Clinical and analytical validation of FoundationOne®CDx, a comprehensive genomic profiling assay for solid tumors

PPP2R1A mutations cause ATR inhibitor sensitivity in ovarian clear cell carcinoma

Identification of ARID1A/ATR synthetic lethality led to ATR inhibitor phase II trials in ovarian clear cell carcinoma (OCCC), a cancer of unmet need. Using multiple CRISPR-Cas9 mutagenesis and interference screens, we show that inactivation of protein phosphatase 2A (PP2A) subunits, including PPP2R1A, enhance ATRi sensitivity in ARID1A mutant OCCC. Analysis of a new OCCC cohort indicates that 52% possess oncogenic PPP2R1A p.R183 mutations and of these, one half possessed both ARID1A as well as PPP2R1A mutations. Using CRISPR-prime editing to generate new isogenic models of PPP2R1A mutant OCCC, we found that PPP2R1A p.R183W and p.R183P mutations cause ATRi-induced S phase stress, premature mitotic entry, genomic instability and ATRi sensitivity in OCCC tumour cells. p.R183 mutation also enhanced both in vitro and in vivo ATRi sensitivity in preclinical models of ARID1A mutant OCCC. These results argue for the assessment of PPP2R1A mutations as a biomarker of ATRi sensitivity.

comprehensive genomic profiling: a public health system perspective

INTRODUCTION

Comprehensive genomic profiling (CGP) is gaining ground in modern precision oncology for its ability to potentially analyze multiple tumor alterations and identify actionable ones, guiding targeted anticancer treatments. However, integrating CGP into healthcare systems demands consideration of the available evidence and collaboration between shareholders.

AREAS COVERED

This review explores CGP's cost-effectiveness and feasibility across diverse healthcare settings, based on searches in PubMed, Google Scholar, gray literature, and extensive snowballing. We further aimed to elucidate barriers to routine CGP implementation and discuss potential solutions.

EXPERT OPINION

Patients generally express satisfaction with CGP, especially if publicly funded, yet face difficulties in understanding test results, and managing lack of actionable mutations and access to novel treatment avenues. Physicians exhibit confidence in recommending and interpreting CGP for patients with refractory disease and considerable life expectancy and performance status, albeit acknowledging potential treatment delays. Health economic studies support CGP's cost-effectiveness, highlighting increased survival, productivity, reduced medical service utilization, and cost diversion to trial sponsors. Nonetheless, challenges persist, including reimbursement policies, limited testing accessibility, and the imperative for physician training and infrastructure enhancement. Addressing these issues through collaborative efforts and policy adjustments is paramount for realizing the full potential of CGP in advancing precision oncology.

Clinical Utility of Liquid-based Comprehensive Genomic Profiling (CGP) in Gastrointestinal Stromal Tumors (GIST)

Treatment for GIST focuses on tyrosine kinase inhibitors (TKI), whose selection depends on specific mutations. We sought to determine the clinical utility of liquid biopsy in advanced GIST. Liquid (n=181) (FoundationOne®Liquid CDx) and tissue (n=2,198) (FoundationOne® and FoundationOne®CDx) CGP of GIST were evaluated. The presence of circulating tumor DNA in liquid was determined via tumor fraction (TF), with elevated TF defined as TF ≥1%. Liquid CGP revealed 30% (54/181) of samples had an elevated TF, among which the prevalence of KIT and PDGFRA alterations were 89% (48/54) and 2% (1/54), respectively. In patient-matched tissue/liquid samples (n=49), positive percent agreement of driver alterations in liquid with elevated TF relative to tissue was 100%. 55% (42/77) of liquid samples with a KIT-driver mutation had a co-occurring imatinib-resistant alteration; a minority of cases harbored non-KIT mechanisms of resistance such as FGFR2 fusion, BRAF or EGFR alterations. The relative prevalence of imatinib-resistance KIT exon 13 and 17 mutations was enriched in liquid compared to tissue. Finally, in the liquid cohort, 2.2%, 1.7% and 1.1% of patients were predicted to harbor germline KIT, SDHx, or NF1 mutations, respectively. In conclusion, known driver and TKI-resistant mutations were identified in liquid biopsies of GIST patients with high concordance to tissue in the presence of elevated TF. Liquid biopsy may be valuable in the molecular classification and medical management of GIST.

The genomic landscape of metastatic clear-cell renal cell carcinoma and its prognostic value: a comprehensive analysis of a large real-world clinico-genomic database

BACKGROUND

Translating findings on the genomic landscape of metastatic clear-cell renal cell carcinoma (mccRCC) into clinical practice remains challenging. A better understanding of the molecular features of mccRCC could identify a prognostic and/or predictive role for ccRCC genomic alterations.

PATIENTS AND METHODS

In this real-world observational study based on the nationwide (US-based) de-identified Flatiron Health-Foundation Medicine, Inc. clinico-genomic database (FH-FMI-CGDB), we investigate the frequency and co-occurrence of genomic alterations in mccRCC patients and assess their prognostic role. Patients (n = 858) were adults diagnosed with mccRCC, with FH electronic health records between 2011 and 2022.

RESULTS

The top 10 mutated genes were VHL (73.9%), PBRM1 (42.4%), SETD2 (25.3%), CDKN2A (20.0%), BAP1 (16.4%), CDKN2B (16.0%), KDM5C (14.5%), TP53 (12.9%), PTEN (11.7%), and TERT (9.2%). Eight genes showed prognostic value: CDKN2A, CDKN2B, TP53, PTEN, NF2, PIK3CA, and MTAP were linked to worse prognosis, whereas PBRM1 was associated with better overall survival (OS). Two of the three identified gene clusters had prognostic value: cluster 1 (VHL, SETD2, PBRM1, KDM5C, NFE2L2) correlated with better OS [adjusted hazard ratio (aHR) 0.63, P < 0.001], whereas cluster 3 (CDKN2A, CDKN2B, BAP1, NF2, MTAP) correlated with shorter OS (aHR 1.36, P = 0.023).

CONCLUSION

We identified eight genes and two gene clusters with prognostic significance for mccRCC. Future research will explore the predictive value of gene clusters in various treatments.

Comprehensive genomic profiling can predict response to neoadjuvant chemotherapy in triple-negative breast cancer

BACKGROUND

The rate of pathological complete response (pCR) after neoadjuvant chemotherapy (NACT) in triple-negative breast cancer (TNBC) varies, and adjuvant therapy treatment for residual cancer remains a challenge. The aim of our study was to assess the added value of FoundationOne®CDx (F1CDx) testing in the non-metastatic TNBC in predicting responses to NACT and disease outcomes.

METHODS

Ninety-three eligible patients with stage II-III TNBC were treated with NACT without immunotherapy. Response to NACT was evaluated postoperatively. Comprehensive genomic profiling with NGS-based molecular test F1CDx was performed on diagnostic biopsies (N = 93). Hierarchical clustering and logistic regression were applied for data analysis.

RESULTS

Genomic profiling and data clustering revealed heterogeneous genetic landscapes of TNBC with subsets displaying multilayered co-amplifications of oncogenes and overlapping changes in crucial signaling pathways. TP53 mutations were detected in 95 % of all TNBCs. BRCA1/BRCA2 mutations were significant molecular factors in predicting favorable responses to NACT (OR = 0.09, p = 0.002), while CCNDs co-mutations with FGFs (OR = 13.4, p = 0.016) and PI3Ks family mutations in AR-positive cases (OR = 6.1, p = 0.008) - poor responses. Low tumor mutational burden (TMB) ≤ 3 (OR = 9.4, p = 0.009) was a significant factor for the disease progression after NACT.

CONCLUSIONS

This study suggests that comprehensive CDx testing can be explored as a prognostic tool in early-stage TNBC to predict responses to NACT and disease progression. Based on these results, genomic analysis should be performed early in the patient journey, possibly guiding adjuvant treatment choices and participation in randomized clinical trials, mainly when pCR is not achieved, as the ultimate goal is improving patient outcomes.

A Case of Intracranial Mesenchymal Tumor, FET::CREB Fusion-positive, Diagnosed by Genomic Profiling with FoundationOne CDx

Intracranial mesenchymal tumor FET::cyclic adenosine monophosphate response element-binding fusion-positive is a soft tissue tumor with an extremely rare intracranial occurrence. Histological diagnosis is sometimes difficult, requiring confirmation of characteristic fusion genes. The patient was a 45-year-old male who presented with a chief complaint of pain and an abnormal sensation in the right trigeminal nerve area, in whom a neoplastic lesion in Meckel's cave was noted. The preoperative diagnoses included meningioma and schwannoma. The tumor was extirpated as much as possible, and the tumor tissue showed a high proliferative potential with rhabdoid features, raising the suspicion of a rhabdoid meningioma. However, immunostaining was positive for desmin and cluster of differentiation 99, suggesting the possibility of angiomatoid fibrous histiocytoma. For diagnosis, Ewing sarcoma breakpoint region1 gene-cyclic adenosine monophosphate response element-binding 1 fusion and Ewing sarcoma breakpoint region1 gene-activating transcription factor 1 fusion were examined at our institution, but were undetectable and did not lead to a diagnosis. Genomic profiling with FoundationOne CDx (Foundation Medicine, Cambridge, MA, USA) confirmed Ewing sarcoma breakpoint region1 gene-cyclic adenosine monophosphate response element modulator fusion and a diagnosis of intracranial mesenchymal tumor FET::cyclic adenosine monophosphate response element-binding fusion-positive was made. Diagnosis of intracranial mesenchymal tumor FET::cyclic adenosine monophosphate response element-binding fusion-positive requires both histological examination and confirmation of the fusion gene. Genomic profiling using the FoundationOne CDx is also useful when the fusion gene cannot be sufficiently confirmed at an individual's institution.

MDM2 inhibition is associated with the emergence of TP53-altered clonal hematopoiesis

Murine double minute 2 (MDM2) inhibitors have shown promising activity in TP53-wild type tumors and are under active investigation across a spectrum of malignancies. Herein, we report a 51-year-old female with MDM2-amplified, TP53-wild type adenoid cystic carcinoma who was treated with a MDM2 inhibitor and developed persistent pancytopenia despite drug discontinuation. Her pancytopenia was associated with 20 distinct pathogenic TP53 mutations in peripheral blood and bone marrow not present in drug-resistant tumor tissue. Plasma TP53 mutations were similarly detected among 4 other patients treated at our institution, with the number of mutations correlating strongly with duration of treatment. This case suggests that MDM2 inhibitors are associated with TP53 clonal hematopoiesis, which may confer a risk of subsequent myeloid malignancy. As multiple MDM2 inhibitor trials are ongoing, our findings underscore the need for further investigation into the potential long-term deleterious effects of these inhibitors in the hematopoietic stem and progenitor compartment.

FGFR2 fusions assessed by NGS, FISH, and immunohistochemistry in intrahepatic cholangiocarcinoma

BACKGROUND

FGFR2 fusion has become a promising therapeutic target in iCCAs; however, the procedure for screening FGFR2 fusion has not been conventionally developed.

METHODS

FGFR2 fusion was identified using DNA + RNA-based NGS and FISH, and the concordance between DNA + RNA-based NGS, FISH, and IHC was compared.

RESULTS

FGFR2 fusions were detected in 9 out of 76 iCCAs (11.8%). The consistency of FISH and DNA + RNA-based NGS for FGFR2 fusions was high (κ value = 0.867, P = 0.001), while the consistency of IHC and DNA + RNA-based NGS was lower (κ value = 0.464, P = 0.072). All nine FGFR2 fusion-positive iCCAs were MSS with a median TMB of 2.1 mut/Mb, and only one had a CPS (PD-L1) above 5. Two FGFR2 fusion-positive iCCA patients were treated with and benefited from FGFR inhibitor therapy.

CONCLUSIONS

FGFR2 fusion should be assessed for advanced iCCA patients. We recommend DNA + RNA-based NGS as the preferred option to supply all possible therapeutic targets. FISH should be preferred if the tumor sample is insufficient for NGS or if the patient is inclined to receive FGFR inhibitors promptly. Although IHC is not the preferred method to identify FGFR2 fusion, it might be used as preliminary screening for FGFR2 alterations if the hospital cannot offer NGS or FISH, and the results need to be validated before FGFR2 inhibitors treatment.

Homologous recombination deficiency testing in patients with high grade ovarian cancer: factors influencing test success

INTRODUCTION

Testing for tumor BRCA mutations and homologous recombination deficiency (HRD) is recommended for all patients with advanced high-grade epithelial ovarian cancer. Delays in the HRD testing process can significantly affect the treatment offered to patients.

METHODS

HRD testing pathways and sampling processes were analyzed for tests sent from a tertiary gynae-oncology referral center between December 2020 and January 2023.

RESULTS

A total of 148 hRD tests were performed in 125 patients. The overall success rate of HRD testing was 69.6%. The success rates of obtaining results were: from diagnostic image-guided biopsy 66.7% (n = 40/60), at primary surgery 91.5% (n = 42/47), and at interval debulking surgery 51.2% (n = 21/41). The use of a larger 16-gauge needle used at image-guided biopsy produced a 100% success rate. Of 148 tests carried out, the median time for result was 28 days (range 14-158 days), with only 27% returned results in 21 or fewer days. In successful tests, 44.7% were classified as HRD-positive. 97% of patients with HRD-positive tumors treated at the center received a PARP inhibitor as part of their first-line maintenance treatment.

CONCLUSIONS

By optimizing the factors affecting HRD test success, we can obtain faster results and offer patients appropriate treatment at earlier time points to improve patient outcomes.

Molecular tumor board in patients with metastatic breast cancer

PURPOSE

Comprehensive genomic profiling is becoming increasingly important in the management of patients with metastatic breast cancer (mBC). Real-world clinical outcomes from applying molecular tumor boards (MTBs) recommendations in this context remain limited. Accordingly, we conducted a retrospective, single-institution analysis to evaluate the clinical impact of discussing patients affected by mBC at the MTB.

METHODS

Clinicogenomic data of patients affected by mBCs referred to the European Institute of Oncology MTB between August 2019 and December 2023 were reviewed. Genomic alterations were classified by ESCAT framework. Clinical outcomes of patients showing actionable alterations and receiving molecular-matched therapy (MMT) were compared to those receiving standard therapy (ST).

RESULTS

Ninety-six patients were included. Following MTB discussion, genetic counseling was recommended in 27% (n = 26) of patients, while additional molecular analyses were requested in 25% (n = 24) cases. Fifty-six patients (58%) displayed at least one actionable alteration. For patients with available follow-up (n = 50), 32 (64%) received MMTs and 18 (36%) ST. No differences in real-world progression-free survival (rwPFS) (4.07 months [95% CI 2.14-8.28] vs. 3.12 months [95% CI 1.51-NE], P = 0.8) and 12-month overall survival (OS) (58% [95%CI 43-78] vs. 57% [95%CI 34-97), P = 0.9) were observed between the MMT- and ST-group. Level I ESCAT alterations yielded longer rwPFS (5.82 months [95% CI 3.12-8.41]) compared to ESCAT II (2.14 months [95%CI 1.61-NE]) and ESCAT III (2.10 months [95% CI 2.04-NE]; P = 0.03). Twenty-four percent of patients showed a PFS2/PFS1 ratio > 1.3 from MMT.

CONCLUSION

Molecular tumor boards can provide additional treatment options for patients affected by mBC. Besides treatment recommendations, MTBs also have the utility to assess the validity of discussed genomic reports and to identify alterations worthy of genetic counseling.

Real-world genomic landscape of colon and rectal cancer

MAPK signaling activation is an important driver event in colorectal cancer (CRC) tumorigenesis that informs therapy selection, but detection by liquid biopsy can be challenging. We analyze real-world comprehensive genomic profiling (CGP) data to explore the landscape of alterations in BRAF or RAS in CRC patients (N = 51 982) and co-occurrence with other biomarkers. A pathogenic RAS or BRAF alteration was found in 63.2% and 57.9% of colon and rectal cancer samples, respectively. In a subset of 140 patients with both tissue- and liquid-based CGP, the sensitivity of liquid for results found by tissue was 100% when ctDNA tumor fraction was at least 1%, illustrating the utility of tissue and liquid biopsy in detecting driver alterations in CRC.

Histopathology and proteomics are synergistic for high-grade serous ovarian cancer platinum response prediction

Patients with High-Grade Serous Ovarian Cancer (HGSOC) exhibit varied responses to treatment, with 20-30% showing de novo resistance to platinum-based chemotherapy. While hematoxylin-eosin (H&E)-stained pathological slides are used for routine diagnosis of cancer type, they may also contain diagnostically useful information about treatment response. Our study demonstrates that combining H&E-stained whole slide images (WSIs) with proteomic signatures using a multimodal deep learning framework significantly improves the prediction of platinum response in both discovery and validation cohorts. This method outperforms the Homologous Recombination Deficiency (HRD) score in predicting platinum response and overall patient survival. Our study suggests that histology and proteomics contain complementary information about biological processes determining response to first line platinum treatment in HGSOC. This integrative approach has the potential to improve personalized treatment and provide insights into the therapeutic vulnerabilities of HGSOC.

Homologous recombination deficiency in ovarian cancer: Global expert consensus on testing and a comparison of companion diagnostics

BACKGROUND

Poly (ADP ribose) polymerase inhibitors (PARPis) are a treatment option for patients with advanced high-grade serous or endometrioid ovarian carcinoma (OC). Recent guidelines have clarified how homologous recombination deficiency (HRD) may influence treatment decision-making in this setting. As a result, numerous companion diagnostic assays (CDx) have been developed to identify HRD. However, the optimal HRD testing strategy is an area of debate. Moreover, recently published clinical and translational data may impact how HRD status may be used to identify patients likely to benefit from PARPi use. We aimed to extensively compare available HRD CDx and establish a worldwide expert consensus on HRD testing in primary and recurrent OC.

METHODS

A group of 99 global experts from 31 different countries was formed. Using a modified Delphi process, the experts aimed to establish consensus statements based on a systematic literature search and CDx information sought from investigators, companies and/or publications.

RESULTS

Technical information, including analytical and clinical validation, were obtained from 14 of 15 available HRD CDx (7 academic; 7 commercial). Consensus was reached on 36 statements encompassing the following topics: 1) the predictive impact of HRD status on PARPi use in primary and recurrent OC; 2) analytical and clinical validation requirements of HRD CDx; 3) resource-stratified HRD testing; and 4) how future CDx may include additional approaches to help address unmet testing needs.

CONCLUSION

This manuscript provides detailed information on currently available HRD CDx and up-to-date guidance from global experts on HRD testing in patients with primary and recurrent OC.

Genomic analysis of comprehensive next generation sequencing data to explore the criteria for MET amplification as an actionable biomarker in NSCLC

INTRODUCTION

MET amplification (METamp) can be a de novo or acquired resistance driver; however, the definition of METamp that best captures patients who may respond to targeted therapy remains debated. We explored the genomic landscape of METamp NSCLC including degree of amplification, co-drivers, amplicon size, and outcomes to MET inhibitors.

METHODS

Hybrid-capture NGS-based genomic profiling from 88,547 tissue and 12,428 liquid NSCLC samples were queried for METamp (copy number (CN) ≥ ploidy + 4, or amplification ratio (AmpRatio; [CN/sample ploidy] ≥ 3). A nationwide de-identified real-world (rw) clinico-genomic database (CGDB) of NGS results linked to deidentified, electronic health record-derived clinical data was used to assess treatment and outcomes.

RESULTS

Among 10,760 evaluable patients in CGDB, 362 (3.4%) had a METamp. In targeted therapy-naïve cases, MET AmpRatio negatively correlated with non-METex14 co-drivers (median 4.1 vs 2.9, p < 0.0001). MET AmpRatio was not significantly correlated with tumor mutational burden (p = 0.79) but was inversely correlated with amplicon size (p < 0.001). Among paired METamp tissue samples, 8/30 had METamp detected in liquid; higher tumor fraction and AmpRatio were associated with liquid detection. Among 39 METamp patients receiving MET inhibitors, longer median real-world progression free survival was observed with MET AmpRatio ≥ 3 vs < 3 (4.9 vs. 1.7mos, HR 0.53 [95 %CI:0.21-1.3]).

CONCLUSIONS

MET AmpRatio positively correlated with focal amplification and absence of co-drivers and trended with increased benefit from MET inhibitors. Further studies evaluatingcombinatorial data including MET AmpRatio, amplicon size and presence of other potential drivers, as predictive biomarkers for therapies targeting MET amplification in NSCLC are warranted.

A phase Ib study evaluating the c-MET inhibitor INC280 (capmatinib) in combination with bevacizumab in patients with high-grade glioma

Background

To improve survival in patients with high-grade glioma, INC280 (capmatinib) a highly selective and potent oral inhibitor of the MET receptor with robust central nervous system (CNS) penetration, was evaluated in combination with bevacizumab (BEV).

Methods

There were 2 phases, dose-escalation (3+3 design) and dose-expansion, which included patients (1) who progressed during or after first-line therapy (no prior BEV), (2) who progressed during or after second-line therapy with BEV, and (3) who had unresectable high-grade glioma (no prior BEV).

Results

Sixty-four patients with high-grade glioma were treated; 18 in escalation cohorts and 46 in expansion Cohorts A (21), B (15), and C (10). The maximum-tolerated dose (MTD) was not reached and the RP2D was 400 mg capmatinib PO BID (800 mg daily). Treatment continued for a median of 14 weeks and up to ~6 years in one patient. Common treatment-related adverse events (65% ≤ Grade 2) included fatigue, peripheral edema, nausea, diarrhea, ALT increased, and constipation. Headaches and seizures occurred in 11 patients; Grade 3+ events included Grade 3 headache (1) and Grade 3 seizures (4). There were no treatment-related deaths. The 12 responders to treatment (2 CRs [1 pt in escalation and 1 pt in Cohort A] and 10 PRs [2 pts in escalation and A = 6, B = 1, and C = 1]) had a median duration of response of 9.2 months. Two patients with durable responses (CR >5 years, PR >1 year) did not harbor baseline c-MET alterations.

Conclusion

Capmatinib + BEV was well-tolerated but had no clear signal of activity in c-MET non-activated high-grade glioma.

Molecular Features of Diffuse Large B-Cell Lymphoma Associated With Primary Treatment Resistance

Diffuse large B-cell lymphoma (DLBCL) patients that fail to achieve a complete metabolic response with frontline immunochemotherapy have a poor prognosis. Genomic profiling has led to a broader understanding of the molecular drivers in DLBCL, but it is unknown how well current classifiers identify patients that will experience primary treatment resistance (PTR). Using whole exome and RNA sequencing data from newly diagnosed DLBCL patients, we evaluated the genomic landscape of PTR and compared it to that of non-PTR DLBCL. We found a significant increase in the frequency of TP53 (34% vs. 15%, p = 0.005) and ARID1A mutations (21% vs. 7%, p = 0.007) in PTR cases, with pathway analysis further demonstrating a downregulation of TP53 and an increase in chromatin modifying pathways. These results suggest that TP53 and ARID1A may be key mediators of PTR and important pathways contributing to the poor outcomes. We found that the current molecular classifiers were unable to identify PTR cases at diagnosis. However, our newly identified high-risk signature identified 46% of PTR cases at diagnosis. Overall, these results contribute to our understanding of the genomic landscape of patients with primary treatment resistance.

Whole genome and transcriptome analysis of pancreatic acinar cell carcinoma elucidates mechanisms of homologous recombination deficiency and unravels novel relevant fusion events

Pancreatic acinar cell carcinoma (PACC) is a rare pancreatic tumor with a heterogeneous clinical course and, except for radical surgery, limited treatment options. We present a comprehensive study encompassing whole-genome and RNA sequencing of 7 tumor samples from 3 metastatic PACC patients to further delineate its genomic landscape and potential therapeutic implications. Our findings reveal distinct signatures of homologous recombination deficiency (HRD) in patients harboring pathogenic germline BRCA1/2 and FANCL mutations, demonstrating favorable responses to poly (ADP-ribose) polymerase 1 (PARP) inhibitors with prolonged disease-free intervals. Additionally, we first describe structural variants in PACC, including BRCA1::TRIM47 fusion and another variant impacting FANCC, both events related to HRD, and we also identify alterations in the mitogen-activated protein kinase (MAPK) pathway, including RAF1 duplication as well as novel BRAF::SORBS2 and MAP7D2::SND1 gene fusions, offering potential targets for therapy. Our study underscores the importance of genome and transcriptome-wide profiling of PACC, to help guide personalized treatment strategies to improve patient outcomes.

Breast cancer brain metastases genomic profiling identifies alterations targetable by immune-checkpoint and PARP inhibitors

Understanding the genomic landscape of breast cancer brain metastases (BCBMs) is key to developing targeted treatments. In this study, targetable genomic profiling was performed on 822 BCBMs, 11,988 local breast cancer (BC) biopsies and 15,516 non-central nervous system (N-CNS) metastases (all unpaired samples) collected during the course of routine clinical care by Foundation Medicine Inc (Boston, MA). Clinically relevant genomic alterations were significantly enriched in BCBMs compared to local BCs and N-CNS metastases. Homologous recombination deficiency as measured by BRCA1/2 alteration prevalence and loss-of-heterozygosity and immune checkpoint inhibitor (ICI) biomarkers [Tumor mutation burden (TMB)-High, Microsatellite instability (MSI)-High, PD-L1/L2)] were significantly more prevalent in BCBM than local BC and N-CNS. High PD-L1 protein expression was observed in ER-negative/HER2-negative BCBMs (48.3% vs 50.0% in local BCs, 21.4% in N-CNS). Our data highlights that a high proportion of BCBMs are potentially amenable to treatment with targeted therapeutic agents including PARP inhibitors and ICIs.

Analysis of PD1, LAG3, TIGIT, and TIM3 expression in human lung adenocarcinoma reveals a 25-gene signature predicting immunotherapy response

Immune checkpoint inhibitors (ICIs) have advanced the treatment of non-small cell lung cancer (NSCLC). This study evaluates the predictive value of CD8+ T cell exhaustion in patients with lung adenocarcinoma treated with ICIs. By analyzing tumor samples from 166 patients through multiplex immunofluorescence, we quantify tumor-infiltrating lymphocytes (TILs) expressing exhaustion markers programmed cell death-1 (PD1), lymphocyte activation gene 3 (LAG3), T cell immunoreceptor with Ig and ITIM domains (TIGIT), and T cell immunoglobulin and mucin domain 3 (TIM3). Their co-expression is associated with ICI resistance, irrespective of programmed cell death ligand-1 (PD-L1) status. We also identify a 25-gene signature indicative of CD8+ T cell exhaustion with high predictive accuracy for ICI response. Validated using several datasets from various clinical trials, this signature accurately predicts ICI responsiveness. Our findings highlight T cell exhaustion's significance in lung adenocarcinoma responses to ICIs and suggest the 25-gene signature as a potential universal biomarker to reinforce precision medicine. This was registered under Clinical Trial registration number NCT02534649.

Current transcriptome database and biomarker discovery for immunotherapy by immune checkpoint blockade

Immune checkpoint blockade (ICB) has revolutionized the current immuno-oncology and significantly improved clinical outcome for cancer treatment. Despite the advancement in clinics, only a small subset of patients derives immune response to the ICB therapy. Therefore, a robust predictive biomarker that identifies potential candidate becomes increasingly crucial in delivering this technology to the public. In this review, we first discuss the biomarkers that focus on tumor genome, tumor microenvironment and tumor-host interaction. Then, we compare existing databases for biomarker discovery for ICB response. We also present IOhub - an interactive web portal that incorporates 36 bulk and 10 single-cell transcriptome datasets for benchmark analysis of the current biomarkers. Finally, we highlight the trending interest in antibody drug conjugate and combination treatment and their use in precision immuno-oncology.

Direct comparison of an ultrasensitive real-time PCR assay with droplet digital PCR for the detection of PIK3CA hotspot mutations in primary tumors, plasma cell-free DNA and paired CTC-derived gDNAs

Introduction

Detection of PIK3CA mutations in primary tumors and liquid biopsy samples is of increasing importance for treatment decisions and therapy resistance in many types of cancer. The aim of the present study was to directly compare the efficacy of a relatively inexpensive ultrasensitive real-time PCR with the well-established and highly sensitive technology of ddPCR for the detection of the three most common hotspot mutations of PIK3CA, in exons 9 and 20, that are all of clinical importance in various types of cancer.

Patients and methods

We analyzed 42 gDNAs from primary tumors (FFPEs), 29 plasma-cfDNA samples, and 29 paired CTC-derived gDNAs, all from patients with ER+ metastatic breast cancer, and plasma from 10 healthy donors. The same blood draws were used for CTC isolation using EpCAM beads for positive immunomagnetic enrichment. All FFPEs and plasma-cfDNA samples were analyzed in parallel for PIK3CA mutations by ultrasensitive real-time PCR assay and droplet digital PCR.

Results

In gDNAs from FFPEs, using ultrasensitive real-time PCR, the p.E545K mutation was detected in 22/42(52.4%), and the p.E542K and p.H1047R mutations were detected in 14/42(33.3%) and 16/42(38.1%), respectively. Using ddPCR, the p.E545K mutation was detected in 22/42(52.4%), p.E542K in 17/42(40.5%), and p.H1047R in 19/42(45.2%) samples, revealing a concordance between the two methodologies of 81%, 78.6% and 78.6% for each mutation respectively. In plasma-cfDNA, using ultrasensitive real-time PCR, the p.E545K mutation was detected in 11/29(38%) and both p.E542K and p.H1047R mutations in 2/29(6.9%).In the same plasma-cfDNA samples using ddPCR, p.E545K was detected in 1/29(3.5%), p.E542K in 2/29(6.9%), and p.H1047R in 3/29(10.5%) samples, revealing a concordance of 65.5%,100% and 93.1% for each mutation respectively. In paired CTC-derived gDNAs p.E545K was detected in 11/29(38%), p.E542K in 3/29(10.3%), and p.H1047R in 7/29(24.1%) samples.

Conclusions

This low-cost, high-throughput and ultrasensitive real-time PCR assay provides accurate and specific detection of PIK3CA hotspot mutations in liquid biopsy samples and gives similar results to ddPCR. This assay can be performed in labs where digital PCR instrumentation is not available. In CTC-derived gDNA and paired plasma-cfDNA, PIK3CA mutations detected were not identical, revealing that CTC and plasma-cfDNA give complementary information.

Genomic Profiling in Glioma Patients to Explore Clinically Relevant Markers

Gliomas are a heterogeneous group of brain tumors, among which the most aggressive subtype is glioblastoma, accounting for 60% of cases in adults. Available systemic treatment options are few and ineffective, so new approaches to therapies for glioblastoma are in high demand. In total, 131 patients with diffuse glioma were studied. Paired tumor–normal samples were sequenced on the Illumina platform; the panel included 812 genes associated with cancer development. Molecular profiles in clinically distinct groups were investigated. In low-grade glioma (LGG) patients (n = 18), the most common mutations were IDH1/2 (78%), ATRX (33%), TP53 (44%), PIK3CA (17%), and co-deletion 1p/19q (22%). In high-grade glioma (HGG) patients (n = 113), more frequently affected genes were CDKN2A/B (33%), TERTp (71%), PTEN (60%), TP53 (27%), and EGFR (40%). The independent predictors of better prognosis were tumor grade and IDH1/2 mutations. In IDH—wildtype glioblastoma patients, a history of other precedent cancer was associated with worse overall survival (OS), while re-operation and bevacizumab therapy increased OS. Also, among genetic alterations, TERTp mutation and PTEN deletion were markers of poor prognosis. Nine patients received molecular targeted therapy, and the results were evaluated. The search for molecular changes associated with tumor growth and progression is important for diagnosis and choice of therapy.

Clinical utility of a comprehensive genomic profiling test for patient with advanced biliary tract cancer

BACKGROUND

Biliary tract cancer (BTC) comprises a heterogeneous group of malignancies with poor prognosis because of the limited treatment options. With the recent advances of next generation sequencing technologies, comprehensive genomic profiling (CGP) tests have been widely introduced into daily clinical practice.

PATIENTS AND METHODS

We performed a retrospective, multicenter, observation cohort study. The genomic and clinical data of 85 BTC patients, who underwent CGP testing from August 2021 to September 2023, were analyzed.

RESULTS

There were 62 (73%) cases in which treatment recommendations were raised during expert meetings, including 34 intrahepatic cholangiocarcinoma (ICC), 20 extrahepatic cholangiocarcinoma (ECC) and 8 gall bladder carcinoma (GBC). The drug accessibility rate of the BTC patients was 15.3% (13 cases): ten ICCs, two ECCs, and one GBC. Five ICC patients (three male and two female) with the FGFR2 fusion gene were treated with pemigatinib. Those patients who received a genomically matched therapy had significantly longer median overall survival than those patients who not received. (n = 13; not reached [95% CI not reached-not reached] vs n = 72; 8.6 months [95% CI 6.6-10.0]; hazard ratio 0.24 [95% CI 0.12-0.49], p = 0.013). The median observation period of pemigatinib treatment was 15.4 months (range 10.1-27.4). The responses were classified as PR in three patients, SD in one patient and PD in one patient. The median progression free survival is 9.0 months. No patient had grade 3/4 AEs requiring discontinuation of the treatment.

CONCLUSION

The drug accessibility rate of ICC is high and pemigatinib is effective and well-tolerated in ICC patients harboring FGFR2 gene fusions.

Mutational landscape of Japanese patients with oral squamous cell carcinoma from comprehensive genomic profiling tests

OBJECTIVES

Oral squamous cell carcinoma (OSCC) is the most common subtype of head and neck squamous cell carcinoma (HNSCC). Treatment options for OSCC are currently limited owing to the lack of identified therapeutic targets. In this study, we aimed to analyze the genomic profiles of Japanese patients with OSCC and compare them to those of patients with HNSCC to identify potential therapeutic targets.

MATERIALS AND METHODS

We extracted the clinical and genomic information of patients with OSCC (n = 242) and those with other HNSCC (n = 402) who underwent comprehensive genomic profiling tests under the National Health Insurance between June 2019 and April 2024 from the Center for Cancer Genomics and Therapeutics database.

RESULTS

The most frequent genomic alterations identified in OSCC were TP53 (85.5 %), followed by TERT (62.4 %), CDKN2A (41.3 %), FGF19 (24.9 %), and CCND1 (23.6 %). FGF19 and CCND1 were co-amplified, and CDKN2A and CDKN2B were co-deleted. The frequencies of TERT, HRAS, and CASP8 alterations were the highest in OSCC among all HNSCC subtypes. The frequency of EGFR alterations was substantially higher in adolescent and young adults than older patients with OSCC. Genes associated with genomic integrity and the RTK-RAS pathway were frequently altered in OSCC.

CONCLUSION

This study analyzed the genomic profiles of patients with OSCC in Japan and the genetic differences between OSCC and other HNSCC subtypes. This analysis offers insights into the development of personalized therapeutics for OSCC.

Lung-MAP Next-Generation Sequencing Analysis of Advanced Squamous Cell Lung Cancers (SWOG S1400)

INTRODUCTION

Squamous cell cancer (SqCC) is a lung cancer subtype with few targeted therapy options. Molecular characterization, that is, by next-generation sequencing (NGS), is needed to identify potential targets. Lung Cancer Master Protocol Southwest Oncology Group S1400 enrolled patients with previously treated stage IV or recurrent SqCC to assess NGS biomarkers for therapeutic sub-studies.

METHODS

Tumors underwent NGS using Foundation Medicine's FoundationOne research platform, which sequenced the exons and/or introns of 313 cancer-related genes. Mutually exclusive gene set analysis and Selected Events Linked by Evolutionary Conditions across Human Tumors were performed to identify mutually exclusive and co-occurring gene alterations. Comparisons were performed with data on 495 lung SqCC downloaded from The Cancer Genome Atlas. Cox proportional hazards models were used to assess associations between genetic variants and survival.

RESULTS

NGS data are reported for 1672 patients enrolled on S1400 between 2014 and 2019. Mutually exclusive gene set analysis identified two non-overlapping sets of mutually exclusive alterations with a false discovery rate of less than 15%: NFE2L2, KEAP1, and PARP4; and CDKN2A and RB1. PARP4, a relatively uncharacterized gene, showed three frequent mutations suggesting functional significance: 3116T>C (I1039T), 3176A>G (Q1059R), and 3509C>T (T1170I). When taken together, NFE2L2 and KEAP1 alterations were associated with poorer survival.

CONCLUSIONS

As the largest dataset to date of lung SqCC profiled on a clinical trial, the S1400 NGS dataset establishes a rich resource for biomarker discovery. Mutual exclusivity of PARP4 and NFE2L2 or KEAP1 alterations suggests that PARP4 may have an uncharacterized role in a key pathway known to impact oxidative stress response and treatment resistance.

Relevant factors for policy concerning comprehensive genomic profiling in oncology: stakeholder perspectives

BACKGROUND

Comprehensive genomic profiling (CGP) can identify targets beyond standard of care, potentially revolutionizing personalized cancer management. However, conducting well designed studies in this rapidly evolving field is complex and demands time and investments. Consequently, the total added value of CGP remains uncertain. Clinical benefit and costs often are driving factors in coverage decisions. Recently, five additional factors were identified in the literature that can influence the choice for targeted profiling vs. CGP, specifically: "feasibility", "test journey patient/physician", "wider implications of diagnostic results", "organization of laboratories", and "scientific spillover". The objective of the current study is to examine the role and importance assigned to these five additional factors for a comprehensive technology assessment by different stakeholders.

METHODS

Purposive sampling was used to identify respondents from 4 stakeholder groups (i.e., medical specialists, molecular specialists, patient representatives, and policymakers) from different regions and hospital types (academic vs. non-academic) in the Netherlands. In semi-structured interviews, respondents scored the importance to decision-making of the five factors on a 0 (not important) to 5 (essential) scale. Reasoning behind the scores were elicited using open-ended follow-up questions. Transcripts were independently double-coded by two researchers using thematic analysis.

RESULTS

Nineteen stakeholders (100% response rate; medical specialists (n = 7), molecular specialists (n = 7), patient representatives (n = 2), and policymakers (n = 3)) were interviewed. We observed differences between stakeholders in the relative importance assigned to the factors (range of median importance scores: 2-5). Overall, "wider implications of diagnostic results", primarily CGP's potential to identify additional treatment options, was deemed the most important factor alongside clinical benefit and costs in decision-making about CGP (median range: 3-5). While the "organization of laboratories" was considered less important (median range: 3-4), opposing arguments and preferences regarding the organization of laboratories were identified, with participants from academic centers preferring a centralized approach whilst non-academics preferred a decentralized approach.

CONCLUSIONS

Stakeholders deemed "wider implications of diagnostic results", "feasibility", and "test journey" the most important considerations for decision-making about targeted profiling vs. CGP alongside clinical benefit and costs. For policy decision-making, it is important to understand the arguments behind the heterogeneous opinions, often related to the setting they originate from.

De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data

In cancer, genetic and transcriptomic variations generate clonal heterogeneity, leading to treatment resistance. Long-read single-cell RNA sequencing (LR scRNA-seq) has the potential to detect genetic and transcriptomic variations simultaneously. Here, we present LongSom, a computational workflow leveraging high-quality LR scRNA-seq data to call de novo somatic single-nucleotide variants (SNVs), including in mitochondria (mtSNVs), copy-number alterations (CNAs), and gene fusions, to reconstruct the tumor clonal heterogeneity. Before somatic variants calling, LongSom re-annotates marker gene based cell types using cell mutational profiles. LongSom distinguishes somatic SNVs from noise and germline polymorphisms by applying an extensive set of hard filters and statistical tests. Applying LongSom to human ovarian cancer samples, we detected clinically relevant somatic SNVs that were validated against matched DNA samples. Leveraging somatic SNVs and fusions, LongSom found subclones with different predicted treatment outcomes. In summary, LongSom enables de novo variant detection without the need for normal samples, facilitating the study of cancer evolution, clonal heterogeneity, and treatment resistance.

Histopathologic, genomic, transcriptomic, and functional characteristics of eight melanocytic tumors with BRAF fusions showing stronger MAPK pathway activation compared to BRAF V600E tumors

BACKGROUND

Activating BRAF gene alterations are central to melanocytic tumor pathogenesis. A small, emerging subset of melanocytic tumors driven by BRAF fusions has distinct therapeutic implications and has been described to have Spitzoid morphology patterns. However, such morphological patterns do not encompass all cases, and little is known about the functional molecular events.

MATERIALS AND METHODS

We conducted a retrospective search through our molecular archives to identify melanocytic tumors with BRAF fusions. We reviewed clinical, histopathological, and genomic features. We further explored transcriptomic and protein-level findings.

RESULTS

Histopathologic patterns varied, with many cases without a distinctive pattern. We identified novel and diverse BRAF gene fusion partners. Differential transcriptomic analysis between low-risk BRAF fusion tumors and reference BRAF V600E tumors showed no differentially expressed genes. However, quantitatively stronger MAPK pathway activation of BRAF fusion tumors over BRAF V600E tumors was demonstrated by statistically significant stronger staining of p-ERK immunohistochemistry. Gene-specific RNA analysis shows comparable BRAF transcript levels between the two groups.

DISCUSSION AND CONCLUSION

The quantitatively stronger activation of the MAPK pathway of BRAF fusion tumors, instead of qualitatively different transcriptomes, may account for the morphology difference from conventional BRAF V600E tumors. BRAF fusions likely act through dysregulated protein function rather than RNA upregulation related to the characteristics of the fusion partners.

Widespread Adoption of Precision Anticancer Therapies After Implementation of Pathologist-Directed Comprehensive Genomic Profiling Across a Large US Health System

PURPOSE

Precision therapies and immunotherapies have revolutionized cancer care, with novel genomic biomarker-associated therapies being introduced into clinical practice rapidly, resulting in notable gains in patient survival. Despite this, there is significant variability in the utilization of tumor molecular profiling that spans the timing of test ordering, comprehensiveness of gene panels, and clinical decision support through therapy and trial recommendations.

METHODS

To standardize testing, we designed a pathologist-directed test ordering system at the time of diagnosis using a 523-gene DNA/RNA hybrid comprehensive genomic profiling (CGP) panel and extensive clinical decision support tools. To comprehensively characterize the clinical impact of this protocol, we developed a novel natural language processing (NLP)-based approach to extract clinical features from physician chart notes. We assessed test actionability rates, therapy choice, and outcomes across a set of 3,216 patients with advanced cancer.

RESULTS

We observed 49% of patients had at least one actionable genomic biomarker-driven-approved and/or guideline-recommended targeted or immunotherapy (IO) and 53% of patients would have been eligible for a precision therapy clinical trial from three large basket trials. When assessing CGP versus an in silico 50-gene panel, 67% of tumors compared with 33% harbored actionable alterations including clinical trials. Among patients with 6 months or more of follow-up, over 52% received a targeted therapy (TT) or IO, versus 32% who received conventional chemotherapy alone. Furthermore, patients receiving TT had significantly improved overall survival compared with patients receiving chemotherapy alone (P < .001).

CONCLUSION

Overall, these data represent a major shift in standard clinical practice toward molecularly guided treatments (targeted and immunotherapies) over conventional systemic chemotherapy. As guidelines continue to evolve and more precision therapeutics gain approval, we expect this gap to continue to widen.

Single-Hit and Multi-hit PIK3CA Short Variant Genomic Alterations in Clinically Advanced Prostate Cancer: A Genomic Landscape Study

BACKGROUND

Tumors harboring two or more PIK3CA short variant (SV) ("multi-hit") mutations have been linked to improved outcomes with anti-PIK3CA-targeted therapies in breast cancer. The landscape and clinical implications of multi-hit PIK3CA alterations in clinically advanced prostate cancer (CAPC) remains elusive.

OBJECTIVE

To evaluate the genomic landscape of single-hit and multi-hit PIK3CA genomic alterations in CAPC.

PATIENTS AND METHODS

The Foundation Medicine FoundationCore database was used to identify 19,978 CAPC tumors that underwent hybrid capture-based comprehensive genomic profiling to evaluate all classes of genomic alterations (GA) and determine tumor mutational burden (TMB), microsatellite instability (MSI), genomic ancestry, single-base substitution mutational signatures, and homologous recombination deficiency signature (HRDsig). Tumor cell PD-L1 expression was determined by IHC (Dako 22C3).

RESULTS

18,741 (93.8%) tumors were PIK3CA wild type (WT), 1155 (5.8%) featured single PIK3CA SV, and 82 (0.4%) featured multi-hit PIK3CA SVs. Single-hit (6.6 versus 3.8; p < 0.0001) and multi-hit (12.8 versus 3.8; p < 0.0001) featured more driver GA per tumor than PIK3CA WT CAPC, as well as higher prevalence of MMR mutational signature, MSI high status, and TMB levels versus PIK3CA WT (p < 0.0001). Other differences in GA included higher frequencies of GA in BRCA2 in multi-hit versus WT (18.3% versus 8.5%; p = 0.0191), ATM in multi-hit versus WT (13.4% versus 5.6%; p = 0.02) and PTEN in single-hit versus WT (40.2% versus 30.1%; p < 0.0001). Homologous recombination deficiency signatures were higher in PIK3CA WT versus single-hit (11.2% versus 7.6%; p = 0.0002). There were no significant differences in PD-L1 expression among the three groups.

CONCLUSIONS

Identification of multi-hit PIK3CA GA in CAPC highlights a potentially unique phenotype that may be associated with response to anti-PIK3CA targeted therapy and checkpoint inhibition, supporting relevant clinical trial designs.

Research on biomarkers using innovative artificial intelligence systems in breast cancer

Cancer is highly diverse and heterogeneous. Accurate and rapid analysis of the characteristics of individual cancer cells, using a complex array of big data that includes various clinicopathological features and molecular mechanisms, is crucial for advancing precision medicine. In recent years, experts in biomedical sciences and data sciences have explored the potential of artificial intelligence (AI) to analyze such extensive data sets. The next phase of AI-based medical research on cancer should focus on the practical applications of AI tools and how they can be effectively used in actual medical research settings. Recently, translational research that leverages AI and comprehensive genetic analysis data has emerged as a significant research focus. This field represents an opportunity for groundbreaking discoveries to be shared globally. To further precision medicine in clinical practice, it is vital to develop sophisticated AI tools for cancer research. These tools should not only identify potential therapeutic targets through comprehensive genetic analysis but also predict therapeutic outcomes in clinical settings.

Comparison of Results from Two Commercially Available In-House Tissue-Based Comprehensive Genomic Profiling Solutions: Research Use Only AVENIO Tumor Tissue Comprehensive Genomic Profiling Kit and TruSight Oncology 500 Assay

Increased adoption of personalized medicine has brought comprehensive genomic profiling (CGP) to the forefront. However, differences in assay, bioinformatics, and reporting systems and lack of understanding of their complex interplay are a challenge for implementation and achieving uniformity in CGP testing. Two commercially available, tissue-based, in-house CGP assays were compared, in combination with a tertiary analysis solution in a research use only (RUO) context: the AVENIO Tumor Tissue CGP RUO Kit paired with navify Mutation Profiler (RUO) software and the TruSight Oncology 500 RUO assay paired with PierianDx Clinical Genomics Workspace software. Agreements and differences between the assays were assessed for short variants, copy number alterations, rearrangements, tumor mutational burden, and microsatellite instability, including variant categorization and clinical trial-matching (CTM) recommendations. Results showed good overall agreement for short variant, known gene fusion, and microsatellite instability detection. Important differences were obtained in tumor mutational burden scoring, copy number alteration detection, and CTM. Differences in variant and biomarker detection could be explained by bioinformatic approaches to variant calling, filtering, tiering, and normalization; differences in CTM, by underlying reported variants and conceptual differences in system parameters. Thus, distinctions between different approaches may lead to inconsistent results. Complexities in calling, filtering, and interpreting variants illustrate key considerations for implementation of any high-quality CGP in the laboratory and bringing uniformity to genomic insight results.

Personalized Medicine in Histiocytic Disorders: Novel Targets in Patients Without MAPK Alterations

PURPOSE

BRAF and MEK inhibitors are standard treatments in histiocytic disorders, such as Erdheim-Chester disease (ECD). Some patients lack MAPK-pathway alterations, making these treatments less effective.

METHODS

We describe three patients with histiocytic disorders who have novel non-MAPK pathway alterations. These alterations were studied through genomic and in silico analyses when applicable, then treated with off-label medications rationally selected on the basis of genomic alterations.

RESULTS

Patient 1 had rapidly progressive ECD involving the CNS. A CSF1R in-frame deletion (p.S560_P566del) was identified, and in silico modeling predicted a gain-of-function mutation. This alteration was targeted with pexidartinib, which led to a clinical complete response (CR) within 2 months, and a partial response (PR) on imaging after 3 months. After 15 months, the disease became resistant to pexidartinib and transformed to histiocytic sarcoma. Patient 2 has skin-only involvement of a xanthogranuloma disorder. A KIF5B-FGFR1 fusion was identified on RNA sequencing and targeted with pemigatinib. At 24 months of follow-up, she remains in a clinical PR. Patient 3 has ECD involving the bone marrow, gastrointestinal tract, and subcutaneous tissues. A MEF2C-FLT3 fusion was identified and targeted with sorafenib. He achieved a clinical CR and radiographic PR within 3 months, which has continued for 30 months.

CONCLUSION

We report three patients with histiocytic disorders harboring novel alterations who had sustained responses to off-label kinase inhibitors specific to their histiocytic disorder. Pathogenic variants outside of the MAPK pathway, including variants of unknown significant, may be targeted with readily available small molecules.

Highly Multiplexed Tissue Imaging in Precision Oncology and Translational Cancer Research

Precision oncology tailors treatment strategies to a patient's molecular and health data. Despite the essential clinical value of current diagnostic methods, hematoxylin and eosin morphology, immunohistochemistry, and gene panel sequencing offer an incomplete characterization. In contrast, highly multiplexed tissue imaging allows spatial analysis of dozens of markers at single-cell resolution enabling analysis of complex tumor ecosystems; thereby it has the potential to advance our understanding of cancer biology and supports drug development, biomarker discovery, and patient stratification. We describe available highly multiplexed imaging modalities, discuss their advantages and disadvantages for clinical use, and potential paths to implement these into clinical practice. Significance: This review provides guidance on how high-resolution, multiplexed tissue imaging of patient samples can be integrated into clinical workflows. It systematically compares existing and emerging technologies and outlines potential applications in the field of precision oncology, thereby bridging the ever-evolving landscape of cancer research with practical implementation possibilities of highly multiplexed tissue imaging into routine clinical practice.

Brachial plexus peripheral nerve sheath tumors (PNSTs): clinical and surgical management in the pediatric population

PURPOSE

Peripheral nerve sheath tumors (PNSTs) are rare in pediatric patients, especially in the brachial plexus. Research on PNSTs is lacking. This article presents a retrospective cohort study of pediatric patients diagnosed and treated with PNSTs, specifically brachial plexus tumors.

METHODS

All pediatric patients intervened in a single center between 2007 and 2023 with brachial plexus tumors were systemically analyzed.

RESULTS

Eleven pediatric patients with 14 brachial plexus PNSTs were studied. The gender distribution was 64% female and 36% male, with an average age of 10.7 years. Ninety-one percent had a previous NF-1 diagnosis. Right brachial plexus presented a higher prevalence (64%). Pain, Tinel's sign, and stiffness masses were common during diagnosis. Motor deficits were noted in 43% of the patients. Surgery was indicated for symptoms, particularly pain and rapid growth, increasing malignancy risk. Due to suspected malignancy, an en bloc resection with safety margins was performed. Among the patients, 57% received a histopathological diagnosis of MPNST (malignant peripheral nerve sheath tumor). Treatment included radiotherapy and chemotherapy. Clinical follow-up was conducted for all cases, involving clinical and oncological evaluations for all MPNSTs.

CONCLUSIONS

This article present a series of pediatric brachial plexus tumors, especially in NF-1, and emphasizes the importance of thorough evaluation for this group. Swift diagnosis is crucial in pediatrics, enabling successful surgery for small lesions with limited neurological symptoms, improving long-term outcomes. Prompt referral to specialized services is urged for suspected masses, irrespective of neurological symptoms. Benign tumor postsurgical progression shows better outcomes than MPNSTs, with complete resection as the primary goal. Needle-guided biopsy is not recommended.

Clinical value of comprehensive genomic profiling on clinical trial enrollment for patients with advanced solid tumors

The use of biomarker testing to inform treatment decisions has emerged as a standard of care in multiple cancer types. However, the rates of patients with genomic testing results in hand to inform treatment decision-making remain variable. Here, we studied the impact of comprehensive genomic profiling (CGP) on clinical trial enrollment rates in patients with advanced-stage non-small cell lung, colorectal, breast, and prostate cancer using a real-world clinicogenomic database. On average, clinical trial enrollment in the therapy line immediately after CGP report receipt was 5.4%, which represents a 3.0 percentage point increase compared to therapy lines preceding CGP report receipt, supporting a meaningful association between CGP report availability and increased clinical trial enrollment.

Low PD-L1 expression, MAP2K2 alterations, and enriched HPV gene signatures characterize brain metastases in head and neck squamous cell carcinoma

BACKGROUND

Brain metastasis (BM) is a rare but severe complication of head and neck squamous cell carcinoma (HNSCC), with limited knowledge of molecular characteristics and immunogenicity.

METHODS

We analyzed 61 cases of HNSCC-BM from three academic institutions (n = 24) and Foundation Medicine Inc (FMI, n = 37). A subset of cases underwent next-generation sequencing, multiple immunofluorescence, and proximity ligation sequencing. Gene enrichment analysis compared alterations in FMI BM samples (n = 37) with local samples (n = 4082).

RESULTS

Demographics included: median age of 59 years, 75% male, 55% current/former smokers, 75% oropharyngeal primary, and 67% human papillomavirus (HPV) +. ATM (54%), KMT2A (54%), PTEN (46%), RB1 (46%), and TP53 (46%) were frequently altered in BM samples from academic centers (62% HPV/p16+). Structural rearrangements ranged from 9 to 90 variants by proximity ligation sequencing. BMs had low densities of CD8+, PD-1+, PD-L1+, and FOXP3 + cells, and 92% had PD-L1 combined positive scores < 1%. CDKN2A (40.5%), TP53 (37.8%), and PIK3CA (27.0%) alterations were common in the FMI BMs (51% HPV+). MAP2K2 alterations and HPV + signature were enriched in FMI BMs compared to local tumors (11.8% vs. 6.4%, P = 0.005 and 51.25% vs. 26.11%, P = 0.001 respectively), and pathogenic TSC1 inactivating mutations were enriched in local tumors (67.3% vs. 37.8%, P = 0.008). Median overall survival from BM diagnosis was 9 months (range 0-27).

CONCLUSIONS

HNSCC patients with BM frequently have oropharyngeal primary sites and are HPV+. Common molecular alterations in BM samples, including targetable PIK3CA and ATM, were identified. MAP2K2 alterations were enriched and densities of immune cells were low, highlighting potential targets for further research and immunotherapy considerations.

Beat-AML 2024 ELN-refined risk stratification for older adults with newly diagnosed AML given lower-intensity therapy

ABSTRACT

Although the 2022 European LeukemiaNet (ELN) acute myeloid leukemia (AML) risk classification reliably predicts outcomes in younger patients treated with intensive chemotherapy, it is unclear whether it applies to adults ≥60 years treated with lower-intensity treatment (LIT). We aimed to test the prognostic impact of ELN risk in patients with newly diagnosed (ND) AML aged ≥60 years given LIT and to further refine risk stratification for these patients. A total of 595 patients were included: 11% had favorable-, 11% intermediate-, and 78% had adverse-risk AML. ELN risk was prognostic for overall survival (OS) (P < .001) but did not stratify favorable- from intermediate-risk (P = .71). Within adverse-risk AML, the impact of additional molecular abnormalities was further evaluated. Multivariable analysis was performed on a training set (n = 316) and identified IDH2 mutation as an independent favorable prognostic factor, and KRAS, MLL2, and TP53 mutations as unfavorable (P < .05). A "mutation score" was calculated for each combination of these mutations, assigning adverse-risk patients to 2 risk groups: -1 to 0 points ("Beat-AML intermediate") vs 1+ points ("Beat-AML adverse"). In the final refined risk classification, ELN favorable- and intermediate-risk were combined into a newly defined "Beat-AML favorable-risk" group, in addition to mutation scoring within the ELN adverse-risk group. This approach redefines risk for older patients with ND AML and proposes refined Beat-AML risk groups with improved discrimination for OS (2-year OS, 48% vs 33% vs 11%, respectively; P < .001), providing patients and providers additional information for treatment decision-making.

Tectal glioma: clinical, radiological, and pathological features, and the importance of molecular analysis

Tectal glioma (TG) is a rare lower grade glioma (LrGG) that occurs in the tectum, mainly affecting children. TG shares pathological similarities with pilocytic astrocytoma (PA), but recent genetic analyses have revealed distinct features, such as alterations in KRAS and BRAF. We conducted a retrospective review of cases clinically diagnosed as TG and treated at our institute between January 2005 and March 2023. Six cases were identified and the median age was 30.5 years. Four patients underwent biopsy and two patients underwent tumor resection. Histological diagnoses included three cases of PA, one case of astrocytoma, and two cases of high-grade glioma. The integrated diagnosis, according to the fifth edition of the World Health Organization Classification of Tumours of the central nervous system, included two cases of PA and one case each of diffuse high-grade glioma; diffuse midline glioma H3 K27-altered; glioblastoma; and circumscribed astrocytic glioma. Among the three patients who underwent molecular evaluation, two had KRAS mutation and one had H3-3A K27M mutation. Our results demonstrate the diverse histological and molecular characteristics of TG distinct from other LrGGs. Given the heterogeneous pathological background and the risk of pathological progression in TG, we emphasize the importance of comprehensive diagnosis, including molecular evaluation.

Spatial oncology: Translating contextual biology to the clinic

Microscopic examination of cells in their tissue context has been the driving force behind diagnostic histopathology over the past two centuries. Recently, the rise of advanced molecular biomarkers identified through single cell profiling has increased our understanding of cellular heterogeneity in cancer but have yet to significantly impact clinical care. Spatial technologies integrating molecular profiling with microenvironmental features are poised to bridge this translational gap by providing critical in situ context for understanding cellular interactions and organization. Here, we review how spatial tools have been used to study tumor ecosystems and their clinical applications. We detail findings in cell-cell interactions, microenvironment composition, and tissue remodeling for immune evasion and therapeutic resistance. Additionally, we highlight the emerging role of multi-omic spatial profiling for characterizing clinically relevant features including perineural invasion, tertiary lymphoid structures, and the tumor-stroma interface. Finally, we explore strategies for clinical integration and their augmentation of therapeutic and diagnostic approaches.

Therapeutic vulnerabilities and pan-cancer landscape of BRAF class III mutations in epithelial solid tumors

BACKGROUND

Kinase-impaired class III BRAF mutations have recently received attention as a possible prognostic factor and therapeutic target. Class III BRAF variants differ from class I and class II mutations in terms of mechanism of pathway activation and therapeutic vulnerabilities. Genomic landscape analyses of tumors in large real-world cohorts represent a great opportunity to further characterize tumor-related molecular events and treatment vulnerabilities, however, such data is not yet available for tumors with BRAF class III mutations.

METHODS

We investigated the pan-cancer genomic landscape of BRAF class III mutations in 376,302 patients. Patients had comprehensive genomic profiling either by FoundationOne® or FoundationOne®CDx from formalin-fixed, paraffin embedded tissue biopsies. 2 patient cases that harbored BRAF class III mutations who demonstrated dramatic response to anti-EGFR treatment were presented.

RESULTS

BRAF class III mutations are likely to co-occur with RAF1, NRAS and HRAS alterations, while concomitant KRAS alterations were rare. Moreover, we found that alterations that predict resistance to anti-EGFR agents were significantly less common in tumors harboring BRAF class III mutations, which is of great importance as anti-EGFR therapies are a potential targeted treatment option in these tumors.

DISCUSSION

Our findings suggest a heterogenous interplay of oncogenic alterations in BRAF class III mutated tumors and have important implications for the molecular mechanisms of carcinogenesis while revealing potential therapeutic vulnerabilities.

HIGHLIGHTS

Tumors harboring BRAF class III (BRAF vIII) mutations comprise a novel subset with distinct genomic heterogeneity. BRAF vIII mutations may sensitize tumors to anti-EGFR treatments. BRAF vIII alterations show significantly less co-occurrence with alterations that predict resistance to anti-EGFR agents. Rare tumors with limited therapy options should be screened for BRAF vIII mutations as they may benefit from anti-EGFR agents.

Real-world pan-tumor comprehensive genomic profiling sample adequacy and success rates in tissue and liquid specimens

Real-world success rate of liquid and tissue-based comprehensive genomic profiling (CGP) is unknown. We analyzed real-world pan-tumor cohorts that underwent CGP during clinical care via FoundationOne CDx (F1CDx) and FoundationOne Liquid CDx (F1LCDx) to determine tissue and liquid sample adequacy based on tumor type. Pan-tumor presequencing adequacy was high (>90%) by both tissue-based F1CDx (median: 92.3%; range: 88.2%-96.9%) and liquid-based F1LCDx (median: 94.8%; range: 86.6%-96.7%). Similarly, postsequencing analysis revealed that most tissue and liquid samples yielded successful sequencing results with a median sequencing success rate of 97.9% and 98.1% for F1CDx and F1LCDx, respectively. One exception is central nervous system (CNS) tumors, for which F1CDx had dramatically higher sample sufficiency (96.9%) and postsequencing success rate (97.0%) compared with F1LCDx (86.6% and 92.9%, respectively). The pan-tumor median sample-to-success rate was 90.4% (range: 84.8%-94.4%) for F1CDx. The equivalent rate for F1LCDx was slightly higher at 93.2% (range: 80.4%-95.7%). Conversely, when examining the prevalence of F1LCDx results with high tumor fraction (TF≥1%), the sample-to-high TF results rate was dramatically lower (median: 37.7%, range: 2.1% [CNS tumors]-46.0%). In conclusion, except in CNS tumors or when accounting for liquid TF, success rates of F1CDx and F1LCDx are equivalently high. These results may guide informed decision on when to pursue tissue vs liquid testing of patients with cancer.

Amplification of MYC and Its Enhancer Correlates With Genetic Ancestry in Lung Squamous Cell Carcinoma

PURPOSE

In lung squamous cell carcinoma (LUSC), Black patients show significantly higher incidence and lower overall survival than White patients. Although socioeconomic factors likely contribute to this survival disparity, genomic factors have yet to be elucidated in LUSC.

METHODS

Using 416 LUSC tumor samples in the Cancer Genome Atlas (TCGA), we assessed genomic and transcriptomic profiles by ancestry. We replicated our analyses in pan-cancer data from TCGA, the American Association of Cancer Research (AACR) Genomics Evidence Neoplasia Information Exchange (GENIE), and Columbia University Medical Center.

RESULTS

We found increased MYC amplification, LUSC-specific MYC enhancer amplification, and chromosome arm 8q (chr8q) gain to be significantly associated with genetic AFR (African) ancestry in LUSC in TCGA. Furthermore, expression of MYC target genes was significantly enriched in AFR samples. Local ancestry analysis identified correlation of chr8q gain with AFR ancestry at the MYC locus in TCGA. We also found a significant correlation between chr8q and AFR ancestry in multiple cancer types and pan-cancer in TCGA. Similarly, in a pan-cancer subset of AACR GENIE data, we found a significant correlation between chr8q gain and race.

CONCLUSION

Together, our data suggest that ancestry may influence amplification of not only MYC but also its enhancer in LUSC. They also suggest a role for genetic ancestry in chr8q aneuploidy in cancer. These studies further define and expand patients who may benefit from future anti-MYC therapeutic approaches.

Intratumoral Escherichia Is Associated With Improved Survival to Single-Agent Immune Checkpoint Inhibition in Patients With Advanced Non-Small-Cell Lung Cancer

PURPOSEThe impact of the intratumoral microbiome on immune checkpoint inhibitor (ICI) efficacy in patients with non-small-cell lung cancer (NSCLC) is unknown. Preclinically, intratumoral Escherichia is associated with a proinflammatory tumor microenvironment and decreased metastases. We sought to determine whether intratumoral Escherichia is associated with outcome to ICI in patients with NSCLC.PATIENTS AND METHODSWe examined the intratumoral microbiome in 958 patients with advanced NSCLC treated with ICI by querying unmapped next-generation sequencing reads against a bacterial genome database. Putative environmental contaminants were filtered using no-template controls (n = 2,378). The impact of intratumoral Escherichia detection on overall survival (OS) was assessed using univariable and multivariable analyses. The findings were further validated in an external independent cohort of 772 patients. Escherichia fluorescence in situ hybridization (FISH) and transcriptomic profiling were performed.RESULTSIn the discovery cohort, read mapping to intratumoral Escherichia was associated with significantly longer OS (16 v 11 months; hazard ratio, 0.73 [95% CI, 0.59 to 0.92]; P = .0065) in patients treated with single-agent ICI, but not combination chemoimmunotherapy. The association with OS in the single-agent ICI cohort remained statistically significant in multivariable analysis adjusting for prognostic features including PD-L1 expression (P = .023). Analysis of an external validation cohort confirmed the association with improved OS in univariable and multivariable analyses of patients treated with single-agent ICI, and not in patients treated with chemoimmunotherapy. Escherichia localization within tumor cells was supported by coregistration of FISH staining and serial hematoxylin and eosin sections. Transcriptomic analysis correlated Escherichia-positive samples with expression signatures of immune cell infiltration.CONCLUSIONRead mapping to potential intratumoral Escherichia was associated with survival to single-agent ICI in two independent cohorts of patients with NSCLC.

Barriers and facilitators to next-generation sequencing use in United States oncology settings: a systematic review

Aim: Next-generation sequencing (NGS) of solid tumors can inform treatment decisions; however, uptake remains low. This objective of this systematic review was to identify barriers to and facilitators of NGS in US oncology settings.Materials & methods: Embase and MEDLINE were searched in March 2023 for articles published from 2012 to 2023 on barriers and facilitators of NGS adoption for solid tumors. Surveys, interviews and observational studies were eligible. Studies on genetic testing for hereditary cancers and non-US studies were excluded. The Motheral scale, Joanna Briggs Institute critical appraisal checklist and McGill Mixed Methods Appraisal Tool were used to assess study quality. Data were synthesized narratively.Results: Twenty-one studies were included. Study participants were clinicians, payers and administrators. Key barriers included complex reimbursement processes and uncertainties around clinical utility. Including recommendations for NGS in clinical practice guidelines was a key facilitator, although insurance policies were often more restrictive than guideline recommendations.Conclusion: Uptake of NGS is increasing but barriers remain. Changes to the current reimbursement frameworks are needed to increase access to NGS. The impact of implementing the 2018 National Coverage Determination, which allows access to NGS for all Medicare beneficiaries with advanced cancer, is not yet evident in the published literature.

Advancing quantitative PCR with color cycle multiplex amplification

Quantitative PCR (qPCR) is the gold standard for detection and quantitation of known DNA targets, but the scarcity of spectrally distinct fluorophores and filter sets limits the number of detectable targets. Here, we introduce color cycle multiplex amplification (CCMA) to significantly increase the number of detectable DNA targets in a single qPCR reaction using standard instrumentation. In CCMA, presence of one DNA target species results in a pre-programmed pattern of fluorescence increases. This pattern is distinguished by cycle thresholds (Cts) through rationally designed delays in amplification. For example, we design an assay wherein Staphylococcus aureus sequentially induces FAM, then Cy5.5, then ROX fluorescence increases with more than 3 cycles between each signal. CCMA offers notably higher potential for multiplexing because it uses fluorescence permutation rather than combination. With 4 distinct fluorescence colors, CCMA theoretically allows the detection of up to 136 distinct DNA target sequences using fluorescence permutation. Experimentally, we demonstrated a single-tube qPCR assay screening 21 sepsis-related bacterial DNA targets in samples of blood, sputum, pleural effusion and bronchoalveolar lavage fluid, with 89% clinical sensitivity and 100% clinical specificity, showing its potential as a powerful tool for advanced quantitative screening in molecular diagnostics.

FGFR2-fusions define a clinically actionable molecular subset of pancreatic cancer

Genomic alterations in fibroblast growth factor receptor (FGFR) genes are present in a small number of metastatic pancreatic ductal adenocarcinomas (PDAC) and may represent an emerging subgroup of patients likely to benefit from FGFR targeted therapies. Here we present four FGFR2 fusion-positive metastatic PDAC patients who exhibited durable responses or disease control to FGFR kinase inhibitors. Utilizing our custom FGFR focused cell-free DNA assay, FGFR-Dx, we serially monitored variant allele fractions of FGFR2 fusions during FGFR inhibitor treatment and observed dynamic changes correlating with clinical responses. Genomic analysis of 30,229 comprehensively profiled pancreatic cancers revealed FGFR1-3 fusions in 245 cases, an incidence of 0.81%. FGFR fusions were generally mutually exclusive from other known oncogenes. Our findings provide clinical evidence for identifying and treating FGFR2 fusion-positive PDAC patients with FGFR targeted therapy.

Pan-tumor validation of a NGS fraction-based MSI analysis as a predictor of response to Pembrolizumab

Microsatellite instability high (MSI-H) and mismatch repair deficient (dMMR) tumor status have been demonstrated to predict patient response to immunotherapies. We developed and validated a next-generation sequencing (NGS)-based companion diagnostic (CDx) to detect MSI-H solid tumors via a comprehensive genomic profiling (CGP) assay, FoundationOne®CDx (F1CDx). To determine MSI status, F1CDx calculates the fraction of unstable microsatellite loci across >2000 loci using a fraction-based (FB) analysis. Across solid tumor types, F1CDx demonstrated a high analytical concordance with both PCR (n = 264) and IHC (n = 279) with an overall percent agreement (OPA) of 97.7% and 97.8%, respectively. As part of a retrospective bridging clinical study from KEYNOTE-158 Cohort K and KEYNOTE-164, patients with MSI-H tumors as determined by F1CDx demonstrated an objective response rate (ORR) of 43.0% to pembrolizumab. In real-world cancer patients from a deidentified clinicogenomic database, F1CDx was at least equivalent in assessing clinical outcome following immunotherapy compared with MMR IHC. Demonstrated analytical and clinical performance of F1CDx led to the pan-tumor FDA approval in 2022 of F1CDx to identify MSI-H solid tumor patients for treatment with pembrolizumab. F1CDx is an accurate, reliable, and FDA-approved method for the identification of MSI-H tumors for treatment with pembrolizumab.

A signal-seeking phase 2 study of Trastuzumab emtansine in tumours harbouring HER2 amplification or mutation

This single-arm phase II non-randomised trial (ACTRN12619001265167) evaluated trastuzumab emtansine in solid cancers with HER2 amplification or mutation detected by comprehensive genomic profiling. The primary objective was objective response (OR), while secondary objectives included the time to progression (TTP) on study to TTP on prior therapy ratio, progression-free survival (PFS) and overall survival (OS). The cohort included 16 tumours with HER2 mutations (group 1) and 16 with HER2 amplification (group 2). After 17 months median follow-up, ORs occurred in 19% of group 1 (1 salivary gland carcinoma (SGC), 2 lung cancers) and 25% of group 2 (3 SGCs, 1 uterine carcinoma). Fourteen of 29 TTP-evaluable patients achieved a TTP ratio ≥1.3, including 10 without an OR. Median PFS and OS were 4.5 (95% CI 2.1-7.0) and 18.2 months (95% CI 8.1-not reached) respectively. Trastuzumab emtansine showed modest ORs and a favourable change in disease trajectory in select HER2-altered solid cancers.