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Supplementary Figure 1 from The Cytoplasmic Deacetylase HDAC6 Is Required for Efficient Oncogenic Tumorigenesis

Histone deacetylase inhibitors (HDACI) are promising antitumor agents. Although transcriptional deregulation is thought to be the main mechanism underlying their therapeutic effects, the exact mechanism and targets by which HDACIs achieve their antitumor effects remain poorly understood. It is not known whether any of the HDAC members support robust tumor growth. In this report, we show that HDAC6, a cytoplasmic-localized and cytoskeleton-associated deacetylase, is required for efficient oncogenic transformation and tumor formation. We found that HDAC6 expression is induced upon oncogenic Ras transformation. Fibroblasts deficient in HDAC6 are more resistant to both oncogenic Ras and ErbB2-dependent transformation, indicating a critical role for HDAC6 in oncogene-induced transformation. Supporting this hypothesis, inactivation of HDAC6 in several cancer cell lines reduces anchorage-independent growth and the ability to form tumors in mice. The loss of anchorage-independent growth is associated with increased anoikis and defects in AKT and extracellular signal-regulated kinase activation upon loss of adhesion. Lastly, HDAC6-null mice are more resistant to chemical carcinogen-induced skin tumors. Our results provide the first experimental evidence that a specific HDAC member is required for efficient oncogenic transformation and indicate that HDAC6 is an important component underlying the antitumor effects of HDACIs. [Cancer Res 2008;68(18):7561–9]

In this work, we demonstrate a novel In0.52Al0.48As based top-illuminated avalanche photodiode (APD), designed to circumvent the problem of serious bandwidth degradation under high gain (>100) and high power operation and significantly enhance the dynamic range in the established frequency modulated continuous wave (FMCW) lidar system. In our APD design, the carriers transiting through the dual multiplication (M-)layers are subjected to a stepped-up electric field profile, so they can be energized by the first step and propagate to the second step to trigger the avalanche processes. Such a cascade avalanche process leads to an ultra-high gain bandwidth product (460 GHz) with a 1 A/W responsivity at unit gain. Compared to the high-performance and commercial p-i-n PD and photo-receiver (PD + trans-impedance amplifier (TIA)) installed in the same lidar test bed, our demonstrated APD receiver (without TIA) has a larger S/N ratio under high operation gain (33 A/W) with less optical local-oscillator (LO) power required (0.25 vs. 0.5 mW), while exhibiting a wider dynamic range in each pixel. These advantages in turn lead to the construction of a better quality of 3-D lidar image by using the demonstrated APD.

We carry out an In0.53Ga0.47As/In0.52Al0.48As single photon avalanche diode which exhibits a single photon detection efficiency exceeding 60% at 1310 nm and neat temporal characteristic of 65 ps. A novel concept of dual multiplication layer is incorporated to avoid the tradeoff between dark count rate, afterpulsing and timing jitter, paving the possibility to improve the overall performance of a single photon detector. Based on this elevated device structure, we further optimize the detection efficiency and timing jitter by employing a delicate mesa structure to better confine the electric field distribution within the central multiplication region. For our detector operated under gated mode, a shorten gate width together with an increase of excess bias percentage leads to a significant improvement in the detection performance. We eventually achieve a single photon detection efficiency of 61.4% without the involvement of afterpulsing at the gating frequency of 10 kHz for 200 K.

Patients with multiple myeloma (MM) who are treated with lenalidomide rarely develop a secondary B-cell acute lymphoblastic leukemia (B-ALL). The clonal and biological relationship between these sequential malignancies is not yet clear. We identified 17 patients with MM treated with lenalidomide, who subsequently developed B-ALL. Patient samples were evaluated through sequencing, cytogenetics/fluorescence in situ hybridization (FISH), immunohistochemical (IHC) staining, and immunoglobulin heavy chain (IgH) clonality assessment. Samples were assessed for shared mutations and recurrently mutated genes. Through whole exome sequencing and cytogenetics/FISH analysis of 7 paired samples (MM vs matched B-ALL), no mutational overlap between samples was observed. Unique dominant IgH clonotypes between the tumors were observed in 5 paired MM/B-ALL samples. Across all 17 B-ALL samples, 14 (83%) had a TP53 variant detected. Three MM samples with sufficient sequencing depth (>500×) revealed rare cells (average of 0.6% variant allele frequency, or 1.2% of cells) with the same TP53 variant identified in the subsequent B-ALL sample. A lack of mutational overlap between MM and B-ALL samples shows that B-ALL developed as a second malignancy arising from a founding population of cells that likely represented unrelated clonal hematopoiesis caused by a TP53 mutation. The recurrent variants in TP53 in the B-ALL samples suggest a common path for malignant transformation that may be similar to that of TP53-mutant, treatment-related acute myeloid leukemia. The presence of rare cells containing TP53 variants in bone marrow at the initiation of lenalidomide treatment suggests that cellular populations containing TP53 variants expand in the presence of lenalidomide to increase the likelihood of B-ALL development.

Quality variables, which are usually measured offline, play important roles in describing process behaviors. However, online data obtained from soft sensors are significant as they provide accurate and immediate information. The reliability of online soft sensors is questionable due to changes in sensors, equipment, raw material availability, and operation conditions. In addition, chemical plants have dynamic properties and complex correlations amidst a large number of process variables. This causes most of the predictions obtained from steady-state soft sensors to be inaccurate in representing the particular chemical process. In this paper, the latent dynamic variational autoencoder is proposed to provide an estimation model and supervise soft-sensors. The input data are encoded in the latent space to remove underlying noises and disturbances in the data. Afterward, the dynamical properties are learned in the latent space through the bi-directional recurrent neural network, whose output (latent variable) is used to reconstruct back the input data. A simulation case study is conducted to show the effectiveness of the proposed method.

In this work, we demonstrate the high-power and high-responsivity performance of the dual multiplication (M-) layers in In0.52Al0.48As based avalanche photodiode (APD). The dual M-layer design in our APD structure effectively constrains the multiplication process to a thin high-field region rather than the whole thick M-layer. It thus minimizes the space charge effect (SCE) within and avoids increasing the tunneling dark current for the case of directly shrinking M-layer thickness in APD. Furthermore, by combining the specially designed mesa shape with this dual M-layer structure, the edge breakdown can be well suppressed. These benefits lead to an ultra-high gain-bandwidth product (450 GHz; 1 A/W at unit gain) and a high saturation current (>12 mA) can be simultaneously achieved in our device. By nonlinearly driving a wavelength sweeping laser in the self-heterodyne lidar setup, it can generate an optical pulse train-like waveform, providing an effective optical modulation depth of 200% to feed into our demonstrated APD at the receiver-end. Under such scheme, the photo-generated RF (1 GHz) power from our APD with a 6.3 A/W responsivity can be as high as +6.95 dBm at a high (7 mA) output photocurrent. Such high-power and high-responsivity characteristics of our APD can further improve the signal-to-noise (S/N) ratio and dynamic range performances in each pixel of the lidar image. A high-quality 3-dimensional (D) FMCW lidar image is constructed based on our APD, without the integration of any electrical amplifier at the receiver end.

Postzygotic (somatic) variants in the mTOR pathway genes cause a spectrum of distinct developmental abnormalities. Accurate classification of somatic variants in this group of disorders is crucial for affected individuals and their families.The ClinGen Brain Malformation Variant Curation Expert Panel was formed to curate somatic variants associated with developmental brain malformations. We selected the genes AKT3, MTOR, PIK3CA, and PIK3R2 as the first set of genes to provide additional specifications to the 2015 American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) sequence variant interpretation guidelines, which currently focus solely on germline variants.A total of 24 of the original 28 ACMG/AMP criteria required modification. Several modifications used could be applied to other genes and disorders in which somatic variants play a role: 1) using variant allele fraction differences as evidence that somatic mutagenesis occurred as a proxy for de novo variation, 2) incorporating both somatic and germline evidence, and 3) delineating phenotype on the basis of variable tissue expression.We have established a framework for rigorous interpretation of somatic mosaic variants, addressing issues unique to somatic variants that will be applicable to many genes and conditions.

Fluorophores with emission in the second near-infrared (NIR-II) window have displayed salient advantages for biomedical applications. However, exploration of new luminogens with high NIR-II fluorescent brightness is still challenging. Herein, based on the "ring-fusion" strategy, a series of heteroatom-inserted rigid-planar cores is proposed to achieve the bathochromic NIR-II fluorophores with aggregation-induced emission (AIE) performance. Interestingly, one of the representative fluorophores, 4,4'-(5,5'-([1,2,5]thiadiazolo[3,4-i]dithieno[2,3-a:3',2'-c]phenazine-8,12-diyl)bis(4-octylthiophene-5,2-diyl))bis(N,N-diphenylaniline) (TTQiT), enjoys a maximum emission beyond 1100 nm because of the efficiently narrowed energy bandgap by electron-rich sulfur-atom-inserted core, which is verified by theoretical calculation. Taking advantage of the bright NIR-II emission of TTQiT nanoparticles, the desirable in vivo NIR-II imaging with high signal-to-background ratios is successfully performed and a long-term stem cell tracking in the detection of acute lung injury is further realized. Therefore, it is anticipated that this work will provide a promising molecular engineering strategy to enrich the scope of NIR-II fluorophores for catering to diverse demands in biomedical applications.

Recessive variants of the SLC26A4 gene are an important cause of hereditary hearing impairment. Several transgenic mice with different Slc26a4 variants have been generated. However, none have recapitulated the auditory phenotypes in humans. Of the SLC26A4 variants identified thus far, the p.T721M variant is of interest, as it appears to confer a more severe pathogenicity than most of the other missense variants, but milder pathogenicity than non-sense and frameshift variants. Using a genotype-driven approach, we established a knock-in mouse model homozygous for p.T721M. To verify the pathogenicity of p.T721M, we generated mice with compound heterozygous variants by intercrossing Slc26a4+/T721M mice with Slc26a4919-2A>G/919-2A>G mice, which segregated the c.919-2A > G variant with abolished Slc26a4 function. We then performed serial audiological assessments, vestibular evaluations, and inner ear morphological studies. Surprisingly, both Slc26a4T721M/T721M and Slc26a4919-2A>G/T721M showed normal audiovestibular functions and inner ear morphology, indicating that p.T721M is non-pathogenic in mice and a single p.T721M allele is sufficient to maintain normal inner ear physiology. The evidence together with previous reports on mouse models with Slc26a4 p.C565Y and p.H723R variants, support our speculation that the absence of audiovestibular phenotypes in these mouse models could be attributed to different protein structures at the C-terminus of human and mouse pendrin.

Background The most common B-cell cancers, chronic lymphocytic leukemia/lymphoma (CLL), follicular and diffuse large B-cell (FL, DLBCL) lymphomas, have distinct clinical courses, yet overlapping “cell-of-origin”. Dynamic changes to the epigenome are essential regulators of B-cell differentiation. Therefore, we reasoned that these distinct cancers may be driven by shared mechanisms of disruption in transcriptional circuitry. Methods We compared purified malignant B-cells from 52 patients with normal B-cell subsets (germinal center centrocytes and centroblasts, naive and memory B-cells) from 36 donor tonsils using >325 high-resolution molecular profiling assays for histone modifications, open chromatin (ChIP-, FAIRE-seq), transcriptome (RNA-seq), transcription factor (TF) binding, and genome copy number (microarrays). Findings From the resulting data, we identified gains in active chromatin in enhancers/super-enhancers that likely promote unchecked B-cell receptor signaling, including one we validated near the immunoglobulin superfamily receptors FCMR and PIGR. More striking and pervasive was the profound loss of key B-cell identity TFs, tumor suppressors and their super-enhancers, including EBF1, OCT2(POU2F2), and RUNX3. Using a novel approach to identify transcriptional feedback, we showed that these core transcriptional circuitries are self-regulating. Their selective gain and loss form a complex, iterative, and interactive process that likely curbs B-cell maturation and spurs proliferation. Interpretation Our study is the first to map the transcriptional circuitry of the most common blood cancers. We demonstrate that a critical subset of B-cell TFs and their cognate enhancers form self-regulatory transcriptional feedback loops whose disruption is a shared mechanism underlying these diverse subtypes of B-cell lymphoma. Funding National Institute of Health, Siteman Cancer Center, Barnes-Jewish Hospital Foundation, Doris Duke Foundation.

Agricultural waste from the hulls of water caltrop (Trapa taiwanesis Nakai, TT-hull) was extracted by either steeping them in cold 95% ethanol (C95E), refluxing 95E, refluxing 50E, or refluxing hot water (HW) to obtain C95EE, 95EE, 50EE, and HWE, respectively. These four extracts showed acetylcholinesterase (AChE) inhibitory activities and free radical scavenging activities, as well as anti-non-enzymatic protein glycation in vitro. Eight compounds were isolated from TT-hull-50EE and were used to plot the chromatographic fingerprints of the TT-hull extracts, among which tellimagrandin-I, tellimagrandin-II, and 1,2,3,6-tetra-galloylglucose showed the strongest AChE inhibitory activities, and they also exhibited anti-amyloid β peptide aggregations. The scopolamine-induced amnesiac ICR mice that were fed with TT-hull-50EE or TT-hull-HWE (100 and 200 mg/kg) or tellimagrandin-II (100 and 200 mg/kg) showed improved learning behavior when evaluated using passive avoidance or water maze evaluation, and they showed significant differences (p &lt, 0.05) compared to those in the control group. The enriched hydrolysable tannins of the recycled TT-hull may be developed as functional foods for the treatment of degenerative disorders.

Disorders of somatic mosaicism (DoSM) are a diverse group of syndromic and non-syndromic conditions caused by mosaic variants in genes that regulate cell survival and proliferation. Despite overlap in gene space and technical requirements, few clinical labs specialize in DoSM compared to oncology. We adapted a high-sensitivity next-generation sequencing cancer assay for DoSM in 2014. Some 343 individuals have been tested over the past 5 years, 58% of which had pathogenic and likely pathogenic (P/LP) findings, for a total of 206 P/LP variants in 22 genes. Parameters associated with the high diagnostic yield were: (1) deep sequencing (∼2,000× coverage), (2) a broad gene set, and (3) testing affected tissues. Fresh and formalin-fixed paraffin embedded tissues performed equivalently for identification of P/LP variants (62% and 71% of individuals, respectively). Comparing cultured fibroblasts to skin biopsies suggested that culturing might boost the allelic fraction of variants that confer a growth advantage, specifically gain-of-function variants in PIK3CA. Buccal swabs showed high diagnostic sensitivity in case subjects where disease phenotypes manifested in the head or brain. Peripheral blood was useful as an unaffected comparator tissue to determine somatic versus constitutional origin but had poor diagnostic sensitivity. Descriptions of all tested individuals, specimens, and P/LP variants included in this cohort are available to further the study of the DoSM population.

Folate receptor α (FRα) is a well-studied tumor biomarker highly expressed in many epithelial tumors such as breast, ovarian, and lung cancers. Mirvetuximab soravtansine (IMGN853) is the antibody-drug conjugate of FRα-binding humanized monoclonal antibody M9346A and cytotoxic maytansinoid drug DM4. IMGN853 is currently being evaluated in multiple clinical trials, in which the immunohistochemical evaluation of an archival tumor or biopsy specimen is used for patient screening. However, limited tissue collection may lead to inaccurate diagnosis due to tumor heterogeneity. Herein, we developed a zirconium-89 (89Zr)-radiolabeled M9346A (89Zr-M9346A) as an immuno-positron emission tomography (immuno-PET) radiotracer to evaluate FRα expression in triple-negative breast cancer (TNBC) patients, providing a novel means to guide intervention with therapeutic IMGN853. In this study, we verified the binding specificity and immunoreactivity of 89Zr-M9346A by in vitro studies in FRαhigh cells (HeLa) and FRαlow cells (OVCAR-3). In vivo PET/computed tomography (PET/CT) imaging in HeLa xenografts and TNBC patient-derived xenograft (PDX) mouse models with various levels of FRα expression demonstrated its targeting specificity and sensitivity. Following PET imaging, the treatment efficiencies of IMGN853, pemetrexed, IMGN853 + pemetrexed, paclitaxel, and saline were assessed in FRαhigh and FRαlow TNBC PDX models. The correlation between 89Zr-M9346A tumor uptake and treatment response using IMGN853 in FRαhigh TNBC PDX model suggested the potential of 89Zr-M9346A PET as a noninvasive tool to prescreen patients based on the in vivo PET imaging for IMGN853-targeted treatment.

In this work, we demonstrate In0.52Al0.48As top/backside-illuminated avalanche photodiodes (APD) with dual multiplication layers for high-speed and wide dynamic range performances. Our fabricated top-illuminated APDs, with a partially depleted p-type In0.53Ga0.47As absorber layer and thin In0.52Al0.48As dual multiplication (M-) layer (60 and 88 nm), exhibit a wide optical-to-electrical bandwidth (16 GHz) with high responsivity (2.5 A/W) under strong light illumination (around 1 mW). The measured bias dependent 3-dB O-E bandwidth was pinned at 16 GHz without any serious degradation near the saturation current output. To further increase the speed, we downscaled the active diameter and adopted a back-side illuminated structure with flip-chip bonding for batter optical alignment tolerance. A significant improvement in maximum bandwidth was demonstrated (25 versus 18 GHz). On the other hand, we adopted a thick dual M-layer (200 and 300 nm) and 2 μm absorber layer in the APD design to circumvent the problem of serious bandwidth degradation under high gain (&gt, 100) and high-power operation which significantly enhanced the dynamic range. Due to dual M-layer, the carriers could be energized in the first M-layer then propagate to the second M-layer to trigger the avalanche process. In both cases, despite variation in thickness of the absorber and M-layer, the cascade avalanche process leads to values close to the ultra-high gain bandwidth product (GBP) of around 460 GHz with a responsivity of 0.4 and 1 A/W at unit gain for the thin and thick M-layer devices, respectively. We successfully achieved a good sensitivity of around −20.6 dBm optical modulation amplitude (OMA) at a data rate of 25.78 Gb/s, by packaging the fabricated APDs (thin dual M-layer (60 and 88 nm) version) with a 25 Gb/s trans-impedance amplifier in a 100 Gb/s ROSA package. The results show that, the incorporation of a dual multiplication (M) layer structure in the APD opens a new window to obtaining the higher GBP in order to meet the requirements for high-speed transmission without the need of further downscaling the multiplication layer.

Development of B-lymphoblastic leukemia/lymphoma (BALL) is uncommon in patients with plasma cell neoplasm (PCN). Currently, little is known about risk factors for and characteristics of BALL arising in patients who have undergone treatment for PCN. We reviewed the clinicopathologic features of 14 patients with PCN who developed subsequent BALL and assessed the clonal relationship between these two neoplasms in 5 of the 14 patients. Clinical and laboratory data were extracted from the electronic medical record in accordance with an institutional review board-approved protocol. For the IgH clonality studies DNA was extracted from formalin fixed paraffin embedded tissue and analyzed utilizing the LymphoTrack® IGH FR2/3 Assay -- S5/PGM™ reagents from Invivoscribe Technologies. Next-generation sequencing of libraries was performed on a ThermoFisher Scientific Ion Torrent S5™ sequencer. The LymphoTrack® Software - S5/PGM™ Version 2.4.5 was used to analyze the IGH rearrangement sequences and relative proportion of the sequences was determined as a percentage of total sequencing reads. All PCN patients in our cohort received an autologous stem cell transplant (auto-SCT) with subsequent lenalidomide maintenance therapy. The mean time from the start of lenalidomide treatment after auto-SCT to BALL development was 62 months. None of the BALL cases were Philadelphia chromosome-positive. There was increased incidence of TP53 mutations and deletions (36%). IgH clones were identified in all but one sample. Comparison of the IgH clones from the original PCN and subsequent BALL revealed distinct clones in all 5 patients tested. In 2 of the 5 patients, the original PCN clone was also identified along with the distinct BALL clone. Our study reveals that BALL cases arising in patients with treated PCN are not clonally related to the original disease, and may represent therapy-related malignancy associated to prior treatment including lenalidomide maintenance therapy. More studies are needed to establish the incidence and understand the pathogenesis of this possible therapy-related complication.

The performance of InGaAs/InAlAs single photon avalanche diodes (SPAD) was improved with fabrication in triple mesa. Current SPADs achieve better dark count rate of 5 × 104 ⁄2 for single photon detection efficiency of 31% at RT.