Spatial proteo-transcriptomic profiling reveals the molecular landscape of borderline ovarian tumors and their invasive progression.

Serous borderline tumors (SBT) are epithelial neoplastic lesions of the ovaries that commonly have a good prognosis. In 10-15% of cases, however, SBT will recur as low-grade serous cancer (LGSC), which is deeply invasive and responds poorly to current standard chemotherapy1,2,3. While genetic alterations suggest a common origin, the transition from SBT to LGSC remains poorly understood4. Here, we integrate spatial proteomics5 with spatial transcriptomics to elucidate the evolution from SBT to LGSC and its corresponding metastasis at the molecular level in both the stroma and the tumor. We show that the transition of SBT to LGSC occurs in the epithelial compartment through an intermediary stage with micropapillary features (SBT-MP), which involves a gradual increase in MAPK signaling. A distinct subset of proteins and transcripts was associated with the transition to invasive tumor growth, including the neuronal splicing factor NOVA2, which was limited to expression in LGSC and its corresponding metastasis. An integrative pathway analysis exposed aberrant molecular signaling of tumor cells supported by alterations in angiogenesis and inflammation in the tumor microenvironment. Integration of spatial transcriptomics and proteomics followed by knockdown of the most altered genes or pharmaceutical inhibition of the most relevant targets confirmed their functional significance in regulating key features of invasiveness. Combining cell-type resolved spatial proteomics and transcriptomics allowed us to elucidate the sequence of tumorigenesis from SBT to LGSC. The approach presented here is a blueprint to systematically elucidate mechanisms of tumorigenesis and find novel treatment strategies.

Quantitative multiorgan proteomics of fatal COVID-19 uncovers tissue-specific effects beyond inflammation.

SARS-CoV-2 may directly and indirectly damage lung tissue and other host organs, but there are few system-wide, untargeted studies of these effects on the human body. Here, we developed a parallelized mass spectrometry (MS) proteomics workflow enabling the rapid, quantitative analysis of hundreds of virus-infected FFPE tissues. The first layer of response to SARS-CoV-2 in all tissues was dominated by circulating inflammatory molecules. Beyond systemic inflammation, we differentiated between systemic and true tissue-specific effects to reflect distinct COVID-19-associated damage patterns. Proteomic changes in the lungs resembled those of diffuse alveolar damage (DAD) in non-COVID-19 patients. Extensive organ-specific changes were also evident in the kidneys, liver, and lymphatic and vascular systems. Secondary inflammatory effects in the brain were related to rearrangements in neurotransmitter receptors and myelin degradation. These MS-proteomics-derived results contribute substantially to our understanding of COVID-19 pathomechanisms and suggest strategies for organ-specific therapeutic interventions.

Profiling the human intestinal environment under physiological conditions.

The spatiotemporal structure of the human microbiome1,2, proteome3 and metabolome4,5 reflects and determines regional intestinal physiology and may have implications for disease6. Yet, little is known about the distribution of microorganisms, their environment and their biochemical activity in the gut because of reliance on stool samples and limited access to only some regions of the gut using endoscopy in fasting or sedated individuals7. To address these deficiencies, we developed an ingestible device that collects samples from multiple regions of the human intestinal tract during normal digestion. Collection of 240 intestinal samples from 15 healthy individuals using the device and subsequent multi-omics analyses identified significant differences between bacteria, phages, host proteins and metabolites in the intestines versus stool. Certain microbial taxa were differentially enriched and prophage induction was more prevalent in the intestines than in stool. The host proteome and bile acid profiles varied along the intestines and were highly distinct from those of stool. Correlations between gradients in bile acid concentrations and microbial abundance predicted species that altered the bile acid pool through deconjugation. Furthermore, microbially conjugated bile acid concentrations exhibited amino acid-dependent trends that were not apparent in stool. Overall, non-invasive, longitudinal profiling of microorganisms, proteins and bile acids along the intestinal tract under physiological conditions can help elucidate the roles of the gut microbiome and metabolome in human physiology and disease.

Immobility-associated thromboprotection is conserved across mammalian species from bear to human.

Venous thromboembolism (VTE) comprising deep venous thrombosis and pulmonary embolism is a major cause of morbidity and mortality. Short-term immobility-related conditions are a major risk factor for the development of VTE. Paradoxically, long-term immobilized free-ranging hibernating brown bears and paralyzed spinal cord injury (SCI) patients are protected from VTE. We aimed to identify mechanisms of immobility-associated VTE protection in a cross-species approach. Mass spectrometry-based proteomics revealed an antithrombotic signature in platelets of hibernating brown bears with heat shock protein 47 (HSP47) as the most substantially reduced protein. HSP47 down-regulation or ablation attenuated immune cell activation and neutrophil extracellular trap formation, contributing to thromboprotection in bears, SCI patients, and mice. This cross-species conserved platelet signature may give rise to antithrombotic therapeutics and prognostic markers beyond immobility-associated VTE.

Transparent Exploration of Machine Learning for Biomarker Discovery from Proteomics and Omics Data.

Biomarkers are of central importance for assessing the health state and to guide medical interventions and their efficacy; still, they are lacking for most diseases. Mass spectrometry (MS)-based proteomics is a powerful technology for biomarker discovery but requires sophisticated bioinformatics to identify robust patterns. Machine learning (ML) has become a promising tool for this purpose. However, it is sometimes applied in an opaque manner and generally requires specialized knowledge. To enable easy access to ML for biomarker discovery without any programming or bioinformatics skills, we developed "OmicLearn" (http://OmicLearn.org), an open-source browser-based ML tool using the latest advances in the Python ML ecosystem. Data matrices from omics experiments are easily uploaded to an online or a locally installed web server. OmicLearn enables rapid exploration of the suitability of various ML algorithms for the experimental data sets. It fosters open science via transparent assessment of state-of-the-art algorithms in a standardized format for proteomics and other omics sciences.

Reproductive failure in an Austrian piglet-producing farm due to porcine circovirus genotype 2d.

Infections of pigs with porcine circovirus type 2 (PCV2) can lead to various clinical conditions including reproductive disorders (PCV2-RD). In general, a transplacental infection of fetuses leads to mummification and stillbirth. So far, PCV2-RD has mainly been described in specific-pathogen-free (SPF) herds or farms with a high proportion of gilts. From December 2018 to February 2019, a high abundance of mummified fetuses (15.5%) was observed in two farrowing groups in an Austrian piglet-producing farm. PCV2 DNA was detected using qPCR in organs of all six investigated fetuses (2.07 × 108-1.09 × 1012 PCV2) genome equivalents/g tissue and via in situ hybridisation in organs from five fetuses, while histologic lesions were not observed in a single fetal heart. All isolates were sequenced and identified as PCV2d. After the implementation of a regular vaccination of all sows against PCV2, the abundance of mummified fetuses dropped to 3.5% in May 2019. In contrast to previous reports about PCV2-RD, this farm was neither an SPF herd nor a start-up herd with a high proportion of gilts. The implementation of regular PCV2 vaccination helped to reduce the abundance of mummified fetuses substantially.

High-resolution serum proteome trajectories in COVID-19 reveal patient-specific seroconversion.

A deeper understanding of COVID-19 on human molecular pathophysiology is urgently needed as a foundation for the discovery of new biomarkers and therapeutic targets. Here we applied mass spectrometry (MS)-based proteomics to measure serum proteomes of COVID-19 patients and symptomatic, but PCR-negative controls, in a time-resolved manner. In 262 controls and 458 longitudinal samples of 31 patients, hospitalized for COVID-19, a remarkable 26% of proteins changed significantly. Bioinformatics analyses revealed co-regulated groups and shared biological functions. Proteins of the innate immune system such as CRP, SAA1, CD14, LBP, and LGALS3BP decreased early in the time course. Regulators of coagulation (APOH, FN1, HRG, KNG1, PLG) and lipid homeostasis (APOA1, APOC1, APOC2, APOC3, PON1) increased over the course of the disease. A global correlation map provides a system-wide functional association between proteins, biological processes, and clinical chemistry parameters. Importantly, five SARS-CoV-2 immunoassays against antibodies revealed excellent correlations with an extensive range of immunoglobulin regions, which were quantified by MS-based proteomics. The high-resolution profile of all immunoglobulin regions showed individual-specific differences and commonalities of potential pathophysiological relevance.

Cohort profile: the MUNICH Preterm and Term Clinical study (MUNICH-PreTCl), a neonatal birth cohort with focus on prenatal and postnatal determinants of infant and childhood morbidity.

PURPOSE: The MUNICH Preterm and Term Clinical (MUNICH-PreTCl) birth cohort was established to uncover pathological processes contributing to infant/childhood morbidity and mortality. We collected comprehensive medical information of healthy and sick newborns and their families, together with infant blood samples for proteomic analysis. MUNICH-PreTCl aims to identify mechanism-based biomarkers in infant health and disease to deliver more precise diagnostic and predictive information for disease prevention. We particularly focused on risk factors for pregnancy complications, family history of genetically influenced health conditions such as diabetes and paediatric long-term health-all to be further monitored and correlated with proteomics data in the future. PARTICIPANTS: Newborns and their parents were recruited from the Perinatal Center at the LMU University Hospital, Munich, between February 2017 and June 2019. Infants without congenital anomalies, delivered at 23-41 weeks of gestation, were eligible. FINDINGS: Findings to date concern the clinical data and extensive personal patient information. A total of 662 infants were recruited, 44% were female (36% in preterm, 46% in term). 90% of approached families agreed to participate. Neonates were grouped according to gestational age: extremely preterm (<28 weeks, N=28), very preterm (28 to <32 weeks, N=36), late preterm (32 to <37 weeks, N=97) and term infants (>37+0 weeks, N=501). We collected over 450 data points per child-parent set, (family history, demographics, pregnancy, birth and daily follow-ups throughout hospitalisation) and 841 blood samples longitudinally. The completion rates for medical examinations and blood samples were 100% and 95% for the questionnaire. FUTURE PLANS: The correlation of large clinical datasets with proteomic phenotypes, together with the use of medical registries, will enable future investigations aiming to decipher mechanisms of disorders in a systems biology perspective. TRIAL REGISTRATION NUMBER: DRKS (00024189); Pre-results.

Molecular Origin of Blood-Based Infrared Spectroscopic Fingerprints*.

Infrared spectroscopy of liquid biopsies is a time- and cost-effective approach that may advance biomedical diagnostics. However, the molecular nature of disease-related changes of infrared molecular fingerprints (IMFs) remains poorly understood, impeding the method's applicability. Here we probe 148 human blood sera and reveal the origin of the variations in their IMFs. To that end, we supplemented infrared spectroscopy with biochemical fractionation and proteomic profiling, providing molecular information about serum composition. Using lung cancer as an example of a medical condition, we demonstrate that the disease-related differences in IMFs are dominated by contributions from twelve highly abundant proteins-that, if used as a pattern, may be instrumental for detecting malignancy. Tying proteomic to spectral information and machine learning advances our understanding of the infrared spectra of liquid biopsies, a framework that could be applied to probing of any disease.

A New Parallel High-Pressure Packing System Enables Rapid Multiplexed Production of Capillary Columns.

Reversed-phase HPLC is the most commonly applied peptide-separation technique in MS-based proteomics. Particle-packed capillary columns are predominantly used in nanoflow HPLC systems. Despite being the broadly applied standard for many years, capillary columns are still expensive and suffer from short lifetimes, particularly in combination with ultra-high-pressure chromatography systems. For this reason, and to achieve maximum performance, many laboratories produce their own in-house packed columns. This typically requires a considerable amount of time and trained personnel. Here, we present a new packing system for capillary columns enabling rapid, multiplexed column packing with pressures reaching up to 3000 bar. Requiring only a conventional gas pressure supply and methanol as the driving fluid, our system replaces the traditional setup of helium-pressured packing bombs. By using 10× multiplexing, we have reduced the production time to just under 2 min for several 50 cm columns with 1.9-µm particle size, speeding up the process of column production 40 to 800 times. We compare capillary columns with various inner diameters and lengths packed under different pressure conditions with our newly designed, broadly accessible high-pressure packing station.

Comparison of prognosis and complications after warning leaks in subarachnoidal hemorrhage--experience with 214 patients following aneurysm clipping.

OBJECTIVES: The 'warning leak', a smaller bleeding event from an aneurysm, which sometimes occurs before an acute massive subarachnoidal hemorrhage (SAH), was first described in 1967. The present study was performed to compare the complications and prognosis for 214 patients with and without a warning leak; aneurysm clipping had been performed in all. METHODS: The interval between the warning headache and the actual SAH was calculated. The following complications were examined: preoperative hemorrhage, intra-operative rupture of the aneurysm, postoperative re-bleeding, symptomatic vasospasm, shunt-requiring hydrocephalus, ventriculitis, postoperative wound infection, and outcome according to the Glasgow Outcome Scale (GOS). RESULTS: Sixty-seven (31%) out of the 214 patients had a warning leak with a median distance of 11 days before suffering from major SAH. Preoperative angiographic vasospasms occurred more frequently in the group with a warning bleeding (22.4 versus 6.1%; p<0.05), which means that the warning leaks induce vascular reactions similar to SAH. The outcome of both groups after a mean follow-up time of 22 months did not show any difference. But 30 out of the 67 patients with a warning leak were graded H&H III-V at admission to hospital after a major SAH. The overall outcome for patients graded H&H I and II was in 92% favorable, compared with only a 54% favorable outcome for H&H III-V patients. Long-term outcome in the warning leak group was not impaired by angiographically proven vasospasm. DISCUSSION: To give patients the chance to start their treatment in a better clinical condition it is important to recognize the early warning signs.

Comparison of tc-99m depreotide and in-111 octreotide in recurrent meningioma.

PURPOSE: For more than a decade, In-111 octreotide has been known to accumulate in meningiomas as a result of the expression of subtype 2 somatostatin receptors. Improved imaging characteristics can be expected with the recently developed radiotracer Tc-99m depreotide, which also binds to subtype 2 somatostatin receptors. MATERIALS AND METHODS: The authors examined a patient with intraorbital and extracranial recurrent meningioma using SPECT with Tc-99m depreotide and In-111 octreotide. The tumor-to-background ratios in the lesions were compared and the findings were correlated with histopathologic findings. RESULTS: Although the tumor-to-background ratios were higher for the In-111-labeled tracer in the largest tumor lesion (5.7 versus 3.3), SPECT with the Tc-99m-labeled compound showed a proved second site of recurrence as a result of the better resolution that can be achieved with that isotope. CONCLUSIONS SPECT: with Tc-99m depreotide appears to be clinically useful for detecting recurrent meningiomas with higher resolution and may outperform In-111 octreotide imaging in patients with meningiomas.

Effect of high power ultrasound on endothelial cells--an in vitro study of the endothelium--hemostasis interaction.

OBJECTIVE: The goal of this study was to develop an in vitro model system in which the hemostatic effects of high power ultrasound applied to the outer surface of blood vessels during tumor dissection can be simulated and measured. METHODS: Monolayers of endothelial cells (HUVEC, ATCC) in cell culture plates were sonicated with an ultrasound dissector (SONOCA II, Soering) at a frequency of 23.5 kHz. The dissector was equipped with a cooling circuit. The cell cultures were exposed to 2 minutes of continuous ultrasound with intensities of 10, 50, or 100 W/cm(2). To differentiate between heat and sound effects, selected monolayers were warmed for 2 minutes. Finally, the cell cultures were stained with trypan blue to assess for cell death due to membrane disruption. Cytomorphological alterations and changes in the concentration of coagulation parameters in the cell culture medium were evaluated. RESULTS: The cytomorphological alterations were found to depend on ultrasound intensity. They included detachment of single endothelial cells, cell cluster formation and cytoplasmic cavitation. Disruption of the cell membrane integrity was infrequently observed. Of 14 screened coagulation parameters, thromboxane B(2) (TXB(2)), prostaglandin F(1alpha) (PGF(1alpha)), plasminogen activator inhibitor type 1 (PAI-1), thrombomodulin (TM), and thrombospondin (TSP) were found to be ultrasound sensitive. TXB(2) concentrations in the medium increased beginning at low ultrasound intensities (p < 0.01) and were independent of temperature. PGF(1alpha) concentrations peaked at high ultrasound intensities (p < 0.05), and heat alone produced a significant increase in concentration (p < 0.05). At high intensities, the ratio of TXB(2) to PGF(1alpha) shifted in favour of PGF(1alpha). PAI-1 was most strongly secreted at low ultrasound intensities (p < 0.01), and heat resulted in a decrease of concentration (p < 0.05). TM and TSP concentrations correlated strongly and reached a non significant peak at low intensities. CONCLUSION: The results demonstrate that during sonication of endothelial cells in vitro, coagulation parameters are released from distant undamaged cells. HUVEC-cells exhibit a differential hemostaseological response at different ultrasound intensities, and the response is also influenced by heat. Additionally, massive morphological damage can be induced at the endothelium.