LncRNA-mediated regulation of SOX9 expression in basal subtype breast cancer cells.

Triple-negative breast cancer (TNBC) is one of the most aggressive breast cancer (BC) subtypes with a poor prognosis and high recurrence rate. Recent studies have identified vital roles played by several lncRNAs (long noncoding RNAs) in BC pathobiology. Cell type-specific expression of lncRNAs and their potential role in regulating the expression of oncogenic and tumor suppressor genes have made them promising cancer drug targets. By performing a transcriptome screen in an isogenic TNBC/basal subtype BC progression cell line model, we recently reported ∼1800 lncRNAs that display aberrant expression during breast cancer progression. Mechanistic studies on one such nuclear-retained lncRNA, linc02095, reveal that it promotes breast cancer proliferation by facilitating the expression of oncogenic transcription factor, SOX9. Both linc02095 and SOX9 display coregulated expression in BC patients as well in basal subtype BC cell lines. Knockdown of linc02095 results in decreased BC cell proliferation, whereas its overexpression promotes cells proliferation. Linc02095-depleted cells display reduced expression of SOX9 concomitant with reduced RNA polymerase II occupancy at the SOX9 gene body as well as defective SOX9 mRNA export, implying that linc02095 positively regulates SOX9 transcription and mRNA export. Finally, we identify a positive feedback loop in BC cells that controls the expression of both linc02095 and SOX9 Thus, our results unearth tumor-promoting activities of a nuclear lncRNA linc02095 by facilitating the expression of key oncogenic transcription factor in BC.

A natural antisense lncRNA controls breast cancer progression by promoting tumor suppressor gene mRNA stability.

The human genome encodes thousands of long noncoding RNA (lncRNA) genes; the function of majority of them is poorly understood. Aberrant expression of a significant number of lncRNAs is observed in various diseases, including cancer. To gain insights into the role of lncRNAs in breast cancer progression, we performed genome-wide transcriptome analyses in an isogenic, triple negative breast cancer (TNBC/basal-like) progression cell lines using a 3D cell culture model. We identified significantly altered expression of 1853 lncRNAs, including ~500 natural antisense transcript (NATs) lncRNAs. A significant number of breast cancer-deregulated NATs displayed co-regulated expression with oncogenic and tumor suppressor protein-coding genes in cis. Further studies on one such NAT, PDCD4-AS1 lncRNA reveal that it positively regulates the expression and activity of the tumor suppressor PDCD4 in mammary epithelial cells. Both PDCD4-AS1 and PDCD4 show reduced expression in TNBC cell lines and in patients, and depletion of PDCD4-AS1 compromised the cellular levels and activity of PDCD4. Further, tumorigenic properties of PDCD4-AS1-depleted TNBC cells were rescued by exogenous expression of PDCD4, implying that PDCD4-AS1 acts upstream of PDCD4. Mechanistically, PDCD4-AS1 stabilizes PDCD4 RNA by forming RNA duplex and controls the interaction between PDCD4 RNA and RNA decay promoting factors such as HuR. Our studies demonstrate crucial roles played by NAT lncRNAs in regulating post-transcriptional gene expression of key oncogenic or tumor suppressor genes, thereby contributing to TNBC progression.

Social-ecological analysis of timely rice planting in Eastern India.

Timely crop planting is a foundation for climate-resilient rice-wheat systems of the Eastern Gangetic Plains-a global food insecurity and poverty hotspot. We hypothesize that the capacity of individual farmers to plant on time varies considerably, shaped by multifaceted enabling factors and constraints that are poorly understood. To address this knowledge gap, two complementary datasets were used to characterize drivers and decision processes that govern the timing of rice planting in this region. The first dataset was a large agricultural management survey (rice-wheat: n = 15,245; of which rice: n = 7597) from a broad geographic region that was analyzed by machine learning methods. The second dataset was a discussion-based survey (n = 112) from a more limited geography that we analyzed with graph theory tools to elicit nuanced information on planting decisions. By combining insights from these methods, we show for the first time that differences in rice planting times are primarily shaped by ecosystem and climate factors while social factors play a prominent secondary role. Monsoon onset, surface and groundwater availability, and land type determine village-scale mean planting times whereas, for resource-constrained farmers who tend to plant later ceteris paribus, planting is further influenced by access to farm machinery, seed, fertilizer, and labor. Also, a critical threshold for economically efficient pumping appears at a groundwater depth of around 4.5 m; below this depth, farmers do not irrigate and delay planting. Without collective action to spread risk through synchronous timely planting, ecosystem factors such as threats posed by pests and wild animals may further deter early planting by individual farmers. Accordingly, we propose a three-pronged strategy that combines targeted strengthening of agricultural input chains, agroadvisory development, and coordinated rice planting and wildlife conservation to support climate-resilient agricultural development in the Eastern Gangetic Plains.

MIR100 host gene-encoded lncRNAs regulate cell cycle by modulating the interaction between HuR and its target mRNAs.

Long non-coding RNAs (lncRNAs) regulate vital biological processes, including cell proliferation, differentiation and development. A subclass of lncRNAs is synthesized from microRNA (miRNA) host genes (MIRHGs) due to pre-miRNA processing, and are categorized as miRNA-host gene lncRNAs (lnc-miRHGs). Presently, the cellular function of most lnc-miRHGs is not well understood. We demonstrate a miRNA-independent role for a nuclear-enriched lnc-miRHG in cell cycle progression. MIR100HG produces spliced and stable lncRNAs that display elevated levels during the G1 phase of the cell cycle. Depletion of MIR100HG-encoded lncRNAs in human cells results in aberrant cell cycle progression without altering the levels of miRNA encoded within MIR100HG. Notably, MIR100HG interacts with HuR/ELAVL1 as well as with several HuR-target mRNAs. Further, MIR100HG-depleted cells show reduced interaction between HuR and three of its target mRNAs, indicating that MIR100HG facilitates interaction between HuR and target mRNAs. Our studies have unearthed novel roles played by a MIRHG-encoded lncRNA in regulating RNA binding protein activity, thereby underscoring the importance of determining the function of several hundreds of lnc-miRHGs that are present in human genome.

Intercomparison of crop establishment methods for improving yield and profitability in the rice-wheat system of Eastern India.

Conventionally managed rice-wheat systems of the eastern Indo-Gangetic Plains (E-IGP) that rely on soil puddling for rice and intensive tillage for wheat are low-yielding and resource-inefficient, leading to low profitability. While a host of alternative tillage and crop establishment (TCE) methods have been advocated as solutions for sustainably enhancing productivity and profitability, few systematic comparisons of these methods are reported. To address this gap, a three-year field study was conducted in Bihar, India with the goal of identifying TCE methods for rice-wheat systems that are high yielding, less resource-intensive, and more profitable. The following systems were evaluated: 1) puddled transplanted rice (PTR) followed by (fb) conventional tillage wheat (CTW) or zero-tillage wheat (ZTW); 2) machine transplanted rice in non-puddled soil (MTR) fb ZTW; 3) the system of rice intensification (SRI) fb system of wheat intensification (SWI); and 4) dry-seeded rice (DSR) fb ZTW. Rice cultivar duration (short versus medium-duration) was incorporated as a subplot treatment in all systems. Rice yields were similar with all methods, except DSR yield was 11 % lower and MTR yield was 7% higher than PTR in the third year. Cost of production was US$ 149 and 77 ha-1 lower in DSR and MTR, respectively, and US$ 84 ha-1 higher in SRI than PTR. The gross margin and benefit-cost (B:C) ratio was highest in MTR followed by DSR and lowest in SRI. In wheat, ZT resulted in a higher yield than CTW, especially when ZTW was cultivated after non-puddled rice (e.g., DSR or MTR). ZTW reduced production costs by US$ 69 ha-1, whereas SWI increased it by US$ 139 ha-1 relative to CTW. The higher yield and lower cost of production resulted in a higher gross margin (US$ 82-355 ha-1 and US$ 129-409 ha-1 higher than CTW and SWI, respectively) and a higher B:C ratio in ZTW treatments than CTW and SWI. At the system level, MTR or DSR followed by ZTW had both superior crop yields and consistently higher gross margins (US $133 to 382 ha-1) than other practices. On the other hand, the SRI fb SWI system had no yield advantage and poorer economic performance than conventional practices. In all systems, the inclusion of a medium-duration rice hybrid resulted in higher rice and system yields. These results suggest that significant gains in profitability are possible with emerging TCE practices in rice-wheat systems, but alternatives such as the SRI and SWI will likely erode farmer incomes.

ADAR2 regulates RNA stability by modifying access of decay-promoting RNA-binding proteins.

Adenosine deaminases acting on RNA (ADARs) catalyze the editing of adenosine residues to inosine (A-to-I) within RNA sequences, mostly in the introns and UTRs (un-translated regions). The significance of editing within non-coding regions of RNA is poorly understood. Here, we demonstrate that association of ADAR2 with RNA stabilizes a subset of transcripts. ADAR2 interacts with and edits the 3΄UTR of nuclear-retained Cat2 transcribed nuclear RNA (Ctn RNA). In absence of ADAR2, the abundance and half-life of Ctn RNA are significantly reduced. Furthermore, ADAR2-mediated stabilization of Ctn RNA occurred in an editing-independent manner. Unedited Ctn RNA shows enhanced interaction with the RNA-binding proteins HuR and PARN [Poly(A) specific ribonuclease deadenylase]. HuR and PARN destabilize Ctn RNA in absence of ADAR2, indicating that ADAR2 stabilizes Ctn RNA by antagonizing its degradation by PARN and HuR. Transcriptomic analysis identified other RNAs that are regulated by a similar mechanism. In summary, we identify a regulatory mechanism whereby ADAR2 enhances target RNA stability by limiting the interaction of RNA-destabilizing proteins with their cognate substrates.

PSIP1/p75 promotes tumorigenicity in breast cancer cells by promoting the transcription of cell cycle genes.

Breast cancer (BC) is a highly heterogeneous disease, both at the pathological and molecular level, and several chromatin-associated proteins play crucial roles in BC initiation and progression. Here, we demonstrate the role of PSIP1 (PC4 and SF2 interacting protein)/p75 (LEDGF) in BC progression. PSIP1/p75, previously identified as a chromatin-adaptor protein, is found to be upregulated in basal-like/triple negative breast cancer (TNBC) patient samples and cell lines. Immunohistochemistry in tissue arrays showed elevated levels of PSIP1 in metastatic invasive ductal carcinoma. Survival data analyses revealed that the levels of PSIP1 showed a negative association with TNBC patient survival. Depletion of PSIP1/p75 significantly reduced the tumorigenicity and metastatic properties of TNBC cell lines while its over-expression promoted tumorigenicity. Further, gene expression studies revealed that PSIP1 regulates the expression of genes controlling cell-cycle progression, cell migration and invasion. Finally, by interacting with RNA polymerase II, PSIP1/p75 facilitates the association of RNA pol II to the promoter of cell cycle genes and thereby regulates their transcription. Our findings demonstrate an important role of PSIP1/p75 in TNBC tumorigenicity by promoting the expression of genes that control the cell cycle and tumor metastasis.

Functional insights into the role of nuclear-retained long noncoding RNAs in gene expression control in mammalian cells.

The mammalian genome harbors thousands of long noncoding RNA (lncRNA) genes. Recent studies have indicated the involvement of several of these lncRNAs in the regulation of gene expression. lncRNAs play crucial roles in various biological processes ranging from epigenetic gene regulation, transcriptional control,to post-transcriptional regulation. lncRNAs are localized in various subcellular compartments, and major proportion of these are retained in the cell nucleus and could be broadly classified as nuclear-retained lncRNAs (nrRNAs). Based on the identified functions,members of the nrRNAs execute diverse roles, including providing architectural support to the hierarchical subnuclear organization and influencing the recruitment of chromatin modifier factors to specific chromatin sites. In this review, we will summarize the recently described roles of mammalian nrRNAs in controlling gene expression by influencing chromatin organization, transcription,pre-mRNA processing, nuclear organization, and their involvement in disease.

NiSi: A New Venue for Antiferromagnetic Spintronics.

Envisaging antiferromagnetic spintronics pivots on two key criteria of high transition temperature and tuning of underlying magnetic order using straightforward application of magnetic field or electric current. Here, it is shown that NiSi metal can provide suitable new platform in this quest. First, the study unveils high-temperature antiferromagnetism in single-crystal NiSi with Néel temperature, TN ⩾ 700 K. Antiferromagnetic order in NiSi is accompanied by non-centrosymmetric magnetic character with small ferromagnetic component in the a-c plane. Second, it is found that NiSi manifests distinct magnetic and electronic hysteresis responses to field applications due to the disparity in two moment directions. While magnetic hysteresis is characterized by one-step switching between ferromagnetic states of uncompensated moment, electronic behavior is ascribed to metamagnetic switching phenomena between non-collinear spin configurations. Importantly, the switching behaviors persist to high temperature. The properties underscore the importance of NiSi in the pursuit of antiferromagnetic spintronics.

5-Azacytidine- and retinoic-acid-induced reprogramming of DCCs into dormancy suppresses metastasis via restored TGF-ß-SMAD4 signaling.

Disseminated cancer cells (DCCs) in secondary organs can remain dormant for years to decades before reactivating into overt metastasis. Microenvironmental signals leading to cancer cell chromatin remodeling and transcriptional reprogramming appear to control onset and escape from dormancy. Here, we reveal that the therapeutic combination of the DNA methylation inhibitor 5-azacytidine (AZA) and the retinoic acid receptor ligands all-trans retinoic acid (atRA) or AM80, an RARα-specific agonist, promotes stable dormancy in cancer cells. Treatment of head and neck squamous cell carcinoma (HNSCC) or breast cancer cells with AZA+atRA induces a SMAD2/3/4-dependent transcriptional program that restores transforming growth factor ß (TGF-ß)-signaling and anti-proliferative function. Significantly, either combination, AZA+atRA or AZA+AM80, strongly suppresses HNSCC lung metastasis formation by inducing and maintaining solitary DCCs in a SMAD4+/NR2F1+ non-proliferative state. Notably, SMAD4 knockdown is sufficient to drive resistance to AZA+atRA-induced dormancy. We conclude that therapeutic doses of AZA and RAR agonists may induce and/or maintain dormancy and significantly limit metastasis development.

Long interspersed nuclear elements (LINEs) show tissue-specific, mosaic genome and methylation-unrestricted, widespread expression of noncoding RNAs in somatic tissues of the rat.

We report strong somatic and germ line expression of LINE RNAs in eight different tissues of rat by using a novel ~2.8 kb genomic PstI-LINE DNA (P1-LINE) isolated from the rat brain. P1-LINE is present in a 93 kb LINE-SINE-cluster in sub-telomeric region of chromosome 12 (12p12) and as multiple truncated copies interspersed in all rat chromosomes. P1-LINEs occur as inverted repeats at multiple genomic loci in tissue-specific and mosaic patterns. P1-LINE RNAs are strongly expressed in brain, liver, lungs, heart, kidney, testes, spleen and thymus into large to small heterogeneous RNAs (~5.0 to 0.2 kb) in tissue-specific and dynamic patterns in individual rats. P1-LINE DNA is strongly methylated at CpG-dinucleotides in most genomic copies in all the tissues and weakly hypomethylated in few copies in some tissues. Small (700-75 nt) P1-LINE RNAs expressed in all tissues may be possible precursors for small regulatory RNAs (PIWI-interacting/piRNAs) bioinformatically derived from P1-LINE. The strong and dynamic expression of LINE RNAs from multiple chromosomal loci and the putative piRNAs in somatic tissues of rat under normal physiological conditions may define functional chromosomal domains marked by LINE RNAs as long noncoding RNAs (lncRNAs) unrestricted by DNA methylation. The tissue-specific, dynamic RNA expression and mosaic genomic distribution of LINEs representing a steady-state genomic flux of retrotransposon RNAs suggest for biological role of LINE RNAs as long ncRNAs and small piRNAs in mammalian tissues independent of their cellular fate for translation, reverse-transcription and retrotransposition. This may provide evolutionary advantages to LINEs and mammalian genomes.

Transfacetal Screw Fixation for Subaxial Cervical Spine.

Background and Introduction: In the modern era of spine surgery for subaxial cervical spine, transfacetal screw fixation has evolved enormously. Transfacetal screw fixation for subaxial cervical spine is a biomechanically effective technique. In this fixation, four cortical surfaces of the facets are purchased by the transfacetal screws. Objectives: In this video, we demonstrated the surgical technique of posterior transfacetal screw fixation. Surgical Technique: Transfacetal screw fixation of subaxial cervical spine was done along with posterior decompression. The entry point of transfacetal screw was defined as 1 mm caudal to mid-point of lateral mass, and screws were directed perpendicular to facet joint in the sagittal plane and straight in the coronal plane. Bone chips were placed over decorticated lateral mass after decompression. Result: Patient had uneventful recovery and maintained good status at follow up. Conclusion: In subaxial cervical spine, transfacetal screw fixation is a biomechanically effective, rigid, and an inexpensive technique to obtain immediate rigid fixation.

Double Anchoring Technique of Occipito-Cervical Fixation Using Innovative Occipital Plate: A Preliminary Study.

Background: Occipito-cervical fixation (OCF) provides immediate rigid fixation to cranio-vertebral junction (CVJ); however, in current practice, the optimal occipito-cervical fixation method is arguable. Aim: The aim of this study was to test the safety and efficacy of a newly designed inside-outside occipital (OC) plate system for the treatment of cranio-vertebral junction instability. Material and Methods: Thirty-two patients of CVJ instability were treated using this new OC plate system. Safety and efficacy of this new OC plate was evaluated radiologically and clinically. Results: Follow-up period ranged from 9 to 23 months. During the follow-up, no implant failure, recurrent subluxation, or newly developed instability at adjacent levels occurred, except in one patient in whom C2 screw pullout occurred due to trauma. All patients showed a satisfactory fusion at three months follow-up examination. Conclusions: These preliminary results suggest that this OC plate system is a simple, safe, and effective method for providing immediate internal rigid fixation of the CV junction. Long-term results are needed to determine the superiority of this OC plate over other methods of occipital fixation.

MacroH2A impedes metastatic growth by enforcing a discrete dormancy program in disseminated cancer cells.

MacroH2A variants have been linked to inhibition of metastasis through incompletely understood mechanisms. Here, we reveal that solitary dormant disseminated cancer cells (DCCs) display increased levels of macroH2A variants in head and neck squamous cell carcinoma PDX in vivo models and patient samples compared to proliferating primary or metastatic lesions. We demonstrate that dormancy-inducing transforming growth factor-ß2 and p38α/ß pathways up-regulate macroH2A expression and that macroH2A variant overexpression is sufficient to induce DCC dormancy and suppress metastasis in vivo. Notably, inducible expression of the macroH2A2 variant in vivo suppresses metastasis via a reversible growth arrest of DCCs. This state does not require the dormancy-regulating transcription factors DEC2 and NR2F1; instead, transcriptomic analysis reveals that macroH2A2 overexpression inhibits cell cycle and oncogenic signaling programs, while up-regulating dormancy and senescence-associated inflammatory cytokines. We conclude that the macroH2A2-enforced dormant phenotype results from tapping into transcriptional programs of both quiescence and senescence to limit metastatic outgrowth.

Primary tumor associated macrophages activate programs of invasion and dormancy in disseminating tumor cells.

Metastases are initiated by disseminated tumor cells (DTCs) that colonize distant organs. Growing evidence suggests that the microenvironment of the primary tumor primes DTCs for dormant or proliferative fates. However, the manner in which this occurs remains poorly understood. Here, using the Window for High-Resolution Intravital Imaging of the Lung (WHRIL), we study the live lung longitudinally and follow the fate of individual DTCs that spontaneously disseminate from orthotopic breast tumors. We find that spontaneously DTCs have increased levels of retention, increased speed of extravasation, and greater survival after extravasation, compared to experimentally metastasized tumor cells. Detailed analysis reveals that a subset of macrophages within the primary tumor induces a pro-dissemination and pro-dormancy DTC phenotype. Our work provides insight into how specific primary tumor microenvironments prime a subpopulation of cells for expression of proteins associated with dissemination and dormancy.

Prostate Cancer Dormancy and Reactivation in Bone Marrow.

Prostate cancer has a variable clinical course, ranging from curable local disease to lethal metastatic spread. Eradicating metastatic cells is a unique challenge that is rarely met with the available therapies. Thus, targeting prostate cancer cells in earlier disease states is a crucial window of opportunity. Interestingly, cancer cells migrate from their primary site during pre-cancerous and malignant phases to seed secondary organs. These cells, known as disseminated cancer cells (DCCs), may remain dormant for months or decades before activating to form metastases. Bone marrow, a dormancy-permissive site, is the major organ for housed DCCs and eventual metastases in prostate cancer. The dynamic interplay between DCCs and the primary tumor microenvironment (TME), as well as that between DCCs and the secondary organ niche, controls the conversion between states of dormancy and activation. Here, we discuss recent discoveries that have improved our understanding of dormancy signaling and the role of the TME in modulating the epigenetic reprogramming of DCCs. We offer potential strategies to target DCCs in prostate cancer.

Magnetic charge's relaxation propelled electricity in two-dimensional magnetic honeycomb lattice.

Emerging new concepts, such as magnetic charge dynamics in two-dimensional magnetic material, can provide novel mechanism for spin-based electrical transport at macroscopic length. In artificial spin ice of single domain elements, magnetic charge's relaxation can create an efficient electrical pathway for conduction by generating fluctuations in local magnetic field that couple with conduction electron spins. In a first demonstration, we show that the electrical conductivity is propelled by more than an order of magnitude at room temperature due to magnetic charge defects sub-picosecond relaxation in artificial magnetic honeycomb lattice. The direct evidence to the proposed electrical conduction mechanism in two-dimensional frustrated magnet points to the untapped potential for spintronic applications in this system.

Vitamin D levels in paediatric intensive care unit patients and its relation to severity of illness: An Indian experience.

Vitamin D deficiency is a common disorder that is associated with morbidity and mortality in the general population. We conducted a cross-sectional study of 384 children admitted to paediatric intensive care to determine its prevalence and association with severity of illness and outcome in critically ill children. The severity of illness was evaluated using the paediatric risk of mortality score (PRISM III), on admission, at 24 and 48 h. Vitamin D deficiency was observed in 175 children (45.6%) and was associated with higher severity of illness, need for mechanical ventilation and increased mortality.

Bone marrow NG2+/Nestin+ mesenchymal stem cells drive DTC dormancy via TGFß2.

In the bone marrow (BM) microenvironment, where breast cancer (BC) disseminated tumour cells (DTCs) can remain dormant for decades, NG2+/Nestin+ mesenchymal stem cells (MSCs) promote hematopoietic stem cell quiescence. Here, we reveal that periarteriolar BM-resident NG2+/Nestin+ MSCs can also instruct BC DTCs to enter dormancy. NG2+/Nestin+ MSCs produce TGFß2 and BMP7 and activate a quiescence pathway dependent on TGFBRIII and BMPRII, which via p38-kinase result in p27 induction. Genetic depletion of MSCs or conditional knock-out of TGFß2 in MSCs using an NG2-CreER driver led to bone metastatic outgrowth of otherwise dormant p27+/Ki67- DTCs. Also ER+ BC patients without systemic recurrence displayed higher frequency of TGFß2 and BMP7 detection in the BM. Our results provide a direct proof that HSC dormancy niches control BC DTC dormancy and suggest that aging or extrinsic factors that affect the NG2+/Nestin+ MSC niche homeostasis may result in a break from dormancy and BC bone relapse.