Post-dispersal seed consumption by rainforest vertebrates on the forest floor can substantially influence the community dynamics of rainforest trees. Studies of rainforest vertebrate seed predators ...at a community level, however, are lacking. Furthermore, there is very limited understanding of the effects of forest fragmentation on seed predators and their feeding behaviour. Here, we test whether communities of vertebrate seed predators, and their patterns of feeding on rainforest tree seeds, are altered when clearing creates forest fragments in an agricultural matrix. Using infra-red trail cameras deployed at stations with and without seeds of 20 local tree species, we identified four mammal and three bird species (from 18 recorded vertebrate taxa at mainly species level) as common post-dispersal seed predators in subtropical rainforest of eastern Australia. Statistical comparisons of species-specific frequencies between six sites in continuous forest and six in small rainforest fragments (4-21 ha) showed that habitat fragmentation substantially altered species composition of seed predator communities. Two species, both small rodents, had lower abundances in fragments than in continuous forest, while higher abundances were observed in fragments for a further four species: two small birds, a medium-sized marsupial and the small non-native rodent Rattus rattus. The abundance of one larger bird species did not change. Predatory interest in seeds was also significantly affected by habitat fragmentation and generally increased in each species' habitat of greater abundance. Collectively, seed predators showed behaviours associated with potential or actual seed consumption on an average of 43% of camera days with seeds, with about 50% of seeds physically removed or damaged after five days' exposure. Camera data have revealed community-level changes in seed predator abundance and feeding that are likely to cause altered patterns of plant recruitment following rainforest fragmentation, but these will be complex in nature.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Background.
The U.S. Food and Drug Administration‐approved method for detecting EML4‐ALK rearrangement is fluorescence in situ hybridization (FISH); however, data supporting the use of ...immunohistochemistry (IHC) for that purpose are accumulating. Previous studies that compared FISH and IHC considered FISH the gold standard, but none compared data with the results of next‐generation sequencing (NGS) analysis.
Materials and Methods.
We studied FISH and IHC (D5F3 antibody) systematically for EML4‐ALK rearrangement in 51 lung adenocarcinoma patients, followed by NGS in case of discordance.
Results.
Of 51 patients, 4 were positive with FISH (7.8%), and 8 were positive with IHC (15.7%). Three were positive with both. NGS confirmed that four of the five patients who were positive with IHC and negative with FISH were positive for ALK. Two were treated by crizotinib, with progression‐free survival of 18 and 6 months. Considering NGS as the most accurate test, the sensitivity and specificity were 42.9% and 97.7%, respectively, for FISH and 100% and 97.7%, respectively, for IHC.
Conclusion.
The FISH‐based method of detecting EML4‐ALK rearrangement in lung cancer may miss a significant number of patients who could benefit from targeted ALK therapy. Screening for EML4‐ALK rearrangement by IHC should be strongly considered, and NGS is recommended in borderline cases. Two patients who were negative with FISH and positive with IHC were treated with crizotinib and responded to therapy.
The U.S. Food and Drug Administration‐approved method for detecting EML4‐ALK rearrangement in lung cancer is fluorescence in situ hybridization (FISH); however, FISH may miss a significant number of patients who could benefit from targeted ALK therapy. Screening for EML4‐ALK rearrangement by immunohistochemistry should be strongly considered, and next‐generation sequencing is recommended for borderline cases.
Background.
Intrahepatic cholangiocarcinoma (ICC) is a subtype of primary liver cancer that is rarely curable by surgery and is rapidly increasing in incidence. Relapsed ICC has a poor prognosis, and ...current systemic nontargeted therapies are commonly extrapolated from those used in other gastrointestinal malignancies. We hypothesized that genomic profiling of clinical ICC samples would identify genomic alterations that are linked to targeted therapies and that could facilitate a personalized approach to therapy.
Methods.
DNA sequencing of hybridization‐captured libraries was performed for 3,320 exons of 182 cancer‐related genes and 36 introns of 14 genes frequently rearranged in cancer. Sample DNA was isolated from 40 μm of 28 formalin‐fixed paraffin‐embedded ICC specimens and sequenced to high coverage.
Results.
The most commonly observed alterations were within ARID1A (36%), IDH1/2 (36%), and TP53 (36%) as well as amplification of MCL1 (21%). Twenty cases (71%) harbored at least one potentially actionable alteration, including FGFR2 (14%), KRAS (11%), PTEN (11%), CDKN2A (7%), CDK6 (7%), ERBB3 (7%), MET (7%), NRAS (7%), BRCA1 (4%), BRCA2 (4%), NF1 (4%), PIK3CA (4%), PTCH1 (4%), and TSC1 (4%). Four (14%) of the ICC cases featured novel gene fusions involving the tyrosine kinases FGFR2 and NTRK1 (FGFR2‐KIAA1598, FGFR2‐BICC1, FGFR2‐TACC3, and RABGAP1L‐NTRK1).
Conclusion.
Two thirds of patients in this study harbored genomic alterations that are associated with targeted therapies and that have the potential to personalize therapy selection for to individual patients.
摘要
摘要. 肝内胆管癌 (intrahepatic cholangiocarcinoma, ICC) 是原发性肝癌的一种亚型，很少可以通过手术治愈，且其发病率在日益增高。复发性肝内胆管癌预后不佳，而目前的非靶向全身疗法通常是从其他胃肠道恶性肿瘤的治疗推演而来。我们提出假设：临床ICC 样本的基因组学特征分析将鉴别与靶向疗法有关的基因组学变化，而且可能有助于制定个体化疗法。
方法. 对 182 个癌症相关基因的 3,320 个外显子以及癌症中频繁重排的 14 个基因的 36 个内含子进行杂交捕获DNA 文库测序。从 28 个 40 μm 厚福尔马林固定、石蜡包埋的 ICC 标本分离出 DNA 样本，并测序到高覆盖率水准。
结果. 最常见的 DNA 变化可见于 ARID1A (36%)、IDH1/2 (36%) 、 TP53 (36%) 以及扩增的 MCL1 (21%)。从至少有一个潜在活性变化的基因中采集了二十例 (71%) 测序结果，这些基因包括 FGFR2 (14%)、KRAS (11%)、 PTEN (11%)、CDKN2A (7%)、CDK6 (7%)、 ERBB3 (7%)、MET (7%)、NRAS (7%)、BRCA1 (4%)、BRCA2 (4%)、NF1 (4%)、PIK3CA (4%)、PTCH1 (4%) 以及 TSC1 (4%)。四例 (14%) ICC病例表现出新基因融合的特征，涉及酪氨酸激酶 FGFR2 和 NTRK1（FGFR2‐KIAA1598、 FGFR2‐ BICC1、FGFR2‐TACC3及 RABGAP1L‐NTRK1）。
结论. 从本研究中三分之二患者采集到的基因组变化与靶向疗法相关，并有可能对患者个体化疗法有帮助。The Oncologist 2014;19:235–242
In this study, the authors hypothesized that genomic profiling of clinical intrahepatic cholangiocarcinoma samples would identify genomic alterations that are linked to targeted therapies and that could facilitate a personalized approach to therapy. Two‐thirds of patients in this study harbored genomic alterations that are associated with targeted therapies and that have the potential to personalize therapy selection for individual patients.
Circulating tumor cells (CTCs) are tumor cells shed from either primary tumors or its metastases that circulate in the peripheral blood of patients with metastatic cancers. The molecular ...characterization of the CTCs is critical to identifying the key drivers of cancer metastasis and devising therapeutic approaches. However, the molecular characterization of CTCs is difficult to achieve because their isolation is a major technological challenge.
CTCs from two triple negative breast cancer patients were enriched using CellSearch and single cells selected by DEPArray™. A TP53 R110 fs*13 mutation identified by next generation sequencing in the breast and chest skin biopsies of both patients was studied in single CTCs.
From 6 single CTC isolated from one patient, 1 CTC had TP53 R110 delC, 1 CTC showed the TP53 R110 delG mutation, and the remaining 4 single CTCs showed the wild type p53 sequence; a pool of 14 CTCs isolated from the same patient also showed TP53 R110 delC mutation. In the tumor breast tissue of this patient, only the TP53 R110 delG mutation was detected. In the second patient a TP53 R110 delC mutation was detected in the chest wall skin biopsy; from the peripheral blood of this patient, 5 single CTC and 6 clusters of 2 to 6 CTCs were isolated; 3 of the 5 single CTCs showed the TP53 R110 delC mutation and 2 CTCs showed the wild type TP53 allele; from the clusters, 5 showed the TP53 R110 delC mutation, and 1 cluster the wild type TP53 allele. Single white blood cells isolated as controls from both patients only showed the wild type TP53 allele.
We are able to isolate uncontaminated CTCs and achieve single cell molecular analysis. Our studies showed the presence of different CTC sub-clones in patients with metastatic breast cancer. Some CTCs had the same TP53 mutation as their matching tumor samples although others showed either a different TP53 mutation or the wild type allele. Our results indicate that CTCs could represent a non-invasive source of cancer cells from which to determine genetic markers of the disease progression and potential therapeutic targets.
There is growing interest in delivering genomically informed cancer therapy. Our aim was to determine the concordance of genomic alterations between primary and recurrent breast cancer. Targeted ...next-generation sequencing was performed on formalin-fixed paraffin-embedded (FFPE) samples, profiling 3,320 exons of 182 cancer-related genes plus 37 introns from 14 genes often rearranged in cancer. Point mutations, indels, copy-number alterations (CNA), and select rearrangements were assessed in 74 tumors from 43 patients (36 primary and 38 recurrence/metastases). Alterations potentially targetable with established or investigational therapeutics were considered "actionable." Alterations were detected in 55 genes (mean 3.95 alterations/sample, range 1-12), including mutations in PIK3CA, TP53, ARID1A, PTEN, AKT1, NF1, FBXW7, and FGFR3 and amplifications in MCL1, CCND1, FGFR1, MYC, IGF1R, MDM2, MDM4, AKT3, CDK4, and AKT2. In 33 matched primary and recurrent tumors, 97 of 112 (86.6%) somatic mutations were concordant. Of identified CNAs, 136 of 159 (85.5%) were concordant: 37 (23.3%) were concordant, but below the reporting threshold in one of the matched samples, and 23 (14.5%) discordant. There was an increased frequency of CDK4/MDM2 amplifications in recurrences, as well as gains and losses of other actionable alterations. Forty of 43 (93%) patients had actionable alterations that could inform targeted treatment options. In conclusion, deep genomic profiling of cancer-related genes reveals potentially actionable alterations in most patients with breast cancer. Overall there was high concordance between primary and recurrent tumors. Analysis of recurrent tumors before treatment may provide additional insights, as both gains and losses of targets are observed.
Inflammatory breast cancer (IBC) is a distinct clinicopathologic entity that carries a worse prognosis relative to non-IBC breast cancer even when matched for standard biomarkers (ER/PR/HER2). The ...objective of this study was to identify opportunities for benefit from targeted therapy, which are not currently identifiable in the standard workup for advanced breast cancer. Comprehensive genomic profiling on 53 IBC formalin-fixed paraffin-embedded specimens (mean, 800× + coverage) using the hybrid capture-based FoundationOne assay. Academic and community oncology clinics. From a series of 2208 clinical cases of advanced/refractory invasive breast cancers, 53 cases with IBC were identified. The presence of clinically relevant genomic alterations (CRGA) in IBC and responses to targeted therapies. CRGA were defined as genomic alterations (GA) associated with on label targeted therapies and targeted therapies in mechanism-driven clinical trials. For the 44 IBCs with available biomarker data, 19 (39 %) were ER−/PR−/HER2− (triple-negative breast cancer, TNBC). For patients in which the clinical HER2 status was known, 11 (25 %) were HER2+ with complete (100 %) concordance with
ERBB2
(
HER2
) amplification detected by the CGP assay. The 53 sequenced IBC cases harbored a total of 266 GA with an average of 5.0 GA/tumor (range 1–15). At least one alteration associated with an FDA approved therapy or clinical trial was identified in 51/53 (96 %) of cases with an average of 2.6 CRGA/case. The most frequently altered genes were
TP53
(62 %),
MYC
(32 %),
PIK3CA
(28 %),
ERBB2
(26 %),
FGFR1
(17 %),
BRCA2
(15 %), and
PTEN
(15 %). In the TNBC subset of IBC, 8/19 (42 %) showed
MYC
amplification (median copy number 8X, range 7–20) as compared to 9/32 (28 %) in non-TNBC IBC (median copy number 7X, range 6–21). Comprehensive genomic profiling uncovered a high frequency of GA in IBC with 96 % of cases harboring at least 1 CRGA. The clinical benefit of selected targeted therapies in individual IBC cases suggests that a further study of CGP in IBC is warranted.
Characterization of the genomic changes that drive an individual patient's disease is critical in management of many cancers. In patients with non-small-cell lung cancer (NSCLC), obtaining tumor ...samples of sufficient size for genomic profiling on recurrence is often challenging. We undertook this study to compare genomic alterations identified in archived primary tumors from patients with NSCLC with those identified in metachronous or synchronous metastases.
Primary and matched metastatic tumor pairs from 15 patients were analyzed by using a targeted next-generation sequencing assay in a Clinical Laboratory Improvement Amendments laboratory. Genomic libraries were captured for 3,230 exons in 182 cancer-related genes plus 37 introns from 14 genes often rearranged in cancer and sequenced to high coverage.
Among 30 tumors, 311 genomic alterations were identified of which 63 were known recurrent (32 in primary tumor, 31 in metastasis) and 248 were nonrecurrent (likely passenger). TP53 mutations were the most frequently observed recurrent alterations (12 patients). Tumors harbored two or more (maximum four) recurrent alterations in 10 patients. Comparative analysis of recurrent alterations between primary tumor and matched metastasis revealed a concordance rate of 94% compared with 63% for likely passenger alterations.
This high concordance suggests that for the purposes of genomic profiling, use of archived primary tumor can identify the key recurrent somatic alterations present in matched NSCLC metastases and may provide much of the relevant genomic information required to guide treatment on recurrence.
Background.
Gastric cancer (GC) is a major global cancer burden and the second most common cause of global cancer‐related deaths. The addition of anti‐ERBB2 (HER2) targeted therapy to chemotherapy ...improves survival for ERBB2‐amplified advanced GC patients; however, the majority of GC patients do not harbor this alteration and thus cannot benefit from targeted therapy under current practice paradigms.
Materials and Methods.
Prospective comprehensive genomic profiling of 116 predominantly locally advanced or metastatic (90.0%) gastric cancer cases was performed to identify genomic alterations (GAs) associated with a potential response to targeted therapies approved by the U.S. Food and Drug Administration or targeted therapy‐based clinical trials.
Results.
Overall, 78% of GC cases harbored one clinically relevant GA or more, with the most frequent alterations being found in TP53 (50%), ARID1A (24%), KRAS (16%), CDH1 (15%), CDKN2A (14%), CCND1 (9.5%), ERBB2 (8.5%), PIK3CA (8.6%), MLL2 (6.9%), FGFR2 (6.0%), and MET (6.0%). Receptor tyrosine kinase genomic alterations were detected in 20.6% of cases, primarily ERBB2, FGFR2, and MET amplification, with ERBB2 alterations evenly split between amplifications and base substitutions. Rare BRAF mutations (2.6%) were also observed. One MET‐amplified GC patient responded for 5 months to crizotinib, a multitargeted ALK/ROS1/MET inhibitor.
Conclusion.
Comprehensive genomic profiling of GC identifies clinically relevant GAs that suggest benefit from targeted therapy including MET‐amplified GC and ERBB2 base substitutions.
摘要
背景. 胃癌（GC）在全球范围都是严重的癌症负担，同时也是全球癌症相关死亡的第二大原因。化疗联合抗ERBB2（HER2）靶向治疗改善了ERBB2扩增的进展期胃癌患者的生存；但是多数胃癌患者的肿瘤中并没有这一基因变异，因此不能从这一治疗范例的靶向治疗中获益。
材料与方法. 对116例患者进行前瞻性综合性基因组分析，以鉴别与靶向治疗（美国食品和药物管理局批准的靶向治疗，或以靶向治疗为基础的临床试验）部分缓解相关的基因变异（GA），患者主要为局部进展期或转移性胃癌（90.0%）。
结果. 总体而言，78%的胃癌病例含有≥ 1个临床相关性GA。最常见的基因变异见于TP53（50%）、ARID1A（24%）、KRAS（16%）、CDH1（15%）、CDKN2A（14%）、CCND1（9.5%）、ERBB2（8.5%）、PIK3CA（8.6%）、MLL2（6.9%）、FGFR2（6.0%）和MET（6.0%）。20.6%的病例可检测到受体酪氨酸激酶基因变异，主要为ERBB2、FGFR2和MET扩增，而ERBB2变异中扩增和碱基置换各占一半。还观察到少量BRAF突变（2.6%）。一例MET扩增胃癌患者经克唑替尼（ALK/ROS1/MET多靶点抑制剂）治疗5个月有应答。
结论. 对胃癌进行综合性基因组分析可鉴别出临床相关性GA，提示可从针对包括MET扩增胃癌和ERBB2碱基置换在内的靶向治疗中获益。The Oncologist 2015;20:499–507
Prospective comprehensive genomic profiling of 116 predominantly locally advanced or metastatic gastric cancer (GC) cases was performed to identify genomic alterations (GAs) associated with a potential response to targeted therapies or targeted therapy‐based clinical trials. Comprehensive genomic profiling of GC identified clinically relevant GAs that suggest benefit from targeted therapy including MET‐amplified GC and ERBB2 base substitutions.
Background.
Targeted ERBB2/HER2 inhibitors are approved by the U.S. Food and Drug Administration for the treatment of breast, gastric, and esophageal cancers that overexpress or amplify HER2/ERBB2, ...as measured by immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH), respectively. Activating mutations in ERBB2 have also been reported and are predicted to confer sensitivity to these targeted agents. Testing for these mutations is not performed routinely, and FISH and IHC are not applied outside of these approved indications.
Materials and Methods.
We explored the spectrum of activating ERBB2 alterations across a collection of ∼7,300 solid tumor specimens that underwent comprehensive genomic profiling using next‐generation sequencing. Results were analyzed for base substitutions, insertions and deletions, select rearrangements, and copy number changes.
Results.
Known oncogenic ERBB2 alterations were identified in tumors derived from 27 tissues, and ERBB2 amplification in breast, gastric, and gastroesophageal cancers accounted for only 30% of these alterations. Activating mutations in ERBB2 were identified in 131 samples (32.5%); amplification was observed in 246 samples (61%). Two samples (0.5%) harbored an ERBB2 rearrangement. Ten samples (2.5%) harbored multiple ERBB2 mutations, yet mutations and amplifications were mutually exclusive in 91% of mutated cases.
Conclusion.
Standard slide‐based tests for overexpression or amplification of ERBB2 would fail to detect the majority of activating mutations that occur overwhelmingly in the absence of copy number changes. Compared with current clinical standards, comprehensive genomic profiling of a more diverse set of tumor types may identify ∼3.5 times the number of patients who may benefit from ERBB2‐targeted therapy.
The authors explored activating ERBB2 alterations in solid tumor specimens that underwent comprehensive genomic profiling using next‐generation sequencing. Results showed that activating events in ERBB2/HER2 occurred across a wide variety of tumors. Additionally, standard slide‐based tests for overexpression or amplification of ERBB2 would fail to detect the majority of activating mutations that occur overwhelmingly in the absence of copy number changes. Comprehensive genomic profiling of a more diverse set of tumor types may identify more patients likely to benefit from ERBB2‐targeted therapy.
Although urothelial carcinoma (UC) of the urinary bladder generally portends a favorable prognosis, metastatic tumors often follow an aggressive clinical course. DNA was extracted from 40 μm of ...formalin-fixed, paraffin-embedded (FFPE) sections from 35 stage IV UCs that had relapsed and progressed after primary surgery and conventional chemotherapy. Next-generation sequencing (NGS) was performed on hybridization-captured, adaptor ligation-based libraries for 3320 exons of 182 cancer-related genes plus 37 introns from 14 genes frequently rearranged in cancer to at an average sequencing depth of 1164 × and evaluated for all classes of genomic alterations (GAs). Actionable GAs were defined as those impacting the selection of targeted anticancer therapies on the market or in registered clinical trials. A total of 139 GAs were identified, with an average of 4.0 GAs per tumor (range 0–10), of which 78 (56%) were considered actionable, with an average of 2.2 per tumor (range 0–7). Twenty-nine (83%) cases harbored at least one actionable GA including: PIK3CA (9 cases; 26%); CDKN2A/B (8 cases; 23%); CCND1 (5 cases; 14%); FGFR1 (5 cases; 14%); CCND3 (4 cases; 11%); FGFR3 (4 cases; 11%); MCL1 (4 cases; 11%); MDM2 (4 cases; 11%); EGFR (2 cases, 6%); ERBB2 (HER2/neu) (2 cases, 6%); NF1 (2 cases, 6%) and TSC1 (2 cases, 6%). Notable additional alterations included TP53 (19 cases, 54%) and RB1 (6 cases; 17%). Genes involved in chromatin modification were altered by nonsense mutation, splice site mutation or frameshift indel in a mutually exclusive manner in nearly half of all cases including KDM6A (10 cases; 29%) and ARID1A (7 cases; 20%). Comprehensive NGS of 35 UCs of the bladder revealed a diverse spectrum of actionable GAs in 83% of cases, which has the potential to inform treatment decisions for patients with relapsed and metastatic disease.
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