Abstract Accurate assessment of the resection margin is of key importance for patient outcome after tumor surgery. Intraoperative assessment is preferable but present methods like fresh-frozen sectioning risk sampling errors and provide only 2D information. Classical 2D histology has better quality but is too slow for intraoperative feedback. In the present proof-of-concept study we show that laboratory x-ray histology based on propagation-based phase-contrast microtomography has potential for 3D intraoperative resection margin assessment. Our system includes a liquid–metal-jet high-brightness microfocus source, precision stages and a high-resolution detector, providing fast, high-contrast, near-cellular-resolution 3D imaging. The tissue is prepared by rapid acetone fixation before the 3D x-ray imaging. We demonstrate the method on several tumor types in liver and pancreas, as well as on different sarcomas. After the x-ray histology, classical histology was performed on the same samples for comparison. The two methods compare excellently on the liver and pancreas samples and reasonably on the morphologically more difficult sarcomas. The imaging currently takes 4–5 h with our prototype instrument, and we outline how to go below 1 h for the full procedure. We conclude that 3D x-ray histology can be developed to provide intraoperative resection margin assessment.

Hepatocellular carcinoma (HCC) remains a major challenge due to its aggressive features, therapeutic resistance, and disease recurrence. Patients with HCC often show anxiety and depression, and mental illness lasts throughout the therapeutic period, exacerbated by treatments such as radiofrequency ablation therapy and liver resection. Exploring novel pathological mechanisms paves the way for the development of HCC treatment with the mitigation of psychiatric issues. Tripartite motif-containing 13 (TRIM13), an E3 ubiquitin ligase, plays a role in central nervous system (CNS) homeostasis and acts as a tumor suppressor in lung and renal cancers. However, its role in HCC is undefined, making it a potentially intriguing target. Here, we demonstrate that TRIM13 expression is significantly downregulated in human HCC Hep3B and HepG2 cells. Adenovirus vector-mediated TRIM13 transgene overexpression (TRIM13 OE) suppresses the viability, proliferation, migration, and invasion of Hep3B and HepG2 cells. TRIM13 OE in the two HCC cell lines increases the levels of apoptosis markers, such as BAX and CASPASE 3, while reducing BCL-2 levels. Additionally, TRIM13 OE cells enhance autophagy by upregulating LC3-I, LC3-II, and BECLIN1, while downregulating P62. Collectively, TRIM13 OE inhibited the proliferation and migration of HCC cells through autophagy.

Background Progressive respiratory failure is the leading cause of death in patients with severe COVID-19. Histopathological findings in acute severe COVID-19 are foremost based on post-mortem findings. On computed tomography (CT), acute COVID-19 pneumonia is characterized by ground-glass opacities (GGOs) and, later, by a crazy-paving pattern (CPP) and consolidations.Purpose To investigate if CT patterns corresponded to histopathological post-mortem findings.Material and Methods Eight patients were identified with a chest CT performed between testing positive for COVID-19 and death. CT images, histological slides, and medical records were retrospectively reviewed. The lungs were photographed during the gross investigation to ascertain the exact position of the tissue blocks in relation to the relevant anatomical structures. Each slide was compared side by side with the in vivo chest CT pattern on the corresponding site.Results At CT, the most predominant finding was GGOs, present in all eight cases. CPP was observed in 6/8 (75%) patients, and consolidation in 7/8 (87.5%) patients, both predominantly located in the lower lung zones. In 5 (62.5%) patients, so-called fibrotic-like changes were present. In four patients with CT angiogram, no findings of pulmonary thromboembolism were present. At autopsy, all patients demonstrated macroscopic consolidation, while pleural effusion was seen in 2 (25%) cases. Microscopically, edema was present in all cases, hyaline membranes in 7/8 (87.5%) cases, but no signs of acute interstitial inflammation were observed. Thromboembolic findings were evident in 4 (50%) patients, of whom two were negative on CT and 3 (37.5%) cases had fibrosis.Conclusion The results demonstrate a clear association between radiological signs of GGO, consolidation and features of organizing pneumonia to microscopical signs of edema and diffuse alveolar damage. However, fibrotic-like changes and thromboembolism in the small vessels had a poorer compliance.

BACKGROUND:Despite the reporting of myocarditis associated with coronavirus disease 2019 vaccination, the correlation between vaccine-related rhabdomyositis and myocarditis incidence remains undocumented. This case offers a new perspective on myocarditis, potentially associated with the coronavirus disease 2019 vaccine, possibly caused by the strong immunostimulatory effects of messenger RNA vaccination-related rhabdomyositis. CASE PRESENTATION:A 25-year-old male athlete of Swedish (white) ethnicity and non-Hispanic origin collapsed during a strenuous ice hockey training session after receiving his third dose of the coronavirus disease 2019 vaccine (BN162b2). He had received standard cardiopulmonary resuscitation, and the electrocardiography showed ventricle fibrillation. According to the laboratory test, elevations were observed in troponin T, aminotransferase, blood glucose, and leucocyte number. Magnetic resonance imaging indicated disseminated myocarditis. A biopsy of the heart revealed mild lymphocytic inflammation and focal myocytolysis. The patient had permanent brain damage and passed away after the breathing tube was removed. The autopsy revealed cardiac muscle necrosis and skeletal muscle rhabdomyolysis. There was a sign of massive expansion of lymphoid compartment in the gastrointestinal tract. Increased hemophagocytosis and eosinophils were seen in the lymph node and bone marrow. The specific case drew attention to a potential association between the coronavirus disease 2019 vaccine and fatal myocarditis. CONCLUSION:We suggest that strenuous training associated with skeletal muscle damage, together with the strong immunostimulatory effect of messenger RNA vaccination, may lead to autoimmune rhabdomyositis that potentially cross-reacts with the myocardium. Athletes should be aware of the potential danger of heavy training in close proximity to vaccination or acute infections.

AIM:Ovarian cancer (OC) is a fatal female malignant tumor that severely impacts the health of women worldwide. Due to the lack of diagnostic biomarkers, 70% of OC patients are considered in the advanced stage at the first diagnosis. Exploring novel biomarkers for OC diagnosis has become an urgent clinical need to address. TRIB1 is a newly discovered oncogene in several malignant tumors, including acute myeloid leukemia, prostate cancer, and breast cancer. However, the biological function of TRIB1 in OC remains uncertain and, therefore, was explored in the present study. METHODS:Levels of TRIB1 in OC and normal tissues were evaluated in the GEPIA database. TRIB1-KD was constructed in ES-2 cells and TRIB1-OE was constructed in OVCAR3 cells using a siRNA and OE vector, respectively. The proliferation ability was determined using the CCK-8 and clone formation assays. The migration ability was detected using the wound healing and Transwell assays. The expression of epithelial-mesenchymal transition (EMT) biomarkers was determined using western blotting. RESULTS:TRIB1 was markedly upregulated in OC tissues compared with normal ovarian tissues in the GEPIA database. The TRIB1 level was slightly altered among ES-2, CAOV3, and SKOV3 cells, with the highest expression in ES-2 cells, which was greatly reduced in OVCAR3 cells. In TRIB1-KD ES-2 cells, a remarkably reduced proliferation ability was observed with the CCK-8 and clone formation assays, accompanied by a reduction in migration distance in the Wound healing assay and the number of migrated cells in the Transwell assay. In contrast, in TRIB1-OE OVCAR3 cells, increased proliferation ability was observed, accompanied by increased migration distance and number of migrated cells. Furthermore, EMT progression was markedly repressed in TRIB1-KD ES-2 cells and remarkably enhanced in TRIB1-OE OVCAR3 cells. CONCLUSION:TRIB1 facilitated the proliferation and migration of OC cells by enhancing EMT progression.

Glioma is a central nervous system (CNS) malignant tumor with high heterogeneity and mortality, which severely threatens the health of patients. The overall survival of glioma patients is relatively short and it is critical to identify new molecular targets for developing effective treatment strategies. UBE2K is a ubiquitin conjugating enzyme with oncogenic function in several malignant tumors. However, whether UBE2K participates in gliomas remains unknown. Herein, in glioma cells, UBE2K was found highly expressed in U87 and U251 cells. Subsequently, U87 and U251 cells were transfected with si-UBE2K to silence UBE2K, with the si-NC transfection as the negative control. In both U87 and U251 cells, the cell viability was sharply reduced by transfecting si-UBE2K for 48 and 72 h. Markedly decreased colony number, reduced number of migrated cells and invaded cells, and declined relative wound healing rate were observed in si-UBE2K transfected U87 and U251 cells. Moreover, the Bcl-2 level was markedly reduced, while the Bax and cleaved-caspase-3 levels were sharply increased in U87 and U251 cells after the si-UBE2K transfection. Furthermore, the p62 level was signally declined, while the Beclin-1 and LC-3 II/I levels were greatly increased in U87 and U251 cells by the si-UBE2K transfection. Furthermore, the facilitating effect of si-UBE2K on the apoptosis and autophagy in U87 and U251 cells was abolished by the coculture of 3-MA, an inhibitor of autophagy. Collectively, UBE2K facilitated the in vitro growth of glioma cells, possibly by inhibiting the autophagy-related apoptosis, which might be a promising target for treating glioma. UBE2K facilitated the in vitro growth of glioma cells, possibly by inhibiting the autophagy-related apoptosis, which might be a promising target for treating glioma. image

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific neutralizing antibodies (NAbs) lack cross-reactivity between SARS-CoV species and variants and fail to mediate long-term protection against infection. The maintained protection against severe disease and death by vaccination suggests a role for cross-reactive T cells. We generated vaccines containing sequences from the spike or receptor binding domain, the membrane and/or nucleoprotein that induced only T cells, or T cells and NAbs, to understand their individual roles. In three models with homologous or heterologous challenge, high levels of vaccine-induced SARS-CoV-2 NAbs protected against neither infection nor mild histological disease but conferred rapid viral control limiting the histological damage. With no or low levels of NAbs, vaccine-primed T cells, in mice mainly CD8+ T cells, partially controlled viral replication and promoted NAb recall responses. T cells failed to protect against histological damage, presumably because of viral spread and subsequent T cell-mediated killing. Neither vaccine- nor infection-induced NAbs seem to provide long-lasting protective immunity against SARS-CoV-2. Thus, a more realistic approach for universal SARS-CoV-2 vaccines should be to aim for broadly cross-reactive NAbs in combination with long-lasting highly cross-reactive T cells. Long-lived cross-reactive T cells are likely key to prevent severe disease and fatalities during current and future pandemics.

The treatment resistance is a problem for lung cancer. In this study, we used a vitro tissue culturing system to select a new therapy strategy for a patient with tyrosine kinase inhibitors (TKIs) resistance. A 42-year-old male Asian patient was diagnosed with advanced lung adenocarcinoma harboring an exon 19 deletion in the epidermal growth factor receptor (EGFR) gene. The patient was treated with Gefitinib, resulting in an almost complete remission for over a year. The patient relapsed after 13 months treatment, and received four cycles of chemotherapy. At 20 months, the patient had developed multiple lung metastases and a solitary cerebellar metastasis. An EGFR T790M mutation was identified in the peripheral blood sample. Subsequent treatment with Osimertinib resulted in a complete response of the intracranial metastasis. By 33 months, the patient had developed a mediastinal tumor mass that responded well to local radiotherapy. By 39 months, an EGFR C797S cis-mutation had been identified and the patient was treated with Brigatinib and Cetuximab. By 44 months, the tumor cells from the pleural effusion had been tested for sensitivity against 30 targeted and cytostatic drugs using the D Sense ex-vivo viability assay. The assay identified 8 drugs with moderate to high sensitivity. Combination therapy of Gemcitabin and Lobaplatin had resulted in disease stabilization. The case showed that individualized treatment aided by D Sense ex-vivo viability assay can be a viable option for patients with advanced lung adenocarcinoma with pleural effusions.

Supplementary Figure Legends 1-2 from Rescue of p53 Function by Small-Molecule RITA in Cervical Carcinoma by Blocking E6-Mediated Degradation

Supplementary Figure 1 from Rescue of p53 Function by Small-Molecule RITA in Cervical Carcinoma by Blocking E6-Mediated Degradation

Supplementary Movie 2 from Rescue of p53 Function by Small-Molecule RITA in Cervical Carcinoma by Blocking E6-Mediated Degradation

Background Homoharringtonine (HHT) is a plant cytotoxic alkaloid derived from the trees of the genus Cephalotaxus. HAG (HHT, low-dose cytarabine, and G-CSF), as a priming regimen, is utilized to treat acute myeloid leukemia (AML). Azacitidine (Aza), a DNA hypomethylation agent, has been a "backbone" for new combinational therapies. However, so far, it has not been well determined the efficacy and safety of adding Aza to HAG regimen. Methods This is a multi-center, single arm, phase 2 clinical trial done in 17 clinical institutions across China between Aug 2019 and Dec 2021 (ClinicalTrials.gov: NCT04248595). Induction therapy consisted of Aza (75mg/m2/d on days 1-7) was given in combination with the HAG regimen (Fig. 1A). Primary endpoints were complete remission (CR) or complete remission with incomplete hematologic recovery (CRi). Secondary endpoints were overall survival (OS), relapse free survival (RFS), and adverse events (AEs). Mutation screening was conducted through next generation sequencing (NGS) by targeting 58 frequently mutated genes. Results A total of 112 patients, including 72 newly diagnosed (ND) (56 de novo, 16 secondary AML [sAML]), and 40 relapsed/refractory (R/R) AML were enrolled. The CR/CRi was achieved in 79.2% (57/72) in the ND and 40.0% (16/40) in R/R AML, respectively (Fig. 1B). CR/CRi were achieved in 80.4% of de novo AML (45/56) and 75.0% of sAML (12/16), respectively. In addition, the median OS and RFS of ND AML patients were 22.8m (95%CI, 12.6 to not reached) and not reached, respectively (Fig. 1C&1D), which were significantly longer than the R/R group (median OS, 10.8m [95%CI, 9.5 to 12.7], P=0.0056; median RFS 5.21m [95%CI, 4.21 to 9.64], P=0.0051) (Fig. 1C&1D). Furthermore, 94.7% (18/19) of patients with favorable-risk reached CR/CRi (Fig. 1E), with median OS and RFS were both not reached (Fig. 1F&1G). 83.9% (26/31) of patients with intermediate-risk reached CR/CRi (Fig. 1E), and the median OS and median RFS were 22.8m (95%CI, 10.5 to not reached) (Fig. 1F) and 16.9m (95%CI, 4.64 to not reached) (Fig. 1G), respectively. Whereas in those with poor-risk, 59.1% (13/22) reached CR/CRi (Fig. 1E), with the median OS 17.3m (95%CI, 3.79 to not reached) (Fig. 1F) and median RFS not reached (Fig. 1G). In this study, infection was the most common non-hematological adverse event, presenting 58.0% (65/112). Common non-hematological AEs of grade 3 or higher includes: infection (38/112, 33.9%), hemorrhage (11/112, 9.82%), fatigue (6/112, 5.36%), hypokalemia (4/112, 3.57%), cardiac arrhythmia (2/112, 1.79%), and fever (2/112, 1.79%). The median duration of neutropenia and thrombocytopenia were 11 d (IQR, 7-19d) and 16d (IQR, 11-25d) among CR/CRi patients. No patients discontinued the induction therapy due to hematological or non-hematological toxicities. The early deaths within 4 weeks of the induction treatment occurred in 1.79% (2/112). Moreover, we detected 228 mutants involving 33 genes in 103 patients at the enrollment. The most frequently mutated genes were DNMT3A (25/103), TET2 (20/103), and NPM1 (18/103) (Fig. 1H), and mostly involved in DNA methylation (DNMT3A, IDH1/2, TET2; 48/103, 46.6%), followed by signal transducers (FLT3, NRAS, KRAS, KIT, PTPN11; 36/103, 35.0%), and transcription regulation (WT1, RUNX1, CEBPA, SETBP1, GATA2; 32/103, 28.2%). Upon Aza+HAG treatment, we observed the high CR/CRi rate in ND patients with mutated BCOR (100%,7/7), KIT (100%,3/3), IDH1 (100%,7/7), NPM1 (93.3%,14/15), ASXL1 (88.9%,8/9), DNMT3A (80. 0%,16/20), RUNX1 (75.0%,6/8), FLT3 (71.4%,5/7), and TET2 (71.4%,10/14) (Fig. 1I). We further observed the clearance of mutated genes after the induction therapy and found the variant allele fraction (VAF) of mutants was dramatically reduced among the CR/CRi patients. Specifically, VAF change of FLT3 mutant from 3 of 4 available patients reduced to <0.01%, with the other one, decreased by 91.9% (Fig. 1J); 4 out of 6 patients with IDH1 mutant reduced to <0.01%, with the other two, decreased 67.6% and 35.9%, respectively (Fig. 1K); 5 out of 6 patients with ASXL1 mutant reduced to <0.01%, with the other one, decreased by 33.4% (Fig. 1L); and 10 out of 14 patients with NPM1 mutant reduced to <0.01%, respectively (Fig. 1M). Conclusion This study demonstrated that the Aza+HAG regimen is a cost-effective first-line therapy with high efficacy and well tolerance for elderly/unfit AML, especially ND AML patients. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Objective. Patients with underlying heart diseases have a higher risk of dying from Covid-19. It has also been suggested that Covid-19 affects the heart through myocarditis. Despite the rapidly growing research on the management of Covid-19 associated complications, most of the ongoing research is focused on the respiratory complications of Covid-19, and little is known about the prevalence of myocarditis. Design. This study aimed to characterize myocardial involvement by using a panel of antibodies to detect hypoxic and inflammatory changes and the presence of SARS-CoV-2 proteins in heart tissues obtained during the autopsy procedure of Covid-19 deceased patients. Thirty-seven fatal COVID-19 cases and 21 controls were included in this study. Results. Overall, the Covid-19 hearts had several histopathological changes like the waviness of myocytes, fibrosis, contract band necrosis, infiltration of polymorphonuclear neutrophils, vacuolization, and necrosis of myocytes. In addition, endothelial damage and activation were detected in heart tissue. However, viral replication was not detected using RNA in situ hybridization. Also, lymphocyte infiltration, as a hallmark of myocarditis, was not seen in this study. Conclusion. No histological sign of myocarditis was detected in any of our cases; our findings are thus most congruent with the hypothesis of the presence of a circulating endothelium activating factor such as VEGF, originating outside of the heart, probably from the hypoxic part of the Covid-19 lungs.

BACKGROUND:The human protein atlas (HPA) is an online database containing large sets of protein expression data in normal and cancerous tissues in image form from immunohistochemically (IHC) stained tissue microarrays. In these, the tissue architecture is preserved and thus provides information on the spatial distribution and localization of protein expression at the cellular and extracellular levels. The database is freely available online through the HPA website but currently without support for large-scale screening and analysis of the images in the database. Features like spatial information are typically lacking in gene expression datasets from homogenized tissues or single-cell analysis. To enable high throughput analysis of the HPA database, we developed the AtlasGrabber software. It is available freely under an open-source license. Based on a predefined gene list, the software fetches the images from the database and displays them for the user. Several filters for specific antibodies or images enable the user to customize her/his image analysis. Up to four images can be displayed simultaneously, which allows for the comparison of protein expression between different tissues and between normal and cancerous tissues. An additional feature is the XML parser that allows the extraction of a list of available antibodies, images, and genes for specific tissues or cancer types from the HPA's database file.RESULTS:Compared to existing software designed for a similar purpose, ours provide more functionality and is easier to use. To demonstrate the software's usability, we identified six new markers of basal cells of the prostate. A comparison to prostate cancer showed that five of them are absent in prostate cancer.CONCLUSIONS:The HPA is a uniquely valuable database. By facilitating its usefulness with the AtlasGrabber, we enable researchers to exploit its full capacity. The loss of basal cell markers is diagnostic for prostate cancer and can help refine the histopathological diagnosis of prostate cancer. As proof of concept, with the AtlasGrabber we identified five new potential biomarkers specific for prostate basal cells which are lost in prostate cancer and thus can be used for prostate cancer diagnostics.

Patients with COVID-19 frequently manifest adipose atrophy, weight loss and cachexia, which significantly contribute to poor quality of life and mortality1,2. Browning of white adipose tissue and activation of brown adipose tissue are effective processes for energy expenditure3-7; however, mechanistic and functional links between SARS-CoV-2 infection and adipose thermogenesis have not been studied. In this study, we provide experimental evidence that SARS-CoV-2 infection augments adipose browning and non-shivering thermogenesis (NST), which contributes to adipose atrophy and body weight loss. In mouse and hamster models, SARS-CoV-2 infection activates brown adipose tissue and instigates a browning or beige phenotype of white adipose tissues, including augmented NST. This browning phenotype was also observed in post-mortem adipose tissue of four patients who died of COVID-19. Mechanistically, high levels of vascular endothelial growth factor (VEGF) in the adipose tissue induces adipose browning through vasculature-adipocyte interaction. Inhibition of VEGF blocks COVID-19-induced adipose tissue browning and NST and partially prevents infection-induced body weight loss. Our data suggest that the browning of adipose tissues induced by COVID-19 can contribute to adipose tissue atrophy and weight loss observed during infection. Inhibition of VEGF signaling may represent an effective approach for preventing and treating COVID-19-associated weight loss.

Critically ill COVID-19 patients with pleural effusion experience longer hospitalization, multisystem inflammatory syndrome, and higher rates of mortality. Generally, pleural effusion can serve as a diagnostic value to differentiate cytokine levels. This study aimed to evaluate the pleural effusions of COVID-19 deceased patients for 182 protein markers. Olink® Inflammation and Organ Damage panels were used to determine the level of 184 protein markers, e.g., ADA, BTC, CA12, CAPG, CD40, CDCP1, CXCL9, ENTPD2, Flt3L, IL-6, IL-8, LRP1, OSM, PD-L1, PTN, STX8, and VEGFA, which were raised significantly in COVID-19 deceased patients, showing over-stimulation of the immune system and ravaging cytokine storm. The rises of DPP6 and EDIL3 also indicate damage caused to arterial and cardiovascular organs. Overall, this study confirms the elevated levels of CA12, CD40, IL-6, IL-8, PD-L1, and VEGFA, proposing their potential either as biomarkers for the severity and prognosis of the disease or as targets for therapy. Particularly, this study reports upregulated ADA, BTC, DPP6, EDIL3, LIF, ENTPD2, Flt3L, and LRP1 in severe COVID-19 patients for the first time. Pearson’s correlation coefficient analysis indicates the involvement of JAK/STAT pathways as a core regulator of hyperinflammation in deceased COVID-19 patients, suggesting the application of JAK inhibitors as a potential efficient treatment.

Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive solid tumors. Based on transcriptomic classifiers, basal-like and classical PDAC subtypes can be defined that differ in prognosis. Single-cell sequencing has recently revealed that these subtypes coexist in individual tumors. However, the contribution of either clonal heterogeneity or microenvironmental cues to subtype heterogeneity is unclear. Here, we report the tumor phenotype dynamics in a cohort of patients in whom PDAC infiltrated the duodenal wall. Using multiplex immunohistochemistry, we show that PDAC cells revert to non-destructive growth and undergo differentiation towards the classical subtype upon integration into the duodenal epithelium. Our results tightly link microenvironmental cues to the PDAC molecular subtype and open the door to a systematic investigation of microenvironmental control in human pancreatic cancer.

Most COVID-19 victims are old and die from unrelated causes. Here we present twelve complete autopsies, including two rapid autopsies of young patients where the cause of death was COVID-19 ARDS. The main virus induced pathology was in the lung parenchyma and not in the airways. Most coagulation events occurred in the intra-alveolar and not in the intra-vascular space and the few thrombi were mainly composed of aggregated thrombocytes. The dominant inflammatory response was the massive accumulation of CD163 + macrophages and the disappearance of T killer, NK and B-cells. The virus was replicating in the pneumocytes and macrophages but not in bronchial epithelium, endothelium, pericytes or stromal cells. The lung consolidations were produced by a massive regenerative response, stromal and epithelial proliferation and neovascularization. We suggest that thrombocyte aggregation inhibition, angiogenesis inhibition and general proliferation inhibition may have a roll in the treatment of advanced COVID-19 ARDS.

The main viral protease (3CLpro) is indispensable for SARS-CoV-2 replication. We delineate the human protein substrate landscape of 3CLpro by TAILS substrate-targeted N-terminomics. We identify more than 100 substrates in human lung and kidney cells supported by analyses of SARS-CoV-2-infected cells. Enzyme kinetics and molecular docking simulations of 3CLpro engaging substrates reveal how noncanonical cleavage sites, which diverge from SARS-CoV, guide substrate specificity. Cleaving the interactors of essential effector proteins, effectively stranding them from their binding partners, amplifies the consequences of proteolysis. We show that 3CLpro targets the Hippo pathway, including inactivation of MAP4K5, and key effectors of transcription, mRNA processing, and translation. We demonstrate that Spike glycoprotein directly binds galectin-8, with galectin-8 cleavage disengaging CALCOCO2/NDP52 to decouple antiviral-autophagy. Indeed, in post-mortem COVID-19 lung samples, NDP52 rarely colocalizes with galectin-8, unlike in healthy lungs. The 3CLpro substrate degradome establishes a foundational substrate atlas to accelerate exploration of SARS-CoV-2 pathology and drug design.

The commonly used laboratory cell lines are the first line of experimental models to study the pathogenicity and performing antiviral assays for emerging viruses. Here, we assessed the tropism and cytopathogenicity of the first Swedish isolate of SARS-CoV-2 in six different human cell lines, compared their growth characteristics, and performed quantitative proteomics for the susceptible cell lines. Overall, Calu-3, Caco2, Huh7, and 293FT cell lines showed a high-to-moderate level of susceptibility to SARS-CoV-2. In Caco2 cells, the virus can achieve high titers in the absence of any prominent cytopathic effect. The protein abundance profile during SARS-CoV-2 infection revealed cell-type-specific regulation of cellular pathways. Type-I interferon signaling was identified as the common dysregulated cellular response in Caco2, Calu-3, and Huh7 cells. Together, our data show cell-type specific variability for cytopathogenicity, susceptibility, and cellular response to SARS-CoV-2 and provide important clues to guide future studies.