Quantifying the Expanding Landscape of Clinical Actionability for Patients with Cancer

Ancestral Differences in Anticancer Treatment Efficacy and Their Underlying Genomic and Molecular Alterations

SIGNIFICANCE

Our study charts a global landscape of ancestry-associated differences in therapeutic efficacy, highlighting the importance of considering ancestry in anticancer therapies.

Decoding the functional impact of the cancer genome through protein-protein interactions

Acquisition of genomic mutations enables cancer cells to gain fitness advantages under selective pressure and, ultimately, leads to oncogenic transformation. Interestingly, driver mutations, even within the same gene, can yield distinct phenotypes and clinical outcomes, necessitating a mutation-focused approach. Conversely, cellular functions are governed by molecular machines and signalling networks that are mostly controlled by protein-protein interactions (PPIs). The functional impact of individual genomic alterations could be transmitted through regulated nodes and hubs of PPIs. Oncogenic mutations may lead to modified residues of proteins, enabling interactions with other proteins that the wild-type protein does not typically interact with, or preventing interactions with proteins that the wild-type protein usually interacts with. This can result in the rewiring of molecular signalling cascades and the acquisition of an oncogenic phenotype. Here, we review the altered PPIs driven by oncogenic mutations, discuss technologies for monitoring PPIs and provide a functional analysis of mutation-directed PPIs. These driver mutation-enabled PPIs and mutation-perturbed PPIs present a new paradigm for the development of tumour-specific therapeutics. The intersection of cancer variants and altered PPI interfaces represents a new frontier for understanding oncogenic rewiring and developing tumour-selective therapeutic strategies.

Deep multi-omics integration approach reveals new molecular features of uterine leiomyosarcoma

Uterine leiomyosarcoma (uLMS) is a rare and aggressive cancer representing approximately 25 % of all uterine malignancies. The molecular heterogeneity and pathogenesis of uLMS are not well understood, and translational studies aimed at discovering the vulnerabilities of this tumor type are of high priority. We conducted an innovative comprehensive multi-omics integration study from DNA to protein using freshly frozen tumors. Here, we show that two tumors harbor actionable therapeutic targets, IDH1_p.Arg132Cys and KRAS_p.Gly12Cys, and homologous recombination deficiency (HRD) is the most predominant genomic signature. Additionally, 80 % of the samples presented a chromothripsis signature, reinforcing the aneuploidy phenotype of these tumors. Tumors with a high proliferation score and high Ki67 expression was associated with worse overall survival (OS). We observed a high frequency of balanced fusion events involving EEF1A1 with enrichment of the EGFR pathway. For the first time, uLMS proteomics analysis showed the enrichment of pathways associated with suppression of the innate immune system and ECM organization. Finally, our comprehensive multi-omics integration analysis identified amplification of the CTHRC1 gene from the matrisome, with a negative impact on OS. Interestingly, the expression of Ki67 and CTHRC1 exhibits a strong negative correlation, underscoring two distinct and mutually exclusive biological profiles in uLMS: (i) highly proliferative tumors, characterized by elevated Ki67 expression, and (ii) tumors driven by ECM remodeling, marked by high CTHRC1 levels. Taken together, this deep functional multi-omics approach contributes to the detection of new molecular features of uLMS and suggests that patients could benefit from precision oncology in clinical practice.

Mismatch repair (MMR) and microsatellite instability (MSI) phenotypes across solid tumors: A comprehensive cBioPortal study on prevalence and prognostic impact

Mismatch repair deficiency (MMR-d) and microsatellite instability (MSI) are prognostic and predictive biomarkers in oncology. Current testing for MMR/MSI relies on immunohistochemistry (IHC) for MMR proteins and molecular assays for MSI detection. This combined diagnostic strategy, however, lacks tumor specificity and does not account for gene variants. This study provides an in-depth analysis of MMR mutations frequency, spectrum, and distribution in solid tumors. Data from 23,893 patients across 11 tumor types, using 66 publicly available studies, were analyzed. MMR-mutated (MMR-m) status was defined by alterations in MLH1, PMS2, MSH2, and/or MSH6; MSI was assessed by MSIsensor. Cases with indeterminate labelling were excluded. Survival was analyzed using the Kaplan-Meier method. Among 19,353 tumors, 949 MMR variants were identified, comprising 432 pathogenic and 517 variants of unknown significance (VUS), as defined by OncoKB. MSH6 mutations were the most frequent (n = 279, 29.4 %), followed by MSH2 (n = 198, 20.9 %), MLH1 (n = 187, 19.7 %), and PMS2 (n = 161, 16.9 %). MMR-m cases were more frequent in endometrial (EC, 20.5 %), colorectal (CRC, 8.2 %), bladder (BLCA, 8.7 %), and gastroesophageal cancers (GEC, 5.4 %). Pathogenic mutations were more common than non-pathogenic in EC, CRC, and GEC (p < 0.001, p = 0.01, p = 0.32, respectively). MMR-m status was not associated with MSI in 247 (48.9 %) cases, including 67 (13.2 %) with pathogenic mutations. The highest concordance between MMR-m and MSI was observed in CRC (65.7 %), EC (91.2 %), and GEC (69.6 %), while the lowest in pancreatic (0.2 %) and lung cancers (0.1 %). MMR-m GECs showed improved overall survival compared to MMR-wt (p = 0.009), a relationship not observed in other tumor types. This study demonstrates that the MMR spectrum is extremely hetoerogeneous in solid tumors, highliting the need for comprehensive and tumor-specific testing strategies.

Homologous recombination repair status in metastatic prostate cancer by next-generation sequencing and functional immunofluorescence

Metastatic prostate cancer (mPC) is enriched for homologous recombination repair (HRR) gene alterations, which have prognostic and predictive value. Routine clinical implementation of next-generation sequencing (NGS) is still limited. We investigated the association between genomic and functional loss of HRR, using NGS and RAD51 immunofluorescence (RAD51-IF) in 219 primary or metastatic biopsies from 187 patients with stage IV prostate cancer. NGS showed frequent genomic alterations in TP53 (40%), AR (15%), PTEN (14%), FOXA1 (12%), MYC (10%), BRCA2 (9%), ATM (8%), and BRCA1 (2%). We pursued RAD51-IF in 206 samples; of those, 139/206 (67%) were evaluable. 21% of samples had RAD51-low score compatible with HRR deficiency (HRD). RAD51-IF showed high sensitivity (71%) and specificity (86%) for BRCA1/2 alterations. Patients with RAD51-low scores experienced longer progression-free survival (PFS) on poly(ADP-ribose) polymerase inhibitors (PARPi) or platinum chemotherapy. RAD51-IF is feasible in routine clinical samples from patients with mPC and is associated with clinically relevant HRR gene alterations.

Mapping kinase domain resistance mechanisms for the MET receptor tyrosine kinase via deep mutational scanning

Mutations in the kinase and juxtamembrane domains of the MET Receptor Tyrosine Kinase are responsible for oncogenesis in various cancers and can drive resistance to MET-directed treatments. Determining the most effective inhibitor for each mutational profile is a major challenge for MET-driven cancer treatment in precision medicine. Here, we used a deep mutational scan (DMS) of ~5764 MET kinase domain variants to profile the growth of each mutation against a panel of 11 inhibitors that are reported to target the MET kinase domain. We validate previously identified resistance mutations, pinpoint common resistance sites across type I, type II, and type I ½ inhibitors, unveil unique resistance and sensitizing mutations for each inhibitor, and verify non-cross-resistant sensitivities for type I and type II inhibitor pairs. We augment a protein language model with biophysical and chemical features to improve the predictive performance for inhibitor-treated datasets. Together, our study demonstrates a pooled experimental pipeline for identifying resistance mutations, provides a reference dictionary for mutations that are sensitized to specific therapies, and offers insights for future drug development.

Association of non-gain-of-function alterations in exportin-1 with improved overall survival in colorectal cancer

BACKGROUND

Upregulation of nuclear export protein exportin-1 (coded by gene XPO1) has been previously demonstrated in multiple cancer subtypes, contributing to pharmacotherapy resistance and increased recurrence rates. This study aimed to explore the effect of non-gain-of-function (GOF) XPO1 alterations in patients with colorectal cancer (CRC).

METHODS

Patients with colon/rectal/colorectal adenocarcinoma were identified from the Memorial Sloan Kettering Clinicogenomic, Harmonized Oncologic Real-World Dataset using cBioPortal. A subpopulation with alterations in XPO1 was identified. Patients with known amplifications and GOF E571K and R749Q alterations were excluded, as were patients with in situ and stage IV disease. Survival analysis was performed via Kaplan-Meier and Cox proportional hazards analyses, adjusted for patient age and disease stage.

RESULTS

Among 5543 patients with CRC, 83 (1.5%) had alterations in the XPO1 locus, and 5460 patients (98.5%) did not. Of patients with XPO1 alteration, 66 (79.5%) had non-GOF alterations, and 17 (21.5%) had GOF point mutations or amplifications. Patients with non-GOF XPO1 alteration had a mortality hazard ratio of 0.601 (95% CI, 0.463-0.805; P =.011). When adjusted for patient age and disease stage, XPO1 co-alteration was associated with improved overall survival (OS) in patients with alterations in TP53, APC, FBXW7, SMAD4, and BRAF genes (all P <.01).

CONCLUSION

XPO1 alterations were associated with improved OS in patients with CRC. Associated survival benefits persisted when co-alterations were present, particularly in co-alterations with intranuclear tumor suppressor proteins.

Extensive molecular profiling of KRAS wild-type as compared to KRAS mutated pancreatic ductal adenocarcinoma on 318 patients

PURPOSE

Molecular profiling is increasingly implemented to guide treatment of advanced pancreatic ductal adenocarcinoma (PDAC), especially when for clinical trials enrollment. This study aimed to describe actionable alterations detected in KRAS mutated (KRASm) versus KRAS wild-type (KRASwt) PDAC, the latter group being considered enriched in molecular alterations.

METHODS

This prospective monocentric study included patients with locally advanced or metastatic PDAC who underwent next-generation sequencing (NGS) on liquid biopsy and/or tissue samples between 2015 and 2023, as part of the BIP academic study (NCT02534649). Actionable alterations were classified using the ESCAT (ESMO Scale for Clinical Actionability of molecular Targets).

RESULTS

A total of 378 patients with a PDAC underwent NGS: 73 on tissue samples, 162 on liquid biopsies, and 143 on both tissue and liquid. Liquid biopsies had a 59.3 % performance (181 informative samples out of 305). Among 318 informative NGS samples, 273 (86 %) were KRASm, and 45 (14 %) were KRASwt. Median overall survival (OS) was 19.35 in KRASwt patients and 16.89 months for KRASm patients (HR 0.67, 95 %CI (0.49-0.90), p = 0.02). ESCAT alterations were found in 15.7 % of total population, with 31.1 % in KRASwt tumors and 13.2 % in KRASm tumors. BRCA1/2 mutations were identified in 7.5 % of the population, and one NTRK fusion was found in a KRASwt PDAC. The molecular tumor board considered 71 patients (22.3 %) eligible for early-phase trials, with 14 treated with matched therapy.

CONCLUSION

Although actionable mutations were more frequent in KRASwt tumors, 13.2 % of KRASm PDAC harbored ESCAT alterations, emphasizing the importance of molecular profiling regardless of KRAS status.

The Landscape of ctDNA in Appendiceal Adenocarcinoma

PURPOSE

Appendiceal adenocarcinoma is a rare malignancy with distinct histopathologic subtypes and a natural history with metastasis primarily limited to the peritoneum. Little is known about the molecular pathogenesis of appendiceal adenocarcinoma relative to common tumors.

EXPERIMENTAL DESIGN

We analyzed molecular data for patients within the Guardant Health database with appendix cancer (n = 718). We then identified patients with appendiceal adenocarcinoma at our institution (from October 2004-September 2022) for whom ctDNA mutation profiling (liquid biopsy) was performed (n = 168) and extracted clinicopathologic and outcomes data. Of these 168 patients, 57 also had tissue-based tumor mutational profiling, allowing for evaluation of concordance between liquid and tissue assays.

RESULTS

The mutational landscape of ctDNA in appendiceal adenocarcinoma is distinct from tissue-based sequencing, with TP53 being the most frequently mutated (46%). Relative to other tumors, appendiceal adenocarcinoma seems less likely to shed ctDNA, with only 38% of patients with metastatic appendiceal adenocarcinoma having detectable ctDNA (OR = 0.26; P < 0.0001 relative to colorectal cancer). When detectable, the median variant allele frequency was significantly lower in appendiceal adenocarcinoma (0.4% vs. 1.3% for colorectal cancer; P ≤ 0.001). High-grade, signet ring, or colonic-type histology, metastatic spread beyond the peritoneum, and TP53 mutation were associated with detectable ctDNA. With respect to clinical translation, patients with detectable ctDNA had worse overall survival (HR = 2.32; P = 0.048). In the Guardant Health cohort, actionable mutations were found in 93 patients (13.0%).

CONCLUSIONS

Although metastatic appendiceal adenocarcinoma tumors are less likely to shed tumor DNA into the blood relative to colorectal cancer, ctDNA profiling in appendiceal adenocarcinoma has clinical utility.

Clinical utility of comprehensive genomic profiling in non-small cell lung cancer: An analysis of a nation-wide database

BACKGROUND

Molecular testing is recommended to patients with advanced non-small cell lung cancer (NSCLC) because those who receive targeted therapy have better prognosis than patients who don't. However, recent studies have raised concerns that first-line companion diagnostic testing at diagnosis may have lower detection rates than previously reported. Therefore, we sought to determine the utility of comprehensive genomic profiling (CGP) tests in NSCLC by analyzing a nation-wide database.

METHODS

We searched the Center for Cancer Genomics and Advanced Therapeutics database and downloaded clinical and genomic data from 3,240 lung cancer cases registered from June 2019 to August 2023. Patients undergoing tissue tests and plasma tests were analyzed separately. NSCLC with previously known driver mutations and those without were further analyzed separately. All 3,240 lung cancer patients were analyzed for the presence of germline findings.

RESULTS

We found that 25 % of patients who had negative companion diagnostic results tested positive for driver oncogene mutations with indications for approved inhibitors when they underwent tissue CGP tests. Tissue CGP tests had lower detection rates for gene fusions compared with gene mutations (93 % for mutations and 73 % for fusions, p < 0.001), and plasma CGP tests had lower detection rates for both mutations and fusions compared with tissue testing (69 % for mutations and 37 % for fusions, p < 0.001). Finally, presumed germline pathogenic variants were detected in 3.9-5.3 % of NSCLC patients.

CONCLUSION

NSCLC patients who tested negative for companion diagnostic tests benefited from CGP tests, especially with tissue-based panels. CGP tests detect germline findings in NSCLC patients at rates similar to previous reports.

Integrating functional proteomics and next generation sequencing reveals potential therapeutic targets for Taiwanese breast cancer

Integrating functional proteomics and next-generation sequencing (NGS) offers a comprehensive approach to unraveling the molecular intricacies of breast cancer. This study investigates the functional interplay between genomic alterations and protein expression in Taiwanese breast cancer patients. By analyzing 61 breast cancer samples using tandem mass tag (TMT) labeling and mass spectrometry, coupled with whole-exome sequencing (WES) or targeted sequencing, we identified key genetic mutations and their impact on protein expression. Notably, pathogenic variants in BRCA1, BRCA2, PTEN, and PIK3CA were found to be clinically relevant, potentially guiding targeted therapy decisions. Additionally, we discovered trans correlations between specific gene alterations (FANCA, HRAS, PIK3CA, MAP2K1, JAK2) and the expression of 22 proteins, suggesting potential molecular mechanisms underlying breast cancer development and progression. These findings highlight the power of integrating proteomics and NGS to identify potential therapeutic targets and enhance personalized medicine strategies for Taiwanese breast cancer patients.

Frank Invasion in Tall Cell Carcinoma With Reversed Polarity of the Breast: Report of Two Cases

Tall cell carcinoma with reversed polarity (TCCRP) is a rare neoplasm of the breast composed of columnar tumor cells arranged in solid and solid-papillary nests with evidence of apical nuclear polarity. No frank invasion is evident despite the lack of a myoepithelial cell layer throughout the tumor. TCCRP has a triple-negative or hormone receptor-low immunophenotype. Recurrent IDH2 R172 hotspot mutation coexisting with genetic alterations in the PI3K pathway characterizes this tumor. Here, we report on 2 postmenopausal patients with TCCRP with frank stromal invasion. IDH2 R172 mutations were detected in both tumors by immunohistochemistry. Targeted sequencing of case 2 demonstrated the presence of IDH2 R172T and RTEL1 E839K mutations. Both patients underwent breast conservation surgery, radiation therapy, and adjuvant endocrine therapy with anastrozole and demonstrated no evidence of disease at 65 and 25 months, respectively. This study suggests that TCCRP may give rise to frank invasive carcinoma, the prognostic significance of which is yet unknown.

Molecular and Immunohistochemical Classification of Extrapulmonary Small Cell Neuroendocrine Carcinomas: A Study of 181 Cases

Extrapulmonary small cell neuroendocrine carcinoma (EP-SCNC) is a rare malignancy with a poor prognosis. Most patients with EP-SCNC have metastatic disease upon presentation, and their average overall survival (OS) is less than 12 months. Our study aimed to conduct a complex analysis of EP-SCNC. One hundred eighty-one EP-SCNC tissue samples were subjected to a complex analysis. One hundred fifty-five tumors were pure EP-SCNC, whereas 26 were combined tumors. Immunohistochemistry for ASCL1, NEUROD1, YAP1, POU2F3, Rb1, p53, cyclin D1, p16, PTEN, DLL3, PD-L1, CD56, synaptophysin, chromogranin A, and INSM1 was performed, and 128 samples were analyzed molecularly using next-generation sequencing, comprising DNA and RNA analyses. Detailed results on immunohistochemical and molecular analyses were provided for each primary origin of EP-SCNC separately. Median survival for the whole cohort of patients was 8.94 months. Patient age (≥70 years), tumor mutational burden <15, and TP53 and BRCA2 mutations were negative prognostic factors. High expression of ASCL-1 was associated with shorter OS, whereas high expression of YAP1 was associated with longer OS. Patients with genitourinary tumors had significantly better OS than those with gastrointestinal tract EP-SCNC tumors. Rb1 expression loss was detected more often in genitourinary tract SCNCs. In contrast, p16 overexpression was found more often in genitourinary tract SCNCs. POU2F3 expression was detected more often in combined tumors, whereas NEUROD1 was detected more often in pure EP-SCNC. Regarding "druggable markers," DLL3 was expressed in 66% of tumors and PD-L1 in 17.4%. Detailed analyses of different prognostic and predictive markers are needed to better understand EP-SCNC biology and create more personalized therapy to improve patient prognosis.

Chromothripsis-Mediated Small Cell Lung Carcinoma

Small cell lung carcinoma (SCLC) is a highly aggressive malignancy that is typically associated with tobacco exposure and inactivation of RB1 and TP53 genes. Here, we performed detailed clinicopathologic, genomic, and transcriptomic profiling of an atypical subset of SCLC that lacked RB1 and TP53 co-inactivation and arose in never/light smokers. We found that most cases were associated with chromothripsis-massive, localized chromosome shattering-recurrently involving chromosome 11 or 12 and resulting in extrachromosomal amplification of CCND1 or co-amplification of CCND2/CDK4/MDM2, respectively. Uniquely, these clinically aggressive tumors exhibited genomic and pathologic links to pulmonary carcinoids, suggesting a previously uncharacterized mode of SCLC pathogenesis via transformation from lower-grade neuroendocrine tumors or their progenitors. Conversely, SCLC in never-smokers harboring inactivated RB1 and TP53 exhibited hallmarks of adenocarcinoma-to-SCLC derivation, supporting two distinct pathways of plasticity-mediated pathogenesis of SCLC in never-smokers. Significance: Here, we provide the first detailed description of a unique SCLC subset lacking RB1/TP53 alterations and identify extensive chromothripsis and pathogenetic links to pulmonary carcinoids as its hallmark features. This work defines atypical SCLC as a novel entity among lung cancers, highlighting its exceptional histogenesis, clinicopathologic characteristics, and therapeutic vulnerabilities. See related commentary by Nadeem and Drapkin, p. 8.

PRMT5 inhibition has a potent anti-tumor activity against adenoid cystic carcinoma of salivary glands

BACKGROUND

Adenoid cystic carcinoma (ACC) is a rare glandular malignancy, commonly originating in salivary glands of the head and neck. Given its protracted growth, ACC is usually diagnosed in advanced stage. Treatment of ACC is limited to surgery and/or adjuvant radiotherapy, which often fails to prevent disease recurrence, and no FDA-approved targeted therapies are currently available. As such, identification of new therapeutic targets specific to ACC is crucial for improved patients' outcomes.

METHODS

After thoroughly evaluating the gene expression and signaling patterns characterizing ACC, we applied PandaOmics (an AI-driven software platform for novel therapeutic target discovery) on the unique transcriptomic dataset of 87 primary ACCs. Identifying protein arginine methyl transferase 5 (PRMT5) as a putative candidate with the top-scored druggability, we next determined the applicability of PRMT5 inhibitors (PRT543 and PRT811) using ACC cell lines, organoids, and patient derived xenograft (PDX) models. Molecular changes associated with response to PRMT5 inhibition and anti-proliferative effect of the combination therapy with lenvatinib was then analyzed.

RESULTS

Using a comprehensive AI-powered engine for target identification, PRMT5 was predicted among potential therapeutic target candidates for ACC. Here we show that monotherapy with selective PRMT5 inhibitors induced a potent anti-tumor activity across several cellular and animal models of ACC, which was paralleled by downregulation of genes associated with ACC tumorigenesis, including MYB and MYC (the recognized drivers of ACC progression). Furthermore, as a subset of genes targeted by lenvatinib is upregulated in ACC, we demonstrate that addition of lenvatinib enhanced the growth inhibitory effect of PRMT5 blockade in vitro, suggesting a potential clinical benefit for patients expressing lenvatinib favorable molecular profile.

CONCLUSION

Taken together, our study underscores the role of PRMT5 in ACC oncogenesis and provides a strong rationale for the clinical development of PRMT5 inhibitors as a targeted monotherapy or combination therapy for treatment of patients with this rare disease, based on the analysis of their underlying molecular profile.

Genetic Ancestry-Based Differences in Biomarker-Based Eligibility for Precision Oncology Therapies

Importance

Although differences in the prevalence of key cancer-specific somatic mutations as a function of genetic ancestry among patients with cancer has been well-established, few studies have addressed the practical clinical implications of these differences for the growing number of biomarker-driven treatments.

Objective

To determine if the approval of precision oncology therapies has benefited patients with cancer from various ancestral backgrounds equally over time.

Design, Setting, and Participants

A retrospective analysis of samples from patients with solid cancers who underwent clinical sequencing using the integrated mutation profiling of actionable cancer targets (MSK-IMPACT) assay between January 2014 and December 2022 was carried out. The annual fraction of patients per ancestral group with at least 1 level 1 biomarker was calculated for FDA drug approvals from January 1998 to December 2023. Analysis began in January 2024.

Main Outcomes and Measures

For each patient, genetic ancestry was quantitatively inferred, and patients were grouped based on predominant reference ancestry. OncoKB was used to identify all Food and Drug Administration (FDA)-recognized somatic biomarkers associated with FDA-approved therapies (level 1 biomarkers) in each tumor sample.

Results

Overall, the study included 59 433 patients. The approval of the EGFR-tyrosine kinase inhibitor erlotinib for patients with EGFR-mutant lung cancers in 2013 disproportionately benefited patients of East Asian and South Asian ancestries, leading to higher patient fractions with level 1 biomarkers in these ancestral groups compared with other populations. Although the increase in precision oncology drug approvals from 2019 to 2020 had a notable positive impact on clinical actionability for patients of European ancestry, patients of African ancestry had the lowest fraction of level 1 biomarkers compared with other groups from 2019 onward.

Conclusion and Relevance

This study systematically assessed and compared temporal changes in genomic biomarker-based eligibility for precision oncology therapies as a function of inferred genetic ancestry derived from DNA sequencing data. Despite the accelerated rate of FDA approvals for precision oncology therapies over the past decade, measurable differences in biomarker-based drug eligibility among patient ancestral groups exist. These differences may exacerbate the systemic disparities in clinical outcomes in patients of African ancestry due to existing deficiencies in their access to cancer care.

Potentially actionable molecular alterations in particular related to poor oncologic outcomes in salivary gland carcinomas

AIM

The study was designed to evaluate molecular alterations, relevant to the prognosis and personalized therapy of salivary gland cancers (SGCs).

MATERIALS AND METHODS

DNA was extracted from archival tissue of 40 patients with various SGCs subtypes. A targeted next-generation sequencing (NGS) panel was used for the identification of small-scale mutations, focal and chromosomal arm-level copy number changes. The final analysis included selected genes with potential actionable aberrations for targeted therapies and outcome predictions in 37 tumours' samples.

RESULTS

The follow-up of the SGCs study cohort revealed disease recurrence or metastasis in 19 patients and indicated poor individual outcomes. The mean disease-free survival (DFS) within the poor outcome group was 2.4 years, and the overall survival (OS) was 5.4 years. The DFS and OS of the remaining 18 patients with favourable outcomes were 8.3 years. The genes most frequently affected with aberrations were NF1 (n = 9, 24%) and TP53 (n = 8, 22%), with increased occurrence observed in the poor outcome group: NF1 (n = 6, 32%) and TP53 (n = 6, 32%). CDKN2A biallelic deletion was the most common copy number variation (n = 5), and was detected in 4 cases with identified disease relapse. TERT promoter mutation and amplification were found in myoepithelial carcinoma. A p.Ile35Thr mutation was discovered in CTNNB1 in two cases of adenoid cystic carcinoma. ERBB2 alterations were remarkable for SDC ex PA. Furthermore, TP53 mutation was established as a relevant negative prognostic factor for overall survival (p = 0,04). The analysis revealed potentially actionable genes in detected alterations in: MECA 100% (1/1), SDC 100% (7/7), AD 92% (11/12), Ca ex PA 82% (18/22), MECA 65% (20/31), AdCC 64% (9/14) and AcCC 0% (0/1).

CONCLUSIONS

SGCs are a heterogeneous group of malignancies with distinct molecular landscape that characterized by poor prognosis and inadequate treatment options. Nonstandard strategies might be beneficial for patients who suffer from salivary gland cancers. Wider utilization of NGS analysis may increase the opportunity for patients with those rare cancers to receive more precise, personalized therapy.

Maximizing the clinical utility and performance of cytology samples for comprehensive genetic profiling

Comprehensive molecular profiling by next-generation sequencing has revolutionized tumor classification and biomarker evaluation. However, routine implementation is challenged by the scant nature of diagnostic material obtained through minimally invasive procedures. Here, we describe our long-term experience in profiling cytology samples with an in-depth assessment of the performance, quality metrics, biomarker identification capabilities, and potential pitfalls. We highlight the impact of several optimization strategies to maximize performance with 4,871 prospectively sequenced clinical cytology samples tested by MSK-IMPACTTM. Special emphasis is given to the use of residual supernatant cell-free DNA (ScfDNA) as a valuable source of tumor DNA. Overall, cytology samples are similar in performance to surgical samples in identifying clinically relevant genomic alterations, achieving success rates up to 93% with full optimization. While cell block (CB) samples have excellent performance overall, low-level cross-contamination is identified in a small proportion of cases (4.7%), a common pitfall intrinsic to the processing of paraffin blocks, suggesting that more stringent precautions and processing modifications should be considered in quality control initiatives. By contrast ScfDNA samples have negligible contamination. Finally, ScfDNA testing exclusively used as a rescue strategy, delivered successful results in 71% of cases where tumor tissue from CB was depleted.

Current and emerging treatment options for BRAFV600-mutant melanoma

INTRODUCTION

BRAF mutations are the most common driver mutation in cutaneous melanoma, present in 40% of cases. Rationally designed BRAF targeted therapy (TT) has been developed in response to this, and alongside immune checkpoint inhibitors (ICI), forms the backbone of systemic therapy options for BRAF-mutant melanoma. Various therapeutic approaches have been studied in the neoadjuvant, adjuvant and advanced settings, and there is a wealth of information to guide clinicians managing these patients. Despite this, certain challenges remain.

AREAS COVERED

We reviewed the available literature regarding BRAF mutation types and resistance mechanisms, neoadjuvant and adjuvant approaches for patients with early-stage disease, management of advanced disease, including patients with brain metastases, as well as identified areas of further research.

EXPERT OPINION

Although there is a significant amount of literature to guide the management of BRAF-mutant melanoma, several questions remain. Thus far, the management of stage III BRAF-mutant patients following neoadjuvant ICI, treatment de-escalation in long-term TT responders in the advanced setting and the management of symptomatic brain metastases remain areas of debate. Further work on predictive and prognostic biomarkers for patients with BRAF-mutant melanoma patients will assist in clinical decision-making.

Actionable Gene Alterations Identified in Patients With Malignant Melanoma by Targeted Sequencing in Japan

PURPOSE

Precision medicine plays an important role in the treatment of patients with advanced melanoma. Despite its high incidence in White patients, advanced melanoma is rare in Asian countries, hampering prospective clinical trials targeting the Asian population. This retrospective study aimed to elucidate the real-world molecular diagnoses and outcomes of Japanese patients with melanoma using comprehensive genome profiling (CGP).

MATERIALS AND METHODS

Patients with melanoma who completed standard anticancer medical treatments (including those expected to complete the treatments) underwent CGP, which is covered by the National Health Insurance. We analyzed the results and clinical annotations of 569 patients registered before August 2023 in a national database.

RESULTS

Skin, mucosal, and uveal melanomas accounted for 64%, 28%, and 7% of cases, respectively. Patients with BRAF, NRAS, NF1, and KIT variants represented 25%, 20%, 17%, and 17%, respectively. Eighty-two percent of BRAF, 97% of NRAS, 69% of NF1, and 54% of KIT were actionable alterations (ie, BRAF classes I, II, and III, NRAS Q61, G12, G13, NF1 loss-of-function, KIT gain-of-function variants). BRAF V600E/K variants occurred in 22% of skin and 2% of mucosal melanomas, but not in uveal melanomas. The mean tumor mutation burden in cutaneous melanomas was 4.2 variants/Mb. Patients previously treated with BRAF-targeted therapy harbored amplifications of BRAF and cell cycle genes more frequently than therapy-naive patients. Thirty-six patients (6.3%) were treated following the molecular tumor board (MTB) recommendations.

CONCLUSION

Actionable gene alterations in BRAF, NRAS, NF1, and KIT are common in Japanese patients with melanoma. However, few patients were treated according to the MTB recommendations, suggesting that there is an unmet need to increase accessibility to gene-matched clinical trials in Japan.

Patient-derived tumor organoids: A preclinical platform for personalized cancer therapy

Patient-derived tumor organoids (PDTOs) represent a significant advancement in cancer research and personalized medicine. These organoids, derived from various cancer types, have shown the ability to retain the genetic and molecular characteristics of the original tumors, allowing for the detailed study of tumor biology and drug responses on an individual basis. The success rates of establishing PDTOs vary widely and are influenced by factors such as cancer type, tissue quality, and media composition. Furthermore, the dynamic nature of organoid cultures may also lead to unique molecular characteristics that deviate from the original tumors, affecting their interpretation in clinical settings without the implementation of rigorous validation and establishment of standardized protocols. Recent studies have supported the correlation between PDTOs and the corresponding patient response. Although these studies involved a small number of patients, they promoted the integration of PDTOs in observational and interventional clinical trials to advance translational cancer therapies.

Rhabdomyosarcoma With EWSR1::NF2 Gene Fusion: A Case Report Potentially Expanding Its Genetic Spectrum

Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in children, presenting with heterogeneous clinical and molecular subtypes. While gene fusions are predominantly associated with alveolar RMS, spindle cell RMS, especially congenital and intraosseous variants, are also linked to specific gene fusions. Furthermore, recently, FGFR1 kinase-driven RMSs were published. Here, we describe a case of RMS harboring an EWSR1::NF2 gene fusion, a deletion-driven genetic alteration that has not been previously documented in RMS or other soft tissue tumors. The patient was a 29-year-old female who presented with a lobulated ankle mass. Histologic examination revealed a malignant round cell tumor extensively infiltrating large nerve bundles. Immunohistochemical analysis demonstrated rhabdomyoblastic differentiation, consistent with rhabdomyosarcoma. While some areas showed features resembling the sclerosing and others the embryonal subtypes, the overall findings were considered unclassifiable. Targeted RNA sequencing revealed EWSR1(exon 9):: NF2(exon 7) gene fusion, which was confirmed on whole genome and targeted DNA sequencing. The latter did not yield specific diagnostic insights but revealed mutations in TSC2 (p.T1330M), ZFHX3 (p.A301T), and a NOTCH3 rearrangement, all of unknown oncogenic significance. MYC gene amplification was detected, but there was no evidence of chromosome 8 amplification or chromosome 11p15 loss of heterozygosity. Whole genome sequencing revealed a low tumor mutation burden (2.69/Mb) and showed no other significant potentially oncogenic events. DNA methylation studies using dimensionality reduction and unsupervised clustering placed the case within the embryonal RMS subtype. Although the absence of other oncogenic driver alterations suggests that the fusion may have played a pivotal role in pathogenesis, we cannot exclude the possibility that it represents a passenger alteration rather than a true driver mutation. If the former is true, further studies will be required to determine whether this fusion represents a novel RMS subtype or a rare driver in existing subtypes of RMS.

MET Exon 14 Skipping and Novel Actionable Variants: Diagnostic and Therapeutic Implications in Latin American Non-Small-Cell Lung Cancer Patients

Targeted therapy indications for actionable variants in non-small-cell lung cancer (NSCLC) have primarily been studied in Caucasian populations, with limited data on Latin American patients. This study utilized a 52-genes next-generation sequencing (NGS) panel to analyze 1560 tumor biopsies from NSCLC patients in Chile, Brazil, and Peru. The RNA sequencing reads and DNA coverage were correlated to improve the detection of the actionable MET exon 14 skipping variant (METex14). The pathogenicity of MET variants of uncertain significance (VUSs) was assessed using bioinformatic methods, based on their predicted driver potential. The effects of the predicted drivers VUS T992I and H1094Y on c-MET signaling activation, proliferation, and migration were evaluated in HEK293T, BEAS-2B, and H1993 cell lines. Subsequently, c-Met inhibitors were tested in 2D and 3D cell cultures, and drug affinity was determined using 3D structure simulations. The prevalence of MET variants in the South American cohort was 8%, and RNA-based diagnosis detected 27% more cases of METex14 than DNA-based methods. Notably, 20% of METex14 cases with RNA reads below the detection threshold were confirmed using DNA analysis. The novel actionable T992I and H1094Y variants induced proliferation and migration through c-Met/Akt signaling. Both variants showed sensitivity to crizotinib and savolitinib, but the H1094Y variant exhibited reduced sensitivity to capmatinib. These findings highlight the importance of RNA-based METex14 diagnosis and reveal the drug sensitivity profiles of novel actionable MET variants from an understudied patient population.

Leukemia-mutated proteins PHF6 and PHIP form a chromatin complex that represses acute myeloid leukemia stemness

Myeloid leukemias are heterogeneous cancers with diverse mutations, sometimes in genes with unclear roles and unknown functional partners. PHF6 and PHIP are two poorly-understood chromatin-binding proteins recurrently mutated in acute myeloid leukemia (AML). PHF6 mutations are associated with poorer outcomes, while PHIP was recently identified as the most common selective mutation in Black patients in AML. Here, we show that PHF6 is a transcriptional repressor that suppresses a stemness gene network, and that PHF6 missense mutations, classified by current clinical algorithms as variants of unknown significance, produce unstable or non-functional protein. We present multiple lines of evidence converging on a critical mechanistic connection between PHF6 and PHIP. We show that PHIP loss phenocopies PHF6 loss, and that PHF6 requires PHIP to occupy chromatin and exert its downstream transcriptional program. Our work unifies PHF6 and PHIP, two disparate leukemia-mutated proteins, into a common functional complex that suppresses AML stemness.

A precision oncology-focused deep learning framework for personalized selection of cancer therapy

Precision oncology matches tumors to targeted therapies based on the presence of actionable molecular alterations. However, most tumors lack actionable alterations, restricting treatment options to cytotoxic chemotherapies for which few data-driven prioritization strategies currently exist. Here, we report an integrated computational/experimental treatment selection approach applicable for both chemotherapies and targeted agents irrespective of actionable alterations. We generated functional drug response data on a large collection of patient-derived tumor models and used it to train ScreenDL, a novel deep learning-based cancer drug response prediction model. ScreenDL leverages the combination of tumor omic and functional drug screening data to predict the most efficacious treatments. We show that ScreenDL accurately predicts response to drugs with diverse mechanisms, outperforming existing methods and approved biomarkers. In our preclinical study, this approach achieved superior clinical benefit and objective response rates in breast cancer patient-derived xenografts, suggesting that testing ScreenDL in clinical trials may be warranted.

Imlunestrant with or without Abemaciclib in Advanced Breast Cancer

BACKGROUND

Imlunestrant is a next-generation, brain-penetrant, oral selective estrogen-receptor (ER) degrader that delivers continuous ER inhibition, even in cancers with mutations in the gene encoding ERα (ESR1).

METHODS

In a phase 3, open-label trial, we enrolled patients with ER-positive, human epidermal growth factor receptor 2 (HER2)-negative advanced breast cancer that recurred or progressed during or after aromatase inhibitor therapy, administered alone or with a cyclin-dependent kinase 4 and 6 (CDK4/6) inhibitor. Patients were assigned in a 1:1:1 ratio to receive imlunestrant, standard endocrine monotherapy, or imlunestrant-abemaciclib. Primary end points were investigator-assessed progression-free survival with imlunestrant as compared with standard therapy among patients with ESR1 mutations and among all patients and with imlunestrant-abemaciclib as compared with imlunestrant among all patients who had undergone randomization concurrently.

RESULTS

Overall, 874 patients underwent randomization, with 331 assigned to imlunestrant, 330 to standard therapy, and 213 to imlunestrant-abemaciclib. Among 256 patients with ESR1 mutations, the median progression-free survival was 5.5 months with imlunestrant and 3.8 months with standard therapy. The estimated restricted mean survival time at 19.4 months was 7.9 months (95% confidence interval [CI], 6.8 to 9.1) with imlunestrant and 5.4 months (95% CI, 4.6 to 6.2) with standard therapy (difference, 2.6 months; 95% CI, 1.2 to 3.9; P<0.001). In the overall population, the median progression-free survival was 5.6 months with imlunestrant and 5.5 months with standard therapy (hazard ratio for progression or death, 0.87; 95% CI, 0.72 to 1.04; P = 0.12). Among 426 patients in the comparison of imlunestrant-abemaciclib with imlunestrant, the median progression-free survival was 9.4 months and 5.5 months, respectively (hazard ratio, 0.57; 95% CI, 0.44 to 0.73; P<0.001). The incidence of grade 3 or higher adverse events was 17.1% with imlunestrant, 20.7% with standard therapy, and 48.6% with imlunestrant-abemaciclib.

CONCLUSIONS

Among patients with ER-positive, HER2-negative advanced breast cancer, treatment with imlunestrant led to significantly longer progression-free survival than standard therapy among those with ESR1 mutations but not in the overall population. Imlunestrant-abemaciclib significantly improved progression-free survival as compared with imlunestrant, regardless of ESR1-mutation status. (Funded by Eli Lilly; EMBER-3 ClinicalTrials.gov number, NCT04975308.).

Genomic differences of patients with hematologic malignancies in different age groups

Hematologic malignancies cause significant morbidity/mortality in both children and young adults (CYAs) as well as older adults (OAs). Yet their biological underpinnings remain inadequately understood. Here, we analyzed clinical and genomic disparities between CYAs and OAs in various hematologic malignancies. We found substantial differences in clinical features such as patient sex, ethnicity, metastasis rates, and tumor subtypes. Genomically, most CYA hematologic malignancies indicated lower mutational burden. Subsequently, we identified differentially mutated genes (DMGs) with varying mutation rates between CYAs and OAs, noting fewer mutations in CYAs for most genes such as TP53, TET2, and DNMT3A. In contrast, several DMGs (i.e., NRAS, KRAS, SMARCA4, ID3, PTPN11, WT1, and KIT) were overrepresented in CYAs. We further investigated human protein interacting partners of these identified DMGs that were highly mutated in CYAs/OAs, respectively, and found significant differences in network topological and functional roles. Notably, CYA malignancies demonstrated extensive copy number alterations (CNAs) and more driver gene fusions. In particular, four CNA differential genes (i.e., ARID1B, MYB, TP53, and ESR1) were overrepresented as amplifications and deletions in CYAs and OAs, respectively. Ultimately, we demonstrated a landscape comparative view of clinically actionable genetic events in CYAs and OAs, providing clues for age-related personalized treatment.

Mapping kinase domain resistance mechanisms for the MET receptor tyrosine kinase via deep mutational scanning

Mutations in the kinase and juxtamembrane domains of the MET Receptor Tyrosine Kinase are responsible for oncogenesis in various cancers and can drive resistance to MET-directed treatments. Determining the most effective inhibitor for each mutational profile is a major challenge for MET-driven cancer treatment in precision medicine. Here, we used a deep mutational scan (DMS) of ~5,764 MET kinase domain variants to profile the growth of each mutation against a panel of 11 inhibitors that are reported to target the MET kinase domain. We validate previously identified resistance mutations, pinpoint common resistance sites across type I, type II, and type I ½ inhibitors, unveil unique resistance and sensitizing mutations for each inhibitor, and verify non-cross-resistant sensitivities for type I and type II inhibitor pairs. We augment a protein language model with biophysical and chemical features to improve the predictive performance for inhibitor-treated datasets. Together, our study demonstrates a pooled experimental pipeline for identifying resistance mutations, provides a reference dictionary for mutations that are sensitized to specific therapies, and offers insights for future drug development.

AEmiGAP: AutoEncoder-Based miRNA-Gene Association Prediction Using Deep Learning Method

MicroRNAs (miRNAs) play a crucial role in gene regulation and are strongly linked to various diseases, including cancer. This study presents AEmiGAP, an advanced deep learning model that integrates autoencoders with long short-term memory (LSTM) networks to predict miRNA-gene associations. By enhancing feature extraction through autoencoders, AEmiGAP captures intricate, latent relationships between miRNAs and genes with unprecedented accuracy, outperforming all existing models in miRNA-gene association prediction. A thoroughly curated dataset of positive and negative miRNA-gene pairs was generated using distance-based filtering methods, significantly improving the model's AUC and overall predictive accuracy. Additionally, this study proposes two case studies to highlight AEmiGAP's application: first, a top 30 list of miRNA-gene pairs with the highest predicted association scores among previously unknown pairs, and second, a list of the top 10 miRNAs strongly associated with each of five key oncogenes. These findings establish AEmiGAP as a new benchmark in miRNA-gene association prediction, with considerable potential to advance both cancer research and precision medicine.

Nivolumab in Patients with Metastatic Castration-Resistant Prostate Cancer with and without DNA Repair Defects

PURPOSE

Despite the success of immune checkpoint inhibitors (ICI) across various cancers, their efficacy in metastatic castration-resistant prostate cancer (mCRPC) is modest, except for a subset of patients who experience significant, yet unpredictable, benefits. DNA repair defects (DRD) are associated with higher neoantigen load, which may predict response. Our study explored the potential of DRD for enhanced responsiveness to the ICI nivolumab.

PATIENTS AND METHODS

We conducted a phase II, multicenter, single-arm trial evaluating nivolumab in patients with mCRPC with prior docetaxel therapy. The DRD were assessed using ctDNA. The primary endpoint was PSA50 response. Secondary endpoints included the objective response rate, radiographic progression-free survival (rPFS), and overall survival. Also, exploratory comprehensive genomic profiling was performed via whole-exome sequencing of tumor samples and matched normal tissues, alongside PD-L1 expression evaluation.

RESULTS

Among the 38 enrolled patients, DRD was identifiable in 30.5% (11/36) through ctDNA and/or whole-exome sequencing analyses. The overall PSA50 response rate was 10.5% (4/38). The PSA50 and objective response rates did not significantly differ between patients with and without DRD (18.2% vs. 8%; P = 0.57 and 50% vs. 17.6%; P = 0.27, respectively). The median PSA-PFS (1.9 vs. 2.8 months; P = 0.52) and rPFS (3.4 vs. 5.5 months; P = 0.7) were not statistically different between patients with and without DRD. Grade ≥ 3 adverse events were reported in 47.3% of participants.

CONCLUSIONS

Nivolumab has clinical activity in a subset of patients with mCRPC; however, DRD does not predict response. These results highlight the necessity of identifying new biomarkers to more accurately determine patients with mCRPC who might respond to ICIs.

Precision Oncology: 2024 in Review

This article discusses the specific advances made in precision oncology in 2024. We comment on the evolving nature of predictive molecular events used to select patients who will most benefit clinically from treatment. We also discuss advances in the development of strategic treatment regimens for combination therapies, rational drug design of small-molecule inhibitors, and structurally informed drug repurposing.

Genomic landscape of cutaneous, acral, mucosal, and uveal melanoma in Japan: analysis of clinical comprehensive genomic profiling data

BACKGROUND

Cutaneous melanoma (CM) is the most common type in Caucasians, while acral melanoma (AM) and mucosal melanoma (MM), which are resistant to immunotherapies and BRAF/MEK-targeted therapies, are more common in East Asians. Genomic profiling is essential for treating melanomas, but such data are lacking in Japan.

METHODS

Comprehensive genomic profiling data compiled in the Center for Cancer Genomics and Advanced Therapeutics (C-CAT) were analyzed.

RESULTS

A total of 380 melanomas was analyzed, including 136 CM, 46 AM, 168 MM, and 30 uveal melanoma (UM). MM included conjunctival, sinonasal, oral, esophageal, anorectal, and vulvovaginal melanomas. No significant difference in the median tumor mutational burden (TMB) of CM (3.39 mutations/megabase), AM (2.76), and MM (3.78) was the key finding. Microsatellite instability-high status was found in one case. BRAF V600E/K was found in only 45 patients (12%). Key driver mutations in CM were BRAF (38%), NRAS (21%), NF1 (8%), and KIT (10%), with frequent copy number alterations (CNAs) of CDKN2A, CDKN2B, and MYC. AM was characterized by altered KIT (30%), NRAS (26%), and NF1 (11%) and CDKN2A, CDKN2B, CDK4, MDM2, and CCND1 CNAs. MM was characterized by altered NRAS (24%), KIT (21%), and NF1 (17%) and MYC, KIT, and CDKN2A CNAs, with differences based on anatomical locations. UM bore GNAQ or GNA11 driver mutations (87%) and frequent mutations in SF3B1 or BAP1.

CONCLUSION

The distinct genomic profiling in Japanese patients, including lower TMB, compared to Caucasians, is associated with poorer treatment outcomes. This result underscores the need for more effective therapeutic agents.

A Comparative Genomic Study of Conventional and Undifferentiated Melanoma

Undifferentiated melanoma, defined as melanoma that has lost all usual phenotypic and immunohistochemical characteristics of conventional melanoma, can pose significant diagnostic challenges. Molecular studies have advanced our understanding of undifferentiated melanoma by demonstrating that a subset of these tumors harbors known melanoma driver alterations in genes such as BRAF, NRAS, and NF1. However, there is a paucity of data describing genetic alterations that may distinguish undifferentiated melanoma from conventional melanoma. In this study, we directly compared the genomic profiles of undifferentiated melanoma to a cohort of conventional melanomas, including 14 undifferentiated melanoma cases (comprised of 2 primary cases, 2 cutaneous recurrences, and 10 metastases) and a cohort of 127 conventional melanomas including primary, recurrent, and metastatic cases. Targeted sequencing of 447 cancer-associated genes was performed, including identification of mutations and copy number alterations. NRAS was the most frequent melanoma driver in undifferentiated melanoma (8/14 cases, 57%), although notably, only 1 undifferentiated melanoma harbored an NRAS Q61R mutation. Compared with the conventional melanoma cohort, undifferentiated melanoma demonstrated statistically significant enrichment of pathogenic activating RAC1 mutations (6/14 total cases, 43%), including P29S (4/6 cases), P29L (1/6 cases), and D11E (1/6 cases). In addition to providing insight into the molecular pathogenesis of undifferentiated melanoma, these findings also suggest that RAS Q61R immunohistochemistry may have limited utility for its diagnosis. The presence of recurrent RAC1 mutations in undifferentiated melanoma is also notable as these alterations may contribute to mitogen-activated protein kinase pathway-targeted therapy resistance. Furthermore, the RAC1 alterations identified in this cohort have been shown to drive a melanocytic to mesenchymal switch in melanocytes, offering a possible explanation for the undifferentiated phenotype of these melanomas.

Discovery of Gene Fusions in Driver-Negative Cancer Samples From the National Cancer Institute-Molecular Analysis for Therapy Choice Screening Cohort

PURPOSE

The National Cancer Institute-Molecular Analysis for Therapy Choice (NCI-MATCH) trial was implemented to identify actionable genetic alterations across cancer types and enroll patients accordingly onto treatment arms, irrespective of tumor histology. Using multiplex polymerase chain reaction (PCR) next-generation sequencing, NCI-MATCH genotyped 5,540 patients, discovering gene fusions in 202/5,540 tumors (3.65%). This result, substantially lower than the fusion detection prevalence of 8.5% across all patients with cancer screened at Massachusetts General Hospital's (MGH) clinical laboratories, supported reanalysis of NCI-MATCH samples identified as mutations-of-interest (MOI)-negative. The assay used by NCI-MATCH requires previous knowledge of both fusion genes, cannot detect novel fusions, and may underestimate fusion-positive patients. Anchored multiplex PCR (AMP) technology permits fusion detection with knowledge of just one gene of the fusion partners.

METHODS

Using AMP-based kits, we reprocessed 663 MOI-negative samples. 200 ng of RNA per sample were shipped from the Eastern Cooperative Oncology Group-American College of Radiology Imaging Network biorepository to MGH (n = 319) and Yale University (n = 344), processed, and sequenced on the NextSeq550. Reported fusions were manually reviewed, and novel fusions orthogonally verified via reverse-transcription PCR and Sanger sequencing.

RESULTS

AMP identified 148 fusions in 142/663 MOI-negative patients (21% [95% CI, 18 to 25]), of which 28 were covered by the Oncomine Comprehensive Assay (OCA) panel but missed, while 120 were not covered by OCA. Among AMP-identified positive patients, 32 had actionable fusions, 24 contained novel fusions, and six had two fusion events. We identified fusions in 12/34 (35% [95% CI, 20 to 54]) cholangiocarcinomas and 43/109 (39% [95% CI, 30 to 49]) sarcomas.

CONCLUSION

Technology and awareness of actionable fusions have improved since the NCI-MATCH trial. With AMP-based technology, we identified 142 patients with fusions not detected during NCI-MATCH screening, many potentially actionable. These striking data underscore the need to optimize the fusion-detection capabilities of genotyping assays used in precision medicine.

Genetic and therapeutic heterogeneity shape the baseline and longitudinal immune ecosystem of ovarian clear cell carcinoma

BACKGROUND

Ovarian clear cell carcinoma (OCCC) is a rare and chemo-resistant subtype of ovarian cancer. While immunotherapy has demonstrated effectiveness in some OCCC cases, the mechanisms for heterogeneous immunoreactivity and potential combinatory strategies remain unclear.

METHODS

Tumor samples from 13 patients with OCCC underwent single-cell mRNA-seq and TCR-seq to generate 1 40 683 cells transcriptome, while additionally 31 formalin-fixed paraffin-embedded samples were used for immunohistochemistry. Spatial transcriptomics of two OCCC samples and bulk RNA-seq of 58 patients were incorporated for spatial and interpatient level explorations. Serum tumor markers and radiologic images of three patients with OCCC who received combinatory VEGF and PD-1 inhibition were retrospectively analyzed.

RESULTS

OCCC exhibited a dynamic immune architecture shaped by genetic and therapeutic pressure. ARID1A mutation linked to baseline immune activation, correlated with an enrichment of neoantigen-reactive CXCL13+ CTLA4+ CD8+ T cells (p<0.001) and enhanced FASLG-FAS interactions. Recurrent OCCC was fibrotic, angiogenic, and immunosuppressive, exhibiting metabolic reprogramming towards activated activity in fatty acid metabolism. High CD36 (log-rank p=0.012, HR: 4.515) and CD47 expression (log-rank p=0.037, HR: 3.246) indicated worse progression-free survival. Treatment with bevacizumab increased intratumoral T cell infiltration and activated T cell interferon-γ signaling. Retrospective analysis of clinical cases revealed that combination therapy with anti-VEGF (vascular endothelial growth factor) and anti-PD-1 agents exerted clinical benefits in patients with OCCC with persistent, recurrent, and metastatic disease.

CONCLUSIONS

ARID1A mutation correlated with OCCC baseline immune activation. Stromal reconstruction and tumor metabolic reprogramming functioned as key processes of OCCC dynamic progression. VEGF inhibition remodeled OCCC stroma, restored T cell function and potentiated immunotherapy. CD36 and CD47 might be potential therapeutic targets for recurrent OCCC.

Integrated analyses of multi-omic data derived from paired primary lung cancer and brain metastasis reveal the metabolic vulnerability as a novel therapeutic target

BACKGROUND

Lung cancer brain metastases (LC-BrMs) are frequently associated with dismal mortality rates in patients with lung cancer; however, standard of care therapies for LC-BrMs are still limited in their efficacy. A deep understanding of molecular mechanisms and tumor microenvironment of LC-BrMs will provide us with new insights into developing novel therapeutics for treating patients with LC-BrMs.

METHODS

Here, we performed integrated analyses of genomic, transcriptomic, proteomic, metabolomic, and single-cell RNA sequencing data which were derived from a total number of 154 patients with paired and unpaired primary lung cancer and LC-BrM, spanning four published and two newly generated patient cohorts on both bulk and single cell levels.

RESULTS

We uncovered that LC-BrMs exhibited a significantly greater intra-tumor heterogeneity. We also observed that mutations in a subset of genes were almost always shared by both primary lung cancers and LC-BrM lesions, including TTN, TP53, MUC16, LRP1B, RYR2, and EGFR. In addition, the genome-wide landscape of somatic copy number alterations was similar between primary lung cancers and LC-BrM lesions. Nevertheless, several regions of focal amplification were significantly enriched in LC-BrMs, including 5p15.33 and 20q13.33. Intriguingly, integrated analyses of transcriptomic, proteomic, and metabolomic data revealed mitochondrial-specific metabolism was activated but tumor immune microenvironment was suppressed in LC-BrMs. Subsequently, we validated our results by conducting real-time quantitative reverse transcription PCR experiments, immunohistochemistry, and multiplexed immunofluorescence staining of patients' paired tumor specimens. Therapeutically, targeting oxidative phosphorylation with gamitrinib in patient-derived organoids of LC-BrMs induced apoptosis and inhibited cell proliferation. The combination of gamitrinib plus anti-PD-1 immunotherapy significantly improved survival of mice bearing LC-BrMs. Patients with a higher expression of mitochondrial metabolism genes but a lower expression of immune genes in their LC-BrM lesions tended to have a worse survival outcome.

CONCLUSIONS

In conclusion, our findings not only provide comprehensive and integrated perspectives of molecular underpinnings of LC-BrMs but also contribute to the development of a potential, rationale-based combinatorial therapeutic strategy with the goal of translating it into clinical trials for patients with LC-BrMs.

Successful Treatment of Abdominal Wall Advanced Endometriosis-Associated Clear Cell Carcinoma with AKT Pathway Inhibitor: Case Report

The emergence of endometriosis-associated clear cell carcinoma (CCC) within the abdominal wall is a notably rare phenomenon. This condition predominantly impacts females who have previously undergone surgical interventions, including hysterectomy or caesarean section (C-section), with the malignant transformation of endometriosis within the post-surgical abdominal scar posited as a likely mechanism. Herein, we delineate a distinctive case of endometriosis-associated CCC emanating from the abdominal wall. The therapeutic approach for the patient encompassed surgical resection, complemented by a regimen of adjuvant chemotherapy, radiotherapy, immunotherapy, and targeted therapy. Despite these measures, the patient experienced disease progression, manifested by bilateral inguinal lymph node involvement and metastasis to the left femoral bone. Advanced molecular diagnostics, specifically next-generation sequencing (NGS) of the resected specimen, identified a targetable PIK3CA E726K mutation. Subsequent treatment with alpelisib and everolimus was initiated, culminating in a sustained complete response.

Precision oncology platforms: practical strategies for genomic database utilization in cancer treatment

In recent years, the expansion of molecularly targeted cancer therapies has significantly advanced precision oncology. Parallel developments in next-generation sequencing (NGS) technologies have also improved precision oncology applications, making genomic analysis of tumors more affordable and accessible. Targeted NGS panels now enable the rapid identification of diverse actionable mutations, requiring clinicians to efficiently assess the predictive value of cancer biomarkers for specific treatments. The urgency for timely and accurate decision-making in oncology emphasizes the importance of reliable precision oncology software. Online clinical decision-making tools and associated cancer databases have been designed by consolidating genomic data into standardized, accessible formats. These new platforms are highly integrated and crucial for identifying actionable somatic genomic biomarkers essential for tumor survival, determining corresponding drug targets, and selecting appropriate treatments based on the mutational profile of each patient's tumor. To help oncologists and translational cancer researchers unfamiliar with these tools, we review the utility, accuracy, and comprehensiveness of several commonly used precision medicine software options currently available. Our analysis categorized selected genomic databases based on their primary content, utility, and how well they provide practical guidance for interpreting somatic biomarker data. We identified several comprehensive, mostly open-access platforms that are easy to use for genetic biomarker searches, each with unique features and limitations. Among the precision oncology tools we evaluated, we found MyCancerGenome and OncoKB to be the first choice, offering comprehensive, accurate up-to-date information on the clinical significance of somatic mutations. To illustrate the application of these precision oncology tools in clinical settings, we evaluated three case studies to see how use of the platforms could have influenced treatment planning. Most of the precision oncology software evaluated could be easily streamlined into clinical workflows to provide updated information on approved drugs and clinical trials related the actionable mutations detected. Some platforms were very intuitive and easy to use, while others, often developed in smaller academic settings, were more difficult to navigate and may not be updated consistently. Future enhancements, incorporating artificial intelligence algorithms, are likely to improve integration of the platforms with diverse big data sources, enabling more accurate predictions of potential therapeutic responses.

Reproducible processing of TCGA regulatory networks

Background

Technological advances in sequencing and computation have allowed deep exploration of the molecular basis of diseases. Biological networks have proven to be a useful framework for interrogating omics data and modeling regulatory gene and protein interactions. Large collaborative projects, such as The Cancer Genome Atlas (TCGA), have provided a rich resource for building and validating new computational methods resulting in a plethora of open-source software for downloading, pre-processing, and analyzing those data. However, for an end-to-end analysis of regulatory networks a coherent and reusable workflow is essential to integrate all relevant packages into a robust pipeline.

Findings

We developed tcga-data-nf, a Nextflow workflow that allows users to reproducibly infer regulatory networks from the thousands of samples in TCGA using a single command. The workflow can be divided into three main steps: multi-omics data, such as RNA-seq and methylation, are downloaded, preprocessed, and lastly used to infer regulatory network models with the netZoo software tools. The workflow is powered by the NetworkDataCompanion R package, a standalone collection of functions for managing, mapping, and filtering TCGA data. Here we show how the pipeline can be used to study the differences between colon cancer subtypes that could be explained by epigenetic mechanisms. Lastly, we provide pre-generated networks for the 10 most common cancer types that can be readily accessed.

Conclusions

tcga-data-nf is a complete yet flexible and extensible framework that enables the reproducible inference and analysis of cancer regulatory networks, bridging a gap in the current universe of software tools.

Clonal Hematopoiesis and Clinical Outcomes in Metastatic Castration-Resistant Prostate Cancer Patients Given Androgen Receptor Pathway Inhibitors (Alliance A031201)

PURPOSE

Mutations in hematopoietic progenitor cells accumulate with age leading to clonal expansion, termed clonal hematopoiesis (CH). CH in the general population is associated with hematopoietic neoplasms and reduced overall survival (OS), predominantly through cardiovascular adverse events (CVAE). Because androgen receptor pathway inhibitors (ARPI) used in metastatic castration-resistant prostate cancer (mCRPC) are also associated with CVAEs and because CH negatively impacted survival in an advanced solid tumor cohort, we hypothesized that CH in mCRPC may be associated with increased CVAEs and inferior survival.

EXPERIMENTAL DESIGN

A targeted DNA sequencing panel captured common CH mutations in pretreatment blood samples from 957 patients enrolled in Alliance A031201: a randomized trial of enzalutamide ± abiraterone/prednisone in the first-line mCRPC setting. The primary outcome was the impact of CH on OS; the secondary outcomes were progression-free survival (PFS) and CVAEs.

RESULTS

Baseline comorbidities were similar by CH status. No differences in OS/progression-free survival were detected regardless of treatment arm or the variant allele frequency threshold used to define CH [primary: 2% (normal-CH, N-CH); exploratory: 0.5% (low-CH) and 10% (high-CH, H-CH)]. Patients with H-CH (7.2%) and TET2-mutated N-CH (6.0%) had greater odds of any CVAE (14.5% vs. 4.0%; P = 0.0004 and 12.3% vs. 4.2%; P = 0.010, respectively). More major CVAEs were observed in patients with H-CH (5.8% vs. 1.9%; P = 0.042) and N-CH (3.4% vs. 1.8%; P = 0.147).

CONCLUSIONS

CH did not affect survival in patients with mCRPC treated with ARPIs in A031201. H-CH and TET2-mutated CH were associated with more CVAEs. These findings inform the risk/benefit discussion about ARPIs in mCRPC.

Obesity-dependent selection of driver mutations in cancer

Obesity is a risk factor for cancer, but whether obesity is linked to specific genomic subtypes of cancer is unknown. We examined the relationship between obesity and tumor genotype in two clinicogenomic corpora. Obesity was associated with specific driver mutations in lung adenocarcinoma, endometrial carcinoma and cancers of unknown primaries, independent of clinical covariates, demographic factors and genetic ancestry. Obesity is therefore a driver of etiological heterogeneity in some cancers.

MSH6-proficient crypt foci in MSH6 constitutional mismatch repair deficiency: reversion of a frameshifted coding microsatellite to its wild-type sequence

The discovery of "mismatch repair deficient (MMRd)-crypt foci" in non-neoplastic intestinal mucosa in Lynch syndrome (LS) has significantly enhanced our understanding of how tumors and tumor immunity form and evolve in LS. In this study, we report the frequent presence of "mismatch repair proficient (MMRp)-crypt foci" in both non-neoplastic and neoplastic intestinal mucosa in a patient with constitutional MMR deficiency (CMMRD), who carried a germline MSH6 pathogenic variant (c.3261dupC) in trans with an MSH6 likely pathogenic variant (c.3724_3726del) and whose tissues were otherwise deficient in MMR globally. The MMRp-crypts occurred at a rate of 1.1/100 crypts in non-neoplastic intestinal mucosa and were readily discernible in adenomas > 1 cm. Sequencing analysis revealed normalization of the MSH6c.3261dupC variant in MMRp-adenoma crypts, indicating reverse frameshifting of the exon 5 C8 microsatellite. Interestingly but not surprisingly, the MMRp-adenoma crypts remained microsatellite-instability-high (MSI-H), and shared oncogenic APC mutations with the background MMRd-adenoma. Contrasting with MSH6-CMMRD, no PMS2-CMMRD individuals (0/5) harbored MMRp-crypts. In conclusion, our study documents distinct MMRp-crypts in MSH6-CMMRD, a phenomenon in keeping with MSH6 being a frequent target of MSI-H due to its coding microsatellite and suggesting that MSH6-CMMRD can potentially serve as a unique model system to further our understanding of MSH6's role in MSI-H tumor formation and evolution. Our findings also bear diagnostic implications; when using MMR immunohistochemistry as an ancillary tool in detecting CMMRD, awareness of these MMRp crypts can help avoid diagnostic pitfalls.

Isoform-level analyses of 6 cancers uncover extensive genetic risk mechanisms undetected at the gene-level

Integrating genome-wide association study (GWAS) and transcriptomic datasets can help identify potential mediators for germline genetic risk of cancer. However, traditional methods have been largely unsuccessful because of an overreliance on total gene expression. These approaches overlook alternative splicing, which can produce multiple isoforms from the same gene, each with potentially different effects on cancer risk. Here, we integrate genetic and multi-tissue isoform-level gene expression data from the Genotype Tissue-Expression Project (GTEx, N = 108-574) with publicly available European-ancestry GWAS summary statistics (all N > 20,000 cases) to identify both isoform- and gene-level risk associations with six cancers (breast, endometrial, colorectal, lung, ovarian, prostate) and six related cancer subtype classifications (N = 12 total). Compared to traditional methods leveraging total gene expression, directly modeling isoform expression through transcriptome-wide association studies (isoTWAS) substantially increases discovery of transcriptomic mechanisms underlying genetic associations. Using the same RNA-seq datasets, isoTWAS identified 164% more significant unique gene associations compared to TWAS (6,163 and 2,336, respectively), with isoTWAS-prioritized genes enriched 4-fold for evolutionarily-constrained genes (P = 6.1 × 10-13). isoTWAS tags transcriptomic associations at 52% more independent GWAS loci compared to TWAS across the six cancers. Additionally, isoform expression mediates an estimated 63% greater proportion of cancer risk SNP heritability compared to gene expression when evaluating cis-genetic influence on isoform expression. We highlight several notable isoTWAS associations that demonstrate GWAS colocalization at the isoform level but not at the gene level, including, CLPTM1L (lung cancer), LAMC1 (colorectal), and BABAM1 (breast). These results underscore the critical importance of modeling isoform-level expression to maximize discovery of genetic risk mechanisms for cancers.

A patient-derived xenograft mouse platform from epithelioid glioblastoma provides possible druggable screening and translational study

Despite advancements in targeted therapy, glioblastoma remains a challenging condition with limited treatment options. While surgical techniques and external radiation therapy have improved, the median survival for glioblastoma stands at around 12-18 months, with a 5-year survival rate of only 6.8%. Epithelioid glioblastoma (eGBM) represents a rare subtype within the glioma spectrum. Utilizing patient-derived xenograft (PDX) models in mice offers a promising avenue for drug screening and translational research, particularly for this specific glioblastoma subtype. Establishing a stable PDX model for eGBM revealed consistent genetic abnormalities, including BRAF V600E mutation and CDKN2A deletion, in both primary and PDX tumors. Leveraging a curated drug database, compounds potentially targeting these aberrations were identified. By using the novel PDX platform, the results presented in this study demonstrate that the treatments with Palbociclib or Dabrafenib/Trametinib significantly reduced tumor size. RNA sequencing analysis further validated the responsiveness of the tumors to these targeted therapies. In conclusion, PDX models offer a deeper understanding of eGBM at the genomic level and facilitate the identification of potential therapeutic targets. Further translational studies of this novel PDX model hold promise for advancing the diagnosis and treatment of this specific subtype of glioblastoma.

Deciphering resistance mechanisms in cancer: final report of MATCH-R study with a focus on molecular drivers and PDX development

BACKGROUND

Understanding the resistance mechanisms of tumor is crucial for advancing cancer therapies. The prospective MATCH-R trial (NCT02517892), led by Gustave Roussy, aimed to characterize resistance mechanisms to cancer treatments through molecular analysis of fresh tumor biopsies. This report presents the genomic data analysis of the MATCH-R study conducted from 2015 to 2022 and focuses on targeted therapies.

METHODS

The study included resistant metastatic patients (pts) who accepted an image-guided tumor biopsy. After evaluation of tumor content (TC) in frozen tissue biopsies, targeted NGS (10 < TC < 30%) or Whole Exome Sequencing and RNA sequencing (TC > 30%) were performed before and/or after the anticancer therapy. Patient-derived xenografts (PDX) were established by implanting tumor fragments into NOD scid gamma mice and amplified up to five passages.

RESULTS

A total of 1,120 biopsies were collected from 857 pts with the most frequent tumor types being lung (38.8%), digestive (16.3%) and prostate (14.1%) cancer. Molecular targetable driver were identified in 30.9% (n = 265/857) of the patients, with EGFR (41.5%), FGFR2/3 (15.5%), ALK (11.7%), BRAF (6.8%), and KRAS (5.7%) being the most common altered genes. Furthermore, 66.0% (n = 175/265) had a biopsy at progression on targeted therapy. Among resistant cases, 41.1% (n = 72/175) had no identified molecular mechanism, 32.0% (n = 56/175) showed on-target resistance, and 25.1% (n = 44/175) exhibited a by-pass resistance mechanism. Molecular profiling of the 44 patients with by-pass resistance identified 51 variants, with KRAS (13.7%), PIK3CA (11.8%), PTEN (11.8%), NF2 (7.8%), AKT1 (5.9%), and NF1 (5.9%) being the most altered genes. Treatment was tailored for 45% of the patients with a resistance mechanism identified leading to an 11 months median extension of clinical benefit. A total of 341 biopsies were implanted in mice, successfully establishing 136 PDX models achieving a 39.9% success rate. PDX models are available for EGFR (n = 31), FGFR2/3 (n = 26), KRAS (n = 18), ALK (n = 16), BRAF (n = 6) and NTRK (n = 2) driven cancers. These models closely recapitulate the biology of the original tumors in term of molecular alterations and pharmacological status, and served as valuable models to validate overcoming treatment strategies.

CONCLUSION

The MATCH-R study highlights the feasibility of on purpose image guided tumor biopsies and PDX establishment to characterize resistance mechanisms and guide personalized therapies to improve outcomes in pre-treated metastatic patients.

CTNNB1 exon 3 mutations in metastatic solid pseudopapillary neoplasm of the pancreas

BACKGROUND AND OBJECTIVES

Solid pseudopapillary neoplasm (SPN) of the pancreas demonstrates an indolent disease course; however, some patients present with a "malignant" phenotype, including distant metastases resistant to chemotherapy. This analysis identifies molecular drivers of metastatic SPN using the world's largest clinicogenomics database.

METHODS

The American Association for Cancer Research Project Genomics Evidence Neoplasia Information Exchange was queried for primary and metastatic SPN samples. Sample-level genomic alterations were compared. A pan-pancreatic cancer analysis assessed relevant mutations among all metastatic pancreatic malignancies.

RESULTS

Among 28 SPN samples identified (n = 17 primary, n = 11 metastatic), the most commonly mutated gene was CTNNB1, (24/28 samples; 85.7%). Most mutations were missense (21/24; 87.5%) or in-frame deletions (3/24; 12.5%). The most common CTNNB1 mutations in primary SPN were exon 3 S37F/C missense mutations (6/16 profiled patients, 37.5%), contrasting exon 3 D32N/Y/H missense mutations in metastatic samples (6/11 profiled patients, 54.5%). Metastatic SPN had higher rates of CTNNB1 mutations than metastases from pancreatic ductal adenocarcinoma (72.7% vs. 1.1%; q < 0.0001), pancreatic neuroendocrine tumor (72.7% vs. 2.5%; q < 0.0001), and pancreatic acinar cell carcinoma (72.7% vs. 11.5%; q = 0.0254).

CONCLUSIONS

Missense mutations along exon 3 of CTNNB1 predominate metastatic SPN, differentiating these patients from those with metastases from analogous pancreatic malignancies.

Comprehensive Genomic Profiling in Non-Myeloid Hematologic Malignancies Identifies Variants That Can Alter Clinical Practice

BACKGROUND

Comprehensive genomic profiling (CGP) is frequently adopted to direct the clinical care of myeloid neoplasms and solid tumors, but its utility in the care of lymphoid and histiocytic cancers is less well defined.

METHODS

In this study, we aimed to evaluate the frequency at which mutations identified by CGP altered management in non-myeloid hematologic malignancies. We retrospectively examined the CGP results of 105 samples from 101 patients with non-myeloid hematologic malignancies treated at an academic medical center who had CGP testing between 2014 and 2021.

RESULTS

CGP revealed one or more pathogenic or likely pathogenic variant in 92 (88%) of samples and 73 (72%) of tested patients had one or more mutations with diagnostic, prognostic, or therapeutic significance. The identification of a resistance variant resulted in the suspension of the active treatment or affected subsequent treatment choice in 9 (69%) out of 13 patients. However, the presence of a therapy sensitizing variant only led to consideration of a biomarker-directed therapy in 6 (10%) out of 61 patients.

CONCLUSIONS

Overall, CGP of non-myeloid hematologic malignancies identified clinically significant variants in 72% of patients and resulted in a change in management in 22% of patients.

A unique interplay of access and selection shapes peritoneal metastasis evolution in colorectal cancer

Whether metastasis in humans can be accomplished by most primary tumor cells or requires the evolution of a specialized trait remains an open question. To evaluate whether metastases are founded by non-random subsets of primary tumor lineages requires extensive, difficult-to-implement sampling. We have realized an unusually dense multi-region sampling scheme in a cohort of 26 colorectal cancer patients with peritoneal metastases, reconstructing the evolutionary history of on average 28.8 tissue samples per patient with a microsatellite-based fingerprinting assay. To assess metastatic randomness, we evaluate inter- and intra-metastatic heterogeneity relative to the primary tumor and find that peritoneal metastases are more heterogeneous than liver metastases but less diverse than locoregional metastases. Metachronous peritoneal metastases exposed to systemic chemotherapy show significantly higher inter-lesion diversity than synchronous, untreated metastases. Projection of peritoneal metastasis origins onto a spatial map of the primary tumor reveals that they often originate at the deep-invading edge, in contrast to liver and lymph node metastases which exhibit no such preference. Furthermore, peritoneal metastases typically do not share a common subclonal origin with distant metastases in more remote organs. Synthesizing these insights into an evolutionary portrait of peritoneal metastases, we conclude that the peritoneal-metastatic process imposes milder selective pressures onto disseminating cancer cells than the liver-metastatic process. Peritoneal metastases' unique evolutionary features have potential implications for staging and treatment.

Germline DNA Damage Repair Gene Alterations in Patients with Metachronous Breast and Colorectal Cancer

A hereditary component of breast (BC) and colorectal cancer (CRC) has been described in approximately one-third of these tumor types. BC patients have an increased risk of developing CRC as a second primary tumor and vice versa. Germline genomic variants (NextSeq550, Illumina) were investigated in 24 unrelated BC and/or CRC patients and 7 relatives from 3 index patients. Fifty-six pathogenic or likely pathogenic variants were identified in 19 of 24 patients. We detected single-nucleotide variants (SNVs) in CRC predisposition genes (MLH1 and MUTYH) and other promising candidates (CDK5RAP3, MAD1L1, NOS3, and POLM). Eighteen patients presented SNVs or copy number variants (CNVs) in DNA damage repair genes. We also identified SNVs recently associated with BC or CRC predisposition (PABPC1, TYRO3, MAP3K1, SLC15A4, and LAMA1). The PABPC1c.1255C>T variant was detected in nine unrelated patients. Each patient presented at least one SNV/CNV in a candidate gene, and most had alterations in more than one gene, reinforcing a polygenic model for BC/CRC predisposition. A significant fraction of BC/CRC patients with a family history of these tumors harbored deleterious germline variants in DNA repair genes. Our findings can lead to strategies to improve the diagnosis, genetic counseling, and treatment of patients and their relatives.