Biology subjects

Fatima, H.

Publications and source records attributed to Fatima, H..

7 recordsLinked to original sources

bioRxiv2026

The membrane distal domain of CD16a allosterically regulates NK cell ADCC

Antibody-dependent cellular cytotoxicity (ADCC) by natural killer (NK) cells is mediated by the activating IgG receptor CD16a (Fc{gamma}RIIIa), yet the molecular mechanisms governing receptor activation remain poorly understood. We demonstrate that the membrane-distal domain 1 (D1) of CD16a functions as an allosteric checkpoint that controls ADCC independently of IgG-Fc binding. A nanobody, C28, that binds an electronegative patch in D1 dose-dependently blocks NK cell ADCC against multiple therapeutic antibodies without affecting direct cytotoxicity. A second nanobody, C21, binding an adjacent D1 epitope has no such effect. Cryo-EM structures of the CD16a-IgG-nanobody complex reveal that C28 allosterically competes with core-fucosylated IgG and stabilizes a closed D1 conformation resembling unliganded receptor, even when Fc is bound. Molecular dynamics simulations show that occupation of the D1 epitope rigidifies the IgG-binding site, stabilizing CD16a overall in contrast with IgG binding alone. The nanobody C28 restricts CD3{zeta} phosphorylation in both resting and ADCC-activated NK cells, revealing tonic inhibitory control upstream of the signaling cascade. Using MINFLUX nanoscopy, we also show that CD16a forms dimers of [~]9 nm spacing on the NK cell surface, a geometry unaltered by the ADCC-enhancing L48H polymorphism. Drawing on structural parallels with the IgE receptor Fc{varepsilon}RI, which is held inactive as a cholesterol-stabilized dimer, we propose that CD16a dimerization through D1 contacts represents a conserved autoinhibitory mechanism among Fc receptors. Consistent with this model, structure-guided disruption of the C28 epitope in NK-92 cells enhances ADCC potency and killing kinetics, providing a blueprint for engineering improved cellular immunotherapeutics.

immunology↗

bioRxiv2025

SRRM1 coordinates an alternative splicing program that promotes expression of oncogenic protein isoforms.

The alternative splicing of the adapter protein NUMB is dysregulated in multiple cancer types, regulating its functional divergence towards either tumor suppression or oncogenesis in an isoform-dependant manner. Here we utilized a NUMB exon 9 (E9) splicing reporter in a genome-wide CRISPR screen to identify splicing regulators SRRM1 and SRSF11 that promote NUMB oncogenic splicing in colorectal, lung and breast cancer cell lines. We show that SRRM1 and SRSF11 share common protein interactors, RNA targets and effects on an oncogenic splicing program which favors the expression of pro-tumorigenic isoforms. In addition to NUMB E9, SRRM1 regulates cancer-associated splicing events in genes encoding signaling proteins, transcription factors and actin cytoskeleton regulators, many of which are also developmentally regulated, including CD44, MKNK2, ECT2, DIAPH1, KAT5, TCF7L2, FOXM1 and TBX3. Loss of SRRM1 in colorectal and lung cancer cells reduces cell proliferation, colony formation and invasion capabilities, as well as expression of tumour promoters Cyclin D1, Notum, and PRDX2. Our data indicate that SRRM1 regulation of alternative splicing represents a node to target multiple properties of malignant cells, with broad effects on cellular signaling, proliferation, EMT, apoptosis resistance and stemness.

cancer biology↗

bioRxiv2024

Complex genomic ancestry in southern regions and drivers of continental-level genetic diversity in the wolves of Asia

Gray wolves (Canis lupus) in Asia encompass most of the species global genetic diversity and many endangered populations. However, a clear understanding of the evolutionary history of wolves from many parts of Asia, especially southern regions, is lacking. We used 98 whole genomes of wolves sampled across Eurasia to better resolve their evolutionary history by investigating phylogenetic and gene flow histories across the genome, and to characterize their demographic history and genetic diversity. The strongest barriers to gene flow coincided with boundaries separating the three major extant wolf lineages - Indian, Tibetan, and Holarctic. Wolves in the central Asian mountain ranges belonged to the Holarctic lineage, and despite their geographic adjacency only share minimal ancestry with the Tibetan lineage. In contrast, wolves from eastern Asia share population-wide ancestry with the Tibetan lineage, which may reflect an unsampled lineage similar, but not exactly to, the modern-day Tibetan lineage. Wolves from southwestern Asia also share population-wide ancestry with the Indian lineage, likely due to old (>6kya) admixture events. Long-term historical declines over the last 100,000 years, geographic isolation, and recent inbreeding have resulted in the Indian and Tibetan wolves having some of the lowest levels of genetic diversity and highest realized genetic loads. In contrast, adjacent populations exhibit some of the highest genetic diversity, due in part to admixture along contact zones. Our study illustrates how using multiple approaches that consider heterogenous signals across the genome can more fully resolve the historical and contemporary processes that have led to present-day species diversity.

evolutionary biology↗

bioRxiv2024

Spatial localization of CD16a at the human NK cell ADCC lytic synapse

Natural Killer (NK) cells utilize effector functions, including antibody-dependent cellular cytotoxicity (ADCC), for the clearance of viral infection and cellular malignancies. NK cell ADCC is mediated by Fc{gamma}RIIIa (CD16a) binding to the fragment crystallizable (Fc) region of immunoglobulin G (IgG) within immune complexes on a target cell surface. While antibody-induced clustering of CD16a is thought to drive ADCC, the molecular basis for this activity has not been fully described. Here we use MINFLUX nanoscopy to map the spatial distribution of stoichiometrically labeled CD16a across the NK cell membrane, revealing the presence of pairs of CD16a molecules with intra-doublet distance of approximately 17 nm. NK cells activated on supported lipid bilayers by Trastuzumab results in an increase of synaptic regions with greater CD16a density. Our results provide the highest spatial resolution yet described for CD16a imaging, offering new insight into how CD16a organization within the immune synapse could influence ADCC activity. MINFLUX holds great promise to further unravel the molecular details driving CD16a-based activation of NK cells.

immunology↗

bioRxiv2023

Replication stress in activated human NK cells induces sensitivity to apoptosis

Natural killer cells are innate immune effectors that kill virally infected or malignant cells. Natural killer cell deficiency (NKD) occurs when NK cell development or function are impaired, and individuals with NKD are susceptible to severe and recurrent viral infections. Several gene deficiencies result in NKD, including variants in MCM4, GINS1, MCM10 and GINS4, which are components of the CDC45-MCM-GINS (CMG) helicase. The CMG helicase unwinds DNA during replication and is expressed in any actively proliferating cell. NK cells are more strongly impacted by mutational deficiencies in helicase proteins than other lymphocytes, though the mechanisms underlying this susceptibility are not completely understood. NK cells from individuals with NKD as a result of helicase deficiency have increased DNA damage, cell cycle arrest, and replication stress. Here, we induced replication stress in activated mature NK cells or T cells by chemical methods, using aphidicolin, and through shRNA knockdown of MCM10 in an NK cell line. We found that the CD56bright subset of NK cells accumulates more DNA damage and replication stress during activation than CD56dim NK cells or activated T cells. Aphidicolin treatment increases apoptosis of CD56bright NK cells through increased pan-caspase expression and decreases perforin expression in surviving cells. This effect is modeled by shRNA mediated knockdown of MCM10, thus linking decreased helicase protein expression to replication stress and impaired NK cell function. These findings show that sensitivity to replication stress affects human NK cell survival and function and can contribute to NK cell deficiency.

immunology↗

bioRxiv2022

The CD58:CD2 axis is co-regulated with PD-L1 via CMTM6 and governs anti-tumor immunity

The cell autonomous balance of immune-inhibitory and -stimulatory signals is a critical yet poorly understood process in cancer immune evasion. Using patient-derived co-culture models and humanized mouse models, we show that an intact CD58:CD2 interaction is necessary for anti-tumor immunity. Defects in this axis lead to multi-faceted immune evasion through impaired CD2-dependent T cell polyfunctionality, T cell exclusion, impaired intra-tumoral proliferation, and concurrent protein stabilization of PD-L1. We performed genome-scale CRISPR-Cas9 and CD58 coimmunoprecipitation mass spectrometry screens identifying CMTM6 as a key stabilizer of CD58, and show that CMTM6 is required for concurrent upregulation of PD-L1 in CD58 loss. Single-cell RNA-seq analysis of patient melanoma samples demonstrates that most TILs lack expression of primary costimulatory signals required for response to PD-1 blockade (e.g. CD28), but maintain strong CD2 expression, thus providing an opportunity to mobilize a so far therapeutically untapped pool of TILs for anti-tumor immunity. We identify two potential therapeutic avenues, including rescued activation of human CD2-expressing TILs using recombinant CD58 protein, and targeted disruption of PD-L1/CMTM6 interactions. Our work identifies an underappreciated yet critical axis at the nexus of cancer immunity and evasion, uncovers a fundamental mechanism of co-inhibitory and -stimulatory signal balancing, and provides new approaches to improving cancer immunotherapies.

cancer biology↗

bioRxiv2021

TRAK proteins encode distinct MIRO-dependent and MIRO-independent mechanisms for associating with the mitochondrial outer membrane

Current models suggest that MIRO GTPases anchor cytoskeletal motors to the mitochondrial outer membrane (MOM). However, our previous findings indicate that the unconventional myosin, MYO19, interacts with MIRO weakly and that a MIRO-independent MOM-localizing domain interacts more tightly with the MOM. To test the hypothesis that other MIRO interactors may also have MIRO-independent MOM-binding, we examined interactions between TRAK proteins (microtubule motor-mitochondria adaptor proteins) and the MOM via quantitative fluorescence microscopy and steady-state kinetic approaches. Using GFP-TRAK truncations expressed in MIRO1-2 double knockout mouse embryonic fibroblasts, we identified a MIRO-independent mitochondrial binding domain in the C-terminus of TRAK1 and TRAK2, sufficient for MOM-localization similar to what we observed for full length GFP-TRAK proteins. The MIRO-binding domains (MBD) of the TRAK proteins were only able to localize to mitochondria in the presence of ectopic expression of MIRO. Importantly, fluorescence recovery after photobleaching (FRAP) demonstrated that the steady-state kinetics of TRAKMBD/MIRO interactions were faster-exchanging than for either full-length TRAK or the TRAK C-terminal MOM-binding domain expressed alone. These data support a model where faster-exchanging TRAK/MIRO associations could support initial association and/or TRAK activation, while MIRO-independent binding contributes significantly to tighter association to the MOM.

cell biology↗