Combining the Tyrosine Kinase Inhibitor Cabozantinib and the mTORC1/2 Inhibitor Sapanisertib Blocks ERK Pathway Activity and Suppresses Tumor Growth in Renal Cell Carcinoma.

Current treatment approaches for renal cell carcinoma (RCC) face challenges in achieving durable tumor responses due to tumor heterogeneity and drug resistance. Combination therapies that leverage tumor molecular profiles could offer an avenue for enhancing treatment efficacy and addressing the limitations of current therapies. To identify effective strategies for treating RCC, we selected ten drugs guided by tumor biology to test in six RCC patient-derived xenograft (PDX) models. The multitargeted tyrosine kinase inhibitor (TKI) cabozantinib and mTORC1/2 inhibitor sapanisertib emerged as the most effective drugs, particularly when combined. The combination demonstrated favorable tolerability and inhibited tumor growth or induced tumor regression in all models, including two from patients who experienced treatment failure with FDA-approved TKI and immunotherapy combinations. In cabozantinib-treated samples, imaging analysis revealed a significant reduction in vascular density, and single-nucleus RNA sequencing (snRNA-seq) analysis indicated a decreased proportion of endothelial cells in the tumors. SnRNA-seq data further identified a tumor subpopulation enriched with cell-cycle activity that exhibited heightened sensitivity to the cabozantinib and sapanisertib combination. Conversely, activation of the epithelial-mesenchymal transition pathway, detected at the protein level, was associated with drug resistance in residual tumors following combination treatment. The combination effectively restrained ERK phosphorylation and reduced expression of ERK downstream transcription factors and their target genes implicated in cell-cycle control and apoptosis. This study highlights the potential of the cabozantinib plus sapanisertib combination as a promising treatment approach for patients with RCC, particularly those whose tumors progressed on immune checkpoint inhibitors and other TKIs. SIGNIFICANCE: The molecular-guided therapeutic strategy of combining cabozantinib and sapanisertib restrains ERK activity to effectively suppress growth of renal cell carcinomas, including those unresponsive to immune checkpoint inhibitors.

Differential chromatin accessibility and transcriptional dynamics define breast cancer subtypes and their lineages.

Breast cancer is a heterogeneous disease, and treatment is guided by biomarker profiles representing distinct molecular subtypes. Breast cancer arises from the breast ductal epithelium, and experimental data suggests breast cancer subtypes have different cells of origin within that lineage. The precise cells of origin for each subtype and the transcriptional networks that characterize these tumor-normal lineages are not established. In this work, we applied bulk, single-cell (sc), and single-nucleus (sn) multi-omic techniques as well as spatial transcriptomics and multiplex imaging on 61 samples from 37 breast cancer patients to show characteristic links in gene expression and chromatin accessibility between breast cancer subtypes and their putative cells of origin. We applied the PAM50 subtyping algorithm in tandem with bulk RNA-seq and snRNA-seq to reliably subtype even low-purity tumor samples and confirm promoter accessibility using snATAC. Trajectory analysis of chromatin accessibility and differentially accessible motifs clearly connected progenitor populations with breast cancer subtypes supporting the cell of origin for basal-like and luminal A and B tumors. Regulatory network analysis of transcription factors underscored the importance of BHLHE40 in luminal breast cancer and luminal mature cells, and KLF5 in basal-like tumors and luminal progenitor cells. Furthermore, we identify key genes defining the basal-like ( PRKCA , SOX6 , RGS6 , KCNQ3 ) and luminal A/B ( FAM155A , LRP1B ) lineages, with expression in both precursor and cancer cells and further upregulation in tumors. Exhausted CTLA4-expressing CD8+ T cells were enriched in basal-like breast cancer, suggesting altered means of immune dysfunction among breast cancer subtypes. We used spatial transcriptomics and multiplex imaging to provide spatial detail for key markers of benign and malignant cell types and immune cell colocation. These findings demonstrate analysis of paired transcription and chromatin accessibility at the single cell level is a powerful tool for investigating breast cancer lineage development and highlight transcriptional networks that define basal and luminal breast cancer lineages.

Epigenetic and transcriptomic characterization reveals progression markers and essential pathways in clear cell renal cell carcinoma.

Identifying tumor-cell-specific markers and elucidating their epigenetic regulation and spatial heterogeneity provides mechanistic insights into cancer etiology. Here, we perform snRNA-seq and snATAC-seq in 34 and 28 human clear cell renal cell carcinoma (ccRCC) specimens, respectively, with matched bulk proteogenomics data. By identifying 20 tumor-specific markers through a multi-omics tiered approach, we reveal an association between higher ceruloplasmin (CP) expression and reduced survival. CP knockdown, combined with spatial transcriptomics, suggests a role for CP in regulating hyalinized stroma and tumor-stroma interactions in ccRCC. Intratumoral heterogeneity analysis portrays tumor cell-intrinsic inflammation and epithelial-mesenchymal transition (EMT) as two distinguishing features of tumor subpopulations. Finally, BAP1 mutations are associated with widespread reduction of chromatin accessibility, while PBRM1 mutations generally increase accessibility, with the former affecting five times more accessible peaks than the latter. These integrated analyses reveal the cellular architecture of ccRCC, providing insights into key markers and pathways in ccRCC tumorigenesis.

Spatiotemporal evolution of global long-term patterns of soil moisture.

Surface soil moisture (SM) is essential for existence of biotic lifeform and geophysical processes. However, with increasing global warming due to climatic changes, its spatiotemporal evolution is uncertain and largely unknown. In this study we detected long-term (40 years; 1981-2020) SM patterns of global vegetated areas through spatial timeseries clustering using the state-of-the-art ERA5-Land dataset. In addition, we also analyzed long-term patterns of precipitation (P), evapotranspiration (bare soil evaporation (BSe) and vegetation transpiration (VT)), and normalized difference vegetation index (NDVI). Our results indicate that surface SM (0-7 cm depth) of about 48 % and 9 % of the global vegetated area is showing drying and wetting pattern over the past 40 years, respectively. The detected soil drying, and wetting patterns were largely consistent across different soil depth, with 90 % and 80 % pattern similarity of surface soil layer with 2nd soil layer (7-28 cm) and 3rd soil layer (28-100 cm), respectively. About 80 % of areas with drying soil pattern also showed increasing evapotranspiration and/or decreasing precipitation. Specifically, decreasing P, increasing BSe and VT pattern were detected for 11 % of the soil drying pattern area. Similarly, increasing BSe and VT pattern, only decreasing P and only increasing VT pattern were detected for 17 %, 25 % and 12 % of soil drying areas, respectively. Both decreasing precipitation and increasing evapotranspiration patterns showed about 40 % similarity with decreasing soil moisture patterns. Across different landcover types, broadleaved forests, and cropland areas showed largest drying pattern. Under the future global warming scenario, the global soil water is expected to decrease as evapotranspiration would increase with inconsistent trend of global precipitation change. Our findings are of utmost importance for global soil water resource conservation and management.

The effects of electrical stimulation on glial cell behaviour.

Neural interface devices interact with the central nervous system (CNS) to substitute for some sort of functional deficit and improve quality of life for persons with disabilities. Design of safe, biocompatible neural interface devices is a fast-emerging field of neuroscience research. Development of invasive implant materials designed to directly interface with brain or spinal cord tissue has focussed on mitigation of glial scar reactivity toward the implant itself, but little exists in the literature that directly documents the effects of electrical stimulation on glial cells. In this review, a survey of studies documenting such effects has been compiled and categorized based on the various types of stimulation paradigms used and their observed effects on glia. A hybrid neuroscience cell biology-engineering perspective is offered to highlight considerations that must be made in both disciplines in the development of a safe implant. To advance knowledge on how electrical stimulation affects glia, we also suggest experiments elucidating electrochemical reactions that may occur as a result of electrical stimulation and how such reactions may affect glia. Designing a biocompatible stimulation paradigm should be a forefront consideration in the development of a device with improved safety and longevity.

Spatially restricted drivers and transitional cell populations cooperate with the microenvironment in untreated and chemo-resistant pancreatic cancer.

Pancreatic ductal adenocarcinoma is a lethal disease with limited treatment options and poor survival. We studied 83 spatial samples from 31 patients (11 treatment-naïve and 20 treated) using single-cell/nucleus RNA sequencing, bulk-proteogenomics, spatial transcriptomics and cellular imaging. Subpopulations of tumor cells exhibited signatures of proliferation, KRAS signaling, cell stress and epithelial-to-mesenchymal transition. Mapping mutations and copy number events distinguished tumor populations from normal and transitional cells, including acinar-to-ductal metaplasia and pancreatic intraepithelial neoplasia. Pathology-assisted deconvolution of spatial transcriptomic data identified tumor and transitional subpopulations with distinct histological features. We showed coordinated expression of TIGIT in exhausted and regulatory T cells and Nectin in tumor cells. Chemo-resistant samples contain a threefold enrichment of inflammatory cancer-associated fibroblasts that upregulate metallothioneins. Our study reveals a deeper understanding of the intricate substructure of pancreatic ductal adenocarcinoma tumors that could help improve therapy for patients with this disease.

Analysing frequent extreme flood incidences in Brahmaputra basin, South Asia.

The present study is focused on the flood inundation in Brahmaputra Basin, which is one of the most recurrent and destructive natural disasters of the region. The flood inundation was assessed using C-Band Sentinel 1A synthetic aperture radar (SAR) during 2015-2020 with precipitation patterns, runoff discharge, and their impacts on land cover in the basin. The study exhibited a very high precipitation during monsoon in the upper catchment resulting in severe flood inundation in downslopes of Brahmaputra Basin. A very high (900-2000 mm) to extremely high (>2000 mm) monthly cumulative precipitation in the south and south-eastern parts of basin led to high discharge (16,000 to 18,000 m3s-1) during July-August months. The river discharge increases with cumulative effects of precipitation and melting of snow cover during late summer and monsoon season, and induced flood inundation in lower parts of basin. This flood has largely affected agricultural land (>77% of total basin), forests (~3%), and settlement (426 to 1758 km2) affecting large wildlife and livelihood during 2015-2020. The study highlights the regions affected with recurrent flood and necessitates adopting an integrated, multi-hazard, multi-stakeholder approach with an emphasis on self-reliance of the community for sustenance with local resources and practices.

Present and future projections of heatwave hazard-risk over India: A regional earth system model assessment.

The heatwave is a disastrous hazard having significant impacts on health and society. This study analyses the heatwave hazards and risk for India's current and future scenarios using socioeconomic vulnerability and temperature datasets during the summer (April-June) season. The Census of India (CoI) 2011 datasets were considered to assess current vulnerability and projected from the SocioEconomic Data And Application Center (SEDAC) population at Shared Socioeconomic Pathway (SSP) 4 for future vulnerability. Whereas IMD temperature data used for hazard assessment for the present scenario (1958-2005) while projected temperature data from regional earth system model REMO-OASIS-MPIOM (ROM) were used for the future (2006-2099) scenario. The study exhibited the most hazardous, vulnerable, and risk-prone regions identified as the south-eastern coast and Indo-Gangetic plains and some populous districts with metropolitan regions (Mumbai, Delhi, and Kolkata) under the current scenario. The coupled model ROM has efficiently captured the critical districts with higher and lower risk, showing its future projection capability. The study highlighted that the heatwave hazard-risk would significantly worsen in future scenarios in all districts under enhanced global warming and largely affecting the districts in the eastern and middle Indo-Gangetic plains and Malabar region. The present study will provide sufficient insights into designing mitigation strategies and future adaptive planning for the heatwave risk, which is one of the targets under Sustainable Development Goal 13 (Goal 13: Climate Action).

Influence of Super Cyclone "Amphan" in the Indian Subcontinent amid COVID-19 Pandemic.

Tropical cyclone "Amphan" developed as a super cyclone on 19 May 2020 and caused severe impact on the landmass with very high torrential precipitation (>250 mm day-1), and extremely high wind speed (>150 km h-1) after landfall on 20 May 2020. The tropical cyclone Amphan largely affected agricultural land (78.2%) and forest, including mangroves (10.8%) in eastern India and Bangladesh. The built-up area over the trajectory of the cyclone and its proximity, including eastern parts of the Kolkata metropolitan area, was considerably affected by the cyclone due to the high population density and poor structural and community planning. Although the regions with close proximities to cyclones' trajectory (2033 km2 area under <2 km proximity) were affected severely, the presence of mangrove forest in Sundarban substantially reduced the magnitude of the tropical cyclone. A considerable decrease (~30%) in aerosol optical depth (AOD) in April-May 2020 as compared to that in 2019 is considered one of the major causes of the development of the warm pool and cyclogenesis in the Bay of Bengal. The number of COVID-19 cases increased by ~70% in the post-cyclonic period (29 May 2020) compared to that in the pre-cyclonic period (19 May 2020) illustrating the impact of the cyclonic hazard.

Google Earth Engine for concurrent flood monitoring in the lower basin of Indo-Gangetic-Brahmaputra plains.

The present study focused on the recent flood inundation (July 2020) that occurred in the lower Indo-Gangetic-Brahmaputra plains (IGBP) using concurrent C-band Sentinel-1A Synthetic Aperture Radar images in Google Earth Engine. The study exhibited that a substantial proportion of IGBP (40,929 km2) was inundated primarily in Bangladesh (9.09% of the total inundation), Assam (8.99%), and Bihar (6.29%) during June-July 2020. The severe impact of flood inundation was observed in croplands (4.41% of the total cropland), followed by settlements (20.98% of the total settlements) that affected a large population (~ 10,046,262) in IGBP. The prevailing COVID-19 pandemic has debilitated the efforts of mitigation and responses to flooding risks. The study necessitates adopting an integrated, multi-hazard, multi-stakeholder approach with an emphasis on self-reliance of the community for sustenance with local resources and practices.

The dark cloud with a silver lining: Assessing the impact of the SARS COVID-19 pandemic on the global environment.

The Severe Acute Respiratory Syndrome-Coronavirus Disease 2019 (COVID-19) pandemic caused by a novel coronavirus known as SARS-CoV-2 has caused tremendous suffering and huge economic losses. We hypothesized that extreme measures of partial-to-total shutdown might have influenced the quality of the global environment because of decreased emissions of atmospheric pollutants. We tested this hypothesis using satellite imagery, climatic datasets (temperature, and absolute humidity), and COVID-19 cases available in the public domain. While the majority of the cases were recorded from Western countries, where mortality rates were strongly positively correlated with age, the number of cases in tropical regions was relatively lower than European and North American regions, possibly attributed to faster human-to-human transmission. There was a substantial reduction in the level of nitrogen dioxide (NO2: 0.00002 mol m-2), a low reduction in CO (<0.03 mol m-2), and a low-to-moderate reduction in Aerosol Optical Depth (AOD: ~0.1-0.2) in the major hotspots of COVID-19 outbreak during February-March 2020, which may be attributed to the mass lockdowns. Our study projects an increasing coverage of high COVID-19 hazard at absolute humidity levels ranging from 4 to 9 g m-3 across a large part of the globe during April-July 2020 due to a high prospective meteorological suitability for COVID-19 spread. Our findings suggest that there is ample scope for restoring the global environment from the ill-effects of anthropogenic activities through temporary shutdown measures.

Interfering with HuR-RNA Interaction: Design, Synthesis and Biological Characterization of Tanshinone Mimics as Novel, Effective HuR Inhibitors.

The human antigen R (HuR) is an RNA-binding protein known to modulate the expression of target mRNA coding for proteins involved in inflammation, tumorigenesis, and stress responses and is a valuable drug target. We previously found that dihydrotanshinone-I (DHTS, 1) prevents the association of HuR with its RNA substrate, thus imparing its function. Herein, inspired by DHTS structure, we designed and synthesized an array of ortho-quinones (tanshinone mimics) using a function-oriented synthetic approach. Among others, compound 6a and 6n turned out to be more effective than 1, showing a nanomolar Ki and disrupting HuR binding to RNA in cells. A combined approach of NMR titration and molecular dynamics (MD) simulations suggests that 6a stabilizes HuR in a peculiar closed conformation, which is incompatible with RNA binding. Alpha screen and RNA-electrophoretic mobility shift assays (REMSA) data on newly synthesized compounds allowed, for the first time, the generation of structure activity relationships (SARs), thus providing a solid background for the generation of highly effective HuR disruptors.

Regulation of HuR structure and function by dihydrotanshinone-I.

The Human antigen R protein (HuR) is an RNA-binding protein that recognizes U/AU-rich elements in diverse RNAs through two RNA-recognition motifs, RRM1 and RRM2, and post-transcriptionally regulates the fate of target RNAs. The natural product dihydrotanshinone-I (DHTS) prevents the association of HuR and target RNAs in vitro and in cultured cells by interfering with the binding of HuR to RNA. Here, we report the structural determinants of the interaction between DHTS and HuR and the impact of DHTS on HuR binding to target mRNAs transcriptome-wide. NMR titration and Molecular Dynamics simulation identified the residues within RRM1 and RRM2 responsible for the interaction between DHTS and HuR. RNA Electromobility Shifts and Alpha Screen Assays showed that DHTS interacts with HuR through the same binding regions as target RNAs, stabilizing HuR in a locked conformation that hampers RNA binding competitively. HuR ribonucleoprotein immunoprecipitation followed by microarray (RIP-chip) analysis showed that DHTS treatment of HeLa cells paradoxically enriched HuR binding to mRNAs with longer 3'UTR and with higher density of U/AU-rich elements, suggesting that DHTS inhibits the association of HuR to weaker target mRNAs. In vivo, DHTS potently inhibited xenograft tumor growth in a HuR-dependent model without systemic toxicity.

Dihydrotanshinone-I interferes with the RNA-binding activity of HuR affecting its post-transcriptional function.

Post-transcriptional regulation is an essential determinant of gene expression programs in physiological and pathological conditions. HuR is a RNA-binding protein that orchestrates the stabilization and translation of mRNAs, critical in inflammation and tumor progression, including tumor necrosis factor-alpha (TNF). We identified the low molecular weight compound 15,16-dihydrotanshinone-I (DHTS), well known in traditional Chinese medicine practice, through a validated high throughput screening on a set of anti-inflammatory agents for its ability to prevent HuR:RNA complex formation. We found that DHTS interferes with the association step between HuR and the RNA with an equilibrium dissociation constant in the nanomolar range in vitro (Ki = 3.74 ± 1.63 nM). In breast cancer cell lines, short term exposure to DHTS influences mRNA stability and translational efficiency of TNF in a HuR-dependent manner and also other functional readouts of its post-transcriptional control, such as the stability of selected pre-mRNAs. Importantly, we show that migration and sensitivity of breast cancer cells to DHTS are modulated by HuR expression, indicating that HuR is among the preferential intracellular targets of DHTS. Here, we disclose a previously unrecognized molecular mechanism exerted by DHTS, opening new perspectives to therapeutically target the HuR mediated, post-transcriptional control in inflammation and cancer cells.

Targeting the multifaceted HuR protein, benefits and caveats.

The RNA-binding protein (RBP) HuR is one of the most widely studied regulators of the eukaryotic posttranscriptional gene expression and it plays a physiological role in mediating the cellular response to apoptotic, proliferating and survival stimuli. Following physiological or stress stimuli, HuR protein binds to Adenylate-Urydinilate rich elements (AREs) generally contained in the 3'UTR of transcripts, then it shuttles from the nucleus to the cytoplasm and regulates the half-life and/or translation of cargo mRNAs. Derangements in sub-cellular localization and expression of HuR have been associated with the pathophysiology of many diseases and this protein has been proposed as a potential drug target. Recent findings also re-evaluated HuR as a splicing and polyadenylation factor, expanding its spectrum of functional activity up to the maturation of pre-mRNAs. In this review, we generate a comprehensive picture of HuR functionality to discuss the implications of considering HuR as pharmacological target and the detrimental or positive impact that can be expected upon its modulation. Firstly, we focus on the recent findings about the mechanistic role of HuR in the nucleus and in the regulation of long non coding RNAs; then we describe the animal models and the clinical association and significance in cancer; finally, we have reviewed the pharmacological tools that influence HuR's post-transcriptional control and the efforts made to identify specific HuR inhibitors.