Cell2location maps fine-grained cell types in spatial transcriptomics

Spatial transcriptomic technologies promise to resolve cellular wiring diagrams of tissues in health and disease, but comprehensive mapping of cell types in situ remains a challenge. Here we present сell2location, a Bayesian model that can resolve fine-grained cell types in spatial transcriptomic data and create comprehensive cellular maps of diverse tissues. Cell2location accounts for technical sources of variation and borrows statistical strength across locations, thereby enabling the integration of single-cell and spatial transcriptomics with higher sensitivity and resolution than existing tools. We assessed cell2location in three different tissues and show improved mapping of fine-grained cell types. In the mouse brain, we discovered fine regional astrocyte subtypes across the thalamus and hypothalamus. In the human lymph node, we spatially mapped a rare pre-germinal center B cell population. In the human gut, we resolved fine immune cell populations in lymphoid follicles. Collectively, our results present сell2location as a versatile analysis tool for mapping tissue architectures in a comprehensive manner.

MultiMAP: dimensionality reduction and integration of multimodal data

Multimodal data is rapidly growing in many fields of science and engineering, including single-cell biology. We introduce MultiMAP, a novel algorithm for dimensionality reduction and integration. MultiMAP can integrate any number of datasets, leverages features not present in all datasets, is not restricted to a linear mapping, allows the user to specify the influence of each dataset, and is extremely scalable to large datasets. We apply MultiMAP to single-cell transcriptomics, chromatin accessibility, methylation, and spatial data and show that it outperforms current approaches. On a new thymus dataset, we use MultiMAP to integrate cells along a temporal trajectory. This enables quantitative comparison of transcription factor expression and binding site accessibility over the course of T cell differentiation, revealing patterns of expression versus binding site opening kinetics.

Correlation between bioelectrical spectroscopy and perometry in assessment of upper extremity swelling

Lymphedema is a common side effect of breast cancer treatment and is associated with increased upper extremity volume, functional impairment, and pain. While there is no cure for lymphedema, physical therapy treatment can often alleviate symptoms. To measure the efficacy of treatment, accurate assessment of the limbs is important. Current methods of assessment are complex (water displacement), marginally accurate (circumferential measurements), or expensive (opto-electrical systems). A new method for estimating tissue fluid is bioelectrical spectroscopy (BIS). This method measures impedance to small currents applied to the body and is easily performed. Acceptance of BIS devices for assessment of limb fluid will be dependent on the establishment of sufficient reliability and validity, and the objective of this study was to evaluate reliability and validity of this device compared to perometry. Both upper limbs of ten subjects previously treated for breast cancer were measured using BIS and perometry. We found that inter-rater reliability (r = 0.987) and intrarater reliability (r = 0.993) were acceptably high for the BIS unit and concurrent validity was r = -0.904, when compared to perometry. These results confirm that BIS can produce valid and reliable data related to the assessment of upper limbs affected by lymphedema.

Epilepsies among twins born in families of Indian probands with epilepsy

Twins have a high frequency of adverse perinatal events and have been reported to have an increased risk of seizures. Contrary to popular belief, a recent study reported that twins do not have an increased risk of seizures. We studied the relationship of twinning and epilepsy in India. The frequency of twinning in families of probands with epilepsy was compared with the frequency of twinning among hospital births in the same region of India. We also compared consecutively ascertained probands with epilepsy for their twin status and the occurrence of epilepsies in their twin and non-twin relatives. The frequency of twin births in families of 524 probands with epilepsy was comparable to the twin births among consecutive deliveries over a 3-year period in another government hospital in the same catchment area (1:99 vs. 1:75). Every 1 in 58 of probands with epilepsy was a twin while a twin was born in these families every 1 in 71 live births. The frequency of epilepsy in non-proband twin relatives was 1.5% compared with 2% among non-proband, non-twin relatives. This data suggests that twin birth is not a major risk factor for seizures even in families of Indian probands with epilepsy. Family data such as ours can be used to study the contribution by genetic factors in the pathogenesis of complex genetic diseases such as human epilepsies.