Biology subjects

Khan, J.

Publications and source records attributed to Khan, J..

At least 19 recordsLinked to original sources

bioRxiv2026

Human skin fibrosis with iPSC-derived organoids reveals RUNX2-mediated fibroblast reprogramming

Fibrotic skin diseases are characterized by persistent fibroblast activation and extracellular matrix remodeling, yet the mechanisms governing fibroblast state transitions remain incompletely understood. Here, we established a human iPSC-derived skin organoid model of fibrosis through chronic TGF-{beta} stimulation. Single-cell RNA sequencing combined with immunofluorescence-based spatial analysis revealed dynamic fibroblast state transitions, spatial reorganization, and expansion of activated fibroblast populations during fibrotic remodeling. Integration with human scleroderma single-cell datasets demonstrated conserved fibroblast states and transcriptional programs between organoids and patient tissues. We further identified broad induction of RUNX2 in the dermal compartment during fibrosis, and RUNX2 depletion attenuated fibrotic marker expression. CUT&RUN profiling revealed RUNX2 occupancy at fibrosis-associated loci, including RUNX1 and LOXL2. Using a machine learning-guided screening approach, we identified F0565-0303, a small molecule that suppressed RUNX2-dependent fibrotic programs in vitro and reduced fibrosis in a bleomycin-induced mouse model. Together, these findings establish human skin organoids as a platform for modeling fibrosis and nominate RUNX2 as a potential therapeutic target.

bioengineering↗

bioRxiv2026

Synergistic targeting of EP300/CBP and EYA co-activators collapses the rhabdomyosarcoma core regulatory circuit

Rhabdomyosarcoma (RMS) is a multi-subtype, high-risk pediatric sarcoma with a low mutational burden. The mutations found in RMS often alter genes involved in transcriptional control. Approaches to target dysregulated RMS transcription have remained elusive. Here, we develop a novel approach to target RMS transcription comprising simultaneous targeting of two distinctly acting transcriptional co-activators. We discover a common identity-controlling pan-RMS core regulatory circuit (CRC) composed of oncogenic and lineage-specific myogenic master transcription factors (mTFs). Using a super-enhancer-based reporter screen, we identify the EP300/CBP inhibitor A485 as a potent inhibitor of the pan-RMS CRC, though with efficacy-limiting toxicities. To enhance efficacy, we identify the mTF-binding co-activator EYA2 as a co-factor of this pan-RMS CRC and exploit a new second-generation EYA1/2 inhibitor, LG1-34, to disrupt its function. Combined co-activator inhibition inactivates the CRC and synergistically reduces RMS growth. This strategy dually targets CRC-associated co-activators to cooperatively suppress the RMS transcriptome and enforce cell death.

cancer biology↗

bioRxiv2026

kache-hash: A dynamic, concurrent, and cache-efficient hash table for streaming k-mer operations

MotivationHash tables are fundamental to computational genomics, where keys are often k-mers--fixed-length substrings that exhibit a "streaming" property: consecutive k-mers share k-1 nucleotides and are processed in order. Existing static data structures exploit this locality but cannot support dynamic updates, while state-of-the-art concurrent hash tables support dynamic operations but ignore k-mer locality. ResultsWe introduce kache-hash, the first dynamic, concurrent, and resizable hash table that exploits k-mer locality. kache-hash builds on Iceberg hashing--a multi-level design achieving stability and low associativity--but replaces generic hashing with minimizer-based hashing, ensuring that consecutive k-mers map to the same buckets. This keeps frequently accessed buckets cache-resident during streaming operations. On the human genome, kache-hash achieves 1.58-2.62x higher insertion throughput than IcebergHT and up to 6.1x higher query throughput, while incurring 7.39x fewer cache misses. kache-hash scales near-linearly to 16 threads and supports dynamic resizing without sacrificing locality. Our theoretical analysis proves that streaming k-mer operations achieve [O](1/r) amortized cache misses per operation, where r is the minimizer run length, explaining the substantial performance gains over general-purpose hash tables. Availabilitykache-hash is implemented in C++20 and is available at https://github.com/jamshed/kache-hash. Contactp.pandey@northeastern.edu Supplementary informationSupplementary material are available for this manuscript.

bioinformatics↗

bioRxiv2026

Long-term Effects of Early Life Adversity On Brain Dopamine and Serotonin Receptor Systems Involved In Cocaine Reinforcement In Adult Macaques: a Positron Emission Tomography study

Early life adverse (ELA) experiences such as child maltreatment (MALT) are associated with physical and mental illness, including substance use disorders (SUDs), but underlying neurobiological mechanisms remain unclear. This study examined long-term effects of infant MALT on adult brain serotonin (5HT) and dopamine (DA) receptors in corticolimbic regions involved in reward and emotional control, using positron emission tomography (PET) imaging, a translational infant MALT macaque model of cocaine use disorder (CUD) risk and a COC self-administration (SA) paradigm. The study focused on regional serotonin 5HT1A, 5HT2A, and dopamine D2/D3 receptor availability (BP) differences between MALT and Control animals using PET, both at baseline (pre-COC SA) and following chronic COC SA (once they reached a total of 100 mg/kg intake). We also examined whether levels of these neurochemical receptors predicted COC SA measures, including reinforcing effects and potency using fixed-ratio (FR) peak response rates and progressive-ratio (PR) peak breakpoint. Our findings showed long-term effects of infant MALT on 5HT, but not DA, receptors in corticolimbic circuits. Specifically, MALT animals showed lower 5HT1A BP in the anterior cingulate cortex (ACC), medial prefrontal cortex (mPFC), and hippocampus compared to Controls. A MALT by Sex interaction effect was detected in 5HT2A BP in the OFC, with lower levels in MALT than Control males, but not in females. In addition, upregulation of 5HT1A and 5HT2A receptors was detected following chronic COC SA in most PFC subregions, hippocampus, and NAcc, particularly in the Control group. These findings suggest long-term effects of ELA on adult 5HT, but not DA, receptors in corticolimbic regions involved in emotional and reward processes. We also found associations between PET baseline (pre-COC SA) receptor BP data and COC SA measures. In particular, a positive correlation between 5HT1A receptor BP in caudate and peak FR Response Rates, whereas amygdala 5HT1A receptor levels were positively correlated with peak PR breakpoint and negatively correlated with peak FR Response Rates. Overall, these findings suggest an important role of 5HT1A and 5HT2A PFC receptors in early COC-related changes in reward circuitry and of amygdala 5HT receptors on cocaine-maintained behaviors. The dynamic change of these 5HT1A and 5HT2A receptors following chronic COC exposure was blunted in animals with ELA. It would be important to understand the biological consequences of these dynamic changes in 5HT receptors and whether they are associated with other stages of the addiction cycle, for example COC relapse, which could inform future pharmacological interventions that target 5HT receptors for treatment of CUD. Simple SummaryWe studied the long-term effects of early life adversity (ELA) on adult brain dopamine (DA) and serotonin (5HT) signaling in corticolimbic regions involved in emotional and reward regulation. We used specific PET radioligands that bind to the DA D2/D3, 5HT1A and 5HT2A receptors, finding lower levels of 5HT, but not DA, receptors binding potential (BP) in animals that experienced ELA. We also found associations between PET receptor BP measures and reinforcing effects of cocaine in i.v. self-administration paradigms using fixed- and progressive-ratio reinforcement schedules. In addition, a strong upregulation of 5HT, but not DA, receptors was identified following chronic cocaine exposure in prefrontal cortex (PFC). Our findings suggest long-term effects of ELA on adult PFC 5HT1A and 5HT2A receptors. The findings also suggest an important role of 5HT1A and 5HT2A, more so than D2/D3, receptors in early cocaine-related changes in reward circuitry. The early dynamic changes of these 5HT receptors could serve as biomarkers for cocaine use disorder (CUD) and inform future pharmacological interventions.

neuroscience↗

bioRxiv2026

Engineering Functionality-Optimized Fully Human B7-H3 CAR T Cells for Enhanced Solid Tumor Therapy

B7-H3 is a cell surface protein overexpressed in many solid tumors and an attractive target for chimeric antigen receptor (CAR) T cell therapy. The most clinically advanced B7-H3 CARs are derived from murine monoclonal antibodies (mAbs) 376.96 and MGA271, which are now in phase 1/11 trials. However, non-human mAb sequences can provoke immune responses, leading to CAR T-cell rejection and therapeutic failure. Although scFv humanization reduces this risk, residual foreign residues within the variable domains remain. To overcome this limitation, we used in vitro phage display to generate fully human B7-H3-specific scFvs for CAR design. In pancreatic cancer, neuroblastoma, and glioblastoma xenograft models, CAR T cells incorporating the lead human binder Y111 were well tolerated and demonstrated superior antitumor activity compared with 376.96- and MGA271-based CARs. Y111 CAR treatment induced complete responses, tumor rejection, and significant survival benefits, identifying Y111 as a promising fully human B7-H3 CAR for solid tumors.

immunology↗

bioRxiv2025

Arsenic Trioxide Underpins Delayed Neuroinflammation and Impaired Synaptic Integrity involving Integrative Stress Response Signaling

Arsenic trioxide (ATO), an industrial and environmental chemical with potential for accidental or intentional exposure, exerts profound neurotoxic effects. Its single acute exposure has been linked to delayed neurological and neurodegenerative outcomes. However, the molecular and cellular pathways driving these long-term manifestations remain poorly defined. In this study, combining human iPSC-derived neuronal and in vivo mouse model, we uncovered that the acute ATO exposure activates cellular stress pathway, which drives long-term neurotoxic and associated functional outcomes. We found that ATO induces integrated stress response (ISR) signaling in human iPSC-derived neurons. To model the impact of accidental ATO exposure in vivo, we administered a single high dose of ATO to C57BL/6J wild type mice. Four weeks post-treatment, ATO-exposed mice displayed neuropsychological symptoms and cognitive deficits. Brain analyses of ATO-challenged mice revealed elevated ISR activity marked by the increased phosphorylation of PERK and eIF2 and upregulation of the transcription factors, CHOP and ATF4. Transcriptomic profiling using bulk RNAseq revealed activation of pathways associated with stress and neuroinflammatory responses. Consistently, increased DNA damage and dysregulation of the STING-mediated innate immune response were also found in the brain of ATO-challenged mice. Pharmacological inhibition of the ISR with a small-molecule inhibitor, ISRIB mitigated ISR activation and preserved synaptic integrity in mouse hippocampal cells. In conclusion, our data identify ISR activation and DNA damage-driven immune dysregulation as key pathogenic drivers of ATO-induced delayed neurotoxicity and cognitive deficits and highlight ISR inhibitors as promising therapeutics to mitigate these effects.

neuroscience↗

bioRxiv2025

Childhood brain tumours instruct cranial haematopoiesis and immunotolerance

Recent research has revealed a remarkable role for immunosurveillance in healthy and diseased brains, dispelling the notion that this organ is a passive immune-privileged site1-3. Better understanding of how this immunosurveillance operates could improve the treatment of neurological diseases. Here, using a novel genetically engineered mouse model of ZFTA-RELA ependymoma4-a childhood brain tumour-we characterised an immune circuit between the tumour and antigen presenting, haematopoietic stem/progenitor cells (HSPCs) in the skull bone marrow. The presentation of antigens in the cerebrospinal fluid (CSF) by HSPCs to CD4+ T cells, biased HSPC lineages toward myelopoiesis and polarised CD4+ T-cells to regulatory T cells (T- regs), culminating in tumour immunotolerance. Remarkably, a single infusion of antibodies directed against cytokines enriched in the CSF of mice bearing ZFTA-RELA ependymomas, choroid plexus carcinomas or Group-3 medulloblastoma-all aggressive childhood brain tumours-disrupted this process and caused profound tumour regression. These data unmask a mechanism by which skull bone marrow-derived HSPCs and CD4+ T cells cooperate to promote the immunotolerance of childhood brain tumours. Antibodies that disrupt this immunosurveillance could prove an effective therapy for these cancers that are less toxic than current treatments.

immunology↗

bioRxiv2025

RUNX2 inhibition disrupts a PAX3::FOXO1-RUNX2 feed-forward loop and dismantles oncogenic gene programs in fusion-positive rhabdomyosarcoma

Fusion-positive rhabdomyosarcoma is an aggressive pediatric cancer of skeletal muscle lineage, with a 5-year overall survival of <30% for high-risk disease, and <8% when metastatic. The PAX3::FOXO1 fusion gene, resulting from t(2:13), is a signature driver of fusion-positive rhabdomyosarcoma, but similar to other transcription-factor based fusion genes in other cancers, not currently pharmacologically tractable. To identify novel druggable proteins in fusion-positive rhabdomyosarcoma tumor tissue and cell lines, we performed mRNA-seq of RMS patient tumors and utilizing the human FP-RMS cell lines Rh30 and Rh4, found that the RUNX2 transcription factor was the top druggable dependency. In vitro loss of function studies using genetic (RNAi) or pharmacologic (small molecule CADD522) inhibition showed that RUNX2 suppression inhibited FP-RMS cell growth, induced myogenic differentiation and apoptosis, and phenocopied PAX3::FOXO1 suppression. In vivo loss of function studies using conditional (dox-inducible) or pharmacologic (small molecule CADD522) blockade of tumor growth in a xenograft model system showed that RUNX2 suppression inhibited tumor growth. Mechanistically, we identify a PAX3::FOXO1 feed-forward loop whereby PAX3::FOXO1 binds a RUNX2 enhancer to upregulate gene expression alongside MYOD1, while RUNX2 expression supports the expression of PAX3::FOXO1 at the mRNA and protein level. SignificanceRUNX2 inhibition reduces PAX3::FOXO1 expression and signaling, which impairs fusion-positive rhabdomyosarcoma oncogenic phenotypes. In vivo treatment with CADD522 decreased tumor growth and increased survival, indicating that RUNX2 is a promising therapeutic target.

cancer biology↗

bioRxiv2025

Oncolytic Maraba virus MG1 mediates direct and natural killer cell-dependent lysis of Ewing sarcoma

Ewing sarcoma (EWS) is a rare cancer of the bone and soft tissue, most prevalent in children and young adults. Treatment of EWS has progressed relatively little in over 30 years. Survival rates for patients, particularly those with metastatic and/or relapsed disease, remain poor, highlighting the urgent need for innovative treatment options. We have explored the therapeutic potential of the oncolytic Maraba virus strain MG1. We show that MG1 undergoes productive replication and exerts direct oncolysis of established EWS cell lines, doxorubicin-resistant EWS cell lines and patient-derived Ewing sarcoma (PDES) cell cultures more recently established from tumours. In contrast, primary mesenchymal stem cells (the likely cell of origin of EWS) were resistant to MG1, with IFN-I being a major determinant of tumour cell selectivity. MG1 treated PBMC produced IFN-I and killed EWS cells in vitro, in a natural killer (NK) cell-dependent manner. The ability of MG1 to kill EWS cells directly and to stimulate NK cell cytotoxicity against this tumour suggests that Maraba virus MG1 may provide therapeutic benefit for EWS patients where the efficacy of conventional treatments is currently limited.

cancer biology↗

bioRxiv2025

Sulfotransferase 4A1 (SULT4a1): A Novel Neuroprotective Protein in Stroke

SULT4a1, a member of the cytosolic sulfotransferase family, is predominantly expressed in neurons and plays potentially vital roles in regulating neural survival and function. SULT4a1 protects against mitochondrial dysfunction and oxidative stress. SULT4a1 levels decrease in experimental stroke models and may play a critical neuroprotective role in mitigating neuronal injury caused by oxygen-glucose deprivation (OGD) and ischemic stroke, as shown in a transient middle cerebral artery occlusion (tMCAO) mouse model. In this study, we investigated the neuroprotective role of SULT4a1 in OGD and tMCAO and highlighted its expression pattern and involvement in maintaining mitochondrial function and reducing oxidative stress, two early pathophysiological features in stroke and related neuronal injury. Our data show that decreased SULT4a1 expression in OGD conditions and in the tMCAO mouse brain leads to enhanced neuronal damage, emphasizing the importance of SULT4a1 in preserving neuronal integrity. Loss of SULT4a1 alone was sufficient to decrease mitochondrial function in mouse cortical neurons. Notably, overexpression of SULT4a1 preserved mitochondrial function, reduced the loss of mitochondrial membrane potential, and diminished oxidative stress, as evidenced by lower reactive oxygen species (ROS) production and reduced protein carbonylation. These results indicate that modulating SULT4a1 expression in stroke could offer a promising strategy for preventing neuronal damage. Indeed, overexpression of SULT4a1 via stereotaxic injection of AAV9 into the mouse brain mitigated tMCAO-related brain injury and functional deficits over time. The findings of this study indicate that SULT4a1 may protect neurons in stroke and related brain injury, possibly by maintaining mitochondrial function and redox homeostasis through mechanisms that are still unknown. It is likely that SULT4a1 regulates neuroprotective processes in both the mitochondria and the cytosol. However, further research is needed to clarify the specific molecular pathways involved in its neuroprotective function.

neuroscience↗

bioRxiv2025

Fast and Scalable Parallel External-Memory Construction of Colored Compacted de Bruijn Graphs with Cuttlefish 3

The exponential growth of genomic data has created an urgent need for scalable sequence analysis algorithms. De Bruijn graphs--along with their colored and compacted variants--have become essential tools in modern bioinformatics pipelines. Colored compacted de Bruijn graphs condense repetitive sequence information, significantly reducing the data burden on downstream analyses like genome assembly, metagenomic clustering, and pan-genomics. Since constructing uncompacted graphs becomes computationally prohibitive at scale, direct construction methods for colored compacted de Bruijn graphs are essential for the scalability of downstream analyses. We present Cuttlefish 3, a parallel external-memory algorithm that delivers state-of-the-art performance for constructing colored compacted de Bruijn graphs. Our approach introduces three algorithmic innovations that enable efficient scaling to massive datasets while maintaining high performance. First, we develop an optimized technique for accelerating local subgraph contractions. Second, we design a deterministic parallel algorithm based on list-ranking to efficiently merge local solutions. Third, we introduce a novel combinable hash-based method for identifying and tracking color-changing nodes, enabling rapid color-set extraction. We evaluate Cuttlefish 3 on diverse large-scale genomic datasets. In our benchmarks, Cuttlefish 3 achieves 3.29-4.09x speedup over GGCAT, the current state-of-the-art tool, while maintaining comparable memory usage. These performance gains make Cuttlefish 3 a practical solution for representing and analyzing the growing volumes of genomic data in modern bioinformatics workflows. Cuttlefish 3 is implemented in C++17 and is available at https://github.com/COMBINE-lab/cuttlefish.

bioinformatics↗

bioRxiv2024

Alevin-fry-atac enables rapid and memory frugal mapping of single-cell ATAC-seq data using virtual colors for accurate genomic pseudoalignment

Ultrafast mapping of short reads via lightweight mapping techniques such as pseudoalignment has significantly accelerated transcriptomic and metagenomic analyses, often with minimal accuracy loss compared to alignment-based methods. However, applying pseudoalignment to large genomic references, like chromosomes, is challenging due to their size and repetitive sequences. We introduce a new and modified pseudoalignment scheme that partitions each reference into "virtual colors.... These are essentially overlapping bins of fixed maximal extent on the reference sequences that are treated as distinct "colors" from the perspective of the pseudoalignment algorithm. We apply this modified pseudoalignment procedure to process and map single-cell ATAC-seq data in our new tool alevin-fry-atac. We compare alevin-fry-atac to both Chromap and Cell Ranger ATAC. Alevin-fry-atac is highly scalable and, when using 32 threads, is approximately 2.8 times faster than Chromap (the second fastest approach) while using approximately one third of the memory and mapping slightly more reads. The resulting peaks and clusters generated from alevin-fry-atac show high concordance with those obtained from both Chromap and the Cell Ranger ATAC pipeline, demonstrating that virtual colorenhanced pseudoalignment directly to the genome provides a fast, memory-frugal, and accurate alternative to existing approaches for single-cell ATAC-seq processing. The development of alevin-fry-atac brings single-cell ATAC-seq processing into a unified ecosystem with single-cell RNA-seq processing (via alevin-fry) to work toward providing a truly open alternative to many of the varied capabilities of CellRanger. Furthermore, our modified pseudoalignment approach should be easily applicable and extendable to other genome-centric mapping-based tasks and modalities such as standard DNA-seq, DNase-seq, Chip-seq and Hi-C.

bioinformatics↗

bioRxiv2023

Exploiting the therapeutic vulnerability of IDH-mutant gliomas with zotiraciclib

Isocitrate dehydrogenase (IDH)-mutant gliomas have distinctive metabolic and biological traits that may render them susceptible to targeted treatments. Here, by conducting a high-throughput drug screen, we pinpointed a specific susceptibility of IDH-mutant gliomas to zotiraciclib (ZTR). ZTR exhibited selective growth inhibition across multiple IDH-mutant glioma in vitro and in vivo models. Mechanistically, ZTR at low doses suppressed CDK9 and RNA Pol II phosphorylation in IDH-mutant cells, disrupting mitochondrial function and NAD+ production, causing oxidative stress. Integrated biochemical profiling of ZTR kinase targets and transcriptomics unveiled that ZTR-induced bioenergetic failure was linked to the suppression of PIM kinase activity. We posit that the combination of mitochondrial dysfunction and an inability to adapt to oxidative stress resulted in significant cell death upon ZTR treatment, ultimately increasing the therapeutic vulnerability of IDH-mutant gliomas. These findings prompted a clinical trial evaluating ZTR in IDH-mutant gliomas towards precision medicine (NCT05588141). HighlightsO_LIZotiraciclib (ZTR), a CDK9 inhibitor, hinders IDH-mutant glioma growth in vitro and in vivo. C_LIO_LIZTR halts cell cycle, disrupts respiration, and induces oxidative stress in IDH-mutant cells. C_LIO_LIZTR unexpectedly inhibits PIM kinases, impacting mitochondria and causing bioenergetic failure. C_LIO_LIThese findings led to the clinical trial NCT 05588141, evaluating ZTR for IDH-mutant gliomas. C_LI

cancer biology↗

bioRxiv2023

Poly(ADP-ribose) mediates bioenergetic defects and redox imbalance in neurons following oxygen and glucose deprivation

PARP-1 over-activation results in cell death via excessive PAR generation in different cell types, including neurons following brain ischemia. Glycolysis, mitochondrial function, and redox balance are key cellular processes altered in brain ischemia. Studies show that PAR generated after PARP-1 over-activation can bind hexokinase-1 (HK-1) and result in glycolytic defects and subsequent mitochondrial dysfunction. HK-1 is the neuronal hexokinase and catalyzes the first reaction of glycolysis, converting glucose to glucose-6-phosphate (G6P), a common substrate for glycolysis, and the pentose phosphate pathway (PPP). PPP is critical in maintaining NADPH and GSH levels via G6P dehydrogenase activity. Therefore, defects in HK-1 will not only decrease cellular bioenergetics but will also cause redox imbalance due to the depletion of GSH. In brain ischemia, whether PAR-mediated inhibition of HK-1 results in bioenergetics defects and redox imbalance is not known. We used oxygen-glucose deprivation (OGD) in mouse cortical neurons to mimic brain ischemia in neuronal cultures and observed that PARP-1 activation via PAR formation alters glycolysis, mitochondrial function, and redox homeostasis in neurons. We used pharmacological inhibition of PARP and adenoviral-mediated overexpression of wild-type HK-1 (wtHK-1) and PAR-binding mutant HK-1 (pbmHK-1). Our data show that PAR inhibition or overexpression of HK-1 significantly improves glycolysis, mitochondrial function, redox homeostasis, and cell survival in mouse cortical neurons exposed to OGD. These results suggest that PAR binding and inhibition of HK-1 during OGD drives bioenergetic defects in neurons due to inhibition of glycolysis and impairment of mitochondrial function.

neuroscience↗

bioRxiv2023

Fulgor: A fast and compact k-mer index for large-scale matching and color queries

The problem of sequence identification or matching -- determining the subset of references from a given collection that are likely to contain a query nucleotide sequence -- is relevant for many important tasks in Computational Biology, such as metagenomics and pan-genome analysis. Due to the complex nature of such analyses and the large scale of the reference collections a resource-efficient solution to this problem is of utmost importance. The reference collection should therefore be pre-processed into an index for fast queries. This poses the threefold challenge of designing an index that is efficient to query, has light memory usage, and scales well to large collections. To solve this problem, we describe how recent advancements in associative, order-preserving, k-mer dictionaries can be combined with a compressed inverted index to implement a fast and compact colored de Bruijn graph data structure. This index takes full advantage of the fact that unitigs in the colored de Bruijn graph are monochromatic (all k-mers in a unitig have the same set of references of origin, or "color"), leveraging the order-preserving property of its dictionary. In fact, k-mers are kept in unitig order by the dictionary, thereby allowing for the encoding of the map from k-mers to their inverted lists in as little as 1 + o(1) bits per unitig. Hence, one inverted list per unitig is stored in the index with almost no space/time overhead. By combining this property with simple but effective compression methods for inverted lists, the index achieves very small space. We implement these methods in a tool called Fulgor. Compared to Themisto, the prior state of the art, Fulgor indexes a heterogeneous collection of 30,691 bacterial genomes in 3.8x less space, a collection of 150,000 Salmonella enterica genomes in approximately 2 x less space, is at least twice as fast for color queries, and is 2 - 6x faster to construct. 2012 ACM Subject ClassificationApplied computing [->] Bioinformatics

bioinformatics↗

bioRxiv2022

High-throughput Approaches to Uncover Synergistic Drug Combinations in Leukemia

We report a comprehensive drug synergy study in acute myeloid leukemia (AML). In this work, we investigate 11 cell lines spanning both MLL-rearranged and non-rearranged subtypes. The work comprises a resource for the community, with many synergistic drug combinations that could not have been predicted a priori, and open source code for automation and analyses. We base our definitions of drug synergy on the Chou-Talalay method, which is useful for visualizations of synergy experiments in isobolograms, and median-effects plots, among other representations. Our key findings include drug synergies affecting the chromatin state, specifically in the context of regulation of the modification state of histone H3 lysine-27. We report open source high throughput methodology such that multidimensional drug screening can be accomplished with equipment that is accessible to most laboratories. This study will enable preclinical investigation of new drug combinations in a lethal blood cancer, with data analysis and automation workflows freely available to the community. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=90 SRC="FIGDIR/small/518409v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@1e85ef9org.highwire.dtl.DTLVardef@b3369eorg.highwire.dtl.DTLVardef@1c6d705org.highwire.dtl.DTLVardef@14ec6b2_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2022

Spectrum preserving tilings enable sparse and modular reference indexing

The reference indexing problem for k-mers is to pre-process a collection of reference genomic sequences[R] so that the position of all occurrences of any queried k-mer can be rapidly identified. An efficient and scalable solution to this problem is fundamental for many tasks in bioinformatics. In this work, we introduce the spectrum preserving tiling (SPT), a general representation of[R] that specifies how a set of tiles repeatedly occur to spell out the constituent reference sequences in[R] . By encoding the order and positions where tiles occur, SPTs enable the implementation and analysis of a general class of modular indexes. An index over an SPT decomposes the reference indexing problem for k-mers into: (1) a k-mer-to-tile mapping; and (2) a tile-to-occurrence mapping. Recently introduced work to construct and compactly index k-mer sets can be used to efficiently implement the k-mer-to-tile mapping. However, implementing the tile-to-occurrence mapping remains prohibitively costly in terms of space. As reference collections become large, the space requirements of the tile-to-occurrence mapping dominates that of the k-mer-to-tile mapping since the former depends on the amount of total sequence while the latter depends on the number of unique k-mers in[R] . To address this, we introduce a class of sampling schemes for SPTs that trade off speed to reduce the size of the tile-to-reference mapping. We implement a practical index with these sampling schemes in the tool pufferfish2. When indexing over 30,000 bacterial genomes, pufferfish2 reduces the size of the tile-to-occurrence mapping from 86.3GB to 34.6GB while incurring only a 3.6x slowdown when querying k-mers from a sequenced readset. Supplementary materialsSections S.1 to S.8 available online at https://doi.org/10.5281/zenodo.7504717 Availabilitypufferfish2 is implemented in Rust and available at https://github.com/COMBINE-lab/pufferfish2.

bioinformatics↗

bioRxiv2022

Transcriptomics based prediction of survival and response to therapy in malignant mesothelioma

Malignant mesothelioma is an aggressive cancer with limited treatment options and poor prognosis. Better understanding of mesothelioma genomics and transcriptomics could advance novel therapies. We performed whole-exome and RNA-sequencing of germline and tumors of 122 patients with pleural, peritoneal, and tunica-vaginalis mesothelioma. We identify a 48 gene prognostic signature that is highly predictive of mesothelioma patient survival including CCNB1, whose expression is highly predictive of patient survival on its own. Using a synthetic-lethality (SL) based pipeline for analyzing the patients transcriptomic data, we identified SL-based signatures predictive of response to an anti-PD1 immune checkpoint inhibitor and combination therapies with pemetrexed. These SL-profiles successfully predict the overall patient-response observed across targeted, immuno- and chemotherapies in 11 independent mesothelioma clinical trials spanning 7 different treatments. These findings lay a basis for future studies aimed specifically at testing the ability of these SL profiles to serve as treatment biomarkers in mesothelioma.

cancer biology↗