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1.
Cell ; 187(7): 1617-1635, 2024 Mar 28.
Article in English | MEDLINE | ID: mdl-38552610

ABSTRACT

The integration of cancer biomarkers into oncology has revolutionized cancer treatment, yielding remarkable advancements in cancer therapeutics and the prognosis of cancer patients. The development of personalized medicine represents a turning point and a new paradigm in cancer management, as biomarkers enable oncologists to tailor treatments based on the unique molecular profile of each patient's tumor. In this review, we discuss the scientific milestones of cancer biomarkers and explore future possibilities to improve the management of patients with solid tumors. This progress is primarily attributed to the biological characterization of cancers, advancements in testing methodologies, elucidation of the immune microenvironment, and the ability to profile circulating tumor fractions. Integrating these insights promises to continually advance the precision oncology field, fostering better patient outcomes.


Subject(s)
Biomarkers, Tumor , Neoplasms , Precision Medicine , Humans , Medical Oncology/methods , Neoplasms/therapy , Neoplasms/drug therapy , Precision Medicine/methods , Tumor Microenvironment
2.
Cancer ; 2024 Sep 30.
Article in English | MEDLINE | ID: mdl-39347608

ABSTRACT

Comprehensive biomarker testing for patients with non-small cell lung cancer is critical for selecting appropriate targeted therapy or immunotherapy. Ensuring timely ordering, processing, and reporting is key to optimizing patient outcomes. However, various factors can prevent or delay patients from being offered the option of treatment selection based on comprehensive biomarker testing. These factors include problems with access to testing, tissue adequacy, turnaround time, and health insurance coverage and billing practices. Turnaround time depends on several logistical and tissue handling factors, which involve institutional policies, processes, resources, testing methodology, and testing algorithms that vary across different practices. In this article, the authors identify key factors that prolong biomarker testing turnaround time, propose strategies to reduce it, and present a process map to aid physicians and key organizational stakeholders in improving testing efficiency.

3.
Oncologist ; 29(7): 638-e952, 2024 Jul 05.
Article in English | MEDLINE | ID: mdl-38815151

ABSTRACT

BACKGROUND: The National Cancer Institute-Children's Oncology Group Pediatric Molecular Analysis for Therapy Choice (MATCH) precision oncology platform trial enrolled children aged 1-21 years with treatment-refractory solid tumors and predefined actionable genetic alterations. Patients with tumors harboring alterations in DNA damage repair (DDR) genes were assigned to receive olaparib. METHODS: Tumor and blood samples were submitted for centralized molecular testing. Tumor and germline sequencing were conducted in parallel. Olaparib was given twice daily for 28-day cycles starting at a dose 30% lower than the adult recommended phase 2 dose (RP2D). The primary endpoint was the objective response. RESULTS: Eighteen patients matched (1.5% of those screened) based on the presence of a deleterious gene alteration in BRCA1/2, RAD51C/D, or ATM detected by tumor sequencing without germline subtraction or analysis of loss of heterozygosity (LOH). Eleven (61%) harbored a germline mutation, with only one exhibiting LOH. Six patients enrolled and received the olaparib starting dose of 135 mg/m2/dose. Two participants were fully evaluable; 4 were inevaluable because <85% of the prescribed dose was administered during cycle 1. There were no dose-limiting toxicities or responses. Minimal hematologic toxicity was observed. CONCLUSION: Most DDR gene alterations detected in Pediatric MATCH were germline, monoallelic, and unlikely to confer homologous recombination deficiency predicting sensitivity to olaparib monotherapy. The study closed due to poor accrual. CLINICALTRIALS.GOV IDENTIFIER: NCT03233204. IRB approved: initial July 24, 2017.


Subject(s)
DNA Repair , Neoplasms , Phthalazines , Piperazines , Adolescent , Adult , Child , Child, Preschool , Female , Humans , Infant , Male , Young Adult , Ataxia Telangiectasia Mutated Proteins/genetics , BRCA1 Protein/genetics , BRCA2 Protein/genetics , DNA Damage/drug effects , DNA Repair/drug effects , DNA Repair/genetics , DNA-Binding Proteins/genetics , Germ-Line Mutation , Neoplasms/drug therapy , Neoplasms/genetics , Phthalazines/therapeutic use , Phthalazines/adverse effects , Phthalazines/administration & dosage , Piperazines/therapeutic use , Piperazines/administration & dosage , Piperazines/adverse effects , Poly(ADP-ribose) Polymerase Inhibitors/therapeutic use , Poly(ADP-ribose) Polymerase Inhibitors/adverse effects
4.
Oncologist ; 29(8): 723-e1093, 2024 Aug 05.
Article in English | MEDLINE | ID: mdl-38873934

ABSTRACT

BACKGROUND: This is a phase II subprotocol of the NCI-COG Pediatric MATCH study evaluating vemurafenib, a selective oral inhibitor of BRAF V600 mutated kinase, in patients with relapsed or refractory solid tumors harboring BRAF V600 mutations. METHODS: Patients received vemurafenib at 550 mg/m2 (maximum 960 mg/dose) orally twice daily for 28-day cycles until progression or intolerable toxicity. The primary aim was to determine the objective response rate and secondary objectives included estimating progression-free survival and assessing the tolerability of vemurafenib. RESULTS: Twenty-two patients matched to the subprotocol and 4 patients (18%) enrolled. Primary reasons for non-enrollment were ineligibility due to exclusions of low-grade glioma (n = 7) and prior BRAF inhibitor therapy (n = 7). Enrolled diagnoses were one each of histiocytosis, ameloblastoma, Ewing sarcoma, and high-grade glioma, all with BRAF V600E mutations. Treatment was overall tolerable with mostly expected grade 1/2 adverse events (AE). Grade 3 or 4 AE on treatment were acute kidney injury, hyperglycemia, and maculopapular rash. One patient came off therapy due to AE. One patient (glioma) had an objective partial response and remained on protocol therapy for 15 cycles. CONCLUSION: There was a low accrual rate on this MATCH subprotocol, with only 18% of those who matched with BRAFV600 mutations enrolling, resulting in early termination, and limiting study results (ClinicalTrials.gov Identifier: NCT03220035).


Subject(s)
Mutation , Proto-Oncogene Proteins B-raf , Vemurafenib , Humans , Proto-Oncogene Proteins B-raf/genetics , Vemurafenib/therapeutic use , Vemurafenib/administration & dosage , Male , Female , Child , Adolescent , Young Adult , Adult , Child, Preschool , Neoplasms/drug therapy , Neoplasms/genetics
5.
Histopathology ; 84(3): 429-439, 2024 Feb.
Article in English | MEDLINE | ID: mdl-37957137

ABSTRACT

Many patients with non-small cell lung cancer do not receive guideline-recommended, biomarker-directed therapy, despite the potential for improved clinical outcomes. Access to timely, accurate, and comprehensive molecular profiling, including targetable protein overexpression, is essential to allow fully informed treatment decisions to be taken. In turn, this requires optimal tissue management to protect and maximize the use of this precious finite resource. Here, a group of leading thoracic pathologists recommend factors to consider for optimal tissue management. Starting from when lung cancer is first suspected, keeping predictive biomarker testing in the front of the mind should drive the development of practices and procedures that conserve tissue appropriately to support molecular characterization and treatment selection.


Subject(s)
Carcinoma, Non-Small-Cell Lung , Lung Neoplasms , Humans , Carcinoma, Non-Small-Cell Lung/therapy , Carcinoma, Non-Small-Cell Lung/drug therapy , Lung Neoplasms/therapy , Lung Neoplasms/drug therapy , Pathologists , Biomarkers, Tumor/metabolism , Molecular Targeted Therapy
6.
J Neurooncol ; 166(1): 39-49, 2024 Jan.
Article in English | MEDLINE | ID: mdl-38160230

ABSTRACT

PURPOSE: Genomic alterations are fundamental for molecular-guided therapy in patients with breast and lung cancer. However, the turn-around time of standard next-generation sequencing assays is a limiting factor in the timely delivery of genomic information for clinical decision-making. METHODS: In this study, we evaluated genomic alterations in 54 cerebrospinal fluid samples from 33 patients with metastatic lung cancer and metastatic breast cancer to the brain using the Oncomine Precision Assay on the Genexus sequencer. There were nine patients with samples collected at multiple time points. RESULTS: Cell-free total nucleic acids (cfTNA) were extracted from CSF (0.1-11.2 ng/µl). Median base coverage was 31,963× with cfDNA input ranging from 2 to 20 ng. Mutations were detected in 30/54 CSF samples. Nineteen (19/24) samples with no mutations detected had suboptimal DNA input (< 20 ng). The EGFR exon-19 deletion and PIK3CA mutations were detected in two patients with increasing mutant allele fraction over time, highlighting the potential of CSF-cfTNA analysis for monitoring patients. Moreover, the EGFR T790M mutation was detected in one patient with prior EGFR inhibitor treatment. Additionally, ESR1 D538G and ESR1::CCDC170 alterations, associated with endocrine therapy resistance, were detected in 2 mBC patients. The average TAT from cfTNA-to-results was < 24 h. CONCLUSION: In summary, our results indicate that CSF-cfTNA analysis with the Genexus-OPA can provide clinically relevant information in patients with brain metastases with short TAT.


Subject(s)
Cell-Free Nucleic Acids , Lung Neoplasms , Humans , Lung Neoplasms/pathology , Cell-Free Nucleic Acids/cerebrospinal fluid , Mutation , ErbB Receptors/genetics , Protein Kinase Inhibitors
7.
J Cutan Pathol ; 51(6): 407-414, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38444194

ABSTRACT

ALK-fused Spitz melanocytic neoplasms are a distinct subgroup of melanocytic lesions exhibiting unique histopathologic characteristics. These lesions often manifest as exophytic or polypoid tumors, characterized by fusiform-to-epithelioid melanocytes arranged in a nested, fascicular, or plexiform growth pattern. Several fusion partners of the ALK gene have been identified in spitzoid melanocytic neoplasms, with TPM3 and DCTN1 being the most prevalent. Less common fusion partners include NPM1, TPR, CLIP1, GTF3C2, EEF2, MYO5A, KANK1, and EHBP1. The MLPH gene, which encodes melanophilin (MLPH), playing a crucial role in regulating skin pigmentation by acting as a linker between RAB27A and myosin Va during melanosome transport, has also recently been recognized as a rare fusion partner of ALK in Spitz melanocytic neoplasms. Currently, there exists a sparse documentation within English literature, illustrating a limited number of cases featuring MLPH::ALK fusion in Spitz melanocytic neoplasms. In this report, we present two additional cases, including a previously unreported instance of Spitz melanoma, contributing to the expanding knowledge on ALK-fused Spitz melanocytic neoplasms. In addition, we provide a comprehensive review of the clinical, histopathologic, and molecular features observed in documented cases with this novel fusion.


Subject(s)
Anaplastic Lymphoma Kinase , Melanoma , Nevus, Epithelioid and Spindle Cell , Skin Neoplasms , Adult , Female , Humans , Adaptor Proteins, Signal Transducing , Anaplastic Lymphoma Kinase/genetics , Melanoma/genetics , Melanoma/pathology , Nevus, Epithelioid and Spindle Cell/genetics , Nevus, Epithelioid and Spindle Cell/pathology , Oncogene Proteins, Fusion/genetics , Skin Neoplasms/genetics , Skin Neoplasms/pathology
8.
Cytopathology ; 33(2): 216-221, 2022 03.
Article in English | MEDLINE | ID: mdl-34816516

ABSTRACT

INTRODUCTION: The diagnosis of solid pseudopapillary neoplasm (SPN) on fine needle aspiration specimens can be challenging because of morphological overlap with other pancreatic neoplasms, including pancreatic neuroendocrine tumour (PanNET). SRY-related high-mobility group box 11 (SOX11) is a recently described sensitive and specific marker for SPN diagnosis. However, SOX11 immunocytochemistry on cytological smears has not been reported. We evaluated the utility of SOX11 for diagnosis of SPN on cytological preparations. METHODS: SOX11 immunocytochemistry was performed on Papanicolaou-stained smears and/or corresponding cell blocks from aspirates of 7 SPN and 10 PanNET cases identified between 2005 and 2020. Findings were compared with those for beta-catenin, a frequently used diagnostic marker for SPN. RESULTS: Six smears and 6 cell blocks from SPN cases and 8 smears and 10 cell blocks from PanNET cases were available for immunostaining. For SPN, nuclear staining for SOX11 was seen in 6 of 6 (100%) smears and 5 of 6 (83%) cell blocks, with equivocal staining in 1 cell block. In contrast, 7 of 8 (88%) smears and 9 of 10 (90%) cell blocks were negative for SOX11 for PanNet, with equivocal staining seen in 1 case. Beta-catenin immunocytochemistry showed nuclear staining in 6 of 7 (86%) SPN cases and no staining in all 10 (100%) PanNET cases. CONCLUSIONS: SOX11 detected by immunocytochemistry can serve as a useful diagnostic marker for SPN, in addition to beta catenin, and can be performed on cytological smears in cases without a cell block preparation.


Subject(s)
Carcinoma, Papillary , Pancreatic Neoplasms , Biopsy, Fine-Needle , Carcinoma, Papillary/diagnosis , Carcinoma, Papillary/pathology , Humans , Immunohistochemistry , Pancreas/pathology , Pancreatic Neoplasms/diagnosis , Pancreatic Neoplasms/pathology , SOXC Transcription Factors/genetics
9.
Gut ; 70(1): 55-66, 2021 01.
Article in English | MEDLINE | ID: mdl-32345613

ABSTRACT

OBJECTIVE: Peritoneal carcinomatosis (PC; malignant ascites or implants) occurs in approximately 45% of advanced gastric adenocarcinoma (GAC) patients and associated with a poor survival. The molecular events leading to PC are unknown. The yes-associated protein 1 (YAP1) oncogene has emerged in many tumour types, but its clinical significance in PC is unclear. Here, we investigated the role of YAP1 in PC and its potential as a therapeutic target. METHODS: Patient-derived PC cells, patient-derived xenograft (PDX) and patient-derived orthotopic (PDO) models were used to study the function of YAP1 in vitro and in vivo. Immunofluorescence and immunohistochemical staining, RNA sequencing (RNA-Seq) and single-cell RNA-Seq (sc-RNA-Seq) were used to elucidate the expression of YAP1 and PC cell heterogeneity. LentiCRISPR/Cas9 knockout of YAP1 and a YAP1 inhibitor were used to dissect its role in PC metastases. RESULTS: YAP1 was highly upregulated in PC tumour cells, conferred cancer stem cell (CSC) properties and appeared to be a metastatic driver. Dual staining of YAP1/EpCAM and sc-RNA-Seq revealed that PC tumour cells were highly heterogeneous, YAP1high PC cells had CSC-like properties and easily formed PDX/PDO tumours but also formed PC in mice, while genetic knockout YAP1 significantly slowed tumour growth and eliminated PC in PDO model. Additionally, pharmacologic inhibition of YAP1 specifically reduced CSC-like properties and suppressed tumour growth in YAP1high PC cells especially in combination with cytotoxics in vivo PDX model. CONCLUSIONS: YAP1 is essential for PC that is attenuated by YAP1 inhibition. Our data provide a strong rationale to target YAP1 in clinic for GAC patients with PC.


Subject(s)
Adaptor Proteins, Signal Transducing/physiology , Adenocarcinoma/secondary , Peritoneal Neoplasms/secondary , Stomach Neoplasms/pathology , Animals , Cell Culture Techniques , Humans , Mice , Xenograft Model Antitumor Assays , YAP-Signaling Proteins
10.
Gut ; 70(11): 2055-2065, 2021 11.
Article in English | MEDLINE | ID: mdl-33334899

ABSTRACT

OBJECTIVE: Prognosis of patients with advanced oesophagogastric adenocarcinoma (mEGAC) is poor and molecular determinants of shorter or longer overall survivors are lacking. Our objective was to identify molecular features and develop a prognostic model by profiling the genomic features of patients with mEGAC with widely varying outcomes. DESIGN: We profiled 40 untreated mEGACs (20 shorter survivors <13 months and 20 longer survivors >36 months) with whole-exome sequencing (WES) and RNA sequencing and performed an integrated analysis of exome, transcriptome, immune profile and pathological phenotypes to identify the molecular determinants, developing an integrated model for prognosis and comparison with The Cancer Genome Atlas (TCGA) cohorts. RESULTS: KMT2C alterations were exclusively observed in shorter survivors together with high level of intratumour heterogeneity and complex clonal architectures, whereas the APOBEC mutational signatures were significantly enriched in longer survivors. Notably, the loss of heterozygosity in chromosome 4 (Chr4) was associated with shorter survival and 'cold' immune phenotype characterised by decreased B, CD8, natural killer cells and interferon-gamma responses. Unsupervised transcriptomic clustering revealed a shorter survivor subtype with distinct expression features (eg, upregulated druggable targets JAK2, MAP3K13 and MECOM). An integrated model was then built based on clinical variables and the identified molecular determinants, which significantly segregated shorter and longer survivors. All the above features and the integrated model have been validated independently in multiple TCGA cohorts. CONCLUSION: This study discovered novel molecular features prognosticating overall survival in patients with mEGAC and identified potential novel targets in shorter survivors.


Subject(s)
Adenocarcinoma/genetics , Esophageal Neoplasms/genetics , Genetic Profile , Stomach Neoplasms/genetics , DNA Copy Number Variations , Female , Humans , Male , Prognosis , Risk Assessment , Sequence Analysis, RNA , Exome Sequencing
11.
Ann Surg Oncol ; 28(1): 258-264, 2021 Jan.
Article in English | MEDLINE | ID: mdl-32556731

ABSTRACT

BACKGROUND: Current national guidelines do not include hyperthermic intraperitoneal chemoperfusion (HIPEC) as treatment for gastric cancer, and there are no completed clinical trials of cytoreduction, gastrectomy, and HIPEC from the US. METHODS: Patients with gastric adenocarcinoma and positive peritoneal cytology or carcinomatosis who had completed systemic chemotherapy and laparoscopic HIPEC underwent cytoreduction, gastrectomy, and HIPEC with 30 mg mitomycin C and 200 mg cisplatin. The primary endpoint was overall survival (OS), with a secondary endpoint of postoperative complications (NCT02891447). RESULTS: We enrolled 20 patients from September 2016 to March 2019. Six patients had positive cytology only and 14 had carcinomatosis. All patients were treated with systemic chemotherapy with a median of eight cycles (range 5-11 cycles) and at least one laparoscopic HIPEC. The median peritoneal carcinomatosis index at cytoreduction/gastrectomy/HIPEC was 2 (range 0-13). After surgery, the 90-day morbidity and mortality rates were 70% and 0%, respectively. Median length of hospital stay was 13 days (range 7-23 days); median follow-up was 33.5 months; median OS from the date of diagnosis of metastatic disease was 24.2 months; and median OS from the date of cytoreduction, gastrectomy, and HIPEC was 16.1 months. 1-, 2-, and 3-year OS rates from the diagnosis of metastatic disease were 90%, 50%, and 28%, respectively. CONCLUSIONS: Survival rates for patients with gastric adenocarcinoma and peritoneal disease treated with cytoreduction, gastrectomy, and HIPEC are encouraging; our early results are similar to those of recent prospective registry studies. Multi-institutional and cooperative group trials should be supported to confirm survival and safety outcomes.


Subject(s)
Hyperthermia, Induced , Peritoneal Neoplasms , Stomach Neoplasms , Antineoplastic Combined Chemotherapy Protocols/therapeutic use , Chemotherapy, Cancer, Regional Perfusion , Combined Modality Therapy , Cytoreduction Surgical Procedures , Gastrectomy , Humans , Perfusion , Peritoneal Neoplasms/therapy , Stomach Neoplasms/drug therapy , Survival Rate
12.
Gastrointest Endosc ; 93(5): 1142-1151.e2, 2021 05.
Article in English | MEDLINE | ID: mdl-33058885

ABSTRACT

BACKGROUND AND AIMS: EUS-guided FNA is recommended as a first-line procedure for the histopathologic diagnosis of pancreatic cancer. Molecular analysis of EUS-FNA samples might be used as an auxiliary tool to strengthen the diagnosis. The current study aimed to evaluate the diagnostic performances of K-ras testing using droplet digital polymerase chain reaction (ddPCR) and a novel single-nucleotide variant (SNV) assay performed on pancreatic EUS-FNA samples. METHODS: EUS-FNA specimens from 31 patients with pancreatic masses (22 pancreatic ductal adenocarcinomas, 7 chronic pancreatitis, and 2 pancreatic neuroendocrine tumors) were included in the study. K-ras testing was initially performed by ddPCR. In addition, mutational status was evaluated using an SNV assay by NanoString technology, using digital enumeration of unique barcoded probes to detect 97 SNVs from 24 genes of clinical significance. RESULTS: The overall specificity and sensitivity of cytologic examination were 100% and 63%, respectively. K-ras mutation testing was performed using ddPCR, and the sensitivity increased to 87% with specificity 90%. The SNV assay detected at least 1 variant in 90% of pancreatic ductal adenocarcinoma samples; the test was able to detect 2 K-ras codon 61 mutations in 2 cases of pancreatic ductal adenocarcinoma, which were missed by ddPCR. The overall diagnostic accuracy of the cytologic examination alone was 74%, and it increased to 91% when the results of both molecular tests were considered for the cases with negative and inconclusive results. CONCLUSIONS: The current study illustrated that integration of K-ras analysis with cytologic evaluation, especially in inconclusive cases, can enhance the diagnostic accuracy of EUS-FNA for pancreatic lesions.


Subject(s)
Carcinoma, Pancreatic Ductal , Pancreatic Neoplasms , Carcinoma, Pancreatic Ductal/diagnosis , Carcinoma, Pancreatic Ductal/genetics , Endoscopic Ultrasound-Guided Fine Needle Aspiration , Endosonography , Humans , Nucleotides , Pancreatic Neoplasms/diagnosis , Pancreatic Neoplasms/genetics , Polymerase Chain Reaction , Sensitivity and Specificity
13.
Semin Diagn Pathol ; 38(5): 109-115, 2021 Sep.
Article in English | MEDLINE | ID: mdl-34119361

ABSTRACT

Cytopathology has emerged as a promising platform in precision oncology especially after the revolutionary change in our understanding of the concept of lung cancer etiopathogenesis. With increasing use of minimally invasive techniques for sample acquisition, it becomes almost mandatory to utilize precious cytology samples maximally and judiciously by appropriate triaging of the specimen and timely action of the cytopathology team. Existing patient management protocols require accurate morphologic and molecular diagnosis of the lung cancer specimens which needs knowledge about evolving techniques related to specimen procurement, updates of genomic variants of lung cancer and recently developed molecular testing platforms and algorithms which are capable enough to use even miniscule amount of diagnostic material. This review provides a brief knowledge about advances in cytology of lung cancer which are helpful for developing correct clinical management strategies.


Subject(s)
Lung Neoplasms , Precision Medicine , Cytodiagnosis , Humans , Lung Neoplasms/diagnosis , Lung Neoplasms/genetics , Lung Neoplasms/pathology , Molecular Diagnostic Techniques
14.
Cytopathology ; 32(5): 604-610, 2021 Sep.
Article in English | MEDLINE | ID: mdl-33792972

ABSTRACT

OBJECTIVES: The practice of cytopathology has evolved over the past decade with a growing need for doing more with less tissue. Changes in clinical practice guidelines and evolving needs in tissue acquisition for diagnosis and treatment have affected various areas of cytopathology in different ways. In this study, we evaluated the changing trends in cytopathological practice at our institution over the past decade. METHODS: We performed a retrospective review of our institutional database for cytopathology cases from calendar years 2009 (n = 28038) and 2019 (n = 31386) to evaluate the changing trends in practice. RESULTS: The overall number of exfoliative cases decreased 10% over the past decade, primarily due to a 64% decrease in gynaecological Pap testing. However, the volume of serous body cavity and cerebrospinal fluids increased 125% and 44%, respectively. The overall volume of fine needle aspiration (FNA) cases increased 38% from 2009 to 2019. The number of FNA cases increased across most body sites, driven primarily by a 180% increase in endobronchial ultrasound-guided transbronchial needle aspiration cases. In contrast, breast FNA volume decreased 43%. Ancillary studies increased substantially over the past decade, including immunostains (476%) and molecular testing (250%). CONCLUSIONS: The trends in our cytopathological practice showed an increased volume of cases, especially in non-gynaecological specimens. As expected, the number of FNA cases used for immunostains and molecular testing increased substantially, indicating an upward trend in ancillary studies in cytopathological practice.


Subject(s)
Cytological Techniques/methods , Endoscopic Ultrasound-Guided Fine Needle Aspiration/methods , Humans , Retrospective Studies , Tertiary Care Centers
15.
Gut ; 69(1): 18-31, 2020 01.
Article in English | MEDLINE | ID: mdl-31171626

ABSTRACT

OBJECTIVE: Peritoneal carcinomatosis (PC) occurs frequently in patients with gastric adenocarcinoma (GAC) and confers a poor prognosis. Multiplex profiling of primary GACs has been insightful but the underpinnings of PC's development/progression remain largely unknown. We characterised exome/transcriptome/immune landscapes of PC cells from patients with GAC aiming to identify novel therapeutic targets. DESIGN: We performed whole-exome sequencing (WES) and whole transcriptome sequencing (RNA-seq) on 44 PC specimens (43 patients with PC) including an integrative analysis of WES, RNA-seq, immune profile, clinical and pathological phenotypes to dissect the molecular pathogenesis, identifying actionable targets and/or biomarkers and comparison with TCGA primary GACs. RESULTS: We identified distinct alterations in PC versus primary GACs, such as more frequent CDH1 and TAF1 mutations, 6q loss and chr19 gain. Alterations associated with aggressive PC phenotypes emerged with increased mutations in TP53, CDH1, TAF1 and KMT2C, higher level of 'clock-like' mutational signature, increase in whole-genome doublings, chromosomal instability (particularly, copy number losses), reprogrammed microenvironment, enriched cell cycle pathways, MYC activation and impaired immune response. Integrated analysis identified two main molecular subtypes: 'mesenchymal-like' and 'epithelial-like' with discriminating response to chemotherapy (31% vs 71%). Patients with the less responsive 'mesenchymal-like' subtype had high expression of immune checkpoint T-Cell Immunoglobulin And Mucin Domain-Containing Protein 3 (TIM-3), its ligand galectin-9, V-domain Ig suppressor of T cell activation (VISTA) and transforming growth factor-ß as potential therapeutic immune targets. CONCLUSIONS: We have uncovered the unique mutational landscape, copy number alteration and gene expression profile of PC cells and defined PC molecular subtypes, which correlated with PC therapy resistance/response. Novel targets and immune checkpoint proteins have been identified with a potential to be translated into clinics.


Subject(s)
Adenocarcinoma/secondary , Peritoneal Neoplasms/secondary , Stomach Neoplasms/genetics , Adenocarcinoma/drug therapy , Adenocarcinoma/genetics , Adenocarcinoma/immunology , Adult , Aged , Aged, 80 and over , Antineoplastic Agents/therapeutic use , Chromosomal Instability , DNA Copy Number Variations/genetics , DNA, Neoplasm/genetics , Female , Gene Expression Profiling/methods , Humans , Male , Middle Aged , Molecular Targeted Therapy/methods , Mutation , Peritoneal Neoplasms/drug therapy , Peritoneal Neoplasms/genetics , Peritoneal Neoplasms/immunology , Ploidies , Stomach Neoplasms/drug therapy , Stomach Neoplasms/immunology , Exome Sequencing/methods
16.
Ann Surg Oncol ; 27(8): 2806-2811, 2020 Aug.
Article in English | MEDLINE | ID: mdl-31974712

ABSTRACT

BACKGROUND: The purpose of this phase I trial is to evaluate the safety and toxicity of laparoscopic hyperthermic intraperitoneal perfusion with chemotherapy (HIPEC), combining mitomycin, cisplatin, and paclitaxel for patients with gastric cancer metastatic to the peritoneum. PATIENTS AND METHODS: A Bayesian optimal interval design was used to prospectively identify the safety and tolerability of escalating doses of paclitaxel in combination with flat doses of mitomycin (30 mg) and cisplatin (200 mg) during laparoscopic HIPEC. The primary objective is to define the maximum tolerated dose. Secondary endpoints include surgical complications and overall survival (OS). RESULTS: A total of 27 patients were treated between 11/2017 and 11/2018. No dose-limiting toxicities were observed. Treatment-related grade 1-2 toxicities were leukopenia (11%), oral dysesthesia (4%), arthralgia (4%), and diarrhea (4%). Treatment-related grade 3-4 toxicities included leukopenia (4%) and neutropenia (4%). The maximum dose for paclitaxel was 60 mg/m2. Rates of Clavien-Dindo surgical complications were grade I 96% (all electrolyte deficiencies requiring replacement), II 4%, III 0%, IV 0%, and V 4%. The median follow-up time was 15 months. One- and 2-year OS rates from date of metastatic disease were 73.9% and 58.1%, respectively. CONCLUSIONS: Laparoscopic HIPEC with mitomycin, cisplatin, and paclitaxel may be safely used at intraperitoneal doses of 30 mg, 200 mg, and 60 mg/m2, respectively. Although electrolyte abnormalities were common, systemic toxicity was low. Survival rates were promising, supporting further research into intraperitoneal therapy for stage IV gastric cancer.


Subject(s)
Adenocarcinoma , Hyperthermia, Induced , Stomach Neoplasms , Adenocarcinoma/therapy , Antineoplastic Combined Chemotherapy Protocols/therapeutic use , Bayes Theorem , Cisplatin/therapeutic use , Combined Modality Therapy , Humans , Mitomycin/therapeutic use , Paclitaxel , Perfusion , Peritoneal Neoplasms/therapy , Stomach Neoplasms/drug therapy
17.
BMC Cancer ; 20(1): 83, 2020 Jan 31.
Article in English | MEDLINE | ID: mdl-32005111

ABSTRACT

BACKGROUND: Gene expression profiling has consistently identified three molecular subtypes of lung adenocarcinoma that have prognostic implications. To facilitate stratification of patients with this disease into similar molecular subtypes, we developed and validated a simple, mutually exclusive classification. METHODS: Mutational status of EGFR, KRAS, and TP53 was used to define seven mutually exclusive molecular subtypes. A development cohort of 283 cytology specimens of lung adenocarcinoma was used to evaluate the associations between the proposed classification and clinicopathologic variables including demographic characteristics, smoking history, fluorescence in situ hybridization and molecular results. For validation and prognostic assessment, 63 of the 283 cytology specimens with available survival data were combined with a separate cohort of 428 surgical pathology specimens of lung adenocarcinoma. RESULTS: The proposed classification yielded significant associations between these molecular subtypes and clinical and prognostic features. We found better overall survival in patients who underwent surgery and had tumors enriched for EGFR mutations. Worse overall survival was associated with older age, stage IV disease, and tumors with co-mutations in KRAS and TP53. Interestingly, neither chemotherapy nor radiation therapy showed benefit to overall survival. CONCLUSIONS: The mutational status of EGFR, KRAS, and TP53 can be used to easily classify lung adenocarcinoma patients into seven subtypes that show a relationship with prognosis, especially in patients who underwent surgery, and these subtypes are similar to classifications based on more complex genomic methods reported previously.


Subject(s)
Adenocarcinoma of Lung/pathology , Lung Neoplasms/pathology , Proto-Oncogene Proteins p21(ras)/genetics , Tumor Suppressor Protein p53/genetics , Adenocarcinoma of Lung/genetics , Adenocarcinoma of Lung/surgery , Adult , Age Factors , Aged , Aged, 80 and over , ErbB Receptors/genetics , Female , Genetic Association Studies , High-Throughput Nucleotide Sequencing , Humans , Lung Neoplasms/genetics , Lung Neoplasms/surgery , Male , Middle Aged , Mutation , Precision Medicine , Prognosis , Retrospective Studies , Sequence Analysis, DNA , Survival Analysis
18.
Pancreatology ; 20(3): 391-393, 2020 Apr.
Article in English | MEDLINE | ID: mdl-32192904

ABSTRACT

Pancreatic cancer patients have not benefited from survival improvements brought about by personalized medicine in other malignancies. Even though this is the era of precision medicine, unfortunately most clinicians in practice either do not embrace or are unaware of the concept of molecular profiling for pancreatic cancer patients. Improving the grim prognosis of this challenging disease requires a paradigm shift. To exploit all potential therapeutic options in this lethal disease, molecular profiling should be performed ideally at the moment of diagnosis to identify potentially trial-eligible tumoral mutations or support off label use of an agent approved for another indication. This perspective article aims to increase awareness of the importance of upfront molecular profiling for pancreatic cancer patients.


Subject(s)
Carcinoma, Pancreatic Ductal/genetics , Gene Expression Profiling , Pancreatic Neoplasms/genetics , Humans , Male , Middle Aged , Precision Medicine
19.
World J Surg Oncol ; 18(1): 39, 2020 Feb 17.
Article in English | MEDLINE | ID: mdl-32066454

ABSTRACT

BACKGROUND: Staging laparoscopy and peritoneal cytology can detect occult metastatic disease prior to treatment of gastric cancer. The yield of peritoneal staging in patients with early stage disease is lacking. We assess the yield of peritoneal staging in early stage gastric cancer and its impact on survival. METHODS: Data were obtained from a prospective database of patients who underwent staging laparoscopy and peritoneal cytology for gastric cancer at our institution between July 1995 and July 2018. Clinical stage was determined by endoscopic ultrasound, and early stage was defined as cT1-2 and cN0. Rates of positive cytology and carcinomatosis at time of laparoscopy were obtained. Univariate analyses were used to compare groups, and Kaplan-Meier survival analyses were used to assess survival outcomes. RESULTS: Eight hundred sixty-seven patients underwent staging laparoscopy and peritoneal cytology; 56 were defined as early stage. Age was 61 ± 12 years, 66.4% were male, and 62.3% were white. Of the patients with early stage disease, 17.9% had either gross carcinomatosis (10.7%) and/or positive peritoneal cytology (10.9%). All cases of peritoneal disease were in patients with cT2 disease. There were no differences in age, gender, or race based on peritoneal disease (all p > 0.05). The presence of carcinomatosis or positive cytology significantly affected overall survival (p < 0.001), regardless of clinical T or N stage. CONCLUSIONS: Peritoneal staging identifies metastatic disease in a significant number of patients with early stage disease. Given its poor prognosis and alternate therapy options, independent staging laparoscopy and peritoneal cytology should be considered in patients with early stage gastric adenocarcinoma.


Subject(s)
Adenocarcinoma/epidemiology , Gastrectomy/methods , Laparoscopy/methods , Peritoneal Neoplasms/epidemiology , Stomach Neoplasms/mortality , Adenocarcinoma/diagnosis , Adenocarcinoma/secondary , Aged , Female , Follow-Up Studies , Gastric Mucosa/pathology , Gastric Mucosa/surgery , Humans , Incidence , Kaplan-Meier Estimate , Male , Middle Aged , Neoplasm Staging , Peritoneal Neoplasms/diagnosis , Peritoneal Neoplasms/secondary , Peritoneum/pathology , Prospective Studies , Retrospective Studies , Stomach Neoplasms/diagnosis , Stomach Neoplasms/pathology , Stomach Neoplasms/surgery , Treatment Outcome
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