Biology subjects

Pradhan, K.

Publications and source records attributed to Pradhan, K..

16 recordsLinked to original sources

bioRxiv2026

Evolutionary divergence V-ATPase function in macropinocytic cup remodeling

Macropinocytosis is an evolutionarily conserved process from unicellular eukaryotes to mammals. This process relies on actin-rich protrusions beneath the plasma membrane to form a macropinocytic cup. Traditionally, V ATPase has been best studied for its role in late endosomal acidification. However, the specific roles of V-ATPase interaction with cytoskeletal machinery and its crosstalk with lipids in the formation of macropinocytic cups have not been investigated. Here, we uncover an unprecedented role of V-ATPase in shaping the macropinocytic cup in the pathogenic amoeba Entamoeba histolytica. Our results showed that the Entamoeba V-ATPase complex is associated with F-actin at macropinocytic cups. Moreover, we found that the V-ATPase complex is dynamically recruited to the macropinocytic cup and dissociates from the macropinosome. We further demonstrated that the V-ATPase V1B subunit directly binds to actin and uniquely promotes actin polymerization. The pH biosensor phosphatidic acid, revealed abundant V-ATPase complex and cytoskeleton associated proteins in its interactome. Surprisingly, the V1B subunit showed reproducible binding to phosphatidic acid and this interaction modulates actin polymerization. Collectively, our work highlights the novel role of V-ATPase in directly driving actin polymerization, in conjunction with phosphatidic acid, to shape the macropinocytic cup.

cell biology↗

bioRxiv2026

Genetic and stochastic basis of phenotypic discordance in 16p11.2 mouse model deletion

Recurrent copy number variations such as the 16p11.2 deletion (del/+) represent a significant genetic risk for neurodevelopmental disorders, showing incomplete penetrance and variable expressivity. Here we describe a striking discordance in a genetic mouse model of human 16p11.2 deletion. Using electrocorticography experiments, we detected that approximately 50% of the isogenic del/+ mice exhibited increased susceptibility to seizures from low doses of the convulsant drug pentylenetetrazole (PTZ). Some of these mice also displayed spontaneous epileptiform brain activity. Next, we used two-photon microscopy tomography (STPT) with c-Fos-GFP (c-Fos+) as a reporter of neuronal activity to obtain images of the entire mouse brain. We examined del/+ mice that exhibited low or high responses to PTZ. Low responders exhibited minimal c-Fos+ activation. However, they had activating circuits that suggest the presence of compensatory mechanisms that suppress seizures. These circuits include the reticular nucleus of the thalamus, the pretectal region, the pedunculopontine nucleus, and the superior colliculus. In contrast, high-responder mice exhibited high c-Fos+ expression, corresponding to a fast seizure phenotype. Using whole-brain imaging, we analyzed brain volume and detected significant differences in the cortex between low- responder and high-responder del/+ mice. In the group with higher seizure susceptibility, we observed a notable decrease in cortical volume with significant differences in several brain regions compared to low responders. Additionally, some high-responder mice showed null expansion areas compared to low-responder mice. During the longitudinal behavioral analysis, the high-responder group of mice exhibited more severe sleep disturbances and an increase in repetitive grooming. Finally, to identify transcriptional correlates of the low- versus high- response phenotypes in adulthood, we performed bulk RNA-seq on somatosensory cortex punches from adult del/+ mice stratified by seizure response. Seizure-prone del/+ mice exhibited reduced activity-dependent immediate early gene signatures and coordinated changes in regulatory programs, including decreased expression of transcriptional regulators and metabotropic glutamate receptor genes, compared to low responders. Together, these findings define two distinct adult del/+ subgroups with convergent circuit, structural, behavioral, and molecular signatures.

neuroscience↗

bioRxiv2026

Phenological Plasticity without Directional Change: Tropical Hornbills Track Temperature but Maintain Reproductive Stability

Climate change is altering breeding phenology in birds worldwide, yet tropical systems remain understudied despite harbouring the greatest avian diversity. We drew upon 26 years (1998-2024) of breeding phenology and reproductive success data on three sympatric Asian hornbill species (Great Hornbill Buceros bicornis, Wreathed Hornbill Rhyticeros undulatus, Oriental Pied Hornbill Anthracoceros albirostris) from a tropical forest in northeast India to examine whether trends in long-term breeding parameters reflect directional climate change or interannual variability. Over the study period, we found no significant directional trends in nest entry timing, occupancy, or breeding success over 26 years, despite modest regional warming. However, breeding parameters showed sensitivity to interannual temperature variation, with pre-breeding temperature (January-February) explaining 36-70% of variance in nest timing. Temperature sensitivity differed among species, with Wreathed Hornbill showing the strongest response (-15.9 days/{degrees}C), followed by Great Hornbill (-9.8 days/{degrees}C), and Oriental Pied Hornbill showing the weakest (-4.8 days/{degrees}C), consistent with predictions that larger, frugivorous species with extended breeding cycles would exhibit greater climatic sensitivity. The underlying mechanism appears related to a body size-phenology-thermal exposure interaction: Oriental Pied Hornbills nest later (mid-April) with shorter breeding cycles ([~]90 days), completing reproduction before peak monsoon heat (June), whereas both larger species nest earlier (mid-February) but endure thermal stress throughout extended breeding cycles ([~]130+ days) into August. Notably, annual occupancy and breeding success remained stable across years despite strong phenological responses to temperature, suggesting that phenological plasticity may help maintain reproductive performance under current climatic variation. These findings indicate that tropical cavity-nesting frugivores exhibit phenological plasticity coupled with demographic stability, though the mechanisms underlying this apparent buffering remain incompletely understood, and body size-dependent differences in thermal exposure suggest heterogeneous vulnerabilities to future warming scenarios.

ecology↗

bioRxiv2026

Assessing heatdome effects on forest dynamics in the Pacific Northwest using Planet imagery

Increasingly frequent extreme heat events are imposing significant stress on forest ecosystems, with implications for forests and the organisms that live in them. This study evaluates the effects of the June 2021 Pacific Northwest (PNW) heatdome (a prolonged high-pressure system that generated record-breaking temperatures) on forest canopy health and its subsequent recovery within the conifer-dominated Ellsworth Creek Preserve in Washington state, USA, using high-resolution Planet Labs satellite imagery. We analyzed normalized difference vegetation index (NDVI) trends from spring to fall from 2017 to 2024 to identify canopy stress and quantify changes in canopy greenness. Experimental forest restoration thinning treatments implemented to test their effectiveness in restoring old-growth forest characteristics at our sites allowed us to assess impacts of the heatdome event relative to these restoration treatments. Our results show a marked decline in summer NDVI following the 2021 heatdome, signaling substantial canopy stress. This decline, different than patterns in the other seven years, was particularly strong in dense, unmanaged (control) forest stands, which exhibited more pronounced NDVI declines than thinned (treatment) stands. These more pronounced stress signals during and after the heat event were associated with greater tree canopy height, canopy complexity, and tree density. The summer NDVI trends over the three post-heatdome years suggest a gradual recovery in tree canopy greenness, with thinned stands showing faster NDVI recovery than controls. In all, these results suggest that restoration thinning may improve canopy resilience to extreme heat. However, recovery trajectories varied widely within stand types, with persistent evidence of stress in high-density areas that suggest incomplete recovery as of 2023. Broadly, these findings show the vulnerability of dense forest canopies to extreme heat events, suggesting that forests with high canopy density may be less adaptable to recurring heat events. Nonetheless, managing forests through restoration thinning may enhance forest resilience to these climate-induced stressors - providing potential guidance for adaptive management strategies to maintain forest health in a world with more extreme climates.

ecology↗

bioRxiv2024

A STAT3 Degrader Demonstrates Pre-clinical Efficacy in Venetoclax resistant Acute Myeloid Leukemia

Acute myeloid leukemia (AML) is an aggressive hematologic malignancy that continues to have poor prognosis despite recent therapeutic advances. Venetoclax (Ven), a BCL2-inhibitor has shown a high response rate in AML; however, relapse is invariable due to mitochondrial dysregulation that includes upregulation of the antiapoptotic protein MCL1, a central mechanism of Ven resistance (Ven-res). We have previously demonstrated that the transcription factor STAT3 is upregulated in AML hematopoietic stem and progenitor cells (HSPCs) and can be effectively targeted to induce apoptosis of these aberrant cells. We now show that overexpression of STAT3 alone is sufficient to initiate a strong AML phenotype in a transgenic murine model. Phospho-proteomic data from Ven treated AML patients show a strong correlation of high total STAT3 and phospho-STAT3 [both p-STAT3(Y705) and p-STAT3(S727)] expression with worse survival and reduced remission duration. Additionally, significant upregulation of STAT3 was observed in Ven-res cell lines, in vivo models and primary patient samples. A novel and specific degrader of STAT3 demonstrated targeted reduction of total STAT3 and resulting inhibition of its active p-STAT3(Y705) and p-STAT3(S727) forms. Treatment with the STAT3 degrader induced apoptosis in parental and Ven-res AML cell lines and decreased mitochondrial depolarisation, and thereby dependency on MCL1 in Ven-res AML cell line, as observed by BH3 profiling assay. STAT3 degrader treatment also enhanced differentiation of myeloid and erythroid colonies in Ven-res peripheral blood mononuclear cells (PBMNCs). Upregulation of p-STAT3(S727) was also associated with pronounced mitochondrial structural and functional dysfunction in Ven-res cell lines, that were restored by STAT3 degradation. Treatment with a clinical-stage STAT3 degrader, KT-333 resulted in a significant reduction in STAT3 and MCL1 protein levels within two weeks of treatment in a cell derived xenograft model of Ven-res AML. Additionally, this treatment significant improvement in the survival of a Ven-res patient-derived xenograft in-vivo study. Degradation of STAT3 resulting in downregulation of MCL1 and improvements in global mitochondrial dysfunction suggests a novel mechanism of overcoming Ven-res in AML. Statement of PurposeFive-year survival from AML is dismal at 30%. Our prior research demonstrated STAT3 over-expression in AML HSPCs to be associated with inferior survival. We now explore STAT3 over-expression in Ven-res AML, explain STAT3 mediated mitochondrial perturbations and describe a novel therapeutic strategy, STAT3 degradation to overcome Ven-res.

cancer biology↗

bioRxiv2024

Broad de-regulated U2AF1 splicing is prognostic and augments leukemic transformation via protein arginine methyltransferase activation

The role of splicing dysregulation in cancer is underscored by splicing factor mutations; however, its impact in the absence of such rare mutations is poorly understood. To reveal complex patient subtypes and putative regulators of pathogenic splicing in Acute Myeloid Leukemia (AML), we developed a new approach called OncoSplice. Among diverse new subtypes, OncoSplice identified a biphasic poor prognosis signature that partially phenocopies U2AF1-mutant splicing, impacting thousands of genes in over 40% of adult and pediatric AML cases. U2AF1-like splicing co-opted a healthy circadian splicing program, was stable over time and induced a leukemia stem cell (LSC) program. Pharmacological inhibition of the implicated U2AF1-like splicing regulator, PRMT5, rescued leukemia mis-splicing and inhibited leukemic cell growth. Genetic deletion of IRAK4, a common target of U2AF1-like and PRMT5 treated cells, blocked leukemia development in xenograft models and induced differentiation. These analyses reveal a new prognostic alternative-splicing mechanism in malignancy, independent of splicing-factor mutations. Statement of significanceUsing a new in silico strategy we reveal counteracting determinants of patient survival in Acute Myeloid Leukemia that co-opt well-defined mutation-dependent splicing programs. Broad poor-prognosis splicing and leukemia stem cell survival could be rescued through pharmacological inhibition (PRMT5) or target deletion (IRAK4), opening the door for new precision therapies. Competing InterestsConflict-of-interest disclosure: DTS. serves on the scientific advisory board at Kurome Therapeutics; is a consultant for and/or received funding from Kurome Therapeutics, Captor Therapeutics, Treeline Biosciences, and Tolero Therapeutics; and has equity in Kurome Therapeutics. AV has received research funding from GlaxoSmithKline, BMS, Jannsen, Incyte, MedPacto, Celgene, Novartis, Curis, Prelude and Eli Lilly and Company, has received compensation as a scientific advisor to Novartis, Stelexis Therapeutics, Acceleron Pharma, and Celgene, and has equity ownership in Throws Exception and Stelexis Therapeutics.

cancer biology↗

bioRxiv2023

Lagged climate-driven range shifts at species' leading, but not trailing, range edges revealed by multispecies seed addition experiment

Climate change is causing many species ranges to shift upslope to higher elevations as species track their climatic requirements. However, many species have not shifted in pace with recent warming (i.e., range stasis), possibly due either to demographic lags or microclimatic buffering. The lagged-response hypothesis posits that range stasis disguises an underlying climatic sensitivity if range shifts lag the velocity of climate change due to slow colonization or mortality. Alternatively, the microclimatic buffering hypothesis proposes that small-scale variation within the landscape, such as canopy cover, creates patches of suitable habitat within otherwise unsuitable macroclimates that create climate refugia and buffer range contractions. To test these two hypotheses, we combined a large seed addition experiment of 25 plant species across macro- and micro-scale climate gradients with local herbaria records to compare patterns of seedling recruitment relative to adult ranges and microclimate in the North Cascades, USA. Despite high species-to-species variability in recruitment, community-level patterns supported the lagged response hypothesis, with a mismatch between where recruitment vs. adults occur. On average, the seedling recruitment optimum shifted from the adult climatic range centre to historically cooler, wetter regions and many species recruited beyond their cold (e.g., leading) range edge. Meanwhile, successful recruitment at warm and dry edges, despite recent climate change, suggests that macroclimatic effects on recruitment do not drive trailing range dynamics. By contrast, we were unable to detect evidence of microclimatic buffering due to canopy cover. Combined, our results suggest apparent range stasis in our system is a lagged response to climate change at the cool ends of species ranges, with range expansions likely to occur slowly or in a punctuated fashion.

ecology↗

bioRxiv2023

Monocytes reprogrammed by 4-PBA potently contribute to the resolution of inflammation and atherosclerosis

BackgroundChronic inflammation initiated by inflammatory monocytes underlies the pathogenesis of atherosclerosis. However, approaches that can effectively resolve chronic low-grade inflammation targeting monocytes are not readily available. The small chemical compound 4-phenylbutyric acid (4-PBA) exhibits broad anti-inflammatory effects in reducing atherosclerosis. Selective delivery of 4-PBA reprogrammed monocytes may hold novel potential in providing targeted and precision therapeutics for the treatment of atherosclerosis. MethodsSystems analyses integrating single-cell RNA-sequencing and complementary immunological approaches characterized key resolving characteristics as well as defining markers of reprogrammed monocytes trained by 4-PBA. Molecular mechanisms responsible for monocyte reprogramming was assessed by integrated biochemical and genetic approaches. The inter-cellular propagation of homeostasis resolution was evaluated by co-culture assays with donor monocytes trained by 4-PBA and recipient naive monocytes. The in vivo effects of monocyte resolution and atherosclerosis prevention by 4-PBA were assessed with the high fat diet-fed ApoE-/- mouse model with i.p. 4-PBA administration. Furthermore, the selective efficacy of 4-PBA trained monocytes were examined by i.v. transfusion of ex vivo trained monocytes by 4-PBA into recipient high fat diet-fed ApoE-/- mice. ResultsIn this study, we found that monocytes can be potently reprogrammed by 4-PBA into an immune-resolving state characterized by reduced adhesion and enhanced expression of anti-inflammatory mediator CD24. Mechanistically, 4-PBA reduced the expression of ICAM-1 via reducing peroxisome stress and attenuating SYK-mTOR signaling. Concurrently, 4-PBA enhanced the expression of resolving mediator CD24 through promoting PPAR{gamma} neddylation mediated by TOLLIP. 4-PBA trained monocytes can effectively propagate anti-inflammation activity to neighboring monocytes through CD24. Our data further demonstrated that 4-PBA trained monocytes effectively reduce atherosclerosis pathogenesis when administered in vivo. ConclusionOur study describes a robust and effective approach to generate resolving monocytes, characterizes novel mechanisms for targeted monocyte reprogramming, and offers a precision-therapeutics for atherosclerosis based on delivering reprogrammed resolving monocytes.

immunology↗

bioRxiv2023

Microclimate buffering varies across forest types during an extreme heat event

Increasing temperatures and extreme heat episodes have become more common with climate change. While forests are known to be buffered from increasing temperatures compared to non-forested areas, whether this buffering is maintained under extreme temperature events, how such events influence forests, and how forest organisms respond to extreme heat is relatively unknown. Here we assess the effects of an extreme heat event (the Pacific Northwest (PNW) heatdome in June 2021) on forest microclimates, forests, and the organisms living within them. We first asked how the PNW heatdome affected microclimates in forests with differing canopy cover (including non-forests) and found that the buffering capacity of forests is greater under denser canopies, even under extreme heat events. We then combined this information with organismal temperature tolerance curves for 12 relevant species and found that canopy buffering can minimize the negative impacts of even extreme heat events on understory organisms, with greater canopy density providing greater microclimate moderation. Finally, we analyzed seasonal NDVI trends in recent years, and found signs of canopy stress following the extreme 2021 heat event. In all, this suggests that although forest canopies may buffer the negative effects of extreme heat events on understory organisms, a greater frequency of extreme heat events may threaten this capacity by damaging forest canopies.

ecology↗

bioRxiv2023

Ribosomal protein control of hematopoietic stem cell transformation through direct, non-canonical regulation of metabolism

We report here that expression of the ribosomal protein, RPL22, is frequently reduced in human myelodysplastic syndrome (MDS) and acute myelogenous leukemia (AML); and, reduced RPL22 expression is associated with worse outcomes. Mice null for Rpl22 display characteristics of an MDS-like syndrome and develop leukemia at an accelerated rate. Rpl22-deficient mice also display enhanced hematopoietic stem cell (HSC) self-renewal and obstructed differentiation potential, which arises not from reduced protein synthesis but from altered metabolism including increased fatty acid oxidation (FAO) and a striking induction of the stemness factor Lin28b in the resulting leukemia. Lin28b promotes a substantial increase in lipid content, upon which the survival of Rpl22-deficient leukemias depends. Altogether, these findings reveal that Rpl22 insufficiency enhances the leukemia potential of HSC through regulation of FAO and promotes leukemogenesis through Lin28b promotion of lipid synthesis. HighlightsO_LIRPL22 insufficiency is observed in MDS/AML and is associated with reduced survival C_LIO_LIRpl22-deficiency produces an MDS-like syndrome and facilitates leukemogenesis C_LIO_LIRpl22-deficiency does not impair global protein synthesis by HSC C_LIO_LIRpl22 controls leukemia survival through control of lipid synthesis C_LI eTOC: Rpl22 controls the function and transformation potential of hematopoietic stem cells through regulation of lipid metabolism.

cancer biology↗

bioRxiv2023

Understanding inter-individual social networks in mixed-species bird flocks

Mixed-species flocks (MSFs) are an important form of social organisation in forest bird communities worldwide. MSFs provide participants with the benefits of reduced predation risk and/or enhanced foraging efficiency. Recent work has shown that participation in MSFs confers long-term survival benefits in the face of anthropogenic change. However, our understanding of MSFs mainly comes from studies that examine species-level networks, where each node is a unique species and the edges or connections between nodes are associations/interactions between species. While valuable, such approaches might not allow us to understand and investigate the mechanisms that drive MSF formation and structure because social interactions and their effects occur at the individual-level. Empirical studies on multi-species, individual-level MSF social networks have seldom been undertaken due to the various complexities and logistical challenges involved. In this study, we use mist-netting and colour-ringing followed by a standardised observation protocol to construct individual-level social networks in MSFs at 2000m ASL in Eaglenest Wildlife Sanctuary, Arunachal Pradesh, Eastern Himalaya, India. First, we found two separate flocktypes at our study site, comprising two distinct sets of understorey species. The mechanisms contributing to individual-level co-occurrences are likely to differ between these flocktypes, and with MSFs in the Neotropics. The Rusty-fronted Barwing (the nuclear species of one flocktype) shows spatially disjunct territories for each flock while the Yellow-throated Fulvetta (nuclear species of the other flocktype) shows large spatial overlap in its MSF networks, which is likely driven by non-individual-specific benefits such as predation risk dilution. Further, the addition of associating individuals to the social networks has opposite impacts on the two networks. The addition of Coral-billed Scimitar Babblers to the barwing networks greatly reduces network modularity because the associating individuals bridge two modules of barwings (both spatially and in the social network). On the contrary, territorial Rufous-capped Babblers and Grey-cheeked Warblers increase the modularity of the spatially overlapping fulvetta network. Our study provides novel insights into flock formation mechanisms in the Eastern Himalaya, likely applicable to other multi-species flock systems in the Old World.

ecology↗

bioRxiv2022

Activation of targetable inflammatory immune signaling is seen in Myelodysplastic Syndromes with SF3B1 mutations

BackgroundMutations in the SF3B1 splicing factor are commonly seen in Myelodysplastic syndromes (MDS) and Acute Myeloid Leukemia (AML), yet the specific oncogenic pathways activated by missplicing have not been fully elucidated. Inflammatory immune pathways have been shown to play roles in pathogenesis of MDS, though the exact mechanisms of their activation in splicing mutant cases are not well understood. MethodsRNA-seq data from SF3B1 mutant samples was analyzed and functional roles of IRAK4 isoforms were determined. Efficacy of IRAK4 inhibition was evaluated in pre-clinical models of MDS/AML ResultsRNA-seq splicing analysis of innate immune mediators in SF3B1 mutant MDS samples revealed retention of full-length exon 6 of interleukin-1 receptor-associated kinase 4 (IRAK4), a critical downstream mediator that links the Myddosome to inflammatory NF-kB activation. Exon 6 retention leads to a longer isoform, encoding a protein (IRAK4-Long) that contains the entire death domain and kinase domain, leading to maximal activation of NF-kB. Cells with wild-type SF3B1 contain smaller IRAK4 isoforms that are targeted for proteosomal degradation. Expression of IRAK4-Long in SF3B1 mutant cells induces TRAF6 activation leading to K63-linked ubiquitination of CDK2, associated with a block in hematopoietic differentiation. Inhibition of IRAK4 with CA-4948, leads to reduction in NF-kB activation, inflammatory cytokine production, enhanced myeloid differentiation in vitro and reduced leukemic growth in xenograft models. ConclusionsSF3B1 mutation leads to expression of a therapeutically targetable, longer, oncogenic IRAK4 isoform in AML/MDS models.

cancer biology↗

bioRxiv2020

Deletion of PI3-Kinase Promotes Myelodysplasia Through Dysregulation of Autophagy in Hematopoietic Stem Cells

Hematopoietic stem cells (HSCs) maintain the blood system through a delicate equilibrium between self-renewal and differentiation. Most hematopoietic growth factors and cytokines signal through phosphoinositide 3-kinase (PI3K) via three Class IA catalytic PI3K isoforms (P110, {beta}, and {delta}), encoded by Pik3ca, Pik3cb, and Pik3cd, respectively. The PI3K/AKT pathway is commonly activated in acute myeloid leukemia (AML), and PI3K is a common therapeutic target in cancer. However, it is not known whether PI3K is required for HSC differentiation or self-renewal. We previously demonstrated that individual PI3K isoforms are dispensable in HSCs1,2. To determine the redundant roles of PI3K isoforms in HSCs, we generated a triple knockout (TKO) mouse model with deletion of all three Class IA PI3K isoforms in the hematopoietic system. Surprisingly, we observed significant expansion of TKO HSCs after transplantation, with decreased differentiation capacity and impaired multilineage repopulation. Additionally, the bone marrow of TKO mice exhibited myelodysplastic features with chromosomal abnormalities. Interestingly, we found that macroautophagy (thereafter autophagy) is impaired in TKO HSCs, and that pharmacologic induction of autophagy improves their differentiation. Therefore, we have uncovered important roles for PI3K in autophagy regulation in HSCs to maintain the balance between self-renewal and differentiation.

cancer biology↗

bioRxiv2020

Relationships between climate and phylogenetic community structure of fossil pollen assemblages are not constant during the last deglaciation

Disentangling the influence of environmental drivers on community assembly is important to understand how multiple processes influence biodiversity patterns and can inform understanding of ecological responses to climate change. Phylogenetic Community Structure (PCS) is increasingly used in community assembly studies to incorporate evolutionary perspectives and as a proxy for trait (dis)similarity within communities. Studies often assume a stationary relationship between PCS and climate, though few if any studies have tested this assumption over long time periods with concurrent community data. We estimated Nearest Taxon Index (NTI) and Net Relatedness index (NRI), two PCS metrics, of fossil pollen assemblages of angiosperms in eastern North America data over the last 21 ka BP at 1ka intervals. We analyzed spatiotemporal relationships between PCS and seven climate variables, evaluated the potential impact of deglaciation on PCS, and tested for the stability of climate-PCS relationships. The broad scale patterns of PCS, with overdispersion increasing towards the southern and eastern parts of the study area, remained largely stable across time. Most importantly, we found that significant relationships between climate variables and PCS (slope) were unstable as climate changed during the last deglaciation and new ice-free regions were colonized. We also found weak, but significant, relationships between both PCS metrics (i.e., NTI and NRI) and climate and time-since-deglaciation, which were stable even though the baselines (intercepts) changed through time. Overall, our results suggest that (1) PCS of fossil Angiosperm assemblages during the last 21ka BP have had predictable spatial patterns, but (2) the instability in the relationships between PCS and climate brings into question their usefulness in predictive modeling of community assembly.

ecology↗

bioRxiv2020

Functional succinate dehydrogenase deficiency is a pathognomonic adverse feature of clear cell renal cancer

BackgroundReduced succinate dehydrogenase (SDH) activity resulting in adverse succinate accumulation was previously thought to be relevant only in 0.05-0.5% of kidney cancers associated with germline SDH mutations (categorized SDH-deficient Renal Cell Carcinoma in the 2016 WHO classification) ResultsWe show that under-expression of SDH subunits resulting in accumulation of oncogenic succinate is a common feature in clear cell renal cell carcinoma (ccRCC) tumors during pathogenesis and progression, with a marked adverse impact on survival in a large cohort (n=516) of ccRCC patients. From a mechanistic standpoint, we show that von Hippel-Lindau (VHL) loss induced hypoxia-inducible factor (HIF) dependent upregulation of mir-210 in ccRCC causes direct inhibition of the SDHD transcript. We demonstrate that reduced expression of SDH subunits is associated with genome-wide increase in methylation and enhancement of epithelial mesenchymal transition (EMT) in ccRCC tumors, consistent with succinate-induced inhibition of TET activity and increase in invasiveness/ migratory ability of ccRCC cells. TET-2 inhibition-induced global regulatory DNA hypermethylation drives SDH loss-induced enrichment of EMT. SDH subunits under-expression had a striking association with CDHI (E-cadherin) loss in ccRCC tumors, in keeping with succinate-induced CDH1 hypermethylation and under-expression in ccRCC cells. Next, in conformity with recombinant TET-2 fluorescence quenching dynamics with succinate and ascorbic acid (AA, a TET enzyme co-factor), AA treatment led to reversal of succinate-induced inhibition of TET activity, CDH1 hypermethylation and under-expression, as well as enhanced invasiveness in ccRCC cells. Furthermore, using immunohistochemical analysis and artificial intelligence quantitation, we report that ccRCC is characterized by a marked loss of ascorbic acid transporter SLC23A1 [median percent positive cells in ccRCC primary tumors (n=104) and normal kidney cortex (n=7) was 0.7 and 32.4 respectively; p=0.0012]. Lower SLC23A1 was associated with worse survival in ccRCC (TCGA). Lastly, intravenous AA significantly prolonged survival in a metastatic ccRCC xenograft model with increased succinate and reduced SLC23A1 expression. ConclusionsTaken together, these findings strongly indicate that functional SDH deficiency is a pathognomonic adverse feature of ccRCC (which accounts for [~]80% of all kidney cancers), and that the WHO category SDH-deficient RCC should be re-named SDH germline mutation-associated RCC. Furthermore, oncogenic accumulation of succinate can be abrogated by TET modulation with AA. STATEMENT OF SIGNIFICANCEIn this study, we show that under-expression of succinate dehydrogenase (SDH) subunits resulting in the accumulation of oncogenic succinate is a common, adverse, epigenetic modulating feature occurring in a vast majority of clear cell renal cell carcinoma (ccRCC), during pathogenesis and progression. Functional SDH deficiency is therefore a pathognomonic feature of ccRCC (which accounts for [~]80% of all kidney cancers), and not just limited to the 0.05-0.5% of kidney cancer patients with germline SDH mutations. Based on the findings reported, we propose that the SDH-deficient RCC category in the 2016 WHO classification of kidney tumors be renamed SDH germline mutation-associated RCC. Furthermore, we demonstrate that oncogenic accumulation of succinate in ccRCC can be countered by TET modulation with ascorbic acid, and that ccRCC is characterized by a marked loss of ascorbic acid transporter SLC23A1. O_FIG O_LINKSMALLFIG WIDTH=172 HEIGHT=200 SRC="FIGDIR/small/188433v2_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@728d5eorg.highwire.dtl.DTLVardef@9f2e24org.highwire.dtl.DTLVardef@8e7011org.highwire.dtl.DTLVardef@15f8d33_HPS_FORMAT_FIGEXP M_FIG Graphical abstract depicting the consequential adverse downregulation of Succinate Dehydrogenase in ccRCC and its central role in oxidative phosphorylation C_FIG

cancer biology↗

bioRxiv2019

Paradoxical role of AT-rich interactive domain 1A in restraining pancreatic carcinogenesis

Background & AimsARID1A is postulated to be a tumor suppressor gene owing to loss-of-function mutations in human pancreatic ductal adenocarcinomas (PDAC). However, its role in pancreatic pathogenesis is not clear despite recent studies using genetically engineered mouse (GEM) models. We aimed at further understanding of its direct functional role in PDAC, using a combination of GEM model, PDAC cell lines. MethodsPancreas-specific mutant Arid1a-driven GEM model (Ptf1a-Cre;KrasG12D;Arid1af/f or "KAC") was generated by crossing Ptf1a-Cre;KrasG12D ("KC") mice with Arid1af/f mice and characterized histologically with timed necropsies. Arid1a was also deleted using CRISPR-Cas9 system in established PDAC cell lines to study the immediate effects of Arid1a loss in isogenic models. Cells lines with or without Arid1a expression were developed from respective autochthonous PDAC GEM models, compared functionally using various culture assays, and subjected to RNA-sequencing for comparative gene expression analysis. DNA damage repair was analyzed in cultured cells using immunofluorescence and COMET assay. ResultsArid1a is critical for early progression of mutant Kras-driven pre-malignant lesions into PDAC, as evident by lower Ki-67 and higher apoptosis staining in "KAC" as compared to "KC" mice. Enforced deletion of Arid1a in established PDAC cell lines caused suppression of cellular growth and migration, accompanied by compromised DNA damage repair. Despite early development of relatively indolent cystic precursor lesions called intraductal papillary mucinous neoplasms (IPMNs), a subset of "KAC" mice developed aggressive PDAC in later ages. PDAC cells obtained from older autochthonous "KAC" mice revealed epigenetic changes underlying the various compensatory mechanisms to overcome the growth suppressive effects of Arid1a loss. ConclusionsArid1a is an essential survival gene whose loss impairs cellular growth, and thus, its expression is critical during early stages of pancreatic tumorigenesis in mouse models.

cancer biology↗