Spindle cell neoplasms with novel LTK fusion - Expanding the spectrum of kinase fusion-positive soft tissue tumors.

AIMS: Kinase fusion-positive soft tissue tumors represent an emerging, molecularly defined group of mesenchymal tumors with a wide morphologic spectrum and diverse activating kinases. Here, we present two cases of soft tissue tumors with novel LTK fusions. METHODS AND RESULTS: Both cases presented as acral skin nodules (big toe and middle finger) in pediatric patients (17-year-old girl and 2-year-old boy). The tumors measured 2 and 3 cm in greatest dimension. Histologically, both cases exhibited bland-looking spindle cells infiltrating adipose tissue and accompanied by collagenous stroma. One case additionally displayed perivascular hyalinization and band-like stromal collagen. Both cases exhibited focal S100 staining, and one case had patchy coexpression of CD34. Targeted RNA-seq revealed the presence of novel in-frame MYH9::LTK and MYH10::LTK fusions, resulting in upregulation of LTK expression. Of interest, DNA methylation-based unsupervised clustering analysis in one case showed that the tumor clustered with dermatofibrosarcoma protuberans (DFSP). One tumor was excised with amputation with no local recurrence or distant metastasis at 18-month follow-up. The other case was initially marginally excised with local recurrence after one year, followed by wide local excision, with no evidence of disease at 10 years of follow-up. CONCLUSIONS: This is the first reported case series of soft tissue tumors harboring LTK fusion, expanding the molecular landscape of soft tissue tumors driven by activating kinase fusions. Furthermore, studies involving a larger number of cases and integrated genomic analyses will be warranted to fully elucidate the pathogenesis and classification of these tumors.

A Collaborative Classroom Investigation of the Evolution of SABATH Methyltransferase Substrate Preference Shifts over 120 My of Flowering Plant History.

Next-generation sequencing has resulted in an explosion of available data, much of which remains unstudied in terms of biochemical function; yet, experimental characterization of these sequences has the potential to provide unprecedented insight into the evolution of enzyme activity. One way to make inroads into the experimental study of the voluminous data available is to engage students by integrating teaching and research in a college classroom such that eventually hundreds or thousands of enzymes may be characterized. In this study, we capitalize on this potential to focus on SABATH methyltransferase enzymes that have been shown to methylate the important plant hormone, salicylic acid (SA), to form methyl salicylate. We analyze data from 76 enzymes of flowering plant species in 23 orders and 41 families to investigate how widely conserved substrate preference is for SA methyltransferase orthologs. We find a high degree of conservation of substrate preference for SA over the structurally similar metabolite, benzoic acid, with recent switches that appear to be associated with gene duplication and at least three cases of functional compensation by paralogous enzymes. The presence of Met in active site position 150 is a useful predictor of SA methylation preference in SABATH methyltransferases but enzymes with other residues in the homologous position show the same substrate preference. Although our dense and systematic sampling of SABATH enzymes across angiosperms has revealed novel insights, this is merely the "tip of the iceberg" since thousands of sequences remain uncharacterized in this enzyme family alone.

A macrodomain-linked immunosorbent assay (MLISA) for mono-ADP-ribosyltransferases.

ADP-ribosyltransferases (ARTs) catalyze reversible additions of mono- and poly-ADP-ribose onto diverse types of proteins by using nicotinamide adenine dinucleotide (NAD+) as a cosubstrate. In the human ART superfamily, 14 out of 20 members are shown to catalyze endogenous protein mono-ADP-ribosylation and play important roles in regulating various physiological and pathophysiological processes. Identification of new modulators of mono-ARTs can thus potentially lead to discovery of novel therapeutics. In this study, we developed a macrodomain-linked immunosorbent assay (MLISA) for characterizing mono-ARTs. Recombinant macrodomain 2 from poly-ADP-ribose polymerase 14 (PARP14) was generated with a C-terminal human influenza hemagglutinin (HA) tag for detecting mono-ADP-ribosylated proteins. Coupled with an anti-HA secondary antibody, the generated HA-tagged macrodomain 2 reveals high specificity for mono-ADP-ribosylation catalyzed by distinct mono-ARTs. Kinetic parameters of PARP15-catalyzed automodification were determined by MLISA and are in good agreement with previous studies. Eight commonly used chemical tools for PARPs were examined by MLISA with PARP15 and PARP14 in 96-well plates and exhibited moderate inhibitory activities for PARP15, consistent with published reports. These results demonstrate that MLISA provides a new and convenient method for quantitative characterization of mono-ART enzymes and may allow identification of potent mono-ART inhibitors in a high-throughput-compatible manner.

Building carbon-carbon bonds using a biocatalytic methanol condensation cycle.

Methanol is an important intermediate in the utilization of natural gas for synthesizing other feedstock chemicals. Typically, chemical approaches for building C-C bonds from methanol require high temperature and pressure. Biological conversion of methanol to longer carbon chain compounds is feasible; however, the natural biological pathways for methanol utilization involve carbon dioxide loss or ATP expenditure. Here we demonstrated a biocatalytic pathway, termed the methanol condensation cycle (MCC), by combining the nonoxidative glycolysis with the ribulose monophosphate pathway to convert methanol to higher-chain alcohols or other acetyl-CoA derivatives using enzymatic reactions in a carbon-conserved and ATP-independent system. We investigated the robustness of MCC and identified operational regions. We confirmed that the pathway forms a catalytic cycle through (13)C-carbon labeling. With a cell-free system, we demonstrated the conversion of methanol to ethanol or n-butanol. The high carbon efficiency and low operating temperature are attractive for transforming natural gas-derived methanol to longer-chain liquid fuels and other chemical derivatives.

Rapid and efficient differentiation of human pluripotent stem cells into intermediate mesoderm that forms tubules expressing kidney proximal tubular markers.

Human pluripotent stem cells (hPSCs) can generate a diversity of cell types, but few methods have been developed to derive cells of the kidney lineage. Here, we report a highly efficient system for differentiating human embryonic stem cells and induced pluripotent stem cells (referred to collectively as hPSCs) into cells expressing markers of the intermediate mesoderm (IM) that subsequently form tubule-like structures. Treatment of hPSCs with the glycogen synthase kinase-3ß inhibitor CHIR99021 induced BRACHYURY(+)MIXL1(+) mesendoderm differentiation with nearly 100% efficiency. In the absence of additional exogenous factors, CHIR99021-induced mesendodermal cells preferentially differentiated into cells expressing markers of lateral plate mesoderm with minimal IM differentiation. However, the sequential treatment of hPSCs with CHIR99021 followed by fibroblast growth factor-2 and retinoic acid generated PAX2(+)LHX1(+) cells with 70%-80% efficiency after 3 days of differentiation. Upon growth factor withdrawal, these PAX2(+)LHX1(+) cells gave rise to apically ciliated tubular structures that coexpressed the proximal tubule markers Lotus tetragonolobus lectin, N-cadherin, and kidney-specific protein and partially integrated into embryonic kidney explant cultures. With the addition of FGF9 and activin, PAX2(+)LHX1(+) cells specifically differentiated into cells expressing SIX2, SALL1, and WT1, markers of cap mesenchyme nephron progenitor cells. Our findings demonstrate the effective role of fibroblast growth factor signaling in inducing IM differentiation in hPSCs and establish the most rapid and efficient system whereby hPSCs can be differentiated into cells with features characteristic of kidney lineage cells.

Regenerating the nephron with human pluripotent stem cells.

PURPOSE OF REVIEW: Nephrogenesis in humans is limited to the period of embryonic kidney development in utero, with no new nephrons formed after birth. Although the kidneys possess the capacity to self-repair segments of the nephron, nephron loss from acute or chronic kidney injury is irreversible and results in impaired function. Human pluripotent stem cells (PSCs), including embryonic stem cells and induced pluripotent stem cells, are an attractive source of cells to regenerate nephron progenitor cells (NPCs) and ultimately functional kidney tissue. NPCs are found exclusively during the period of embryonic development, but their nephron-forming capacity makes them an ideal cell population to regenerate with PSCs. RECENT FINDINGS: Significant progress has been made in the effort to direct the differentiation of human PSCs into NPCs. Differentiation protocols designed to recapitulate the complex process of kidney organogenesis in vitro can generate cells that express characteristic NPC markers and these cells can assemble into three-dimensional nephron-like structures. Additional studies are required to evaluate the functionality of these putative kidney cells and to test their ability to integrate into three-dimensional organized kidney tissue structures, either spontaneously or facilitated by bioengineered structures or scaffolds with appropriate matrix materials. SUMMARY: The successful recreation of human nephrons from PSCs would offer a novel therapeutic approach to treating patients with kidney disease.

Membranous nephropathy as a manifestation of graft-versus-host disease: association with HLA antigen typing, phospholipase A2 receptor, and C4d.

Glomerulopathy is an uncommon but increasingly recognized complication of hematopoietic cell transplantation. It typically manifests as membranous nephropathy, less commonly as minimal change disease, and rarely as proliferative glomerulonephritis. There is evidence to suggest that these glomerulopathies might represent manifestations of chronic graft-versus-host disease. In this report, we focus on membranous nephropathy as the most common form of glomerulopathy after hematopoietic cell transplantation. We present a case of membranous nephropathy that developed 483 days post-allogeneic hematopoietic stem cell transplantation in a patient with a history of acute graft-versus-host disease. We also share our experience with 4 other cases of membranous nephropathy occurring after allogeneic hematopoietic stem cell transplantation. Clinicopathologic correlates, including the association with graft-versus-host-disease, HLA antigen typing, glomerular deposition of immunoglobulin G (IgG) subclasses, subepithelial colocalization of IgG deposits with phospholipase A2 receptor staining, C4d deposition along the peritubular capillaries, and treatment, are discussed with references to the literature.

Reduced ciliary polycystin-2 in induced pluripotent stem cells from polycystic kidney disease patients with PKD1 mutations.

Heterozygous mutations in PKD1 or PKD2, which encode polycystin-1 (PC1) and polycystin-2 (PC2), respectively, cause autosomal dominant PKD (ADPKD), whereas mutations in PKHD1, which encodes fibrocystin/polyductin (FPC), cause autosomal recessive PKD (ARPKD). However, the relationship between these proteins and the pathogenesis of PKD remains unclear. To model PKD in human cells, we established induced pluripotent stem (iPS) cell lines from fibroblasts of three ADPKD and two ARPKD patients. Genetic sequencing revealed unique heterozygous mutations in PKD1 of the parental ADPKD fibroblasts but no pathogenic mutations in PKD2. Undifferentiated PKD iPS cells, control iPS cells, and embryonic stem cells elaborated primary cilia and expressed PC1, PC2, and FPC at similar levels, and PKD and control iPS cells exhibited comparable rates of proliferation, apoptosis, and ciliogenesis. However, ADPKD iPS cells as well as somatic epithelial cells and hepatoblasts/biliary precursors differentiated from these cells expressed lower levels of PC2 at the cilium. Additional sequencing confirmed the retention of PKD1 heterozygous mutations in iPS cell lines from two patients but identified possible loss of heterozygosity in iPS cell lines from one patient. Furthermore, ectopic expression of wild-type PC1 in ADPKD iPS-derived hepatoblasts rescued ciliary PC2 protein expression levels, and overexpression of PC1 but not a carboxy-terminal truncation mutant increased ciliary PC2 expression levels in mouse kidney cells. Taken together, these results suggest that PC1 regulates ciliary PC2 protein expression levels and support the use of PKD iPS cells for investigating disease pathophysiology.

A ribose-functionalized NAD+ with versatile activity for ADP-ribosylation.

An NAD+ featuring an adenosyl 4'-azido functions as a general substrate for poly-ADP-ribose polymerases. Its derived mono- and poly-ADP-ribosylated proteins can be adequately recognized by distinct ADP-ribosylation-specific readers. This molecule represents the first ribose-functionalized NAD+ with versatile activities across different ADP-ribosyltransferases and provides insight into developing new probes for ADP-ribosylation.

Novel MAP4::RAF1 Fusion in a Primary Bone Sarcoma: Expanding the spectrum of RAF1 Fusion Sarcoma.

Soft tissue tumors with RAF1 fusion had been emerging as a group of tumors with peculiar histology and immunoprofile. While a case series and rare case reports of RAF1 translocated sarcoma had been reported, to our knowledge a primary bone tumor with RAF1 translocation and fusion partner with MAP4 had not been described in the literature. The patient was a 60-year-old lady, with strong family history of breast cancer, who presented with pathological fracture of right humerus. X-ray revealed a 9.7 cm juxta-articular lesion of the proximal humerus, which was expansile and lytic with a non-sclerotic well defined border distally, radiologically suggestive of a giant cell tumor of bone. Excision was performed after initial biopsy. Histology showed a monomorphic low grade spindle cell lesion with prominent hyalinized stroma. Immunohistochemistry demonstrated diffuse CD34 staining, with focal staining for S100. Gene sequencing for histone 3 H3 genes was negative for hotspot mutation. Targeted RNA-seq sequencing revealed the presence of MAP4::RAF1 fusion, which was confirmed by reverse transcriptase-polymerase chain reaction (RT-PCR) and fluorescence in-situ hybridization (FISH) break-apart probes involving both genes. The overall features were consistent with a primary bone sarcoma with RAF1 fusion. This report expanded the spectrum of RAF1 fusion sarcoma and was the first report documenting its primary occurrence in bone.

Effectiveness of population-based colorectal cancer screening programme in down-staging.

BACKGROUND: This is the first evaluation study to assess the demographic characteristics of the colorectal cancer (CRC) cases detected in the prevalent round of the population-based Colorectal Cancer Screening Programme (CRCSP) in Hong Kong and to explore the effectiveness of the programme on the stage distribution of CRC. METHODS: This study covered the period between 28 September 2016 and 31 December 2018. Information on CRC diagnosis, age and stage at diagnosis were retrieved and reviewed by the Hong Kong Cancer Registry (HKCaR). The CRC detection rate among CRCSP-screened participants and incidence rate among the Hong Kong general population were calculated respectively. The odds ratio (OR) was calculated to measure the strength of association and quantify the effect of CRCSP on stage shift between CRCSP-detected CRC cases and an age-matched cohort of CRC cases diagnosed outside the programme. RESULTS: The CRC detection rate among participants of the CRCSP during the study period was 736.0/100,000, whereas the overall CRC incidence rate among general population of similar age groups was 393.7/100,000. For all ages and both sexes, the OR of stage I CRCSP-detected CRC compared to the CRC from the age-matched cohort was 3.91 (95%CI=3.41-4.48) and the OR dropped to 0.54 (95%CI=0.41-0.70) at stage IV. Meanwhile, the overall OR of CRCSP-detected CRC compared to CRC from the age-matched cohort dropped from 2.24 (95%CI=1.97-2.56) to 1.62 (95%CI=1.40-1.87) with increasing age. CONCLUSION: The present study has demonstrated the initial impact of the CRCSP on shifting the stage at diagnosis towards earlier stage. The benefit of stage-shift was similar for all ages from 60 to 77 in both sexes and seems to increase with younger age. Given the stage-dependent survival outcomes, this stage-shift could lead to a reduction in CRC-associated mortality in Hong Kong in future.

Discovery of an NAD+ analogue with enhanced specificity for PARP1.

Among various protein posttranslational modifiers, poly-ADP-ribose polymerase 1 (PARP1) is a key player for regulating numerous cellular processes and events through enzymatic attachments of target proteins with ADP-ribose units donated by nicotinamide adenine dinucleotide (NAD+). Human PARP1 is involved in the pathogenesis and progression of many diseases. PARP1 inhibitors have received approvals for cancer treatment. Despite these successes, our understanding about PARP1 remains limited, partially due to the presence of various ADP-ribosylation reactions catalyzed by other PARPs and their overlapped cellular functions. Here we report a synthetic NAD+ featuring an adenosyl 3'-azido substitution. Acting as an ADP-ribose donor with high activity and specificity for human PARP1, this compound enables labelling and profiling of possible protein substrates of endogenous PARP1. It provides a unique and valuable tool for studying PARP1 in biology and pathology and may shed light on the development of PARP isoform-specific modulators.

Disturbance-Aware Neuro-Optimal System Control Using Generative Adversarial Control Networks.

Disturbance, which is generally unknown to the controller, is unavoidable in real-world systems and it may affect the expected system state and output. Existing control methods, like robust model predictive control, can produce robust solutions to maintain the system stability. However, these robust methods trade the solution optimality for stability. In this article, a method called generative adversarial control networks (GACNs) is proposed to train a controller via demonstrations of the optimal controller. By formulating the optimal control problem in the presence of disturbance, the controller trained by GACNs obtains neuro-optimal solutions without knowing the future disturbance and determines the objective function explicitly. A joint loss, composed of the adversarial loss and the least square loss, is designed to be used in the training of the generator. Experimental results on simulated systems with disturbance show that GACNs outperform other compared control methods.

Surgeon Performed Ultrasound for Diagnosis of Intussusception - A Pilot Study.

Aim: To study the diagnostic accuracy of surgeon performed ultrasound (SPU) in the diagnosis of children presenting with clinical suspicion of intussusception to a tertiary paediatric facility in NSW, Australia. Methods: Children under the age of 16 presenting to the emergency department with clinical features suggestive of intussusception were recruited. After obtaining consent SPU was performed by a Paediatric surgeon. All patients subsequently had an ultrasound performed in radiology department (RPU) on which management was based. Diagnosis and images of SPU were reviewed by an independent radiologist blinded to results of the formal study. Results: Of 7 children enrolled 5 were male. Age ranged from 3 months to 7 years (mean 2.64, SD 2.282), weight from 5.2kgs to 25.2kgs (mean 13.69, SD 6.721). Five out of the 7 children presented during day hours i.e. 8a.m.-5 p.m. (mean 12.72, SD 4.049). Mean time to SPU was 6.3 hours (SD7.1) and RPU was 8.3 hours (SD 7.6). SPU was earlier by 2 hours and correlation between SPU and RPU was 100 percent. Conclusion: SPU for intussusception can be performed early and accurately. Surgeons should train and use ultrasound as a reliable tool in evaluating the child with suspected intussusception.

Case report on metastatic pelvic bone tumor treated with frozen autograft by liquid nitrogen.

INTRODUCTION AND IMPORTANCE: Frozen autograft recycling has been used for biological reconstruction of bone defects following tumor excision, more commonly in extremities. We report on the histological outcome of a pelvic recycled frozen autograft. CASE PRESENTATION: We investigated the pelvic frozen autograft removed in 2 years and 8 months after surgery because of soft tissue recurrence in pelvic floor. The autograft bone showed no evidence of revitalization and was non-viable with patchy inflammation, and no residual tumor. There was only fibrous union but the autograft bone remained mechanically stable. CLINICAL DISCUSSION: We confirmed the clearance of tumor cells with the treatment with liquid nitrogen. The union at the host-graft junction might be affected by the previous radiotherapy, the presence of infection, the small contact area limited by the anatomy, and the inadequate compression across the osteotomy interface with the fixation. CONCLUSION: Frozen autograft treated by liquid nitrogen can be used safely for biological reconstructions after pelvic tumor excision.

A Bifunctional NAD+ for Profiling Poly-ADP-Ribosylation-Dependent Interacting Proteins.

Protein poly-ADP-ribosylation (PARylation) is a heterogeneous and dynamic post-translational modification regulated by various writers, readers, and erasers. It participates in a variety of biological events and is involved in many human diseases. Currently, tools and technologies have yet to be developed for unambiguously defining readers and erasers of individual PARylated proteins or cognate PARylated proteins for known readers and erasers. Here, we report the generation of a bifunctional nicotinamide adenine dinucleotide (NAD+) characterized by diazirine-modified adenine and clickable ribose. By serving as an excellent substrate for poly-ADP-ribose polymerase 1 (PARP1)-catalyzed PARylation, the generated bifunctional NAD+ enables photo-cross-linking and enrichment of PARylation-dependent interacting proteins for proteomic identification. This bifunctional NAD+ provides an important tool for mapping cellular interaction networks centered on protein PARylation, which are essential for elucidating the roles of PARylation-based signals or activities in physiological and pathophysiological processes.

A child with acute myeloid leukemia complicated by calcaneal osteomyelitis due to Mycobacterium abscessus infection after induction chemotherapy successfully salvaged with bedaquiline and clofazimine.

Our patient was a 4-year-old female with acute myeloid leukemia complicated with right calcaneal osteomyelitis due to Mycobacterium abscessus with subcutaneous abscesses extending to the popliteal and groin regions after two courses of induction chemotherapy according to NOPHO-AML 2012 protocol. She required multiple operations and prolonged anti-mycobacterial therapy. A high index of suspicion for mycobacterial infection is required for immunocompromised patients with prolonged fever or unusual presentation. Mycobacterial osteomyelitis is rare, difficult to diagnose and treat, and may necessitate prolonged interruption of anti-leukemic therapy. Multidisciplinary collaboration in patient management is crucial. Long-term toxicity of antimicrobials with uncertain efficacy should not be overlooked.

Anti-FLT3 nanoparticles for acute myeloid leukemia: Preclinical pharmacology and pharmacokinetics.

FLT3 receptor is an important therapeutic target in acute myeloid leukemia due to high incidence of mutations associated with poor clinical outcome. Targeted therapies against the FLT3 receptor, including small-molecule FLT3 tyrosine kinase inhibitors (TKIs) and anti-FLT3 antibodies, have demonstrated promising preclinical and even clinical efficacy. Yet, even with the current FDA approval for two FLT3 inhibitors, these modalities were unable to cure AML or significantly extend the lives of patients with a common mutation called FLT3-ITD. While FLT3 is a viable target, the approaches to inhibit its activity were inadequate. To develop a new modality for targeting FLT3, our team engineered an α-FLT3-A192 fusion protein composed of a single chain variable fragment antibody conjugated with an elastin-like polypeptide. These fusion proteins assemble into multi-valent nanoparticles with excellent stability and pharmacokinetic properties as well as in vitro and in vivo pharmacological activity in cellular and xenograft murine models of AML. In conclusion, α-FLT3-A192 fusions appear to be a viable new modality for targeting FLT3 in AML and warrant further preclinical development to bring it into the clinic.

Transfer of the anterior gluteus maximus to address abductor deficiency following soft tissue tumour excision.

Hip abductor deficiency is most commonly encountered in the context of degeneration of the hip, and techniques for reconstruction pioneered by arthroplasty surgeons. We adopted a local muscle transfer technique utilizing the anterior half of the gluteus maximus for abductor reconstruction following soft tissue tumour excision in a young female patient. The patient of concern had a solitary fibrous tumour located between the right gluteus medius and minimus detected as an incidental finding. Marginal excision of the mass resulted in removal of the gluteus medius. The anterior half of the gluteus maximus was transferred and attached to the decorticated lateral greater trochanter by means of suture anchors and transosseous sutures. The patient initially demonstrated a Trendelenburg gait and limited abduction against gravity. By 1-year post-operation, there was return of normal gait and recovery of hip abductor power. This is the first report of anterior gluteus maximus transfer being successfully applied for soft tissue reconstruction around the hip subsequent to tumour excision.