Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness

Clear cell renal cell carcinomas (ccRCCs) represent ∼75% of RCC cases and account for most RCC-associated deaths. Inter- and intratumoral heterogeneity (ITH) results in varying prognosis and treatment outcomes. To obtain the most comprehensive profile of ccRCC, we perform integrative histopathologic, proteogenomic, and metabolomic analyses on 305 ccRCC tumor segments and 166 paired adjacent normal tissues from 213 cases. Combining histologic and molecular profiles reveals ITH in 90% of ccRCCs, with 50% demonstrating immune signature heterogeneity. High tumor grade, along with BAP1 mutation, genome instability, increased hypermethylation, and a specific protein glycosylation signature define a high-risk disease subset, where UCHL1 expression displays prognostic value. Single-nuclei RNA sequencing of the adverse sarcomatoid and rhabdoid phenotypes uncover gene signatures and potential insights into tumor evolution. In vitro cell line studies confirm the potential of inhibiting identified phosphoproteome targets. This study molecularly stratifies aggressive histopathologic subtypes that may inform more effective treatment strategies.

Fetal fibronectin, endotoxin, bacterial vaginosis and cervical length as predictors of preterm birth and neonatal morbidity in twin pregnancies

OBJECTIVE

To evaluate the predictive values of fetal fibronectin, bacterial vaginosis, endotoxin and cervical length for preterm birth (< 35 and < 37 weeks) and neonatal morbidity in twin pregnancies.

PARTICIPANTS

One-hundred and twenty-one women with twin pregnancies recruited into a prospective longitudinal study at three antenatal clinics in the southwest of Sweden.

METHODS

Cervical or vaginal fluid was sampled and determined for fetal fibronectin (> or = 0.05 microgram/mL was used as cutoff), endotoxin (> or = 100 pg/mL) and bacterial vaginosis (presence of clue cells) at two week intervals from 24 to 34 weeks of gestation. The cervical length was measured with transvaginal sonography at the same time intervals.

MAIN OUTCOME MEASURES

Occurrence of preterm birth (< 35 and < 37 weeks of gestation) and neonatal morbidity.

RESULTS

All positive fetal fibronectin samples obtained at screening between 24 and 34 weeks predicted birth < 35 weeks (RR 18.0; 95% CI 2.2-145.9). A positive fetal fibronectin at 28 weeks of gestation predicted delivery < 35 weeks (RR 6.3; 95% CI 2.6-15.1) with a sensitivity, specificity, positive and negative predictive value of 50.0, 92.0, 62.5 and 87.3%, respectively. An independent association between fetal fibronectin at 28 weeks and preterm birth (< 35 weeks) was verified with logistic regression (P = 0.03). A positive fetal fibronectin at 28 weeks of gestation predicted neonatal morbidity (RR 5.1; 95% CI 2.4-11.0) and a longer period of care at the neonatal intensive care unit. The predictive power of cervical sonography was generally low but cervical length (cutoff < or = 33 mm) measured at 28 weeks of gestation was significantly associated with birth < 37 weeks (RR 2.2; 95% CI 1.1-4.2). The presence of endotoxin correlated to bacterial vaginosis, but these tests were not significantly related to preterm birth or neonatal morbidity.

CONCLUSIONS

Fetal fibronectin predicted preterm birth and neonatal morbidity in twin pregnancies. The predictive value of cervical length determinations was low. Endotoxin and bacterial vaginosis had no predictive power for preterm delivery in this study.

Proteogenomic analysis of chemo-refractory high-grade serous ovarian cancer

To improve the understanding of chemo-refractory high-grade serous ovarian cancers (HGSOCs), we characterized the proteogenomic landscape of 242 (refractory and sensitive) HGSOCs, representing one discovery and two validation cohorts across two biospecimen types (formalin-fixed paraffin-embedded and frozen). We identified a 64-protein signature that predicts with high specificity a subset of HGSOCs refractory to initial platinum-based therapy and is validated in two independent patient cohorts. We detected significant association between lack of Ch17 loss of heterozygosity (LOH) and chemo-refractoriness. Based on pathway protein expression, we identified 5 clusters of HGSOC, which validated across two independent patient cohorts and patient-derived xenograft (PDX) models. These clusters may represent different mechanisms of refractoriness and implicate putative therapeutic vulnerabilities.

Patients with hyperhidrosis have changed grip force, coefficient of friction and safety margin

OBJECTIVE

To evaluate whether subjects with palmar hyperhidrosis have functional problems with the handgrip caused by the wet slippery surface of palm and fingertips. We used two different dosages of botulinum toxin to explore its impact on sweating and on muscle strength in the hand.

METHOD

Using an object equipped with force sensors we measured the muscle strength and calculated the coefficients of friction and safety margin (SM) in the precision grip before and 2, 4, 6, 8 10-12 weeks and 6 months after treatment of 13 patients with two different doses of botulinum toxin. Sweat evaporation was measured simultaneously.

RESULTS

A significant decrease in evaporation and a parallel reduction of grip force in the dominant hand of the patients were observed. The SM used by the patients was significantly lower after the treatment, and increased gradually when sweating reappeared.

CONCLUSION

These measurements showed, for the first time, that hyperhidrosis of the palms may cause an objective perturbation of the hand function which may be partially corrected by botulinum toxin treatment.

Different Helicobacter pylori strains colonize the antral and duodenal mucosa of duodenal ulcer patients

BACKGROUND

We have investigated the possibility that the same patients may be colonized by Helicobacter pylori strains of different genotypes or phenotypes in the antrum as compared to in the duodenum. The strains were typed for DNA fingerprints, different lipopolysaccharides (LPS), and Lewis antigen expression on the O-side chains of LPS.

MATERIALS AND METHODS

Polymerase chain reaction (PCR) amplifications using primer sequences (i.e., the Enterobacterial Repetitive Intergenic Consensus [ERIC]) and randomly amplified polymorphic DNA (RAPD) elements were performed to asses chromosomal DNA diversity between H. pylori strains. The expression of different LPS types and Lewis antigens in the various H. pylori isolates were determined by whole bacterial enzyme-linked immunosorbent assays using monoclonal antibodies.

RESULTS

Duodenal ulcer patients had different H. pylori genotypes in the duodenum as compared to in the antrum as shown by ERIC-PCR (44%) and by RAPD-PCR (75%). Different DNA patterns were found among the strains that were isolated from various regions of the duodenum in 4 of 16 patients (25%) as shown by ERIC-PCR and in 8 of 16 patients (50%) as shown by RAPD-PCR. Sixty-three percent of the duodenal ulcer patients had H. pylori strains with a different Lewis antigen phenotype in the duodenum as compared to in the antrum, and 3 of 16 patients (19%) had strains with different Lewis antigens expressed by strains from different duodenal biopsies from the same patient.

CONCLUSION

The results suggest that a mixed population of different H. pylori strains with marked variation, both genotypically and phenotypically, colonize the same patient.

Sleep disorders in systemic lupus erythematosus. Does vitamin D play a role?

Objectives

Sleep disorders are common among patients with systemic lupus erythematosus (SLE) with unclear underlying mechanisms. We assessed the role of vitamin D in sleep quality of patients with SLE.

Methods

A retrospective study was conducted on women with SLE for whom the following data were available at the same time; sleep quality (Pittsburgh Sleep Quality Index (PSQI)), disease activity, cumulative disease damage, psychological state (Hospital Anxiety and Depression Scale (HADS)), and serum vitamin D level. Bivariate and regression analyses were computed to find contributors of sleep quality.

Results

In total, 63 women were studied. Serum vitamin D level was correlated with physical activity ( r = 0.310, p = 0.015), season of assessment ( r = −0.302, p = 0.016), the PSQI global score ( r = −0.262, p = 0.043), anxiety score ( r = −0.298, p = 0.021), and non-significantly with depression score ( r = −0.218, p = 0.094). Including all variables into a linear regression model, vitamin D level was independently associated with the global PSQI score (beta = −0.364, p = 0.042). Association of vitamin D level with psychological state disappeared after controlling for season of assessment (beta = −0.248, p = 0.154).

Conclusions

We found a role for vitamin D in sleep quality of SLE patients. Further studies are warranted to confirm these results and to find possible mechanisms of action.

Two-stage Cox-nnet: biologically interpretable neural-network model for prognosis prediction and its application in liver cancer survival using histopathology and transcriptomic data

Pathological images are easily accessible data with the potential of prognostic biomarkers. Moreover, integration of heterogeneous data types from multi-modality, such as pathological image and gene expression data, is invaluable to help predicting cancer patient survival. However, the analytical challenges are significant. Here, we take the hepatocellular carcinoma (HCC) pathological image features extracted by CellProfiler, and apply them as the input for Cox-nnet, a neural network-based prognosis prediction model. We compare this model with the conventional Cox proportional hazards (Cox-PH) model, CoxBoost, Random Survival Forests and DeepSurv, using C-index and log-rank P-values. The results show that Cox-nnet is significantly more accurate than Cox-PH and Random Survival Forests models and comparable with CoxBoost and DeepSurv models, on pathological image features. Further, to integrate pathological image and gene expression data of the same patients, we innovatively construct a two-stage Cox-nnet model, and compare it with another complex neural-network model called PAGE-Net. The two-stage Cox-nnet complex model combining histopathology image and transcriptomic RNA-seq data achieves much better prognosis prediction, with a median C-index of 0.75 and log-rank P-value of 6e-7 in the testing datasets, compared to PAGE-Net (median C-index of 0.68 and log-rank P-value of 0.03). Imaging features present additional predictive information to gene expression features, as the combined model is more accurate than the model with gene expression alone (median C-index 0.70). Pathological image features are correlated with gene expression, as genes correlated to top imaging features present known associations with HCC patient survival and morphogenesis of liver tissue. This work proposes two-stage Cox-nnet, a new class of biologically relevant and interpretable models, to integrate multiple types of heterogenous data for survival prediction.

Load force during manual transport in Parkinson's disease

OBJECTIVES

To search for a physiological method for the measurement of upper extremity dexterity during activities of daily life in Parkinson's disease (PD).

MATERIALS AND METHODS

We examined load force output during manual transport in seven patients with PD and 10 healthy controls. PD patients were measured in both the non-medicated and medicated states. The test movement included two continuous sub-movements: an upward-forward transport of an object from the table to the stand, and a downward-backward transport of the object from the stand to the table. Hand movements were recorded using an optoelectronic camera, and load force was measured using a force sensor installed in the test object.

RESULTS

Compared with the controls, PD patients had a different pattern of load force output characterized by slower force development and release, lower peak force, and less dynamic force generation during movement. After medication, the speed of force development and the level of peak force increased in the patients.

CONCLUSIONS

These findings suggest that PD impairs the production of preprogrammed movements. The movements observed in the PD patients may result from compensatory strategies relying more on feedback mechanisms.

The stimulatory effects of topical application of radioactive lantern mantle powder on wound healing

Some people in different parts of Iran use burned mantles as a wound healing medicine. To perform surface area measurement, twenty rats were divided randomly into two groups of 10 animals each. The 1st group received topical burned radioactive lantern mantle powder at 1st-3rd day after making excision wounds. The 2nd group received non-radioactive lantern mantle powder. For histological study, 36 male rats randomly divided into two groups of 18 animals each. Full thickness excision wound (314+/-31.4 mm(2)) was made on the dorsal neck in all animals after inducing general anesthesia. For the first 3 days, cases received topical application of the radioactive lantern mantle powder. Finally, to measure the tensile strength, an incision was made on the dorsal neck of the rats. Surface area measurement of the wounds showed a progressive surface reduction in both groups. Histological study showed a significant statistically difference between cases and controls with respect to fibrinoid necrosis and neutrophilic exudate at the days 3 and 14. Considering the existence of granulation tissue, a significant difference was observed between case and control groups at days 3 and 7. Tensile strength study showed no significant difference between the cases and controls until 30 days after excision.

On automatic determination of movement phases in manual transport during the precision grip

Integrated movement and force analysis of the precision grip-lift sequence (grasping an object between index finger and thumb) is a useful tool in studies on manipulative hand functions. The everyday Manual Transport tasks, moving objects from one place to another, exhibits powerful test possibilities because it includes the precision grip. In this study, as a step towards the exploitation of these possibilities, we created an algorithm that extracts sequence of phases in this task. The mathematical and dynamical properties of the movement and force signals were used to determine the start and the end of each phase. The grip-lift synergy was quantified by the correlation coefficient during each phase. Eight patients with Parkinson's Disease (PD) and 10 healthy persons were studied. The PD patients were tested both in the medicated (ON) and the unmedicated (OFF) state. The object was lifted with the index finger and the thumb, moved a short distance, and put down on a shelf. The preliminary results of these experiments displayed significantly higher coordination between the grip and load forces in the initial phases, before the lift was completely established, than during the transport phases. This was evident both in PD patients and healthy subjects. This method provides an automatic analysis of the motor performance during an arm-hand movement that is important in daily life to aid in clinical diagnosis.

A monolithic MEMS position sensor for closed-loop high-speed atomic force microscopy

The accuracy and repeatability of atomic force microscopy (AFM) imaging significantly depend on the accuracy of the piezoactuator. However, nonlinear properties of piezoactuators can distort the image, necessitating sensor-based closed-loop actuators to achieve high accuracy AFM imaging. The advent of high-speed AFM has made the requirements on the position sensors in such a system even more stringent, requiring higher bandwidths and lower sensor mass than traditional sensors can provide. In this paper, we demonstrate a way for high-speed, high-precision closed-loop AFM nanopositioning using a novel, miniaturized micro-electro-mechanical system position sensor in conjunction with a simple PID controller. The sensor was developed to respond to the need for small, lightweight, high-bandwidth, long-range and sub-nm-resolution position measurements in high-speed AFM applications. We demonstrate the use of this sensor for closed-loop operation of conventional as well as high-speed AFM operation to provide distortion-free images. The presented implementation of this closed-loop approach allows for positioning precision down to 2.1 Å, reduces the integral nonlinearity to below 0.2%, and allows for accurate closed loop imaging at line rates up to 300 Hz.

Distinct mutational processes shape selection of MHC class I and class II mutations across primary and metastatic tumors

Disruption of antigen presentation via loss of major histocompatibility complex (MHC) expression is a strategy whereby cancer cells escape immune surveillance and develop resistance to immunotherapy. Here, we develop the personalized genomics algorithm Hapster and accurately call somatic mutations within the MHC genes of 10,001 primary and 2,199 metastatic tumors, creating a catalog of 1,663 non-synonymous mutations that provide key insights into MHC mutagenesis. We find that MHC class I genes are among the most frequently mutated genes in both primary and metastatic tumors, while MHC class II mutations are more restricted. Recurrent deleterious mutations are found within haplotype- and cancer-type-specific hotspots associated with distinct mutational processes. Functional classification of MHC residues reveals significant positive selection for mutations disruptive to the B2M, peptide, and T cell binding interfaces, as well as to MHC chaperones.

Disturbed grip function in women with rheumatoid arthritis

OBJECTIVE

Hand dysfunction is a frequent cause of disability in rheumatoid arthritis (RA). In patients with RA, we studied the precision grip-lift sequence in relation to pain, stiffness, and observer assessed hand function and their relation to patients' experience of clumsiness and tendency to drop objects.

METHODS

Performance of the precision grip-lift sequence was studied in 23 women with RA and 7 age and sex matched controls. The results were correlated to self-estimation of pain and stiffness of hands and to observer assessed measurements of hand function.

RESULTS

A prolongation of the preload and loading phases and of the acceleration part of the transition phase as well as a disturbance of the safety margin (SM) during precision grip-lift were noted. Patients with good hand function (low Grip Ability Test score; GAT) displayed normal or increased SM compared to the healthy controls, whereas patients with more pronounced disease exhibited a lower SM. Disturbances seen in the precision grip-lift performance were related to stiffness, range of motion, and GAT score. In RA patients with decreased hand function the SM was correlated to feeling of clumsiness, but did not explain the frequency of object dropping.

CONCLUSION

A disturbance in the precision grip-lift performance was noted in patients with RA. These grip performance changes need further investigation to determine possible mechanisms.

Comprehensive proteogenomic characterization of rare kidney tumors

Non-clear cell renal cell carcinomas (non-ccRCCs) encompass diverse malignant and benign tumors. Refinement of differential diagnosis biomarkers, markers for early prognosis of aggressive disease, and therapeutic targets to complement immunotherapy are current clinical needs. Multi-omics analyses of 48 non-ccRCCs compared with 103 ccRCCs reveal proteogenomic, phosphorylation, glycosylation, and metabolic aberrations in RCC subtypes. RCCs with high genome instability display overexpression of IGF2BP3 and PYCR1. Integration of single-cell and bulk transcriptome data predicts diverse cell-of-origin and clarifies RCC subtype-specific proteogenomic signatures. Expression of biomarkers MAPRE3, ADGRF5, and GPNMB differentiates renal oncocytoma from chromophobe RCC, and PIGR and SOSTDC1 distinguish papillary RCC from MTSCC. This study expands our knowledge of proteogenomic signatures, biomarkers, and potential therapeutic targets in non-ccRCC.

Abstract 2036: Distinct mutational processes shape selection of MHC class I and class II mutations across primary and metastatic tumors

Disruption of antigen presentation via loss of MHC expression is a strategy whereby cancer cells escape immune surveillance and develop resistance to immunotherapy. We developed the personalized genomics algorithm Hapster and accurately called somatic mutations within the MHC genes of 10,001 primary and 2,199 metastatic tumors, creating a catalog of 1663 nonsynonymous mutations that provide key insights into MHC mutagenesis. We found that MHC-I genes are among the most frequently mutated genes in both primary and metastatic tumors, while MHC-II mutations are more restricted. Recurrent deleterious mutations are found within haplotype and cancer-type specific hotspots associated with distinct mutational processes. Functional classification of MHC residues revealed significant positive selection for mutations disruptive to the B2M, peptide, and T-cell binding interfaces, as well as MHC chaperones. At the cohort level, all cancers with positive selection for MHC mutations are responsive to immune checkpoint inhibitors, underscoring the translational relevance of our findings.

Citation Format: Michael Mumphrey, Noshad Hosseini, Abhijit Parolia, Jie Geng, Weiping Zou, Malini Raghavan, Arul Chinnaiyan, Marcin Cieslik. Distinct mutational processes shape selection of MHC class I and class II mutations across primary and metastatic tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2036.

Waveguide-based absorption measurement system for visible wavelength applications

We present a miniaturized waveguide-based absorption measurement system operating at a wavelength of 635 nm, based on a silicon nitride integrated photonic platform, suitable for lab-on-chip applications. We experimentally demonstrate a high correlation between the bulk dye concentration and the measured absorption loss levels in the waveguides. We explain a photonic design process for choosing the ideal waveguide to minimize the coefficient of variation on the analyte concentration. The approach is designed for camera readout, allowing multiple readouts and easy integration for lab-on chip cartridge approach.

IL-1beta, IL-6, TNFalpha, fetal fibronectin, and endotoxin in the lower genital tract of pregnant women with bacterial vaginosis

BACKGROUND

In our studies on women with bacterial vaginosis (BV) in early pregnancy a strong association has been found between BV and the levels of endotoxin or interleukin-1alpha (IL-1alpha) in the lower genital tract. In the present study we investigated if an association could be found between BV and other cytokines (IL-1beta, IL-6, tumor necrosis factor alpha, TNF) or fetal fibronectin (FFN). The cytokine-inducing capacity of endotoxins present in the cervical mucus was explored in a monocytic cell assay.

METHODS

Cervical mucus or cervicovaginal fluid was collected from women with (BV) and without BV (nonBV) attending a family planning unit for first trimester abortion. The concentrations of IL-1beta, IL-6, TNF and FFN were determined by quantitative enzyme immunoassays. TNF was determined in 63 women (BV, n=25) out of whom 37 (BV, n=11) were analyzed for IL-1beta and the remaining 26 for IL-6 (BV, n=14). FFN was determined in another 36 women (BV, n= 19). The cytokine-inducing capacity of endotoxin-containing cervical mucus and purified endotoxin of Prevotella bivia were studied by an in vitro cell assay using a human monocytic cell line (THP-1).

RESULTS

IL-lbeta and IL-6 were found in almost all women. The levels of IL-1beta, but not IL-6, TNF or FFN, were significantly increased in women with BV compared with the nonBV women (p<0.05). Purified endotoxin from P. bivia, and cervical mucus from BV women containing high levels of endotoxin were able to induce a cytokine response (IL-6) in monocytic cells in vitro.

CONCLUSION

BV is associated with increased levels of IL-1beta in the lower genital tract of pregnant women in the first trimester. The ability of BV-associated endotoxins to induce cytokine production in monocytic cells may partly explain the increased IL-1beta levels.

Surgical Duration Estimation via Data Mining and Predictive Modeling: A Case Study

Operating rooms (ORs) are one of the most expensive and profitable resources within a hospital system. OR managers strive to utilize these resources in the best possible manner. Traditionally, surgery durations are estimated using a moving average adjusted by the scheduler (adjusted system prediction or ASP). Other methods based on distributions, regression and data mining have also been proposed. To overcome difficulties with numerous procedure types and lack of sufficient sample size, and avoid distributional assumptions, the main objective is to develop a hybrid method of duration prediction and demonstrate using a case study.

The UBA1-STUB1 Axis Mediates Cancer Immune Escape and Resistance to Checkpoint Blockade

SIGNIFICANCE

Our study reveals UBA1 as a predictive biomarker for clinical outcomes in ICB cohorts, mediating cancer immune evasion and ICB resistance. We further highlight JAK1 stabilization as a key mechanism of UBA1 inhibition and nominate the UBA1-STUB1 axis as an immuno-oncology therapeutic target to improve the efficacy of ICB.

An X–FEM technique for numerical simulation of variable-density flow in fractured porous media

Solute transport is one of the major topics in geological studies. Fracture is a significant characteristic of natural porous media, where the solute can transport due to its higher density with respect to the density of fluid. As the solute migrates in the medium, the density of the fluid changes with time. In this paper, the mass transport problem in the fractured porous media is modeled using the extended finite element method (X-FEM). An advection-diffusion equation is adopted to define the transport phenomenon in conjunction with the continuity equation of fluid. Transport regimes including diffusion, dispersion and advection are taken into the computational model. The presence of fractures within a porous medium substantially affects the transport behavior. In order to resolve the issue of discontinuity in the field variables, the X-FEM is implemented to discretize the discontinuity of medium. The Newmark integration scheme is adopted to discretize the governing equations in time domain. The nonlinear equations are solved by the Newton-Raphson iterative technique in a fully coupled manner. Finally, in order to illustrate the performance of the proposed computational model, two conventional problems, including the Schincariol problem and the Elder problem as well as the fractured Elder problem are solved numerically. Different patterns of fractures including horizontal and vertical intersecting cracks are adopted to study the effect of fracture density as well as the capability and versatility of the proposed computational model. The method is described in details and the pitfalls of the whole approach are demonstrated. •The density-driven fluid flow in naturally fractured porous media is modeled using an enhanced-FEM technique.•The effect of fractures (faults) in the porous medium is investigated by modeling the transport of saltwater in the fractured Elder problem.•The proposed computational model provides an accurate prediction of subsurface hydrology for a field-scale closed desert basin.

Abstract 3127: Comprehensive proteogenomic characterization of rare kidney tumors

Non-clear cell renal cell carcinomas (non-ccRCCs) represent ~15-20% RCCs cases comprising nearly 20 different disease subtypes and a wide spectrum of clinical behavior from benign to highly aggressive course. Clinically, metastatic non-ccRCC patients, regardless of subtypes with distinct genomic aberrations, are all treated with the same standard of care therapies, underscoring the need for precision therapeutic strategies. Diagnostic challenges also exist as benign and malignant entities often display overlapping histomorphologies that current diagnostic cytokeratin markers cannot resolve. Therefore, identification of more reliable diagnostic and prognostic non-ccRCC biomarkers remains an unmet need in this field.

As part of the Clinical Tumor Analysis Consortium (CPTAC), we performed integrative analysis of multi-omics data including genomic next generation sequencing-based whole exome, whole genome, RNAseq, snRNAseq and mass spectrometry-based proteomics, post translational modifications (glycosylation and phosphorylation) and metabolomic profiles generated by CPTAC. The composition of the kidney tumor cohort (n=151) included 103 ccRCC, 15 oncocytomas, 13 papillary RCC (PRCC), 11 other rare tumors and 8 unclassified RCCs. Our multi-omic analysis revealed both unique and shared molecular features of RCC subtypes. We characterized proteogenomic, PTM and glycoproteome impact of genome instability (GI), a feature that is associated with poor prognosis in both ccRCC and non-ccRCC and affects 10-15% of cases. These analyses identified new prognostic signatures, outlier targetable kinase expression patterns, kinase-substrate relationships and differential protein glycosylation events. Glycoproteome analysis also revealed variation in cell-type specific marker expression among RCC subtypes such as FUT8 (core-fucosyltransferase) associated protein glycosylation in PRCC. Integrative analysis of snRNA-seq data predicted diverse tumor cell-of-origin and stratified RCC subtype specific proteogenomic signatures. Differential expression analysis revealed several novel diagnostic makers including MAPRE3, GPNMB, PIGR, SOSTDC1. These biomarkers were validated by IHC and their addition to existing panels results in improved diagnostic specificity. Metabolic characterization revealed RCC subtype-specific differences and increased oncometabolite SAICAR in oncocytomas that may have functional significance. The valuable proteogenomic data resource we generated contains several rare tumor types that are hard to obtain for proteogenomic characterization at the scale described here, and will certainly aid in future pan-RCC studies.

Citation Format: Ginny Xiaohe Li, Yi Hsiao, Lijun Chen, Rahul Mannan, Yuping Zhang, Francesca Petralia, Hanbyul Cho, Noshad Hosseini, Anna Calinawan, Yize Li, Shankara Anand, Aniket Dagar, Yifat Geffen, Felipe V. Leprevost, Anne Le, Sean Ponce, Michael Schnaubelt, Nataly Naser Al Deen, Wagma Caravan, Andrew Houston, Chandan Kumar-Sinha, Xiaoming Wang, Seema Chugh, Gilbert S. Omenn, Daniel W. Chan, Christopher Ricketts, Rohit Mehra, Arul Chinnaiyan, Li Ding, Marcin Cieslik, Hui Zhang, Saravana M. Dhanasekaran, Alexey I. Nesvizhskii. Comprehensive proteogenomic characterization of rare kidney tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3127.

Rise Time Reduction of Thermal Actuators Operated in Air and Water through Optimized Pre-Shaped Open-Loop Driving

Electrothermal actuators have many advantages compared to other actuators used in Micro-Electro-Mechanical Systems (MEMS). They are simple to design, easy to fabricate and provide large displacements at low voltages. Low voltages enable less stringent passivation requirements for operation in liquid. Despite these advantages, thermal actuation is typically limited to a few kHz bandwidth when using step inputs due to its intrinsic thermal time constant. However, the use of pre-shaped input signals offers a route for reducing the rise time of these actuators by orders of magnitude. We started with an electrothermally actuated cantilever having an initial 10-90% rise time of 85 μs in air and 234 μs in water for a standard open-loop step input. We experimentally characterized the linearity and frequency response of the cantilever when operated in air and water, allowing us to obtain transfer functions for the two cases. We used these transfer functions, along with functions describing desired reduced rise-time system responses, to numerically simulate the required input signals. Using these pre-shaped input signals, we improved the open-loop 10-90% rise time from 85 μs to 3 μs in air and from 234 μs to 5 μs in water, an improvement by a factor of 28 and 47, respectively. Using this simple control strategy for MEMS electrothermal actuators makes them an attractive alternative to other high speed micromechanical actuators such as piezoelectric stacks or electrostatic comb structures which are more complex to design, fabricate, or operate.