Pathology Review Research Articles

Pathologic Features of Anti-Ku Myositis.

Characteristics of myositis with anti-Ku antibodies are poorly understood. The purpose of this study was to elucidate the pathologic features of myositis associated with anti-Ku antibodies, compared with immune-mediated necrotizing myopathy (IMNM) with anti-signal recognition particle (SRP) and anti-3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGCR) antibodies, in muscle biopsy-oriented registration cohorts in Japan and Germany. We performed a retrospective pathology review of patients with anti-Ku myositis samples diagnosed in the Japanese and German cohorts. We evaluated histologic features and performed HLA phenotyping. Fifty biopsied muscle samples in the Japanese cohort and 10 in the German cohort were obtained. After exclusion of myositis-specific autoantibodies or other autoimmune connective tissue diseases, 26 samples (43%) of anti-Ku antibody-positive myositis were analyzed. All the samples shared some common features with IMNM, whereas they showed expression of MHC class II and clusters of perivascular inflammatory cells more frequently than the anti-SRP/HMGCR IMNM samples (71% vs 7%/16%; p < 0.005/<0.005; 64% vs 0%/0%; p < 0.005/<0.005). Anti-Ku myositis biopsies could be divided into 2 subgroups based on the extent of necrosis and regeneration. The group with more abundant necrosis and regeneration showed a higher frequency of MHC class II expression and perivascular inflammatory cell clusters. HLA phenotyping in the 44 available patients showed possible associations of HLA-DRB1*03:01, HLA-DRB1*11:01, and HLA-DQB1*03:01 (p = 0.0045, 0.019, and 0.027; odds ratio [OR] 50.2, 4.6, and 2.8; 95% CI 2.6-2942.1, 1.1-14.5, and 1.0-7.0) in the group with less conspicuous necrosis and regeneration. On the contrary, in the group of more abundant necrosis and regeneration, the allele frequencies of HLA-A*24:02, HLA-B*52:01, HLA-C*12:02, and HLA-DRB1*15:02 were lower than those of healthy controls (p = 0.0036, 0.027, 0.016, and 0.026; OR = 0.27, 0, 0, and 0; 95% CI 0.1-0.7, 0-0.8, 0-0.8, and 0-0.8). However, these HLA associations did not remain significant after statistical correction for multiple testing. While anti-Ku myositis shows necrotizing myopathy features, they can be distinguished from anti-SRP/HMGCR IMNM by their MHC class II expression and clusters of perivascular inflammatory cells. The HLA analyses suggest that anti-Ku myositis may have different subsets associated with myopathologic subgroups.

Prognostic Factors after Hepatectomy for Hepatocellular Carcinoma—The Importance of Pathological Immunophenotyping, the Steatohepatitic Subtype and the Impact of the Hepatic Pedicle Clamping

Introduction: Hepatectomy (HP) is, along with liver transplantation, the only potentially curative treatment for Hepatocellular Carcinoma (HCC). The high prevalence of Metabolic Syndrome (MS) may be causing a shift in the HCC spectrum. Hepatic Pedicle Clamping (HPC), used to reduce perioperative bleeding during HP, has been theorized to increase the risk of recurrence. Cytokeratin 19 (CK19) and glypican-3 (GLP-3) have been identified as markers of worse prognosis in HCC. Materials and Methods: A clinical and pathological review of 59 patients undergoing HP for HCC between 2005 and 2013 was performed. Chronic liver disease was observed in 53 patients (89.8%), with cirrhosis in 54.2% [most frequent etiologies: ethylism (47.5%), HCV (25.4%) and HBV (11.9%)]. MS was in 36% of patients. In addition, 95% of patients had Child–Pugh class A and 5% class B, and there was a median MELD of 8 (6–18). A single nodule was observed in 46 patients (78%) with an average size of 5.4 cm. Microscopic vascular invasion (MiVI) was in 49% of patients and macroscopic (MaVI) in 17. HPC was in 43 patients (74.1%). Statistical analysis was performed with SPSS™ 21.0. Survival tests (Kaplan–Meier, log-rank and Cox regression). Statistical significance was with p &lt; 0.05. Results: Major morbidity in 22% of patients. Mortality in 5.1%. Median overall survival (OS) of 71 months and median disease-free survival (DFS) of 37. In a multivariate analysis: MaVI (p = 0.001), MiVI (p = 0.005) and HCV infection (p = 0.002) were associated with worse OS; MS was associated with better OS (p = 0.001); MaVI (p = 0.000), MiVI (p = 0.035) and HPC (p = 0.012) were associated with worse DFS. CK19+/GLP-3− (p = 0.007) and CK19−/GLP-3+ (p = 0.029) patients were associated with worse DFS and CK19−/GLP-3− (p = 0.031) with better DFS. Discussion/Conclusions: HPC was an independent factor of worse DFS. The ischemia-reperfusion injury (IRI) produced by HPC could promote a more angiogenic and angioinvasive phenotype of tumor cells, resulting in higher recurrence. HCV etiology was associated with worse OS. MS was associated with better OS, highlighting the importance of a hepatectomy in these cases. The combined detection of CK19 and GLP-3 was an independent prognostic factor in HCC patients allowing for the identification of more aggressive tumors.

Hepatic lipid accumulation is associated with multiple metabolic pathway alterations but not dyslipidemia and insulin resistance in central bearded dragons (Pogona vitticeps).

To investigate associations between hepatic fat accumulation, fibrosis, and plasma values of primary metabolites, biochemical measurands, insulin, and lipoproteins in bearded dragons. 48 adult central bearded dragons (Pogona vitticeps). Dragons were sedated with alfaxalone, and a blood sample was collected. Plasma was submitted for untargeted primary metabolomics using gas chromatography time-of-flight mass spectrometry, a biochemistry panel, and a lipoprotein panel determined by PAGE. Hepatic lipid content was quantified by liver attenuation measurements from CT images and digital image analysis of standardized histologic sections of the liver. Fibrosis was quantified by digital image analysis on Masson's trichrome-stained histologic sections. Severity was determined from pathologic review of liver sections according to a standardized grading system. Statistical associations were investigated using serial linear models adjusted for false discovery rate and multivariate statistics. Both hepatic fat and fibrosis had a significant effect on CT liver attenuation values. Several oligosaccharides (maltotriose, maltose, ribose, trehalose) and alkaline phosphatase were significantly and linearly increased with hepatic lipid content (all q < .05). On partial least square-discriminant analysis, β-hydroxybutyric acid was the most important discriminatory variable between fatty liver severity grades on histology. No significant associations were found with insulin, lipoproteins, and succinic acid. Bearded dragons with hepatic lipid accumulation experienced multiple metabolic pathway disruptions, some being compatible with mitochondrial dysfunction. No evidence of insulin resistance or dyslipidemia was found. Hepatic biopsy and histopathology remain recommended for reliably diagnosing and staging fatty liver disease in bearded dragons.

Histologic correlates of "Choroidal abnormalities" in Neurofibromatosis type 1 (NF1).

Neurofibromatosis type 1 (NF1) is a rare autosomal dominant disorder characterized by proliferation of cells from neural crest origin. The most common manifestations are cutaneous, neurologic, skeletal and ocular. The distinction of NF1 from other syndromes with multiple café-au-lait macules may be difficult in the pediatric age group, and ocular findings, especially Lisch nodules (i.e., melanocytic hamartomas on the irides), are a useful, early diagnostic tool. In recent years, novel ocular manifestations descriptively referred to as "choroidal abnormalities", choroidal "hyperpigmented spots" and "retinal vascular abnormalities" have been recognized in NF1. Choroidal abnormalities (CA) appear as bright patchy nodules that can be best detected with near-infrared ocular coherence tomography imaging (NIR-OCT). Because of their high specificity and sensitivity for NF1, CA have been added as an ocular diagnostic criterion of NF1 as an alternative to Lisch nodules. Although CA are important ocular diagnostic criteria for NF1, the histologic correlates are controversial. We present the postmortem ocular pathology findings of an NF1 patient for whom clinical notes and ocular imaging were available. Findings in this patient included choroidal hyperpigmented spots on funduscopy and retinal vascular abnormalities, both of which have been reported to be closely associated with CA. Histologic examination of the eyes showed multiple clusters of melanocytes of varying sizes in the choroid. Pathologic review of 12 additional postmortem eyes from 6 NF1 patients showed multiple, bilateral choroidal melanocytic aggregates in all eyes. These findings suggest that the CA seen on NIR-OCT and the hyperpigmented spots seen clinically in NF1 patients are manifestations of multifocal choroidal melanocytic clusters, consistent with choroidal melanocytic hamartomas. Lisch nodules, often multiple, were present in all eyes with morphology that differed from the choroidal hamartomas. As such, although CA and Lisch nodules are melanocytic hamartomas, there are clear phenotypical differences in their morphologies.

Abstract NG07: Association between somatic microsatellite instability, hypermutation status, and specific T cell subsets in colorectal cancer tumors

Abstract Background: Colorectal cancer (CRC) is a critical public health concern as the third most commonly diagnosed cancer and second leading cause of cancer death globally. CRC is a heterogeneous disease with many different mechanisms and molecular subtypes. Around 15% of sporadic CRCs are classified as exhibiting high microsatellite instability (MSI-high) due to deficient DNA mismatch repair (dMMR). In the presence of MSI-high, colorectal tumors accumulate somatic mutations, resulting in high neoantigen burden, which, in turn, elicits a strong T cell response. Several previous studies have shown that MSI-high status is associated with overall levels of T cell infiltration in CRC and, specifically, with CD45RO+ T cell density. However, many studies have measured T cell densities using single-plex immunohistochemistry assays of individual T cell markers, which fail to capture the complexity of the T cell response in tumors, and the contributions of different T cell subsets. Using a multiplex immunofluorescence panel, we aimed to characterize the composition of the T cell response in CRC tumors in relation to MSI-high and hypermutation status in CRC. Methods: This study was conducted within a subset of participants from three well-characterized epidemiologic studies included in the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO): the Ontario Family Colon Cancer Registry (OFCCR), the Nurses’ Health Study (NHS), the Health Professionals Follow-up Study (HPFS). In a total of N=637 participants with CRC, we profiled the in-situ T cell landscape of CRC using digital imaging, machine learning, and a multiplexed immunofluorescence panel. Our customized 9-plex panel included antibodies directed against CD3, CD4, CD8, CD45RA, CD45RO, FOXP3, and MKI67, as well as a pan-cytokeratin antibody to identify tumor/epithelial cells and nuclear DAPI (4’, 6-diamidino-2-phenylindole) stain. Assays were conducted using tissue microarrays (TMAs) where all slides were sent to Dana Farber Cancer Institute for analysis. In brief, core selection from donor FFPE blocks was guided by pathologist review of H&amp;E-stained slides. For each CRC case, TMA blocks have 2-4 cores (0.6 mm) from tumor areas. T cell immune microenvironment is assessed for each tumor histologically using a multispectral imaging platform (PerkinElmer Vectra 3.0) for multiplexed immunofluorescence (mIF), where TMAs are stained with all markers concurrently and imaged. With pathologist supervision, a machine learning algorithm segmented tissue into epithelial and stromal area regions as well as phenotyped individual cells. The mIF panel has been validated against traditional chromogenic IHC. Based on these markers, we quantified counts and densities of naive, memory, and regulatory subsets of helper (CD3+CD4+) and cytotoxic (CD3+CD8+) T cells, and looked separately at these subsets within epithelial and stromal tissue, resulting in 12 unique subsets. Microsatellite instability and hypermutation status were determined from one of two targeted sequencing panels that included either 205 or 298 genes. MSI status was called using mSINGS. Hypermutation status was defined by plotting point mutations for all samples and observing different peaks, separately by panel. The minimum value between the two peaks was 23 and 26 point mutations per sample, respectively, which were used as cut-points. We used multivariable ordinal logistic regression to estimate odds ratios (ORs) and 95% confidence intervals (CIs) for the association between MSI/hypermutation status with quantiles of specific T cell densities in CRC. As an alternative approach where counts were modeled directly, we used negative binomial count models with an offset term for area. Ordinal logistic regression either used quartiles or tertiles of T cell densities as the outcome, where different subsets were assessed for zero-inflation considering both epithelial and stromal tissue, so the same subset used the same categorization in each tissue. Subsets with less than 25% zero counts were divided into quartiles, subsets with greater than 25% zero counts into tertiles. Study-specific quantile cut points were used to limit potential batch effects across TMAs. Models were adjusted for age, sex, and study, and p-values were adjusted for multiple testing using the false discovery rate method for 12 independent tests. Results: Among 637 CRC tumors with targeted tumor sequencing and T cell immune profile available, 107 were classified as MSI-high, and 106 were classified as hypermutated. 98 tumors were both MSI-high and hypermutated. Compared to tumors with low microsatellite instability (MSI-low) or microsatellite stable (MSS) tumors, MSI-high tumors were strongly associated (ORs around 2 or higher) with higher T cell densities for all epithelial area CD3+CD4+, epithelial area CD3+CD8+, and stromal area CD3+CD8+ T cells (adjusted p-values &amp;lt;0.001). Compared to MSI-low/MSS tumors, MSI-high tumors had 3 times the odds of greater quantile of epithelial area CD3+CD8+ subsets defined as naive, memory, and regulatory [OR= 3.2 95% CI (2.14, 4.79), OR=3.19 (2.15, 4.72), OR=3.31 (2.20, 4.97), respectively]. MSI-high tumors were not associated with higher densities of stromal area CD3+CD4+ naive, memory, or regulatory cells. Effect estimates for hypermutation status showed consistent results and the same conclusions as MSI. Effect estimates from negative binomial models showed consistent findings with the ordinal logistic results presented. Conclusions: While it is well known that T cells overall are strongly associated with MSI status in CRC, the present study improves our understanding of what specific T cell subsets in what location in the tumor are associated with MSI and hypermutation status. Additionally, given the high level of T cell infiltration in MSI-high/dMMR tumors, these tumors are more likely to respond favorably to immune checkpoint inhibitors (ICIs). A more granular understanding of specific T cell subsets that are associated with these tumor phenotypes may improve our understanding of underlying biology and help inform targeted immunotherapy treatment decision-making for the MSI-high/dMMR CRC subtype. In future work we aim to examine increasing mutation frequency as a continuous variable and with more specific categorization of mutation frequency than binary cut-points in association with T cell profile. Citation Format: Claire Elizabeth Thomas, Yasutoshi Takashima, Tomotaka Ugai, Daniel D. Buchanan, Conghui Qu, Li Hsu, Andressa Dias Costa, Stephen Gallinger, Robert C. Grant, Jeroen R. Huyghe, Sushma S. Thomas, Robert S. Steinfelder, Shuji Ogino, Amanda I. Phipps, Jonathan A. Nowak, Ulrike Peters. Association between somatic microsatellite instability, hypermutation status, and specific T cell subsets in colorectal cancer tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr NG07.

Reevaluation of negative cervical conizations: Frequency, diagnostic errors, risk factors and management

ObjectiveCervical conization is an effective treatment for precancerous lesions. However, in cases where no high-grade lesion is identified in the surgical specimen, managing these patients may be challenging due to the absence of established follow-up protocols for negative conizations. This study aimed to assess the negative conization rates at our institution by histopathological review, identify diagnostic errors, possible risk and recurrence factors and propose follow-up strategies for this group of patients. MethodsA retrospective study from January-2010 to December-2020 analyzed patients with negative conization including all surgical techniques and procedure indications. Biopsy and cervical conizations slides were reviewed and patients who kept a negative result underwent deeper levels sectioning of the paraffin blocks with immunohistochemical stains application: p16, Ki-67 and geminin. Data were compared with a control group composed by 29 women with CIN3. ResultsOut of 1022 conizations, 186 were negative (18.1%), with 151 cases selected for the study after excluding 35 patients. Following pathology review, 4 patients were excluded due to false-positive cervical biopsy results, 16 for false-negative conization results and 9 for hidden dysplasia identified after deeper sectioning. The remaining 122 patients were considered truly negative cones (11.9%) and exhibited IHC staining with p16 positive in 20.4% of cases, low Ki-67 expression, and low geminin score in most cases. Specimens with CIN 1 had higher prevalence of p16 staining, Ki-67 expression and geminin score when compared to absence of neoplasia, nevertheless geminin had no statistical difference. Older age, higher parity and IHC pattern with negative p16, low Ki-67 and geminin expressions were identified as risk factors for negative cones (p<0.05). Only 10 patients recurred for high-grade lesions, with no statistically significant risk factors identified. ConclusionsThe negative conization rate was 11.9%, with diagnostic errors identified across pre-surgical biopsy, cone specimen, and deeper levels. Risk factors included older age, higher parity, low expression of p16, Ki-67 and geminin (p<0.05). Recurrence represented 8.1% of the negative cones, without identification of statistically significant risk factors. Pathological review with deeper level sections and 2-year follow-up are recommended for patients with negative conizations.

Perineural invasion in cervical cancer: A multicenter retrospective study

ObjectiveThe study aimed to evaluate the accuracy of perineural invasion (PNI) diagnosis in cervical cancer, and to analyze the impact of PNI on the prognosis and postoperative adjuvant treatment decisions for cervical cancer. MethodsA retrospective pathological review of PNI in cervical cancer was conducted from 2004 to 2016 in 15 hospitals. ResultsThis study included a total of 1208 cases, comprising 273 cases with PNI and 935 cases without. The false positive rate and false negative rate of PNI diagnosis were 5.35% (50/935) and 33.33% (91/273), respectively. Adenocarcinoma, deep stromal invasion, lymphovascular space invasion (LVSI) (+), and margin involvement were independent risk factors for PNI. Both 5-year overall survival rate (OS) and 5-year disease-free survival rate (DFS) of PNI group were worse than non-PNI group. PNI was an independent risk factor for 5-year OS and 5-year DFS. In cases receiving standard postoperative adjuvant treatment, among those with two intermediate-risk factors, both 5-year OS and DFS were worse in the PNI group. Among cases with three intermediate-risk factors or at least one high-risk factor, there was no difference in 5-year OS between the two groups, but 5-year DFS was worse in the PNI group. ConclusionThe diagnosis of PNI in cervical cancer was not accurate. Adenocarcinoma, deep stromal invasion, LVSI, and margin involvement were independent risk factors for PNI. PNI was an independent risk factor for 5-year OS and DFS. PNI has the potential to serve as a new high-risk factor, thus providing guidance for postoperative adjuvant therapy.

Abstract 4627: Metastatic renal cell carcinoma with occult primary: Clinical and biological evidence for a new entity of cancers of unknown primary that beneficiates from tissue-tailored treatment

Abstract Background: Cancers of unknown primary (CUP) is a heterogenous group of malignancies characterized by distant metastases in the absence of detectable primary. Specifics subgroups of CUP that share similarities with cancers of known primary beneficiate from tissue-tailored therapeutic strategies. The objective of this study was to characterize the clinical and biological presentation of a cohort of patients with suspected CUP of renal origin (rCUP) and to evaluate their optimal therapeutic management. Methods: All Patients with rCUP identified prospectively between 2020 and 2023 within the French National Multidisciplinary Tumor Board for CUP were included. Centralized pathological review and immunohistochemical stainings were performed. Whole Exome Sequencing (WES), whole transcriptomic sequencing (RNAseq) and application of the deep-learning based algorithm TransCUPtomics for prediction of tissue of origin, and DNA methylation analysis were performed and compared to public renal cell carcinomas (RCC). Progression Free Survival (PFS) and Overall Survival (OS) were calculated using Kaplan-Meier estimates. Results: 23 patients were included. The median age at diagnosis was 57 yo and 17/23 were male. The most common metastatic sites were the bones (N=17) and the lymph nodes (N=14). 19/23 patients presented with at least two distinct distant metastatic sites. Genomic analyses performed in 10 patients led to the identification of recurrent inactivating mutations in genes commonly altered in RCC, including NF2 (N=7), SETD2 (N=3), or VHL (N=1). 10/11 samples analyzed by RNAseq were predicted as RCC by the TransCUPtomics classifier based on their gene expression profiles. DNA methylation profiling performed in 7 samples showed major similarity with known RCC subtypes.Centralized pathological review and integration of molecular characteristics led to the final diagnoses of papillary RCC (N=2), clear cell RCC (N=7), renal medullary carcinoma (N=1), TFEB-amplified RCC (N=1) and unclassified RCC (N=12). 20/23 patients received at least one line of systemic treatment based on the renal origin, including anti-angiogenic TKI, anti-PD1/PDL1 antibody, anti-CTLA4 antibody or mTOR inhibitor. The median PFS under the first renal-oriented systemic treatment was 5 months and 10 patients remained progression-free for more than 6 months under tailored-treatment. The median OS was 31 months, and 11 patients are still alive in October 2023. Conclusions: This study shows that rCUP represent a new entity within CUPs that shares major similarities with classical RCC despite the more frequent presentation of unfavorable prognostic factors. Prolonged survival can be observed with renal-tailored systemic treatment, supporting the individualization of these patients within CUP. Citation Format: Nicolas Jacquin, Julien Masliah-Planchon, Guillaume Grisay, Ronan Flippot, Riwan Brillet, Célia Dupain, Maud Kamal, Isabelle Guillou, Nadège Gruel, Nicolas Servant, Pierre Gestraud, Jennifer Wong, Vincent Cockenpot, Andreia Goncalves, Janick Selves, Hélène Blons, Etienne Rouleau, Oliver Delattre, Christophe Le Tourneau, Ivan Bièche, Yves Allory, Laurence Albigès, Sarah Watson. Metastatic renal cell carcinoma with occult primary: Clinical and biological evidence for a new entity of cancers of unknown primary that beneficiates from tissue-tailored treatment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4627.

Abstract 4944: Divergent proteogenomic gene expression is driven by microenvironment across tumor types

Abstract Solid tumors develop through a complex series of genome and downstream expression alterations that interact with the local tissue microenvironment, leading to a transformed cell and malignant phenotype. With massive multi-omic data, recent proteogenomics studies have jointly analyzed RNA and protein expression to uncover new gene regulatory relationships; however, many of these studies focused on single tumor types and lack a generalizable view of joint RNA and protein expression. Here, we present the first pan-cancer analysis of sample-wise RNA to protein correlation (SRPC). We re-analyzed over 1,000 tumors across 10 tumor types from published proteogenomic data from the Clinical Proteomic Tumor Analysis Consortium (CPTAC) and the Applied Proteogenomics OrganizationaL Learning and Outcomes (APOLLO) Research Network. We identified a wide range of SRPC across all tumors (ρ range: -0.08 to 0.70, median: 0.45). We then analyzed tumor pathologic and molecular characteristics versus the range of SRPC. High SRPC tumors had high tumor purity by pathology review, by somatic DNA whole exome sequencing, and by RNA and protein purity scores. In contrast, low SRPC tumors had high immune cell and stromal cell expression scores as inferred by either protein or RNA based signatures. We observed marked differences in cell type populations estimated by expression in different SRPC tumor tranches (low SRPC: macrophages, endothelial cells, cancer-associated fibroblasts; high SRPC: CD4+ Th2 cells). Tumors expressed signaling pathways depending on their SRPC (low SRPC: hypoxia, inflammatory response, and KRAS signaling; high SRPC: DNA repair and E2F targets). SRPC also stratifies tumors with distinct somatic DNA alterations (low SRPC: HRAS and NF2; high SRPC: TP53, MEN1, high Tumor Mutational Burden and high DNA chromosomal instability). Finally, we found that cancer driver genes displayed divergent gene-wise RNA to protein correlations (GRPC) among tumor types with a median absolute deviation interquartile range of 0.1 - 0.2, suggesting tumor-type-specific regulation. In summary, divergent RNA and protein expression is driven, in part, by tumor microenvironment composition across tumor types. Tumors with a diverse cellular microenvironment display a summation of RNA and protein expression resulting from this cell type diversity leading to a low SRPC, while tumors predominated by tumor cells display coordinated RNA and protein expression levels resulting from a pure clonal or cell type leading to a high SRPC. This first deep analysis into sample-wise RNA to protein correlation represents a large proteogenomic community resource for informing biomarker analysis by modality and by tranches of tumor microenvironment. The views expressed in this abstract are solely of the authors and do not reflect the official policy of the Departments of Army/Navy/Air Force, Department of Defense, USUHS, HJF, or U.S. Government. Citation Format: Joseph LaMorte, Nicholas Bateman, Thomas Conrads, Robert F. Browning, Craig D. Shriver, Robert L. Kortum, Matthew D. Wilkerson. Divergent proteogenomic gene expression is driven by microenvironment across tumor types [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4944.

Abstract 3626: Day 21 early bone marrow response does not offer high concordance with response bone marrow in the induction chemotherapy setting of FLT3 mutant acute myeloid leukemia

Abstract Purpose: Day 14 early bone marrow biopsies are routinely initiated to determine need for reinduction chemotherapy, but poorly predict true response and risk overtreatment. Day 21 (D21) bone marrow biopsies have been performed in the context of trials utilizing FLT3-targeted therapies in combination with induction chemotherapy (Stone et al. NEJM 2017). However, the utility of D21 bone marrow responses is not well defined. Methods: We retrospectively identified 26 newly diagnosed FLT3 mutant AML patients who underwent induction chemotherapy with midostaurin and Next Generation Sequencing (NGS) of bone marrow aspirate within a week of diagnosis. Results: 19/26 (73%) of patients had both D21 and response bone marrow biopsy. Of the remaining 7 patients, 4 patients did not have D21 bone marrow, 2 died of unrelated complications prior to response bone marrow, and 1 did not have recovery marrow available for assessment. Our cohort included 13 (50%) men with a median age of 57 years (range, 21 - 73 years). All patients had ECOG of 0 - 1. 96% of cases were de novo AML and 81% had normal cytogenetics. FLT3 ITD mutations were detected in 17 (65%) patients with a median FLT3 ITD ratio of 0.305 (range, 0.03 - 1) and median FLT3 VAF of 23.8% (range, 3.2 - 80.6%). 7 patients (26.9%) underwent additional allogeneic stem cell transplant. In the 19 patients evaluable for analysis, 13/13 (100%) patients with blast % ≤ 5 at D21 achieved a complete response (CR) based on recovery marrow. 4/6 (67%) patients with blast % &amp;gt; 5 at D21 which were considered to have residual disease based on pathology review (median blast % 11 (range, 6 - 17%) ultimately achieved a CR. The 2 patients that did not achieve a CR has a blast % of 29% and 9% on D21 marrow. Thus, the positive predictive value of D21 early bone marrow response corresponding with the response bone marrow was only 33% in our patient cohort. Of the 4 patients that did not have D21 marrow but had recovery marrows available for review, the CR rate was 100%. No other significant differences in initial disease characteristics were seen. There were no differences proportion of co-mutations in NPM1, DNMT3A, TP53, IDH2, and IDH1, and higher FLT3 ITD ratio nor FLT3 VAF corresponded with ability to clear D21 bone marrow. Additionally, there were no differences in minimal residual disease (MRD) and overall survival (OS) between the groups. Conclusions: Our study suggests early bone marrow response in the context of FLT3-mutant disease is not dependent on inherent disease characteristics and does not correspond to overall response to targeted induction chemotherapy. The utility of these marrows in is this population needs to be studied further in a larger cohort to better understand the clinical necessity to avoid unnecessary cost/procedures to patients and even more importantly unnecessary reinductions. Citation Format: Vincent Lok, Su Bin Hahn, Nikesh N. Shah, Daniel A. Kerr, Ivan M. Borrello, Eduardo M. Sotomayor, David M. Swoboda. Day 21 early bone marrow response does not offer high concordance with response bone marrow in the induction chemotherapy setting of FLT3 mutant acute myeloid leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3626.

Abstract 4869: Efficient study design for the discovery of a gene expression signature predicting metastasis in cutaneous squamous cell carcinoma

Abstract Background: The StepIdent study aims to develop a gene signature predicting metastasis in patients with cutaneous squamous cell carcinoma (cSCC) to improve risk stratification, thus enabling personalized decisions about follow-up schedules and treatment options. Here we describe the unique characteristics, challenges, and best practices for an efficient design of a discovery cohort for a rare outcome (metastasis prevalence: 2-5%); for retrieving, curating, and linking the clinical and pathological data through nationwide databases; and for measuring gene expression through sequencing of archived Formalin-Fixed Paraffin-Embedded (FFPE) primary tumor samples. Methods: Following a predefined protocol, we identified a nested-case control cohort (NCC) of 305 cases and 305 controls from a nationwide cohort of 19,120 patients with a first cSCC in the Netherlands from 2007 to 2009, followed up until 2020. We chose an NCC design since it is an efficient study design in a rare outcome setting (weighting is needed to accommodate the under-sampling of the controls). Patients were identified from the Dutch National Cancer Registry (NCR) and the clinical information was retrieved from the NCR which is linked to the nationwide registry of histo- and cytopathology (PALGA). Tumor blocks were requested from PALGA, and pathological characteristics were assessed by dermatopathologists. We matched controls to cases, based on a risk score estimated by a clinicopathological model. Gene expression was measured using the Illumina RNA Prep with Enrichment kit combined with the whole exome panel and paired-end sequenced on the NextSeq 550. Results: Tissue slides for 541 samples were retrieved for sequencing. 151 samples were excluded after pathology review or due to low pre-library concentration. The final cohort includes 195 case-control pairs (n=390). The median sequencing depth was 43M (Q1-Q3: 35-52M); the median Q30 was 85% (Q1-Q3: 83-87%); the median GC content was 51% (Q1-Q3: 50-52%); a median of 1.8% of base pairs (Q1-Q3: 1.4-2.1%) was trimmed prior to the mapping/alignment; a median of 69% (Q1-Q3: 65-74%) of reads were aligned as protein-coding and a median of 7% (Q1-Q3: 6-10%) as rRNA; a median of 95% (Q1-Q3: 93-96%) of reads were aligned by STAR. Two samples were excluded based on quality control. Conclusion: We described an efficient design and implementation of a nationwide discovery study in cSCC, involving the retrieval of clinicopathological data, the collection of FFPE materials, and the execution of omics measurements. This study presents the largest cohort to date, incorporating omics measurements of primary cSCC samples, combined with simultaneous access to well-curated clinical and pathological information and follow-up data. Our findings can provide guidance for similar studies involving a rare clinical endpoint, where an efficient study design is a necessity. Citation Format: Barbara Rentroia-Pacheco, Lara Pozza, Yan Ting Chen, Daphne Huigh, Celeste J. Eggermont, Olivia FM Steijlen, Sheril Alex, Jvalini Dwarkasing, Domenico Bellomo, Harmen JG van de Werken, Antien L. Mooyaart, Marlies Wakkee, Loes M. Hollestein. Efficient study design for the discovery of a gene expression signature predicting metastasis in cutaneous squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4869.

Abstract 3910: The Atlas of Blood Cancer Genomes: A resource for therapeutic and biomarker development

Abstract Developing a novel cancer therapy is an expensive, time-consuming, high-risk endeavor that involves identifying a molecular target as well as target indications. This process could be accelerated by a comprehensive interrogation of driver variants and gene expression profiles across cancer types. The Atlas of Blood Cancer Genomes (ABCG) project was initiated to elucidate the molecular basis of all leukemias and lymphomas, building on advances in genomic technologies, our capabilities for data analysis, and economies of scale. The ABCG project includes collaborators from 25 institutions worldwide who contributed samples from 10,512 patients comprising every type of blood cancer in the World Health Organization classifications. All cases were de-identified and their associated pathology and clinical information entered into a purpose-built web-based system. All cases underwent pathology and clinical data review by experienced hematopathologists and oncologists. Samples were subjected to whole exome DNA and RNA sequencing. We examined three classes of therapeutic targets with selected examples of application: 1. Surface markers: Surface markers are targets of many approved and experimental therapies in blood cancers (CAR-T cells, monoclonal and bispecific antibodies). We found that CD22, which has been evaluated as a target in diffuse large B-cell lymphoma (DLBCL), is also highly expressed in follicular lymphoma, adult ALL, mantle cell lymphoma, and high-grade B cell lymphoma, all areas of clinical need. We can evaluate the expression of virtually any marker or combination of markers across all blood cancers while noting areas of greatest clinical need within and across diseases, providing the basis to reclassify diseases by therapeutic target. 2. Genetic targets: Our work assesses the entire spectrum of genetic alterations including mutations and fusions. We found targetable alterations including BCR-ABL1 fusions, EZH2 Y641, IDH2 R140Q and BRAF V600E mutations in multiple cancers, albeit at low frequency, pointing to potential new indications for existing drugs in subsets of rare diseases. 3. Complex targets (immune or expression signatures or combinations of gene variants): Past work defined DLBCL immune and other signatures associated with response to avadomide, a novel cereblon inhibitor. We found that these signatures are also highly expressed in large subsets of peripheral T-cell lymphomas and acute myeloid leukemia, both areas of major unmet clinical need. Thus, we can interrogate immune and other signatures across the spectrum of cancers to uncover potential biomarkers of response. The ABCG project will enable the comprehensive study of genomic and clinicopathological features of all blood cancers. We anticipate that our data, approaches and results will provide a lasting resource for molecular classification and therapeutic development in all leukemias and lymphomas. Citation Format: Jennifer Shingleton, Raju Pillai, Sarah Ondrejka, Govind Bhagat, Amy Chadburn, Matthew McKinney, Jean Koff, Dina Soliman, Magdalena Czader, Abner Louissaint, Shaoying Li, Choon Kiat Ong, Amir Behdad, Andrew Evens, Yaso Natkunam, Mette Pedersen, Sirpa Leppa, Eric Tse, Jennifer Chapman, Catalina Amador-Ortiz, Yuri Fedoriw, Andrew Evans, Jiong Yan, Mina Xu, Kikkeri Naresh, Clay Parker, David Hsu, Sandeep Dave. The Atlas of Blood Cancer Genomes: A resource for therapeutic and biomarker development [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3910.

Abstract 5094: Immunotherapy in advanced cutaneous non-melanomatous spindle cell neoplasms

Abstract Background: Non-melanomatous cutaneous spindle cell neoplasms (NMCSpC) are a rare group of malignancies including pleomorphic dermal sarcoma (PDS) and spindle-cell cutaneous squamous cell carcinoma (SpSCC). They present a diagnostic challenge with overlapping morphological features and variable patterns of immunohistochemical (IHC) staining. There is a lack of consensus on how to best manage advanced NMCSpC and limited reports of immunotherapy (IO) responses. This study reviews the efficacy of IO in NMCSpC and performs comprehensive tumor profiling to identify biological rationale for IO use in this rare group of tumors. Methods: We performed a single-center retrospective review of all locally-advanced or metastatic NMCSpCs treated with IO. Blinded histopathology reviews occurred to confirm each diagnosis. Overall response rates (ORR) were collected as per Response Evaluation Criteria in Solid Tumors 1.1 or Positron Emission Tomography Response Criteria 1.0. Comprehensive tumor profiling included whole exome sequencing for tumor mutational burden (TMB) and ultraviolet(UV)-signatures, and IHC for immune-cell infiltration (CD103/CD4/CD3/CD8/CD20) and immune-checkpoint expression (PD-L1/TIGIT/LAG3). Results: 7 patients were identified. Median follow up was 18.1 months (range: 5.3-34.7). ORR 86% (6/7) with five complete responses (CR). One patient who achieved stable disease progressed. Responses were durable with two patients in CR &amp;gt;30 months after IO commencement. Blinded pathological review identified 3 SpSCC, 2 PDS and 2 spindle cell tumors of unclear sub-classification. All patients had high TMB and UV-signatures. One patient had PD-L1 100% (combined positive score) with abundant immune-cell infiltration and LAG3 expression (Table 1). Conclusion: In advanced NMCSpC, excellent responses to IO with durable disease control was observed. IO is worthy of further exploration in these patients. UV-signatures and high TMB could be used to help select patients for treatment. Immunohistochemistry (IHC)^, tumor mutational burden and ultraviolet signatures Patient T-cell markers B-cell marker Immune-checkpoints Tumor mutational burden (mutations/megabase) Ultraviolet-mutational signature Best response assessment# CD103 CD4 CD3 CD8 CD20 PD-L1 TIGIT LAG3 1 1 20 1 1 0 7 0 0 17.94 Yes Stable metabolic response 2 1 20 30 10 0 100 0 10 35.34 Yes Complete metabolic response 3 1 10 10 5 0 5 0 0 104.87 Yes Complete metabolic response 4 1 0 1 0 0 0 0 0 74.04 Yes Partial metabolic response 5* NA NA NA NA NA NA NA NA 29 Yes Complete metabolic response 6 1 0 0 5 0 0 0 4 12.02 Yes Complete metabolic response 7 1 0 5 1 0 0 0 0 41.17 Yes Complete response ^IHC scores are % of positively stained cells, except for PD-L1 which is combined positive score (CPS). *Insufficient tissue for IHC on Patient 5. #As per PERCIST 1.0 on FDG-PET/CT or RECIST1.1 on CT. Citation Format: Luke S. McLean, Annette M. Lim, Christopher Angel, Richard J. Young, Angela Pizzolla, Stuart Archer, Alesha A. Thai, Benjamin Solomon, Jeremy Lewin, Danny Rischin. Immunotherapy in advanced cutaneous non-melanomatous spindle cell neoplasms [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5094.

Abstract 225: Integration of patient-derived tumor organoids and patient clinical multimodal data to investigate the role of organoids in predicting treatment response

Abstract Introduction: Patient-derived organoids (PDOs) enable the ex vivo study of tumor heterogeneity and its effect on response to treatment. Our previous work demonstrated that our robust pan-cancer organoid platform shows genetic and transcriptomic concordance with clinical tumor samples and can be deployed for high-throughput drug response screening. Here, we ran a standard of care (SOC) panel on PDOs with paired de-identified clinically curated data to enable a comparison of patient response to the same drugs ex vivo and exploration of potentially more effective treatment alternatives. Methods: Patient tumor samples were cultivated into tumor PDOs in extracellular matrix + chemically defined media. PDOs underwent pathological review to ensure development of malignant tissue. PDOs were identified by clusters of Hoechst-positive cells and live and dead cell counts for each PDO were determined using fluorescent stains. The median number of cells per PDO in the well was calculated, excluding PDOs with &amp;lt;3 cells and the top 1% of PDOs by area. Drug screens were run with 6 doses of the compound and the inverse area under the curve of ToPro3 live cell measurements was calculated to quantify response. Tempus xT DNA-seq and xR whole-transcriptome assays were used to perform NGS on organoids and patient samples where available. Data was processed through our standard pipeline to identify targetable mutations, neoantigens, copy number variants (CNVs) and fusions. Results: We analyzed 38 PDOs with paired patient data across 9 different cancer types comprising mostly lung (n=14) and colorectal (n=12); 17 PDOs had responses associated with treatment given close to the biopsy collection date. Across the full PDO cohort, we observed a range of responses to SOC compounds, providing a platform to better understand biomarkers and mechanisms of response. Treatment response in PDOs correlated with patient response in many cases. In the 3 patients with progression-free survival &amp;gt;1 year and outcomes of either complete response or stable disease, all showed strong responses to the corresponding drugs in the SOC panel. For most patients with progressive disease recorded after treatment the corresponding PDO cluster showed limited response to treatment. The SOC panel includes several targeted therapies that provide insight into how patients respond to treatment beyond chemotherapy. For two patients with limited response to treatment in both patient and PDO, we identified targeted therapies relevant to their clinico-genomic landscape. One patient showed improved clinical outcomes to a later line of therapy with a similar mechanism of action to the drug that showed response in the organoid. Conclusion: These results suggest that PDOs may serve as a powerful tool for predicting patient response to treatment and aid the development of new therapies. Citation Format: Kathleen A. Burke, Brian Larsen, Yi-Hung Carol Tan, Jessica Barbeau, Curtis Brinkman, Elle Moore, Nick Callamaras, Jonathan R. Dry, Iker Huerga, Kate Sasser, Jeffrey A. Borgia. Integration of patient-derived tumor organoids and patient clinical multimodal data to investigate the role of organoids in predicting treatment response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 225.

Abstract 5656: Longitudinal spatial profiling reveals chemoresistance mechanisms and characteristics of minimal residual disease in high-grade serous ovarian cancer

Abstract High-grade serous ovarian cancer (HGSOC) is the most lethal gynecologic malignancy globally. Despite an initial response to upfront surgery and platinum-based chemotherapy in most cases, over 70% will relapse. A critical source of recurrence is minimal residual disease (MRD), which persists after upfront treatment yet is clinically undetectable. In this study, we performed second look laparoscopy (SLL) on advanced stage HGSOC patients who had received neoadjuvant chemotherapy (NACT) followed by interval debulking surgery and adjuvant chemotherapy and were in complete clinical remission by imaging and CA-125 tumor marker. Surgical MRD status was determined by pathological review of SLL biopsies. Matched samples from pre-treatment biopsy, interval debulking surgery and SLL in 4 MRD+ and 3 MRD- cases were analyzed using GeoMx Digital Spatial Profiling. Among them, samples from 1 MRD+ and 1 MRD- case were also profiled with Visium. The tumor cells of MRD+ cases exhibited stronger signaling related to hypoxia, angiogenesis, and epithelial-mesenchymal transition at baseline as well as diminished apoptosis signaling after NACT. In addition, progressively upregulated expressions of ATP binding cassette transporters were also observed over time in the tumor compartment of MRD+ cases, potentially contributing to chemoresistance. In the tumor microenvironment, MRD- cases displayed increased abundance of plasma cells, conventional dendritic cells and lymphocytes in both pre-treatment and interval debulking samples compared to MRD+ cases. Notably, Visium data of the MRD- case revealed tertiary lymphoid structures (TLS) in the pre-treatment sample, which became better organized following NACT, with plasma cells disseminating into adjacent tumor areas. Conversely, TLS were fewer and poorly organized in the MRD+ case. Longitudinal comparison of the 3 timepoints in MRD+ cases revealed more regulatory T cells in the stromal compartments of the MRD lesions. Furthermore, from Visium data, exclusion of CD8 T and plasma cells from the tumor core was evident in the MRD lesion. In line with this, strong TGF-β, IL-1β, IL6 and FGF2 signaling surrounding the tumor were noted, likely contributing to immune exclusion. The spatial distribution of multiple immune checkpoint molecules highly overlapped with that of CD8 T cells, indicating T cell exhaustion in the MRD lesion. In summary, these data suggested distinct cancer phenotypic states and immune features in surgically detected MRD+ HGSOC, shedding light on potential chemoresistance and immune evasion mechanisms that contribute to the MRD phase of disease. This study represents the first systemic characterization of ovarian cancer MRD by leveraging SLL, providing insights for designing personalized therapies aimed at eradicating these chemoresistant lesions and ultimately preventing disease recurrence. Citation Format: Yibo Dai, Anne Knisely, Barrett Craig Lawson, Sanghoon Lee, Khalida M. Wani, Rossana N. Lazcano Segura, Brenda Melendez, Jianfeng Chen, Yunhe Liu, Manoj Chelvanambi, Laura A. Gibson, Sarah B. Johnson, Chih-Chen Yeh, Davis R. Ingram, Courtney W. Hudgens, Kyung Serk Cho, Guangsheng Pei, Jiahui Jiang, Yanshuo Chu, Alexander J. Lazar, Jianjun Gao, Jennifer Wargo, Linghua Wang, Amir A. Jazaeri. Longitudinal spatial profiling reveals chemoresistance mechanisms and characteristics of minimal residual disease in high-grade serous ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5656.

Abstract 6997: Elucidating the tumorigenic properties of alveolar epithelial type 1 cells in EGFR-mediated LUAD tumorigenesis

Abstract Originating from within the distal lung, lung adenocarcinoma (LUAD) is the most common pathologic subtype of non-small cell lung carcinoma (NSCLC) and encompasses an assortment of histologic presentations. Colocalized within the distal alveolar epithelium are two alveolar epithelial cell (AEC) subpopulations: alveolar epithelial type 1 (AT1) and alveolar epithelial type 2 (AT2) cells. We previously demonstrated that signatures unique to each AEC subpopulation were detected in LUAD tumors formed by oncogenic KRASG12D activation in mice and were associated with disparate survival outcomes, transcriptomic patterning, and histologic presentation. Epithelial growth factor receptor (EGFR) mutations are among the most frequent oncogenic drivers in thoracic oncology. Therefore, we set out to determine if EGFR oncogenic activation resulted in differential LUAD presentation and outcomes based on the cell of origin in which it was activated. To activate EGFR oncogenic mutations in AT1 or AT2 cells, we employed triple transgenic mouse models (AT1: Gramd2-CreERT2:EF1-LSL-tTA:TetO-EGFRdel20/T790 and AT2: Sftpc-CreERT2:EF1-LSL-tTA:TetO-EGFRdel20/T790), which allowed for EGFR activation in either Gramd2+ AT1 or Sftpc+ AT2 cells. Longitudinal analysis of hematoxylin and eosin-stained lungs over the course of 20 weeks was performed. Blinded pathology review demonstrated that EGFR oncogenic activation in Gramd2+ AT1 cells resulted in histologically defined LUAD with lepidic properties at early time points and solid adenocarcinoma properties at later time points. This differed from EGFR activation in Sftpc+ AT2 cells, which resulted in pre-carcinogenic atypical adenomatous hyperplasia (AAH) formation that did not progress to adenocarcinoma. While preliminary, our results suggest that cell of origin strongly influences EGFR-mediated lung oncogenesis and concomitant pathology and histologic presentation. This work may advance our understanding while informing patient stratification and treatment strategies for LUAD patients. Citation Format: Aaron M. Neely, Andrea Lanz, William Dean Wallace, Anthony W. Kim, Zea Borok, Crystal N. Marconett. Elucidating the tumorigenic properties of alveolar epithelial type 1 cells in EGFR-mediated LUAD tumorigenesis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6997.

Clinical, Epidemiologic, and Pathologic Significance of ERBB2-Low Expression in Breast Cancer

It is unclear whether breast cancer (BC) with low ERBB2 expression (ERBB2-low) is a distinct clinical, pathological, and epidemiological entity from BC classified as no ERBB2 expression (ERBB2-negative). To evaluate the clinical, pathological, and epidemiologic features of BC with ERBB2-low expression compared with ERBB2-negative BC in a large population study. This cohort study was conducted as part of the Pathways Study, a prospective, racially and ethnically diverse cohort study of women with BC enrolled between 2006 and 2013 in Kaiser Permanente Northern California (KPNC). The hematoxylin and eosin slides underwent centralized pathology review, including the percentage of tumor infiltrating lymphocytes (TILs). Breast biomarker results were extracted from pathology reports, and women were included if they had a documented ERBB2 value that was not classified ERBB2-positive. Data were analyzed from February 2023 through January 2024. Clinical and tumor characteristics associated with BC and ERBB2-low or ERBB2-negative status. ERBB2-low was defined as immunohistochemistry score of 1+ or 2+ (negative by in situ hybridization); ERBB2-negative was defined as immunohistochemistry score of 0+. Other data were collected by self-report or extraction from electronic health records, including BC risk factors, tumor characteristics, treatment modality, and survival outcomes, with recurrence-free survival (RFS) as the primary outcome and overall survival (OS) and BC-specific mortality (BCSM) as secondary outcomes. The clinical, pathological, and epidemiological variables were compared between ERBB2-low and ERBB2-negative BC. Of 2200 eligible patients (all female; with mean [SD] age, 60.4 [11.9] years), 1295 (57.2%) had tumors that were ERBB2-low. Hormone receptors were positive in 1956 patients (88.9%). The sample included 291 Asian patients (13.2%), 166 Black patients (7.5%), 253 Hispanic patients (11.5%), 1439 White patients (65.4%), and 51 patients (2.3%) who identified as other race or ethnicity (eg, American Indian or Alaska Native and Pacific Islander). Within the hormone receptor-negative group, patients whose tumors had ERBB2-low staining, compared with those with ERBB2-negative tumors, had better OS (hazard ratio [HR], 0.54; 95% CI, 0.33-0.91; P = .02), RFS (HR, 0.53; 95% CI, 0.30-0.95; P = .03), and BCSM (HR, 0.43; 95% CI, 0.22-0.84; P = .01). In multivariable survival analysis stratified by hormone receptor status and adjusted for key covariates, patients with ERBB2-low and hormone receptor-negative tumors had lower overall mortality (HR, 0.48; 95% CI, 0.27-0.83; P = .009), RFS (HR, 0.45; 95% CI, 0.24-0.86; P = .02), and BCSM (subdistribution HR, 0.21; 95% CI, 0.10-0.46; P < .001) compared with patients with ERBB2-negative and hormone receptor-negative tumors. Within the hormone receptor-negative subtype, patients with ERBB2-low and high TILs tumors had better survival across all 3 outcomes compared with patients with ERBB2-negative and low TILs tumors. Additionally, patients with ERBB2-low and low TILs tumors had better BCSM (subdistribution HR, 0.36; 95% CI, 0.14-0.92; P = .03). These findings suggest that there were clinical, pathological, and epidemiological differences between ERBB2-low and ERBB2-negative BC, raising the possibility that ERBB2-low might be a unique biologic entity.

Epigenetic MLH1 silencing concurs with mismatch repair deficiency in sporadic, naturally occurring colorectal cancer in rhesus macaques

BackgroundNaturally occurring colorectal cancers (CRC) in rhesus macaques share many features with their human counterparts and are useful models for cancer immunotherapy; but mechanistic data are lacking regarding the comparative molecular pathogenesis of these cancers.MethodsWe conducted state-of-the-art imaging including CT and PET, clinical assessments, and pathological review of 24 rhesus macaques with naturally occurring CRC. Additionally, we molecularly characterized these tumors utilizing immunohistochemistry (IHC), microsatellite instability assays, DNAseq, transcriptomics, and developed a DNA methylation-specific qPCR assay for MLH1, CACNA1G, CDKN2A, CRABP1, and NEUROG1, human markers for CpG island methylator phenotype (CIMP). We furthermore employed Monte-Carlo simulations to in-silico model alterations in DNA topology in transcription-factor binding site-rich promoter regions upon experimentally demonstrated DNA methylation.ResultsSimilar cancer histology, progression patterns, and co-morbidities could be observed in rhesus as reported for human CRC patients. IHC identified loss of MLH1 and PMS2 in all cases, with functional microsatellite instability. DNA sequencing revealed the close genetic relatedness to human CRCs, including a similar mutational signature, chromosomal instability, and functionally-relevant mutations affecting KRAS (G12D), TP53 (R175H, R273*), APC, AMER1, ALK, and ARID1A. Interestingly, MLH1 mutations were rarely identified on a somatic or germline level. Transcriptomics not only corroborated the similarities of rhesus and human CRCs, but also demonstrated the significant downregulation of MLH1 but not MSH2, MSH6, or PMS2 in rhesus CRCs. Methylation-specific qPCR suggested CIMP-positivity in 9/16 rhesus CRCs, but all 16/16 exhibited significant MLH1 promoter hypermethylation. DNA hypermethylation was modelled to affect DNA topology, particularly propeller twist and roll profiles. Modelling the DNA topology of a transcription factor binding motif (TFAP2A) in the MLH1 promoter that overlapped with a methylation-specific probe, we observed significant differences in DNA topology upon experimentally shown DNA methylation. This suggests a role of transcription factor binding interference in epigenetic silencing of MLH1 in rhesus CRCs.ConclusionsThese data indicate that epigenetic silencing suppresses MLH1 transcription, induces the loss of MLH1 protein, abrogates mismatch repair, and drives genomic instability in naturally occurring CRC in rhesus macaques. We consider this spontaneous, uninduced CRC in immunocompetent, treatment-naïve rhesus macaques to be a uniquely informative model for human CRC.Graphical abstract

A Rare Case Report of Intraosseous Spindle and Epithelioid Rhabdomyosarcoma With TFCP2 Rearrangement: A Pathological Diagnostic Conundrum and Literature Review.

Rhabdomyosarcoma is a highly malignant tumor with striated muscle differentiation, which is histologically classified as alveolar, embryonal, pleomorphic, and spindle cell/sclerosing histological subtype. Rhabdomyosarcoma with TFCP2 rearrangement, which usually occurs in the bone, is a newly identified rare spindle and epithelioid rhabdomyosarcoma with characteristic clinicopathological features and molecular alterations. We report a 39-year-old female patient who underwent local excision of the mandibular lesion. Microscopically, the intraosseous tumor was composed of spindle-shaped, epithelioid, and rhabdomyoblastic cells with atypical nuclei and atypical mitotic figures. In addition, TFCP2 rearrangement was revealed by the fluorescence in situ hybridization. The tumor was thus correctly diagnosed as rhabdomyosarcoma with TFCP2 rearrangement. The patient was scheduled to undergo radiotherapy, and triple-agent chemotherapy after surgery, and no tumor recurrence or metastasis was detected during the 3-month postoperative follow up. Since this tumor is relatively rare and newly recognized, it can be easily misdiagnosed or missed and might be a conundrum of pathological diagnosis. Familiarity with its clinicopathological features and molecular alterations is essential for its correct diagnosis. Therefore, we summarized the clinicopathological, immunohistochemical, and molecular alterations of 43 cases of this rare rhabdomyosarcoma variant in the English-language literature. In addition, the differential diagnosis of this lesion is crucial either.

HER2-low and tumor infiltrating lymphocytes in triple-negative breast cancer: Are they connected?

Most patients with triple-negative breast cancer (TNBC) are not candidates for targeted therapy, leaving chemotherapy as the primary treatment option. Recently, immunotherapy has demonstrated promising results in TNBC, due to its immunogenicity. In addition, a novel antibody–drug conjugate, namely, trastuzumab-deruxtecan, has shown effectiveness in TNBC patients with low-HER2 expression (HER2-low). These novel treatment options raise the question about the potential association between the density of stromal tumor-infiltrating lymphocytes (sTILs) and the level of HER2 expression. We aimed to evaluate the association between the level of HER2 expression (HER2-low versus HER2-0) and density of sTILs in TNBC patients, and how they impact the response to neoadjuvant chemotherapy (NAC). This was a retrospective multicenter study including all TNBC patients diagnosed between 2018 and 2022. Central pathology review included sTILs percentages and level of HER2 expression. Tumors were reclassified as either HER2-0 (HER2 IHC 0) or HER2-low (IHC 1 + or 2 + with negative reflex test). Various clinicopathologic characteristics, including sTILs density, and response to NAC were compared between HER2-0 and HER2-low cases. In total, 753 TNBC patients were included in this study, of which 292 patients received NAC. Interobserver agreement between the original pathology report and central review was moderate (77% had the same IHC status after reclassification in either HER2-0 or HER2-low; k = 0.45). HER2-low TNBC represented about one third (36%) of the tumors. No significant difference in sTILs density or complete pathologic response rate was found between HER2-0 and HER2-low cases (p = 0.476 and p = 0.339, respectively). The density of sTILs (≥ 10% sTILs vs. < 10%) was independently associated with achieving a pCR (p = 0.011). In conclusion, no significant association was found between HER2-low status and density of sTILs nor response to NAC. Nonetheless, sTILs could be an independent biomarker for predicting NAC response in TNBC patients.