Biology subjects

Kamm, J.

Publications and source records attributed to Kamm, J..

10 recordsLinked to original sources

bioRxiv2026

scLANTERN: High-Throughput Retrospective Lineage Tracing via Full-Length Single-Cell Transcriptomics and Expressed Repeat Variation

Understanding the lineage relationships among individual cells is a key pursuit of modern biology, essential for unraveling the complexities of developmental processes and the adaptive mechanisms of disease progression, particularly in oncology. Retrospective single-cell clonal tracing has emerged as a transformative approach, offering a unique window into the evolutionary trajectories of cancer within clinical samples. While short-read single-cell transcriptomics (scRNA-seq) has revolutionized our ability to map cell states across human tumor atlases, it remains fundamentally limited in its capacity to link these states with high-resolution genomic alterations and the evolutionary trajectories inferred from these natural variants. Integrating somatic mutation discovery with transcriptomic profiles at single-cell resolution often requires separate, costly, and low-throughput genomic assays. Furthermore, existing methods frequently rely on exogenous genetic labeling or are restricted to short-read sequencing, which typically fails to resolve complex genomic rearrangements, large indels, or variations within highly repetitive regions,such as short tandem repeats (STRs), that could serve as potent endogenous clonal markers.

evolutionary biology↗

bioRxiv2026

Joint analysis of multiply perturbed cells improves statistical power and cost efficiency in Perturb-seq

Perturb-seq measures transcriptomic responses to genetic perturbations at scale, but conventional designs that enrich for one guide RNA per cell remain resource-intensive. Standard analyses discard cells carrying multiple guides, further limiting the usable yield from each experiment. Here, we characterize how incorporating these guide multiplets affects signal recovery, information loss, and cost reduction. At the highest guide burden, cells showed increased stress and suppressed cell-cycle progression. We develop PerturbMatch, a scalable statistical framework to analyze guide multiplets. Among different classes of guide multiplets, doublets and triplets recovered perturbation responses more accurately than higher-order multiplets. Across three 5000-gene Perturb-seq screens with increasing guide loading, per-cell costs decreased by up to 81% while information loss remained within 1.5-fold of the loss observed between technical replicates. In existing genome-wide Perturb-seq data, incorporating previously discarded guide multiplets increased usable cell numbers and improved statistical power. Compared with a singlet holdout set, adding guide multiplets moved signal recovery closer to the theoretical expected reproducibility. Overall, we recommend a design that intentionally includes single-guide cells, guide doublets, and guide triplets to improve cost efficiency while preserving signal recovery.

genomics↗

bioRxiv2026

Linking live-cell behavior to transcriptional responses across perturbations using dynamic caging

Single-cell technologies, encompassing molecular, morphological, and functional assays, have emerged as cornerstones of modern biological research and discovery. However, current experimental methods often fail to explicitly link these omic modalities, especially in live cells or longitudinally through time, impeding the study of multi-scale interactions and mechanisms of regulation. CellCage Enclosure (CCE) technology overcomes these limitations by dynamically compartmentalizing cells, allowing for scalable, live-cell, longitudinal exploration and simultaneous analysis of transcriptomic, proteomic, and morphological profiles. Using this novel technology, we generate previously inaccessible insights across various in vitro cellular systems under a diverse set of perturbations, including the discovery of morphological and proteomic features linked to immune suppressive gene set expression in human primary regulatory T cells (Tregs), as well as direct association of morphological and proteomic features with inflammatory gene modules in human colonic fibroblasts. We then develop a novel pooled CRISPR genetic screening technology using CCEs, PERTURB-LINK (PERTURBational LINKage of transcriptomics and imaging in single cells via enclosure-based screening) and apply this approach in murine bone marrow derived macrophages (BMDMs), enabling multiomic dissection of NF-{kappa}B pathway regulation in response to lipopolysaccharide (LPS) stimulation. Together, these findings demonstrate the broad impact that advancements in live-cell, paired multimodal technologies, especially upon perturbation, may offer in deepening our understanding of cellular biology.

cell biology↗

bioRxiv2026

Fishash: A contingency table approach to Perturb-seq guide assignment

BackgroundSingle-cell pooled CRISPR screens (Perturb-seq) are a powerful tool in functional genomics. A key preprocessing step is to determine which cells received which perturbations based on possibly noisy sequencing counts of the guide RNA library. Many existing approaches to this problem require fitting probabilistic models which may be computationally expensive on large screens with 10s of thousands of cells and guides. ResultsWe propose to view the guide count matrix as a contingency table and use Fishers Exact Test to test for associations between cell and guide barcodes. This approach is fast, normalizes for both cell and guide-specific size factors, and provides a p-value for each cell-guide pair. Our method further uses a multiple testing correction approach that accounts for the correlation structure between the tests, and a correction for Simpsons paradox that arises due to hidden confounding. Additionally, to facilitate the development and benchmarking of guide assignment methods, we propose a framework for simulating guide counts with a realistic model of sequencing noise. ConclusionsWe find that our method compares favorably to existing methods in both accuracy and runtime on simulated and real datasets. We provide our method in an easy to use R package, fishash, available at https://github.com/jackkamm/fishash. Additionally, the code to reproduce the results of this manuscript is available at https://github.com/jackkamm/fishash_analysis.

genomics↗

bioRxiv2025

Deficiency in POLE exonuclease causes synthetic lethality in highly aneuploid cancer cells

Aneuploidy is a hallmark of cancer and is associated with drug resistance and poor clinical outcomes across diverse cancer types. However, no therapies have been clinically established to target highly aneuploid tumors. By analyzing a real-world dataset comprising nearly half a million tumor samples subjected to comprehensive genomic profiling, we identified a striking mutual exclusivity between POLE exonuclease domain mutations and high aneuploidy burden. This observation was independently validated using data from The Cancer Genome Atlas (TCGA) and the Cancer Cell Line Encyclopedia (CCLE). Probabilistic modeling revealed that the elevated quantity and unique spectrum of mutations induced by POLE exonuclease deficiency increase the likelihood of inactivating essential genes on chromosome arms harboring losses, leading to a synthetic lethal phenotype in highly aneuploid cells. Functional experiments demonstrated that POLE exonuclease activity is essential for the viability of highly aneuploid cancer cell lines but is dispensable in diploid cells. These findings suggest that selective inhibition of POLE exonuclease may represent a promising therapeutic strategy for targeting highly aneuploid tumors.

cancer biology↗

bioRxiv2024

Fine-scale cellular deconvolution via generalized maximum entropy on canonical correlation features

We propose a method for estimating probability distributions over single cells, which we apply to fine-scale cellular deconvolution, which quantifies the composition of external bulk RNAseq samples at high resolution (i.e. at the single-cell or neighborhood level). Our method is based on a computationally-efficient convex optimization problem, which is also generalization of the Maximum Entropy method. Our method has a much higher resolution than traditional approaches that require computing gene expression profiles at the cell-type level, and also compares favorably to recent high-resolution cellular deconvolution methods, with orders-of-magnitude speedup in computational efficiency. We implement this method in a Python package quipcell, available at https://github.com/genentech/quipcell.

bioinformatics↗

bioRxiv2022

3MDR, a microcomputer-controlled visual stimulation device for psychotherapy-like treatments of mice

Post-traumatic stress disorder and other mental disorders can be treated by an established psychotherapy called Eye Movement Desensitization and Reprocessing (EMDR). In EMDR, patients are confronted with traumatic memories while they are stimulated with alternating bilateral stimuli (ABS). How ABS affect the brain and whether ABS could be adapted to different patients or mental disorders is unknown. Interestingly, ABS reduced conditioned fear in mice. Yet, an approach to systematically test complex visual stimuli and compare respective differences in emotional processing based on (semi-)automated behavioral analysis is lacking. We developed 3MDR (Model for MultiModal visual stimulation to Desensitize Rodents) - a novel, open-source, low-cost, customizable device that can be integrated in and TTL-controlled by commercial rodent behavioral setups. 3MDR allows to design and precisely steer multimodal visual stimuli in the head direction of freely-moving mice. Optimized videography allows to semi-automatically analyze rodent behavior during visual stimulation. Detailed building, integration, and treatment instructions along with open-source software provide easy access for inexperienced users. Using 3MDR, we confirmed that EMDR-like ABS persistently improve fear extinction in mice and showed for the first time that ABS-mediated anxiolytic effects strongly depend on physical stimulus properties such as ABS brightness. 3MDR not only enables researchers to interfere with mouse behavior in an EMDR-like setting, but demonstrates that visual stimuli can be used as a noninvasive brain stimulation to differentially alter emotional processing in mice. SIGNIFICANCE STATEMENTAlternating bilateral stimuli (ABS) reduce fear in post-traumatic stress disorder patients and in mice. The mechanism of how classic ABS - typically used in Eye Movement Desensitization and Reprocessing (EMDR) - reduce fear is enigmatic. We provide detailed resources to build a cost-effective, computer-controlled device called 3MDR to perform and semi-automatically analyze EMDR-like treatments in freely-moving mice and to test behavioral effects of multiple ABS variants. Using the 3MDR device, this study confirmed that classic ABS strongly and persistently improve the extinction of conditioned fear in mice - an effect that depended on the brightness of ABS. This novel method may ultimately contribute to a deeper translational and neurobiological understanding of how visual stimuli affect emotional processing in mice.

neuroscience↗

bioRxiv2020

Identification of a polymorphism in the N gene of SARS-CoV-2 that adversely impacts detection by a widely-used RT-PCR assay

We identify a mutation in the N gene of SARS-CoV-2 that adversely affects annealing of a commonly used RT-PCR primer; epidemiologic evidence suggests the virus retains pathogenicity and competence for spread. This reinforces the importance of using multiple targets, preferably in at least 2 genes, for robust SARS-CoV-2 detection. Article Summary LineA SARS-CoV-2 variant that occurs worldwide and has spread in California significantly affects diagnostic sensitivity of an N gene assay, highlighting the need to employ multiple viral targets for detection.

molecular biology↗

bioRxiv2019

Insights into human genetic variation and population history from 929 diverse genomes

Genome sequences from diverse human groups are needed to understand the structure of genetic variation in our species and the history of, and relationships between, different populations. We present 929 high-coverage genome sequences from 54 diverse human populations, 26 of which are physically phased using linked-read sequencing. Analyses of these genomes reveal an excess of previously undocumented private genetic variation in southern and central Africa and in Oceania and the Americas, but an absence of fixed, private variants between major geographical regions. We also find deep and gradual population separations within Africa, contrasting population size histories between hunter-gatherer and agriculturalist groups in the last 10,000 years, a potentially major population growth episode after the peopling of the Americas, and a contrast between single Neanderthal but multiple Denisovan source populations contributing to present-day human populations. We also demonstrate benefits to the study of population relationships of genome sequences over ascertained array genotypes. These genome sequences are freely available as a resource with no access or analysis restrictions.

genomics↗

bioRxiv2019

Investigating Transfusion-Related Sepsis using Culture-Independent Metagenomic Sequencing

BackgroundTransfusion-related sepsis remains an important hospital infection control challenge. Investigating septic transfusion events is often restricted by the limitations of bacterial culture in terms of time requirements and low yield in the setting of prior antibiotic administration.\n\nMethodsIn three Gram-negative septic transfusion cases, we performed mNGS of direct clinical blood specimens in addition to standard culture-based approaches utilized for infection control investigations. Pathogen detection leveraged IDSeq, a new open-access microbial bioinformatics portal. Phylogenetic analysis was performed to assess microbial genetic relatedness and understand transmission events.\n\nResultsmNGS of direct clinical blood specimens afforded precision detection of pathogens responsible for each case of transfusion-related sepsis, and enabled discovery of a novel Acinetobacter species in a platelet product that had become contaminated despite photochemical pathogen reduction. In each case, longitudinal assessment of pathogen burden elucidated the temporal sequence of events associated with each transfusion-transmitted infection. We found that informative data could be obtained from culture-independent mNGS of residual platelet products and leftover blood specimens that were either unsuitable or unavailable for culture, or that failed to grow due to prior antibiotic administration. We additionally developed methods to enhance accuracy for detecting transfusion-associated pathogens sharing taxonomic similarity to contaminants commonly found in mNGS library preparations.\n\nConclusionsCulture-independent mNGS of blood products afforded rapid and precise assessment of pathogen identity, abundance and genetic relatedness. Together, these challenging cases demonstrated the potential for metagenomics to advance existing methods for investigating transfusion-transmitted infections.

microbiology↗