Fusion Gene Detection Research Articles

Chromosomal Aberrations in Chronic Myeloid Leukemia: Response to Conventional TKIs and Risk of Blastic Transformation

Background and Purpose: Chronic Myeloid Leukemia (CML) is a common hematological malignancy. The characteristic molecular abnormality is the presence of Philadelphia chromosome or BCR-ABL fusion gene which is the result of 9:22 translocation. Tyrosine kinase inhibitors (TKIs) form the main stay of treatment in CML with excellent responses. The purpose of this study was to determine the impact of additional chromosomal abnormalities on outcomes in CML.Methods: This is a retrospective chart review of all patients who were diagnosed with CML in chronic phase (CP) with additional chromosomal abnormalities (ACAs) over a period of 5 years from 2010 to 2015 at Shaukat Khanum Memorial Cancer Hospital and Research Centre, Lahore, Pakistan. Results: A total of 283 patients were diagnosed with CML from January 2010 to January 2015. 31 patients out of these were found to have additional chromosomal abnormalities at the time of diagnosis in addition to BCR-ABL fusion gene or Philadelphia chromosome detection. Out of these 31 patients, 23 (74.2%) were males whereas 8 (25.8%) were females. 13 (41.9%) were in the age group of 31 to 50 years whereas the other two groups that is 18 to 30 years and 51 to 70 years had 9 patients each. After approval from the government which usually takes a standard 2-3 weeks’ time, these patients were started on tyrosine kinase inhibitors which was Imatinib in 30 (96.8%) and Nilotinib in 1 (3.2%) patient. Conventional cytogenetic analysis performed for each patient at the time of diagnosis revealed that 11 (35.5%) of patients had variant Philadelphia chromosome followed by 7 patients (22.6%) with trisomy 8. 5 patients (16.1%) had multiple chromosomal abnormalities including trisomy 8, deletion 1 and isochrome 17q. 2 patents each had isochrome 17q, inversion 3 and deletion 9 abnormalities. 1 patient had deletion 7 whereas 1 had variant Philadelphia chromosome with other chromosomal abnormalities. Conclusion: It was evident that frequently occurring ACAs In our CML population were Variant Philadelphia chromosome and trisomy 8.

Calcified chondroid mesenchymal neoplasms with FN1-receptor tyrosine kinase gene fusions including FGFR2, FGFR1, MERTK, NTRK1, and TEK: a molecular and clinicopathologic analysis.

Translocations involving FN1 have been described in a variety of neoplasms that share the presence of a cartilage matrix and may also contain a variable extent of calcification. Fusions of FN1 to FGFR1 or FGFR2 have been reported in nine soft tissue chondromas, mostly demonstrated indirectly by FISH analysis. Delineation of FN1 fusions with various partner genes will facilitate our understanding of the pathogenesis and diagnostic classification of these neoplasms. In this study, we present molecular, clinical, and pathologic features of 12 cartilaginous soft tissue neoplasms showing a predilection for the TMJ region and the distal extremities. We analyzed for gene fusions with precise breakpoints using targeted RNA-seq with a 115-gene panel. We detected gene fusions in ten cases, including three novel fusions, FN1-MERTK, FN1-NTRK1, and FN1-TEK, each in one case, recurrent FN1-FGFR2 fusion in five cases, FN1-FGFR1 in one case, and FGFR1-PLAG1 in one case. The breakpoints in the 5' partner gene FN1 ranged from exons 11-48, retaining the domains of a signal peptide, FN1, FN2, and/or FN3, while the 3' partner genes retained the transmembrane domain, tyrosine kinase (TK) domains, and/or Ig domain. The tumors are generally characterized by nodular/lobular growth of polygonal to stellate cells within a chondroid matrix, often accompanied by various patterns of calcification, resembling those described for the chondroblastoma-like variant of soft tissue chondroma. Additional histologic findings include extensive calcium pyrophosphate dihydrate deposition in two cases and features resembling tenosynovial giant cell tumor (TGCT). Overall, while the tumors from our series show significant morphologic overlap with chondroblastoma-like soft tissue chondroma, we describe findings that expand the morphologic spectrum of these neoplasms and therefore refer to them as "calcified chondroid mesenchymal neoplasms." These neoplasms represent a spectrum of chondroid/cartilage matrix-forming tumors harboring FN1-receptor TK fusions that include those classified as soft tissue chondroma as well as chondroid TGCT.

Detection of gene fusions using targeted next-generation sequencing: a comparative evaluation

BackgroundGene fusions represent promising targets for cancer therapy in lung cancer. Reliable detection of multiple gene fusions is therefore essential.MethodsFive commercially available parallel sequencing assays were evaluated for their ability to detect gene fusions in eight cell lines and 18 FFPE tissue samples carrying a variety of known gene fusions. Four RNA-based assays and one DNA-based assay were compared; two were hybrid capture-based, TruSight Tumor 170 Assay (Illumina) and SureSelect XT HS Custom Panel (Agilent), and three were amplicon-based, Archer FusionPlex Lung Panel (ArcherDX), QIAseq RNAscan Custom Panel (Qiagen) and Oncomine Focus Assay (Thermo Fisher Scientific).ResultsThe Illumina assay detected all tested fusions and showed the smallest number of false positive results. Both, the ArcherDX and Qiagen panels missed only one fusion event. Among the RNA-based assays, the Qiagen panel had the highest number of false positive events. The Oncomine Focus Assay (Thermo Fisher Scientific) was the least adequate assay for our purposes, seven fusions were not covered by the assay and two fusions were classified as uncertain. The DNA-based SureSelect XT HS Custom Panel (Agilent) missed three fusions and nine fusions were only called by one software version. Additionally, many false positive fusions were observed.ConclusionsIn summary, especially RNA-based parallel sequencing approaches are potent tools for reliable detection of targetable gene fusions in clinical diagnostics.

Identification of tumors with NRG1 rearrangement, including a novel putative pathogenic UNC5D-NRG1 gene fusion in prostate cancer by data-drilling a de-identified tumor database.

The fusion genes containing neuregulin-1 (NRG1) are newly described potentially actionable oncogenic drivers. Initial clinical trials have shown a positive response to targeted treatment in some cases of NRG1 rearranged lung adenocarcinoma, cholangiocarcinoma, and pancreatic carcinoma. The cost-effective large scale identification of NRG1 rearranged tumors is an open question. We have tested a data-drilling approach by performing a retrospective assessment of a de-identified molecular profiling database of 3263 tumors submitted for fusion testing. Gene fusion detection was performed by RNA-based targeted next-generation sequencing using the Archer Fusion Plex kits for Illumina (ArcherDX Inc., Boulder, CO). Novel fusion transcripts were confirmed by a custom-designed RT-PCR. Also, the aberrant expression of CK20 was studied immunohistochemically. The frequency of NRG1 rearranged tumors was 0.2% (7/3263). The most common histologic type was lung adenocarcinoma (n = 5). Also, renal carcinoma (n = 1) and prostatic adenocarcinoma (n = 1) were found. Identified fusion partners were of a wide range (CD74, SDC4, TNC, VAMP2, UNC5D), with CD74, SDC4 being found twice. The UNC5D is a novel fusion partner identified in prostate adenocarcinoma. There was no co-occurrence with the other tested fusions nor KRAS, BRAF, and the other gene mutations specified in the applied gene panels. Immunohistochemically, the focal expression of CK20 was present in 2 lung adenocarcinomas. We believe it should be considered as an incidental finding. In conclusion, the overall frequency of tumors with NRG1 fusion was 0.2%. All tumors were carcinomas. We confirm (invasive mucinous) lung adenocarcinoma as being the most frequent tumor presenting NRG1 fusion. Herein novel putative pathogenic gene fusion UNC5D-NRG1 is described. The potential role of immunohistochemistry in tumor identification should be further addressed.

Targeting rare and non-canonical driver variants in NSCLC – An uncharted clinical field

ObjectivesImplementation of tyrosine kinase inhibitors (TKI) and other targeted therapies was a main advance in thoracic oncology with survival gains ranging from several months to years for non-small-cell lung cancer (NSCLC) patients. High-throughput comprehensive molecular profiling is of key importance to identify patients that can potentially benefit from these novel treatments. Material and MethodsNext-generation sequencing (NGS) was performed on 4500 consecutive formalin-fixed, paraffin-embedded specimens of advanced NSCLC (n = 4172 patients) after automated extraction of DNA and RNA for parallel detection of mutations and gene fusions, respectively. Results and ConclusionBesides the 24.9 % (n = 1040) of cases eligible for approved targeted therapies based on the presence of canonical alterations in EGFR exons 18–21, BRAF, ROS1, ALK, NTRK, and RET, an additional n = 1260 patients (30.2 %) displayed rare or non-canonical mutations in EGFR (n = 748), BRAF (n = 135), ERBB2 (n = 30), KIT (n = 32), PIK3CA (n = 221), and CTNNB1 (n = 94), for which targeted therapies could also be potentially effective. A systematic literature search in conjunction with in silico evaluation identified n = 232 (5.5 %) patients, for which a trial of targeted treatment would be warranted according to available evidence (NCT level 1, i.e. published data showing efficacy in the same tumor entity).In conclusion, a sizeable fraction of NSCLC patients harbors rare or non-canonical alterations that may be associated with clinical benefit from currently available targeted drugs. Systematic identification and individualized management of these cases can expand applicability of precision oncology in NSCLC and extend clinical gain from established molecular targets. These results can also inform clinical trials.

Abstract SP021: Understanding current platforms

Abstract Next-generation sequencing (NGS) of breast cancer is becoming increasingly integrated into clinical practice. The fast pace of advances coupled with the dizzying array of technologies and platforms challenges the oncologist to select the right test for each patient. The choice could depend on a host of factors including the accessibility of clinical trials, clinical scenario and sample type, and the interest in turning up improbable but profoundly useful findings. Here, I will review the various types of clinical NGS platforms—including tumor and circulating-tumor DNA—particularly highlighting the unique features of commercial platforms that are widely available. Performance characteristics differ by technology: amplification technologies can detect mutations with smaller specimens, whereas capture-based NGS platforms may perform better for detecting novel genomic alterations. Assays integrating RNA-based analysis may enhance detection of rare but impactful gene fusions, such as of FGFR1-3 and NTRK1-3. Some potentially actionable genomic alterations only emerge after therapy, and are detected only with repeat tumor biopsy or cell-free DNA. Some assays include parallel germline testing which can clearly distinguish inherited from somatic (tumor-specific) findings, but may offer logistical challenges. An ever expanding set of ‘genomic phenotypes’ may be captured in these updated assays, with their limitations, including tumor mutational burden, microsatellite instability and homologous recombination. Newer platforms are now including exome and whole-genome sequencing, which may require more tissue and offer research insights, but currently add little to directing clinical care. New technologies, such as long-read and single-cell platforms of the future, may elucidate genomic features that are undetectable with current bulk short-read platforms, and will enable new genomic biomarkers. Despite the differences in genomics platforms, practical matters such as reimbursement, ease of use, and turn-around-time will likely govern platform selection for most oncologists in the near future. Citation Format: M Burkard. Understanding current platforms [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr SP021.

Fusion Genes and RNAs in Cancer Development.

Fusion RNAs are a hallmark of some cancers. They result either from chromosomal rearrangements or from splicing mechanisms that are non-chromosomal rearrangements. Chromosomal rearrangements that result in gene fusions are particularly prevalent in sarcomas and hematopoietic malignancies; they are also common in solid tumors. The splicing process can also give rise to more complex RNA patterns in cells. Gene fusions frequently affect tyrosine kinases, chromatin regulators, or transcription factors, and can cause constitutive activation, enhancement of downstream signaling, and tumor development, as major drivers of oncogenesis. In addition, some fusion RNAs have been shown to function as noncoding RNAs and to affect cancer progression. Fusion genes and RNAs will therefore become increasingly important as diagnostic and therapeutic targets for cancer development. Here, we discuss the function, biogenesis, detection, clinical relevance, and therapeutic implications of oncogenic fusion genes and RNAs in cancer development. Further understanding the molecular mechanisms that regulate how fusion RNAs form in cancers is critical to the development of therapeutic strategies against tumorigenesis.

Accurate and efficient detection of gene fusions from RNA sequencing data.

The identification of gene fusions from RNA sequencing data is a routine task in cancer research and precision oncology. However, despite the availability of many computational tools, fusion detection remains challenging. Existing methods suffer from poor prediction accuracy and are computationally demanding. We developed Arriba, a novel fusion detection algorithm with high sensitivity and short runtime. When applied to a large collection of published pancreatic cancer samples (n = 803), Arriba identified a variety of driver fusions, many of which affected druggable proteins, including ALK, BRAF, FGFR2, NRG1, NTRK1, NTRK3, RET, and ROS1. The fusions were significantly associated with KRAS wild-type tumors and involved proteins stimulating the MAPK signaling pathway, suggesting that they substitute for activating mutations in KRAS. In addition, we confirmed the transforming potential of two novel fusions, RRBP1-RAF1 and RASGRP1-ATP1A1, in cellular assays. These results show Arriba's utility in both basic cancer research and clinical translation.

Intraarticular nodular fasciitis-detection of USP6 gene fusions in three cases by targeted RNA sequencing.

Intraarticular nodular fasciitis arising in the joint synovium is an uncommon lesion. Most cases have been reported in the knee and rarely in other joints. A USP6 gene fusion has so far been documented in only four cases of intraarticular nodular fasciitis, three were located in the knee and one in the proximal interphalangeal joint. In all three caseslocated in the knee, MYH9 was detected as a USP6 fusion partner. We analysed three cases of intraarticular nodular fasciitis for the presence of USP6 fusion by targeted RNA sequencing. Two cases were located in the hip (a 25-year-old female and 48-year-old male) and one in the shoulder (a 38-year-old male). We detected a MYH9-USP6 fusion in the two hip cases and a COL1A1-USP6 fusion in the shoulder case. Our findings provide additional evidence that intraarticular nodular fasciitis is a form of nodular fasciitis arising in the joint synovium, harbouring a USP6 fusion. Although a MYH9-USP6 fusion seems to predominate in intraarticular nodular fasciitis, other fusion partners of the USP6 gene may also be involved. Detection of a USP6 fusion by targeted RNA sequencing may assist in confirming the diagnosis in selected cases.

PATH-26. RNA SEQUENCING OF FORMALIN-FIXED PARAFFIN-EMBEDDED SPECIMENS IN DIAGNOSTIC ROUTINE IDENTIFIES CLINICALLY RELEVANT GENE FUSIONS

Pediatric brain tumor entities harbor a variety of gene fusions. Whilst other molecular parameters like somatic mutations and copy number alterations have become pivotal for brain tumor diagnostics, gene fusions are only less well covered by routinely applied methylation arrays or targeted next-generation sequencing of DNA. In a routine diagnostic setting we established and optimized a workflow for investigation of gene fusions in formalin-fixed paraffin-embedded (FFPE) tumor tissues by using RNA sequencing. Assessing different tools for calling fusions from raw data, we found relevant fusions in 66 out of 101 (65%) analyzed cases in a prospective cohort collected over 26 months. In 43 (43%) cases the fusions were of decisive diagnostic relevance and in 40 (40%) cases the fusion genes rendered a druggable target. Besides the relevance of pathognomonic fusions for diagnostics, especially the detection of druggable gene fusions yields direct benefit to the patients. This approach allows for an unbiased search for fusion events in the tested samples. Besides rare variants of established fusions which were not detected by prior targeted analyses, we identified previously unreported fusion events. Exemplified on KIAA1549:BRAF fusion, we in addition provide an overview of the detection accuracy of different methods, including breakpoint detection in DNA methylation array data and fusion gene detection in DNA panel sequencing data. Our data show that RNA sequencing has great diagnostic as well as therapeutic value by clinically detecting relevant alterations.

LongGF: computational algorithm and software tool for fast and accurate detection of gene fusions by long-read transcriptome sequencing

BackgroundLong-read RNA-Seq techniques can generate reads that encompass a large proportion or the entire mRNA/cDNA molecules, so they are expected to address inherited limitations of short-read RNA-Seq techniques that typically generate < 150 bp reads. However, there is a general lack of software tools for gene fusion detection from long-read RNA-seq data, which takes into account the high basecalling error rates and the presence of alignment errors.ResultsIn this study, we developed a fast computational tool, LongGF, to efficiently detect candidate gene fusions from long-read RNA-seq data, including cDNA sequencing data and direct mRNA sequencing data. We evaluated LongGF on tens of simulated long-read RNA-seq datasets, and demonstrated its superior performance in gene fusion detection. We also tested LongGF on a Nanopore direct mRNA sequencing dataset and a PacBio sequencing dataset generated on a mixture of 10 cancer cell lines, and found that LongGF achieved better performance to detect known gene fusions over existing computational tools. Furthermore, we tested LongGF on a Nanopore cDNA sequencing dataset on acute myeloid leukemia, and pinpointed the exact location of a translocation (previously known in cytogenetic resolution) in base resolution, which was further validated by Sanger sequencing.ConclusionsIn summary, LongGF will greatly facilitate the discovery of candidate gene fusion events from long-read RNA-Seq data, especially in cancer samples. LongGF is implemented in C++ and is available at https://github.com/WGLab/LongGF.

Detection of tmprss2-erg and tmprss2-egr1 gene fusion in prostate cancer from a Chinese population

BackgroundTMPRSS2: ETS gene fusion occurs recurrently in a high proportion of prostate cancer (PCa) patients in Western countries. However, for Chinese PCa patients, no solid conclusion could be drawn from the present studies, as the results varied considerably between the limited reports.ResultsIn this study, we evaluated the prevalence of such gene rearrangements in a small number of Chinese PCa patients and discovered that 6 out of 27 (22.2%) were found to harbor the TMPRSS2: ERG fusion, the ratio was much lower than that in Western countries. Furthermore, we first identified TMPRSS2: EGR1 gene fusion, suggesting other chromosome rearrangements besides ETS gene family harbor in prostate cancer. The hybrid transcript was predicted to encode a truncated EGR1 protein by ORF finder, which might play a key role in prostate cancer.ConclusionsWe reported that the total occurrence rate of TMPRSS2: ERG fusion gene in this small group of Chinese patients was lower than the reported frequencies in European descent patients but comparable to other reported frequencies in Asian populations. The occurrence of TMPRSS2: EGR1 gene fusion suggested other chromosome rearrangements in prostate cancer.

Narrative review of molecular pathways of kinase fusions and diagnostic approaches for their detection in non-small cell lung carcinomas.

The discovery of actionable oncogenic driver alterations has significantly improved treatment options for patients with advanced non-small cell lung cancer (NSCLC). In lung adenocarcinoma (LUAD), approved drugs or drugs in clinical development can target more than half of these altered oncogenic driver genes. In particular, several gene fusions have been discovered in LUAD, including ALK, ROS1, NTRK, RET, NRG1 and FGFR. All these fusions involve tyrosine kinases (TK), which are activated due to structural rearrangements on the DNA level. Although the overall prevalence of these fusions in LUAD is rare, their detection is extremely important, as they are linked to an excellent response to TK inhibitors. Therefore, reliable screening methods applicable to small tumor samples (biopsies and cytology specimens) are required in the diagnostic workup of advanced NSCLC. Several methods are at disposal in a routine laboratory to demonstrate, directly or indirectly, the presence of a gene fusion. These methods include immunohistochemistry (IHC), fluorescence in-situ hybridization (FISH), reverse transcriptase-polymerase chain reaction (RT-PCR), multiplex digital color-coded barcode technology or next-generation sequencing (NGS) either on DNA or RNA level. In our review, we will summarize the increasing number of relevant fusion genes in NSCLC, point out their underlining molecular mechanisms and discuss different methods for the detection of fusion genes.

Development and Validation of an RNA Sequencing Assay for Gene Fusion Detection in Formalin-Fixed, Paraffin-Embedded Tumors

RNA sequencing (RNA-seq) is a well-validated tool for detecting gene fusions in fresh-frozen tumors; however, RNA-seq is much more challenging to use with formalin-fixed, paraffin-embedded (FFPE) tumor samples. We evaluated the performance of RNA-seq to detect gene fusions in clinical FFPE tumor samples. Our assay identified all 15 spiked-in NTRK fusions from RNA reference material and six known fusions from five cancer cell lines. Limit of detection for the assay was assessed with a series of dilutions of RNA from the cell line H2228. These fusions can be detected when the dilution is down to 10%. Good intra-assay and interassay reproducibility was observed in three specimens. For clinical validation, the assay detected 10 of 12 fusions initially identified by a DNA panel (covering 23 gene fusions) in clinical specimens (83.3% sensitivity), whereas one fusion (MET fusion) was identified in another 34 fusion-negative tumor specimens as determined by the DNA panel (negative prediction value of 94.3%). This MET fusion was confirmed by RT-PCR and Sanger sequencing, which found that this is a false-negative result for the DNA panel. The assay also identified 26 extra fusions not covered by the DNA panel, 20 (76.9%) of which were validated by RT-PCR and Sanger sequencing. Therefore, this RNA assay has reasonable performance and could complement DNA-based next-generation sequencing assays.

18473 Pseudomyogenic hemangioendothelioma: An aggressive case of a rare vascular tumor

A 19-year-old otherwise healthy man presented with new painful necrotic lesions on the left fifth toe and heel for four months. Symptoms began months after stepping on a foreign object and progressed rapidly despite multiple antibiotic courses. Imaging showed indeterminate findings of osteomyelitis. Noninvasive vascular studies revealed mild peroneal artery insufficiency. The patient started Aspirin and daily wound care without relief. He was then referred to Dermatology and biopsies were obtained. Histologic sections from both lesions showed a dense dermal proliferation of epitheliod to spindled cells with admixed neutrophils and eosinophils. Several immunohistochemical stains were performed: AE1/AE3(+), ERG(+), HHV8(−), Melan A(−), SOX-10(−), INI-1 (retained). Laboratory work-up was unremarkable including CBC, CMP, ESR, CRP, PT, PTT, ANA, ANCA, urinalysis, and blood cultures. The diagnosis of pseudomyogenic hemangioendothelioma was made and staging was initiated. Imaging revealed multiple tumor foci in the left metatarsal, tibia, groin, and lungs. Treatment consisted of toe amputation, wide local excision of the heel, and systemic everolimus. Pseudomyogenic hemangioendotheliomas are rare vascular tumors of intermediate malignant potential which classically present as multifocal painful nodules on the lower extremities of young males. While concurrent bone involvement can be seen in 20% of cases, distant metastases are exceedingly rare. Treatment is predominately surgical though recent detection of SERPINE1-FOSB gene fusions has prompted the use of mTOR inhibitors in unresectable tumors given their shared signaling pathways. This case represents an aggressive presentation of pseudomyogenic hemangioendothelioma with novel use of mTOR inhibitors as treatment.

Evaluation of NTRK immunohistochemistry as a screening method for NTRK gene fusion detection in non-small cell lung cancer

PurposeThe small molecule inhibitors larotrectinib and entrectinib have recently been approved as cancer agnostic drugs in patients with tumours harbouring a rearrangement of the neurotrophic tropomyosin receptor kinase (NTRK). These oncogenic fusions are estimated to occur in 0.1–3 % of non-small cell lung cancers (NSCLC). Although molecular techniques are most reliable for fusion detection, immunohistochemical analysis is considered valuable for screening. Therefore, we evaluated the newly introduced diagnostic immunohistochemical assay (clone EPR17341) on a representative NSCLC cohort. MethodsCancer tissue from 688 clinically and molecularly extensively annotated NSCLC patients were comprised on tissue microarrays and stained with the pan-TRK antibody clone EPR17341. Positive cases were further analysed with the TruSight Tumor 170 RNA assay (Illumina). Selected cases were also tested with a NanoString NTRK fusion assay. For 199 cases, NTRK RNA expression data were available from previous RNA sequencing analysis. ResultsAltogether, staining patterns for 617 NSCLC cases were evaluable. Of these, four cases (0.6 %) demonstrated a strong diffuse cytoplasmic and membranous staining, and seven cases a moderate staining (1.1 %). NanoString or TST170-analysis could not confirm an NTRK fusion in any of the IHC positive cases, or any of the cases with high mRNA levels. In the four cases with strong staining intensity in the tissue microarray, whole section staining revealed marked heterogeneity of NTRK protein expression. ConclusionThe presence of NTRK fusion genes in non-small cell lung cancer is exceedingly rare. The use of the immunohistochemical NTRK assay will result in a small number of false positive cases. This should be considered when the assay is applied as a screening tool in clinical diagnostics.

An aggressive nodular fasciitis lesion protruding from the palm (USP6 gene fusion helps differentiate from sarcomas): A case report.

Nodular fasciitis is a mesenchymal lesion, which has been viewed as a reactive process. The MYH9-USP6 fusion gene was recently detected in nodular fasciitis, and nodular fasciitis is now considered to be a self-limiting neoplastic process. Recently, a case of nodular fasciitis that recurred a number of times and metastasized to soft tissues was reported, and the features of aggressive cases of nodular fasciitis are currently under investigation. Here, a case of locally aggressive nodular fasciitis is presented, in which the lesion grew rapidly and caused ulnar nerve palsy. The lesion was locally controlled via marginal excision, and no metastasis was identified at 24 months post-operation. Histologically, the lesion was consistent with nodular fasciitis, and the detection of the MYH9-USP6 fusion gene supported the diagnosis. Although most nodular fasciitis lesions are benign, some may be locally aggressive or even metastasize. In the case outlined in the present study, marginal excision was sufficient to locally control the lesion.

Integration of whole-exome and anchored PCR-based next generation sequencing significantly increases detection of actionable alterations in precision oncology

BackgroundFrequency of clinically relevant mutations in solid tumors by targeted and whole-exome sequencing is ∼30%. Transcriptome analysis complements detection of actionable gene fusions in advanced cancer patients. Goal of this study was to determine the added value of anchored multiplex PCR (AMP)-based next-generation sequencing (NGS) assay to identify further potential drug targets, when coupled with whole-exome sequencing (WES). MethodsSelected series of fifty-six samples from 55 patients enrolled in our precision medicine study were interrogated by WES and AMP-based NGS. RNA-seq was performed in 19 cases. Clinically relevant and actionable alterations detected by three methods were integrated and analyzed. ResultsAMP-based NGS detected 48 fusions in 31 samples (55.4%); 31.25% (15/48) were classified as targetable based on published literature. WES revealed 29 samples (51.8%) harbored targetable alterations. TMB-high and MSI-high status were observed in 12.7% and 1.8% of cases. RNA-seq from 19 samples identified 8 targetable fusions (42.1%), also captured by AMP-based NGS. When number of actionable fusions detected by AMP-based NGS were added to WES targetable alterations, 66.1% of samples had potential drug targets. When both WES and RNA-seq were analyzed, 57.8% of samples had targetable alterations. ConclusionsThis study highlights importance of an integrative genomic approach for precision oncology, including use of different NGS platforms with complementary features. Integrating RNA data (whole transcriptome or AMP-based NGS) significantly enhances detection of potential targets in cancer patients. In absence of fresh frozen tissue, AMP-based NGS is a robust method to detect actionable fusions using low-input RNA from archival tissue.

Efficient DNA Walker Guided with Well-Regulated Interfacial Tracks for Ultrasensitive Electrochemiluminescence Biosensing.

Herein, highly efficient deoxyribonucleic acid (DNA) walking on electrode surfaces was realized by regulating DNA tracks, which was applied to construct an ultrasensitive electrochemiluminescent (ECL) biosensor for BCR/ABL fusion gene detection. The well-regulated DNA tracks were constructed via supersandwich hybridization chain reaction of two DNA strands (L1 and L2) to generate periodic linear dsDNA concatemers, where an exposed L1 domain closed with blocking strands (BS). The prepared DNA tracks were further assembled onto the surface of the Au nanoparticle-functionalized g-C3N4 nanohybrid (Au@g-C3N4 NHs)-modified electrode, achieving well-regulated interfacial tracks for the DNA walker. On this state, folic acid-labeled BS (FA-BS) were close to Au@g-C3N4 NHs, performing a quenched ECL emission. With existence of the BCR/ABL fusion gene, the target combined two walking DNA strands (WD1 and WD2) to form the bipedal DNA walkers, which walked on the well-regulated interfacial DNA tracks and replaced the FA-BS to light up the ECL emission, realizing DNA walker-based signal amplification. Compared to randomly constructed DNA tracks, the well-regulated DNA tracks reduced the kinetics barrier and fitted the step size of the DNA walker, thus promoting the DNA walking efficiency and decreasing the risk of interruption in the walking process. As a result, the designed DNA walker presented higher efficiency and capacity in signal amplification. Benefiting from this efficient DNA walker strategy, the ECL biosensor achieved sensitive detection of the BCR/ABL fusion gene with a detection limit of 0.18 fM. This smart strategy proposed a brief strategy to promote the working efficiency of the biosensor, which presented great application potential in clinical molecular diagnosis.

Long-Term Outcomes Following Donor-Derived Anti-CD19 CAR-T Cell Therapy for B-Cell Acute Lymphoblastic Leukemia Patients Relapsed after Allogenic Stem Cell Transplantation

Background: Patients with B cell acute lymphoblastic leukemia (B-ALL) relapsed after allogenic hematopoietic stem cell transplantation(alloHSCT) have poor prognosis and the median survival after relapse was 4 - 5.5 months, estimated 2-year post-relapse survival rates were 10 - 16%. Donor lymphocyte infusion (DLI) have shown limited success in the setting of relapse by a mere increase in median survival by 6 months and a significant risk of acute and chronic graft-versus-host disease (GVHD) and additional risk of marrow aplasia. The donor chimeric antigen receptor-T cell (CAR-T) for CD19 is a promising treatment for relapsed and refractory B-ALL, but the effectiveness and safety of donor-derived CD19 CAR-T cell infusion for relapsed B-ALL after alloHSCT have not been determined. Methods: Between July 2017 and Nov 2018, 10 adult patients with B-ALL relapsed (4 patients were hematologic relapsed, 3 patients were extramedullary relapse, the other 3 patients were bone marrow MRD-positive, Table) after alloHSCT were enrolled, including 9 sibling-matched stem cell transplantation and 1 haploidentical transplantation. About 100 - 200 ml venous blood form each donor was obtained and the T cells were separated. Then donor's T cells were infected with lentivirus carrying CD19 CAR plasmid which containing CD19 scfv (HI-19 clone) and 4-1BB-CD3ζ signaling domains to generate CAR-T cells. ALL the 10 Patients received FAC (fludarabine: 25-30mg/m2/d*3, cyclophosphamide:350mg/m2/d*2, cytosine arabinoside:100mg/m2/d*4) pretreatment and then a total of 5.01 × 106/kg (range, 3.39 - 6.53 × 106/kg) donor T cells including donor-derived anti-CD19 CAR-T cell (1.82 × 106/kg, (range, 1.26 - 4.67 × 106/kg)) was infused on 2 or 3 consecutive days for each patient. The levels of cytokines including IL-1,IL-2R,IL-6,IL-8,IL-10 and the percentage of the donor anti-CD19 CAR-T cells were monitored serially . Clinical manifest and the severity of cytokine release syndrome (CRS) were recorded and evaluated. The bone marrow examination was performed every 2 weeks after CAR T-cell infusion to assess the response for the first 2 months and then was performed every 1-3 months including bone marrow smear, MRD detection by flow cytometry, fusion gene detection by quantitative real-time polymerase chain reaction (qPCR), donor chimera rate by short tandem repeat(STR). Results: The median transduction efficiency of the final donor-derived CD19 CAR-T cells was 35.8%(range 25 - 70.6%). The peak of donor-derived anti-CD19 CAR-T cell expansion in the recipients was about 7 - 14days after infusion and then decreased rapidly. The serum cytokines levels varied differently: the serum IL-6 and IL-2R levels increased overtly and reached the peak during day 5 - day 7 in most of the patients, whereas the serum levels of IL-1, IL-8 and IL-10 did not vary obviously. one patient experienced Grade 3 CRS, 4 patients experienced Grade 2 CRS and the other 5 patients only experienced Grade 1 CRS. Four patients showed encephalopathy and 2 patients received glucocorticoid treatment. All the 10 patients achieved MRD negative remission and complete donor chimerism within 14days to 42days after donor's CAR-T cells infusion. No patients developed acute or chronic graft-versus-host disease (GVHD). After a median follow-up of 20.6 months (range, 13.4-30.3), 5 patients (including all the 3 patients with extramedullary relapse) relapsed with leukemia cells CD19-dim and 4 of them died due to disease progression. Only one patient received a successful secondary alloHSCT from a haplo-identical donor. The other 5 patients showed persistent complete donor chimerism with MRD negative remission(Figure). The estimated 2-year overall survival and leukemia-free survival were 68.6% and 48.0%, 2.5-year OS and LFS were 51.4% and 48.0%. Conclusion: Donor-derived CD19 CAR-T cell infusion seems to be an effective and safe treatment for B-ALL relapsed after alloHSCT, especially for those without extramedullary disease, which may be confirmed with more clinical studies. Disclosures No relevant conflicts of interest to declare.