Biology subjects

Goode, B.

Publications and source records attributed to Goode, B..

5 recordsLinked to original sources

bioRxiv2024

Does PERM1 Regulate Systolic Cardiac Function? A Game of Numbers.

We and others demonstrated that PERM1 is a positive regulator of mitochondrial bioenergetics in the heart. However, discrepant results have emerged with regard to whether PERM1 loss-of-function affect cardiac contractility. In order to exclude the possibility that the reported negative results can be due to insufficient power of statistical test, we conducted a more robust echocardiography (Echo) analysis by increasing the sample size. We used Perm1-KO and their respective wildtype (WT) littermates, which were destined to tissue harvest. This yielded 84 WT mice and 88 Perm1-KO mice. We analyzed Echo-derived parameters of left ventricular (LV) systolic function. At the end of the study, ejection fraction (EF) was 65.43 {+/-} 7.13 in WT vs. 53.98 {+/-} 8.80 in Perm1-KO yielding p < 0.00000000000000004. Other parameters which reached statistically significant difference between WT and Perm1-KO (at p < 0.05) included LV fractional shortening (FS), LV diastolic and systolic diameters, LV anterior and posterior systolic wall thickness, LV posterior wall systolic thickening, stroke volume, and cardiac output (CO). Retrospectively, a p value < 0.05 was consistently achieved in assessment of EF only after average N per group reached 13. Larger minimal N per group were required for other parameters. Of interest, in both groups there were no correlation between EF% and CO. At the same time, in both groups EF strongly inversely correlated with LV diastolic diameter. This led us to a speculation that low EF may be in part compensated by an increased LV circumference, for the purpose of maintaining invariant CO. Indeed, the intergroup difference in CO (6%) was much smaller than the intergroup difference in EF (18%). We conclude that PERM1 does regulate cardiac mechanics. Changes caused by constitutive Perm1-KO can be conceptualized as reduced contractility partially compensated by increased LV circumference. This study underscores the importance of sufficiently large sample size for detecting significant differences in Echo data.

physiology↗

bioRxiv2023

Length control emerges from cytoskeletal network geometry

Many cytoskeletal networks consist of individual filaments that are organized into elaborate higher order structures. While it is appreciated that the size and architecture of these networks are critical for their biological functions, much of the work investigating control over their assembly has focused on mechanisms that regulate the turnover of individual filaments through size-dependent feedback. Here, we propose a very different, feedback-independent mechanism to explain how yeast cells control the length of their actin cables. Our findings, supported by quantitative cell imaging and mathematical modeling, indicate that actin cable length control is an emergent property that arises from the cross-linked and bundled organization of the filaments within the cable. Using this model, we further dissect the mechanisms that allow cables to grow longer in larger cells, and propose that cell length-dependent tuning of formin activity allows cells to scale cable length with cell length. This mechanism is a significant departure from prior models of cytoskeletal filament length control and presents a new paradigm to consider how cells control the size, shape, and dynamics of higher order cytoskeletal structures. Significance StatementCells control the sizes of their cytoskeletal networks to ensure that these structures can efficiently perform their cellular functions. Until now, this ability has been attributed to molecular feedback mechanisms that control the rates at which individual filaments are assembled and disassembled. We find that size control of cytoskeletal networks does not require this type of feedback and can instead be encoded through the physical arrangement of the filaments within that network. These findings have important implications for understanding how the underlying geometry of higher order cytoskeletal networks contributes to cellular control over these structures.

cell biology↗

bioRxiv2019

Cofilin loss in Drosophila muscles contributes to myopathy through defective sarcomerogenesis

Sarcomeres, the fundamental contractile units of muscles, are conserved structures composed of actin thin filaments and myosin thick filaments. How sarcomeres are formed and maintained is not well understood. Here, we show that knockdown of Drosophila Cofilin (DmCFL), an actin depolymerizing factor, leads to the progressive disruption of sarcomere structure and muscle function in vivo. Loss of DmCFL also results in the formation of sarcomeric protein aggregates and impairs sarcomere addition during growth. Strikingly, activation of the proteasome delayed muscle deterioration in our model. Further, we investigate how a point mutation in CFL2 that causes nemaline myopathy (NM) in humans, affects CFL function and leads to the muscle phenotypes observed in vivo. Our data provide significant insights to the role of CFLs during sarcomere formation as well as mechanistic implications for disease progression in NM patients.

developmental biology↗

bioRxiv2019

Multi-region exome sequencing of ovarian teratomas reveals 2N near-diploid genomes, paucity of somatic mutations, and extensive allelic imbalances shared across mature, immature, and disseminated components

Immature teratoma is a subtype of malignant germ cell tumor of the ovary that occurs most commonly in the first three decades of life, frequently with bilateral ovarian disease. Despite being the second most common malignant germ cell tumor of the ovary, little is known about its genetic underpinnings. Here we performed multi-region whole exome sequencing to interrogate the genetic zygosity, clonal relationship, DNA copy number, and mutational status of 52 pathologically distinct tumor components from 10 females with ovarian immature teratomas, with bilateral tumors present in 5 cases and peritoneal dissemination in 7 cases. We found that ovarian immature teratomas are genetically characterized by 2N near-diploid genomes with extensive loss of heterozygosity and an absence of genes harboring recurrent somatic mutations or known oncogenic variants. All components within a single ovarian tumor (immature teratoma, mature teratoma with different histologic patterns of differentiation, and yolk sac tumor) were found to harbor an identical pattern of loss of heterozygosity across the genome, indicating a shared clonal origin. In contrast, the 4 analyzed bilateral teratomas showed distinct patterns of zygosity changes in the right versus left sided tumors, indicating independent clonal origins. All disseminated teratoma components within the peritoneum (including gliomatosis peritonei) shared a clonal pattern of loss of heterozygosity with either the right or left primary ovarian tumor. The observed genomic loss of heterozygosity patterns indicate that diverse meiotic errors contribute to the formation of ovarian immature teratomas, with 11 out of the 15 genetically distinct clones determined to result from the failure of meiosis I or II. Overall, these findings suggest that copy-neutral loss of heterozygosity resulting from meiotic abnormalities may be sufficient to generate ovarian immature teratomas from germ cells.

cancer biology↗

bioRxiv2019

Cell-substrate adhesion drives Scar/WAVE activation and phosphorylation, which controls pseudopod lifetime

The Scar/WAVE complex is the principal catalyst of pseudopod and lamellipod formation. Here we show that Scar/WAVEs proline-rich domain is polyphosphorylated after the complex is activated. Treatments that stop activation block phosphorylation in both Dictyostelium and mammalian cells. This implies that phosphorylation modulates pseudopods after they have been formed, rather than controlling whether a protrusion is initiated. Unexpectedly, activation-dependent phosphorylation is not promoted by chemotactic signalling, or by signal-dependent kinases such as ERKs, but is greatly stimulated by cell:substrate adhesion. Scar/WAVE that has been mutated to be either unphosphorylatable or phosphomimetic is activated normally, and rescues the phenotype of scar- cells, demonstrating that phosphorylation is dispensible for activation and actin regulation. However, pseudopods and patches of Scar/WAVE complex recruitment last substantially longer in unphosphorylatable mutants, altering cell polarisation and the efficiency of migration. We conclude that pseudopod engagement with substratum is more important than extracellular signals at regulating Scar/WAVEs activity, and that phosphorylation acts as a timer, restricting pseudopod lifetime by promoting Scar/WAVE turnover.

cell biology↗