Molecular profiling of clear cell renal cell carcinoma (ccRCC) tumors of patients in a clinical trial has identified distinct transcriptomic signatures with predictive value, yet data in non-clear ...cell variants (nccRCC) are lacking. We examined the transcriptional profiles of RCC tumors representing key molecular pathways, from a multi-institutional, real-world patient cohort, including ccRCC and centrally reviewed nccRCC samples. ccRCC had increased angiogenesis signature scores compared with the heterogeneous group of nccRCC tumors, while cell cycle, fatty acid oxidation/AMPK signaling, and fatty acid synthesis/pentose phosphate signature scores were increased in one or more nccRCC subtypes. Among both ccRCC and nccRCC tumors, T effector scores statistically correlated with increased immune cell infiltration and were more commonly associated with immunotherapy-related markers (PD-L1+/TMBhi/MSIhi). In conclusion, this study provides evidence of differential gene transcriptional profiles among ccRCC versus nccRCC tumors, providing insights for optimizing personalized and histology-specific therapeutic strategies for patients with advanced RCC.
Canine malignant melanoma, a significant cause of mortality in domestic dogs, is a powerful comparative model for human melanoma, but little is known about its genetic etiology. We mapped the genomic ...landscape of canine melanoma through multi-platform analysis of 37 tumors (31 mucosal, 3 acral, 2 cutaneous, and 1 uveal) and 17 matching constitutional samples including long- and short-insert whole genome sequencing, RNA sequencing, array comparative genomic hybridization, single nucleotide polymorphism array, and targeted Sanger sequencing analyses. We identified novel predominantly truncating mutations in the putative tumor suppressor gene PTPRJ in 19% of cases. No BRAF mutations were detected, but activating RAS mutations (24% of cases) occurred in conserved hotspots in all cutaneous and acral and 13% of mucosal subtypes. MDM2 amplifications (24%) and TP53 mutations (19%) were mutually exclusive. Additional low-frequency recurrent alterations were observed amidst low point mutation rates, an absence of ultraviolet light mutational signatures, and an abundance of copy number and structural alterations. Mutations that modulate cell proliferation and cell cycle control were common and highlight therapeutic axes such as MEK and MDM2 inhibition. This mutational landscape resembles that seen in BRAF wild-type and sun-shielded human melanoma subtypes. Overall, these data inform biological comparisons between canine and human melanoma while suggesting actionable targets in both species.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
BackgroundMerkel cell carcinoma (MCC) is a rare, aggressive neuroendocrine cancer with rapid progression and mortality rates of 33–46%.1 The majority of MCC is caused by Merkel Cell Polyomavirus ...(MCPyV) with the remainder induced by UV-mediated damage.1 2 Regardless of virus positivity or tumor mutational burden (TMB), immune checkpoint inhibitors (ICIs) are first line treatment for MCC1 with half of patients not responding or developing resistance. Few options exist for those refractory to immunotherapy.3 There is a need to identify the MCC-specific factors driving resistance and to identify alternate molecular targets.Methods205 MCC tumors were analyzed using next-generation sequencing (592, NextSeq; WES, NovaSeq) and WTS (NovaSeq) (Caris Life Sciences, Phoenix, AZ). TMB was measured by totaling somatic mutations per tumor (TMB-H: >10 mutations/MB). MCPy viral (MCPyV) status was determined for 68 WES profiled cases using a cut-off of 1000 reads after concordance testing with IHC. Immune cell infiltrates were estimated by Quantiseq. Significance was determined using Chi-square and Mann-Whitney U tests and adjusted for multiple comparisons (q-value <0.05).ResultsThe majority (89.3%) of MCPyV-negative MCC tumors were TMB-high (>10 mutations/Mb), with 96.4% having mutations in TP53 and 80.8% in RB1. Other gene mutations included NOTCH1 (37%), KMT2C (28.6%), TERT (17.9%), FAT1 (14.3%), and PIK3CA (14.3%). In contrast, MCPyV-positive tumors were frequently TMB-low (100%) and rarely harbored mutations in TP53 and RB1 (10.3% and 2.6%, respectively). Immune checkpoint gene (CD80, CD86, CD274, PD1, PD1L, and CTLA4) expression was similar between MCPyV-positive and -negative tumors. Estimated NK cell infiltration was significantly higher in MCPyV-negative tumors. MCPyV-negative MCC also had significantly higher expression of a MAPK pathway activation signature (MPAS).ConclusionsMCPyV-positive and -negative MCC represent two classes of molecularly distinct tumors and can be differentiated based on their TMB and mutational profile. The significantly increased NK cell infiltration seen in MCPyV-negative MCC represents a potential therapeutic pathway with the efficacy of NK cell-stimulating agents currently under investigation in the Quilt-3.063 trial.4 MPAS up-regulation in MCPyV-negative MCC suggests that MAPK inhibitors could be used as an alternative to ICIs, which is supported by preclinical data.3 5 MCPyV-negative and -positive MCC are distinct tumor subtypes whose molecular and immune cell profiles warrant further investigation to optimize use of current ICIs and identify therapeutic targets.ReferencesPark SY, Doolittle-Amieva C, Moshiri Y, Akaike T, Parvathaneni U, Bhatia S, Zaba LC, Nghiem P. How we treat Merkel cell carcinoma: within and beyond current guidelines. Future Oncol. 2021 Apr;17(11):1363−1377.Knepper TC, Montesion M, Russell JS, Sokol ES, Frampton GM, Miller VA, Albacker LA, McLeod HL, Eroglu Z, Khushalani NI, Sondak VK, Messina JL, Schell MJ, DeCaprio JA, Tsai KY, Brohl AS. The Genomic Landscape of Merkel Cell Carcinoma and Clinicogenomic Biomarkers of Response to Immune Checkpoint Inhibitor Therapy. Clin Cancer Res. 2019 Oct 1;25(19):5961−5971.Fang B, Kannan A, Zhao S, Nguyen QH, Ejadi S, Yamamoto M, Barreto JC, Zhao H, Gao L. Inhibition of PI3K by copanlisib exerts potent antitumor effects on Merkel cell carcinoma cell lines and mouse xenografts. Sci Rep. 2020 Jun 1;10(1):8867.ImmunityBio,Inc. QUILT-3.063: A Study of N-803, haNK and Avelumab in Patients With Merkel Cell Carcinoma That Has Progressed After Checkpoint Therapy. ClinicalTrials.gov identifier: NCT03853317. Updated June 18, 2023. Accessed June 27, 2023.Temblador A, Topalis D, Andrei G, Snoeck R. Synergistic targeting of the PI3K/mTOR and MAPK/ERK pathways in Merkel cell carcinoma. Tumour Virus Res. 2022 Dec;14:200244.Ethics ApprovalThis study was conducted in accordance with guidelines of the Declaration of Helsinki, Belmont report, and U.S. Common rule utilizing retrospective, deidentified clinical data in keeping with 45 CFR 46.101(b)(4). Therefore, this study is considered Institutional Review Board (IRB) exempt and no consent was necessary from the subjects.
Background
Primary Extra‐mammary Paget's disease (EMPD) is a very rare cutaneous adenocarcinoma affecting anogenital or axillary regions. It is characterized by a prolonged course with recurrences ...and eventually distant metastatic spread for which no specific therapy is known.
Methods
Eighteen EMPD (13 vulvar and five scrotal) and ten mammary Paget's disease (MPD) cases were comprehensively profiled for gene mutations, fusions and copy number alterations, and for therapy‐relevant protein biomarkers).
Results
Mutations in TP53 and PIK3CA were the most frequent in both cohorts: 7/15 and 5/15 in EMPD; 1/6 and 4/7 in MPD HER2 gene amplification was detected in 4/18 EMPD (3 vulvar and 1 scrotal case) in contrast to MPD where it was detected in the majority (7/8) of cases. TOP2A gene amplification was seen in 2/12 EMPD and 1/6 MPD, respectively. Similarly, no difference in estrogen receptor expression was seen between the EMPD (4/15) and MPD (3/10). Androgen receptor was also expressed in the majority of both cohorts (12/16 EMPD) and (7/8 MPD).Here ARv7 splice variant was detected in 1/7 EMPD and 1/4 MPD cases, respectively. PD‐L1 expression on immune cells was exclusively observed in three vulvar EMPD. In contrast to MPD, six EMPDs harbored a “high” tumor mutation burden (≥10 mutations/Mb). All tested cases from both cohorts were MSI stable.
Conclusions
EMPD shares some targetable biomarkers with its mammary counterpart (steroid receptors, PIK3CA signaling pathways, TOP2A amplification). HER2 positivity is notably lower in EMPD while biomarkers to immune checkpoint inhibitors (high TMB and PD‐L1) were observed in some EMPD. Given that no consistent molecular alteration characterizes EMPD, comprehensive theranostic profiling is required to identify individual patients with targetable molecular alterations.
Comprehensive molecular profiling of primary Extra‐mammary Paget's Disease (EMPD) indicates that individually profiled cases harbor potentially targetable molecular alterations. EMPD shares some but not all molecular features with its mammary counterpart. Potential therapeutic targets in EMPD include steroid receptors (ER and AR), HER2, and PIK3CA signaling pathways, TOP2A amplification, and immune checkpoints (PD‐L1).
Microsatellite instability (MSI) is a key secondary effect of a defective DNA mismatch repair mechanism resulting in incorrectly replicated microsatellites in many malignant tumors. Historically, MSI ...detection has been performed by fragment analysis (FA) on a panel of representative genomic markers. More recently, using next‐generation sequencing (NGS) to analyze thousands of microsatellites has been shown to improve the robustness and sensitivity of MSI detection. However, NGS‐based MSI tests can be prone to population biases if NGS results are aligned to a reference genome instead of patient‐matched normal tissue. We observed an increased rate of false positives in patients of African ancestry with an NGS‐based diagnostic for MSI status utilizing 7317 microsatellite loci. We then minimized this bias by training a modified calling model that utilized 2011 microsatellite loci. With these adjustments 100% (95% CI: 89.1% to 100%) of African ancestry patients in an independent validation test were called correctly using the updated model. This poses not only a significant technical improvement but also has an important clinical impact on directing immune checkpoint inhibitor therapy.
This work presents observations of a significant population bias in an NGS‐based MSI test and minimizes this bias using a computational‐based approach. The research poses not only a significant technical improvement to the NGS‐based MSI diagnostic, but has an important clinical impact on directing immune‐check point inhibitor therapy for late‐stage cancer patients of non‐European descent.
Invasive melanoma is the deadliest type of skin cancer, with 101,110 expected cases to be diagnosed in 2021. Recurrent
and
mutations are well documented in melanoma. Biologic implications of gene ...fusions and the efficacy of therapeutically targeting them remains unknown. Retrospective review of patient samples that underwent next-generation sequencing of the exons of 592 cancer-relevant genes and whole transcriptome sequencing for the detection of gene fusion events and gene expression profiling. Expression of PDL1 and ERK1/2 was assessed by immunohistochemistry (IHC). There were 33 (2.6%) cases with oncogenic fusions (14 novel), involving
,
,
,
,
, and
. MAPK pathway-associated genes were over-expressed in
and
fusion-positive tumors in absence of other driver alterations. Increased expression in tumors with
and
fusions was concurrent with MAPK pathway alterations. For a subset of samples with available tissue, increased phosphorylation of ERK1/2 was observed in
,
, and
fusion-positive tumors. Oncogenic gene fusions are associated with transcriptional activation of the MAPK pathway, suggesting they could be therapeutic targets with available inhibitors. Additional analyses to fully characterize the oncogenic effects of these fusions may support biomarker driven clinical trials.
BackgroundBasal cell carcinoma (BCC) is considered an immunogenic tumor based on the high tumor mutational burden (TMB), increased incidence in immunocompromised patients, and responsiveness to ...imiquimod, a toll-like receptor agonist therapy. However, anti-PD-1 immunotherapy response rates in patients with advanced BCC appear less than that seen with other advanced cutaneous malignancies. Molecular profiles of BCC tumors were analyzed to determine immune phenotypes and resistance mechanisms in comparison to other anti-PD-1 therapy responsive cutaneous malignancies.MethodsNext generation sequencing on DNA (NGS; NextSeq and Novaseq), PD-L1 immunohistochemistry (SP-142 and 28–8 antibody clones, cutoff >5% tumor staining) and mRNA gene expression level (Whole Transcriptome Sequencing, NovaSeq) data from BCC (N=69), melanoma (N=914), and cutaneous squamous cell carcinoma (SCC) tumors (N=165) at Caris Life Sciences (Phoenix, AZ) were analyzed. Tumor mutational burden (TMB) was calculated by counting all non-synonymous missense mutations that had not been previously described as germline alterations. Microenvironment cell population counter1 was used to estimate cell population abundance in the TME. Gene set enrichment analysis (GSEA) was performed on transcriptomes.2 Statistical significance was set at P value or false discovery rate (FDR) < 0.05.ResultsOf the 69 BCC tumors with NGS data, the most frequent mutations were in PTCH1 (82%), P53 (73%) and ARID1A (42%); additional relevant mutations included SMO (18%), JAK1 (9%), PI3KCA (6%), APC (4%), and CTNNB1 (3%). TMB was significantly greater in BCC compared to melanoma (median 30.5 vs 12 mut/Mb, P<0.0001) and similar to SCC (median 29.5 mut/Mb, P=0.9389). PD-L1 positivity was 1/23 (4%) in BCC, 215/831 (26%) in melanoma, and 81/147 (56%) in SCC. Interferon gamma and T-effector immune gene analyses showed significantly lower expression in BCC compared to melanoma and SCC (e.g., IFNg TPM=0.26 (BCC) vs 0.65 and 0.58 (melanoma, SCC, both P<0.01). BCC demonstrated the lowest CD-8 T-cell fractions and the highest neutrophil and cancer associated fibroblast (CAF) fractions compared to melanoma and SCC. Angiogenesis and TGF-beta gene sets were enriched in BCC compared to melanoma (NES=1.5, FDR=0.046 and NES=1.35, FDR=0.055, respectively), but not compared to SCC (NES=0.90, FDR=0.57 and NES=0.94, FDR=0.60, respectively).ConclusionsWhile BCC tumors demonstrated a high TMB, a markedly lower level of adaptive anti-tumor immunity in comparison to other cutaneous malignancies was observed. T-cell exclusion mechanisms mediated through CAFs and desmoplasia, with upregulation of TGF-beta and angiogenic signaling, may play a role. Further investigation into abrogation of these mechanisms is warranted to develop improved anti-PD-1 based therapies for BCC.ReferencesBecht E, Giraldo NA, Lacroix L, Buttard B, Elarouci N, Petitprez F, Selves J, Laurent-Puig P, Sautès-Fridman C, Fridman WH, de Reyniès A. Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression. Genome Biol 2016; 17(1):218.Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 2005;102(43):15545–50.
BRAF mutations are relatively common in many cancers, particularly melanoma, colorectal cancer, and thyroid cancer and to a lesser extent in lung cancer. These mutations can be targeted by BRAF and ...MEK inhibitors, which exhibit good clinical activity. There are conflicting reports of the various relative rates of BRAF Class I mutations (V600 locus), defined as those that exhibit extremely strong kinase activity by stimulating monomeric activation of BRAF, Class II, define as non-V600 mutations that activate BRAF to signal as a RAS-independent dimer, and Class III mutations, defined as “kinase-dead” with low kinase activity as compared to wild type BRAF. Prospective studies have largely focused on patients with tumors harboring Class I BRAF mutations (limited to the V600 locus) where response rates up to 70% with BRAF plus MEK inhibition have been demonstrated. We report on the relative prevalence of various types of BRAF mutations across human cancers in a cohort of 114,662 patients that received comprehensive genomic profiling using next-generation sequencing. Of these patients, 4517 (3.9%) a pathogenic or presumed pathogenic BRAF mutation (3.9%). Of these, 1271 were seen in melanoma, representing 39.7% of all melanomas sequenced, representing the highest rate in all tumors. Class I (V600) mutations were seen overall in 2841 patients (62.1% of BRAF mutations, 2.4% of total cancers). Class II mutations were seen in 746 tumors (16.5% of BRAF mutant, 0.7% of total), and Class III mutations were seen in 801 tumors (17.7% of BRAF, 0.7% of total). Knowledge of the relative prevalence of these types of mutations can aid in the development of agents that might better address non-V600 mutations in cancer.
Impact statement
These data represent the largest aggregation of BRAF mutations within a single clinical database to our knowledge. The relative proportions of both BRAF V600 mutations and non-V600 mutations are informative in all cancers and by malignancy, and can serve as a definitive gold-standard for BRAF mutation cancer incidence by malignancy. The rate of BRAF mutation in human cancer in a real-world large database is lower than previously reported likely representing testing more broadly across tumor types. The relative percentages of Class II and Class III BRAF mutations are higher than previously reported, representing almost 35% of BRAF mutations in cancer. These findings provide support for the development of effective treatments for non-V600 BRAF mutations in cancer.
5015 Background: Neuroendocrine prostate cancer (NEPC) is a relatively androgen receptor (AR)-independent and aggressive variant of PC that can arise from adenocarcinoma with varied degrees of ...adenocarcinoma and high-grade neuroendocrine histologic features seen during its progression. This study evaluated the clinical and molecular features of histologic subtypes of prostate tumors (adenocarcinoma, NEPC, mixed adeno-NE) based on previously validated AR signaling and NEPC transcriptomic signatures of PC. Methods: Whole exome (WES) and whole transcriptome sequencing (WTS) were performed on PC tumors. Molecular subsets were defined by AR signaling signature AR score positive (+) vs negative (-) and NEPC gene signature NE score positive (+) vs negative (-). The prevalence of key molecular alterations (RB1, TP53, PTEN, AR, FANC, SLFN11 expression) were investigated. Genes encoding cell surface antigens with potential therapeutic implications were described across signature groups. Overall survival (OS) was obtained from claims data and analyzed with Kaplan-Meier estimator. Results: A total of 4,476 prostate tumors were analyzed in this study including: 3,623 prostate adenocarcinoma, 56 NEPC, and 25 tumors with mixed adeno-NE. Tissue from 2,641 (67%) tumors were collected from prostate and 1,326 (33%) were metastatic tumors lymph node (14%), bone (9%), liver (7%), lung (2%), CNS (2%). The four AR/NEPC signature-defined subtypes were AR+/NE+ (N=649, 14%), AR+/NE- (N=1614, 36%), AR-/NE+ (N=875, 20%), and AR-/NE- (N=1358, 30%). AR+/NE- was most common in prostate (39%), LN (42%) and lung metastasis (35%); AR-/NE+ was most common in bone (34%) and liver metastasis (43%); AR-/NE- was most common in CNS metastasis. The most common gene alterations in each molecular subtype are defined in Table. AR-/NE+ tumors had the lowest mRNA expression of FOLH1(PSMA), STEAP1, TACSTD2 (Trop-2), CD276 (B7-H3), and PSCA among the four groups. DLL3 expression was higher among NE+ subtypes. FOLH1 and PSCA expression were higher among NE- subtypes. The median OS (months) was longer in NE- than NE+ subtypes AR+/NE- (78.3), AR-/NE- (78.7) vs AR+/NE+ (70.7), AR-/NE+ (69.1). In the platinum-treated subgroup (N=146), the median OS was numerically longer among tumors with SLFN11 overexpression (17.6 vs 12.0) although this was not statistically significant (p-value: 0.99). Conclusions: Molecularly distinct subtypes of PC can be further characterized by AR signaling signature, NEPC gene expression signature, and co-occurring molecular alterations. The phase II biomarker-driven PREDICT trial will integrate the above signatures/molecular alterations to allocate treatment regimens in metastatic castration-resistant PC. Table: see text
GEP-NENs are rare malignancies with increasing incidence. Their molecular characteristics are still undefined. We explored the underlying biology of GEP-NENs and the differences between ...gastrointestinal (GI) and pancreatic (PNEN), high-grade (HG), and low-grade (LG) tumors.
GEP-NENs were analyzed using next-generation sequencing (NGS; MiSeq on 47 genes, NextSeq on 592 genes), IHC, and
hybridization. Tumor mutational burden (TMB) was calculated on the basis of somatic nonsynonymous missense mutations, and microsatellite instability (MSI) was evaluated by NGS of known MSI loci.
In total, 724 GEP-NENs were examined: GI (
= 469), PNEN (
= 255), HG (
= 135), and LG (
= 335). Forty-nine percent were female, and median age was 59. Among LG tumors, the most frequently mutated genes were
(13%),
(10%), and
(10%). HG tumors showed
(51%),
(30%),
(27%), and
(23%). Immune-related biomarkers yielded a lower prevalence in LG tumors compared with HG MSI-H 0% vs. 4% (
= 0.04), PD-L1 overexpression 1% vs. 6% (
= 0.03), TMB-high 1% vs. 7% (
= 0.05). Compared with LG, HG NENs showed a higher mutation rate in
(5.4% vs. 0%,
< 0.0001),
(29.4% vs. 2.6%,
< 0.0001), and
(7% vs. 0.3%,
< 0.0001). When compared with GI, PNEN carried higher frequency of
(25.9% vs. 0.0%,
< 0.0001),
(8.6% vs. 0.8%,
= 0.005),
(20.6% vs. 2.0%,
= 0.007), and
(6.3% vs. 0.0%,
= 0.007), but lower frequency of mutations in
(1.0% vs. 13.8%,
< 0.0001).
Significant molecular differences were observed in GEP-NENs by tumor location and grade, indicating differences in carcinogenic pathways and biology.
PDF
