Pub Date : 2024-11-05DOI: 10.1016/j.labinv.2024.102178
Jonathan Lai, Vrinda Madan, Aasheen Qadri, Ludmila Danilova, Long Yuan, Victoria Jacobs, Aleksandra Ogurtsova, Logan L Engle, Joel C Sunshine
Merkel Cell Carcinoma (MCC) is an aggressive cutaneous malignancy with a poor prognosis. One of the major mechanisms of immune evasion in MCC involves downregulation of MHC-I. Anti-PD-1/PD-L1 checkpoint inhibitors (CKIs) have revolutionized treatment for MCC, producing objective responses in ∼50% of patients, and are now standard of care; however, a substantial proportion of patients either fail to respond or develop resistance to CKIs. Given these recent successes, identification of other targetable immune checkpoints in the MCC tumor microenvironment (TME) is of great interest. Additionally, γ-delta (γδ) T cells may play critical roles in the response to MHC-I deficient cancers; therefore, evaluating γδ-T cells as a prognostic biomarker is warranted. We characterized the expression of PD-L1, PD-1, CD3, CD8, LAG-3, MHC-I, and γδ-T cells by IHC in a pre-immunotherapy retrospective cohort of 54 cases of MCC, and quantified expression levels and marker density via HALO. The increased density of LAG-3 and γδ-T cells correlated with other markers of an inflamed TME, with significant positive associations across all six markers (p<.002). Reflective of their putative role in the response to MHC-I suppressed cancers, cases with low HLA-I density showed a trend towards a higher ratio of γδ-T cells:CD3+ T cells (Spearman's r=-0.1582, p=0.21). Importantly, high CD3 density (HR=0.23, p=0.002), LAG-3 density (HR=0.47, p=0.037), γδ-T cell density (HR=0.26, p=0.02), and CD8 density (HR=0.27, p=0.03) showed associations with improved progression-free survival. Conditional tree analysis demonstrated that high CD8 and TCRδ expression were non-significant predictors of improved PFS and OS. Overall, LAG-3 is expressed in MCC infiltrates and is prognostic in pre-immunotherapy MCC, suggesting a potential role for LAG-3 inhibition in MCC. Additionally, CD8 and γδ-T cells may play a critical role in the response to MCC, and γδ-T cell density may represent a novel biomarker in MCC.
{"title":"LAG-3 Expression, γδ-T cell/MHC-I Interactions and Prognosis in Merkel Cell Carcinoma.","authors":"Jonathan Lai, Vrinda Madan, Aasheen Qadri, Ludmila Danilova, Long Yuan, Victoria Jacobs, Aleksandra Ogurtsova, Logan L Engle, Joel C Sunshine","doi":"10.1016/j.labinv.2024.102178","DOIUrl":"https://doi.org/10.1016/j.labinv.2024.102178","url":null,"abstract":"<p><p>Merkel Cell Carcinoma (MCC) is an aggressive cutaneous malignancy with a poor prognosis. One of the major mechanisms of immune evasion in MCC involves downregulation of MHC-I. Anti-PD-1/PD-L1 checkpoint inhibitors (CKIs) have revolutionized treatment for MCC, producing objective responses in ∼50% of patients, and are now standard of care; however, a substantial proportion of patients either fail to respond or develop resistance to CKIs. Given these recent successes, identification of other targetable immune checkpoints in the MCC tumor microenvironment (TME) is of great interest. Additionally, γ-delta (γδ) T cells may play critical roles in the response to MHC-I deficient cancers; therefore, evaluating γδ-T cells as a prognostic biomarker is warranted. We characterized the expression of PD-L1, PD-1, CD3, CD8, LAG-3, MHC-I, and γδ-T cells by IHC in a pre-immunotherapy retrospective cohort of 54 cases of MCC, and quantified expression levels and marker density via HALO. The increased density of LAG-3 and γδ-T cells correlated with other markers of an inflamed TME, with significant positive associations across all six markers (p<.002). Reflective of their putative role in the response to MHC-I suppressed cancers, cases with low HLA-I density showed a trend towards a higher ratio of γδ-T cells:CD3+ T cells (Spearman's r=-0.1582, p=0.21). Importantly, high CD3 density (HR=0.23, p=0.002), LAG-3 density (HR=0.47, p=0.037), γδ-T cell density (HR=0.26, p=0.02), and CD8 density (HR=0.27, p=0.03) showed associations with improved progression-free survival. Conditional tree analysis demonstrated that high CD8 and TCRδ expression were non-significant predictors of improved PFS and OS. Overall, LAG-3 is expressed in MCC infiltrates and is prognostic in pre-immunotherapy MCC, suggesting a potential role for LAG-3 inhibition in MCC. Additionally, CD8 and γδ-T cells may play a critical role in the response to MCC, and γδ-T cell density may represent a novel biomarker in MCC.</p>","PeriodicalId":17930,"journal":{"name":"Laboratory Investigation","volume":" ","pages":"102178"},"PeriodicalIF":5.1,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142604508","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-04DOI: 10.1016/j.labinv.2024.102168
Shayan Monabbati , Pingfu Fu , Sylvia L. Asa , Tilak Pathak , Joseph E. Willis , Qiuying Shi , Anant Madabhushi
Papillary thyroid carcinoma (PTC) is the most prevalent form of thyroid cancer, with a disease recurrence rate of around 20%. Lymphoid formations, which occur in nonlymphoid tissues during chronic inflammatory, infectious, and immune responses, have been linked with tumor suppression. Lymphoid aggregates potentially enhance the body’s antitumor response, offering an avenue for attracting tumor-infiltrating lymphocytes and fostering their coordination. Increasing evidence highlights the role of lymphoid aggregate density in managing tumor invasion and metastasis, with a favorable impact noted on overall and disease-free survival (DFS) across various cancer types. In this study, we present a machine vision model to predict recurrence in different histologic subtypes of PTC using measurements related to peritumoral lymphoid aggregate density. We demonstrated that quantifying peritumoral lymphocytic presence not only is associated with better prognosis but also, along with tumor-infiltrating lymphocytes within the tumor, adds additional prognostic value in the absence of well-known second mutations including TERT. Annotations of peritumoral lymphoid aggregates on 171 well-differentiated PTCs in the Cancer Genome Atlas Thyroid Carcinoma (TCGA-THCA) data set were used to train a deep-learning model to predict regions of lymphoid aggregates across the entire tissue. The fractional area of the tissue regions covered by these lymphocytes was dichotomized to determine the following 2 risk groups: a significant and low density of peritumoral lymphocytes. DFS prognosticated using these risk groups via the Kaplan-Meier analysis revealed a hazard ratio (HR) of 2.51 (95% CI: 2.36, 2.66), tested on 170 new patients also from the TCGA-THCA data set. The prognostic performance of peritumoral lymphocyte aggregate density was compared against the univariate Kaplan-Meier analysis of DFS using the fractional area of intratumoral lymphocytes within the primary tumor with an HR of 2.04 (95% CI: 1.89, 2.19). Combining the lymphocyte features in and around the tumor yielded a statistically significant improvement in prognostic performance (HR, 3.17 [95% CI: 3.02, 3.32]) on training and were independently evaluated against 62 patients outside TCGA-THCA with an HR of 2.44 (95% CI: 2.19, 2.69). Multivariable Cox regression analysis on the validation set revealed that the density of peritumoral and intratumoral lymphocytes was prognostic independent of histologic subtype with a concordance index of 0.815.
{"title":"Machine Vision–Detected Peritumoral Lymphocytic Aggregates Are Associated With Disease-Free Survival in Patients With Papillary Thyroid Carcinoma","authors":"Shayan Monabbati , Pingfu Fu , Sylvia L. Asa , Tilak Pathak , Joseph E. Willis , Qiuying Shi , Anant Madabhushi","doi":"10.1016/j.labinv.2024.102168","DOIUrl":"10.1016/j.labinv.2024.102168","url":null,"abstract":"<div><div>Papillary thyroid carcinoma (PTC) is the most prevalent form of thyroid cancer, with a disease recurrence rate of around 20%. Lymphoid formations, which occur in nonlymphoid tissues during chronic inflammatory, infectious, and immune responses, have been linked with tumor suppression. Lymphoid aggregates potentially enhance the body’s antitumor response, offering an avenue for attracting tumor-infiltrating lymphocytes and fostering their coordination. Increasing evidence highlights the role of lymphoid aggregate density in managing tumor invasion and metastasis, with a favorable impact noted on overall and disease-free survival (DFS) across various cancer types. In this study, we present a machine vision model to predict recurrence in different histologic subtypes of PTC using measurements related to peritumoral lymphoid aggregate density. We demonstrated that quantifying peritumoral lymphocytic presence not only is associated with better prognosis but also, along with tumor-infiltrating lymphocytes within the tumor, adds additional prognostic value in the absence of well-known second mutations including <em>TERT</em>. Annotations of peritumoral lymphoid aggregates on 171 well-differentiated PTCs in the Cancer Genome Atlas Thyroid Carcinoma (TCGA-THCA) data set were used to train a deep-learning model to predict regions of lymphoid aggregates across the entire tissue. The fractional area of the tissue regions covered by these lymphocytes was dichotomized to determine the following 2 risk groups: a significant and low density of peritumoral lymphocytes. DFS prognosticated using these risk groups via the Kaplan-Meier analysis revealed a hazard ratio (HR) of 2.51 (95% CI: 2.36, 2.66), tested on 170 new patients also from the TCGA-THCA data set. The prognostic performance of peritumoral lymphocyte aggregate density was compared against the univariate Kaplan-Meier analysis of DFS using the fractional area of intratumoral lymphocytes within the primary tumor with an HR of 2.04 (95% CI: 1.89, 2.19). Combining the lymphocyte features in and around the tumor yielded a statistically significant improvement in prognostic performance (HR, 3.17 [95% CI: 3.02, 3.32]) on training and were independently evaluated against 62 patients outside TCGA-THCA with an HR of 2.44 (95% CI: 2.19, 2.69). Multivariable Cox regression analysis on the validation set revealed that the density of peritumoral and intratumoral lymphocytes was prognostic independent of histologic subtype with a concordance index of 0.815.</div></div>","PeriodicalId":17930,"journal":{"name":"Laboratory Investigation","volume":"104 12","pages":"Article 102168"},"PeriodicalIF":5.1,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142590999","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Leptin (LEP) is implicated in the pathogenesis of polycystic ovary syndrome (PCOS). This study investigates the mechanism of LEP in PCOS. The baseline information of 80 PCOS patients and matched controls was analyzed, with serum and follicular fluid (FF) LEP and LEP receptor (LEPR) levels, telomerase activity, and relative telomere length (TL) measured. The correlation of FF LEP with telomerase activity and TL was analyzed. The viability and apoptosis of KGN cells (the ovarian granulosa cells) treated with gradient LEP were assessed. LEP-LEPR interaction was examined. LEPR, c-MYC, and TERT levels and c-MYC protein expression in the TERT promoter region were determined. Nuclear c-MYC translocation was detected. LEP was upregulated in sera and FF of PCOS patients. FF LEP positively-correlated with telomerase activity and TL. Low-concentration LEP facilitated KGN cell proliferation and high-concentration LEP dose-dependently suppressed cell proliferation, promoted apoptosis, upregulated LEPR and increased telomerase activity and relative TL. LEP-LEPR interaction upregulated c-MYC and facilitated its nuclear accumulation. c-MYC enrichment in the TERT promoter region upregulated TERT, altering telomerase activity and TL and inducing cell apoptosis. Briefly, LEP/LEPR activate c-MYC, modulate TERT expression, and increase telomerase activity and TL, thus inducing ovarian granulosa cell apoptosis and participating in PCOS.
{"title":"Leptin modulates ovarian granulosa cell apoptosis by regulating telomerase activity and telomere length in polycystic ovary syndrome.","authors":"Feijing Zhou, Zhimin Sun, Luyao Cheng, Yuezhi Dong","doi":"10.1016/j.labinv.2024.102169","DOIUrl":"https://doi.org/10.1016/j.labinv.2024.102169","url":null,"abstract":"<p><p>Leptin (LEP) is implicated in the pathogenesis of polycystic ovary syndrome (PCOS). This study investigates the mechanism of LEP in PCOS. The baseline information of 80 PCOS patients and matched controls was analyzed, with serum and follicular fluid (FF) LEP and LEP receptor (LEPR) levels, telomerase activity, and relative telomere length (TL) measured. The correlation of FF LEP with telomerase activity and TL was analyzed. The viability and apoptosis of KGN cells (the ovarian granulosa cells) treated with gradient LEP were assessed. LEP-LEPR interaction was examined. LEPR, c-MYC, and TERT levels and c-MYC protein expression in the TERT promoter region were determined. Nuclear c-MYC translocation was detected. LEP was upregulated in sera and FF of PCOS patients. FF LEP positively-correlated with telomerase activity and TL. Low-concentration LEP facilitated KGN cell proliferation and high-concentration LEP dose-dependently suppressed cell proliferation, promoted apoptosis, upregulated LEPR and increased telomerase activity and relative TL. LEP-LEPR interaction upregulated c-MYC and facilitated its nuclear accumulation. c-MYC enrichment in the TERT promoter region upregulated TERT, altering telomerase activity and TL and inducing cell apoptosis. Briefly, LEP/LEPR activate c-MYC, modulate TERT expression, and increase telomerase activity and TL, thus inducing ovarian granulosa cell apoptosis and participating in PCOS.</p>","PeriodicalId":17930,"journal":{"name":"Laboratory Investigation","volume":" ","pages":"102169"},"PeriodicalIF":5.1,"publicationDate":"2024-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142567318","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
High pigmentation and the abundance of M2 macrophages have been identified as negative predictors in uveal melanoma (UM). Risk factors associated with UM that are prevalent in high-risk White populations are still present, although less common, in relatively low-risk Asian populations. Research indicates that proangiogenic M2 macrophages and monosomy 3 play significant roles in UM progression. Our aim was to investigate the impact of tumor-associated macrophages in UM and examine their correlation with monosomy 3 and pigmentation. Transmission electron microscopy was used to analyze the morphology of macrophages in UM. Forty UM samples underwent fluorescent in situ hybridization for monosomy 3 identification. Immunohistochemistry was done to assess M2/M1 macrophages on 82 UM tissue samples. IL-10 and IL-12 expressions were quantified in UM serum samples by enzyme-linked immunosorbent assay. The expression of all markers was correlated with pigmentation markers (tyrosinase-related protein 1, tyrosinase-related protein 2, silver protein, and microphthalmia-associated transcription factor). Prognostic outcomes were determined using the Cox proportional hazard model and log-rank tests. Increased expression of M2/M1 macrophages was observed in 31 UM cases, which correlated with the high expression of pigmentation markers. IL-10 concentration was high in UM cases. Monosomy 3 was evident in 50% of UM cases and significantly associated with increased immunoexpression of M2/M1 macrophages and pigmentation markers. Reduced metastasis-free survival was observed in patients with UM with high M2/M1 macrophage expression (P = .001). High pigmentation and increased M2 macrophage density could impact the tumor microenvironment in UM. This could contribute to ineffective antitumor immune responses in patients with UM. Our findings suggest avenues for developing novel therapeutic approaches to counteract these immunosuppressive effects in UM.
高色素沉着和大量的 M2 巨噬细胞已被确定为葡萄膜黑色素瘤(UM)的负面预测因素。在高风险的白人人群中普遍存在的与葡萄膜黑色素瘤相关的风险因素,在风险相对较低的亚裔人群中仍然存在,但并不常见。研究表明,促血管生成的 M2 巨噬细胞和单体 3 在黑色素瘤的发展过程中起着重要作用。我们的目的是研究肿瘤相关巨噬细胞对脐带癌的影响,并探讨其与单体3型和色素沉着的相关性。TEM 被用来分析 UM 中巨噬细胞的形态。对 40 份 UM 样本进行 FISH 检测,以确定单体 3 型。对 82 个 UM 组织样本的 M2/M1 巨噬细胞进行了免疫组化评估。用酶联免疫吸附法对 UM 血清样本中 IL-10 和 IL-12 的表达进行了量化。所有标记物的表达均与色素标记物(TYRP1、TYRP2、SILV和MITF)相关。采用 Cox 比例危险模型和对数秩检验确定预后结果。在 31 例 UM 病例中观察到 M2/M1 巨噬细胞表达增加,这与色素沉着标记物的高表达相关。UM病例中IL-10浓度较高。50%的 UM 病例中存在明显的单体 3,并且与 M2/M1 巨噬细胞和色素标记物的免疫表达增加有显著关联。在 M2/M1 巨噬细胞高表达的 UM 患者中观察到 MFS 降低(p=0.001)。高色素沉着和 M2 巨噬细胞密度增加可能会影响 UM 的肿瘤微环境。这可能会导致 UM 患者的抗肿瘤免疫反应无效。我们的发现为开发新型治疗方法提供了途径,以抵消 UM 的这些免疫抑制效应。
{"title":"Deciphering the Intricate Relationship Between Macrophages, Pigmentation, and Prognosis in Uveal Melanoma","authors":"Jayanti Jha , Mithalesh Kumar Singh , Lata Singh , Neelam Pushker , Aanchal Kakkar , Rachna Meel , Neiwete Lomi , Sameer Bakhshi , Tapas Chandra Nag , Chanda Panwar , Seema Sen , Seema Kashyap","doi":"10.1016/j.labinv.2024.102167","DOIUrl":"10.1016/j.labinv.2024.102167","url":null,"abstract":"<div><div>High pigmentation and the abundance of M2 macrophages have been identified as negative predictors in uveal melanoma (UM). Risk factors associated with UM that are prevalent in high-risk White populations are still present, although less common, in relatively low-risk Asian populations. Research indicates that proangiogenic M2 macrophages and monosomy 3 play significant roles in UM progression. Our aim was to investigate the impact of tumor-associated macrophages in UM and examine their correlation with monosomy 3 and pigmentation. Transmission electron microscopy was used to analyze the morphology of macrophages in UM. Forty UM samples underwent fluorescent in situ hybridization for monosomy 3 identification. Immunohistochemistry was done to assess M2/M1 macrophages on 82 UM tissue samples. IL-10 and IL-12 expressions were quantified in UM serum samples by enzyme-linked immunosorbent assay. The expression of all markers was correlated with pigmentation markers (tyrosinase-related protein 1, tyrosinase-related protein 2, silver protein, and microphthalmia-associated transcription factor). Prognostic outcomes were determined using the Cox proportional hazard model and log-rank tests. Increased expression of M2/M1 macrophages was observed in 31 UM cases, which correlated with the high expression of pigmentation markers. IL-10 concentration was high in UM cases. Monosomy 3 was evident in 50% of UM cases and significantly associated with increased immunoexpression of M2/M1 macrophages and pigmentation markers. Reduced metastasis-free survival was observed in patients with UM with high M2/M1 macrophage expression (<em>P</em> = .001). High pigmentation and increased M2 macrophage density could impact the tumor microenvironment in UM. This could contribute to ineffective antitumor immune responses in patients with UM. Our findings suggest avenues for developing novel therapeutic approaches to counteract these immunosuppressive effects in UM.</div></div>","PeriodicalId":17930,"journal":{"name":"Laboratory Investigation","volume":"104 12","pages":"Article 102167"},"PeriodicalIF":5.1,"publicationDate":"2024-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142567313","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-01DOI: 10.1016/j.labinv.2024.102149
Fangyi Han , Xingdi Fan , Minxuan Hu , Jing Wen , Junrao Wang , Dan Zhang , Shuyang Wang , Yanqing Ding , Yaping Ye , Hongli Jiao
The nuclear pore complex (NPC) regulates nucleoplasmic transport, transcription, and genomic integrity in eukaryotic cells. However, little is known about how NPC works in cancer. In this study, we investigated the role of the nuclear pore protein 210 (Nucleoporin 210, Nup210) in colorectal cancer (CRC). Bioinformatics analysis revealed that the expression of Nup210 was increased in CRC and was associated with poor patient prognosis, but it was not a statistically significant independent prognostic factor. Moreover, knockdown of Nup210 in CRC cells inhibited the proliferation, invasion, and metastasis of CRC cells in vivo and in vitro. Additionally, nuclear size and nuclear plasma material transport capacity decreased along with the number and density of NPCs on the surface of CRC cells when Nup210 expression was inhibited. Furthermore, Nup210 required nuclear localization sequences (NLS) to localize to the nuclear membrane surface and interact with importin-α/β, which in turn affected the transit of nuclear plasma material. Importazole, a small molecule inhibitor of importin, along with therapy that targets the Nup210 protein is anticipated to be a novel strategy for CRC treatment. Their combination may be able to more effectively lower CRC tumor load. In conclusion, Nup210 modulates cellular nucleoplasmic transport capability and cell surface NPC density via NLS, thus promoting CRC progression. This discovery validates the molecular function of NPC in the development of CRC and provides a theoretical foundation for NPC-regulated nuclear import targeting as a therapeutic strategy for CRC.
{"title":"Nup210 Promotes Colorectal Cancer Progression by Regulating Nuclear Plasma Transport","authors":"Fangyi Han , Xingdi Fan , Minxuan Hu , Jing Wen , Junrao Wang , Dan Zhang , Shuyang Wang , Yanqing Ding , Yaping Ye , Hongli Jiao","doi":"10.1016/j.labinv.2024.102149","DOIUrl":"10.1016/j.labinv.2024.102149","url":null,"abstract":"<div><div>The nuclear pore complex (NPC) regulates nucleoplasmic transport, transcription, and genomic integrity in eukaryotic cells. However, little is known about how NPC works in cancer. In this study, we investigated the role of the nuclear pore protein 210 (Nucleoporin 210, Nup210) in colorectal cancer (CRC). Bioinformatics analysis revealed that the expression of Nup210 was increased in CRC and was associated with poor patient prognosis, but it was not a statistically significant independent prognostic factor. Moreover, knockdown of Nup210 in CRC cells inhibited the proliferation, invasion, and metastasis of CRC cells in vivo and in vitro. Additionally, nuclear size and nuclear plasma material transport capacity decreased along with the number and density of NPCs on the surface of CRC cells when Nup210 expression was inhibited. Furthermore, Nup210 required nuclear localization sequences (NLS) to localize to the nuclear membrane surface and interact with importin-α/β, which in turn affected the transit of nuclear plasma material. Importazole, a small molecule inhibitor of importin, along with therapy that targets the Nup210 protein is anticipated to be a novel strategy for CRC treatment. Their combination may be able to more effectively lower CRC tumor load. In conclusion, Nup210 modulates cellular nucleoplasmic transport capability and cell surface NPC density via NLS, thus promoting CRC progression. This discovery validates the molecular function of NPC in the development of CRC and provides a theoretical foundation for NPC-regulated nuclear import targeting as a therapeutic strategy for CRC.</div></div>","PeriodicalId":17930,"journal":{"name":"Laboratory Investigation","volume":"104 11","pages":"Article 102149"},"PeriodicalIF":5.1,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142406581","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-01DOI: 10.1016/j.labinv.2024.102146
Hannah C. Beird , Jeffrey M. Cloutier , Nalan Gokgoz , Christopher Eeles , Anthony M. Griffin , Davis R. Ingram , Khalida M. Wani , Rossana Lazcano Segura , Luca Cohen , Carl Ho , Jay S. Wunder , Irene L. Andrulis , P. Andrew Futreal , Benjamin Haibe-Kains , Alexander J. Lazar , Wei-Lien Wang , Joanna Przybyl , Elizabeth G. Demicco
A solitary fibrous tumor (SFT) is a rare mesenchymal neoplasm that can arise at any anatomical site and is characterized by recurrent NAB2::STAT6 fusions and metastatic progression in 10% to 30%. The cell of origin has not been identified. Despite some progress in understanding the contribution of heterogeneous fusion types and secondary mutations to SFT biology, epigenetic alterations in extrameningeal SFT remain largely unexplored, and most sarcoma research to date has focused on the use of methylation profiling for tumor classification. We interrogated genome-wide DNA methylation in 79 SFTs to identify informative epigenetic changes. RNA-seq data from targeted panels and data from the Cancer Genome Atlas (TCGA) were used for orthogonal validation of selected findings. In unsupervised clustering analysis, the top 500 most variable cytosine-guanine sites segregated SFTs by primary anatomical site. Differentially methylated genes associated with the primary SFT site included EGFR; TBX15; multiple HOX genes; and their cofactors EBF1, EBF3, and PBX1; as well as RUNX1 and MEIS1. Of the 20 DMGs interrogated on the RNA-seq panel, 12 were significantly differentially expressed according to site. However, except TBX15, most of these also showed differential expression according to NAB2::STAT6 fusion type, suggesting that the fusion oncogene contributes to the transcriptional regulation of these genes. Transcriptomic data confirmed an inverse correlation between gene methylation and the expression of TBX15 in both SFT and TCGA sarcomas. TBX15 also showed differential mRNA expression and 5′ UTR methylation between tumors in different anatomical sites in TCGA data. In all analyses, TBX15 methylation and mRNA expression retained the strongest association with tissue of origin in SFT and other sarcomas, suggesting a possible marker to distinguish metastatic tumors from new primaries without genomic profiling. Epigenetic signatures may further help to identify SFT progenitor cells at different anatomical sites.
{"title":"Epigenomic and Transcriptomic Profiling of Solitary Fibrous Tumors Identifies Site-Specific Patterns and Candidate Genes Regulated by DNA Methylation","authors":"Hannah C. Beird , Jeffrey M. Cloutier , Nalan Gokgoz , Christopher Eeles , Anthony M. Griffin , Davis R. Ingram , Khalida M. Wani , Rossana Lazcano Segura , Luca Cohen , Carl Ho , Jay S. Wunder , Irene L. Andrulis , P. Andrew Futreal , Benjamin Haibe-Kains , Alexander J. Lazar , Wei-Lien Wang , Joanna Przybyl , Elizabeth G. Demicco","doi":"10.1016/j.labinv.2024.102146","DOIUrl":"10.1016/j.labinv.2024.102146","url":null,"abstract":"<div><div>A solitary fibrous tumor (SFT) is a rare mesenchymal neoplasm that can arise at any anatomical site and is characterized by recurrent <em>NAB2::STAT6</em> fusions and metastatic progression in 10% to 30%. The cell of origin has not been identified. Despite some progress in understanding the contribution of heterogeneous fusion types and secondary mutations to SFT biology, epigenetic alterations in extrameningeal SFT remain largely unexplored, and most sarcoma research to date has focused on the use of methylation profiling for tumor classification. We interrogated genome-wide DNA methylation in 79 SFTs to identify informative epigenetic changes. RNA-seq data from targeted panels and data from the Cancer Genome Atlas (TCGA) were used for orthogonal validation of selected findings. In unsupervised clustering analysis, the top 500 most variable cytosine-guanine sites segregated SFTs by primary anatomical site. Differentially methylated genes associated with the primary SFT site included <em>EGFR</em>; <em>TBX15</em>; multiple <em>HOX</em> genes; and their cofactors <em>EBF1</em>, <em>EBF3</em>, and <em>PBX1</em>; as well as <em>RUNX1</em> and <em>MEIS1</em>. Of the 20 DMGs interrogated on the RNA-seq panel, 12 were significantly differentially expressed according to site. However, except <em>TBX15</em>, most of these also showed differential expression according to <em>NAB2::STAT6</em> fusion type, suggesting that the fusion oncogene contributes to the transcriptional regulation of these genes. Transcriptomic data confirmed an inverse correlation between gene methylation and the expression of <em>TBX15</em> in both SFT and TCGA sarcomas<em>. TBX15</em> also showed differential mRNA expression and 5′ UTR methylation between tumors in different anatomical sites in TCGA data. In all analyses, <em>TBX15</em> methylation and mRNA expression retained the strongest association with tissue of origin in SFT and other sarcomas, suggesting a possible marker to distinguish metastatic tumors from new primaries without genomic profiling. Epigenetic signatures may further help to identify SFT progenitor cells at different anatomical sites.</div></div>","PeriodicalId":17930,"journal":{"name":"Laboratory Investigation","volume":"104 11","pages":"Article 102146"},"PeriodicalIF":5.1,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142365739","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-25DOI: 10.1016/j.labinv.2024.102165
Sachin S Surwase, Xin Ming M Zhou, Kathryn M Luly, Qingfeng Zhu, Robert A Anders, Jordan J Green, Stephany Y Tzeng, Joel C Sunshine
Spatial proteomics profiling is an emerging set of technologies that has the potential to elucidate the cell types, interactions, and molecular signatures that make up complex tissue microenvironments, with applications in the study of cancer, immunity, and much more. An emerging technique in the field is Co-Detection-by-indEXing (CODEX), recently renamed as the PhenoCycler system. This is a highly-multiplexed immunofluorescence imaging technology that relies on oligonucleotide-barcoded antibodies and cyclic immunofluorescence to visualize many antibody markers in a single specimen while preserving tissue architecture. Existing PhenoCycler panels are primarily designed for fresh-frozen tissues. Formalin-fixed paraffin-embedded (FFPE) blocks offer several advantages in preclinical research, but few antibody clones have been identified in this setting for PhenoCycler imaging. Here, we present a novel PhenoCycler panel of 28 validated antibodies for murine FFPE tissues. We describe our workflow for selecting and validating clones, barcoding antibodies, designing our panel, and performing multiplex imaging. We further detail our analysis pipeline for comparing marker expressions, clustering and phenotyping single-cell proteomics data, and quantifying spatial relationships. We then apply our panel and analysis protocol to profile the effects of three gene-delivery nanoparticle formulations, in combination with systemic anti-PD1, on the murine melanoma tumor immune microenvironment. Intralesional delivery of genes expressing the costimulatory molecule 4-1BBL and the cytokine IL-12 led to a shift towards intratumoral M1 macrophage polarization and promoted closer associations between intratumoral CD8 T cells and macrophages. Delivery of IFNγ, in addition to 4-1BBL and IL-12, further increased markers of antigen presentation on tumor cells and intratumoral antigen-presenting cells but also promoted greater expression of checkpoint marker PD-L1 and closer associations between intratumoral CD8 T cells and PD-L1-expressing tumor cells. These findings help to explain the benefits of 4-1BBL and IL-12 delivery while offering additional mechanistic insights into the limitations of IFNγ therapeutic efficacy.
{"title":"Highly-Multiplexed Immunofluorescence PhenoCycler Panel for Murine FFPE Yields Insight into Tumor Microenvironment Immunoengineering.","authors":"Sachin S Surwase, Xin Ming M Zhou, Kathryn M Luly, Qingfeng Zhu, Robert A Anders, Jordan J Green, Stephany Y Tzeng, Joel C Sunshine","doi":"10.1016/j.labinv.2024.102165","DOIUrl":"https://doi.org/10.1016/j.labinv.2024.102165","url":null,"abstract":"<p><p>Spatial proteomics profiling is an emerging set of technologies that has the potential to elucidate the cell types, interactions, and molecular signatures that make up complex tissue microenvironments, with applications in the study of cancer, immunity, and much more. An emerging technique in the field is Co-Detection-by-indEXing (CODEX), recently renamed as the PhenoCycler system. This is a highly-multiplexed immunofluorescence imaging technology that relies on oligonucleotide-barcoded antibodies and cyclic immunofluorescence to visualize many antibody markers in a single specimen while preserving tissue architecture. Existing PhenoCycler panels are primarily designed for fresh-frozen tissues. Formalin-fixed paraffin-embedded (FFPE) blocks offer several advantages in preclinical research, but few antibody clones have been identified in this setting for PhenoCycler imaging. Here, we present a novel PhenoCycler panel of 28 validated antibodies for murine FFPE tissues. We describe our workflow for selecting and validating clones, barcoding antibodies, designing our panel, and performing multiplex imaging. We further detail our analysis pipeline for comparing marker expressions, clustering and phenotyping single-cell proteomics data, and quantifying spatial relationships. We then apply our panel and analysis protocol to profile the effects of three gene-delivery nanoparticle formulations, in combination with systemic anti-PD1, on the murine melanoma tumor immune microenvironment. Intralesional delivery of genes expressing the costimulatory molecule 4-1BBL and the cytokine IL-12 led to a shift towards intratumoral M1 macrophage polarization and promoted closer associations between intratumoral CD8 T cells and macrophages. Delivery of IFNγ, in addition to 4-1BBL and IL-12, further increased markers of antigen presentation on tumor cells and intratumoral antigen-presenting cells but also promoted greater expression of checkpoint marker PD-L1 and closer associations between intratumoral CD8 T cells and PD-L1-expressing tumor cells. These findings help to explain the benefits of 4-1BBL and IL-12 delivery while offering additional mechanistic insights into the limitations of IFNγ therapeutic efficacy.</p>","PeriodicalId":17930,"journal":{"name":"Laboratory Investigation","volume":" ","pages":"102165"},"PeriodicalIF":5.1,"publicationDate":"2024-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142567314","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-24DOI: 10.1016/j.labinv.2024.102166
Julie Stein Deutsch, Daphne Wang, Krista Y Chen, Ashley Cimino-Mathews, Elizabeth D Thompson, Jaroslaw Jedrych, Robert A Anders, Edward Gabrielson, Peter B Illei, Sonali Uttam, Alexa Fiorante, Emily Cohen, Michael Fotheringham, Logan L Engle, Joel C Sunshine, Hao Wang, Dimple Pandya, Vipul Baxi, Joseph Fiore, Kurex Sidik, James Pratt, Alexander S Baras, Tricia R Cottrell, Janis M Taube
Pathologic response is an endpoint in many ongoing clinical trials for neoadjuvant regimens, including immune checkpoint blockade and chemotherapy. Whole slide scanning of glass slides generates high resolution digital images and allows for remote review and potential measurement with image analysis tools, but concordance of pathologic response assessment on digital scans compared to glass slides has yet to be evaluated. Such a validation goes beyond previous concordance studies which focused on establishing surgical pathology diagnoses, as it requires quantitative assessment of tumor, necrosis, and regression. Further, as pathologic response assessment is being used as an endpoint, such concordance studies have regulatory implications. The purpose of this study was two fold: firstly, to determine the concordance between pathologic response assessed on glass slides and on digital scans; and secondly, to determine if pathologists benefited from using measurement tools when determining pathologic response. To that end, H&E-stained glass slides from 64 non-small cell lung carcinoma specimens were visually assessed for percent residual viable tumor (%RVT). The sensitivity and specificity for digital vs. glass reads of complete pathologic response (pCR, 0% RVT) and major pathologic response (MPR, ≤10% RVT) were all >95%. When %RVT was considered as a continuous variable, intraclass correlation coefficient of digital vs. glass reads was 0.94. The visual assessments of pathologic response were supported by pathologist annotations of residual tumor and tumor bed areas. In a separate subset of H&E-stained glass slides, several measurement approaches to quantifying %RVT were performed. Pathologist estimates strongly reflected measured %RVT. This study demonstrates the high level of concordance between glass slides evaluated using light microscopy and digital whole slide images for pathologic response assessments. Pathologists did not require measurement tools to generate robust %RVT values from slide annotations. These findings have broad implications for improving clinical workflows and multisite clinical trials.
{"title":"Concordance of whole slide imaging and conventional light microscopy for assessment of pathologic response following neoadjuvant therapy for lung cancer.","authors":"Julie Stein Deutsch, Daphne Wang, Krista Y Chen, Ashley Cimino-Mathews, Elizabeth D Thompson, Jaroslaw Jedrych, Robert A Anders, Edward Gabrielson, Peter B Illei, Sonali Uttam, Alexa Fiorante, Emily Cohen, Michael Fotheringham, Logan L Engle, Joel C Sunshine, Hao Wang, Dimple Pandya, Vipul Baxi, Joseph Fiore, Kurex Sidik, James Pratt, Alexander S Baras, Tricia R Cottrell, Janis M Taube","doi":"10.1016/j.labinv.2024.102166","DOIUrl":"https://doi.org/10.1016/j.labinv.2024.102166","url":null,"abstract":"<p><p>Pathologic response is an endpoint in many ongoing clinical trials for neoadjuvant regimens, including immune checkpoint blockade and chemotherapy. Whole slide scanning of glass slides generates high resolution digital images and allows for remote review and potential measurement with image analysis tools, but concordance of pathologic response assessment on digital scans compared to glass slides has yet to be evaluated. Such a validation goes beyond previous concordance studies which focused on establishing surgical pathology diagnoses, as it requires quantitative assessment of tumor, necrosis, and regression. Further, as pathologic response assessment is being used as an endpoint, such concordance studies have regulatory implications. The purpose of this study was two fold: firstly, to determine the concordance between pathologic response assessed on glass slides and on digital scans; and secondly, to determine if pathologists benefited from using measurement tools when determining pathologic response. To that end, H&E-stained glass slides from 64 non-small cell lung carcinoma specimens were visually assessed for percent residual viable tumor (%RVT). The sensitivity and specificity for digital vs. glass reads of complete pathologic response (pCR, 0% RVT) and major pathologic response (MPR, ≤10% RVT) were all >95%. When %RVT was considered as a continuous variable, intraclass correlation coefficient of digital vs. glass reads was 0.94. The visual assessments of pathologic response were supported by pathologist annotations of residual tumor and tumor bed areas. In a separate subset of H&E-stained glass slides, several measurement approaches to quantifying %RVT were performed. Pathologist estimates strongly reflected measured %RVT. This study demonstrates the high level of concordance between glass slides evaluated using light microscopy and digital whole slide images for pathologic response assessments. Pathologists did not require measurement tools to generate robust %RVT values from slide annotations. These findings have broad implications for improving clinical workflows and multisite clinical trials.</p>","PeriodicalId":17930,"journal":{"name":"Laboratory Investigation","volume":" ","pages":"102166"},"PeriodicalIF":5.1,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142503126","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Tumor-associated chronic lung inflammation depends on tumor necrosis factor (TNF)-α to activate several cytokines as part of an inflammatory loop, which plays a critical role in tumor progression in lung adenocarcinoma. High mobility group box 1 (HMGB1) is a cytokine that mediates inflammation. Whether TNF-α-induced inflammation regulates HMGB1 to contribute to tumor progression and promotion in lung adenocarcinoma remains unclear. Thus, human samples and a urethane-induced inflammation-driven lung adenocarcinoma (IDLA) mouse model were used to explore the involvement of HMGB1 in tumorigenesis, tumor progression, and efficacy of anti-programmed cell death protein (PD)-1 immunotherapy. High levels of HMGB1 were observed in human lung adenocarcinoma associated with poor overall survival in patients. HMGB1 upregulation was positively correlated with TNF-α-related inflammation and TIM3+ infiltration. TNF-α upregulated intracellular and extracellular HMGB1 expression to contribute to tumor promotion in A549 cells in vitro. Using a urethane-induced IDLA mouse model, we found HMGB1 upregulation was associated with increased TIM3+ T cell infiltration. Blocking TNF-α-dependent inflammation downregulated HMGB1 expression and inhibited tumorigenesis in the IDLA. Anti-PD-1 treatment alone did not inhibit tumor growth in the TNF-α-dependent IDLA, whereas anti-PD-1 combined with TNF-α blockade overcame anti-PD-1 immunotherapy resistance. Furthermore, anti-PD-1 combined with anti-HMGB1 also inhibited tumor growth in IDLA, suggesting increased HMGB1 release by TNF-α contributes to the resistance of anti-PD-1 immunotherapy in IDLA. Thus, tumor-associated TNF-α-dependent inflammation upregulated intracellular and extracellular HMGB1 expression in an inflammatory loop, contributing to tumor promotion and anti-PD-1 immunotherapy resistance in lung adenocarcinoma.
{"title":"Tumor necrosis factor-α-dependent inflammation upregulates high mobility group box 1 to induce tumor promotion and anti-programmed cell death protein-1 immunotherapy resistance in lung adenocarcinoma.","authors":"Lifei Kang, Jingjing Cao, Wenli Guo, Xiaohui Cui, Yangxuan Wei, Jiayu Zhang, Feiran Liu, Chenyang Duan, Qiang Lin, Ping Lv, Zhiyu Ni, Jing Zuo, Haitao Shen","doi":"10.1016/j.labinv.2024.102164","DOIUrl":"https://doi.org/10.1016/j.labinv.2024.102164","url":null,"abstract":"<p><p>Tumor-associated chronic lung inflammation depends on tumor necrosis factor (TNF)-α to activate several cytokines as part of an inflammatory loop, which plays a critical role in tumor progression in lung adenocarcinoma. High mobility group box 1 (HMGB1) is a cytokine that mediates inflammation. Whether TNF-α-induced inflammation regulates HMGB1 to contribute to tumor progression and promotion in lung adenocarcinoma remains unclear. Thus, human samples and a urethane-induced inflammation-driven lung adenocarcinoma (IDLA) mouse model were used to explore the involvement of HMGB1 in tumorigenesis, tumor progression, and efficacy of anti-programmed cell death protein (PD)-1 immunotherapy. High levels of HMGB1 were observed in human lung adenocarcinoma associated with poor overall survival in patients. HMGB1 upregulation was positively correlated with TNF-α-related inflammation and TIM3<sup>+</sup> infiltration. TNF-α upregulated intracellular and extracellular HMGB1 expression to contribute to tumor promotion in A549 cells in vitro. Using a urethane-induced IDLA mouse model, we found HMGB1 upregulation was associated with increased TIM3<sup>+</sup> T cell infiltration. Blocking TNF-α-dependent inflammation downregulated HMGB1 expression and inhibited tumorigenesis in the IDLA. Anti-PD-1 treatment alone did not inhibit tumor growth in the TNF-α-dependent IDLA, whereas anti-PD-1 combined with TNF-α blockade overcame anti-PD-1 immunotherapy resistance. Furthermore, anti-PD-1 combined with anti-HMGB1 also inhibited tumor growth in IDLA, suggesting increased HMGB1 release by TNF-α contributes to the resistance of anti-PD-1 immunotherapy in IDLA. Thus, tumor-associated TNF-α-dependent inflammation upregulated intracellular and extracellular HMGB1 expression in an inflammatory loop, contributing to tumor promotion and anti-PD-1 immunotherapy resistance in lung adenocarcinoma.</p>","PeriodicalId":17930,"journal":{"name":"Laboratory Investigation","volume":" ","pages":"102164"},"PeriodicalIF":5.1,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142503128","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-10-21DOI: 10.1016/j.labinv.2024.102161
Petra Pokorna , Hana Palova , Sona Adamcova , Robin Jugas , Dagmar Al Tukmachi , Michal Kyr , Dana Knoflickova , Katerina Kozelkova , Vojtech Bystry , Sona Mejstrikova , Tomas Merta , Karolina Trachtova , Eliska Podlipna , Peter Mudry , Zdenek Pavelka , Viera Bajciova , Pavel Tinka , Marie Jarosova , Tina Catela Ivkovic , Sibylle Madlener , Ondrej Slaby
Despite significant improvement in the survival of pediatric patients with cancer, treatment outcomes for high-risk, relapsed, and refractory cancers remain unsatisfactory. Moreover, prolonged survival is frequently associated with long-term adverse effects due to intensive multimodal treatments. Accelerating the progress of pediatric oncology requires both therapeutic advances and strategies to mitigate the long-term cytotoxic side effects, potentially through targeting specific molecular drivers of pediatric malignancies. In this report, we present the results of integrative genomic and transcriptomic profiling of 230 patients with malignant solid tumors (the “primary cohort”) and 18 patients with recurrent or otherwise difficult-to-treat nonmalignant conditions (the “secondary cohort”). The integrative workflow for the primary cohort enabled the identification of clinically significant single nucleotide variants, small insertions/deletions, and fusion genes, which were found in 55% and 28% of patients, respectively. For 38% of patients, molecularly informed treatment recommendations were made. In the secondary cohort, known or potentially driving alteration was detected in 89% of cases, including a suspected novel causal gene for patients with inclusion body infantile digital fibromatosis. Furthermore, 47% of findings also brought therapeutic implications for subsequent management. Across both cohorts, changes or refinements to the original histopathological diagnoses were achieved in 4% of cases. Our study demonstrates the efficacy of integrating advanced genomic and transcriptomic analyses to identify therapeutic targets, refine diagnoses, and optimize treatment strategies for challenging pediatric and young adult malignancies and underscores the need for broad implementation of precision oncology in clinical settings.
{"title":"Real-World Performance of Integrative Clinical Genomics in Pediatric Precision Oncology","authors":"Petra Pokorna , Hana Palova , Sona Adamcova , Robin Jugas , Dagmar Al Tukmachi , Michal Kyr , Dana Knoflickova , Katerina Kozelkova , Vojtech Bystry , Sona Mejstrikova , Tomas Merta , Karolina Trachtova , Eliska Podlipna , Peter Mudry , Zdenek Pavelka , Viera Bajciova , Pavel Tinka , Marie Jarosova , Tina Catela Ivkovic , Sibylle Madlener , Ondrej Slaby","doi":"10.1016/j.labinv.2024.102161","DOIUrl":"10.1016/j.labinv.2024.102161","url":null,"abstract":"<div><div>Despite significant improvement in the survival of pediatric patients with cancer, treatment outcomes for high-risk, relapsed, and refractory cancers remain unsatisfactory. Moreover, prolonged survival is frequently associated with long-term adverse effects due to intensive multimodal treatments. Accelerating the progress of pediatric oncology requires both therapeutic advances and strategies to mitigate the long-term cytotoxic side effects, potentially through targeting specific molecular drivers of pediatric malignancies. In this report, we present the results of integrative genomic and transcriptomic profiling of 230 patients with malignant solid tumors (the “primary cohort”) and 18 patients with recurrent or otherwise difficult-to-treat nonmalignant conditions (the “secondary cohort”). The integrative workflow for the primary cohort enabled the identification of clinically significant single nucleotide variants, small insertions/deletions, and fusion genes, which were found in 55% and 28% of patients, respectively. For 38% of patients, molecularly informed treatment recommendations were made. In the secondary cohort, known or potentially driving alteration was detected in 89% of cases, including a suspected novel causal gene for patients with inclusion body infantile digital fibromatosis. Furthermore, 47% of findings also brought therapeutic implications for subsequent management. Across both cohorts, changes or refinements to the original histopathological diagnoses were achieved in 4% of cases. Our study demonstrates the efficacy of integrating advanced genomic and transcriptomic analyses to identify therapeutic targets, refine diagnoses, and optimize treatment strategies for challenging pediatric and young adult malignancies and underscores the need for broad implementation of precision oncology in clinical settings.</div></div>","PeriodicalId":17930,"journal":{"name":"Laboratory Investigation","volume":"104 12","pages":"Article 102161"},"PeriodicalIF":5.1,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142503127","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}