR) for the drug combination in each cohort and for the total study population. Overall survival is not an endpoint of this protocol.

Citation Format: Ezra Y. Rosen, Payal Patel, Nenad Sarapa, Badreddin Edris, Alexia Iasonos, Komal Jhaveri, Pedram Razavi, Mark Robson, Alexander Drilon, Michael F. Berger, David B. Solit, Sarat Chandarlapaty. A Phase 1b/2a, open-label platform study to evaluate mirdametinib in combination with fulvestrant in ER+ metastatic breast cancers harboring MAPK-activating mutations [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr OT2-23-01.

Genomic characterization of metastatic patterns from prospective clinical sequencing of 25,000 patients

Metastatic progression is the main cause of death in cancer patients, whereas the underlying genomic mechanisms driving metastasis remain largely unknown. Here, we assembled MSK-MET, a pan-cancer cohort of over 25,000 patients with metastatic diseases. By analyzing genomic and clinical data from this cohort, we identified associations between genomic alterations and patterns of metastatic dissemination across 50 tumor types. We found that chromosomal instability is strongly correlated with metastatic burden in some tumor types, including prostate adenocarcinoma, lung adenocarcinoma, and HR+/HER2+ breast ductal carcinoma, but not in others, including colorectal cancer and high-grade serous ovarian cancer, where copy-number alteration patterns may be established early in tumor development. We also identified somatic alterations associated with metastatic burden and specific target organs. Our data offer a valuable resource for the investigation of the biological basis for metastatic spread and highlight the complex role of chromosomal instability in cancer progression.

Defining and Targeting Esophagogastric Cancer Genomic Subsets With Patient-Derived Xenografts

PURPOSE

Comprehensive genomic profiling has defined key oncogenic drivers and distinct molecular subtypes in esophagogastric cancer; however, the number of clinically actionable alterations remains limited. To establish preclinical models for testing genomically driven therapeutic strategies, we generated and characterized a large collection of esophagogastric cancer patient-derived xenografts (PDXs).

MATERIALS AND METHODS

We established a biobank of 98 esophagogastric cancer PDX models derived from primary tumors and metastases. Clinicopathologic features of each PDX and the corresponding patient sample were annotated, including stage at diagnosis, treatment history, histology, and biomarker profile. To identify oncogenic DNA alterations, we analyzed and compared targeted sequencing performed on PDX and parent tumor pairs. We conducted xenotrials in genomically defined models with oncogenic drivers.

RESULTS

From April 2010 to June 2019, we implanted 276 patient tumors, of which 98 successfully engrafted (35.5%). This collection is enriched for PDXs derived from patients with human epidermal growth factor receptor 2-positive esophagogastric adenocarcinoma (62 models, 63%), the majority of which were refractory to standard therapies including trastuzumab. Factors positively correlating with engraftment included advanced stage, metastatic origin, intestinal-type histology, and human epidermal growth factor receptor 2-positivity. Mutations in TP53 and alterations in receptor tyrosine kinases (ERBB2 and EGFR), RAS/PI3K pathway genes, cell-cycle mediators (CDKN2A and CCNE1), and CDH1 were the predominant oncogenic drivers, recapitulating clinical tumor sequencing. We observed antitumor activity with rational combination strategies in models established from treatment-refractory disease.

CONCLUSION

The Memorial Sloan Kettering Cancer Center PDX collection recapitulates the heterogeneity of esophagogastric cancer and is a powerful resource to investigate mechanisms driving tumor progression, identify predictive biomarkers, and develop therapeutic strategies for molecularly defined subsets of esophagogastric cancer.

Distinct differences in genomic profile of gastric and gastroesophageal junction adenocarcinoma

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Background: Gastroesophageal junction cancer (GEJC) and gastric cancer (GC) are frequently studied together as one disease. Genomic profiles between the two disease sites have not been well characterized. We aimed to characterize molecular differences between the two disease sites. Methods: We collected data between January 2010 and December 2019 from a prospectively maintained database of GEJC and GC at our center. GEJC was defined according to the Siewert type 1 to 3 classification. Patients who underwent surgical resection and had MSK-IMPACT (MSK-Integrated Mutation Profiling of Actionable Cancer Targets) sequencing performed on their primary tumor were included in this analysis. Results: Two hundred and seventy-four samples were analyzed; 156 (56.9%) GEJC and 118 (43.1%) GC patients. Regarding molecular subtypes, the GEJC group had a higher frequency of chromosomally instable tumors compared to the GC cohort (55.1% vs. 25.4%, p < 0.001). The fraction of genome altered (FGA) was significantly higher in the GEJC group (p < 0.001). TP53 (75.3% vs. 31.9%, p < 0.001, q < 0.001), CDKN2A (17.1% vs. 4.3%, p = 0.002, q = 0.02), and MDM2 (6.8% vs. 0%, p = 0.007, q = 0.033) were more frequently altered in the GEJC group, whereas CDH1 (2.7% vs. 9.6%, p = 0.037, q = 0.118) and RHOA (0% vs. 6.4%, p = 0.003, q = 0.02) were more frequently altered in the GC group. The GEJC group also had a higher frequency of alterations in the cell cycle pathway compared to the GC patients (36.3% vs. 11.7%, p < 0.001, q < 0.001). Conclusions: There are distinct differences in genomic profiles between GEJC and GC with a higher frequency of mutations in TP53, CDKN2A, MDM2, and cell cycle pathway in the GEJC patients, that may have potential implications in evaluating optimal treatment strategies with targeted therapy.

Differences in Prostate Cancer Genomes by Self-reported Race: Contributions of Genetic Ancestry, Modifiable Cancer Risk Factors, and Clinical Factors

PURPOSE

Black men die from prostate cancer twice as often as White men, a disparity likely due to inherited genetics, modifiable cancer risk factors, and healthcare access. It is incompletely understood how and why tumor genomes differ by self-reported race and genetic ancestry.

EXPERIMENTAL DESIGN

Among 2,069 men with prostate cancer (1,841 self-reported White, 63 Asian, 165 Black) with access to clinical-grade sequencing at the same cancer center, prevalence of tumor and germline alterations was assessed in cancer driver genes reported to have different alteration prevalence by race.

RESULTS

Clinical characteristics such as prostate-specific antigen and age at diagnosis as well as cancer stage at sample procurement differed by self-reported race. However, most genomic differences persisted when adjusting for clinical characteristics. Tumors from Black men harbored fewer PTEN mutations and more AR alterations than those from White men. Tumors from Asian men had more FOXA1 mutations and more ZFHX3 alterations than White men. Despite fewer TP53 mutations, tumors from Black men had more aneuploidy, particularly chromosome arm 8q gains, an adverse prognostic factor. Genetic ancestry was associated with similar tumor alterations as self-reported race, but also with modifiable cancer risk factors. Community-level average income was associated with chr8q gains after adjusting for race and ancestry.

CONCLUSIONS

Tumor genomics differed by race even after accounting for clinical characteristics. Equalizing access to care may not fully eliminate such differences. Therapies for alterations more common in racial minorities are needed. Tumor genomic differences should not be assumed to be entirely due to germline genetics.

BRAF Mutations: The Discovery of Allele- and Lineage-Specific Differences

Cancer treatment is increasingly guided by molecular analyses designed to identify clinically actionable genomic alterations in individual patients. The discovery of BRAF mutations in human cancer, and the subsequent development and FDA authorization of selective BRAF inhibitors highlight the potential clinical impact and current limitations of precision oncology paradigms. In 2002, Brose and colleagues reported that the distribution of BRAF mutations differed in melanoma and lung cancer and that not all BRAF mutations were functionally equivalent. Here, we discuss this landmark paper, which foreshadowed subsequent research elucidating how biochemical differences among mutant alleles within the same gene and lineage-specific differences among cancer types impact drug sensitivity. Such translational studies provided a road map for the development of novel RAF inhibitors and rational combination strategies that promise greater clinical activity and/or more favorable toxicity profiles.See related article by Brose and colleagues, Cancer Res 2002;62:6997-7000.

CD274 (PD-L1) Copy Number Changes (Gain) & Response to Immune Checkpoint Blockade Therapy in Carcinomas of the Urinary Tract

BACKGROUND: Immune checkpoint inhibitors are an important therapeutic option for urothelial carcinoma, but durable responses are achieved in a minority of patients. Identifying pre-treatment biomarkers that may predict response to these therapies or who exhibit intrinsic resistance, is of paramount importance. OBJECTIVE: To explore the prevalence of PD-L1 copy number alteration in urothelial carcinoma and correlate with response to immune checkpoint inhibitors. METHODS: We analyzed a cohort of 1050 carcinomas of the bladder and upper urinary tract that underwent targeted next generation sequencing, prospectively. We assessed PD-L1 protein expression, copy number status (next generation sequencing/FISH), and detailed treatment response. RESULTS: We identified 9 tumors with PD-L1 amplification and 9 tumors with PD-L1 deletion. PD-L1 protein expression was the highest in PD-L1 amplified tumors. Of the 9 patients whose tumors harbored PD-L1 amplification, 6 received immunotherapy with 4 deriving clinical benefit, and 2 achieving durable response. Of the 9 patients whose tumors had PD-L1 copy number losses, 4 received immunotherapy with 3 experiencing disease progression. CONCLUSIONS: PD-L1 copy number alterations may serve as potential biomarkers of response to immunotherapy in urothelial carcinoma patients, if validated in larger cohorts.

Molecular and phenotypic profiling of colorectal cancer patients in West Africa reveals biological insights

Understanding the molecular and phenotypic profile of colorectal cancer (CRC) in West Africa is vital to addressing the regions rising burden of disease. Tissue from unselected Nigerian patients was analyzed with a multigene, next-generation sequencing assay. The rate of microsatellite instability is significantly higher among Nigerian CRC patients (28.1%) than patients from The Cancer Genome Atlas (TCGA, 14.2%) and Memorial Sloan Kettering Cancer Center (MSKCC, 8.5%, P < 0.001). In microsatellite-stable cases, tumors from Nigerian patients are less likely to have APC mutations (39.1% vs. 76.0% MSKCC P < 0.001) and WNT pathway alterations (47.8% vs. 81.9% MSKCC, P < 0.001); whereas RAS pathway alteration is more prevalent (76.1% vs. 59.6%, P = 0.03). Nigerian CRC patients are also younger and more likely to present with rectal disease (50.8% vs. 33.7% MSKCC, P < 0.001). The findings suggest a unique biology of CRC in Nigeria, which emphasizes the need for regional data to guide diagnostic and treatment approaches for patients in West Africa.

Understanding the molecular and phenotypic profile of colorectal cancer (CRC) in West Africa is important for early detection and treatment. Here, the authors use a multigene next-generation sequencing panel to identify genomic differences in Nigerian CRCs compared to those from TCGA and MSKCC cohorts.

Multiple Primary Cancers in Patients Undergoing Tumor-Normal Sequencing Define Novel Associations

BACKGROUND

Cancer survivors are developing more subsequent tumors. We sought to characterize patients with multiple (≥2) primary cancers (MPC) to assess associations and genetic mechanisms.

METHODS

Patients were prospectively consented (01/2013-02/2019) to tumor-normal sequencing via a custom targeted panel (MSK-IMPACT). A subset consented to return of results of ≥76 cancer predisposition genes. International Agency for Research on Cancer (IARC) 2004 rules for defining MPC were applied. Tumor pairs were created to assess relationships between cancers. Age-adjusted, sex-specific, standardized incidence ratios (SIR) for first to second cancer event combinations were calculated using SEER rates, adjusting for confounders and time of ascertainment. Associations were made with germline and somatic variants.

RESULTS

Of 24,241 patients, 4,340 had MPC (18%); 20% were synchronous. Most (80%) had two primaries; however, 4% had ≥4 cancers. SIR analysis found lymphoma-lung, lymphoma-uterine, breast-brain, and melanoma-lung pairs in women and prostate-mesothelioma, prostate-sarcoma, melanoma-stomach, and prostate-brain pairs in men in excess of expected after accounting for synchronous tumors, known inherited cancer syndromes, and environmental exposures. Of 1,580 (36%) patients who received germline results, 324 (21%) had 361 pathogenic/likely pathogenic variants (PV), 159 (44%) in high penetrance genes. Of tumor samples analyzed, 55% exhibited loss of heterozygosity at the germline variant. In those with negative germline findings, melanoma, prostate, and breast cancers were common.

CONCLUSIONS

We identified tumor pairs without known predisposing mutations that merit confirmation and will require novel strategies to elucidate genetic mechanisms of shared susceptibilities.

IMPACT

If verified, patients with MPC with novel phenotypes may benefit from targeted cancer surveillance.

HER2 + breast cancers evade anti-HER2 therapy via a switch in driver pathway

Inhibition of HER2 in HER2-amplified breast cancer has been remarkably successful clinically, as demonstrated by the efficacy of HER-kinase inhibitors and HER2-antibody treatments. Whilst resistance to HER2 inhibition is common in the metastatic setting, the specific programs downstream of HER2 driving resistance are not established. Through genomic profiling of 733 HER2-amplified breast cancers, we identify enrichment of somatic alterations that promote MEK/ERK signaling in metastatic tumors with shortened progression-free survival on anti-HER2 therapy. These mutations, including NF1 loss and ERBB2 activating mutations, are sufficient to mediate resistance to FDA-approved HER2 kinase inhibitors including tucatinib and neratinib. Moreover, resistant tumors lose AKT dependence while undergoing a dramatic sensitization to MEK/ERK inhibition. Mechanistically, this driver pathway switch is a result of MEK-dependent activation of CDK2 kinase. These results establish genetic activation of MAPK as a recurrent mechanism of anti-HER2 therapy resistance that may be effectively combated with MEK/ERK inhibitors.

The context-specific role of germline pathogenicity in tumorigenesis

Human cancers arise from environmental, heritable and somatic factors, but how these mechanisms interact in tumorigenesis is poorly understood. Studying 17,152 prospectively sequenced patients with cancer, we identified pathogenic germline variants in cancer predisposition genes, and assessed their zygosity and co-occurring somatic alterations in the concomitant tumors. Two major routes to tumorigenesis were apparent. In carriers of pathogenic germline variants in high-penetrance genes (5.1% overall), lineage-dependent patterns of biallelic inactivation led to tumors exhibiting mechanism-specific somatic phenotypes and fewer additional somatic oncogenic drivers. Nevertheless, 27% of cancers in these patients, and most tumors in patients with pathogenic germline variants in lower-penetrance genes, lacked particular hallmarks of tumorigenesis associated with the germline allele. The dependence of tumors on pathogenic germline variants is variable and often dictated by both penetrance and lineage, a finding with implications for clinical management.

Novel Mouse Models of Bladder Cancer Identify a Prognostic Signature Associated with Risk of Disease Progression

To study the progression of bladder cancer from non-muscle-invasive to muscle-invasive disease, we have developed a novel toolkit that uses complementary approaches to achieve gene recombination in specific cell populations in the bladder urothelium in vivo, thereby allowing us to generate a new series of genetically engineered mouse models (GEMM) of bladder cancer. One method is based on the delivery of adenoviruses that express Cre recombinase in selected cell types in the urothelium, and a second uses transgenic drivers in which activation of inducible Cre alleles can be limited to the bladder urothelium by intravesicular delivery of tamoxifen. Using both approaches, targeted deletion of the Pten and p53 tumor suppressor genes specifically in basal urothelial cells gave rise to muscle-invasive bladder tumors. Furthermore, preinvasive lesions arising in basal cells displayed upregulation of molecular pathways related to bladder tumorigenesis, including proinflammatory pathways. Cross-species analyses comparing a mouse gene signature of early bladder cancer with a human signature of bladder cancer progression identified a conserved 28-gene signature of early bladder cancer that is associated with poor prognosis for human bladder cancer and that outperforms comparable gene signatures. These findings demonstrate the relevance of these GEMMs for studying the biology of human bladder cancer and introduce a prognostic gene signature that may help to stratify patients at risk for progression to potentially lethal muscle-invasive disease. SIGNIFICANCE: Analyses of bladder cancer progression in a new series of genetically engineered mouse models has identified a gene signature of poor prognosis in human bladder cancer.

Anti-PD-1/L1 lead-in before MAPK inhibitor combination maximizes antitumor immunity and efficacy

Rationally sequencing and combining PD-1/L1-and MAPK-targeted therapies may overcome innate and acquired resistance. Since increased clinical benefit of MAPK inhibitors (MAPKi) is associated with previous immune checkpoint therapy, we compare the efficacies of sequential and/or combinatorial regimens in subcutaneous murine models of melanoma driven by BrafV600, Nras, or Nf1 mutations as well as colorectal and pancreatic carcinoma driven by KrasG12C. Anti-PD-1/L1 lead-in preceding MAPKi combination optimizes response durability by promoting pro-inflammatory polarization of macrophages and clonal expansion of interferon-γhi, and CD8+ cytotoxic and proliferative (versus CD4+ regulatory) T cells that highly express activation genes. Since therapeutic resistance of melanoma brain metastasis (MBM) limits patient survival, we demonstrate that sequencing anti-PD-1/L1 therapy before MAPKi combination suppresses MBM and improves mouse survival with robust T cell clonal expansion in both intracranial and extracranial metastatic sites. We propose clinically testing brief anti-PD-1/L1 (± anti-CTLA-4) dosing before MAPKi co-treatment to suppress therapeutic resistance.

Genetic Determinants of Outcome in Intrahepatic Cholangiocarcinoma

BACKGROUND AND AIM

Genetic alterations in intrahepatic cholangiocarcinoma (iCCA) are increasingly well characterized, but their impact on outcome and prognosis remains unknown.

APPROACH AND RESULTS

This bi-institutional study of patients with confirmed iCCA (n = 412) used targeted next-generation sequencing of primary tumors to define associations among genetic alterations, clinicopathological variables, and outcome. The most common oncogenic alterations were isocitrate dehydrogenase 1 (IDH1; 20%), AT-rich interactive domain-containing protein 1A (20%), tumor protein P53 (TP53; 17%), cyclin-dependent kinase inhibitor 2A (CDKN2A; 15%), breast cancer 1-associated protein 1 (15%), FGFR2 (15%), polybromo 1 (12%), and KRAS (10%). IDH1/2 mutations (mut) were mutually exclusive with FGFR2 fusions, but neither was associated with outcome. For all patients, TP53 (P < 0.0001), KRAS (P = 0.0001), and CDKN2A (P < 0.0001) alterations predicted worse overall survival (OS). These high-risk alterations were enriched in advanced disease but adversely impacted survival across all stages, even when controlling for known correlates of outcome (multifocal disease, lymph node involvement, bile duct type, periductal infiltration). In resected patients (n = 209), TP53mut (HR, 1.82; 95% CI, 1.08-3.06; P = 0.03) and CDKN2A deletions (del; HR, 3.40; 95% CI, 1.95-5.94; P < 0.001) independently predicted shorter OS, as did high-risk clinical variables (multifocal liver disease [P < 0.001]; regional lymph node metastases [P < 0.001]), whereas KRASmut (HR, 1.69; 95% CI, 0.97-2.93; P = 0.06) trended toward statistical significance. The presence of both or neither high-risk clinical or genetic factors represented outcome extremes (median OS, 18.3 vs. 74.2 months; P < 0.001), with high-risk genetic alterations alone (median OS, 38.6 months; 95% CI, 28.8-73.5) or high-risk clinical variables alone (median OS, 37.0 months; 95% CI, 27.6-not available) associated with intermediate outcome. TP53mut, KRASmut, and CDKN2Adel similarly predicted worse outcome in patients with unresectable iCCA. CDKN2Adel tumors with high-risk clinical features were notable for limited survival and no benefit of resection over chemotherapy.

CONCLUSIONS

TP53, KRAS, and CDKN2A alterations were independent prognostic factors in iCCA when controlling for clinical and pathologic variables, disease stage, and treatment. Because genetic profiling can be integrated into pretreatment therapeutic decision-making, combining clinical variables with targeted tumor sequencing may identify patient subgroups with poor outcome irrespective of treatment strategy.

Therapeutic Implications of Germline Testing in Patients With Advanced Cancers

PURPOSE

Tumor mutational profiling is increasingly performed in patients with advanced cancer. We determined the extent to which germline mutation profiling guides therapy selection in patients with advanced cancer.

METHODS

Patients with cancer undergoing tumor genomic profiling were prospectively consented for germline cancer predisposition gene analysis (2015-2019). In patients harboring germline likely pathogenic or pathogenic (LP/P) alterations, therapeutic actionability was classified using a precision oncology knowledge base. Patients with metastatic or recurrent cancer receiving germline genotype-directed therapy were determined.

RESULTS

Among 11,947 patients across > 50 malignancies, 17% (n = 2,037) harbored a germline LP/P variant. By oncology knowledge base classification, 9% (n = 1042) had an LP/P variant in a gene with therapeutic implications (4% level 1; 4% level 3B; < 1% level 4). BRCA1/2 variants accounted for 42% of therapeutically actionable findings, followed by CHEK2 (13%), ATM (12%), mismatch repair genes (11%), and PALB2 (5%). When limited to the 9,079 patients with metastatic or recurrent cancer, 8% (n = 710) harbored level 1 or 3B genetic findings and 3.2% (n = 289) received germline genotype-directed therapy. Germline genotype-directed therapy was received by 61% and 18% of metastatic cancer patients with level 1 and level 3B findings, respectively, and by 54% of BRCA1/2, 75% of mismatch repair, 43% of PALB2, 35% of RAD51C/D, 24% of BRIP1, and 19% of ATM carriers. Of BRCA1/2 patients receiving a poly(ADP-ribose) polymerase inhibitor, 45% (84 of 188) had tumors other than breast or ovarian cancer, wherein the drug, at time of delivery, was delivered in an investigational setting.

CONCLUSION

In a pan-cancer analysis, 8% of patients with advanced cancer harbored a germline variant with therapeutic actionability with 40% of these patients receiving germline genotype-directed treatment. Germline sequence analysis is additive to tumor sequence analysis for therapy selection and should be considered for all patients with advanced cancer.

TNFR2/14-3-3ε signaling complex instructs macrophage plasticity in inflammation and autoimmunity

TNFR1 and TNFR2 have received prominent attention because of their dominance in the pathogenesis of inflammation and autoimmunity. TNFR1 has been extensively studied and primarily mediates inflammation. TNFR2 remains far less studied, although emerging evidence demonstrates that TNFR2 plays an antiinflammatory and immunoregulatory role in various conditions and diseases. Herein, we report that TNFR2 regulates macrophage polarization, a highly dynamic process controlled by largely unidentified intracellular regulators. Using biochemical copurification and mass spectrometry approaches, we isolated the signaling molecule 14-3-3ε as a component of TNFR2 complexes in response to progranulin stimulation in macrophages. In addition, 14-3-3ε was essential for TNFR2 signaling-mediated regulation of macrophage polarization and switch. Both global and myeloid-specific deletion of 14-3-3ε resulted in exacerbated inflammatory arthritis and counteracted the protective effects of progranulin-mediated TNFR2 activation against inflammation and autoimmunity. TNFR2/14-3-3ε signaled through PI3K/Akt/mTOR to restrict NF-κB activation while simultaneously stimulating C/EBPβ activation, thereby instructing macrophage plasticity. Collectively, this study identifies 14-3-3ε as a previously unrecognized vital component of the TNFR2 receptor complex and provides new insights into the TNFR2 signaling, particularly its role in macrophage polarization with therapeutic implications for various inflammatory and autoimmune diseases with activation of the TNFR2/14-3-3ε antiinflammatory pathway.

Identification of a Novel Inflamed Tumor Microenvironment Signature as a Predictive Biomarker of Bacillus Calmette-Guérin Immunotherapy in Non-Muscle-Invasive Bladder Cancer

PURPOSE

Improved risk stratification and predictive biomarkers of treatment response are needed for non-muscle-invasive bladder cancer (NMIBC). Here we assessed the clinical utility of targeted RNA and DNA molecular profiling in NMIBC.

EXPERIMENTAL DESIGN

Gene expression in NMIBC samples was profiled by NanoString nCounter, an RNA quantification platform, from two independent cohorts (n = 28, n = 50); targeted panel sequencing was performed in a subgroup (n = 50). Gene signatures were externally validated using two RNA sequencing datasets of NMIBC tumors (n = 438, n = 73). Established molecular subtype classifiers and novel gene expression signatures were assessed for associations with clinicopathologic characteristics, somatic tumor mutations, and treatment outcomes.

RESULTS

Molecular subtypes distinguished between low-grade Ta tumors with FGFR3 mutations and overexpression (UROMOL-class 1) and tumors with more aggressive clinicopathologic characteristics (UROMOL-classes 2 and 3), which were significantly enriched with TERT promoter mutations. However, UROMOL subclasses were not associated with recurrence after bacillus Calmette-Guérin (BCG) immunotherapy in two independent cohorts. In contrast, a novel expression signature of an inflamed tumor microenvironment (TME) was associated with improved recurrence-free survival after BCG. Expression of immune checkpoint genes (PD-L1/PD-1/CTLA-4) was associated with an inflamed TME, but not with higher recurrence rates after BCG. FGFR3 mutations and overexpression were both associated with low immune signatures.

CONCLUSIONS

Assessment of the immune TME, rather than molecular subtypes, is a promising predictive biomarker of BCG response. Modulating the TME in an immunologically "cold" tumor warrants further investigation. Integrated transcriptomic and exome sequencing should improve treatment selection in NMIBC.

Clinical cancer genomic profiling

Technological innovation and rapid reduction in sequencing costs have enabled the genomic profiling of hundreds of cancer-associated genes as a component of routine cancer care. Tumour genomic profiling can refine cancer subtype classification, identify which patients are most likely to benefit from systemic therapies and screen for germline variants that influence heritable cancer risk. Here, we discuss ongoing efforts to enhance the clinical utility of tumour genomic profiling by integrating tumour and germline analyses, characterizing allelic context and identifying mutational signatures that influence therapy response. We also discuss the potential clinical utility of more comprehensive whole-genome and whole-transcriptome sequencing and ultra-sensitive cell-free DNA profiling platforms, which allow for minimally invasive, serial analyses of tumour-derived DNA in blood.

Prevalence of Germline Alterations on Targeted Tumor-Normal Sequencing of Esophagogastric Cancer

Importance

Among patients with esophagogastric cancers, only individuals who present with known features of heritable cancer syndromes are referred for genetic testing. Broader testing might identify additional patients with germline alterations.

Objectives

To examine the prevalence of likely pathogenic or pathogenic (LP/P) germline alterations among patients with esophagogastric cancer and to assess associations between germline variant prevalence and demographic and clinicopathologic features.

Design, Setting, and Participants

This cross-sectional study was performed at a tertiary referral cancer center from January 1, 2014, to December 31, 2019, in 515 patients with esophagogastric cancer who consented to tumor and blood sequencing.

Main Outcomes and Measures

Presence or absence of LP/P variants in up to 88 genes associated with cancer predisposition syndromes as identified by targeted sequencing (Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets).

Results

Among 515 patients (median age, 59 years; range, 18-87 years; 368 [71.5%] male; 398 [77.3%] White), 243 (47.2%) had gastric cancer, 111 (21.6%) had gastroesophageal junction (GEJ) cancer, and 161 (31.3%) had esophageal cancer. A total of 48 patients with gastric cancer (19.8%), 16 (14.4%) with GEJ cancer, and 17 (10.6%) with esophageal cancer had LP/P germline variants. The number of LP/P variants in high- and moderate-penetrance genes was significantly higher in patients with gastric cancer (29 [11.9%]; 95% CI, 8.1%-16.7%) vs patients with esophageal cancer (8 [5.0%]; 95% CI, 2.2%-9.6%; P = .03), and the difference was greater for high-penetrance germline alterations in patients with gastric cancer (25 [10.3%]; 95% CI, 6.8%-14.8%) vs in patients with esophageal cancer (3 [1.9%]; 95% CI, 0.38%-5.3%; P = .001). The most frequent high- and moderate-penetrance LP/P alterations were in BRCA1/2 (14 [2.7%]), ATM (11 [2.1%]), CDH1 (6 [1.2%]), and MSH2 (4 [0.8%]). Those with early-onset disease (≤50 years of age at diagnosis) were more likely to harbor an LP/P germline variant (29 [21.0%]; 95% CI, 14.5%-28.8%) vs those with late-onset disease (patients >50 years of age at diagnosis) (52 [13.8%]; 95% CI, 10.5%-17.7%; P = .046). ATM LP/P variants occurred in 6 patients (4.3%; 95% CI, 1.6%-9.1%) with early-onset esophagogastric cancer vs 5 (1.3%; 95% CI, 0.4%-3.1%; P = .08) of those with late-onset esophagogastric cancer.

Conclusions and Relevance

These results suggest that pathogenic germline variants are enriched in gastric and early-onset esophagogastric cancer and that germline testing should be considered in these populations. The role of ATM alterations in esophagogastric cancer risk warrants further investigation.

Enhanced specificity of clinical high-sensitivity tumor mutation profiling in cell-free DNA via paired normal sequencing using MSK-ACCESS

Circulating cell-free DNA from blood plasma of cancer patients can be used to non-invasively interrogate somatic tumor alterations. Here we develop MSK-ACCESS (Memorial Sloan Kettering - Analysis of Circulating cfDNA to Examine Somatic Status), an NGS assay for detection of very low frequency somatic alterations in 129 genes. Analytical validation demonstrated 92% sensitivity in de-novo mutation calling down to 0.5% allele frequency and 99% for a priori mutation profiling. To evaluate the performance of MSK-ACCESS, we report results from 681 prospective blood samples that underwent clinical analysis to guide patient management. Somatic alterations are detected in 73% of the samples, 56% of which have clinically actionable alterations. The utilization of matched normal sequencing allows retention of somatic alterations while removing over 10,000 germline and clonal hematopoiesis variants. Our experience illustrates the importance of analyzing matched normal samples when interpreting cfDNA results and highlights the importance of cfDNA as a genomic profiling source for cancer patients.

Liquid biopsies allow the non-invasive detection of somatic mutations from tumours. Here, the authors develop and test MSK-ACCESS, an NGS-based clinical assay for identifying low frequency mutations in 129 genes and describe how it benefits patients in the clinic.

Molecular classification and diagnostics of upper urinary tract urothelial carcinoma

Upper urinary tract urothelial carcinoma (UTUC) is one of the common urothelial cancers. Its molecular pathogenesis, however, is poorly understood, with no useful biomarkers available for accurate diagnosis and molecular classification. Through an integrated genetic study involving 199 UTUC samples, we delineate the landscape of genetic alterations in UTUC enabling genetic/molecular classification. According to the mutational status of TP53, MDM2, RAS, and FGFR3, UTUC is classified into five subtypes having discrete profiles of gene expression, tumor location/histology, and clinical outcome, which is largely recapitulated in an independent UTUC cohort. Sequencing of urine sediment-derived DNA has a high diagnostic value for UTUC with 82.2% sensitivity and 100% specificity. These results provide a solid basis for better diagnosis and management of UTUC.

Tumor fraction-guided cell-free DNA profiling in metastatic solid tumor patients

BACKGROUND

Cell-free DNA (cfDNA) profiling is increasingly used to guide cancer care, yet mutations are not always identified. The ability to detect somatic mutations in plasma depends on both assay sensitivity and the fraction of circulating DNA in plasma that is tumor-derived (i.e., cfDNA tumor fraction). We hypothesized that cfDNA tumor fraction could inform the interpretation of negative cfDNA results and guide the choice of subsequent assays of greater genomic breadth or depth.

METHODS

Plasma samples collected from 118 metastatic cancer patients were analyzed with cf-IMPACT, a modified version of the FDA-authorized MSK-IMPACT tumor test that can detect genomic alterations in 410 cancer-associated genes. Shallow whole genome sequencing (sWGS) was also performed in the same samples to estimate cfDNA tumor fraction based on genome-wide copy number alterations using z-score statistics. Plasma samples with no somatic alterations detected by cf-IMPACT were triaged based on sWGS-estimated tumor fraction for analysis with either a less comprehensive but more sensitive assay (MSK-ACCESS) or broader whole exome sequencing (WES).

RESULTS

cfDNA profiling using cf-IMPACT identified somatic mutations in 55/76 (72%) patients for whom MSK-IMPACT tumor profiling data were available. A significantly higher concordance of mutational profiles and tumor mutational burden (TMB) was observed between plasma and tumor profiling for plasma samples with a high tumor fraction (z-score≥5). In the 42 patients from whom tumor data was not available, cf-IMPACT identified mutations in 16/42 (38%). In total, cf-IMPACT analysis of plasma revealed mutations in 71/118 (60%) patients, with clinically actionable alterations identified in 30 (25%), including therapeutic targets of FDA-approved drugs. Of the 47 samples without alterations detected and low tumor fraction (z-score<5), 29 had sufficient material to be re-analyzed using a less comprehensive but more sensitive assay, MSK-ACCESS, which revealed somatic mutations in 14/29 (48%). Conversely, 5 patients without alterations detected by cf-IMPACT and with high tumor fraction (z-score≥5) were analyzed by WES, which identified mutational signatures and alterations in potential oncogenic drivers not covered by the cf-IMPACT panel. Overall, we identified mutations in 90/118 (76%) patients in the entire cohort using the three complementary plasma profiling approaches.

CONCLUSIONS

cfDNA tumor fraction can inform the interpretation of negative cfDNA results and guide the selection of subsequent sequencing platforms that are most likely to identify clinically-relevant genomic alterations.

Early predictors of benefit to dual anti-PD1/HER2 inhibition: Biomarker analysis from phase 2 trial of pembrolizumab/trastuzumab in HER2-positive metastatic esophagogastric (mEG) cancer

4058

Background: Pembrolizumab and trastuzumab (P&T) and chemotherapy demonstrated 27 month mOS, 13 month mPFS, and 91% response rate in first-line HER2-positive mEG cancer irrespective of PD-L1 status (Janjigian Lancet Oncology 2020). Biomarkers including 89Zr-trastuzumab PET, blood, and tumor analysis were correlated with progression-free survival. Methods: Twenty-five patients received P&T once 3 weeks prior to addition of chemotherapy to P&T. Pre-treatment tumor biopsies, 89Zr-trastuzumab PET scans, serial plasma ctDNA (Guardant360, Redwood City, CA) and CT scans were performed. Tumor-matched DNA alterations were identified by correlating ctDNA and tissue-NGS variant calls. Pre-, on-, and post-treatment biopsies were analyzed using WES and IHC (HER2, PD-L1). Biomarkers were correlated with mPFS and 6-month PFS, the primary endpoint. Results: Of patients with tumor-matched mutations ctDNA at baseline, 12 of 16 had a decline in their maxVAF by week 3, corresponding to a mPFS of 14.7 (11.0-NR) vs 5.9 (95% CI 4.1-NR) months (p=0.009) and a mOS of 29.7 (95% CI 27.2-NR) vs 7.71 (95% CI 6.6-NR) months (p=0.006). 9 of 12 (75%) patients with decline in ctDNA at 3 weeks post-P&T achieved the 6-month PFS primary endpoint while the 4 patients with no decline in ctDNA all progressed in under 6-months. Similarly, 7 of 9 (78%) patients who had a decline in CT-measurements in all disease sites achieved the 6 month PFS primary endpoint, versus 10 of 16 (62.5%) of patients who did not respond in all sites (p=0.66), suggesting that ctDNA is superior to CT as an early predictive biomarker of response. Lack of ERBB2 amplification (amp) by NGS in ctDNA and/or tumor was associated with lack of response to P&T alone prior to addition of chemotherapy. Interestingly, no lesions from patients lacking ERBB2 ctDNA amp (n=3) responded to induction P&T by CT, while lesions from 3/9 patients lacking ERBB2 tissue amp responded to P&T by 3-week CT, suggesting intrapatient HER2 heterogeneity. Eight patients also underwent 89Zr-Trastuzumab PET scans prior to P&T and up to 5 lesions per disease site were measured on serial CT scans. All 15 lesions with intense uptake (SUVmax>10) responded to P&T, but only 9/24 lesions with SUVmax<10. All 4 patients who had at least 1 intense lesion achieved a post-P&T CT response and later 6+ month PFS. All 3 of 3 evaluable patients with intense uptake had baseline ctDNA ERBB2 amp. Conclusions: Patients with a decline in tumor-matched maxVAF after one dose of P&T were more likely to achieve durable PFS. Pre-treatment ctDNA ERBB2 amp and/or intense 89Zr-trastuzumab PET avidity are non-invasive predictive biomarkers of response to HER2-directed therapy. Evaluation of tumor immune environment digital spatial profiling is underway. Clinical trial information: NCT02954536.

Large cell neuroendocrine carcinoma of the urothelial tract (LNEC): The MSKCC experience

4526

Background: LNEC is a rare, poorly characterized entity morphologically resembling small cell NEC of the urothelial tract (SNEC). Methods: Pure and partial LNEC and SNEC cases were identified by histopathologic re-review; clinical outcomes were compared. A subset was sequenced with MSK-IMPACT (279-505 genes). Results: Between 1992-2020, 43 patients (pts) with LNEC were identified (42 bladder, 1 upper tract); 19 (44%) had concomitant SNEC. LNEC cases were compared to 192 SNEC without LNEC (SNEC-only) (Table 1). Compared to SNEC-only pts, LNEC pts experienced longer overall survival (OS), adjusting for age and M0 vs M1 (median OS not reached vs 22.4 months [mos]; HR 0.34, 95% CI 0.16-0.74, p =.006). Neoadjuvant chemo (NAC) use increased over time. Pathologic response rate (<ypT2N0) after NAC was 25% for LNEC and 50% for SNEC-only (p =.13); the ypT0N0 rate was 25% for LNEC and 40% for SNEC-only (p =.52). Perioperative chemo did not improve OS compared to surgery alone in LNEC, adjusting for age and concurrent SNEC (HR 1.46, 95% CI 0.12-17.5, p =.76), but was associated with longer OS among SNEC-only pts (n = 98; HR 0.39, 95% CI 0.22-0.69, p =.001). Two M1 LNEC pts received immunotherapy (IO) in the first-line: 1 atezolizumab, 1 atezolizumab + chemo. Both remained free of progression on IO at a follow-up of 20 and 12 mos, respectively. Of 18 sequenced LNEC tumors, 89% had TERT promoter alterations (alts), similar to 85% seen in 52 SNEC tumors. All LNEC tumors had alts of TP53 or RB1, and 10 (56%) had both. Median tumor mutational burden (TMB) was 14 (IQR 8-38) in LNEC and 30 (IQR 15-55) in SNEC. Epigenetic modifiers were altered in 78% LNEC and 79% SNEC. Two LNEC pts had ERCC2 alts and received platinum chemo; both were alive at last follow-up from NEC diagnosis of 30.7-39.1 mos. Conclusions: LNEC pts experienced longer OS compared to pts with SNEC-only in this cohort, but did not appear more chemo-sensitive. Genomic profiles of LNEC and SNEC-only tumors were similar; TERT promoter mutations suggest a potential urothelial precursor. Further investigation of IO for LNEC is warranted.[Table: see text]

Detection of FGFR3 alt in plasma cfDNA in metastatic UC patients receiving Erda therapy

e16519

Background: The pan-FGFR inhibitor erdafitinib (erda) is FDA-approved for pretreated mUC pts harboring FGFR2/3 alterations. We explored concordance of FGFR3 alt profiles between primary tumor and cfDNA using the next generation sequencing assay MSK-ACCESS. We also correlated changes in FGFR3 cfDNA mutant allele fraction (MAF) with response to erda. Methods: After consent on an approved biomarker protocol, plasma samples were collected from mUC pts on erda at baseline, on treatment (tx), and at progression along with patient clinical characteristics. Baseline tumors were sequenced with MSK-IMPACT and plasma samples sequenced with MSK-ACCESS, a cfDNA platform that sequences select exons and introns of 129 genes and uses unique molecular indexes to detect somatic mutations down to 0.1% MAF. Results: Between 8/2019-12/2020, 18 pts started erda 8mg daily and had plasma drawn for MSK-ACCESS. Three pts increased to 9mg daily, 7 required dose reductions and 10 had dose interruptions. Treatment was discontinued in 13 pts for disease progression and 3 for toxicity. Median PFS was 3.7 months. FGFR3 S249C was the most frequent alt detected (11/18, 61%), then Y373C (3/18, 16%), and R248C (2/18, 11%) (Table). FGFR3 alt were detected in 15/18 (83%) baseline plasma samples, all of which were of the same alt as tumor tissues. In 3 samples, additional FGFR3 alt were detected, including 1 pt with an FGFR3-TACC3 fusion and hotspot mutations found only in cfDNA. FGFR3 MAF decreased in 7 of 9 pts on erda, 2 of whom declined to undetectable levels. Conclusions: A high degree of concordance of FGFR3 alt was observed between primary tumors and cfDNA. Most erda responders displayed reduction of FGFR3 cfDNA MAF. FGFR3 alts exclusive to cfDNA were found in a small subset of pts. Further pt accrual and follow-up are ongoing to assess for correlations between erda response/progression and changes in FGFR3 cfDNA MAF, and to assess whether cfDNA can identify resistance mechanisms.[Table: see text]

Overall survival with circulating tumor DNA-guided therapy in advanced non-small cell lung cancer

9009

Background: The effectiveness of circulating tumor DNA (ctDNA) at matching patients to life prolonging therapy has been studied mostly in small cohorts with limited follow up. The prognostic value of ctDNA alterations, particularly those absent on tissue, is also unclear. To address these questions, we studied survival outcomes in a prospective cohort of patients (N = 1002) with non-small cell lung cancer (NSCLC). Methods: Adults with metastatic or recurrent NSCLC were eligible if they had no known driver mutation or a known driver with progression following targeted therapy. Patients were enrolled at Memorial Sloan Kettering Cancer Center (New York, NY) starting October 21, 2016; analysis here is from a snapshot November 1, 2020. All patients had ctDNA sequenced via the Resolution ctDx Lung platform. To reduce inclusion of incidental germline mutations, we excluded non-functionally significant mutations with an allele frequency 35-65% that were present in gnomAD. Patients could also receive, at their provider’s discretion, tissue sequencing with MSK-IMPACT, which filters germline and clonal hematopoietic (CH) mutations with matched white blood cell sequencing. We performed survival analyses using Cox proportional hazards models from time of diagnosis of advanced disease to death, left truncating at time of study entry. Results: Of 1002 patients, 348 (35%) were treated with targeted therapy; in 181 of these (52%) the targetable alteration was detected in ctDNA. Patients treated with targeted therapy had prolonged survival whether matched by tissue-based methods (HR 0.39, 95%CI 0.30-0.51) or ctDNA (HR 0.47, 95%CI 0.37-0.61). These benefits persisted across multiple subgroups. ctDNA alterations themselves were associated with worse survival (HR 2.2, 95%CI 1.8-2.8), in a manner that scaled with allele fraction and burden. Of 401 patients with time-matched tissue sampling, 62 (15%) had ctDNA alterations that were absent on IMPACT (“unique” ctDNA alterations). Three such patients had unique ctDNA EGFR T790M mutations leading to changes in therapy. However, unique ctDNA alterations were generally associated with worse survival than no ctDNA alterations (HR 2.5, 95%CI 1.7-3.7) and even tissue-matched ctDNA alterations (HR 1.7, 95%CI 1.1-2.4). Of 98 unique ctDNA mutations, 48 (49%) were detectable in tissue at subthreshold levels, 12 (12%) were filtered by IMPACT as CH or germline, and 38 mutations (39%) were absent even at subthreshold levels. ctDNA alteration burden correlated with radiographic disease extent. In multivariate models with radiographic disease extent and other clinical variables, ctDNA alterations were the strongest independent predictor of worse survival. Conclusions: Our results show that ctDNA may match patients to life-prolonging targeted therapy and have prognostic importance. ctDNA may provide data about a patient’s cancer missed by spatially restricted tissue sequencing. Clinical trial information: NCT01775072.

Identifying treatment options for BRAFV600 wild-type metastatic melanoma: A SU2C/MRA genomics-enabled clinical trial

Although combination BRAF and MEK inhibitors are highly effective for the 40-50% of cutaneous metastatic melanomas harboring BRAFV600 mutations, targeted agents have been ineffective for BRAFV600wild-type (wt) metastatic melanomas. The SU2C Genomics-Enabled Medicine for Melanoma Trial utilized a Simon two-stage optimal design to assess whether comprehensive genomic profiling improves selection of molecular-based therapies for BRAFV600wt metastatic melanoma patients who had progressed on standard-of-care therapy, which may include immunotherapy. Of the response-evaluable patients, binimetinib was selected for 20 patients randomized to the genomics-enabled arm, and nine were treated on the alternate treatment arm. Response rates for 27 patients treated with targeted recommendations included one (4%) partial response, 18 (67%) with stable disease, and eight (30%) with progressive disease. Post-trial genomic and protein pathway activation mapping identified additional drug classes that may be considered for future studies. Our results highlight the complexity and heterogeneity of metastatic melanomas, as well as how the lack of response in this trial may be associated with limitations including monotherapy drug selection and the dearth of available single and combination molecularly-driven therapies to treat BRAFV600wt metastatic melanomas.

Next-Generation Sequencing of 487 Esophageal Adenocarcinomas Reveals Independently Prognostic Genomic Driver Alterations and Pathways

PURPOSE

To delineate recurrent oncogenic driver alterations and dysregulated pathways in esophageal adenocarcinoma and to assess their prognostic value.

EXPERIMENTAL DESIGN

We analyzed a large cohort of patients with lower esophageal and junctional adenocarcinoma, prospectively sequenced by MSK-IMPACT with high-quality clinical annotation. Patients were subdivided according to treatment intent, curative versus palliative, which closely mirrored clinical staging. Genomic features, alterations, and pathways were examined for association with overall survival using Cox proportional hazard models, adjusted for relevant clinicopathologic factors knowable at the time of diagnosis.

RESULTS

Analysis of 487 patients revealed 16 oncogenic driver alterations, mostly amplifications, present in ≥5% of patients. Patients in the palliative-intent cohort, compared with those in the curative-intent cohort, were more likely to have metastatic disease, ERBB2 amplifications, Cell-cycle and RTK-RAS pathway alterations, as well as a higher fraction of genome altered and rate of whole-genome doubling. In multivariable analyses, CDKN2A alterations, SMAD4 alterations, KRAS amplifications, Cell-cycle and TGFβ pathways, and overall number of oncogenic drivers were independently associated with worse overall survival. ERBB2 amplification was associated with improved survival, presumably due to trastuzumab therapy.

CONCLUSIONS

Our study suggests that higher levels of genomic instability are associated with more advanced disease in esophageal adenocarcinoma. Furthermore, CDKN2A, KRAS, and SMAD4 represent prognostic biomarkers, given their strong association with poor survival.

Targeting Germline- and Tumor-Associated Nucleotide Excision Repair Defects in Cancer

PURPOSE

Nucleotide excision repair (NER) gene alterations constitute potential cancer therapeutic targets. We explored the prevalence of NER gene alterations across cancers and putative therapeutic strategies targeting these vulnerabilities.

EXPERIMENTAL DESIGN

We interrogated our institutional dataset with mutational data from more than 40,000 patients with cancer to assess the frequency of putative deleterious alterations in four key NER genes. Gene-edited isogenic pairs of wild-type and mutant ERCC2 or ERCC3 cell lines were created and used to assess response to several candidate drugs.

RESULTS

We found that putative damaging germline and somatic alterations in NER genes were present with frequencies up to 10% across multiple cancer types. Both in vitro and in vivo studies showed significantly enhanced sensitivity to the sesquiterpene irofulven in cells harboring specific clinically observed heterozygous mutations in ERCC2 or ERCC3. Sensitivity of NER mutants to irofulven was greater than to a current standard-of-care agent, cisplatin. Hypomorphic ERCC2/3-mutant cells had impaired ability to repair irofulven-induced DNA damage. Transcriptomic profiling of tumor tissues suggested codependencies between DNA repair pathways, indicating a potential benefit of combination therapies, which were confirmed by in vitro studies.

CONCLUSIONS

These findings provide novel insights into a synthetic lethal relationship between clinically observed NER gene deficiencies and sensitivity to irofulven and its potential synergistic combination with other drugs.See related commentary by Jiang and Greenberg, p. 1833.

The Genetic Evolution of Treatment-Resistant Cutaneous, Acral, and Uveal Melanomas

PURPOSE

Melanoma is a biologically heterogeneous disease composed of distinct clinicopathologic subtypes that frequently resist treatment. To explore the evolution of treatment resistance and metastasis, we used a combination of temporal and multilesional tumor sampling in conjunction with whole-exome sequencing of 110 tumors collected from 7 patients with cutaneous (n = 3), uveal (n = 2), and acral (n = 2) melanoma subtypes.

EXPERIMENTAL DESIGN

Primary tumors, metastases collected longitudinally, and autopsy tissues were interrogated. All but 1 patient died because of melanoma progression.

RESULTS

For each patient, we generated phylogenies and quantified the extent of genetic diversity among tumors, specifically among putative somatic alterations affecting therapeutic resistance.

CONCLUSIONS

In 4 patients who received immunotherapy, we found 1-3 putative acquired and intrinsic resistance mechanisms coexisting in the same patient, including mechanisms that were shared by all tumors within each patient, suggesting that future therapies directed at overcoming intrinsic resistance mechanisms may be broadly effective.

Prevalence and Characterization of Biallelic and Monoallelic NTHL1 and MSH3 Variant Carriers From a Pan-Cancer Patient Population

NTHL1 and MSH3 have been implicated as autosomal recessive cancer predisposition genes. Although individuals with biallelic NTHL1 and MSH3 pathogenic variants (PVs) have increased cancer and polyposis risk, risks for monoallelic carriers are uncertain. We sought to assess the prevalence and characterize NTHL1 and MSH3 from a large pan-cancer patient population.

MATERIALS AND METHODS

Patients with pan-cancer (n = 11,081) underwent matched tumor-normal sequencing with consent for germline analysis. Medical records and tumors were reviewed and analyzed. Prevalence of PVs was compared with reference controls (Genome Aggregation Database).

RESULTS

NTHL1-PVs were identified in 40 patients including 39 monoallelic carriers (39/11,081 = 0.35%) and one with biallelic variants (1/11,081 = 0.009%) and a diagnosis of isolated early-onset breast cancer. NTHL1-associated mutational signature 30 was identified in the tumors of the biallelic patient and two carriers. Colonic polyposis was not identified in any NTHL1 patient. MSH3-PVs were identified in 13 patients, including 12 monoallelic carriers (12/11,081 = 0.11%) and one with biallelic MSH3 variants (1/11,081 = 0.009%) and diagnoses of later-onset cancers, attenuated polyposis, and abnormal MSH3-protein expression. Of the 12 MSH3 carriers, two had early-onset cancer diagnoses with tumor loss of heterozygosity of the wild-type MSH3 allele. Ancestry-specific burden tests demonstrated that NTHL1 and MSH3 prevalence was not significantly different in this pan-cancer population versus controls.

CONCLUSION

NTHL1 and MSH3 germline alterations were not enriched in this pan-cancer patient population. However, tumor-specific findings, such as mutational signature 30 and loss of heterozygosity of the wild-type allele, suggest the potential contribution of monoallelic variants to tumorigenesis in a subset of patients.

Treatment results from a phase I study of WST11 phototherapy (VTP) for upper tract urothelial carcinoma

460

Background: Localized treatment of upper tract urothelial carcinoma (UTUC) is technically challenging which limits the ability to provide organ-sparing therapies to preserve renal function and representing a serious unmet need. Vascular-targeted photodynamic therapy (VTP) using intravascular photosensitizing agent padeliporfin (WTS11) has demonstrated preclinical safety and effective tumoricidal activity. Endoluminal application of this therapy offers a promising alternative to radical surgery for patients with upper tract cancers seeking to avoid extirpative surgery. Herein we present early results from a phase I dose-finding study of padeliporfin VTP for UTUC. Methods: Fourteen patients with recurrent UTUC were treated with up to 2 sessions of endoscopic padeliporfin VTP treatment. Eligibility included residual or recurrent urothelial carcinoma of the ureter or renal pelvis failing prior endoscopic treatment in patients who were unable or unwilling to undergo surgical management by resection of the involved ureter or kidney. WST-11 was administered at 4mg/kg and infused over 10 minutes. An intermedic diode laser was used to illuminate tumors with light at a wavelength 753 nm through a flexible ureteroscope. A light dose escalation model was employed with increasing light fluence from 100mW/cm up to a maximally tolerated dose of 200mW/cm. The primary endpoint was the determination of maximally tolerated laser light fluence rate, with the secondary objective to evaluate treatment efficacy defined by absence of visible tumor and negative urine cytology following treatment. Results: Among 14 treated patients, complete response and tumor recurrence rates at 30 days after treatment were 64% and 29%, respectively. A second VTP treatment was performed in 6 (43%) patients. The efficacy rates were comparable among patients who received the intermediate and highest light fluence and between the first and second treatment. At the last follow-up (mean: 11.5 months), 13 patients (93%) had maintained their affected kidney and renal function was not significantly affected. Graded adverse events related to treatment were rigorously evaluated prospectively as the primary endpoint of the trial to be reported separately in detail. Treatment related toxicities were limited, and no ureteral strictures were identified with the procedure. No evidence of increased toxicity was identified among patients who received a second VTP treatment. Conclusions: WST11-VTP shows promising evidence of therapeutic treatment effect in low- and high-grade upper tract urothelial tumors with limited treatment related toxicity. These early results provide support for further investigation to evaluate the curative potential for this therapy in a planned multicenter trial. Clinical trial information: NCT03617003.

Genomic characterization of bladder cancer with variant histology

470

Background: Up to 25% of tumors are of pure variant or mixed urothelial and variant histology. The presence of variant histology may be associated with more advanced stage at presentation and a poorer response to systemic therapy. While histomorphologic assessment provides important prognostic information, genomic analysis of tumors can provide important insight into the biology of disease and inform treatment. In this analysis we performed genomic sequencing of tumors from patients with bladder cancer with variant histology. Methods: Our prospectively generated institutional cohort of molecularly profiled bladder and upper tract tumors contains over 2,000 samples including nearly 300 primary bladder tumor samples from patients with variant histology. Targeted sequencing with MSK-IMPACT was used to identify alterations in cancer-associated genes and to describe trends across variant subtypes. To explore and compare tumor and immune cell heterogeneity, single-cell RNA sequencing (scRNA-seq) was performed on a subset of specimens. Results: Our cohort included patients with pure urothelial carcinoma not otherwise specified (NOS), as well as squamous, small cell, pure adenocarcinoma and urothelial carcinoma with glandular differentiation, micropapillary, nested, and plasmacytoid variants. Compared with urothelial carcinoma NOS, nearly all small cell tumors had mutations in TP53, RB1, and TERT. Squamous tumors had similar mutational frequencies as urothelial carcinoma NOS. Pure adenocarcinoma had frequent mutations in TP53, KRAS, and PIK3CA, resembling colorectal adenocarcinomas, while urothelial carcinoma with glandular differentiation resembled NOS. Micropapillary variant commonly had ERBB2 amplifications. Nested variant was more commonly found to have RHOA mutations and FOXA1 amplifications. Finally, nearly all plasmacytoid variants had pathognomonic alterations in CDH1. To further explore heterogeneity in tumor and immune cell populations, scRNA-seq was performed on four samples from patients with urothelial carcinoma NOS, squamous, micropapillary, and nested variants, showing distinct tumor cell clusters and varying contributions of immune cells from each variant. Conclusions: While the distribution of oncogenic mutations differed among distinct histologic variants, a pathognomonic DNA alteration was not found for most variant histologic subtypes. Within the context of a larger effort to characterize bladder cancer with variant histology, scRNA-seq may reveal differences in immune cell population infiltrates. Further efforts will aim to characterize these cohorts with whole exome sequencing and mutational signatures, and increase the number of samples per histology and representation of variant histologies for scRNA-seq.

A phase I trial of chemoimmunotherapy combining bacillus Calmette-Guerin (BCG) and intravesical gemcitabine for patients with BCG-relapsing high-grade nonmuscle-invasive bladder cancer

TPS509

Background: Intravesical BCG is the most effective treatment for high-grade non-muscle invasive bladder cancer (NMIBC), yet recurrences are common. Patients with BCG-relapsing NMIBC are often re-treated with BCG or BCG with interferon (IFN) with an expected response rate of only 40–60%. Several studies show that a major mechanism of resistance to BCG is high levels of myeloid-derived suppressor cells (MDSCs) and regulatory T cells (Tregs) in the pretreatment tumor microenvironment. Gemcitabine is a commonly used intravesical treatment for NMIBC that, in addition to direct anti-tumor cytotoxic effects, may also reduce MDSCs and Tregs. Prior trials combining BCG with intravesical mitomycin C have shown improved efficacy over BCG alone but with higher toxicity. While gemcitabine has been shown to be better tolerated than mitomycin as an intravesical treatment, no study has looked at combined BCG and intravesical gemcitabine. We hypothesize that combining BCG and intravesical gemcitabine will be well tolerated and result in higher response rates by reducing levels of MDSCs and Tregs. A novel aspect of our trial design is the use of a modified continual reassessment method to more accurately identify the maximum tolerated dose instead of the traditional 3 + 3 design used in most NMIBC phase I trials. Methods: This is an investigator-initiated phase I trial (NCT04179162) that will study the safety of alternating intravesical gemcitabine and BCG. Inclusion and exclusion criteria are designed so most patients who would ordinarily be re-treated with BCG or BCG/IFN would be eligible. Patients must have recurrent high-grade NMIBC within 24 months of their last BCG treatment without meeting the criteria for BCG-unresponsive NMIBC. Intravesical gemcitabine is given twice a week on weeks 1, 4, 7, and 10, for a total of 8 doses. BCG (50 mg) is given once a week on weeks 2, 3, 5, 6, 8, and 9, for a total of 6 doses. The trial is monitored using a modified continual reassessment method with increasing dose levels of gemcitabine (500 mg, 1,000 mg, 1,500 mg, and 2,000 mg) being evaluated. Adverse events are assessed using the Common Terminology Criteria for Adverse Events version 5.0. The primary objective is to determine the maximum tolerated dose of this combination to inform our planned phase II trial. Correlative studies will look at the immunomodulating effects of gemcitabine by evaluating changes in immune cell populations in serial blood and urine specimens. Tissue and urine will also be evaluated for molecular determinants of response and resistance to the combination. The trial is open to enrollment with 10 of 25 planned patients accrued to date. Clinical trial information: NCT04179162.

Single cell RNA sequencing of upper tract urothelial carcinoma to reveal significant heterogeneity of the tumor and immune microenvironment

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Background: Upper tract urothelial carcinoma (UTUC) comprises 5-10% of urothelial malignancies but demonstrates unique clinical and molecular characteristics compared to urothelial carcinoma of the bladder. Prior investigations have used bulk profiling of tumor tissue to identify molecular subtypes, classifying the majority of UTUC as luminal and T-cell depleted. However, bulk sequencing does not allow for analysis of the significant heterogeneity known to be present in urothelial tumors. Single-cell RNA sequencing (scRNA-seq) allows examination of intra-tumoral heterogeneity, clonality, and the complex interactions of the immune tumor microenvironment (TME). We sought to apply this technology to better characterize UTUC and the TME. Methods: Single cell RNA sequencing (scRNA-seq) was performed on nine UTUC tissue specimens from six different patients collected fresh via ureteroscopic biopsy using an established institutional process and the 10X Genomics platform. Sequencing reads were normalized and analyzed using R/Seurat package. We assessed the composition of each tumor specimen with known marker genes for molecular subtypes (luminal, basal, squamous, EMT, and claudin-low). We then assessed the composition of immune cells in each specimen using known marker genes. We compared high- and low-grade specimens by subtype composition and immune cell infiltrates. Results: Lineage density analyses demonstrate the intra- and inter-tumoral heterogeneity of the nine endoscopic samples analyzed by molecular subtype composition. There is higher expression of luminal and claudin-low subtypes across all samples. The high-grade samples have higher expression of squamous markers. There is significant heterogeneity of immune cell infiltrates in seven specimens (two specimens were excluded due to low CD45+ cell counts). There is higher macrophage infiltration in high-grade samples, which was the only significant difference (Wilcoxon two-sided p-value = 0.05). Conclusions: This is the first known study using scRNA-seq expression analysis to characterize the notable heterogeneity of high and low-grade UTUC and the associated TME. Lineage density analysis demonstrates high luminal gene expression across samples, which has been demonstrated on prior bulk sequencing studies. The immune TME is also heterogeneous, with notable increased infiltration of macrophages in high-grade disease. There are unique limitations to performing and analyzing scRNA-seq of fresh UTUC tissue specimens, thus data should be interpreted cautiously. However, this study demonstrates the marked heterogeneity of UTUC tumors and frames our current approaches to bulk molecular subtyping of urothelial cancers and immune deconvolution. Further high-resolution studies are needed to characterize UTUC and inform bulk-sequencing efforts.

Germ cell tumors and associated hematologic malignancies evolve from a common shared precursor

Germ cell tumors (GCTs) are the most common cancer in men between the ages of 15 and 40. Although most patients are cured, those with disease arising in the mediastinum have distinctly poor outcomes. One in every 17 patients with primary mediastinal nonseminomatous GCTs develop an incurable hematologic malignancy and prior data intriguingly suggest a clonal relationship exists between hematologic malignancies and GCTs in these cases. To date, however, the precise clonal relationship between GCTs and the diverse additional somatic malignancies arising in such individuals have not been determined. Here, we traced the clonal evolution and characterized the genetic features of each neoplasm from a cohort of 15 patients with GCTs and associated hematologic malignancies. We discovered that GCTs and hematologic malignancies developing in such individuals evolved from a common shared precursor, nearly all of which harbored allelically imbalanced p53 and/or RAS pathway mutations. Hematologic malignancies arising in this setting genetically resembled mediastinal GCTs rather than de novo myeloid neoplasms. Our findings argue that this scenario represents a unique clinical syndrome, distinct from de novo GCTs or hematologic malignancies, initiated by an ancestral precursor that gives rise to the parallel evolution of GCTs and blood cancers in these patients.