Detection of Novel Tyrosine Kinase Fusion Genes as Potential Therapeutic Targets in Bone and Soft Tissue Sarcomas Using DNA/RNA-based Clinical Sequencing.
Approximately 1% of clinically treatable tyrosine kinase fusions, including anaplastic lymphoma kinase, neurotrophic tyrosine receptor kinase, RET proto-oncogene, and ROS proto-oncogene 1, have been identified in soft tissue sarcomas via comprehensive genome profiling based on DNA sequencing. Histologic tumor-specific fusion genes have been reported in approximately 20% of soft tissue sarcomas; however, unlike tyrosine kinase fusion genes, these fusions cannot be directly targeted in therapy. Approximately 80% of tumor-specific fusion-negative sarcomas, including myxofibrosarcoma and leiomyosarcoma, that are defined in complex karyotype sarcomas remain genetically uncharacterized; this mutually exclusive pattern of mutations suggests that other mutually exclusive driver oncogenes are yet to be discovered. Tumor-specific, fusion-negative sarcomas may be associated with unique translocations, and oncogenic fusion genes, including tyrosine kinase fusions, may have been overlooked in these sarcomas.
(1) Can DNA- or RNA-based analysis reveal any characteristic gene alterations in bone and soft tissue sarcomas? (2) Can useful and potential tyrosine kinase fusions in tumors from tumor-specific, fusion-negative sarcomas be detected using an RNA-based screening system? (3) Do the identified potential fusion tumors, especially in neurotrophic tyrosine receptor kinase gene fusions in bone sarcoma, transform cells and respond to targeted drug treatment in in vitro assays? (4) Can the identified tyrosine kinase fusion genes in sarcomas be useful therapeutic targets?
Between 2017 and 2020, we treated 100 patients for bone and soft tissue sarcomas at five institutions. Any biopsy or surgery from which a specimen could be obtained was included as potentially eligible. Ninety percent (90 patients) of patients were eligible; a further 8% (8 patients) were excluded because they were either lost to follow-up or their diagnosis was changed, leaving 82% (82 patients) for analysis here. To answer our first and second questions regarding gene alterations and potential tyrosine kinase fusions in eight bone and 74 soft tissue sarcomas, we used the TruSight Tumor 170 assay to detect mutations, copy number variations, and gene fusions in the samples. To answer our third question, we performed functional analyses involving in vitro assays to determine whether the identified tyrosine kinase fusions were associated with oncogenic abilities and drug responses. Finally, to determine usefulness as therapeutic targets, two pediatric patients harboring an NTRK fusion and an ALK fusion were treated with tyrosine kinase inhibitors in clinical trials.
DNA/RNA-based analysis demonstrated characteristic alterations in bone and soft tissue sarcomas; DNA-based analyses detected TP53 and copy number alterations of MDM2 and CDK4 . These single-nucleotide variants and copy number variations were enriched in specific fusion-negative sarcomas. RNA-based screening detected fusion genes in 24% (20 of 82) of patients. Useful potential fusions were detected in 19% (11 of 58) of tumor-specific fusion-negative sarcomas, with nine of these patients harboring tyrosine kinase fusion genes; five of these patients had in-frame tyrosine kinase fusion genes ( STRN3-NTRK3, VWC2-EGFR, ICK-KDR, FOXP2-MET , and CEP290-MET ) with unknown pathologic significance. The functional analysis revealed that STRN3-NTRK3 rearrangement that was identified in bone had a strong transforming potential in 3T3 cells, and that STRN3-NTRK3 -positive cells were sensitive to larotrectinib in vitro. To confirm the usefulness of identified tyrosine kinase fusion genes as therapeutic targets, patients with well-characterized LMNA-NTRK1 and CLTC-ALK fusions were treated with tyrosine kinase inhibitors in clinical trials, and a complete response was achieved.
We identified useful potential therapeutic targets for tyrosine kinase fusions in bone and soft tissue sarcomas using RNA-based analysis. We successfully identified STRN3-NTRK3 fusion in a patient with leiomyosarcoma of bone and determined the malignant potential of this fusion gene via functional analyses and drug effects. In light of these discoveries, comprehensive genome profiling should be considered even if the sarcoma is a bone sarcoma. There seem to be some limitations regarding current DNA-based comprehensive genome profiling tests, and it is important to use RNA testing for proper diagnosis and accurate identification of fusion genes. Studies on more patients, validation of results, and further functional analysis of unknown tyrosine kinase fusion genes are required to establish future treatments.
DNA- and RNA-based screening systems may be useful for detecting tyrosine kinase fusion genes in specific fusion-negative sarcomas and identifying key therapeutic targets, leading to possible breakthroughs in the treatment of bone and soft tissue sarcomas. Given that current DNA sequencing misses fusion genes, RNA-based screening systems should be widely considered as a worldwide test for sarcoma. If standard treatments such as chemotherapy are not effective, or even if the sarcoma is of bone, RNA sequencing should be considered to identify as many therapeutic targets as possible.
Hasegawa N
，Hayashi T
，Niizuma H
，Kikuta K
，Imanishi J
，Endo M
，Ikeuchi H
，Sasa K
，Sano K
，Hirabayashi K
，Takagi T
，Ishijima M
，Kato S
，Kohsaka S
，Saito T
，Suehara Y
... -
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Cognitive stimulation to improve cognitive functioning in people with dementia.
Cognitive stimulation (CS) is an intervention for people with dementia offering a range of enjoyable activities providing general stimulation for thinking, concentration and memory, usually in a social setting, such as a small group. CS is distinguished from other approaches such as cognitive training and cognitive rehabilitation by its broad focus and social elements, aiming to improve domains such as quality of life (QoL) and mood as well as cognitive function. Recommended in various guidelines and widely implemented internationally, questions remain regarding different modes of delivery and the clinical significance of any benefits. A systematic review of CS is important to clarify its effectiveness and place practice recommendations on a sound evidence base. This review was last updated in 2012.
To evaluate the evidence for the effectiveness of CS for people with dementia, including any negative effects, on cognition and other relevant outcomes, accounting where possible for differences in its implementation.
We identified trials from a search of the Cochrane Dementia and Cognitive Improvement Group Specialized Register, last searched on 3 March 2022. We used the search terms: cognitive stimulation, reality orientation, memory therapy, memory groups, memory support, memory stimulation, global stimulation, cognitive psychostimulation. We performed supplementary searches in a number of major healthcare databases and trial registers to ensure the search was up-to-date and comprehensive.
We included all randomised controlled trials (RCTs) of CS for dementia published in peer review journals in the English language incorporating a measure of cognitive change.
We used standard methodological procedures expected by Cochrane. As CS is a psychosocial intervention, we did not expect those receiving or delivering CS to be blinded to the nature of the intervention. Where necessary, we contacted study authors requesting data not provided in the papers. Where appropriate, we undertook subgroup analysis by modality (individual versus group), number of sessions and frequency, setting (community versus care home), type of control condition and dementia severity. We used GRADE methods to assess the overall quality of evidence for each outcome.
We included 37 RCTs (with 2766 participants), 26 published since the previous update. Most evaluated CS groups; eight examined individual CS. Participants' median age was 79.7 years. Sixteen studies included participants resident in care homes or hospitals. Study quality showed indications of improvement since the previous review, with few areas of high risk of bias. Assessors were clearly blinded to treatment allocation in most studies (81%) and most studies (81%) reported use of a treatment manual by those delivering the intervention. However, in a substantial number of studies (59%), we could not find details on all aspects of the randomisation procedures, leading us to rate the risk of selection bias as unclear. We entered data in the meta-analyses from 36 studies (2704 participants; CS: 1432, controls: 1272). The primary analysis was on changes evident immediately following the treatment period (median length 10 weeks; range 4 to 52 weeks). Only eight studies provided data allowing evaluation of whether effects were subsequently maintained (four at 6- to 12-week follow-up; four at 8- to 12-month follow-up). No negative effects were reported. Overall, we found moderate-quality evidence for a small benefit in cognition associated with CS (standardised mean difference (SMD) 0.40, 95% CI 0.25 to 0.55). In the 25 studies, with 1893 participants, reporting the widely used MMSE (Mini-Mental State Examination) test for cognitive function in dementia, there was moderate-quality evidence of a clinically important difference of 1.99 points between CS and controls (95% CI: 1.24, 2.74). In secondary analyses, with smaller total sample sizes, again examining the difference between CS and controls on changes immediately following the intervention period, we found moderate-quality evidence of a slight improvement in self-reported QoL (18 studies, 1584 participants; SMD: 0.25 [95% CI: 0.07, 0.42]) as well as in QoL ratings made by proxies (staff or caregivers). We found high-quality evidence for clinically relevant improvements in staff/interviewer ratings of communication and social interaction (5 studies, 702 participants; SMD: 0.53 [95% CI: 0.36, 0.70]) and for slight benefits in instrumental Activities of Daily Living, self-reported depressed mood, staff/interviewer-rated anxiety and general behaviour rating scales. We found moderate-quality evidence for slight improvements in behaviour that challenges and in basic Activities of Daily Living and low-quality evidence for a slight improvement in staff/interviewer-rated depressed mood. A few studies reported a range of outcomes for family caregivers. We found moderate-quality evidence that overall CS made little or no difference to caregivers' mood or anxiety. We found a high level of inconsistency between studies in relation to both cognitive outcomes and QoL. In exploratory subgroup analyses, we did not identify an effect of modality (group versus individual) or, for group studies, of setting (community versus care home), total number of group sessions or type of control condition (treatment-as-usual versus active controls). However, we did find improvements in cognition were larger where group sessions were more frequent (twice weekly or more versus once weekly) and where average severity of dementia among participants at the start of the intervention was 'mild' rather than 'moderate'. Imbalance in numbers of studies and participants between subgroups and residual inconsistency requires these exploratory findings to be interpreted cautiously.
In this updated review, now with a much more extensive evidence base, we have again identified small, short-term cognitive benefits for people with mild to moderate dementia participating in CS programmes. From a smaller number of studies, we have also found clinically relevant improvements in communication and social interaction and slight benefits in a range of outcomes including QoL, mood and behaviour that challenges. There are relatively few studies of individual CS, and further research is needed to delineate the effectiveness of different delivery methods (including digital and remote, individual and group) and of multi-component programmes. We have identified that the frequency of group sessions and level of dementia severity may influence the outcomes of CS, and these aspects should be studied further. There remains an evidence gap in relation to the potential benefits of longer-term CS programmes and their clinical significance.
Woods B
，Rai HK
，Elliott E
，Aguirre E
，Orrell M
，Spector A
... -
《Cochrane Database of Systematic Reviews》
ResearchGate
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钛学术
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