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Serhan HA, Bao L, Cheng X, Qin Z, Liu CJ, Heth JA, Udager AM, Soellner MB, Merajver SD, Morikawa A, Merrill NM. Targeting fatty acid synthase in preclinical models of TNBC brain metastases synergizes with SN-38 and impairs invasion. NPJ Breast Cancer 2024; 10:43. [PMID: 38858374 PMCID: PMC11164988 DOI: 10.1038/s41523-024-00656-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 06/01/2024] [Indexed: 06/12/2024] Open
Abstract
Fatty acid synthesis (FAS) has been shown to play a key role in the survival of brain-metastatic (BM) breast cancer. We demonstrate that the fatty acid synthase inhibitor TVB-2640 synergizes with the topoisomerase inhibitor SN-38 in triple-negative breast cancer (TNBC) BM cell lines, upregulates FAS and downregulates cell cycle progression gene expression, and slows the motility of TNBC BM cell lines. The combination of SN-38 and TVB-2640 warrants further consideration as a potential therapeutic option in TNBC BMs.
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Affiliation(s)
- Habib A Serhan
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Liwei Bao
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Xu Cheng
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Zhaoping Qin
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Chia-Jen Liu
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jason A Heth
- Department of Neurosurgery, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Aaron M Udager
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Matthew B Soellner
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Sofia D Merajver
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Aki Morikawa
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Nathan M Merrill
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA.
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2
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Singhal U, Nallandhighal S, Tosoian JJ, Hu K, Pham TM, Stangl-Kremser J, Liu CJ, Karim R, Plouffe KR, Morgan TM, Cieslik M, Lucianò R, Shariat SF, Finocchio N, Dambrosio L, Doglioni C, Chinnaiyan AM, Tomlins SA, Briganti A, Palapattu GS, Udager AM, Salami SS. Integrative multi-region molecular profiling of primary prostate cancer in men with synchronous lymph node metastasis. Nat Commun 2024; 15:4341. [PMID: 38773085 PMCID: PMC11109137 DOI: 10.1038/s41467-024-48629-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 05/08/2024] [Indexed: 05/23/2024] Open
Abstract
Localized prostate cancer is frequently composed of multiple spatially distinct tumors with significant inter- and intra-tumoral molecular heterogeneity. This genomic diversity gives rise to many competing clones that may drive the biological trajectory of the disease. Previous large-scale sequencing efforts have focused on the evolutionary process in metastatic prostate cancer, revealing a potential clonal progression to castration resistance. However, the clonal origin of synchronous lymph node (LN) metastases in primary disease is still unknown. Here, we perform multi-region, targeted next generation sequencing and construct phylogenetic trees in men with prostate cancer with synchronous LN metastasis to better define the pathologic and molecular features of primary disease most likely to spread to the LNs. Collectively, we demonstrate that a combination of histopathologic and molecular factors, including tumor grade, presence of extra-prostatic extension, cellular morphology, and oncogenic genomic alterations are associated with synchronous LN metastasis.
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Affiliation(s)
- Udit Singhal
- Department of Urology, Michigan Medicine, Ann Arbor, MI, USA.
- Department of Urology, Mayo Clinic, Rochester, MN, USA.
- Rogel Cancer Center, Michigan Medicine, Ann Arbor, MI, USA.
- Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI, USA.
| | | | - Jeffrey J Tosoian
- Department of Urology, Vanderbilt University, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Kevin Hu
- Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA
| | - Trinh M Pham
- Department of Urology, Michigan Medicine, Ann Arbor, MI, USA
| | - Judith Stangl-Kremser
- Department of Urology, Michigan Medicine, Ann Arbor, MI, USA
- Department of Urology, Medical University of Vienna, Vienna, Austria
| | - Chia-Jen Liu
- College of Literature, Science, and Arts, University of Michigan, Ann Arbor, MI, USA
| | - Razeen Karim
- College of Literature, Science, and Arts, University of Michigan, Ann Arbor, MI, USA
| | - Komal R Plouffe
- Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI, USA
- Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA
| | - Todd M Morgan
- Department of Urology, Michigan Medicine, Ann Arbor, MI, USA
- Rogel Cancer Center, Michigan Medicine, Ann Arbor, MI, USA
| | - Marcin Cieslik
- Rogel Cancer Center, Michigan Medicine, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI, USA
- Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA
| | - Roberta Lucianò
- Department of Pathology, Universita Vita-Salute San Raffaele, Milan, Italy
| | | | - Nadia Finocchio
- Department of Urology, Universita Vita-Salute San Raffaele, Milan, Italy
| | - Lucia Dambrosio
- Department of Urology, Universita Vita-Salute San Raffaele, Milan, Italy
| | - Claudio Doglioni
- Department of Pathology, Universita Vita-Salute San Raffaele, Milan, Italy
| | - Arul M Chinnaiyan
- Department of Urology, Michigan Medicine, Ann Arbor, MI, USA
- Rogel Cancer Center, Michigan Medicine, Ann Arbor, MI, USA
- Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI, USA
- Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
| | - Scott A Tomlins
- Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA
| | - Alberto Briganti
- Department of Urology, Universita Vita-Salute San Raffaele, Milan, Italy
| | - Ganesh S Palapattu
- Department of Urology, Michigan Medicine, Ann Arbor, MI, USA
- Rogel Cancer Center, Michigan Medicine, Ann Arbor, MI, USA
- Department of Urology, Medical University of Vienna, Vienna, Austria
| | - Aaron M Udager
- Rogel Cancer Center, Michigan Medicine, Ann Arbor, MI, USA.
- Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI, USA.
- Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA.
| | - Simpa S Salami
- Department of Urology, Michigan Medicine, Ann Arbor, MI, USA.
- Rogel Cancer Center, Michigan Medicine, Ann Arbor, MI, USA.
- Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI, USA.
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3
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Mehra R, Nallandhighal S, Cotta B, Knuth Z, Su F, Kasputis A, Zhang Y, Wang R, Cao X, Udager AM, Dhanasekaran SM, Cieslik MP, Morgan TM, Salami SS. Discovery and Validation of a 15-Gene Prognostic Signature for Clear Cell Renal Cell Carcinoma. JCO Precis Oncol 2024; 8:e2300565. [PMID: 38810179 DOI: 10.1200/po.23.00565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 01/11/2024] [Accepted: 03/15/2024] [Indexed: 05/31/2024] Open
Abstract
PURPOSE Develop and validate gene expression-based biomarker associated with recurrent disease to facilitate risk stratification of clear cell renal cell carcinoma (ccRCC). MATERIALS AND METHODS We retrospectively identified 110 patients who underwent radical nephrectomy for ccRCC (discovery cohort). Patients who recurred were matched on the basis of grade/stage to patients without recurrence. Capture whole-transcriptome sequencing was performed on RNA isolated from archival tissue using the Illumina platform. We developed a gene-expression signature to predict recurrence-free survival/disease-free survival (DFS) using a 15-fold lasso and elastic-net regularized linear Cox model. We derived the 31-gene cell cycle progression (mxCCP) score using RNA-seq data for each patient. Kaplan-Meier (KM) curves and multivariable Cox proportional hazard testing were used to validate the independent prognostic impact of the gene-expression signature on DFS, disease-specific survival (DSS), and overall survival (OS) in two validation data sets (combined n = 761). RESULTS After quality control, the discovery cohort comprised 50 patients with recurrence and 41 patients without, with a median follow-up of 26 and 36 months, respectively. We developed a 15-gene (15G) signature, which was independently associated with worse DFS and DSS (DFS: hazard ratio [HR], 11.08 [95% CI, 4.9 to 25.1]; DSS: HR, 9.67 [95% CI, 3.4 to 27.7]) in a multivariable model adjusting for clinicopathologic parameters (including stage, size, grade, and necrosis [SSIGN] score and Memorial Sloan Kettering Cancer Center nomogram) and mxCCP score. The 15G signature was also independently associated with worse DFS and DSS in both validation data sets (Validation A [n = 382], DFS: HR, 2.6 [95% CI, 1.6 to 4.3]; DSS: HR, 3 [95% CI, 1.4 to 6.1] and Validation B (n = 379), DFS: HR, 2.1 [95% CI, 1.2 to 3.6]; OS: HR, 3 [95% CI, 1.6 to 5.7]) adjusting for clinicopathologic variables and mxCCP score. CONCLUSION We developed and validated a novel 15G prognostic signature to improve risk stratification of patients with ccRCC. Pending further validation, this signature has the potential to facilitate optimal treatment allocation.
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Affiliation(s)
- Rohit Mehra
- University of Michigan Rogel Cancer Center, Ann Arbor, MI
- Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI
- Department of Pathology, Michigan Medicine, Ann Arbor, MI
| | | | | | - Zayne Knuth
- Department of Urology, Michigan Medicine, Ann Arbor, MI
| | - Fengyun Su
- Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI
- Department of Pathology, Michigan Medicine, Ann Arbor, MI
| | - Amy Kasputis
- Department of Urology, Michigan Medicine, Ann Arbor, MI
| | - Yuping Zhang
- Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI
- Department of Pathology, Michigan Medicine, Ann Arbor, MI
| | - Rui Wang
- Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI
- Department of Pathology, Michigan Medicine, Ann Arbor, MI
| | - Xuhong Cao
- Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI
- Department of Pathology, Michigan Medicine, Ann Arbor, MI
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI
| | - Aaron M Udager
- University of Michigan Rogel Cancer Center, Ann Arbor, MI
- Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI
- Department of Pathology, Michigan Medicine, Ann Arbor, MI
| | - Saravana M Dhanasekaran
- Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI
- Department of Pathology, Michigan Medicine, Ann Arbor, MI
| | - Marcin P Cieslik
- Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI
- Department of Pathology, Michigan Medicine, Ann Arbor, MI
- Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI
| | - Todd M Morgan
- University of Michigan Rogel Cancer Center, Ann Arbor, MI
- Department of Urology, Michigan Medicine, Ann Arbor, MI
| | - Simpa S Salami
- University of Michigan Rogel Cancer Center, Ann Arbor, MI
- Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI
- Department of Urology, Michigan Medicine, Ann Arbor, MI
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Hashemi Gheinani A, Kim J, You S, Adam RM. Bioinformatics in urology - molecular characterization of pathophysiology and response to treatment. Nat Rev Urol 2024; 21:214-242. [PMID: 37604982 DOI: 10.1038/s41585-023-00805-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2023] [Indexed: 08/23/2023]
Abstract
The application of bioinformatics has revolutionized the practice of medicine in the past 20 years. From early studies that uncovered subtypes of cancer to broad efforts spearheaded by the Cancer Genome Atlas initiative, the use of bioinformatics strategies to analyse high-dimensional data has provided unprecedented insights into the molecular basis of disease. In addition to the identification of disease subtypes - which enables risk stratification - informatics analysis has facilitated the identification of novel risk factors and drivers of disease, biomarkers of progression and treatment response, as well as possibilities for drug repurposing or repositioning; moreover, bioinformatics has guided research towards precision and personalized medicine. Implementation of specific computational approaches such as artificial intelligence, machine learning and molecular subtyping has yet to become widespread in urology clinical practice for reasons of cost, disruption of clinical workflow and need for prospective validation of informatics approaches in independent patient cohorts. Solving these challenges might accelerate routine integration of bioinformatics into clinical settings.
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Affiliation(s)
- Ali Hashemi Gheinani
- Department of Urology, Boston Children's Hospital, Boston, MA, USA
- Department of Surgery, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Urology, Inselspital, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Jina Kim
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Sungyong You
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Rosalyn M Adam
- Department of Urology, Boston Children's Hospital, Boston, MA, USA.
- Department of Surgery, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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5
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Werner R, Connolly A, Bennett M, Hand CK, Burke L. Implementation of an ISO15189 accredited next-generation sequencing service with the fully automated Ion Torrent Genexus: the experience of a clinical diagnostic laboratory. J Clin Pathol 2024; 77:278-283. [PMID: 36522176 PMCID: PMC10958377 DOI: 10.1136/jcp-2022-208625] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/03/2022] [Indexed: 12/23/2022]
Abstract
AIMS Next-generation sequencing (NGS) is integral to the delivery of personalised medicine for targeted cancer therapy. Average turnaround times (TAT) from reference laboratories with advanced expertise in sequencing are typically 2-3 weeks. Prolonged TAT for biomarker analysis can adversely affect patient outcomes. The project aim was to establish an accredited NGS service integrated within a routine clinical diagnostic laboratory, in a designated tertiary cancer centre with no previous experience in NGS or bioinformatics. METHODS Platform selected was the novel Ion Torrent Genexus Sequencer with automated onboard library preparation, templating, sequencing and data analysis, with subsequent reporting using Oncomine Reporter software.Entire workflow validation was performed with a targeted panel, the Oncomine Precision Assay, on formalin-fixed paraffin embedded clinical tumour samples. Oncomine Reporter software was used to report on variants including mutations, copy number variations and fusions across 50 key genes.Samples included surgical resections, biopsies, cytology and commercial reference material. Assessment of criteria included analytical sensitivity, specificity, limit of detection, accuracy, repeatability and reproducibility, with the establishment of performance metrics and quality parameters. RESULTS High sensitivity, specificity and reproducibility were achieved. DNA/RNA input requirements optimised to >10 ng, and sequencing performance established with a limit of detection of 5% when depth of coverage of 2500X was reached. This NGS service attained ISO15189 accreditation with no non-conformances and >56% reduction in TAT. CONCLUSION Successful implementation, clinical validation and accreditation of a novel NGS technology was achieved in this institution, with a significantly improved TAT of results to oncologists.
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Affiliation(s)
- Réiltín Werner
- Pathology Department, Cork University Hospital, Cork, Ireland
- Department of Pathology, School of Medicine, University College Cork, Cork, Ireland
| | - Amy Connolly
- Pathology Department, Cork University Hospital, Cork, Ireland
| | - Michael Bennett
- Pathology Department, Cork University Hospital, Cork, Ireland
| | - Collette K Hand
- Department of Pathology, School of Medicine, University College Cork, Cork, Ireland
| | - Louise Burke
- Pathology Department, Cork University Hospital, Cork, Ireland
- Department of Pathology, School of Medicine, University College Cork, Cork, Ireland
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Kolekar P, Balagopal V, Dong L, Liu Y, Foy S, Tran Q, Mulder H, Huskey AL, Plyler E, Liang Z, Ma J, Nakitandwe J, Gu J, Namwanje M, Maciaszek J, Payne-Turner D, Mallampati S, Wang L, Easton J, Klco JM, Ma X. SJPedPanel: A pan-cancer gene panel for childhood malignancies. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.11.27.23299068. [PMID: 38076942 PMCID: PMC10705664 DOI: 10.1101/2023.11.27.23299068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Background Large scale genomics projects have identified driver alterations for most childhood cancers that provide reliable biomarkers for clinical diagnosis and disease monitoring using targeted sequencing. However, there is lack of a comprehensive panel that matches the list of known driver genes. Here we fill this gap by developing SJPedPanel for childhood cancers. Results SJPedPanel covers 5,275 coding exons of 357 driver genes, 297 introns frequently involved in rearrangements that generate fusion oncoproteins, commonly amplified/deleted regions (e.g., MYCN for neuroblastoma, CDKN2A and PAX5 for B-/T-ALL, and SMARCB1 for AT/RT), and 7,590 polymorphism sites for interrogating tumors with aneuploidy, such as hyperdiploid and hypodiploid B-ALL or 17q gain neuroblastoma. We used driver alterations reported from an established real-time clinical genomics cohort (n=253) to validate this gene panel. Among the 485 pathogenic variants reported, our panel covered 417 variants (86%). For 90 rearrangements responsible for oncogenic fusions, our panel covered 74 events (82%). We re-sequenced 113 previously characterized clinical specimens at an average depth of 2,500X using SJPedPanel and recovered 354 (91%) of the 389 reported pathogenic variants. We then investigated the power of this panel in detecting mutations from specimens with low tumor purity (as low as 0.1%) using cell line-based dilution experiments and discovered that this gene panel enabled us to detect ∼80% variants with allele fraction of 0.2%, while the detection rate decreases to ∼50% when the allele fraction is 0.1%. We finally demonstrate its utility in disease monitoring on clinical specimens collected from AML patients in morphologic remission. Conclusions SJPedPanel enables the detection of clinically relevant genetic alterations including rearrangements responsible for subtype-defining fusions for childhood cancers by targeted sequencing of ∼0.15% of human genome. It will enhance the analysis of specimens with low tumor burdens for cancer monitoring and early detection.
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Ha GW, Hwang HP, Cho YG, Park J. Clinical and Genetic Characteristics of Early and Advanced Gastric Cancer. Curr Issues Mol Biol 2024; 46:1208-1218. [PMID: 38392195 PMCID: PMC10887908 DOI: 10.3390/cimb46020077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 02/24/2024] Open
Abstract
Gastric cancer (GC) persists as the fourth most prevalent cause of global cancer-related mortality, presenting a challenge due to the scarcity of available therapeutic strategies. Precision medicine is crucial not only in the treatment but also in the management of GC. We performed gene panel sequencing with Oncomine focus assay comprising 52 cancer-associated genes and MSI analysis in 100 case-matched gastric cancer cases. A comprehensive analysis of clinical and genetic characteristics was conducted on these genetic results and clinicopathological findings. Upon comparison of clinicopathological characteristics, significant differences between early gastric cancer (EGC) and advanced gastric cancer (AGC) were observed in tumor location (p = 0.003), Lauren classification (p = 0.015), T stage (p = 0.000), and N stage (p = 0.015). The six most frequently mutated genes were PIK3CA (29%, 10/35), ERBB2 (17%, 6/35), KRAS (14%, 5/35), ALK (6%, 2/35), ESR1 (6%, 2/35), and FGFR3 (6%, 2/35). Regarding genetic variation, there was a tendency for the N stage to be higher in GC patients with mutated genes (p = 0.014). The frequency of mutations in GC patients was statistically significantly higher in AGC (n = 24) compared to EGC (n = 11) (odds ratio, 2.792; 95% confidence interval, 1.113 to 7.007; p = 0.026). Six of the ten GC patients carrying mutated genes and exhibiting MSI were classified into intestinal-type and undifferentiated GC, with the location of the tumor being in the lower-third. Among these patients, five harbored mutated PIK3CA, while the remaining patient had a mutation in ALK. Conclusions: AGC patients more frequently exhibited alterations of PIK3CA, KRAS, and ERBB2 as somatic oncogenic drivers, and displayed a higher prevalence of cumulative genetic events, including increased rates of PIK3CA mutations, enhanced detection of immunotherapy biomarkers, and mutations of the ESR1 gene.
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Affiliation(s)
- Gi Won Ha
- Department of Surgery, Jeonbuk National University Medical School and Hospital, Jeonju 54907, Republic of Korea
| | - Hong Pil Hwang
- Department of Surgery, Jeonbuk National University Medical School and Hospital, Jeonju 54907, Republic of Korea
| | - Yong Gon Cho
- Department of Laboratory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju 54907, Republic of Korea
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju 54907, Republic of Korea
| | - Joonhong Park
- Department of Laboratory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju 54907, Republic of Korea
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju 54907, Republic of Korea
- Department of Laboratory Medicine, Daejeon St. Mary's Hospital, Daejeon 34943, Republic of Korea
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Singh H, Kang A, Bloudek L, Hsu LI, Corinna Palanca-Wessels M, Stecher M, Siadak M, Ng K. Systematic literature review and meta-analysis of HER2 amplification, overexpression, and positivity in colorectal cancer. JNCI Cancer Spectr 2024; 8:pkad082. [PMID: 37815820 PMCID: PMC10868379 DOI: 10.1093/jncics/pkad082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 08/25/2023] [Accepted: 09/21/2023] [Indexed: 10/11/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is the second most common cause of cancer death globally. Recent clinical trials suggest an emerging role for HER2 as a potential clinically relevant biomarker in CRC. Testing for HER2 in CRC is not standard practice; consequently, the prevalence of HER2 positivity (HER2+) in patients with CRC remains uncertain. METHODS A systematic literature review and meta-analysis were conducted to generate estimates of proportions of patients with CRC with HER2 overexpression or HER2 amplification and HER2+ (either overexpression or amplification), overall and in patients with rat sarcoma virus (RAS) wild-type cancer. HER2+ was defined as 1) immunohistochemistry with a score of 3+, 2) immunohistochemistry with a score of 2+ and in situ hybridization+, or 3) next-generation sequencing positive. RESULTS Of 224 studies identified with information on HER2 in CRC, 52 studies used a US Food and Drug Administration-approved assay and were selected for further analysis. Estimated HER2+ rate was 4.1% (95% confidence interval [CI] = 3.4% to 5.0%) overall (n = 17 589). HER2+ rates were statistically higher in RAS wild-type (6.1%, 95% CI = 5.4% to 6.9%) vs RAS mutant CRC (1.1%, 95% CI = 0.3% to 4.4%; P < .0001). Despite limited clinical information, we confirmed enrichment of HER2+ CRC in patients with microsatellite stable and left-sided CRC. CONCLUSION This meta-analysis provides an estimate of HER2+ CRC and confirms enrichment of HER2 in microsatellite stable, left-sided, RAS wild-type CRC tumors. Our work is important given the recently described clinical efficacy of HER2-targeted therapies in HER2+ CRC and informs strategies for incorporation of HER2 testing into standard of care.
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Affiliation(s)
- Harshabad Singh
- Division of Gastrointestinal Cancers, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | | | | | | | | | - Kimmie Ng
- Division of Gastrointestinal Cancers, Dana-Farber Cancer Institute, Boston, MA, USA
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9
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Kukita Y, Kunimasa K, Akazawa T, Mizote Y, Tahara H. A Method for Extending Target Regions of Genomic Profiling by Combining a Custom Probe Pool with a Commercial Targeted Panel. J Appl Lab Med 2023; 8:1065-1073. [PMID: 37748758 DOI: 10.1093/jalm/jfad069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 08/25/2023] [Indexed: 09/27/2023]
Abstract
BACKGROUND Next-generation sequencing (NGS)-based genomic profiling is becoming widespread in determining treatment policies for patients with tumors. Commercially available gene panels for pan-tumor targets comprise hundreds of tumor-related genes but frequently lack genes of interest in specific tumor types. In this study, we demonstrate a method for extending target regions of genomic profiling by combining a custom probe pool with a commercial targeted panel. METHODS We used TruSight Oncology 500 (TSO500) as a commercial targeted panel and a custom probe pool designed for all exons of the SMARCA2 gene. Sequencing libraries of custom targets were constructed using a portion of the TSO500 library solution before the hybridization-capture process. After hybridization capture, both libraries were combined and sequenced using a next-generation sequencer. RESULTS Sequencing results showed that >96.8% and 100% of the target exons were covered at a depth of over 100× using the TSO500 and custom panels, respectively. The custom panels had slightly better median exon coverage than the TSO500. The combined libraries of the custom and TSO500 panels showed a mapped read ratio close to the mixing ratio. Analysis of mutation-free regions showed similar accuracies between the TSO500 and custom panels regarding variant calling. CONCLUSIONS Our devised method easily and affordably extends the targets beyond a ready-made panel. This method provides a valuable solution until the widespread adoption of whole-exome sequencing, which is costly for large target sizes.
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Affiliation(s)
- Yoji Kukita
- Laboratory of Genomic Pathology, Research Center, Osaka International Cancer Institute, Osaka, Japan
| | - Kei Kunimasa
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Takashi Akazawa
- Department of Cancer Drug Discovery and Development, Research Center, Osaka International Cancer Institute, Osaka, Japan
| | - Yu Mizote
- Department of Cancer Drug Discovery and Development, Research Center, Osaka International Cancer Institute, Osaka, Japan
| | - Hideaki Tahara
- Department of Cancer Drug Discovery and Development, Research Center, Osaka International Cancer Institute, Osaka, Japan
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10
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Sakai T, Matsumoto S, Ueda Y, Shibata Y, Ikeda T, Nakamura A, Kodani M, Ohashi K, Furuya N, Izumi H, Nosaki K, Umemura S, Zenke Y, Udagawa H, Sugiyama E, Yoh K, Goto K. Clinicogenomic Features and Targetable Mutations in NSCLCs Harboring BRAF Non-V600E Mutations: A Multi-Institutional Genomic Screening Study (LC-SCRUM-Asia). J Thorac Oncol 2023; 18:1538-1549. [PMID: 37543207 DOI: 10.1016/j.jtho.2023.07.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 07/08/2023] [Accepted: 07/29/2023] [Indexed: 08/07/2023]
Abstract
INTRODUCTION BRAF non-V600E mutations occur in 1% to 2% of NSCLCs. Because of their rarity, the clinical backgrounds and outcomes of cytotoxic chemotherapy or immunotherapy remain unclear, and no targeted therapies are approved for BRAF non-V600E-mutant NSCLC. METHODS In this multi-institutional prospective lung cancer genomic screening project (LC-SCRUM-Asia), we evaluated the clinicogenomic characteristics and therapeutic outcomes of BRAF non-V600E-mutant NSCLC. RESULTS From March 2015 to November 2021, a total of 11,929 patients with NSCLC were enrolled. BRAF mutations were detected in 380 (3.5%), including the V600E (class I) in 119 (31%) and non-V600E in 261; the non-V600E were functionally classified into class II (122, 32%), class III (86, 23%), and non-classes I to III. Smokers and having concurrent RAS gene family or TP53 mutations were more frequently associated with class II or III than with class I. In patients with class III as compared with class I, the progression-free survival in response to platinum-containing chemotherapies (median, 5.3 versus 11.5 mo, p < 0.01) and the overall survival (median, 14.5 versus 34.8 mo, p < 0.02) were significantly shorter. Furthermore, class IIa mutations were significantly more frequent in our Asian cohort than in previously reported cohorts. The clinicogenomic features associated with class IIa were similar to those associated with class I, and one patient with NSCLC with K601E had a good response to dabrafenib plus trametinib. CONCLUSIONS Patients with NSCLCs with BRAF non-V600E, especially class III, were associated with poorer therapeutic outcomes than those with V600E. Furthermore, patients with NSCLC with class IIa had distinct clinicogenomic features, and further preclinical and clinical studies are needed to evaluate class IIa mutations as a therapeutic target.
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Affiliation(s)
- Tetsuya Sakai
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Shingo Matsumoto
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Japan.
| | - Yasuto Ueda
- Department of Respiratory Medicine, Tottori Prefectural Central Hospital, Tottori, Japan
| | - Yuji Shibata
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Takaya Ikeda
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Atsushi Nakamura
- Department of Pulmonary Medicine, Sendai Kousei Hospital, Sendai, Japan
| | - Masahiro Kodani
- Division of Respiratory Medicine and Rheumatology, Department of Multidisciplinary Internal Medicine, Faculty of Medicine, Tottori University, Yonago, Japan
| | - Kadoaki Ohashi
- Department of Respiratory Medicine, Okayama University Hospital, Okayama, Japan
| | - Naoki Furuya
- Division of Respiratory Medicine, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Hiroki Izumi
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Kaname Nosaki
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Shigeki Umemura
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Yoshitaka Zenke
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Hibiki Udagawa
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Eri Sugiyama
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Kiyotaka Yoh
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Koichi Goto
- Department of Thoracic Oncology, National Cancer Center Hospital East, Kashiwa, Japan
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11
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Fürstberger A, Ikonomi N, Kestler AMR, Marienfeld R, Schwab JD, Kuhn P, Seufferlein T, Kestler HA. AMBAR - Interactive Alteration annotations for molecular tumor boards. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2023; 240:107697. [PMID: 37441893 DOI: 10.1016/j.cmpb.2023.107697] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 05/23/2023] [Accepted: 06/24/2023] [Indexed: 07/15/2023]
Abstract
MOTIVATION Personalized decision-making for cancer therapy relies on molecular profiling from sequencing data in combination with database evidence and expert knowledge. Molecular tumor boards (MTBs) bring together clinicians and scientists with diverse expertise and are increasingly established in the clinical routine for therapeutic interventions. However, the analysis and documentation of patients data are still time-consuming and difficult to manage for MTBs, especially as few tools are available for the amount of information required. RESULTS To overcome these limitations, we developed an interactive web application AMBAR (Alteration annotations for Molecular tumor BoARds), for therapeutic decision-making support in MTBs. AMBAR is an R shiny-based application that allows customization, interactive filtering, visualization, adding expert knowledge, and export to clinical systems of annotated mutations. AVAILABILITY AMBAR is dockerized, open source and available at https://sysbio.uni-ulm.de/?Software:Ambar Contact:hans.kestler@uni-ulm.de.
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Affiliation(s)
- Axel Fürstberger
- Institute of Medical Systems Biology, Ulm University, Ulm 89081, Germany; Department of Pathology, Ulm University Hospital, Ulm 89081, Germany; Zentrum Personalisierte Medizin, Ulm University Hospital, Ulm 89081, Germany
| | - Nensi Ikonomi
- Institute of Medical Systems Biology, Ulm University, Ulm 89081, Germany
| | - Angelika M R Kestler
- Department of Internal Medicine I, Ulm University Hospital, Ulm 89081, Germany; Zentrum Personalisierte Medizin, Ulm University Hospital, Ulm 89081, Germany
| | - Ralf Marienfeld
- Department of Pathology, Ulm University Hospital, Ulm 89081, Germany; Zentrum Personalisierte Medizin, Ulm University Hospital, Ulm 89081, Germany
| | - Julian D Schwab
- Institute of Medical Systems Biology, Ulm University, Ulm 89081, Germany
| | - Peter Kuhn
- Comprehensive Cancer Center, Ulm University Hospital, Ulm 89081, Germany; Zentrum Personalisierte Medizin, Ulm University Hospital, Ulm 89081, Germany
| | - Thomas Seufferlein
- Department of Internal Medicine I, Ulm University Hospital, Ulm 89081, Germany; Zentrum Personalisierte Medizin, Ulm University Hospital, Ulm 89081, Germany
| | - Hans A Kestler
- Institute of Medical Systems Biology, Ulm University, Ulm 89081, Germany; Zentrum Personalisierte Medizin, Ulm University Hospital, Ulm 89081, Germany.
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12
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Ahn SY, Bae GE, Park SY, Yeo MK. Differences in the Clinical and Molecular Profiles of Subungual Melanoma and Acral Melanoma in Asian Patients. Cancers (Basel) 2023; 15:4417. [PMID: 37686691 PMCID: PMC10486359 DOI: 10.3390/cancers15174417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/01/2023] [Accepted: 09/01/2023] [Indexed: 09/10/2023] Open
Abstract
Subungual melanoma (SUM) is a rare type of malignant melanoma that arises beneath the nails. SUM is categorized as a type of acral melanoma (AM), which occurs on the hands and feet. SUM is an aggressive type of cutaneous melanoma that is most common among Asian patients. Recent studies reveal that SUM and AM might have different molecular characteristics. Treatment of melanoma relies on analysis of both clinical and molecular data. Therefore, the clinical and molecular characteristics of SUM need to be established, especially during metastasis. To define the mutation profiles of SUM and compare them with those of AM, we performed next-generation sequencing of primary and metastatic tumors of SUM and AM patients. Subungual location was a better independent prognostic factor than acral location for better overall survival (p = 0.001). Patients with SUM most commonly had the triple wild-type (75%) driven by GNAQ (58%) and KIT (25%) mutations, whereas patients with AM had BRAF (28.6%) and RAF (14.3%) molecular types of mutations. Single-nucleotide variations (SNVs) were more common in SUM than in AM, whereas copy number alterations (CNAs) were more common metastatic lesions of AM. Metastatic tumors in patients with SUM and AM showed increases in CNAs (43% and 80%, respectively), but not in SNVs. The number of CNAs increased during metastasis. When compared with AM, SUM has distinct clinical and molecular characteristics.
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Affiliation(s)
- So-Young Ahn
- Department of Rehabilitation Medicine, Chungnam National University School of Medicine, Daejeon 35015, Republic of Korea;
| | - Go-Eun Bae
- Department of Pathology, Chungnam National University School of Medicine, Daejeon 35015, Republic of Korea;
| | - Seung-Yeol Park
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Gyeongbuk, Republic of Korea
| | - Min-Kyung Yeo
- Department of Pathology, Chungnam National University School of Medicine, Daejeon 35015, Republic of Korea;
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13
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Chao TC, Tsai YF, Liu CY, Lien PJ, Lin YS, Feng CJ, Chen YJ, Lai JI, Hsu CY, Lynn JJ, Huang CC, Tseng LM. Prevalence of PIK3CA mutations in Taiwanese patients with breast cancer: a retrospective next-generation sequencing database analysis. Front Oncol 2023; 13:1192946. [PMID: 37655108 PMCID: PMC10466395 DOI: 10.3389/fonc.2023.1192946] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 07/25/2023] [Indexed: 09/02/2023] Open
Abstract
Background Breast cancer is the most common cancer type that affects women. In hormone receptor-positive (HR+), human epidermal growth factor receptor 2-negative (HER2-) advanced breast cancer (ABC), phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) is the most frequently mutated gene associated with poor prognosis. This study evaluated the frequency of PIK3CA mutations in the Taiwanese breast cancer population. Methodology This is a retrospective study; patient data were collected for 2 years from a next-generation sequencing database linked to electronic health records (EHRs). The primary endpoint was the regional prevalence of PIK3CA mutation. The secondary endpoints were to decipher the mutation types across breast cancer subtype, menopausal status, and time to treatment failure after everolimus (an mTOR inhibitor) or cyclin-dependent kinase 4/6 (CDK4/6) inhibitor treatment. Results PIK3CA mutations were identified in 278 of 728 patients (38%). PIK3CA mutations were reported in 43% of patients with HR-/HER2+ subtype and 42% of patients with HR+/HER2- postmenopausal status. A lower prevalence of PIK3CA mutations was observed in triple-negative (27%) and HR+/HER2- premenopausal patients (29%). The most common mutation was at exon 20 (H1047R mutation, 41.6%), followed by exon 9 (E545K mutation, 18.9% and E542K mutation, 10.3%). Among patients treated with CDK4/6 inhibitors, the median time to treatment failure was 12 months (95% CI: 7-21 months) in the PIK3CA mutation cohort and 16 months (95% CI: 11-23 months) in the PIK3CA wild-type cohort, whereas patients receiving an mTOR inhibitor reported a median time to treatment failure of 20.5 months (95% CI: 8-33 months) in the PIK3CA mutation cohort and 6 months (95% CI: 2-9 months) in the PIK3CA wild-type cohort. Conclusion A high frequency of PIK3CA mutations was detected in Taiwanese patients with breast cancer, which was consistent with previous studies. Early detection of PIK3CA mutations might influence therapeutic decisions, leading to better treatment outcomes.
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Affiliation(s)
- Ta-Chung Chao
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
- School of Medicine, College of Medicine, National Yang-Ming Chiao Tung University, Taipei, Taiwan
- Division of Cancer Prevention, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Yi-Fang Tsai
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
- School of Medicine, College of Medicine, National Yang-Ming Chiao Tung University, Taipei, Taiwan
- Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chun-Yu Liu
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
- School of Medicine, College of Medicine, National Yang-Ming Chiao Tung University, Taipei, Taiwan
- Division of Transfusion Medicine, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Pei-Ju Lien
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
- Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Yen-Shu Lin
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
- Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chin-Jung Feng
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
- Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Yen-Jen Chen
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
- School of Medicine, College of Medicine, National Yang-Ming Chiao Tung University, Taipei, Taiwan
- Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Jiun-I. Lai
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
- Division of Medical Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan
- Institute of Clinical Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Chih-Yi Hsu
- School of Medicine, College of Medicine, National Yang-Ming Chiao Tung University, Taipei, Taiwan
- Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Jiun Jen Lynn
- Medical Affairs, Novartis (Taiwan) Co. Ltd, Taipei, Taiwan
| | - Chi-Cheng Huang
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
- Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Ling-Ming Tseng
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
- School of Medicine, College of Medicine, National Yang-Ming Chiao Tung University, Taipei, Taiwan
- Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
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14
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Frenster JD, Erdjument-Bromage H, Stephan G, Ravn-Boess N, Wang S, Liu W, Bready D, Wilcox J, Kieslich B, Jankovic M, Wilde C, Horn S, Sträter N, Liebscher I, Schöneberg T, Fenyo D, Neubert TA, Placantonakis DG. PTK7 is a positive allosteric modulator of GPR133 signaling in glioblastoma. Cell Rep 2023; 42:112679. [PMID: 37354459 PMCID: PMC10445595 DOI: 10.1016/j.celrep.2023.112679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 04/24/2023] [Accepted: 05/23/2023] [Indexed: 06/26/2023] Open
Abstract
The adhesion G-protein-coupled receptor GPR133 (ADGRD1) supports growth of the brain malignancy glioblastoma. How the extracellular interactome of GPR133 in glioblastoma modulates signaling remains unknown. Here, we use affinity proteomics to identify the transmembrane protein PTK7 as an extracellular binding partner of GPR133 in glioblastoma. PTK7 binds the autoproteolytically generated N-terminal fragment of GPR133 and its expression in trans increases GPR133 signaling. This effect requires the intramolecular cleavage of GPR133 and PTK7's anchoring in the plasma membrane. PTK7's allosteric action on GPR133 signaling is additive with but topographically distinct from orthosteric activation by soluble peptide mimicking the endogenous tethered Stachel agonist. GPR133 and PTK7 are expressed in adjacent cells in glioblastoma, where their knockdown phenocopies each other. We propose that this ligand-receptor interaction is relevant to the pathogenesis of glioblastoma and possibly other physiological processes in healthy tissues.
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Affiliation(s)
- Joshua D Frenster
- Department of Neurosurgery, NYU Grossman School of Medicine, New York, NY 10016, USA; Kimmel Center for Stem Cell Biology, NYU Grossman School of Medicine, New York, NY 10016, USA.
| | - Hediye Erdjument-Bromage
- Department of Cell Biology, NYU Grossman School of Medicine, New York, NY 10016, USA; Kimmel Center for Biology and Medicine at the Skirball Institute, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Gabriele Stephan
- Department of Neurosurgery, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Niklas Ravn-Boess
- Department of Neurosurgery, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Shuai Wang
- Department of Neurosurgery, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Wenke Liu
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Devin Bready
- Department of Neurosurgery, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Jordan Wilcox
- Department of Neurosurgery, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Björn Kieslich
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, University of Leipzig, 04103 Leipzig, Germany; Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, University of Leipzig, 04103 Leipzig, Germany
| | - Manuel Jankovic
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, University of Leipzig, 04103 Leipzig, Germany
| | - Caroline Wilde
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, University of Leipzig, 04103 Leipzig, Germany
| | - Susanne Horn
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, University of Leipzig, 04103 Leipzig, Germany
| | - Norbert Sträter
- Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, University of Leipzig, 04103 Leipzig, Germany
| | - Ines Liebscher
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, University of Leipzig, 04103 Leipzig, Germany
| | - Torsten Schöneberg
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, University of Leipzig, 04103 Leipzig, Germany
| | - David Fenyo
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Thomas A Neubert
- Department of Cell Biology, NYU Grossman School of Medicine, New York, NY 10016, USA; Kimmel Center for Biology and Medicine at the Skirball Institute, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Dimitris G Placantonakis
- Department of Neurosurgery, NYU Grossman School of Medicine, New York, NY 10016, USA; Kimmel Center for Stem Cell Biology, NYU Grossman School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY 10016, USA; Brain and Spine Tumor Center, NYU Grossman School of Medicine, New York, NY 10016, USA; Neuroscience Institute, NYU Grossman School of Medicine, New York, NY 10016, USA.
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15
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Mehra R, Shah T, Liu CJ, Plouffe KR, Wang X, Mannan R, Cao X, Chinnaiyan AM, Tomlins SA, Udager AM. Highly Recurrent IDH1 Mutations in Prostate Cancer With Psammomatous Calcification. Mod Pathol 2023; 36:100146. [PMID: 36828361 DOI: 10.1016/j.modpat.2023.100146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 02/13/2023] [Accepted: 02/16/2023] [Indexed: 02/24/2023]
Abstract
Prostate cancer is a heterogeneous disease with several well-recognized morphologic subtypes and histologic variants-subsets of which are enriched for or associated with specific genomic alterations. Herein, we report a cohort of 4 unique prostate cancers characterized by intratumoral psammomatous calcification-which we have termed prostate cancer with psammomatous calcification (PCWPC). Clinicopathologic review demonstrates that PCWPCs are high-grade (grade group ≥3) tumors that involve the anterior prostate, and integrative targeted next-generation sequencing reveals recurrent hotspot IDH1 mutations. This morphology-molecular correlation is independently confirmed in The Cancer Genome Atlas prostatic adenocarcinoma cohort, with 3 of the 5 IDH1-mutant prostate cancers showing psammomatous calcification (rφ = 0.67; Fisher exact test, P < .0001). Overall, these findings suggest that PCWPC represents a novel subtype of prostate cancer enriched for an anterior location and the presence of hotspot IDH1 mutations. Recognition of these unique morphologic features could help identify IDH1-mutant prostate cancer cases retrospectively and prospectively-facilitating future large research studies and enabling clinical trial enrollment and precision medicine approaches for patients with advanced and/or aggressive disease.
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Affiliation(s)
- Rohit Mehra
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan; University of Michigan Rogel Cancer Center, Ann Arbor, Michigan; Michigan Center for Translational Pathology, Ann Arbor, Michigan
| | - Tanmay Shah
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Chia-Jen Liu
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Komal R Plouffe
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Xiaoming Wang
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan; Michigan Center for Translational Pathology, Ann Arbor, Michigan
| | - Rahul Mannan
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan; Michigan Center for Translational Pathology, Ann Arbor, Michigan
| | - Xuhong Cao
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan; Michigan Center for Translational Pathology, Ann Arbor, Michigan
| | - Arul M Chinnaiyan
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan; University of Michigan Rogel Cancer Center, Ann Arbor, Michigan; Michigan Center for Translational Pathology, Ann Arbor, Michigan; Department of Urology, University of Michigan Medical School, Ann Arbor, Michigan; Howard Hughes Medical Institute, Ann Arbor, Michigan
| | - Scott A Tomlins
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Aaron M Udager
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan; University of Michigan Rogel Cancer Center, Ann Arbor, Michigan; Michigan Center for Translational Pathology, Ann Arbor, Michigan.
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16
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Harada G, Yang SR, Cocco E, Drilon A. Rare molecular subtypes of lung cancer. Nat Rev Clin Oncol 2023; 20:229-249. [PMID: 36806787 PMCID: PMC10413877 DOI: 10.1038/s41571-023-00733-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2023] [Indexed: 02/22/2023]
Abstract
Oncogenes that occur in ≤5% of non-small-cell lung cancers have been defined as 'rare'; nonetheless, this frequency can correspond to a substantial number of patients diagnosed annually. Within rare oncogenes, less commonly identified alterations (such as HRAS, NRAS, RIT1, ARAF, RAF1 and MAP2K1 mutations, or ERBB family, LTK and RASGRF1 fusions) can share certain structural or oncogenic features with more commonly recognized alterations (such as KRAS, BRAF, MET and ERBB family mutations, or ALK, RET and ROS1 fusions). Over the past 5 years, a surge in the identification of rare-oncogene-driven lung cancers has challenged the boundaries of traditional clinical grade diagnostic assays and profiling algorithms. In tandem, the number of approved targeted therapies for patients with rare molecular subtypes of lung cancer has risen dramatically. Rational drug design has iteratively improved the quality of small-molecule therapeutic agents and introduced a wave of antibody-based therapeutics, expanding the list of actionable de novo and resistance alterations in lung cancer. Getting additional molecularly tailored therapeutics approved for rare-oncogene-driven lung cancers in a larger range of countries will require ongoing stakeholder cooperation. Patient advocates, health-care agencies, investigators and companies with an interest in diagnostics, therapeutics and real-world evidence have already taken steps to surmount the challenges associated with research into low-frequency drivers.
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Affiliation(s)
- Guilherme Harada
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Soo-Ryum Yang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Emiliano Cocco
- Department of Biochemistry and Molecular Biology/Sylvester Comprehensive Cancer Center, University of Miami/Miller School of Medicine, Miami, FL, USA.
| | - Alexander Drilon
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
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17
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Yamaguchi T, Hayashi S, Hayashi D, Matsuyama T, Koitabashi N, Ogiwara K, Noda M, Nakada C, Fujiki S, Furutachi A, Tanabe Y, Yamanaka M, Ishikawa A, Mizukami M, Mizuguchi A, Sugiura K, Sumi M, Yamazawa H, Izawa A, Wada Y, Fujikawa T, Takiguchi Y, Wakui K, Takano K, Nishio SY, Kosho T. Comprehensive genetic screening for vascular Ehlers-Danlos syndrome through an amplification-based next-generation sequencing system. Am J Med Genet A 2023; 191:37-51. [PMID: 36189931 PMCID: PMC10092364 DOI: 10.1002/ajmg.a.62982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/28/2022] [Accepted: 09/11/2022] [Indexed: 12/14/2022]
Abstract
Vascular Ehlers-Danlos syndrome (vEDS) is a hereditary connective tissue disorder (HCTD) characterized by arterial dissection/aneurysm/rupture, sigmoid colon rupture, or uterine rupture. Diagnosis is confirmed by detecting heterozygous variants in COL3A1. This is the largest Asian case series and the first to apply an amplification-based next-generation sequencing through custom panels of causative genes for HCTDs, including a specific method of evaluating copy number variations. Among 429 patients with suspected HCTDs analyzed, 101 were suspected to have vEDS, and 33 of them (32.4%) were found to have COL3A1 variants. Two patients with a clinical diagnosis of Loeys-Dietz syndrome and/or familial thoracic aortic aneurysm and dissection were also found to have COL3A1 variants. Twenty cases (57.1%) had missense variants leading to glycine (Gly) substitutions in the triple helical domain, one (2.9%) had a missense variant leading to non-Gly substitution in this domain, eight (22.9%) had splice site alterations, three (8.6%) had nonsense variants, two (5.7%) had in-frame deletions, and one (2.9%) had a multi-exon deletion, including two deceased patients analyzed with formalin-fixed and paraffin-embedded samples. This is a clinically useful system to detect a wide spectrum of variants from various types of samples.
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Affiliation(s)
- Tomomi Yamaguchi
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto, Japan.,Center for Medical Genetics, Shinshu University Hospital, Matsumoto, Japan.,Division of Clinical Sequencing, Shinshu University School of Medicine, Matsumoto, Japan
| | - Shujiro Hayashi
- Department of Dermatology, Dokkyo Medical University, Mibu, Japan
| | - Daisuke Hayashi
- Department of Dermatology, Osaka Metropolitan University, Osaka, Japan
| | | | - Norimichi Koitabashi
- Department of Cardiovascular Medicine, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Kenichi Ogiwara
- Department of Pediatrics, Nara Medical University, Nara, Japan
| | - Masaaki Noda
- Department of Hematology, Hiroshima City Hiroshima Citizens Hospital, Hiroshima, Japan.,Noda Family Clinic, Hiroshima, Japan
| | - Chiai Nakada
- Division of Rheumatology, Yuuai Medical Center, Tomigusuku, Japan
| | - Shinya Fujiki
- Division of Cardiology, Department of Medicine, Tsuruoka Municipal Shonai Hospital, Tsuruoka, Japan.,Department of Cardiovascular Medicine, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Akira Furutachi
- Department of Thoracic and Cardiovascular Surgery, National Hospital Organization Ureshino Medical Center, Saga, Japan
| | - Yasuhiko Tanabe
- Department of Cardiology, Niigata Prefectural Shibata Hospital, Shibata, Japan
| | - Michiko Yamanaka
- Center for Medical Genetics, St. Luke's International Hospital, Tokyo, Japan
| | - Aki Ishikawa
- Department of Medical Genetics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Miyako Mizukami
- Department of Medical Genetics, Sapporo Medical University School of Medicine, Sapporo, Japan.,Department of Pediatrics, Sapporo Maternity Women's Hospital, Sapporo, Japan
| | - Asako Mizuguchi
- Department of Neurosurgery, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Kazumitsu Sugiura
- Department of Dermatology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Makoto Sumi
- Department of Cardiovascular Surgery, Saitama Cardiovascular and Respiratory Center, Saitama, Japan
| | - Hirokuni Yamazawa
- Department of Pediatrics, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan.,Division of Clinical Genetics, Hokkaido University Hospital, Sapporo, Japan
| | - Atsushi Izawa
- Department of Cardiovascular Medicine, Shinshu University School of Medicine, Matsumoto, Japan.,School of Health Sciences, Shinshu University, Matsumoto, Japan
| | - Yuko Wada
- Division of Cardiovascular Surgery, Department of Surgery, Shinshu University School of Medicine, Matsumoto, Japan
| | - Tomomi Fujikawa
- Division of Clinical Sequencing, Shinshu University School of Medicine, Matsumoto, Japan
| | - Yuri Takiguchi
- Division of Clinical Sequencing, Shinshu University School of Medicine, Matsumoto, Japan
| | - Keiko Wakui
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto, Japan.,Center for Medical Genetics, Shinshu University Hospital, Matsumoto, Japan
| | - Kyoko Takano
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto, Japan.,Center for Medical Genetics, Shinshu University Hospital, Matsumoto, Japan
| | - Shin-Ya Nishio
- Department of Hearing Implant Science, Shinshu University School of Medicine, Matsumoto, Japan
| | - Tomoki Kosho
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto, Japan.,Center for Medical Genetics, Shinshu University Hospital, Matsumoto, Japan.,Division of Clinical Sequencing, Shinshu University School of Medicine, Matsumoto, Japan.,Research Center for Supports to Advanced Science, Shinshu University, Matsumoto, Japan
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18
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Westbrook TC, Guan X, Rodansky E, Flores D, Liu CJ, Udager AM, Patel RA, Haffner MC, Hu YM, Sun D, Beer TM, Foye A, Aggarwal R, Quigley DA, Youngren JF, Ryan CJ, Gleave M, Wang Y, Huang J, Coleman I, Morrissey C, Nelson PS, Evans CP, Lara P, Reiter RE, Witte O, Rettig M, Wong CK, Weinstein AS, Uzunangelov V, Stuart JM, Thomas GV, Feng FY, Small EJ, Yates JA, Xia Z, Alumkal JJ. Transcriptional profiling of matched patient biopsies clarifies molecular determinants of enzalutamide-induced lineage plasticity. Nat Commun 2022; 13:5345. [PMID: 36109521 PMCID: PMC9477876 DOI: 10.1038/s41467-022-32701-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 08/11/2022] [Indexed: 11/08/2022] Open
Abstract
The androgen receptor (AR) signaling inhibitor enzalutamide (enza) is one of the principal treatments for metastatic castration-resistant prostate cancer (CRPC). Several emergent enza clinical resistance mechanisms have been described, including lineage plasticity in which the tumors manifest reduced dependency on the AR. To improve our understanding of enza resistance, herein we analyze the transcriptomes of matched biopsies from men with metastatic CRPC obtained prior to treatment and at progression (n = 21). RNA-sequencing analysis demonstrates that enza does not induce marked, sustained changes in the tumor transcriptome in most patients. However, three patients' progression biopsies show evidence of lineage plasticity. The transcription factor E2F1 and pathways linked to tumor stemness are highly activated in baseline biopsies from patients whose tumors undergo lineage plasticity. We find a gene signature enriched in these baseline biopsies that is strongly associated with poor survival in independent patient cohorts and with risk of castration-induced lineage plasticity in patient-derived xenograft models, suggesting that tumors harboring this gene expression program may be at particular risk for resistance mediated by lineage plasticity and poor outcomes.
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Affiliation(s)
- Thomas C Westbrook
- Division of Hematology and Oncology, Department of Internal Medicine, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Xiangnan Guan
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Eva Rodansky
- Division of Hematology and Oncology, Department of Internal Medicine, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Diana Flores
- Division of Hematology and Oncology, Department of Internal Medicine, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Chia Jen Liu
- Department of Pathology, Michigan Center for Translational Pathology, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Aaron M Udager
- Department of Pathology, Michigan Center for Translational Pathology, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Radhika A Patel
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Michael C Haffner
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ya-Mei Hu
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Duanchen Sun
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Tomasz M Beer
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Adam Foye
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Rahul Aggarwal
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - David A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Jack F Youngren
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Charles J Ryan
- Masonic Cancer Center, University of Minnesota; Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Martin Gleave
- Department of Urological Sciences and Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - Yuzhuo Wang
- Department of Urological Sciences and Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
- Department of Experimental Therapeutics, BC Cancer, University of British Columbia, Vancouver, BC, Canada
| | | | - Ilsa Coleman
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Peter S Nelson
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Primo Lara
- University of California Davis, Davis, CA, USA
| | | | - Owen Witte
- Department of Microbiology, Immunology, and Molecular Genetics at the David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Matthew Rettig
- University of California Los Angeles, Los Angeles, CA, USA
- VA Greater Los Angeles Healthcare System, Los Angeles, CA, USA
| | - Christopher K Wong
- UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Alana S Weinstein
- UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Vlado Uzunangelov
- UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Josh M Stuart
- UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - George V Thomas
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Felix Y Feng
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Departments of Radiation Oncology and Urology, University of California San Francisco, San Francisco, CA, USA
| | - Eric J Small
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Joel A Yates
- Division of Hematology and Oncology, Department of Internal Medicine, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Zheng Xia
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
| | - Joshi J Alumkal
- Division of Hematology and Oncology, Department of Internal Medicine, Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.
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19
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Cani AK, Hu K, Liu CJ, Siddiqui J, Zheng Y, Han S, Nallandhighal S, Hovelson DH, Xiao L, Pham T, Eyrich NW, Zheng H, Vince R, Tosoian JJ, Palapattu GS, Morgan TM, Wei JT, Udager AM, Chinnaiyan AM, Tomlins SA, Salami SS. Development of a Whole-urine, Multiplexed, Next-generation RNA-sequencing Assay for Early Detection of Aggressive Prostate Cancer. Eur Urol Oncol 2022; 5:430-439. [PMID: 33812851 DOI: 10.1016/j.euo.2021.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 02/22/2021] [Accepted: 03/08/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND Despite biomarker development advances, early detection of aggressive prostate cancer (PCa) remains challenging. We previously developed a clinical-grade urine test (Michigan Prostate Score [MiPS]) for individualized aggressive PCa risk prediction. MiPS combines serum prostate-specific antigen (PSA), the TMPRSS2:ERG (T2:ERG) gene fusion, and PCA3 lncRNA in whole urine after digital rectal examination (DRE). OBJECTIVE To improve on MiPS with a novel next-generation sequencing (NGS) multibiomarker urine assay for early detection of aggressive PCa. DESIGN, SETTING, AND PARTICIPANTS Preclinical development and validation of a post-DRE urine RNA NGS assay (Urine Prostate Seq [UPSeq]) assessing 84 PCa transcriptomic biomarkers, including T2:ERG, PCA3, additional PCa fusions/isoforms, mRNAs, lncRNAs, and expressed mutations. Our UPSeq model was trained on 73 patients and validated on a held-out set of 36 patients representing the spectrum of disease (benign to grade group [GG] 5 PCa). OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS The area under the receiver operating characteristic curve (AUC) of UPSeq was compared with PSA, MiPS, and other existing models/biomarkers for predicting GG ≥3 PCa. RESULTS AND LIMITATIONS UPSeq demonstrated high analytical accuracy and concordance with MiPS, and was able to detect expressed germline HOXB13 and somatic SPOP mutations. In an extreme design cohort (n = 109; benign/GG 1 vs GG ≥3 PCa, stratified to exclude GG 2 cancer in order to capture signal difference between extreme ends of disease), UPSeq showed differential expression for T2:ERG.T1E4 (1.2 vs 78.8 median normalized reads, p < 0.00001) and PCA3 (1024 vs 2521, p = 0.02), additional T2:ERG splice isoforms, and other candidate biomarkers. Using machine learning, we developed a 15-transcript model on the training set (n = 73) that outperformed serum PSA and sequencing-derived MiPS in predicting GG ≥3 PCa in the held-out validation set (n = 36; AUC 0.82 vs 0.69 and 0.69, respectively). CONCLUSIONS These results support the potential utility of our novel urine-based RNA NGS assay to supplement PSA for improved early detection of aggressive PCa. PATIENT SUMMARY We have developed a new urine-based test for the detection of aggressive prostate cancer, which promises improvement upon current biomarker tests.
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Affiliation(s)
- Andi K Cani
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Molecular and Cellular Pathology Graduate Program, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Kevin Hu
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Chia-Jen Liu
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Javed Siddiqui
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Yingye Zheng
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Sumin Han
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Daniel H Hovelson
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Lanbo Xiao
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Trinh Pham
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Nicholas W Eyrich
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Heng Zheng
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Randy Vince
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Jeffrey J Tosoian
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Ganesh S Palapattu
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Todd M Morgan
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - John T Wei
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Aaron M Udager
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Molecular and Cellular Pathology Graduate Program, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Scott A Tomlins
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Molecular and Cellular Pathology Graduate Program, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA.
| | - Simpa S Salami
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA.
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20
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Comprehensive Development and Implementation of Good Laboratory Practice for NGS Based Targeted Panel on Solid Tumor FFPE Tissues in Diagnostics. Diagnostics (Basel) 2022; 12:diagnostics12051291. [PMID: 35626446 PMCID: PMC9141409 DOI: 10.3390/diagnostics12051291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/03/2022] [Accepted: 05/09/2022] [Indexed: 11/25/2022] Open
Abstract
The speed, accuracy, and increasing affordability of next-generation sequencing (NGS) have revolutionized the advent of precision medicine. To date, standardized validation criteria for diagnostic accreditation do not exist due to variability across the multitude of NGS platforms and within NGS processes. In molecular diagnostics, it is necessary to ensure that the primary material of the FFPE sample has good quality and optimum quantity for the analysis, otherwise the laborious and expensive NGS test may result in unreliable information. Therefore, stringent quality control of DNA and RNA before, during, and after library preparation is an essential parameter. Considering the various challenges with the FFPE samples, we aimed to set a benchmark in QC metrics that can be utilized by molecular diagnostic laboratories for successful library preparation and high-quality NGS data output. In total, 144 DNA and 103 RNA samples of various cancer types with a maximum storage of 2 years were processed for 52 gene focus panels. During the making of DNA and RNA libraries, extensive QC check parameters were imposed at different checkpoints. The decision tree approach can be set as a benchmark for FFPE samples and as a guide to establishing a good clinical laboratory practice for targeted NGS panels.
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21
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Rodriguez-Calero A, Gallon J, Akhoundova D, Maletti S, Ferguson A, Cyrta J, Amstutz U, Garofoli A, Paradiso V, Tomlins SA, Hewer E, Genitsch V, Fleischmann A, Vassella E, Rushing EJ, Grobholz R, Fischer I, Jochum W, Cathomas G, Osunkoya AO, Bubendorf L, Moch H, Thalmann G, Ng CKY, Gillessen S, Piscuoglio S, Rubin MA. Alterations in homologous recombination repair genes in prostate cancer brain metastases. Nat Commun 2022; 13:2400. [PMID: 35504881 PMCID: PMC9065149 DOI: 10.1038/s41467-022-30003-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 04/12/2022] [Indexed: 12/31/2022] Open
Abstract
Improved survival rates for prostate cancer through more effective therapies have also led to an increase in the diagnosis of metastases to infrequent locations such as the brain. Here we investigate the repertoire of somatic genetic alterations present in brain metastases from 51 patients with prostate cancer brain metastases (PCBM). We highlight the clonal evolution occurring in PCBM and demonstrate an increased mutational burden, concomitant with an enrichment of the homologous recombination deficiency mutational signature in PCBM compared to non-brain metastases. Focusing on known pathogenic alterations within homologous recombination repair genes, we find 10 patients (19.6%) fulfilling the inclusion criteria used in the PROfound clinical trial, which assessed the efficacy of PARP inhibitors (PARPi) in homologous recombination deficient prostate cancer. Eight (15.7%) patients show biallelic loss of one of the 15 genes included in the trial, while 5 patients (9.8%) harbor pathogenic alterations in BRCA1/2 specifically. Uncovering these molecular features of PCBM may have therapeutic implications, suggesting the need of clinical trial enrollment of PCBM patients when evaluating potential benefit from PARPi.
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Affiliation(s)
- Antonio Rodriguez-Calero
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - John Gallon
- Visceral Surgery and Precision Medicine Research Laboratory, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Dilara Akhoundova
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Department of Medical Oncology and Hematology, University Hospital Zurich, Zurich, Switzerland
| | - Sina Maletti
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Alison Ferguson
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Department of Oncology, Ludwig Cancer Centre, University of Lausanne, Lausanne, Switzerland
| | - Joanna Cyrta
- Department of Pathology, Institut Curie, University Paris Sciences et Lettres, Paris, France
| | - Ursula Amstutz
- Department of Clinical Chemistry, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Andrea Garofoli
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Viola Paradiso
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Scott A Tomlins
- Departments of Pathology and Urology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Ekkehard Hewer
- Institute of Pathology, University of Bern, Bern, Switzerland
- Institute of Pathology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Vera Genitsch
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - Achim Fleischmann
- Institute of Pathology, University of Bern, Bern, Switzerland
- Institute of Pathology, Cantonal Hospital Thurgau, Münsterlingen, Switzerland
| | - Erik Vassella
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - Elisabeth J Rushing
- Institute of Neuropathology, University Hospital Zurich, Zurich, Switzerland
| | - Rainer Grobholz
- Institute of Pathology, Cantonal Hospital Aarau, Aarau, Switzerland
| | - Ingeborg Fischer
- Institute of Pathology, Cantonal Hospital Aarau, Aarau, Switzerland
| | - Wolfram Jochum
- Institute of Pathology, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Gieri Cathomas
- Institute of Pathology, Cantonal Hospital Baselland, Liestal, Switzerland
| | - Adeboye O Osunkoya
- Departments of Pathology and Laboratory Medicine, and Urology, Emory University School of Medicine, Atlanta, USA
| | - Lukas Bubendorf
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - George Thalmann
- Department of Urology, Inselspital, Bern University Hospital, Bern, Switzerland
| | - Charlotte K Y Ng
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Silke Gillessen
- Faculty of Biomedical Sciences, USI, Lugano, Switzerland
- Department of Oncology, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
- Division of Cancer Sciences, University of Manchester, Manchester, United Kingdom
| | - Salvatore Piscuoglio
- Visceral Surgery and Precision Medicine Research Laboratory, Department of Biomedicine, University of Basel, Basel, Switzerland.
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland.
| | - Mark A Rubin
- Department for BioMedical Research, University of Bern, Bern, Switzerland.
- Bern Center for Precision Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.
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22
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Cani AK, Dolce EM, Darga EP, Hu K, Liu C, Pierce J, Bradbury K, Kilgour E, Aung K, Schiavon G, Carroll D, Carr TH, Klinowska T, Lindemann J, Marshall G, Rowlands V, Harrington EA, Barrett JC, Sathiyayogan N, Morrow C, Sero V, Armstrong AC, Baird R, Hamilton E, Im S, Jhaveri K, Patel MR, Dive C, Tomlins SA, Udager AM, Hayes DF, Paoletti C. Serial monitoring of genomic alterations in circulating tumor cells of ER-positive/HER2-negative advanced breast cancer: feasibility of precision oncology biomarker detection. Mol Oncol 2022; 16:1969-1985. [PMID: 34866317 PMCID: PMC9120891 DOI: 10.1002/1878-0261.13150] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/02/2021] [Accepted: 12/01/2021] [Indexed: 12/18/2022] Open
Abstract
Nearly all estrogen receptor (ER)-positive (POS) metastatic breast cancers become refractory to endocrine (ET) and other therapies, leading to lethal disease presumably due to evolving genomic alterations. Timely monitoring of the molecular events associated with response/progression by serial tissue biopsies is logistically difficult. Use of liquid biopsies, including circulating tumor cells (CTC) and circulating tumor DNA (ctDNA), might provide highly informative, yet easily obtainable, evidence for better precision oncology care. Although ctDNA profiling has been well investigated, the CTC precision oncology genomic landscape and the advantages it may offer over ctDNA in ER-POS breast cancer remain largely unexplored. Whole-blood (WB) specimens were collected at serial time points from patients with advanced ER-POS/HER2-negative (NEG) advanced breast cancer in a phase I trial of AZD9496, an oral selective ER degrader (SERD) ET. Individual CTC were isolated from WB using tandem CellSearch® /DEPArray™ technologies and genomically profiled by targeted single-cell DNA next-generation sequencing (scNGS). High-quality CTC (n = 123) from 12 patients profiled by scNGS showed 100% concordance with ctDNA detection of driver estrogen receptor α (ESR1) mutations. We developed a novel CTC-based framework for precision medicine actionability reporting (MI-CTCseq) that incorporates novel features, such as clonal predominance and zygosity of targetable alterations, both unambiguously identifiable in CTC compared to ctDNA. Thus, we nominated opportunities for targeted therapies in 73% of patients, directed at alterations in phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA), fibroblast growth factor receptor 2 (FGFR2), and KIT proto-oncogene, receptor tyrosine kinase (KIT). Intrapatient, inter-CTC genomic heterogeneity was observed, at times between time points, in subclonal alterations. Our analysis suggests that serial monitoring of the CTC genome is feasible and should enable real-time tracking of tumor evolution during progression, permitting more combination precision medicine interventions.
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23
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Stover EH, Oh C, Keskula P, Choudhury AD, Tseng YY, Adalsteinsson VA, Lohr JG, Thorner AR, Ducar M, Kryukov GV, Ha G, Rosenberg M, Freeman SS, Zhang Z, Wu X, Van Allen EM, Takeda DY, Loda M, Wu CL, Taplin ME, Garraway LA, Boehm JS, Huang FW. Implementation of a prostate cancer-specific targeted sequencing panel for credentialing of patient-derived cell lines and genomic characterization of patient samples. Prostate 2022; 82:584-597. [PMID: 35084050 PMCID: PMC8887817 DOI: 10.1002/pros.24305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 12/24/2021] [Accepted: 12/30/2021] [Indexed: 11/10/2022]
Abstract
BACKGROUND Primary and metastatic prostate cancers have low mutation rates and recurrent alterations in a small set of genes, enabling targeted sequencing of prostate cancer-associated genes as an efficient approach to characterizing patient samples (compared to whole-exome and whole-genome sequencing). For example, targeted sequencing provides a flexible, rapid, and cost-effective method for genomic assessment of patient-derived cell lines to evaluate fidelity to initial patient tumor samples. METHODS We developed a prostate cancer-specific targeted next-generation sequencing (NGS) panel to detect alterations in 62 prostate cancer-associated genes as well as recurring gene fusions with ETS family members, representing the majority of common alterations in prostate cancer. We tested this panel on primary prostate cancer tissues and blood biopsies from patients with metastatic prostate cancer. We generated patient-derived cell lines from primary prostate cancers using conditional reprogramming methods and applied targeted sequencing to evaluate the fidelity of these cell lines to the original patient tumors. RESULTS The prostate cancer-specific panel identified biologically and clinically relevant alterations, including point mutations in driver oncogenes and ETS family fusion genes, in tumor tissues from 29 radical prostatectomy samples. The targeted panel also identified genomic alterations in cell-free DNA and circulating tumor cells (CTCs) from patients with metastatic prostate cancer, and in standard prostate cancer cell lines. We used the targeted panel to sequence our set of patient-derived cell lines; however, no prostate cancer-specific mutations were identified in the tumor-derived cell lines, suggesting preferential outgrowth of normal prostate epithelial cells. CONCLUSIONS We evaluated a prostate cancer-specific targeted NGS panel to detect common and clinically relevant alterations (including ETS family gene fusions) in prostate cancer. The panel detected driver mutations in a diverse set of clinical samples of prostate cancer, including fresh-frozen tumors, cell-free DNA, CTCs, and cell lines. Targeted sequencing of patient-derived cell lines highlights the challenge of deriving cell lines from primary prostate cancers and the importance of genomic characterization to credential candidate cell lines. Our study supports that a prostate cancer-specific targeted sequencing panel provides an efficient, clinically feasible approach to identify genetic alterations across a spectrum of prostate cancer samples and cell lines.
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Affiliation(s)
- Elizabeth H. Stover
- Dana-Farber Cancer Institute, Boston MA
- Broad Institute, Cambridge MA
- Harvard Medical School, Boston MA
| | - Coyin Oh
- Broad Institute, Cambridge MA
- Harvard Medical School, Boston MA
| | | | - Atish D. Choudhury
- Dana-Farber Cancer Institute, Boston MA
- Broad Institute, Cambridge MA
- Harvard Medical School, Boston MA
| | | | | | - Jens G. Lohr
- Dana-Farber Cancer Institute, Boston MA
- Broad Institute, Cambridge MA
- Harvard Medical School, Boston MA
| | | | | | - Gregory V. Kryukov
- Dana-Farber Cancer Institute, Boston MA
- Broad Institute, Cambridge MA
- Harvard Medical School, Boston MA
| | - Gavin Ha
- Fred Hutchinson Cancer Research Center, Seattle WA
| | | | | | - Zhenwei Zhang
- Dana-Farber Cancer Institute, Boston MA
- University of Massachusetts Memorial Medical Center, Worcester MA
| | | | - Eliezer M. Van Allen
- Dana-Farber Cancer Institute, Boston MA
- Broad Institute, Cambridge MA
- Harvard Medical School, Boston MA
| | | | - Massimo Loda
- Dana-Farber Cancer Institute, Boston MA
- Broad Institute, Cambridge MA
- New York-Presbyterian/Weill Cornell Medical Center, New York, NY
| | - Chin-Lee Wu
- Harvard Medical School, Boston MA
- Massachusetts General Hospital, Boston MA
| | - Mary-Ellen Taplin
- Dana-Farber Cancer Institute, Boston MA
- Harvard Medical School, Boston MA
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Song P, Wu LR, Yan YH, Zhang JX, Chu T, Kwong LN, Patel AA, Zhang DY. Limitations and opportunities of technologies for the analysis of cell-free DNA in cancer diagnostics. Nat Biomed Eng 2022; 6:232-245. [PMID: 35102279 PMCID: PMC9336539 DOI: 10.1038/s41551-021-00837-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 05/27/2021] [Indexed: 12/15/2022]
Abstract
Cell-free DNA (cfDNA) in the circulating blood plasma of patients with cancer contains tumour-derived DNA sequences that can serve as biomarkers for guiding therapy, for the monitoring of drug resistance, and for the early detection of cancers. However, the analysis of cfDNA for clinical diagnostic applications remains challenging because of the low concentrations of cfDNA, and because cfDNA is fragmented into short lengths and is susceptible to chemical damage. Barcodes of unique molecular identifiers have been implemented to overcome the intrinsic errors of next-generation sequencing, which is the prevailing method for highly multiplexed cfDNA analysis. However, a number of methodological and pre-analytical factors limit the clinical sensitivity of the cfDNA-based detection of cancers from liquid biopsies. In this Review, we describe the state-of-the-art technologies for cfDNA analysis, with emphasis on multiplexing strategies, and discuss outstanding biological and technical challenges that, if addressed, would substantially improve cancer diagnostics and patient care.
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Affiliation(s)
- Ping Song
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Lucia Ruojia Wu
- Department of Bioengineering, Rice University, Houston, TX, USA
| | | | | | - Tianqing Chu
- Department of Respiratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Lawrence N Kwong
- Department of Translational Molecular Pathology, MD Anderson Cancer Center, Houston, TX, USA
| | - Abhijit A Patel
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, USA
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25
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Imamura T, Okamura Y, Ohshima K, Uesaka K, Sugiura T, Ito T, Yamamoto Y, Ashida R, Ohgi K, Otsuka S, Ohnami S, Nagashima T, Hatakeyama K, Kakuda Y, Sugino T, Urakami K, Akiyama Y, Yamaguchi K. Hepatocellular carcinoma after a sustained virological response by direct-acting antivirals harbors TP53 inactivation. Cancer Med 2022; 11:1769-1786. [PMID: 35174643 PMCID: PMC9041076 DOI: 10.1002/cam4.4571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 12/01/2021] [Accepted: 12/15/2021] [Indexed: 12/24/2022] Open
Abstract
Introduction The genomic characteristics of hepatocellular carcinoma (HCC) after a sustained virological response (SVR) and its differences according to whether an SVR was achieved by treatment with direct‐acting antivirals (DAA) or interferon (IFN) are still not fully understood. Methods Sixty‐nine surgically resected HCCs from patients with hepatitis C virus infection were analyzed by gene expression profiling and whole‐exome sequencing. Results Among the 69 HCC patients, 34 HCCs in which an SVR was not achieved at the time of surgery were classified as HCV‐positive, and 35 HCCs in which an SVR was achieved at the time of surgery were classified as HCV‐SVR. According to the HCV treatment, 35 HCV‐SVR HCCs were classified into two groups: eight tumors with DAA (HCV‐SVR‐DAA) and 24 tumors with interferon (HCV‐SVR‐IFN). The frequency of samples with ARID2 mutations was significantly lower in HCV‐SVR than in HCV‐positive tumors (p = 0.048). In contrast, the frequency of samples with PREX2 mutations was significantly higher in HCV‐SVR samples than in HCV‐positive samples (p = 0.048). Among the patients with HCV‐SVR, the frequency of samples with TP53 mutations was significantly higher in HCV‐SVR‐DAA tumors than in HCV‐SVR‐IFN tumors (p = 0.030). TP53 inactivation scores in HCV‐SVR‐DAA tumors were found to be significantly enhanced in comparison to HCV‐SVR‐IFN tumors (p = 0.022). In addition, chromosomal instability and PI3K/AKT/mTOR pathway signatures were enhanced in HCV‐SVR‐DAA tumors. HCV‐SVR‐DAA was significantly associated with portal vein invasion (p = 0.003) in comparison to HCV‐SVR‐IFN. Conclusion Our dataset potentially serves as a fundamental resource for the genomic characteristics of HCV‐SVR‐DAA tumors. Our comprehensive genetic profiling by WES revealed significant differences in the mutation rate of several driver genes between HCV‐positive tumors and HCV‐SVR tumors. Furthermore, it was revealed that the frequency of samples with mutations in TP53 was significantly higher in HCV‐SVR‐DAA tumors than in HCV‐SVR‐IFN tumors.
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Affiliation(s)
- Taisuke Imamura
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center, Shizuoka, Japan
| | - Yukiyasu Okamura
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center, Shizuoka, Japan.,Department of Digestive Surgery, Nihon University School of Medicine, Tokyo, Japan
| | - Keiichi Ohshima
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Katsuhiko Uesaka
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center, Shizuoka, Japan
| | - Teiichi Sugiura
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center, Shizuoka, Japan
| | - Takaaki Ito
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center, Shizuoka, Japan
| | - Yusuke Yamamoto
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center, Shizuoka, Japan
| | - Ryo Ashida
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center, Shizuoka, Japan
| | - Katsuhisa Ohgi
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center, Shizuoka, Japan
| | - Shimpei Otsuka
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center, Shizuoka, Japan
| | - Sumiko Ohnami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Takeshi Nagashima
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan.,SRL, Inc., Tokyo, Japan
| | - Keiichi Hatakeyama
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Yuko Kakuda
- Division of Pathology, Shizuoka Cancer Center, Shizuoka, Japan
| | - Takashi Sugino
- Division of Pathology, Shizuoka Cancer Center, Shizuoka, Japan
| | - Kenichi Urakami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Yasuto Akiyama
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Ken Yamaguchi
- Shizuoka Cancer Center Hospital and Research Institute, Shizuoka, Japan
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Huang CC, Liu CY, Huang CJ, Hsu YC, Lien HH, Wong JU, Tai FC, Ku WH, Hung CF, Lin JT, Huang CS, Chiang HS. Deciphering Genetic Alterations of Taiwanese Patients with Pancreatic Adenocarcinoma through Targeted Sequencing. Int J Mol Sci 2022; 23:1579. [PMID: 35163506 PMCID: PMC8835797 DOI: 10.3390/ijms23031579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 01/26/2022] [Accepted: 01/26/2022] [Indexed: 02/01/2023] Open
Abstract
Pancreatic adenocarcinoma (PAC) is the 8th leading cause of cancer-related deaths in Taiwan, and its incidence is increasing. The development of PAC involves successive accumulation of multiple genetic alterations. Understanding the molecular pathogenesis and heterogeneity of PAC may facilitate personalized treatment for PAC and identify therapeutic agents. We performed tumor-only next-generation sequencing (NGS) with targeted panels to explore the molecular changes underlying PAC patients in Taiwan. The Ion Torrent Oncomine Comprehensive Panel (OCP) was used for PAC metastatic lesions, and more PAC samples were sequenced with the Ion AmpliSeq Cancer Hot Spot (CHP) v2 panel. Five formalin-fixed paraffin-embedded (FFPE) metastatic PAC specimens were successfully assayed with OCP, and KRAS was the most prevalent alteration, which might contraindicate the use of anti-EGFR therapy. One PAC patient harbored a FGFR2 p. C382R mutation, which might benefit from FGFR tyrosine kinase inhibitors. An additional 38 samples assayed with CHP v2 showed 100 hotspot variants, collapsing to 54 COSMID IDs. The most frequently mutated genes were TP53, KRAS, and PDGFRA (29, 23, 10 hotspot variants), impacting 11, 23, and 10 PAC patients. Highly pathogenic variants, including COSM22413 (PDGFRA, FATHMM predicted score: 0.88), COSM520, COSM521, and COSM518 (KRAS, FATHMM predicted score: 0.98), were reported. By using NGS with targeted panels, somatic mutations with therapeutic potential were identified. The combination of clinical and genetic information is useful for decision making and precise selection of targeted medicine.
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Affiliation(s)
- Chi-Cheng Huang
- Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan;
- Comprehensive Breast Health Center, Taipei Veterans General Hospital, Taipei 11217, Taiwan
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei 100, Taiwan
| | - Chih-Yi Liu
- Department of Pathology, Cathay General Hospital SiJhih, New Taipei 221, Taiwan;
| | - Chi-Jung Huang
- Department of Medical Research, Cathay General Hospital, Taipei 106, Taiwan;
- Department of Biochemistry, National Defense Medical Center, Taipei 114, Taiwan
| | - Yao-Chun Hsu
- Division of Gastroenterology, Department of Internal Medicine, E-da Hospital, Kaohsiung 82445, Taiwan;
| | - Heng-Hui Lien
- Division of General Surgery, Department of Surgery, Cathay General Hospital, Taipei 106, Taiwan; (H.-H.L.); (F.-C.T.)
- School of Medicine, College of Medicine, Fu-Jen Catholic University, New Taipei 242, Taiwan;
| | - Jia-Uei Wong
- Division of General Surgery, Department of Surgery, Fu-Jen Catholic University Hospital, New Taipei 243, Taiwan;
| | - Feng-Chuan Tai
- Division of General Surgery, Department of Surgery, Cathay General Hospital, Taipei 106, Taiwan; (H.-H.L.); (F.-C.T.)
| | - Wen-Hui Ku
- Department of Clinical Pathology and Molecular Medicine, Taipei Institute of Pathology, Taipei 10374, Taiwan;
| | - Chi-Feng Hung
- School of Medicine, College of Medicine, Fu-Jen Catholic University, New Taipei 242, Taiwan;
| | - Jaw-Town Lin
- Digestive Medicine Center, China Medical University Hospital, Taichung 404, Taiwan;
| | - Ching-Shui Huang
- Division of General Surgery, Department of Surgery, Cathay General Hospital, Taipei 106, Taiwan; (H.-H.L.); (F.-C.T.)
- School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
| | - Han-Sun Chiang
- School of Medicine, College of Medicine, Fu-Jen Catholic University, New Taipei 242, Taiwan;
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Mesonephric-like Adenocarcinoma of the Ovary: Clinicopathological and Molecular Characteristics. Diagnostics (Basel) 2022; 12:diagnostics12020326. [PMID: 35204416 PMCID: PMC8871294 DOI: 10.3390/diagnostics12020326] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 01/21/2022] [Accepted: 01/25/2022] [Indexed: 01/02/2023] Open
Abstract
Mesonephric-like adenocarcinoma (MLA) arising in the ovary is a rare malignant tumor of the female genital tract. Although the clinicopathological and molecular characteristics of uterine MLA have been accumulated, those of ovarian MLA have not been firmly clarified. In this study, we investigated the clinicopathological, immunohistochemical, and genetic features of five ovarian MLAs. A review of electronic medical records and pathology slides, immunostaining, and targeted sequencing was performed. On imaging, ovarian MLA presented as either a mixed solid and cystic mass or a purely solid mass. One, three, and one patient were diagnosed as having FIGO stage IA, IC, and II MLA, respectively. Four patients with stage IC–II tumor underwent post-operative adjuvant chemotherapy. Three of the four patients whose follow-up information was available did not experience recurrence. In contrast, the remaining patient with stage IA tumor who did not receive any adjuvant treatment developed multiple metastatic recurrences at post-operative 13 months. Histologically, ovarian MLAs characteristically displayed architectural diversity, compactly aggregated small tubules, and eosinophilic intraluminal secretions. Four tumors were found to be associated with endometriotic cysts. Two cases showed some areas of high-grade nuclear atypia, brisk mitotic activity, and necrosis. Immunohistochemically, all cases showed positive immunoreactivities for at least three of the four examined mesonephric markers (GATA3, PAX2, TTF1, and CD10), lack of WT1 expression, non-diffuse p16 immunoreactivity, and wild-type p53 immunostaining pattern. Targeted sequencing analysis revealed that all four examined cases harbored pathogenic KRAS mutations: p.G12V (2/4); p.G12D (1/4); and p.G12C (1/4). In addition, we reviewed the previous literature reporting 60 cases of ovarian MLA. Our findings corroborate those of the previous data regarding the clinical presentation, histological features, immunophenotypes, and molecular alterations. Our observations should encourage pathologists to recognize and accurately diagnose this rare but distinct entity.
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28
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Wang XQ, Goytain A, Dickson BC, Nielsen TO. Advances in Sarcoma Molecular Diagnostics. Genes Chromosomes Cancer 2022; 61:332-345. [DOI: 10.1002/gcc.23025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 01/10/2022] [Accepted: 01/15/2022] [Indexed: 11/11/2022] Open
Affiliation(s)
- Xue Qi Wang
- Faculty of Medicine University of British Columbia Vancouver Canada
- Genetic Pathology Evaluation Centre, Department of Pathology and Laboratory Medicine University of British Columbia Vancouver Canada
| | - Angela Goytain
- Genetic Pathology Evaluation Centre, Department of Pathology and Laboratory Medicine University of British Columbia Vancouver Canada
| | - Brendan C. Dickson
- Department of Pathology & Laboratory Medicine, Mount Sinai Hospital; Department of Laboratory Medicine and Pathobiology University of Toronto Toronto ON Canada
| | - Torsten Owen Nielsen
- Genetic Pathology Evaluation Centre, Department of Pathology and Laboratory Medicine University of British Columbia Vancouver Canada
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29
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Conroy JM, Pabla S, Glenn ST, Seager RJ, Van Roey E, Gao S, Burgher B, Andreas J, Giamo V, Mallon M, Lee YH, DePietro P, Nesline M, Wang Y, Lenzo FL, Klein R, Zhang S. A scalable high-throughput targeted next-generation sequencing assay for comprehensive genomic profiling of solid tumors. PLoS One 2021; 16:e0260089. [PMID: 34855780 PMCID: PMC8639101 DOI: 10.1371/journal.pone.0260089] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 11/03/2021] [Indexed: 11/18/2022] Open
Abstract
Timely and accurate identification of molecular alterations in solid tumors is essential for proper management of patients with advanced cancers. This has created a need for rapid, scalable comprehensive genomic profiling (CGP) systems that detect an increasing number of therapeutically-relevant variant types and molecular signatures. In this study, we assessed the analytical performance of the TruSight Oncology 500 High-Throughput assay for detection of somatic alterations from formalin-fixed paraffin-embedded tissue specimens. In parallel, we developed supporting software and automated sample preparation systems designed to process up to 70 clinical samples in a single NovaSeq 6000TM sequencing run with a turnaround time of <7 days from specimen receipt to report. The results demonstrate that the scalable assay accurately and reproducibly detects small variants, copy number alterations, microsatellite instability (MSI) and tumor mutational burden (TMB) from 40ng DNA, and multiple gene fusions, including known and unknown partners and splice variants from 20ng RNA. 717 tumor samples and reference materials with previously known alterations in 96 cancer-related genes were sequenced to evaluate assay performance. All variant classes were reliably detected at consistent and reportable variant allele percentages with >99% overall accuracy and precision. Our results demonstrate that the high-throughput CGP assay is a reliable method for accurate detection of molecular alterations in support of precision therapeutics in oncology. The supporting systems and scalable workflow allow for efficient interpretation and prompt reporting of hundreds of patient cancer genomes per week with excellent analytical performance.
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Affiliation(s)
- Jeffrey M. Conroy
- Research and Development, OmniSeq Inc., Buffalo, New York, United States of America
- Research Support Services, Roswell Park Comprehensive Cancer Center, Buffalo, New York, United States of America
| | - Sarabjot Pabla
- Bioinformatics, OmniSeq Inc., Buffalo, New York, United States of America
| | - Sean T. Glenn
- Research and Development, OmniSeq Inc., Buffalo, New York, United States of America
- Laboratory Operations, OmniSeq Inc., Buffalo, New York, United States of America
- HemePath Molecular, Roswell Park Comprehensive Cancer Center, Buffalo, New York, United States of America
| | - R. J. Seager
- Bioinformatics, OmniSeq Inc., Buffalo, New York, United States of America
| | - Erik Van Roey
- Bioinformatics, OmniSeq Inc., Buffalo, New York, United States of America
| | - Shuang Gao
- Bioinformatics, OmniSeq Inc., Buffalo, New York, United States of America
| | - Blake Burgher
- Research and Development, OmniSeq Inc., Buffalo, New York, United States of America
| | - Jonathan Andreas
- Research and Development, OmniSeq Inc., Buffalo, New York, United States of America
| | - Vincent Giamo
- Research and Development, OmniSeq Inc., Buffalo, New York, United States of America
| | - Melissa Mallon
- Research and Development, OmniSeq Inc., Buffalo, New York, United States of America
| | - Yong Hee Lee
- Clinical Evidence Development, OmniSeq Inc., Buffalo, New York, United States of America
| | - Paul DePietro
- Clinical Evidence Development, OmniSeq Inc., Buffalo, New York, United States of America
| | - Mary Nesline
- Clinical Evidence Development, OmniSeq Inc., Buffalo, New York, United States of America
| | - Yirong Wang
- Information Technology, OmniSeq Inc., Buffalo, New York, United States of America
| | - Felicia L. Lenzo
- Research and Development, OmniSeq Inc., Buffalo, New York, United States of America
| | - Roger Klein
- Medical Affairs, OmniSeq Inc., Buffalo, New York, United States of America
| | - Shengle Zhang
- Laboratory Operations, OmniSeq Inc., Buffalo, New York, United States of America
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Eefsen RL, Simonsen KS, Grundtvig P, Klarskov L, Chen IM, Høgdall D, Jensen BV, Lorentzen T, Poulsen TS, Theile S, Nielsen D, Høgdall E. Genomic landscape of treatment refractory metastatic colorectal cancer. Acta Oncol 2021; 60:1621-1628. [PMID: 34606390 DOI: 10.1080/0284186x.2021.1984575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
BACKGROUND Metastatic colorectal cancer (mCRC) is a complex and heterogeneous disease with few standard and targeted treatment options. Next-generation sequencing of tumor tissue was performed to identify cancer driver mutations to discover possible personalized treatment options, as targeted treatment possibilities are limited for this patient population. Results of genomic sequencing in patients with treatment-refractory mCRC are described in this retrospective analysis. MATERIAL AND METHODS Clinico-pathological characteristics and genomic sequence results of consecutive patients with refractory mCRC, referred to the Experimental Cancer Therapy Unit (ECTU) at Department of Oncology, Herlev & Gentofte Hospital in the period from 1 October 2015 to 14 December 2018 were reviewed in this retrospective analysis. Tumor tissue from the patients was analyzed by next-generation sequencing using the Oncomine Comprehensive primer panel to detect actionable variants of cancer driver mutations and microsatellite instability status. From August 2018 tumor mutational burden was also analyzed. RESULTS A total of 80 patients with treatment-refractory mCRC and in a fairly good performance were referred to the ECTU during this period. Genomic sequencing of tumor tissue was performed for all 80 patients and a cancer driver mutation was identified in 90% (n = 72) of the patients. A total of 31.3% (n = 25) of the patients received therapy either as targetable therapy outside an available trial (n = 2), FDA approved therapy (n = 2), or treatment in phase 1 or 2 trials, independent of the genomic signature 26.3% (n = 21). CONCLUSION Most mCRC patients refractory to standard anti-neoplastic therapies, presented with a cancer driver mutation, however, only a few of these mutations gave rise to matched therapies as only 2.5% of the patients from this period received targeted therapy.
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Affiliation(s)
- R. L. Eefsen
- Department of Oncology, Herlev Gentofte Hospital, Herlev, Denmark
| | - K. S. Simonsen
- Department of Oncology, Herlev Gentofte Hospital, Herlev, Denmark
| | - P. Grundtvig
- Department of Oncology, Herlev Gentofte Hospital, Herlev, Denmark
| | - L. Klarskov
- Department of Pathology, Herlev Gentofte Hospital, Herlev, Denmark
| | - I. M. Chen
- Department of Oncology, Herlev Gentofte Hospital, Herlev, Denmark
| | - D. Høgdall
- Department of Oncology, Herlev Gentofte Hospital, Herlev, Denmark
| | - B. V. Jensen
- Department of Oncology, Herlev Gentofte Hospital, Herlev, Denmark
| | - T. Lorentzen
- Department of Surgery, Herlev Gentofte Hospital, Herlev, Denmark
| | - T. S. Poulsen
- Department of Pathology, Herlev Gentofte Hospital, Herlev, Denmark
| | - S. Theile
- Department of Oncology, Herlev Gentofte Hospital, Herlev, Denmark
| | - D. Nielsen
- Department of Oncology, Herlev Gentofte Hospital, Herlev, Denmark
| | - E. Høgdall
- Department of Pathology, Herlev Gentofte Hospital, Herlev, Denmark
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31
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Wang S, Yang X, Xie W, Fu S, Chen Q, Li Z, Zhang Z, Sun T, Gong B, Ma M. LncRNA GAPLINC Promotes Renal Cell Cancer Tumorigenesis by Targeting the miR-135b-5p/CSF1 Axis. Front Oncol 2021; 11:718532. [PMID: 34722262 PMCID: PMC8551964 DOI: 10.3389/fonc.2021.718532] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 09/27/2021] [Indexed: 12/12/2022] Open
Abstract
Background Long noncoding RNAs (lncRNAs) are closely related to the occurrence and development of cancer. Gastric adenocarcinoma-associated, positive CD44 regulator, long intergenic noncoding RNA (GAPLINC) is a recently identified lncRNA that can actively participate in the tumorigenesis of various cancers. Here, we investigated the functional roles and mechanism of GAPLINC in renal cell carcinoma (RCC) development. Methods Differentially expressed lncRNAs between RCC tissues and normal kidney tissues were detected by using a microarray technique. RNA sequencing was applied to explore the mRNA expression profile changes after GAPLINC silencing. After gain- and loss-of-function approaches were implemented, the effect of GAPLINC on RCC in vitro and in vivo was assessed by cell proliferation and migration assays. Moreover, rescue experiments and luciferase reporter assays were used to study the interactions between GAPLINC, miR-135b-5p and CSF1. Results GAPLINC was significantly upregulated in RCC tissues and cell lines and was associated with a poor prognosis in RCC patients. Knockdown of GAPLINC repressed RCC growth in vitro and in vivo, while overexpression of GAPLINC exhibited the opposite effect. Mechanistically, we found that GAPLINC upregulates oncogene CSF1 expression by acting as a sponge of miR-135b-5p. Conclusion Taken together, our results suggest that GAPLINC is a novel prognostic marker and molecular therapeutic target for RCC.
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Affiliation(s)
- Siyuan Wang
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiaorong Yang
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Wenjie Xie
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Shengqiang Fu
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Qiang Chen
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhilong Li
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhicheng Zhang
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Ting Sun
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Binbin Gong
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Ming Ma
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, China
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Bartlett J, Amemiya Y, Arts H, Bayani J, Eng B, Grafodatskaya D, Kamel Reid S, Lariviere M, Lo B, McClure R, Mittal V, Sadikovic B, Sadis S, Seth A, Smith J, Zhang X, Feilotter H. Multisite verification of the accuracy of a multi-gene next generation sequencing panel for detection of mutations and copy number alterations in solid tumours. PLoS One 2021; 16:e0258188. [PMID: 34597339 PMCID: PMC8486135 DOI: 10.1371/journal.pone.0258188] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 09/22/2021] [Indexed: 11/29/2022] Open
Abstract
Molecular variants including single nucleotide variants (SNVs), copy number variants (CNVs) and fusions can be detected in the clinical setting using deep targeted sequencing. These assays support low limits of detection using little genomic input material. They are gaining in popularity in clinical laboratories, where sample volumes are limited, and low variant allele fractions may be present. However, data on reproducibility between laboratories is limited. Using a ring study, we evaluated the performance of 7 Ontario laboratories using targeted sequencing panels. All laboratories analysed a series of control and clinical samples for SNVs/CNVs and gene fusions. High concordance was observed across laboratories for measured CNVs and SNVs. Over 97% of SNV calls in clinical samples were detected by all laboratories. Whilst only a single CNV was detected in the clinical samples tested, all laboratories were able to reproducibly report both the variant and copy number. Concordance for information derived from RNA was lower than observed for DNA, due largely to decreased quality metrics associated with the RNA components of the assay, suggesting that the RNA portions of comprehensive NGS assays may be more vulnerable to variations in approach and workflow. Overall the results of this study support the use of the OFA for targeted sequencing for testing of clinical samples and suggest specific internal quality metrics that can be reliable indicators of assay failure. While we believe this evidence can be interpreted to support deep targeted sequencing in general, additional studies should be performed to confirm this.
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Affiliation(s)
- John Bartlett
- Diagnostic Development, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Edinburgh Cancer Research Centre, Edinburgh, United Kingdom
| | - Yutaka Amemiya
- SRI Genomics Laboratory and Department of Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, University of Toronto, Ontario, Canada
| | - Heleen Arts
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Jane Bayani
- Diagnostic Development, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Barry Eng
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, Ontario, Canada
| | - Daria Grafodatskaya
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, Ontario, Canada
| | - Suzanne Kamel Reid
- Department of Clinical Laboratory Genetics, The University Health Network, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Mathieu Lariviere
- Thermo Fisher Scientific, South San Francisco, CA, United States of America
| | - Bryan Lo
- Dept of Pathology and Laboratory Medicine, The Ottawa Hospital, Ottawa, Ontario, Canada
| | - Rebecca McClure
- Health Sciences North/Horizon Sante-Nord, Sudbury, Ontario, Canada
| | - Vinay Mittal
- Thermo Fisher Scientific, South San Francisco, CA, United States of America
| | - Bekim Sadikovic
- Molecular Diagnostics Laboratoroy, Victoria Hospital, London Health Sciences Centre, London, Ontario, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Seth Sadis
- Thermo Fisher Scientific, South San Francisco, CA, United States of America
| | - Arun Seth
- SRI Genomics Laboratory and Department of Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, University of Toronto, Ontario, Canada
| | - Jeff Smith
- Thermo Fisher Scientific, South San Francisco, CA, United States of America
| | - Xiao Zhang
- Department of Pathology and Molecular Medicine, Queen’s University, Kingston, Ontario, Canada
| | - Harriet Feilotter
- Department of Pathology and Molecular Medicine, Queen’s University, Kingston, Ontario, Canada
- Laboratory Genetics, Kingston Health Sciences Center, Kingston Ontario, Canada
- * E-mail:
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Balikov DA, Hu K, Liu CJ, Betz BL, Chinnaiyan AM, Devisetty LV, Venneti S, Tomlins SA, Cani AK, Rao RC. Comparative Molecular Analysis of Primary Central Nervous System Lymphomas and Matched Vitreoretinal Lymphomas by Vitreous Liquid Biopsy. Int J Mol Sci 2021; 22:9992. [PMID: 34576156 PMCID: PMC8471952 DOI: 10.3390/ijms22189992] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/12/2021] [Accepted: 09/14/2021] [Indexed: 12/13/2022] Open
Abstract
Primary Central Nervous System Lymphoma (PCNSL) is a lymphoid malignancy of the brain that occurs in ~1500 patients per year in the US. PCNSL can spread to the vitreous and retina, where it is known as vitreoretinal lymphoma (VRL). While confirmatory testing for diagnosis is dependent on invasive brain tissue or cerebrospinal fluid sampling, the ability to access the vitreous as a proximal biofluid for liquid biopsy to diagnose PCNSL is an attractive prospect given ease of access and minimization of risks and complications from other biopsy strategies. However, the extent to which VRL, previously considered genetically identical to PCNSL, resembles PCNSL in the same individual with respect to genetic alterations, diagnostic strategies, and precision-medicine based approaches has hitherto not been explored. Furthermore, the degree of intra-patient tumor genomic heterogeneity between the brain and vitreous sites has not been studied. In this work, we report on targeted DNA next-generation sequencing (NGS) of matched brain and vitreous samples in two patients who each harbored VRL and PCSNL. Our strategy showed enhanced sensitivity for molecular diagnosis confirmation over current clinically used vitreous liquid biopsy methods. We observed a clonal relationship between the eye and brain samples in both patients, which carried clonal CDKN2A deep deletions, a highly recurrent alteration in VRL patients, as well as MYD88 p.L265P activating mutation in one patient. Several subclonal alterations, however, in the genes SETD2, BRCA2, TERT, and broad chromosomal regions showed heterogeneity between the brain and the eyes, between the two eyes, and among different regions of the PCNSL brain lesion. Taken together, our data show that NGS of vitreous liquid biopsies in PCNSL patients with VRL highlights shared and distinct genetic alterations that suggest a common origin for these lymphomas, but with additional site-specific alterations. Liquid biopsy of VRL accurately replicates the findings for PCNSL truncal (tumor-initiating) genomic alterations; it can also nominate precision medicine interventions and shows intra-patient heterogeneity in subclonal alterations. To the best of our knowledge, this study represents the first interrogation of genetic underpinnings of PCNSL with matched VRL samples. Our findings support continued investigation into the utility of vitreous liquid biopsy in precision diagnosis and treatment of PCNSL/VRL.
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Affiliation(s)
- Daniel A. Balikov
- W.K. Kellogg Eye Center, Department of Ophthalmology and Visual Science, University of Michigan, Ann Arbor, MI 48109, USA; (D.A.B.); (L.V.D.)
| | - Kevin Hu
- Center of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Chia-Jen Liu
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; (C.-J.L.); (B.L.B.); (A.M.C.); (S.V.); (S.A.T.)
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Bryan L. Betz
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; (C.-J.L.); (B.L.B.); (A.M.C.); (S.V.); (S.A.T.)
| | - Arul M. Chinnaiyan
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; (C.-J.L.); (B.L.B.); (A.M.C.); (S.V.); (S.A.T.)
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Laxmi V. Devisetty
- W.K. Kellogg Eye Center, Department of Ophthalmology and Visual Science, University of Michigan, Ann Arbor, MI 48109, USA; (D.A.B.); (L.V.D.)
| | - Sriram Venneti
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; (C.-J.L.); (B.L.B.); (A.M.C.); (S.V.); (S.A.T.)
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Scott A. Tomlins
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; (C.-J.L.); (B.L.B.); (A.M.C.); (S.V.); (S.A.T.)
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Andi K. Cani
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
- Hematology/Oncology Division, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rajesh C. Rao
- W.K. Kellogg Eye Center, Department of Ophthalmology and Visual Science, University of Michigan, Ann Arbor, MI 48109, USA; (D.A.B.); (L.V.D.)
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; (C.-J.L.); (B.L.B.); (A.M.C.); (S.V.); (S.A.T.)
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI 48109, USA
- Division of Ophthalmology, Surgical Service, Veterans Administration Ann Arbor Healthcare System, Ann Arbor, MI 48109, USA
- A. Alfred Taubman Medical Research Institute, University of Michigan, Ann Arbor, MI 48109, USA
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Choi S, Kim SW, Kim HS. Invasive Stratified Mucin-producing Carcinoma (ISMC) of the Uterine Cervix: Clinicopathological and Molecular Characteristics With Special Emphasis on the First Description of Consistent Programmed Death-ligand 1 (PD-L1) Over-expression. Cancer Genomics Proteomics 2021; 18:685-698. [PMID: 34479920 DOI: 10.21873/cgp.20290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND/AIM Invasive stratified mucin-producing carcinoma (ISMC) of the uterine cervix has been reported to be more aggressive than other subtypes of endocervical adenocarcinoma. We investigated the clinicopathological and molecular characteristics of eight ISMCs. PATIENTS AND METHODS We reviewed the electronic medical records and pathology slides of eight patients with ISMC and conducted programmed death-ligand 1 (PD-L1) immunostaining and targeted sequencing. RESULTS The patients were between 31 and 54 years. Six tumors were pure ISMCs, and two showed co-existing squamous cell carcinoma and usual-type endocervical adenocarcinoma. Lymph node metastases were detected in three cases. Three patients developed distant metastases to the adnexa, lungs, inguinal lymph nodes, and small intestine. Two patients experienced disease progression, and three developed postoperative local recurrences. All tumors showed PD-L1 over-expression, with a mean combined positive score of 73.8 (range=30-100). One tumor harbored erb-b2 receptor tyrosine kinase 2 amplification. CONCLUSION ISMC of the uterine cervix exhibits a high risk of recurrence, metastasis, and resistance to chemoradiation therapy. PD-L1 over-expression was consistently observed in all ISMCs. This finding raises the possibility that patients with ISMC may benefit from PD-L1 immunotherapy.
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Affiliation(s)
- Sangjoon Choi
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - So-Woon Kim
- Department of Pathology, Kyung Hee University Hospital, Kyung Hee University College of Medicine, Seoul, Republic of Korea
| | - Hyun-Soo Kim
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea;
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Yeo MK, Yoon N, Bae GE. Clinicopathologic and Molecular Characteristics of Gastrointestinal MiNENs. Front Oncol 2021; 11:709097. [PMID: 34422662 PMCID: PMC8371704 DOI: 10.3389/fonc.2021.709097] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/12/2021] [Indexed: 12/31/2022] Open
Abstract
Background A mixed neuroendocrine–non-neuroendocrine neoplasm (MiNEN) is a recently defined entity that comprises a neuroendocrine tumor (NEN) component and a non-neuroendocrine tumor (nNEN) component. As MiNEN is a recently defined entity, its molecular nature is not well known. Here, we evaluated the clinicopathologic and molecular characteristics of gastrointestinal (GI) MiNENs. Methods We performed a genomic analysis of 31 samples from 12 GI MiNEN cases using next-generation sequencing. We examined the primary NEN and nNEN components, as well as the metastatic NENs and nNENs. The relationships between the clinical tumor features (component, location, and grade) and their molecular characteristics were examined. Results The 12 MiNENs included in the study were found in the stomach (n=10), distal rectum (n=1), and anus (n=1). Primary MiNENs that had NENs as the major component showed a worse clinical outcome than those that had nNENs as the major component. All distant metastatic tumors originating from MiNENs were NENs. In addition, NENs generally carried 1.5 times more gene mutations and copy number variations than nNENs. The ATRX gene deletion and TP53 gene mutation were the most common variants in both components of GI MiNENs. Conclusions We have revealed the detailed clinicopathologic and molecular findings with distinguishable alterations of GI MiNENs. To our knowledge, this is the first study to report the ATRX gene deletion in GI MiNENs. The molecular characteristics of GI MiNENs could provide clues to the pathogenic origin and progression of GI MiNENs.
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Affiliation(s)
- Min-Kyung Yeo
- Department of Pathology, Chungnam National University School of Medicine, Daejeon, South Korea
| | - Nara Yoon
- Departments of Pathology, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Incheon, South Korea
| | - Go Eun Bae
- Department of Pathology, Chungnam National University School of Medicine, Daejeon, South Korea
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MET Mutation Is a Potential Therapeutic Target for Advanced Endometrial Cancer. Cancers (Basel) 2021; 13:cancers13164231. [PMID: 34439385 PMCID: PMC8392057 DOI: 10.3390/cancers13164231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/05/2021] [Accepted: 08/19/2021] [Indexed: 12/30/2022] Open
Abstract
Simple Summary Endometrial cancer is the most common gynecological cancer in developed countries. At initial diagnosis, extra-uterine spread is observed in about 25% of patients. Chemotherapy is the suggested mode of treatment for patients with extra-uterine metastasis; however, the 5-year overall survival rate of these patients remains poor. The development of new therapeutic strategies to improve the poor clinical outcome of patients with advanced endometrial cancer is still in great demand. In this study, we aim to understand the genomic landscape of advanced endometrial cancer and identify new therapeutic targets. Integrated genomic, pathological, and clinical data are analyzed to identify the survival-associated genomic alterations. In addition, the impacts of the genomic alterations are examined in silico, in vitro, and in vivo. The results of this study may aid in developing biomarker-guided treatments for patients with advanced endometrial cancer. Abstract An optimal therapeutic regimen for endometrial cancer with extra-uterine metastasis is unavailable. This study aims to improve our understanding of the genomic landscape of advanced endometrial cancer and identify potential therapeutic targets. The clinical and genomic profiles of 81 patients with stage III or IV endometrial cancer were integrated. To identify genomic aberrations associated with clinical outcomes, Cox proportional hazard regression was used. The impacts of the genomic aberrations were validated in vitro and in vivo. The mutation status of MET, U2AF1, BCL9, PPP2R1A, IDH2, CBL, BTK, and CHEK2 were positively correlated with poor clinical outcomes. MET mutations occurred in 30% of the patients who presented with poor overall survival (hazard ratio, 2.606; 95% confidence interval, 1.167~5.819; adjusted p-value, 0.067). Concurrent MET and KRAS mutations presented with the worst outcomes. MET mutations in hepatocyte growth factor (HGF)-binding (58.1%) or kinase (16.2%) domains resulted in differential HGF-induced c-MET phosphorylation. Different types of MET mutations differentially affected tumor growth and displayed different sensitivities to cisplatin and tyrosine kinase inhibitors. MET N375S mutation is a germline variant that causes chemoresistance to cisplatin, with a high incidence in Eastern Asia. This study highlights the ethnic differences in the biology of the disease, which can influence treatment recommendations and the genome-guided clinical trials of advanced endometrial cancer.
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Mesonephric-like Differentiation of Endometrial Endometrioid Carcinoma: Clinicopathological and Molecular Characteristics Distinct from Those of Uterine Mesonephric-like Adenocarcinoma. Diagnostics (Basel) 2021; 11:diagnostics11081450. [PMID: 34441384 PMCID: PMC8391898 DOI: 10.3390/diagnostics11081450] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 07/25/2021] [Accepted: 08/05/2021] [Indexed: 11/18/2022] Open
Abstract
When diagnosing endometrial carcinoma cases, we encountered histological features that strikingly resembled uterine mesonephric-like adenocarcinoma (MLA), but the differential diagnosis remained challenging after performing immunostaining. Considering the aggressive biological behavior and poor prognosis of uterine MLA, we believe that the accurate recognition of mesonephric-like differentiation (MLD) is important in the diagnosis of endometrial carcinoma. We aimed to investigate the clinicopathological and molecular characteristics of such cases and compared them with those of uterine MLAs. Five patients diagnosed with endometrioid carcinoma (EC) with MLD were included in this study. Histological evaluation, immunostaining, and targeted sequencing were performed. All five tumors showed typical morphological features of MLA, including densely aggregated tubular structures, deep basophilia under low-power magnification microscopy, eosinophilic intraluminal secretions, and diverse growth patterns. Immunostaining revealed moderate-to-strong nuclear immunoreactivity for estrogen and progesterone receptors in more than 50% tumor cells. The staining intensities and proportions of PAX2 and GATA3 were variable. None of the tumors harbored KRAS mutations. Considering the prognostic implications, ancillary tests, including immunostaining and targeted sequencing, should be performed to accurately differentiate between endometrial EC-MLD and uterine MLA.
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Gaiser T, Sauer C, Marx A, Jakob J, Kasper B, Hohenberger P, Hirsch D, Ronellenfitsch U. Molecular and Pathological Profiling of Corresponding Treatment-Naïve and Neoadjuvant Pazopanib-Treated High-Risk Soft Tissue Sarcoma Samples of the GISG-04/NOPASS Study. BIOLOGY 2021; 10:biology10070639. [PMID: 34356494 PMCID: PMC8301157 DOI: 10.3390/biology10070639] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/07/2021] [Indexed: 01/25/2023]
Abstract
In the framework of the German Interdisciplinary Sarcoma Group GISG-04/NOPASS trial, we evaluated soft tissue sarcoma samples taken before and after neoadjuvant pazopanib therapy using histopathology and next generation sequencing (NGS) to find potential predictive biomarkers. We also aimed to improve the genetically based sarcoma classification and to elucidate additional potentially druggable mutations. In total, 30 tumor samples from 18 patients consisting of 12 pre-therapeutic biopsies and 18 resection specimens following neoadjuvant pazopanib therapy were available for analyses. NGS was performed with the Oncomine Focus Assay (Ion Torrent) covering 0.03 Mb of DNA and enabled the detection of genetic variants in 52 cancer-relevant genes. Pathological analysis showed significant regression (≥50%) after pazopanib treatment in only one undifferentiated (pleomorphic) sarcoma. NGS analyses revealed a very high frequency of CDK4 amplification (88%; 7/8) in the group of dedifferentiated liposarcoma. In addition, two potentially druggable mutations, a MAP2K1 missense mutation (E203K) and a BRAF missense mutation (V600E), were traceable in two undifferentiated (pleomorphic) sarcoma patients (11%; 2/18). Our findings demonstrate that NGS testing is a powerful technology helping to improve diagnostic accuracy and offering some patients the chance for personalized medicine even in a "mutation unlikely" cohort like STS.
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Affiliation(s)
- Timo Gaiser
- Institute of Pathology, University Medical Centre Mannheim, University of Heidelberg, 68305 Mannheim, Germany; (C.S.); (A.M.); (D.H.)
- Correspondence: ; Tel.: +49-621-383-2876; Fax: +49-621-383-2005
| | - Christian Sauer
- Institute of Pathology, University Medical Centre Mannheim, University of Heidelberg, 68305 Mannheim, Germany; (C.S.); (A.M.); (D.H.)
| | - Alexander Marx
- Institute of Pathology, University Medical Centre Mannheim, University of Heidelberg, 68305 Mannheim, Germany; (C.S.); (A.M.); (D.H.)
| | - Jens Jakob
- Department of General, Visceral and Child Surgery, University Medical Center Göttingen, 37075 Göttingen, Germany;
| | - Bernd Kasper
- Sarcoma Unit, Interdisciplinary Tumor Center Mannheim, Mannheim University Medical Center, 68305 Mannheim, Germany;
| | - Peter Hohenberger
- Division of Surgical Oncology and Thoracic Surgery, University Medical Center Mannheim, 68167 Mannheim, Germany;
| | - Daniela Hirsch
- Institute of Pathology, University Medical Centre Mannheim, University of Heidelberg, 68305 Mannheim, Germany; (C.S.); (A.M.); (D.H.)
| | - Ulrich Ronellenfitsch
- Department of Abdominal, Vascular, and Endocrine Surgery, University Hospital Halle (Saale), 06120 Halle (Saale), Germany;
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Concordance Analysis of ALK Gene Fusion Detection Methods in Patients with Non-Small-Cell Lung Cancer from Chile, Brazil, and Peru. J Mol Diagn 2021; 23:1127-1137. [PMID: 34186175 DOI: 10.1016/j.jmoldx.2021.05.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 05/08/2021] [Accepted: 05/27/2021] [Indexed: 11/23/2022] Open
Abstract
About 4% to 7% of the non-small-cell lung cancer patients have anaplastic lymphoma kinase (ALK) rearrangements, and specific targeted therapies improve patients' outcomes significantly. ALK gene fusions are detected by immunohistochemistry or fluorescent in situ hybridization as gold standards in South America. Next-generation sequencing-based assays are a reliable alternative, able to perform simultaneous detection of multiple events from a single sample. We analyzed 4240 non-small-cell lung cancer samples collected in 37 hospitals from Chile, Brazil, and Peru, where ALK rearrangements were determined as part of their standard of care (SofC) using either immunohistochemistry or fluorescent in situ hybridization. A subset of 1450 samples was sequenced with the Oncomine Focus Assay (OFA), and the concordance with the SofC tests was measured. An orthogonal analysis was performed using a real-time quantitative PCR echinoderm microtubule-associated protein-like 4-ALK fusion detection kit. ALK fusion prevalence is similar for Chile (3.67%; N = 2142), Brazil (4.05%; N = 1013), and Peru (4.59%; N = 675). Although a comparison between OFA and SofC assays showed similar sensitivity, OFA had significantly higher specificity and higher positive predictive value, which opens new opportunities for a more specific determination of ALK gene rearrangements.
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Yoon N, Kim HS, Lee JW, Lee EJ, Maeng LS, Yoon WS. Targeted Genomic Sequencing Reveals Different Evolutionary Patterns Between Locally and Distally Recurrent Glioblastomas. Cancer Genomics Proteomics 2021; 17:803-812. [PMID: 33099481 DOI: 10.21873/cgp.20234] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 09/23/2020] [Accepted: 10/01/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND/AIM Glioblastoma is the most malignant form of astrocytoma. The purpose of this study was to analyze the genetic characteristics of primary and recurrent glioblastomas using targeted sequencing and investigate the differences in mutational profiles between the locations of tumor recurrence. MATERIALS AND METHODS Fourteen glioblastoma patients who developed local (n=10) or distal (n=4) recurrence were included in the study. Targeted sequencing analysis was performed using the primary (n=14) and corresponding recurrent (n=14) tumor tissue samples. RESULTS The local and distal recurrence groups showed different genetic evolutionary patterns. Most of the locally recurrent glioblastomas demonstrated concordant mutational profiles between the primary and recurrent tumors, suggesting a linear evolution. In contrast, all cases of distally recurrent glioblastomas showed changes in mutational profiles with newly acquired mutations when compared to the corresponding primary tumors, suggesting a branching evolution. CONCLUSION Locally and distally recurrent glioblastomas exhibit different evolutionary patterns.
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Affiliation(s)
- Nara Yoon
- Department of Pathology, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Incheon, Republic of Korea
| | - Hyun-Soo Kim
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jung Whee Lee
- Department of Radiology, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Incheon, Republic of Korea
| | - Eui-Jin Lee
- Institute of Catholic Integrative Medicine, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Incheon, Republic of Korea
| | - Lee-So Maeng
- Department of Pathology, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Incheon, Republic of Korea
| | - Wan Soo Yoon
- Department of Neurosurgery, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Incheon, Republic of Korea
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Kim H, Yoon N, Woo HY, Lee EJ, DO SI, Na K, Kim HS. Atypical Mesonephric Hyperplasia of the Uterus Harbors Pathogenic Mutation of Kirsten Rat Sarcoma 2 Viral Oncogene Homolog ( KRAS) and Gain of Chromosome 1q. Cancer Genomics Proteomics 2021; 17:813-826. [PMID: 33099482 DOI: 10.21873/cgp.20235] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND/AIM Mesonephric carcinoma (MNC) is a rare but notable entity of the female genital tract. While many researchers have acknowledged and studied MNC, much remains unknown on the characteristics of mesonephric remnant (MNR) or hyperplasia (MNH). There has not been any study examining the molecular features of MNR and MNH so far. The aim of this study was to investigate the clinicopathological and molecular characteristics of ten uterine mesonephric lesions, including two MNRs without atypia, four MNHs without atypia, and three MNHs with atypia. MATERIALS AND METHODS We reviewed the electronic medical records and all available slides of ten cases from multiple institutions. Targeted sequencing and array comparative genomic hybridization were performed. RESULTS Three atypical MNHs displayed nuclear enlargement, mild-to-moderate nuclear pleomorphism, and nuclear membrane irregularity, and harbored pathogenic Kirsten rat sarcoma 2 viral oncogene homolograt sarcoma 2 viral oncogene homolog (KRAS) mutation. Two of those that co-existed with MNC harbored the same sequence alterations as each of their adjacent MNC. One of the three atypical MNHs harbored chromosome 1q gain. CONCLUSION Atypical MNH is a potential premalignant lesion in which KRAS mutation and chromosome 1q gain play an important role in the early stage of mesonephric carcinogenesis.
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Affiliation(s)
- Hyunjin Kim
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Nara Yoon
- Department of Pathology, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Incheon, Republic of Korea
| | - Ha Young Woo
- Department of Pathology, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Eui-Jin Lee
- Institute of Catholic Integrative Medicine, Incheon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Incheon, Republic of Korea
| | - Sung-Im DO
- Department of Pathology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Kiyong Na
- Department of Pathology, Kyung Hee University Hospital, Kyung Hee University College of Medicine, Seoul, Republic of Korea
| | - Hyun-Soo Kim
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
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Cani AK, Toral MA, Balikov DA, Betz BL, Hu K, Liu CJ, Prifti MV, Chinnaiyan AM, Tomlins SA, Mahajan VB, Rao RC. Molecular Characterization of a Rare Case of Bilateral Vitreoretinal T Cell Lymphoma through Vitreous Liquid Biopsy. Int J Mol Sci 2021; 22:6099. [PMID: 34198843 PMCID: PMC8201094 DOI: 10.3390/ijms22116099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/19/2021] [Accepted: 05/30/2021] [Indexed: 02/04/2023] Open
Abstract
Vitreoretinal lymphoma (VRL) is an uncommon eye malignancy, and VRLs of T cell origin are rare. They are difficult to treat, and their molecular underpinnings, including actionable genomic alterations, remain to be elucidated. At present, vitreous fluid liquid biopsies represent a valuable VRL sample for molecular analysis to study VRLs. In this study, we report the molecular diagnostic workup of a rare case of bilateral T cell VRL and characterize its genomic landscape, including identification of potentially targetable alterations. Using next-generation sequencing of vitreous-derived DNA with a pan-cancer 126-gene panel, we found a copy number gain of BRAF and copy number loss of tumor suppressor DNMT3A. To the best of our knowledge, this represents the first exploration of the T cell VRL cancer genome and supports vitreous liquid biopsy as a suitable approach for precision oncology treatments.
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Affiliation(s)
- Andi K. Cani
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48105, USA;
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Marcus A. Toral
- Medical Scientist Training Program, University of Iowa, Iowa City, IA 52242, USA;
- Graduate Program in Molecular Medicine, University of Iowa, Iowa City, IA 52242, USA
- Molecular Surgery Laboratory, Byers Eye Institute, Stanford University, Palo Alto, CA 94303, USA
| | - Daniel A. Balikov
- W.K. Kellogg Eye Center, Department of Ophthalmology and Visual Science, University of Michigan, Ann Arbor, MI 48105, USA;
| | - Bryan L. Betz
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; (B.L.B.); (K.H.); (C.-J.L.); (S.A.T.)
| | - Kevin Hu
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; (B.L.B.); (K.H.); (C.-J.L.); (S.A.T.)
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Chia-Jen Liu
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; (B.L.B.); (K.H.); (C.-J.L.); (S.A.T.)
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Matthew V. Prifti
- A. Alfred Taubman Medical Research Institute, University of Michigan, Ann Arbor, MI 48105, USA;
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Arul M. Chinnaiyan
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA;
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; (B.L.B.); (K.H.); (C.-J.L.); (S.A.T.)
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Scott A. Tomlins
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; (B.L.B.); (K.H.); (C.-J.L.); (S.A.T.)
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Vinit B. Mahajan
- Molecular Surgery Laboratory, Byers Eye Institute, Stanford University, Palo Alto, CA 94303, USA
- Palo Alto Veterans Health Care System, Palo Alto, CA 94304, USA
| | - Rajesh C. Rao
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA;
- W.K. Kellogg Eye Center, Department of Ophthalmology and Visual Science, University of Michigan, Ann Arbor, MI 48105, USA;
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; (B.L.B.); (K.H.); (C.-J.L.); (S.A.T.)
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
- A. Alfred Taubman Medical Research Institute, University of Michigan, Ann Arbor, MI 48105, USA;
- Division of Ophthalmology, Surgical Service, Veterans Administration Ann Arbor Healthcare System, Ann Arbor, MI 48105, USA
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TP53 mutations and CDKN2A mutations/deletions are highly recurrent molecular alterations in the malignant progression of sinonasal papillomas. Mod Pathol 2021; 34:1133-1142. [PMID: 33203919 PMCID: PMC8126579 DOI: 10.1038/s41379-020-00716-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/23/2020] [Accepted: 10/24/2020] [Indexed: 01/08/2023]
Abstract
Sinonasal papillomas are benign epithelial tumors of the sinonasal tract that are associated with a synchronous or metachronous sinonasal carcinoma in a subset of cases. Our group recently identified mutually exclusive EGFR mutations and human papillomavirus (HPV) infection in inverted sinonasal papillomas and frequent KRAS mutations in oncocytic sinonasal papillomas. We also demonstrated concordant mutational and HPV infection status in sinonasal papilloma-associated sinonasal carcinomas, confirming a clonal relationship between these tumors. Despite our emerging understanding of the oncogenic mechanisms driving formation of sinonasal papillomas, little is currently known about the molecular mechanisms of malignant progression to sinonasal carcinoma. In the present study, we utilized targeted next-generation DNA sequencing to characterize the molecular landscape of a large cohort of sinonasal papilloma-associated sinonasal carcinomas. As expected, EGFR or KRAS mutations were present in the vast majority of tumors. In addition, highly recurrent TP53 mutations, CDKN2A mutations, and/or CDKN2A copy-number losses were detected; overall, nearly all tumors (n = 28/29; 96.6%) harbored at least one TP53 or CDKN2A alteration. TERT copy-number gains also occurred frequently (27.6%); however, no TERT promoter mutations were identified. Other recurrent molecular alterations included NFE2L2 and PIK3CA mutations and SOX2, CCND1, MYC, FGFR1, and EGFR copy-number gains. Importantly, TP53 mutations and CDKN2A alterations were not detected in matched sinonasal papillomas, suggesting that these molecular events are associated with malignant transformation. Compared to aerodigestive tract squamous cell carcinomas from The Cancer Genome Atlas (TCGA) project, sinonasal papilloma-associated sinonasal carcinomas have a distinct molecular phenotype, including more frequent EGFR, KRAS, and CDKN2A mutations, TERT copy-number gains, and low-risk human papillomavirus (HPV) infection. These findings shed light on the molecular mechanisms of malignant progression of sinonasal papillomas and may have important diagnostic and therapeutic implications for patients with advanced sinonasal cancer.
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Functional impact of intramolecular cleavage and dissociation of adhesion G protein-coupled receptor GPR133 (ADGRD1) on canonical signaling. J Biol Chem 2021; 296:100798. [PMID: 34022221 PMCID: PMC8215292 DOI: 10.1016/j.jbc.2021.100798] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/04/2021] [Accepted: 05/16/2021] [Indexed: 12/22/2022] Open
Abstract
GPR133 (ADGRD1), an adhesion G protein–coupled receptor (GPCR) whose canonical signaling activates GαS-mediated generation of cytosolic cAMP, has been shown to be necessary for the growth of glioblastoma (GBM), a brain malignancy. The extracellular N terminus of GPR133 is thought to be autoproteolytically cleaved into N-terminal and C- terminal fragments (NTF and CTF, respectively). However, the role of this cleavage in receptor activation remains unclear. Here, we used subcellular fractionation and immunoprecipitation approaches to show that the WT GPR133 receptor is cleaved shortly after protein synthesis and generates significantly more canonical signaling than an uncleavable point mutant GPR133 (H543R) in patient-derived GBM cultures and HEK293T cells. After cleavage, the resulting NTF and CTF remain noncovalently bound to each other until the receptor is trafficked to the plasma membrane, where we demonstrated NTF–CTF dissociation occurs. Using a fusion of the CTF of GPR133 and the N terminus of thrombin-activated human protease-activated receptor 1 as a controllable proxy system to test the effect of intramolecular cleavage and dissociation, we also showed that thrombin-induced cleavage and shedding of the human protease-activated receptor 1 NTF increased intracellular cAMP levels. These results support a model wherein dissociation of the NTF from the CTF at the plasma membrane promotes GPR133 activation and downstream signaling. These findings add depth to our understanding of the molecular life cycle and mechanism of action of GPR133 and provide critical insights that will inform therapeutic targeting of GPR133 in GBM.
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Overcoming therapy resistance in EGFR-mutant lung cancer. NATURE CANCER 2021; 2:377-391. [PMID: 35122001 DOI: 10.1038/s43018-021-00195-8] [Citation(s) in RCA: 187] [Impact Index Per Article: 62.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 03/11/2021] [Indexed: 02/01/2023]
Abstract
Tyrosine kinase inhibitors (TKIs) have dramatically changed the clinical prospects of patients with non-small cell lung cancer harboring epidermal growth factor receptor (EGFR)-activating mutations. Despite prolonged disease control and high tumor response rates, all patients eventually progress on EGFR TKI treatment. Here, we review the mechanisms of acquired EGFR TKI resistance, the methods for monitoring its appearance, as well as current and future efforts to define treatment strategies to overcome resistance.
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Salami SS, Tosoian JJ, Nallandhighal S, Jones TA, Brockman S, Elkhoury FF, Bazzi S, Plouffe KR, Siddiqui J, Liu CJ, Kunju LP, Morgan TM, Natarajan S, Boonstra PS, Sumida L, Tomlins SA, Udager AM, Sisk AE, Marks LS, Palapattu GS. Serial Molecular Profiling of Low-grade Prostate Cancer to Assess Tumor Upgrading: A Longitudinal Cohort Study. Eur Urol 2021; 79:456-465. [PMID: 32631746 PMCID: PMC7779657 DOI: 10.1016/j.eururo.2020.06.041] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 06/17/2020] [Indexed: 11/26/2022]
Abstract
BACKGROUND The potential for low-grade (grade group 1 [GG1]) prostate cancer (PCa) to progress to high-grade disease remains unclear. OBJECTIVE To interrogate the molecular and biological features of low-grade PCa serially over time. DESIGN, SETTING, AND PARTICIPANTS Nested longitudinal cohort study in an academic active surveillance (AS) program. Men were on AS for GG1 PCa from 2012 to 2017. INTERVENTION Electronic tracking and resampling of PCa using magnetic resonance imaging/ultrasound fusion biopsy. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS ERG immunohistochemistry (IHC) and targeted DNA/RNA next-generation sequencing were performed on initial and repeat biopsies. Tumor clonality was assessed. Molecular data were compared between men who upgraded and those who did not upgrade to GG ≥ 2 cancer. RESULTS AND LIMITATIONS Sixty-six men with median age 64 yr (interquartile range [IQR], 59-69) and prostate-specific antigen 4.9 ng/mL (IQR, 3.3-6.4) underwent repeat sampling of a tracked tumor focus (median interval, 11 mo; IQR, 6-13). IHC-based ERG fusion status was concordant at initial and repeat biopsies in 63 men (95% vs expected 50%, p < 0.001), and RNAseq-based fusion and isoform expression were concordant in nine of 13 (69%) ERG+ patients, supporting focal resampling. Among 15 men who upgraded with complete data at both time points, integrated DNA/RNAseq analysis provided evidence of shared clonality in at least five cases. Such cases could reflect initial undersampling, but also support the possibility of clonal temporal progression of low-grade cancer. Our assessment was limited by sample size and use of targeted sequencing. CONCLUSIONS Repeat molecular assessment of low-grade tumors suggests that clonal progression could be one mechanism of upgrading. These data underscore the importance of serial tumor assessment in men pursuing AS of low-grade PCa. PATIENT SUMMARY We performed targeted rebiopsy and molecular testing of low-grade tumors on active surveillance. Our findings highlight the importance of periodic biopsy as a component of monitoring for cancer upgrading during surveillance.
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Affiliation(s)
- Simpa S Salami
- Department of Urology, Michigan Medicine, Ann Arbor, MI, USA; University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA; Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI, USA.
| | - Jeffrey J Tosoian
- Department of Urology, Michigan Medicine, Ann Arbor, MI, USA; University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA; Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI, USA
| | | | - Tonye A Jones
- Department of Urology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Scott Brockman
- Department of Urology, Michigan Medicine, Ann Arbor, MI, USA
| | - Fuad F Elkhoury
- Department of Urology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Selena Bazzi
- Department of Urology, Michigan Medicine, Ann Arbor, MI, USA
| | - Komal R Plouffe
- Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA
| | - Javed Siddiqui
- Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI, USA; Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA
| | - Chia-Jen Liu
- Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI, USA; Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA
| | - Lakshmi P Kunju
- Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA
| | - Todd M Morgan
- Department of Urology, Michigan Medicine, Ann Arbor, MI, USA; University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA
| | - Shyam Natarajan
- Department of Urology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Philip S Boonstra
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Lauren Sumida
- Department of Pathology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Scott A Tomlins
- Department of Urology, Michigan Medicine, Ann Arbor, MI, USA; University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA; Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI, USA; Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA
| | - Aaron M Udager
- University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA; Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, MI, USA; Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA
| | - Anthony E Sisk
- Department of Pathology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Leonard S Marks
- Department of Urology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Ganesh S Palapattu
- Department of Urology, Michigan Medicine, Ann Arbor, MI, USA; University of Michigan Rogel Cancer Center, Ann Arbor, MI, USA; Department of Urology, Medical University of Vienna, Vienna, Austria
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Huang CC, Tsai YF, Liu CY, Chao TC, Lien PJ, Lin YS, Feng CJ, Chiu JH, Hsu CY, Tseng LM. Comprehensive molecular profiling of Taiwanese breast cancers revealed potential therapeutic targets: prevalence of actionable mutations among 380 targeted sequencing analyses. BMC Cancer 2021; 21:199. [PMID: 33632156 PMCID: PMC7908797 DOI: 10.1186/s12885-021-07931-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 02/18/2021] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Breast cancer is one of the leading causes of cancer-related deaths in women, and there is a demand in developing an Asian-based genetic profiling database for breast cancer in improving the treatment response. This study aimed to determine molecular alternations and identify potential therapeutic targets by analyzing the genetic profiling from a cohort of Taiwanese breast cancers using a commercialized next-generation sequencing (NGS) targeted panel. METHODS The study population comprised a broad spectrum of breast cancer patients in Taiwan, including Group 1: planned to receive first-line surgery and followed by adjuvant therapy, or early relapse within three years, Group 2: planned to receive first-line neoadjuvant therapy and followed by surgery, and Group 3: de novo stage IV, or stage IV with recurrence beyond three years. Molecular profiles were determined using Thermo Fisher™ Oncomine™ Comprehensive Assay version 3 (TMO comprehensive assay) from Formalin-Fixed Paraffin-Embedded (FFPE) tissues. Level of actionability was evaluated with the ESMO Scale of clinical actionability of molecular targets (ESCAT). RESULTS A total of 380 TMO comprehensive assays were conducted on 372 patients, and we presented targeted sequencing analyses of Tier I: alteration-drug match associated with improved outcome in clinical trials including ERBB2 amplification, BRCA1/2 germline mutation, PIK3CA mutation, and NTRK translocation, and Tier II: antitumor activity associated with the matched alteration-drug but lack of prospective outcome data including PTEN loss, ESR1 mutation, AKT1 mutation, and ERBB2 mutation, and Tier III: matched drug-alteration that led to clinical benefit in another tumor type including MDM2 amplification, and ERBB3 mutation. Among them, 249 (66%) showed at least one actionable alternation based on the ESCAT criteria. The most frequent impacted genes (all variants combined within each sample) were PIK3CA (38%), followed by ERBB2 (23%), ESR1 (10%), AKT1 (6%), and BRCA2 (5%), and the remaining rare variants (less than 5% of assayed cohort) were BRCA1 (3%), MDM2 (2.2%), and ERBB3 (1.1%). CONCLUSION Targeted sequencing of actionable genes is believed to provide clinical applicability and substantial benefits for Taiwanese breast cancer patients. A valid scale of clinical actionability should be adopted for precision medicine practice under multidisciplinary molecular tumor board.
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Affiliation(s)
- Chi-Cheng Huang
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei City, Taiwan
- Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
- Department of Public Health, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Yi-Fang Tsai
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei City, Taiwan
- Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
- Faculty of Medicine, College of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Chun-Yu Liu
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei City, Taiwan
- Faculty of Medicine, College of Medicine, National Yang-Ming University, Taipei, Taiwan
- Division of Transfusion Medicine, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Ta-Chung Chao
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei City, Taiwan
- Faculty of Medicine, College of Medicine, National Yang-Ming University, Taipei, Taiwan
- Division of Chemotherapy, Department of Oncology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Pei-Ju Lien
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei City, Taiwan
- Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Yen-Shu Lin
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei City, Taiwan
- Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chin-Jung Feng
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei City, Taiwan
| | - Jen-Hwey Chiu
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei City, Taiwan
- Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
- Institute of Traditional Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Chih-Yi Hsu
- Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
- School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Ling-Ming Tseng
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei City, Taiwan.
- Division of General Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan.
- Faculty of Medicine, College of Medicine, National Yang-Ming University, Taipei, Taiwan.
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Park K, Tran H, Eng KW, Ramazanoglu S, Marrero Rolon RM, Scognamiglio T, Borczuk A, Mosquera JM, Pan Q, Sboner A, Rubin MA, Elemento O, Rennert H, Fernandes H, Song W. Performance Characteristics of a Targeted Sequencing Platform for Simultaneous Detection of Single Nucleotide Variants, Insertions/Deletions, Copy Number Alterations, and Gene Fusions in Cancer Genome. Arch Pathol Lab Med 2021; 144:1535-1546. [PMID: 32045275 DOI: 10.5858/arpa.2019-0162-oa] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2020] [Indexed: 11/06/2022]
Abstract
CONTEXT.— An increasing number of molecular laboratories are implementing next-generation sequencing platforms to identify clinically actionable and relevant genomic alterations for precision oncology. OBJECTIVE.— To describe the validation studies as per New York State-Department of Health (NYS-DOH) guidelines for the Oncomine Comprehensive Panel v2, which was originally tailored to the National Cancer Institute Molecular Analysis for Therapy Choice (NCI-MATCH) trial. DESIGN.— Accuracy, precision, and reproducibility were investigated by using 130 DNA and 18 RNA samples from cytology cell blocks; formalin-fixed, paraffin-embedded tissues; and frozen samples. Analytic sensitivity and specificity were tested by using ATCC and HapMap cell lines. RESULTS.— High accuracy and precision/reproducibility were observed for single nucleotide variants and insertion/deletions. We also share our experience in the detection of gene fusions and copy number alterations from an amplicon-based sequencing platform. After sequencing analysis, variant annotation and report generation were performed by using the institutional knowledgebase. CONCLUSIONS.— This study serves as an example for validating a comprehensive targeted next-generation sequencing assay with both DNASeq and RNASeq components for NYS-DOH.
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Affiliation(s)
- Kyung Park
- From the Department of Pathology and Laboratory Medicine (Park, Marrero Rolon, Scognamiglio, Borczuk, Mosquera, Pan, Rubin, Rennert, Fernandes, Song), Weill Cornell Medicine, New York, New York
| | - Hung Tran
- Englander Institute for Precision Medicine (Tran, Eng, Ramazanoglu, Mosquera, Pan, Sboner, Rubin, Elemento, Song), Weill Cornell Medicine-New York Presbyterian Hospital, New York, New York
| | - Kenneth W Eng
- Institute for Computational Biomedicine (Eng, Ramazanoglu, Sboner, Elemento), Weill Cornell Medicine, New York, New York.,Englander Institute for Precision Medicine (Tran, Eng, Ramazanoglu, Mosquera, Pan, Sboner, Rubin, Elemento, Song), Weill Cornell Medicine-New York Presbyterian Hospital, New York, New York
| | - Sinan Ramazanoglu
- Institute for Computational Biomedicine (Eng, Ramazanoglu, Sboner, Elemento), Weill Cornell Medicine, New York, New York.,Englander Institute for Precision Medicine (Tran, Eng, Ramazanoglu, Mosquera, Pan, Sboner, Rubin, Elemento, Song), Weill Cornell Medicine-New York Presbyterian Hospital, New York, New York
| | - Rebecca M Marrero Rolon
- From the Department of Pathology and Laboratory Medicine (Park, Marrero Rolon, Scognamiglio, Borczuk, Mosquera, Pan, Rubin, Rennert, Fernandes, Song), Weill Cornell Medicine, New York, New York
| | - Theresa Scognamiglio
- From the Department of Pathology and Laboratory Medicine (Park, Marrero Rolon, Scognamiglio, Borczuk, Mosquera, Pan, Rubin, Rennert, Fernandes, Song), Weill Cornell Medicine, New York, New York
| | - Alain Borczuk
- From the Department of Pathology and Laboratory Medicine (Park, Marrero Rolon, Scognamiglio, Borczuk, Mosquera, Pan, Rubin, Rennert, Fernandes, Song), Weill Cornell Medicine, New York, New York
| | - Juan Miguel Mosquera
- From the Department of Pathology and Laboratory Medicine (Park, Marrero Rolon, Scognamiglio, Borczuk, Mosquera, Pan, Rubin, Rennert, Fernandes, Song), Weill Cornell Medicine, New York, New York.,Englander Institute for Precision Medicine (Tran, Eng, Ramazanoglu, Mosquera, Pan, Sboner, Rubin, Elemento, Song), Weill Cornell Medicine-New York Presbyterian Hospital, New York, New York
| | - Qiulu Pan
- From the Department of Pathology and Laboratory Medicine (Park, Marrero Rolon, Scognamiglio, Borczuk, Mosquera, Pan, Rubin, Rennert, Fernandes, Song), Weill Cornell Medicine, New York, New York.,Englander Institute for Precision Medicine (Tran, Eng, Ramazanoglu, Mosquera, Pan, Sboner, Rubin, Elemento, Song), Weill Cornell Medicine-New York Presbyterian Hospital, New York, New York
| | - Andrea Sboner
- Institute for Computational Biomedicine (Eng, Ramazanoglu, Sboner, Elemento), Weill Cornell Medicine, New York, New York.,Englander Institute for Precision Medicine (Tran, Eng, Ramazanoglu, Mosquera, Pan, Sboner, Rubin, Elemento, Song), Weill Cornell Medicine-New York Presbyterian Hospital, New York, New York
| | - Mark A Rubin
- From the Department of Pathology and Laboratory Medicine (Park, Marrero Rolon, Scognamiglio, Borczuk, Mosquera, Pan, Rubin, Rennert, Fernandes, Song), Weill Cornell Medicine, New York, New York.,Englander Institute for Precision Medicine (Tran, Eng, Ramazanoglu, Mosquera, Pan, Sboner, Rubin, Elemento, Song), Weill Cornell Medicine-New York Presbyterian Hospital, New York, New York
| | - Olivier Elemento
- Institute for Computational Biomedicine (Eng, Ramazanoglu, Sboner, Elemento), Weill Cornell Medicine, New York, New York.,Englander Institute for Precision Medicine (Tran, Eng, Ramazanoglu, Mosquera, Pan, Sboner, Rubin, Elemento, Song), Weill Cornell Medicine-New York Presbyterian Hospital, New York, New York
| | - Hanna Rennert
- From the Department of Pathology and Laboratory Medicine (Park, Marrero Rolon, Scognamiglio, Borczuk, Mosquera, Pan, Rubin, Rennert, Fernandes, Song), Weill Cornell Medicine, New York, New York
| | - Helen Fernandes
- From the Department of Pathology and Laboratory Medicine (Park, Marrero Rolon, Scognamiglio, Borczuk, Mosquera, Pan, Rubin, Rennert, Fernandes, Song), Weill Cornell Medicine, New York, New York
| | - Wei Song
- From the Department of Pathology and Laboratory Medicine (Park, Marrero Rolon, Scognamiglio, Borczuk, Mosquera, Pan, Rubin, Rennert, Fernandes, Song), Weill Cornell Medicine, New York, New York.,Englander Institute for Precision Medicine (Tran, Eng, Ramazanoglu, Mosquera, Pan, Sboner, Rubin, Elemento, Song), Weill Cornell Medicine-New York Presbyterian Hospital, New York, New York
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Bahcivan A, Gamsizkan M, Kantarcioglu Coskun S, Cangur S, Yuksel A, Ceyhan A, Onal B. KRAS, BRAF, PIK3CA mutation frequency of radical prostatectomy samples and review of the literature. Aging Male 2020; 23:1627-1641. [PMID: 33878842 DOI: 10.1080/13685538.2021.1901274] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVE The molecular basis of prostate cancer is highly heterogeneous. Our study aimed to perform the mutation analysis of KRAS, BRAF, PIK3CA, and immunohistochemical (IHC) evaluation of EGFR, HER2, p16, and PTEN to demonstrate new areas for targeted therapies. METHODS A total of 24 prostatectomy samples diagnosed with adenocarcinoma were analyzed by microarray hybridization. Also, these samples were IHC stained for EGFR, HER2, P16, and PTEN. The cases were divided into two groups based on low and high Gleason scores. All findings were compared with the clinicopathological parameters of the patients. RESULTS While KRAS mutation was in 3/24 (12.5%) of our cases, BRAF and PIK3CA mutations were not detected. There was no significant difference between the groups in terms of KRAS mutation frequency. HER2 was immunohistochemically negative in all samples. There was no correlation between EGFR, P16 immunopositivity, and clinicopathological features. CONCLUSION KRAS mutation frequency is similar to those in Asian populations. BRAF and PIK3CA mutation frequencies have been reported in the literature in the range of 0-15% and 0-10.4%, respectively, consistent with our study findings. HER2 immunoexpression is a controversial issue in the literature. EGFR and p16 expressions may not correlate with the stage.
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Affiliation(s)
- Atike Bahcivan
- Department of Pathology, Duzce University, Duzce, Turkey
| | | | | | - Sengul Cangur
- Department of Biostatistics and Medical Informatics, Duzce University, Duzce, Turkey
| | | | - Aysegul Ceyhan
- Department of Pathology, Duzce University, Duzce, Turkey
| | - Binnur Onal
- Department of Pathology, Duzce University, Duzce, Turkey
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Yao H, Liang Q, Qian X, Wang J, Sham PC, Li MJ. Methods and resources to access mutation-dependent effects on cancer drug treatment. Brief Bioinform 2020; 21:1886-1903. [PMID: 31750520 DOI: 10.1093/bib/bbz109] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 07/31/2019] [Accepted: 08/01/2019] [Indexed: 12/13/2022] Open
Abstract
In clinical cancer treatment, genomic alterations would often affect the response of patients to anticancer drugs. Studies have shown that molecular features of tumors could be biomarkers predictive of sensitivity or resistance to anticancer agents, but the identification of actionable mutations are often constrained by the incomplete understanding of cancer genomes. Recent progresses of next-generation sequencing technology greatly facilitate the extensive molecular characterization of tumors and promote precision medicine in cancers. More and more clinical studies, cancer cell lines studies, CRISPR screening studies as well as patient-derived model studies were performed to identify potential actionable mutations predictive of drug response, which provide rich resources of molecularly and pharmacologically profiled cancer samples at different levels. Such abundance of data also enables the development of various computational models and algorithms to solve the problem of drug sensitivity prediction, biomarker identification and in silico drug prioritization by the integration of multiomics data. Here, we review the recent development of methods and resources that identifies mutation-dependent effects for cancer treatment in clinical studies, functional genomics studies and computational studies and discuss the remaining gaps and future directions in this area.
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Affiliation(s)
- Hongcheng Yao
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Qian Liang
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xinyi Qian
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Junwen Wang
- Department of Health Sciences Research & Center for Individualized Medicine, Mayo Clinic, Scottsdale, USA
| | - Pak Chung Sham
- Center for Genomic Sciences, The University of Hong Kong, Hong Kong SAR, China.,Departments of Psychiatry, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Mulin Jun Li
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.,Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
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